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Fanfan D, Larios F, Gonzalez MR, Rodriguez A, Nichols D, Alvarez JC, Pretell-Mazzini J. A Bibliometric Analysis of the 500 Most Cited Papers in Orthopaedic Oncology. J Am Acad Orthop Surg Glob Res Rev 2024; 8:01979360-202401000-00004. [PMID: 38236058 PMCID: PMC10796143 DOI: 10.5435/jaaosglobal-d-23-00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND Despite notable progress over time, broad insight into the scientific landscape of orthopaedic oncology is lacking. We conducted a bibliometric analysis of the 500 most cited papers in the field. METHODS We searched the Science Citation Index Expanded database of the Web of Science Core Collection to find the 500 most cited articles in the field. RESULTS Citation count ranged from 81 to 1,808. Articles were published from 1965 to 2018. Over half of all articles were published in the United States (53.6%). The 2000s was the most productive decade with 170 (34%) articles. All articles were written in English and were published across 29 journals. Female participation as first authors significantly increased from the 1960s to the 2010s (0% vs 14.6%, P = 0.0434). Similarly, female involvement as senior authors grew from the 1960s to the 2010s (0% vs 12.2%, P = 0.0607). Primary bone sarcomas were the most cited topic among articles from the 1970s to the 1980s. From studies produced in the 1990s up until the 2010s, reconstruction procedures were the most cited topic. CONCLUSION Trends over the years have resulted in an emphasis on a surgical technique. Notable progress has been made regarding gender diversity, yet disparities still exist.
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Affiliation(s)
- Dino Fanfan
- From the Herbert Wertheim College of Medicine, Florida International University, Miami, FL (Mr. Fanfan, Mr. Rodriguez, Ms. Nichols, and Mr. Alvarez Jr); the Facultad de Medicina Universidad Peruana Cayetano Heredia, Lima, Peru (Dr. Larios); the Division of Orthopaedic Oncology, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA (Dr. Gonzalez); and the Miami Cancer Institute, Division of Orthopedic Oncology, Baptist Health System South Florida, Plantation, FL (Dr. Pretell-Mazzini)
| | - Felipe Larios
- From the Herbert Wertheim College of Medicine, Florida International University, Miami, FL (Mr. Fanfan, Mr. Rodriguez, Ms. Nichols, and Mr. Alvarez Jr); the Facultad de Medicina Universidad Peruana Cayetano Heredia, Lima, Peru (Dr. Larios); the Division of Orthopaedic Oncology, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA (Dr. Gonzalez); and the Miami Cancer Institute, Division of Orthopedic Oncology, Baptist Health System South Florida, Plantation, FL (Dr. Pretell-Mazzini)
| | - Marcos R. Gonzalez
- From the Herbert Wertheim College of Medicine, Florida International University, Miami, FL (Mr. Fanfan, Mr. Rodriguez, Ms. Nichols, and Mr. Alvarez Jr); the Facultad de Medicina Universidad Peruana Cayetano Heredia, Lima, Peru (Dr. Larios); the Division of Orthopaedic Oncology, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA (Dr. Gonzalez); and the Miami Cancer Institute, Division of Orthopedic Oncology, Baptist Health System South Florida, Plantation, FL (Dr. Pretell-Mazzini)
| | - Alexander Rodriguez
- From the Herbert Wertheim College of Medicine, Florida International University, Miami, FL (Mr. Fanfan, Mr. Rodriguez, Ms. Nichols, and Mr. Alvarez Jr); the Facultad de Medicina Universidad Peruana Cayetano Heredia, Lima, Peru (Dr. Larios); the Division of Orthopaedic Oncology, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA (Dr. Gonzalez); and the Miami Cancer Institute, Division of Orthopedic Oncology, Baptist Health System South Florida, Plantation, FL (Dr. Pretell-Mazzini)
| | - Domonique Nichols
- From the Herbert Wertheim College of Medicine, Florida International University, Miami, FL (Mr. Fanfan, Mr. Rodriguez, Ms. Nichols, and Mr. Alvarez Jr); the Facultad de Medicina Universidad Peruana Cayetano Heredia, Lima, Peru (Dr. Larios); the Division of Orthopaedic Oncology, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA (Dr. Gonzalez); and the Miami Cancer Institute, Division of Orthopedic Oncology, Baptist Health System South Florida, Plantation, FL (Dr. Pretell-Mazzini)
| | - Juan C. Alvarez
- From the Herbert Wertheim College of Medicine, Florida International University, Miami, FL (Mr. Fanfan, Mr. Rodriguez, Ms. Nichols, and Mr. Alvarez Jr); the Facultad de Medicina Universidad Peruana Cayetano Heredia, Lima, Peru (Dr. Larios); the Division of Orthopaedic Oncology, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA (Dr. Gonzalez); and the Miami Cancer Institute, Division of Orthopedic Oncology, Baptist Health System South Florida, Plantation, FL (Dr. Pretell-Mazzini)
| | - Juan Pretell-Mazzini
- From the Herbert Wertheim College of Medicine, Florida International University, Miami, FL (Mr. Fanfan, Mr. Rodriguez, Ms. Nichols, and Mr. Alvarez Jr); the Facultad de Medicina Universidad Peruana Cayetano Heredia, Lima, Peru (Dr. Larios); the Division of Orthopaedic Oncology, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA (Dr. Gonzalez); and the Miami Cancer Institute, Division of Orthopedic Oncology, Baptist Health System South Florida, Plantation, FL (Dr. Pretell-Mazzini)
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Cifuentes P, Jaramillo M, Garrote F, Bravo D, Alvarez JC, Quintero RM, Mouhanna S, Nair RR. Impact of Insurance Type on Access to Pain Management Specialists for the Treatment of Lower Back Pain. Cureus 2024; 16:e51668. [PMID: 38313953 PMCID: PMC10838162 DOI: 10.7759/cureus.51668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2024] [Indexed: 02/06/2024] Open
Abstract
Background Low back pain is known to be one of the leading causes of disability among the young and elderly population. Low back pain can stem from multiple sources, including spinal degeneration, injury, herniated discs, sciatica, and other contributing causes. This symptom significantly influences the quality of life of affected individuals. Its implications include extensive social and economic costs. Economic considerations arise from the fact that not all healthcare facilities accept the insurance plans available to retired individuals under Medicare. This places an additional burden on patients who must bear the financial responsibility for healthcare services not covered by their insurance plan. Florida, renowned as a favored state for retirement, consists of a demographic composition wherein 21% of its residents are aged 65 or older. A significant proportion of this demographic qualifies for Traditional Medicare (TM) and/or Medicare Advantage (MA) plans. Thus, understanding the disparities in healthcare access between Medicare and Medicare Advantage plans is crucial. This study aims to evaluate different Medicare insurances available in the market and their impact on the ease of accessibility to pain management specialists for the treatment of lower back pain in Florida patients. Methods We analyzed the Florida Department of Health database to identify the four counties in Florida with the highest Medicare enrollment rates in 2022: Miami-Dade, Palm Beach, Broward, and Pinellas County. Using the U.S. News and Report directory, 25 Pain Management-trained anesthesiologists were randomly selected from each of the four counties. Each office was contacted four times via telephone by four different team members to assess appointment availability for a fictional 65-year-old grandfather seeking treatment for chronic low back pain. The study examined appointment availability and accepted insurance types, including Cigna (commercial insurance), TM, Humana Gold Plus HMO (Medicare Advantage plan), and Blue Medicare Select PPO (Medicare Advantage plan). Practices without contact information or retired physicians were excluded from the analysis. Time to appointment was measured in business days. Results Of the 100 Pain Management Physicians contacted, 44 fit the inclusion criteria of being non-retired physicians, still practicing in one of the four counties with open offices and valid contact information. Blue Medicare Select PPO was accepted by 47.73%, Humana Gold Plus HMO by 56.82%, TM by 93.18%, and Cigna by 93.18% of the encounters. Blue Medicare select PPO and Humana Gold Plus HMO were accepted at significantly lower rates when compared to Traditional Medicare and Cigna with P values of P < .00001 and P < .000176, respectively. There was no significant difference found in the time to appointment between insurances with P value < 7. Conclusion The study found that patients enrolled in Medicare Advantage plans have significantly decreased access to care when compared to those enrolled in TM or commercial insurance. Further research is needed to elucidate the reasons behind differences in access to care across different insurances, as identified in the study.
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Affiliation(s)
- Phillip Cifuentes
- Anesthesiology, Florida International University, Herbert Wertheim College of Medicine, Miami, USA
| | - Manuela Jaramillo
- Anesthesiology, Florida International University, Herbert Wertheim College of Medicine, Miami, USA
| | - Fabio Garrote
- Anesthesiology, Florida International University, Herbert Wertheim College of Medicine, Miami, USA
| | - Daniel Bravo
- Internal Medicine, Albert Einstein College of Medicine, New York City, USA
| | - Juan C Alvarez
- Anesthesiology, Florida International University, Herbert Wertheim College of Medicine, Miami, USA
| | - Ramon M Quintero
- Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, USA
| | | | - Rakesh R Nair
- Cellular Biology & Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, USA
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Fanfan D, Alvarez JC, Gonzalez MR, Larios F, Shae J, Pretell-Mazzini J. Foot and Ankle Soft Tissue Sarcomas-Treatment and Oncologic Outcomes: A Systematic Review of the Literature. Foot Ankle Int 2023; 44:1199-1207. [PMID: 37750365 DOI: 10.1177/10711007231198516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
BACKGROUND Foot and ankle soft tissue sarcomas (STSs) are rare neoplasms associated with a high risk of local recurrence and metastasis. Although amputation is often performed, its impact on prognosis remains unknown. The aims of our systematic review were identifying risk factors for (1) disease-specific death, (2) local recurrence, (3) metastasis, and assessing (4) whether the type of surgery (amputation or limb-salvage) affected disease-specific survival. METHODS This systematic review was conducted following PRISMA guidelines. The PubMed, Embase, and Scopus databases were searched. Our study was registered in PROSPERO (ID: 415624). Quality appraisal was done using STROBE guidelines. RESULTS A total of 7 studies and 123 patients were included. Metastasis was the only risk factor for disease-specific death (OR = 107.85, P< .001). Previous unplanned excision (OR = 22.29, P = .009) and positive margins (OR = 64.48, P = .011) were associated with higher risk of local recurrence. Patients with high-grade tumors (OR = 13.22, P = .023) and tumors ≥6 cm (OR = 7.40, P = .022) were more likely to develop metastases. After adjusting for confounders (age, sex, and presence of metastasis), amputation was not associated with poorer disease-specific survival. CONCLUSION Metastasis was the single most important risk factor for death with foot and ankle soft tissue sarcoma. Positive margins and history of previous unplanned excision are risk factors for local recurrence. The most important risk factors for metastasis are tumor grade and size ≥6 cm. Amputation was not associated with poorer disease-specific survival.
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Affiliation(s)
- Dino Fanfan
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Juan C Alvarez
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Marcos R Gonzalez
- Division of Orthopaedic Oncology, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Felipe Larios
- Facultad de Medicina Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jillian Shae
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Juan Pretell-Mazzini
- Miami Cancer Institute, Division of Orthopedic Oncology, Baptist Health System South Florida, Plantation, FL, USA
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Ramirez JC, Alvarez JC, Cifuentes P, Castro G, Barengo NC. Time Period of Treatment's Effect on the Association Between Race and Survival in Patients With Malignant Colorectal Adenocarcinoma. Cureus 2023; 15:e45641. [PMID: 37868544 PMCID: PMC10589074 DOI: 10.7759/cureus.45641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND Colorectal cancer is one of the most common malignancies diagnosed in the United States, with 126,240 new cases diagnosed in 2020. Past studies have shown that disparities may exist between certain patient populations, but it is unknown how they are affected over time as treatments evolve. The purpose of this study was to determine whether the decade of treatment modifies the association between race and five-year survival in adults diagnosed and treated for malignant colorectal adenocarcinomas since the 1970s. METHODS This was a non-concurrent retrospective cohort study using data from the Surveillance, Epidemiology, and End Results (SEER) database of the National Cancer Institute. The inclusion criteria involved patients with primary malignant colorectal adenocarcinoma between the years 1975 and 2018. Exclusion criteria included previous malignancies or missing information on any of the variables. The exposure variable was the patient's race, and the main outcome variable was average five-year survival rates. The effect modifier was the time period in which the patient received treatment. The covariates of the study included age, sex, Hispanic status, surgical intervention recommendation, and disease stage. Unadjusted and adjusted hazard ratios (HRs) and corresponding 95% confidence intervals (CIs) were calculated using Cox regression models. RESULTS As the interaction term between race/ethnicity and year of diagnosis was statistically significant, the data were stratified according to year of diagnosis. Black patients in both time periods had a higher mortality rate from malignant colorectal carcinoma after adjustment for the covariates (1975-1990: HR 1.10, 95% CI 1.06-1.15; 1991-2018: HR 1.19, 95% CI 1.16-1.23) when compared with White patients. American Indian, Alaskan Native, and Asian patients were found to have lower mortality in both time periods when compared with White patients (1975-1990: HR 0.90, 95% CI 0.85-0.95; 1991-2018: HR 0.93, 95% CI 0.89-0.96). CONCLUSION Our data found that despite the evolution in the standard of care treatment for malignant colorectal adenocarcinoma since the year 1975, Black patients had lower five-year survival rates when compared with their White counterparts as well as increased rates of being diagnosed with this disease. Overall, addressing these disparities in colorectal cancer outcomes is critical for improving public health and reducing healthcare costs.
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Affiliation(s)
- Juan C Ramirez
- Department of Translational Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, USA
| | - Juan C Alvarez
- Department of Translational Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, USA
| | - Phillip Cifuentes
- Department of Translational Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, USA
| | - Grettel Castro
- Department of Medical and Population Health Sciences Research, Herbert Wertheim College of Medicine, Florida International University, Miami, USA
| | - Noel C Barengo
- Department of Medicine, Riga Stradins University, Riga, LVA
- Department of Global Health, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, USA
- Department of Translational Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, USA
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Lopes JE, Fisher JL, Flick HL, Wang C, Sun L, Ernstoff MS, Alvarez JC, Losey HC. ALKS 4230: a novel engineered IL-2 fusion protein with an improved cellular selectivity profile for cancer immunotherapy. J Immunother Cancer 2021; 8:jitc-2020-000673. [PMID: 32317293 PMCID: PMC7204809 DOI: 10.1136/jitc-2020-000673] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Interleukin-2 (IL-2) plays a pivotal role in immune homeostasis due to its ability to stimulate numerous lymphocyte subsets including natural killer (NK) cells, effector CD4+ and CD8+ T cells, and regulatory T cells (Tregs). Low concentrations of IL-2 induce signaling through the high-affinity IL-2 receptor (IL-2R) comprised of IL-2Rα, IL-2Rβ, and common γ chain (γc), preferentially expressed on Tregs. Higher concentrations of IL-2 are necessary to induce signaling through the intermediate-affinity IL-2R, composed of IL-2Rβ and γc, expressed on memory CD8+ T cells and NK cells. Recombinant human IL-2 (rhIL-2) is approved for treatment of metastatic melanoma and renal cell carcinoma (RCC), but adverse events including capillary leak syndrome, potentially mediated through interaction with the high-affinity IL-2R, limit its therapeutic use. Furthermore, antitumor efficacy of IL-2 may also be limited by preferential expansion of immunosuppressive Tregs. ALKS 4230 is an engineered fusion protein comprised of a circularly-permuted IL-2 with the extracellular domain of IL-2Rα, designed to selectively activate effector lymphocytes bearing the intermediate-affinity IL-2R. RESULTS ALKS 4230 was equipotent to rhIL-2 in activating human cells bearing the intermediate-affinity IL-2R, and less potent than rhIL-2 on cells bearing the high-affinity IL-2R. As observed in vitro with primary human cells from healthy donors and advanced cancer patients, ALKS 4230 induced greater activation and expansion of NK cells with reduced expansion of Tregs relative to rhIL-2. Similarly, in mice, ALKS 4230 treatment stimulated greater expansion of NK cells and memory-phenotype CD8+ T cells at doses that did not expand or activate Tregs. ALKS 4230 treatment induced significantly lower levels of proinflammatory cytokines, including tumor necrosis factor alpha, interleukin-6, and interferon gamma relative to rhIL-2. Furthermore, ALKS 4230 exhibited superior antitumor efficacy in the mouse B16F10 lung tumor model, where ALKS 4230 could be administered via multiple routes of administration and dosing schedules while achieving equivalent antitumor efficacy. CONCLUSIONS ALKS 4230 exhibited enhanced pharmacokinetic and selective pharmacodynamic properties resulting in both improved antitumor efficacy and lower indices of toxicity relative to rhIL-2 in mice. These data highlight the potential of ALKS 4230 as a novel cancer immunotherapy, and as such, the molecule is being evaluated clinically.
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Affiliation(s)
- Jared E Lopes
- Research, Alkermes, Inc, Waltham, Massachusetts, USA
| | - Jan L Fisher
- Department of Medicine, The Geisel School of Medicine at Dartmouth and Norris Cotton Cancer Center, Lebanon, New Hampshire, USA
| | | | - Chunhua Wang
- Research, Alkermes, Inc, Waltham, Massachusetts, USA
| | - Lei Sun
- Research, Alkermes, Inc, Waltham, Massachusetts, USA
| | - Marc S Ernstoff
- Department of Medicine, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Juan C Alvarez
- Computational and Structural Chemistry, Merck & Co, Boston, Massachusetts, USA
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Brueckner AC, Deng Q, Cleves AE, Lesburg CA, Alvarez JC, Reibarkh MY, Sherer EC, Jain AN. Conformational Strain of Macrocyclic Peptides in Ligand-Receptor Complexes Based on Advanced Refinement of Bound-State Conformers. J Med Chem 2021; 64:3282-3298. [PMID: 33724820 DOI: 10.1021/acs.jmedchem.0c02159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Macrocyclic peptides are an important modality in drug discovery, but molecular design is limited due to the complexity of their conformational landscape. To better understand conformational propensities, global strain energies were estimated for 156 protein-macrocyclic peptide cocrystal structures. Unexpectedly large strain energies were observed when the bound-state conformations were modeled with positional restraints. Instead, low-energy conformer ensembles were generated using xGen that fit experimental X-ray electron density maps and gave reasonable strain energy estimates. The ensembles featured significant conformational adjustments while still fitting the electron density as well or better than the original coordinates. Strain estimates suggest the interaction energy in protein-ligand complexes can offset a greater amount of strain for macrocyclic peptides than for small molecules and non-peptidic macrocycles. Across all molecular classes, the approximate upper bound on global strain energies had the same relationship with molecular size, and bound-state ensembles from xGen yielded favorable binding energy estimates.
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Affiliation(s)
- Alexander C Brueckner
- Computational & Structural Chemistry, Merck & Co Inc, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Qiaolin Deng
- Computational & Structural Chemistry, Merck & Co Inc, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ann E Cleves
- Bioengineering and Therapeutic Sciences, University of California San Francisco, Box 0128, San Francisco, California 94158, United States
| | - Charles A Lesburg
- Computational and Structural Chemistry, Merck and Co Inc, 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Juan C Alvarez
- Computational and Structural Chemistry, Merck and Co Inc, 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Mikhail Y Reibarkh
- Analytical Research and Development, Merck & Co Inc, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Edward C Sherer
- Analytical Research and Development, Merck & Co Inc, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Ajay N Jain
- Bioengineering and Therapeutic Sciences, University of California San Francisco, Box 0128, San Francisco, California 94158, United States
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Alvarez JC, Mayer-Duverneuil C, Cappy J, Lorin de la Grandamison G, Knapp-Gisclon A. Postmortem fatal and non-fatal concentrations of amlodipine. Forensic Sci Int 2020; 316:110555. [PMID: 33152659 DOI: 10.1016/j.forsciint.2020.110555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 11/29/2022]
Abstract
Amlodipine is a dihydropyridine calcium channel blocker widely used in the treatment of high blood pressure and coronary heart disease. Intoxication can lead to reflex tachycardia following massive hypotension and death. The objective of this work was to study the post-mortem concentrations of amlodipine in 62 patients in order to determine whether the use of the reference concentrations from the living patients was applicable in postmortem setting, and to define more precisely the fatal and non-fatal postmortem concentrations of amlodipine. The amlodipine concentrations were measured in femoral whole blood by LC-MS/MS validated method. When sufficient information was available, the data were classified into 2 different groups, based on the conclusions of the autopsy and toxicological results: G1: non-toxic death and G2: fatal poisoning involving amlodipine alone or as part of a multidrug poisoning. The median concentration of amlodipine [1st quartile - 3rd quartile] of the whole population (n = 62) was 81 [42-134] ng/mL. Twenty-two cases were classified as G1 and thirteen as G2. The observed median [1st quartile - 3rd quartile] concentration of amlodipine was 66 [40.5-79.5] ng/mL in G1 and 240 [170-404] ng/mL in G2. The median concentrations observed in "non-toxic" deaths (66 ng/mL) were three times higher than those usually observed in living patients. Amlodipine distribution ratio between plasma and whole blood concentrations seems insufficient to explain this difference and postmortem redistribution from organs should be considered, and could suggest the same redistribution pattern for other drugs belonging to the same family.
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Affiliation(s)
- J C Alvarez
- Laboratoire de Pharmacologie - Toxicologie, Centre Hospitalier Universitaire Raymond Poincaré, AP-HP, 104 boulevard Raymond Poincaré, 92380, Garches, France; Plateforme de Spectrométrie de Masse MassSpecLab, INSERM UMR 1173, UFR des Sciences de la Santé Simone Veil, Université Versailles Saint-Quentin, 2 avenue de la source de la Bièvre, 78180, Montigny le Bretonneux, France.
| | - C Mayer-Duverneuil
- Laboratoire de Pharmacologie - Toxicologie, Centre Hospitalier Universitaire Raymond Poincaré, AP-HP, 104 boulevard Raymond Poincaré, 92380, Garches, France
| | - J Cappy
- Institut de Médecine Légale, Centre Hospitalier Universitaire Raymond Poincaré, AP-HP, 104 boulevard Raymond Poincaré, 92380, Garches, France
| | - G Lorin de la Grandamison
- Institut de Médecine Légale, Centre Hospitalier Universitaire Raymond Poincaré, AP-HP, 104 boulevard Raymond Poincaré, 92380, Garches, France
| | - A Knapp-Gisclon
- Laboratoire de Pharmacologie - Toxicologie, Centre Hospitalier Universitaire Raymond Poincaré, AP-HP, 104 boulevard Raymond Poincaré, 92380, Garches, France
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Struble TJ, Alvarez JC, Brown SP, Chytil M, Cisar J, DesJarlais RL, Engkvist O, Frank SA, Greve DR, Griffin DJ, Hou X, Johannes JW, Kreatsoulas C, Lahue B, Mathea M, Mogk G, Nicolaou CA, Palmer AD, Price DJ, Robinson RI, Salentin S, Xing L, Jaakkola T, Green WH, Barzilay R, Coley CW, Jensen KF. Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis. J Med Chem 2020; 63:8667-8682. [PMID: 32243158 PMCID: PMC7457232 DOI: 10.1021/acs.jmedchem.9b02120] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Artificial
intelligence and machine learning have demonstrated
their potential role in predictive chemistry and synthetic planning
of small molecules; there are at least a few reports of companies
employing in silico synthetic planning into their
overall approach to accessing target molecules. A data-driven synthesis
planning program is one component being developed and evaluated by
the Machine Learning for Pharmaceutical Discovery and Synthesis (MLPDS)
consortium, comprising MIT and 13 chemical and pharmaceutical company
members. Together, we wrote this perspective to share how we think
predictive models can be integrated into medicinal chemistry synthesis
workflows, how they are currently used within MLPDS member companies,
and the outlook for this field.
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Affiliation(s)
- Thomas J Struble
- Department of Chemical Engineering, MIT, Cambridge, Massachusetts 02139, United States
| | - Juan C Alvarez
- Computational and Structural Chemistry, Merck & Co. Inc., Kenilworth, New Jersey 07033, United States
| | - Scott P Brown
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Milan Chytil
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Justin Cisar
- Janssen Research & Development LLC, Spring House, Pennsylvania 19477, United States
| | - Renee L DesJarlais
- Janssen Research & Development LLC, Spring House, Pennsylvania 19477, United States
| | - Ola Engkvist
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Scott A Frank
- Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Daniel R Greve
- LEO Pharma A/S, Industriparken 55, DK-2750 Ballerup, Denmark
| | | | - Xinjun Hou
- Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Jeffrey W Johannes
- Medicinal Chemistry, Early Oncology, Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | | | - Brian Lahue
- Computational and Structural Chemistry, Merck & Co. Inc., Kenilworth, New Jersey 07033, United States
| | - Miriam Mathea
- BASF SE, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany
| | | | | | - Andrew D Palmer
- BASF SE, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany
| | - Daniel J Price
- GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Richard I Robinson
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | | | - Li Xing
- WuXi AppTec, Cambridge, Massachusetts 02142, United States
| | - Tommi Jaakkola
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, United States
| | - William H Green
- Department of Chemical Engineering, MIT, Cambridge, Massachusetts 02139, United States
| | - Regina Barzilay
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, United States
| | - Connor W Coley
- Department of Chemical Engineering, MIT, Cambridge, Massachusetts 02139, United States
| | - Klavs F Jensen
- Department of Chemical Engineering, MIT, Cambridge, Massachusetts 02139, United States
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Larabi IA, Fabresse N, Etting I, Nadour L, Pfau G, Raphalen JH, Philippe P, Edel Y, Alvarez JC. Prevalence of New Psychoactive Substances (NPS) and conventional drugs of abuse (DOA) in high risk populations from Paris (France) and its suburbs: A cross sectional study by hair testing (2012-2017). Drug Alcohol Depend 2019; 204:107508. [PMID: 31670189 DOI: 10.1016/j.drugalcdep.2019.06.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/12/2019] [Accepted: 06/03/2019] [Indexed: 01/12/2023]
Abstract
BACKGROUND The aim of the present study is to describe the prevalence of NPS and conventional DOA in Paris and its suburbs over a six-year period using hair testing approach. METHOD Hair was sampled in patients admitted to different departments of Paris hospitals between 2012 and 2017. Two high-risk populations were mainly considered: 1) drug-dependent and 2) acutely intoxicated patients. Segmental hair analysis was performed by validated LC-MS/MS method to screen for DOA and 83 NPS. RESULTS 480 patients (280 M/200 F, 15-70 years) were included. 141 patients tested positive for NPS (99 M/42 F; median age: 33). NPS prevalence was 29%, that of amphetamines, cocaine and opioids were 32%, 38.5% and 52%, respectively. 27 NPS were identified, 4-MEC and mephedrone (number of cases n = 24 each) were the most detected cathinones. JWH-122 (n = 1) was the only detected synthetic cannabinoid while ketamine (n = 104) was present in numerous NPS users (67%). 3-fluorofentanyl (n = 1), furanylfentanyl (n = 1), N-ethylpentylone (n = 2), pentedrone (n = 2), mexedrone (n = 1), methcathinone (n = 3), 6-APDB (n = 2), TFMPP (n = 2), 2-CE (n = 1), 3,4-MD-αPHP (n = 1) and dextromethorphan (n = 27) were identified for the first time in hair. Users were found to have more than one NPS in 53% of cases, mostly in combination with conventional DOA. The number of detected NPS rose from 5 in 2012 to 42 in 2017. A broad range of hair concentrations (0.001-318 ng/mg) was found, but the low median concentrations seem to show an occasional exposure more than chronic use. CONCLUSION NPS screening should be assessed in routine clinical practice, especially in high-risk populations.
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Affiliation(s)
- I A Larabi
- Department of Pharmacology and Toxicology, Versailles Saint-Quentin-en-Yvelines University, Inserm U-1173, Raymond Poincaré Hospital, AP-HP, 104, Raymond Poincaré Blvd., 92380 Garches, France
| | - N Fabresse
- Department of Pharmacology and Toxicology, Versailles Saint-Quentin-en-Yvelines University, Inserm U-1173, Raymond Poincaré Hospital, AP-HP, 104, Raymond Poincaré Blvd., 92380 Garches, France
| | - I Etting
- Department of Pharmacology and Toxicology, Versailles Saint-Quentin-en-Yvelines University, Inserm U-1173, Raymond Poincaré Hospital, AP-HP, 104, Raymond Poincaré Blvd., 92380 Garches, France
| | - L Nadour
- Talan Solutions, 21 Dumont d'Urville Street, 75016, Paris, France
| | - G Pfau
- Addiction Clinic, Pitié Salpétrière Hospital, AP-HP, 47-83 Boulevard de l'Hôpital, 75013 Paris, France
| | - J H Raphalen
- Intensive Care Unit, AP-HP, Necker Hospital, 149 Sèvres Street, 75015 Paris, France
| | - P Philippe
- Intensive Care Unit, AP-HP, Necker Hospital, 149 Sèvres Street, 75015 Paris, France
| | - Y Edel
- Addiction Clinic, Pitié Salpétrière Hospital, AP-HP, 47-83 Boulevard de l'Hôpital, 75013 Paris, France
| | - J C Alvarez
- Department of Pharmacology and Toxicology, Versailles Saint-Quentin-en-Yvelines University, Inserm U-1173, Raymond Poincaré Hospital, AP-HP, 104, Raymond Poincaré Blvd., 92380 Garches, France.
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Campos KR, Coleman PJ, Alvarez JC, Dreher SD, Garbaccio RM, Terrett NK, Tillyer RD, Truppo MD, Parmee ER. The importance of synthetic chemistry in the pharmaceutical industry. Science 2019; 363:363/6424/eaat0805. [PMID: 30655413 DOI: 10.1126/science.aat0805] [Citation(s) in RCA: 224] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Innovations in synthetic chemistry have enabled the discovery of many breakthrough therapies that have improved human health over the past century. In the face of increasing challenges in the pharmaceutical sector, continued innovation in chemistry is required to drive the discovery of the next wave of medicines. Novel synthetic methods not only unlock access to previously unattainable chemical matter, but also inspire new concepts as to how we design and build chemical matter. We identify some of the most important recent advances in synthetic chemistry as well as opportunities at the interface with partner disciplines that are poised to transform the practice of drug discovery and development.
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Affiliation(s)
- Kevin R Campos
- Global Chemistry, Merck & Co. Inc., Kenilworth, NJ 07033, USA.
| | - Paul J Coleman
- Global Chemistry, Merck & Co. Inc., Kenilworth, NJ 07033, USA.
| | - Juan C Alvarez
- Global Chemistry, Merck & Co. Inc., Kenilworth, NJ 07033, USA
| | | | | | | | | | | | - Emma R Parmee
- Global Chemistry, Merck & Co. Inc., Kenilworth, NJ 07033, USA
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Losey HC, Lopes JE, Dean RL, Huff MR, Moroso RA, Alvarez JC. Abstract 591: Efficacy of ALKS 4230, a novel immunotherapeutic agent, in murine syngeneic tumor models alone and in combination with immune checkpoint inhibitors. Immunology 2017. [DOI: 10.1158/1538-7445.am2017-591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Lopes JE, Losey HC, Dean RL, Flick HL, Huff MR, Moroso RA, Sun L, Alvarez JC. Abstract 2663: Characterization of the pharmacodynamic immune response to a novel immunotherapeutic agent, ALKS 4230, in mice and non-human primates. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
ALKS 4230 is a selective agonist of the intermediate-affinity IL-2 receptor (IL-2R). A phase 1 study is ongoing to evaluate the safety and tolerability of ALKS 4230 in the treatment of patients with refractory solid tumors. The selectivity of ALKS 4230 is achieved through the stable fusion of circularly permuted IL-2 to the extracellular portion of the IL-2Rα chain, CD25. The resulting fusion protein is sterically prevented from binding to the high-affinity IL-2R complex, comprised of IL-2Rα, IL-2Rβ, and common gamma chain, expressed preferentially on CD4+ FOXP3+ regulatory T cells (CD4+ Tregs) yet retains full ability to signal through the intermediate-affinity IL-2R complex, comprised of IL-2Rβ and common gamma chain, expressed on memory CD8+ T cells and NK cells. Repeated dosing of ALKS 4230 drives the significant expansion of various CD8+ T cell and NK cell populations without activation and minimal expansion of CD4+ Tregs in mice and non-human primates (NHP). The kinetics of the immunological responses in mice and NHP demonstrate that the pharmacodynamic effects persist beyond systemic exposure of ALKS 4230. Data demonstrating the effects of ALKS 4230 on tumor-infiltrating lymphocyte populations in syngeneic tumor models will also be presented.
Citation Format: Jared E. Lopes, Heather C. Losey, Reginald L. Dean, Heather L. Flick, Michael R. Huff, Rosemarie A. Moroso, Lei Sun, Juan C. Alvarez. Characterization of the pharmacodynamic immune response to a novel immunotherapeutic agent, ALKS 4230, in mice and non-human primates [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2663. doi:10.1158/1538-7445.AM2017-2663
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Lopes JE, Fisher JL, Losey HC, Ernstoff MS, Alvarez JC. Abstract 3158: Ex vivo expansion and activation of human lymphocytes with a selective activator of effector cells. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-3158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
RDB 1450 is an engineered fusion protein of circularly permuted IL-2 and IL-2Rα that is selective for the intermediate-affinity IL-2 receptor. The intermediate-affinity receptor is comprised of the IL-2 receptor beta chain (CD122) and common gamma chain (CD132) expressed on lymphocytes with effector function, whereas the high-affinity receptor, which additionally includes the alpha chain (CD25), is expressed primarily on immunosuppressive CD4+CD25+ regulatory T cells (Tregs). Ex vivo proliferation of subsets of human lymphocytes in response to RDB 1450 or rhIL-2 were evaluated. RDB 1450 supports the selective activation and expansion of effector lymphocytes based on higher observed memory CD8 T/Treg and NK/Treg ratios. Both RDB 1450 and IL-2 drive expansion of NK cells, however, a greater proportion of CD25+ NK cells are observed in response to RDB 1450. Furthermore, unlike IL-2, RDB 1450 does not effectively expand highly suppressive ICOS+ Tregs. The immunological profile resulting from the ex vivo treatment of human PBMCs with RDB 1450 supports its use as a novel immunotherapy for cancer.
Citation Format: Jared E. Lopes, Jan L. Fisher, Heather C. Losey, Marc S. Ernstoff, Juan C. Alvarez. Ex vivo expansion and activation of human lymphocytes with a selective activator of effector cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3158. doi:10.1158/1538-7445.AM2015-3158
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Affiliation(s)
| | - Jan L. Fisher
- 2Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Lebanon, NH
| | | | - Marc S. Ernstoff
- 3Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH
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Losey HC, Lopes JE, Dean RL, Flick H, Gomes M, Huff MR, Moroso RA, Sun L, Wang C, Waters JF, Alvarez JC. Abstract 4280: Utilizing a selective agonist of the intermediate-affinity IL-2 receptor with an improved pharmacokinetic profile leads to an enhanced immunostimulatory response With reduced toxicity in mice. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-4280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
RDB 1450 is an engineered fusion protein which selectively activates the intermediate-affinity IL-2 receptor present on NK cells and memory CD8 T cells. In rodents, RDB 1450 has a half-life of 6-8 hours, compared to a half-life of minutes for recombinant human IL-2 (rhIL-2). Repeat daily dosing (QD) of RDB 1450 in mice results in marked expansion of NK cells and CD8+CD44high T cells, with minimal expansion of CD4+ regulatory T cells (Tregs). Higher QD doses elicit more pronounced effector cell expansion with modest pulmonary edema. TID delivery of the same total daily dose of RDB 1450 enhances the immunological responses in the absence of pulmonary edema. These results suggest that prolonged delivery of reduced concentrations of RDB 1450 drive the desired immune responses with improved tolerability. In contrast, high circulating concentrations of rhIL-2 are required to stimulate effector cells due to its preferential activation of Tregs at lower concentrations. The selectivity profile and favorable pharmacokinetics of RDB 1450 highlight its potential as a novel, differentiated immunotherapeutic agent for the treatment of cancer.
Citation Format: Heather C. Losey, Jared E. Lopes, Reginald L. Dean, Heather Flick, Madison Gomes, Michael R. Huff, Rosemarie A. Moroso, Lei Sun, Chunhua Wang, Julie F. Waters, Juan C. Alvarez. Utilizing a selective agonist of the intermediate-affinity IL-2 receptor with an improved pharmacokinetic profile leads to an enhanced immunostimulatory response With reduced toxicity in mice. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4280. doi:10.1158/1538-7445.AM2015-4280
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Rosentrater EE, Flick H, Lopes JE, Losey HC, Wang C, Alvarez JC. Abstract 4281: Determination of the Relative Potency of a Selective Agonist of the Intermediate-Affinity IL-2 Receptor on Lymphocytes from Human, Cynomolgus Monkey and Mouse. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-4281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
RDB 1450 is an engineered fusion protein designed to selectively activate the intermediate-affinity IL-2 receptor versus the high-affinity IL-2 receptor. The potencies of RDB 1450 and IL-2 for activation of distinct subsets of effector and regulatory lymphocytes from murine, non-human primate and human donors were determined. Splenocytes isolated from mice or leukocytes isolated from human or cyno blood were stimulated with either RDB 1450 or IL-2. Multicolor flow cytometry was used to identify distinct subpopulations and the extent of phosphorylation of STAT5 was measured. Whereas IL-2 is 2-3 orders of magnitude more potent on immunosuppressive Tregs relative to NK cells and memory CD8 T cells, RDB 1450 induces activation of NK cells, memory CD8 T cells and Tregs at comparable concentrations within each species. The non-differentiated potency of RDB 1450 on the lymphocyte subpopulations examined suggests that its effects are mediated through the intermediate affinity receptors even on CD25-expressing Tregs. The preferential activation of Tregs by IL-2 may lead to immunosuppression and limit its antitumor efficacy. In contrast, RDB 1450 does not exhibit the same preference for Treg activation and is expected to be more effective in driving antitumor immune responses. These results highlight the differentiated immunological profile of RDB 1450 and support its potential as a novel human immunotherapy.
Citation Format: Emily E. Rosentrater, Heather Flick, Jared E. Lopes, Heather C. Losey, Chunhua Wang, Juan C. Alvarez. Determination of the Relative Potency of a Selective Agonist of the Intermediate-Affinity IL-2 Receptor on Lymphocytes from Human, Cynomolgus Monkey and Mouse. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4281. doi:10.1158/1538-7445.AM2015-4281
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Funck-Brentano E, Alvarez JC, Longvert C, Abe E, Beauchet A, Funck-Brentano C, Saiag P. Plasma vemurafenib concentrations in advanced BRAFV600mut melanoma patients: impact on tumour response and tolerance. Ann Oncol 2015; 26:1470-5. [PMID: 25899783 DOI: 10.1093/annonc/mdv189] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 04/13/2015] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Vemurafenib improves survival in advanced BRAFV600(mut) melanoma patients, but tolerance is often poor and resistance frequently occurs, without predictive factor. Our aim was to investigate for the first time a relationship between plasma vemurafenib concentration (PVC) and efficacy or tolerance. METHODS Plasma samples from unresectable metastatic BRAFV600(mut) melanoma patients treated with vemurafenib monotherapy were prospectively collected at each tumour response evaluation (RECIST 1.1) or when adverse event occurred (CTCAE 4.0). PVC was measured with liquid chromatography-tandem mass spectrometry. Herein, we report on PVC at steady state (≥14 days after vemurafenib introduction or dose modification). Samples collected after first melanoma progression were excluded from the response analysis. All samples were analysed in the tolerance analysis. We kept the closest collected sample from the onset of each adverse effect or the one with the highest PVC in the absence of this adverse effect. Comparisons of means (Student's t-tests and Wilcoxon rank sum tests) and of frequencies (χ(2) tests) were carried out. A logistic regression analysis identified predictors of progression. RESULTS We included 105 plasma samples in 23 patients (10M/13F). Initial vemurafenib dose was 960 mg b.i.d., reduced by 25% (8 patients) or 50% (2 patients) for intolerance in 10 patients (44%). PVC displayed high inter-individual variability (13.0-109.8 µg/ml, median 54.0). Mean PVC was lower at time of first progression (38.8 ± 19.7 µg/ml) than mean PVC found when tumour was stable or in partial or complete response (56.4 ± 21.0 µg/ml, P = 0.013, 21 patients). Logistic regression revealed that having a low PVC (P = 0.01) or brain metastasis (P = 0.01) were both significantly and independently associated with tumour progression. High PVC was not statistically significantly associated with the occurrence of adverse effects. CONCLUSION PVC at steady state is highly variable and low PVC was associated with tumour progression, suggesting a new path to melanoma resistance to vemurafenib.
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Affiliation(s)
- E Funck-Brentano
- Department of Dermatology, AP-HP, Ambroise Paré Hospital, Boulogne-Billancourt University of Versailles-Saint-Quentin-en-Yvelines, Research Unit EA 4340 'Biomarkers in Cancerology and in Hemato-oncology', Boulogne-Billancourt
| | - J C Alvarez
- Department of Toxicology, AP-HP, Raymond Poincaré Hospital, Boulogne-Billancourt University of Versailles-Saint-Quentin-en-Yvelines, Boulogne-Billancourt
| | - C Longvert
- Department of Dermatology, AP-HP, Ambroise Paré Hospital, Boulogne-Billancourt University of Versailles-Saint-Quentin-en-Yvelines, Research Unit EA 4340 'Biomarkers in Cancerology and in Hemato-oncology', Boulogne-Billancourt
| | - E Abe
- Department of Toxicology, AP-HP, Raymond Poincaré Hospital, Boulogne-Billancourt University of Versailles-Saint-Quentin-en-Yvelines, Boulogne-Billancourt
| | - A Beauchet
- University of Versailles-Saint-Quentin-en-Yvelines, Boulogne-Billancourt Department of Public Health, AP-HP, Ambroise Paré Hospital, Boulogne-Billancourt
| | - C Funck-Brentano
- INSERM, CIC-1421 and UMR ICAN 1166, Paris Department of Pharmacology and CIC-1421, AP-HP, Pitié-Salpêtrière Hospital, Paris Department of Pharmacology and UMR ICAN 1166, Faculty of Medicine, Sorbonne Universités, UPMC Univ Paris 06, Paris, France
| | - P Saiag
- Department of Dermatology, AP-HP, Ambroise Paré Hospital, Boulogne-Billancourt University of Versailles-Saint-Quentin-en-Yvelines, Research Unit EA 4340 'Biomarkers in Cancerology and in Hemato-oncology', Boulogne-Billancourt
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Abstract
Usual human motion capture systems are designed to work in controlled laboratory conditions. For occupational health, instruments that can measure during normal daily life are essential, as the evaluation of the workers' movements is a key factor to reduce employee injury- and illness-related costs. In this paper, we present a method for joint angle measurement, combining inertial sensors (accelerometers and gyroscopes) and magnetic sensors. This method estimates wrist flexion, wrist lateral deviation, elbow flexion, elbow pronation, shoulder flexion, shoulder abduction and shoulder internal rotation. The algorithms avoid numerical integration of the signals, which allows for long-time estimations without angle estimation drift. The system has been tested both under laboratory and field conditions. Controlled laboratory tests show mean estimation errors between 0.06° and of 1.05°, and standard deviation between 2.18° and 9.20°. Field tests seem to confirm these results when no ferromagnetic materials are close to the measurement system.
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Affiliation(s)
- Diego Álvarez
- a SiMuR Lab, Department of Electrical and Computer Engineering , University of Oviedo , Viesques, Ed. 2, 33204 , Gijón , Spain
| | - Juan C Alvarez
- a SiMuR Lab, Department of Electrical and Computer Engineering , University of Oviedo , Viesques, Ed. 2, 33204 , Gijón , Spain
| | - Rafael C González
- a SiMuR Lab, Department of Electrical and Computer Engineering , University of Oviedo , Viesques, Ed. 2, 33204 , Gijón , Spain
| | - Antonio M López
- a SiMuR Lab, Department of Electrical and Computer Engineering , University of Oviedo , Viesques, Ed. 2, 33204 , Gijón , Spain
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Alvarez-Cubero MJ, Saiz M, Martinez-Gonzalez LJ, Alvarez JC, Eisenberg AJ, Budowle B, Lorente JA. Genetic identification of missing persons: DNA analysis of human remains and compromised samples. Pathobiology 2012; 79:228-38. [PMID: 22722562 DOI: 10.1159/000334982] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Human identification has made great strides over the past 2 decades due to the advent of DNA typing. Forensic DNA typing provides genetic data from a variety of materials and individuals, and is applied to many important issues that confront society. Part of the success of DNA typing is the generation of DNA databases to help identify missing persons and to develop investigative leads to assist law enforcement. DNA databases house DNA profiles from convicted felons (and in some jurisdictions arrestees), forensic evidence, human remains, and direct and family reference samples of missing persons. These databases are essential tools, which are becoming quite large (for example the US Database contains 10 million profiles). The scientific, governmental and private communities continue to work together to standardize genetic markers for more effective worldwide data sharing, to develop and validate robust DNA typing kits that contain the reagents necessary to type core identity genetic markers, to develop technologies that facilitate a number of analytical processes and to develop policies to make human identity testing more effective. Indeed, DNA typing is integral to resolving a number of serious criminal and civil concerns, such as solving missing person cases and identifying victims of mass disasters and children who may have been victims of human trafficking, and provides information for historical studies. As more refined capabilities are still required, novel approaches are being sought, such as genetic testing by next-generation sequencing, mass spectrometry, chip arrays and pyrosequencing. Single nucleotide polymorphisms offer the potential to analyze severely compromised biological samples, to determine the facial phenotype of decomposed human remains and to predict the bioancestry of individuals, a new focus in analyzing this type of markers.
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Affiliation(s)
- M J Alvarez-Cubero
- Laboratory of Genetic Identification, Department of Legal Medicine and Toxicology, Medical Faculty, University of Granada, Granada, Spain.
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Alvarez-Cubero MJ, Martinez-Gonzalez LJ, Virgen-Ponce D, Delgado-Najar EA, Moscoso-Caloca GH, Alvarez JC, Lorente JA. Genetic variation of 15 autosomal microsatellite loci in a Nayarit population (Mexico). Leg Med (Tokyo) 2011; 13:323-7. [PMID: 21944851 DOI: 10.1016/j.legalmed.2011.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 07/22/2011] [Accepted: 07/25/2011] [Indexed: 11/30/2022]
Abstract
Fifteen STRs are studied to determine the allele frequencies' distribution and to evaluate the homogeneity of Nayarit populations. This study allows the identification of forensic efficiency parameters to be used in forensic genetics and to explore the genetic similarities between Nayarit and the neighboring countries such as Mexico, Brazil, Puerto Rico, Guatemala, Honduras, Bolivia and Costa Rica. The Hardy-Weinberg equilibrium, expected heterozygosity, matching probability, and power of discrimination, were calculated in the Nayarit population. We found that with respect to the studied markers, Nayarit genetic structure is homogeneous. In this study, it is established that Nayarit is genetically similar to the South American Mestizo population. The distribution of a set of these 15 STRs was analyzed with other South American populations as well as in the extensive set of neighboring populations from the literature (USA, Europe and Africa). We found significant differences exist between the isolated populations (Huastecos, Otomi from Sierra Madre and from Ixmiquilpan Valley) and Mestizo populations. Statistical analysis supports that Americans actual inhabitants and Europeans are genetically similar, while Africans and isolated populations from South America have more genetic differences.
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Affiliation(s)
- M J Alvarez-Cubero
- Laboratory of Genetic Identification, Department of Legal Medicine, University of Granada, Granada, Spain
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Schlehuber LD, McFadyen IJ, Shu Y, Carignan J, Duprex WP, Forsyth WR, Ho JH, Kitsos CM, Lee GY, Levinson DA, Lucier SC, Moore CB, Nguyen NT, Ramos J, Weinstock BA, Zhang J, Monagle JA, Gardner CR, Alvarez JC. Towards ambient temperature-stable vaccines: The identification of thermally stabilizing liquid formulations for measles virus using an innovative high-throughput infectivity assay. Vaccine 2011; 29:5031-9. [DOI: 10.1016/j.vaccine.2011.04.079] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 04/18/2011] [Accepted: 04/20/2011] [Indexed: 11/16/2022]
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Gibson TJ, Mccarty K, McFadyen IJ, Cash E, Dalmonte P, Hinds KD, Dinerman AA, Alvarez JC, Volkin DB. Application of a High-Throughput Screening Procedure with PEG-Induced Precipitation to Compare Relative Protein Solubility During Formulation Development with IgG1 Monoclonal Antibodies. J Pharm Sci 2011; 100:1009-21. [DOI: 10.1002/jps.22350] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 08/20/2010] [Accepted: 08/23/2010] [Indexed: 11/09/2022]
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Vale A, Rojas D, Alvarez JC, Navarro L. Breeding system and factors limiting fruit production in the nectarless orchid Broughtonia lindenii. Plant Biol (Stuttg) 2011; 13 Suppl 1:51-61. [PMID: 21134087 DOI: 10.1111/j.1438-8677.2010.00366.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Low fruit set values in most orchids (especially epiphytic and tropical species) are normally thought to be the consequence of pollination constraints and limited resources. In particular, pollination constraints are modulated by pollinator visitation rates, pollinator visitation behaviour (promoting crossing or selfing), the type and number of pollinia deposited on stigmas (in the case of orchids with subequal pollinia) and the amount of pollen loaded per inflorescence. In order to assess to what extent these factors can affect fruit set in specific orchid-pollinator systems, the repercussions of some of these aspects on reproduction of Broughtonia lindenii were examined in a coastal population in western Cuba. The study focused on plant breeding system, importance of pollen load and type of pollinia on subsequent fruit and seed, limiting factors of seed production and interaction with pollinators. This species presents long-lasting flowers that senesce after all forms of effective visit. Pollinator dependence for fruit production was demonstrated, while hand-pollination experiments revealed self-compatibility and inbreeding depression at seed level. More pollinia on stigmas enhance the proportion of well-developed seeds. In contrast, the pollinia type used in pollination is not important for seed quality of fruits, suggesting that small pollinia are not rudimentary. Natural fruit set in two consecutive years was substantially affected by pollinator activity, and also by systematic depredatory activity of ants and a caterpillar. Considering that this orchid completely lacks nectar and that the local assemblage of pollinators and predators influenced its reproduction, a minor importance of resource constraints in this epiphyte (with long-lasting reserve structures) is confirmed at least for a short time.
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Affiliation(s)
- A Vale
- Departamento de Biología Vegetal y Ciencias del Suelo, Universidad de Vigo, Vigo, España
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Monteagudo B, Cabanillas M, Suárez-Amor O, Ramírez-Santos A, Alvarez JC, de Las Heras C. [Adult blaschkitis (lichen striatus) in a patient treated with adalimumab]. Actas Dermosifiliogr 2010; 101:891-892. [PMID: 21159267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
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González RC, Alvarez D, López AM, Alvarez JC. Ambulatory estimation of mean step length during unconstrained walking by means of COG accelerometry. Comput Methods Biomech Biomed Engin 2010; 12:721-6. [PMID: 19408138 DOI: 10.1080/10255840902896000] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
It has been reported that spatio-temporal gait parameters can be estimated using an accelerometer to calculate the vertical displacement of the body's centre of gravity. This method has the potential to produce realistic ambulatory estimations of those parameters during unconstrained walking. In this work, we want to evaluate the crude estimations of mean step length so obtained, for their possible application in the construction of an ambulatory walking distance measurement device. Two methods have been tested with a set of volunteers in 20 m excursions. Experimental results show that estimations of walking distance can be obtained with sufficient accuracy and precision for most practical applications (errors of 3.66 +/- 6.24 and 0.96 +/- 5.55%), the main difficulty being inter-individual variability (biggest deviations of 19.70 and 15.09% for each estimator). Also, the results indicate that an inverted pendulum model for the displacement during the single stance phase, and a constant displacement per step during double stance, constitute a valid model for the travelled distance with no need of further adjustments. It allows us to explain the main part of the erroneous distance estimations in different subjects as caused by fundamental limitations of the simple inverted pendulum approach.
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Affiliation(s)
- R C González
- Multisensor Systems & Robotics Lab (SiMuR), Electrical and Computer Engineering Department, University of Oviedo, Gijón, Spain
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25
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Lopez AM, Alvarez D, Gonzalez RC, Alvarez JC. Validity of four gait models to estimate walked distance from vertical COG acceleration. J Appl Biomech 2008; 24:360-367. [PMID: 19075305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Pedometers are basically step counters usually used to estimate the distance walked by a pedestrian. Although their precision to compute the number of steps is quite accurate (about 1%), their feasibility to estimate the walked distance is very poor, as they do not consider the intrinsic variability of human gait. Reported results show values of 10% of precision in optimal conditions, increasing to 50% when conditions differ. Electronic accelerometer-based pedometers base their functioning on a basic processing of the vertical acceleration of the waist. Recently, different approaches have been proposed to relate such signals to the step length. This can lead to an improvement of the performance of this kind of device for estimating the walked distance. In this article, we analyze four gait models applied to the vertical accelerations of the body's center of gravity, three biomechanical and one empirical. We compare their precision and accuracy. Results support the superior performance of three of them over an ideal pedometer. We also analyze their feasibility to be implemented in pedometer-like devices.
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Affiliation(s)
- Antonio M Lopez
- Electrical Engineering Department, University of Oviedo, Spain
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26
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Alvarez JC, Santiveri FX, Rodrígueza B, González I, González-Rivero MA, Escolano F. [Utility of bispectral vs auditory evoked potential monitoring during anesthetic maintenance in combined sevoflurane-regional anesthesia in pediatric patients: comparison with standard practice]. Rev Esp Anestesiol Reanim 2008; 55:527-534. [PMID: 19086719 DOI: 10.1016/s0034-9356(08)70648-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
OBJECTIVES To compare the indices computed by a bispectral (BIS) monitor and an auditory evoked potential (AEP) monitor during maintenance of anesthesia in pediatric patients. A secondary objective was to compare anesthetic consumption and recovery times. MATERIAL AND METHODS Patients aged 6 months to 12 years under inhaled anesthesia with sevoflurane were administered a penile or caudal nerve block. BIS and AEP monitoring was then started. The patients were randomized to 3 groups in which the sevoflurane dosage was guided by the BIS index, the A-line ARX index (AAI), or standard procedures (control group). The BIS index, the AAI, the fraction of expired sevoflurane, hemodynamic parameters, and recovery time were the variables recorded for all patients. RESULTS Thirty-five patients were enrolled. Significant differences between the 2 monitor groups were observed. The mean (SD) AAI was lower in patients whose dosage was controlled by the BIS index (19 [2]) than in those whose dosage was based on the AEP monitor's reading (22 [4]) (P=.04). According to a Bland and Altman plot, there was good agreement between the BIS index and the AAI except for the highest and, in particular, the lowest values. The volumes of sevoflurane used and the recovery times were similar between groups. There was a positive correlation between the 2 indices (Pearson correlation coefficient, 0.207; P<.001). CONCLUSIONS BIS monitoring provided a more stable index than did AEP monitoring and BIS-index guidance achieved a deeper level of hypnosis. There was good correlation between the 2 indices during maintenance of anesthesia. Neither monitor offered advantages over standard procedures with regard to movement, volume of anesthetic consumed, or recovery time.
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Affiliation(s)
- J C Alvarez
- Servicio de Anestesia, Reanimación y Terapéutica del Dolor. Hospital Mar-Esperança. IMAS, Barcelona.
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Alvarez JC, González RC, Alvarez D, López AM, Rodríguez-Uría J. Multisensor approach to walking distance estimation with foot inertial sensing. ACTA ACUST UNITED AC 2008; 2007:5720-3. [PMID: 18003311 DOI: 10.1109/iembs.2007.4353645] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Walking distance estimation is an important issue in areas such as gait analysis, sport training or pedestrian localization. A natural location for portable inertial sensors for gait monitoring is to attach them to the user shoes. Step length can be computed by means of a biaxial accelerometer and a gyroscope on the sagittal plane. But estimations based on the direct signal integration are prone to error. This paper shows the results achieved by using a multisensor model approach to reduce uncertainty. Unbounded growth of error is reduced by means of sensor fusion techniques. The method has been tested, and early experimental results show that it provides an estimation of the walking distance with a standard deviation smaller than with single IMU similar systems.
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Affiliation(s)
- Juan C Alvarez
- Multisensor Systems & Robotics Lab (SiMuR), Electrical Eng. Dept., University of Oviedo, Viesques, Ed. 2, 33204 Gijón, Spain.
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Abstract
Step length estimation is an important issue in areas such as gait analysis, sport training or pedestrian localization. It has been shown that the mean step length can be computed by means of a triaxial accelerometer placed near the center of gravity of the human body. Estimations based on the inverted pendulum model are prone to underestimate the step length, and must be corrected by calibration. In this paper we present a modified pendulum model in which all the parameters correspond to anthropometric data of the individual. The method has been tested with a set of volunteers, both males and females. Experimental results show that this method provides an unbiased estimation of the actual displacement with a standard deviation lower than 2.1%.
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Affiliation(s)
- Rafael C González
- Multisensor Systems & Robotics Lab (SiMuR), Electrical Engineering Department, University of Oviedo, Viesques, Ed. 2, 33204 Gijón, Spain.
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Fernández JA, Suárez C, Navarro A, Díaz C, Alvarez JC, González del Rey C, Tolivia J. Aging in the vestibular nuclear complex of the male golden hamster (Mesocricetus auratus): anatomic and morphometric study. Histol Histopathol 2007; 22:855-68. [PMID: 17503342 DOI: 10.14670/hh-22.855] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To study the effects of senescence on the vestibular nuclear complex twenty brainstems from male golden hamsters between 3 and 27 months-old were used and the possible variations in the number of neurons, neuronal morphology and nuclear volume were studied. The neuron profiles were drawn with a camera lucida and Abercrombie's method was used to estimate the total number of neurons. The test of Kolmogorov-Smirnov with the correction of Lilliefors was used to evaluate the fit of our data to a normal distribution and a regression analysis was done to decide if the variation of our data with age was statistically significant. The results of the present study are relevant only for male animals and the effect of senescence could be different in female vestibular nuclear complex. Aging affects the volume of the superior and lateral vestibular nuclei, as well as the nuclear neuronal diameter of the medial vestibular nucleus, but no significant neuronal loss has been appreciated in vestibular nuclear complex related with age. During the aging process we have observed that the distribution of neurons within the vestibular nuclei of the golden hamster does not show important changes and most of their morphometric parameters do not vary significantly.
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Affiliation(s)
- J A Fernández
- Service of Otorrinolaringology of the Burela Coast Hospital, Lugo, Spain
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30
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Monteagudo B, Ginarte M, Ramírez A, Labandeira J, Alvarez JC, de las Heras C, Cacharrón JM. [Violaceus plaque in the left leg]. Actas Dermosifiliogr 2007; 98:281-2. [PMID: 17506963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Affiliation(s)
- B Monteagudo
- Servicios de Dermatología, Complejo Hospitalario Arquitecto Marcide-Novoa Santos, Ferrol, España.
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Salaniwal S, Manas ES, Alvarez JC, Unwalla RJ. Critical evaluation of methods to incorporate entropy loss upon binding in high-throughput docking. Proteins 2007; 66:422-35. [PMID: 17068803 DOI: 10.1002/prot.21180] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Proper accounting of the positional/orientational/conformational entropy loss associated with protein-ligand binding is important to obtain reliable predictions of binding affinity. Herein, we critically examine two simplified statistical mechanics-based approaches, namely a constant penalty per rotor method, and a more rigorous method, referred to here as the partition function-based scoring (PFS) method, to account for such entropy losses in high-throughput docking calculations. Our results on the estrogen receptor beta and dihydrofolate reductase proteins demonstrate that, while the constant penalty method over-penalizes molecules for their conformational flexibility, the PFS method behaves in a more "DeltaG-like" manner by penalizing different rotors differently depending on their residual entropy in the bound state. Furthermore, in contrast to no entropic penalty or the constant penalty approximation, the PFS method does not exhibit any bias towards either rigid or flexible molecules in the hit list. Preliminary enrichment studies using a lead-like random molecular database suggest that an accurate representation of the "true" energy landscape of the protein-ligand complex is critical for reliable predictions of relative binding affinities by the PFS method.
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Affiliation(s)
- Sumeet Salaniwal
- Structural Biology and Computational Chemistry Department, Chemical and Screening Sciences Division, Wyeth Research, Collegeville, Pennsylvania 19426, USA
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Monteagudo B, León A, Durana C, de las Heras C, Used MM, Alvarez JC, Cacharrón JM. [Type 1 segmental manifestation of multiple glomangiomas]. Actas Dermosifiliogr 2006; 97:358-9. [PMID: 16956575 DOI: 10.1016/s0001-7310(06)73421-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Tsao DHH, Sutherland AG, Jennings LD, Li Y, Rush TS, Alvarez JC, Ding W, Dushin EG, Dushin RG, Haney SA, Kenny CH, Malakian AK, Nilakantan R, Mosyak L. Discovery of novel inhibitors of the ZipA/FtsZ complex by NMR fragment screening coupled with structure-based design. Bioorg Med Chem 2006; 14:7953-61. [PMID: 16919463 DOI: 10.1016/j.bmc.2006.07.050] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Revised: 07/19/2006] [Accepted: 07/26/2006] [Indexed: 11/21/2022]
Abstract
ZipA is a membrane anchored protein in Escherichia coli that interacts with FtsZ, a homolog of eukaryotic tubulins, forming a septal ring structure that mediates bacterial cell division. Thus, the ZipA/FtsZ protein-protein interaction is a potential target for an antibacterial agent. We report here an NMR-based fragment screening approach which identified several hits that bind to the C-terminal region of ZipA. The screen was performed by 1H-15N HSQC experiments on a library of 825 fragments that are small, lead-like, and highly soluble. Seven hits were identified, and the binding mode of the best one was revealed in the X-ray crystal structure. Similar to the ZipA/FtsZ contacts, the driving force in the binding of the small molecule ligands to ZipA is achieved through hydrophobic interactions. Analogs of this hit were also evaluated by NMR and X-ray crystal structures of these analogs with ZipA were obtained, providing structural information to help guide the medicinal chemistry efforts.
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Affiliation(s)
- Désirée H H Tsao
- Structural Biology and Computational Chemistry, Wyeth Research, Cambridge, MA 02140, USA.
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34
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Alvarez D, Gonzalez RC, Lopez A, Alvarez JC. Comparison of step length estimators from weareable accelerometer devices. Conf Proc IEEE Eng Med Biol Soc 2006; 2006:5964-5967. [PMID: 17946351 DOI: 10.1109/iembs.2006.259593] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Wearable accelerometry provides easily portable systems that supply real-time data adequate for gait analysis. When they do not provide direct measurement of a spatio-temporal parameter of interest, such as step length, it has to be estimated with a mathematical model from indirect sensor measurements. In this work we are concerned with the accelerometry-based estimation of the step length in straight line human walking. We compare five step length estimators. Measurements were taken from a group of four adult men, adding up a total of 800 m per individual of walking data. Also modifications to these estimators are proposed, based on biomechanical considerations. Results show that this modifications lead to improvements of interest over previous methods.
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35
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Kaila N, Somers WS, Thomas BE, Thakker P, Janz K, DeBernardo S, Tam S, Moore WJ, Yang R, Wrona W, Bedard PW, Crommie D, Keith JC, Tsao DHH, Alvarez JC, Ni H, Marchese E, Patton JT, Magnani JL, Camphausen RT. Quinic Acid Derivatives as Sialyl Lewisx-Mimicking Selectin Inhibitors: Design, Synthesis, and Crystal Structure in Complex with E-Selectin. J Med Chem 2005; 48:4346-57. [PMID: 15974587 DOI: 10.1021/jm050049l] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A search for noncarbohydrate sLe(x) mimics led to the development of quinic acid derivatives as selectin inhibitors. At Wyeth we solved the first cocrystal structure of a small molecule, quinic acid, with E-selectin. In the cocomplex two hydroxyls of quinic acid mimic the calcium-bound fucose of the tetrasaccharide sLe(x). The X-ray structure, together with structure based computational methods, was used to design quinic acid based libraries that were synthesized and evaluated for their ability to block the interaction of sLex with P-selectin. A large number of analogues were prepared using solution-phase parallel synthesis. Selected compounds showed decrease in leukocyte rolling in the IVM mouse model. Compound 2 inhibited neutrophil influx in the murine TIP model and demonstrated good plasma exposure.
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Affiliation(s)
- Neelu Kaila
- Chemical & Screening Sciences and Cardiovascular and Metabolic Disease Research, Wyeth, Cambridge, Massachusetts 02140, USA.
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36
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Abstract
Cholesterol crystal embolism (CCE) is an infrequent entity that primarily appears in males over the age of 60 with generalized arteriosclerosis after angiographic procedures, vascular surgery or, more rarely, with oral anticoagulant treatment with heparin or with fibrinolytics. We present the case of a patient with several risk factors for CCE, who presented with the pathognomonic triad of leg and foot pain, livedo reticularis and palpable pedal pulses. The diagnosis was based on the fact that cholesterol crystals were seen in the arterioles in the skin biopsy. Due to the frequency with which the skin manifestations appear and the importance of early diagnosis and treatment, an awareness of these crystals is fundamental in diagnosing these processes.
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Affiliation(s)
- María T Bordel
- Servicio de Dermatología, Complejo Hospitalario Arquitecto Marcide-Profesor Novoa Santos, Ferrol, A Coruña, Spain.
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Manas ES, Unwalla RJ, Xu ZB, Malamas MS, Miller CP, Harris HA, Hsiao C, Akopian T, Hum WT, Malakian K, Wolfrom S, Bapat A, Bhat RA, Stahl ML, Somers WS, Alvarez JC. Structure-based design of estrogen receptor-beta selective ligands. J Am Chem Soc 2005; 126:15106-19. [PMID: 15548008 DOI: 10.1021/ja047633o] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present the structure-based optimization of a series of estrogen receptor-beta (ERbeta) selective ligands. X-ray cocrystal structures of these ligands complexed to both ERalpha and ERbeta are described. We also discuss how molecular modeling was used to take advantage of subtle differences between the two binding cavities in order to optimize selectivity for ERbeta over ERalpha. Quantum chemical calculations are utilized to gain insight into the mechanism of selectivity enhancement. Despite only two relatively conservative residue substitutions in the ligand binding pocket, the most selective compounds have greater than 100-fold selectivity for ERbeta relative to ERalpha when measured using a competitive radioligand binding assay.
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Affiliation(s)
- Eric S Manas
- Department of Chemical and Screening Sciences, Wyeth Research, 500 Arcola Road, Collegeville, Pennsylvania 19426, USA.
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Abstract
Receptor-based virtual screening has become a viable source of novel leads in the pharmaceutical industry. The rapidly growing availability of structural information across protein families, the accessibility to increased computational power at affordable cost, as well as an improved understanding on how to effectively apply virtual screening technologies has contributed to their emergence. Nonetheless, continued improvement in the accuracy of scoring functions and a greater understanding of protein mobility is critical to advance the technology further.
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Affiliation(s)
- Juan C Alvarez
- Chemical and Screening Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge Massachusetts 02140, USA.
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McKew JC, Lovering F, Clark JD, Bemis J, Xiang Y, Shen M, Zhang W, Alvarez JC, Joseph-McCarthy D. Structure–activity relationships of indole cytosolic phospholipase A 2 α inhibitors: substrate mimetics. Bioorg Med Chem Lett 2003; 13:4501-4. [PMID: 14643356 DOI: 10.1016/j.bmcl.2003.08.070] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An SAR effort focused on generating cPLA(2)alpha inhibitors using a substrate mimetic approach is reported. Indole inhibitors of cPLA(2)alpha with promising pharmacokinetic parameters that were active in both an isolated enzyme assay and in cell-based assays were discovered. Modeling these compounds into the cPLA(2)alpha structure validated the assumptions made at the start of the SAR effort.
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Affiliation(s)
- John C McKew
- Departments of Chemical and Screening Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, MA 02140, USA.
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Abstract
Rapid computational mining of large 3D molecular databases is central to generating new drug leads. Accurate virtual screening of large 3D molecular databases requires consideration of the conformational flexibility of the ligand molecules. Ligand flexibility can be included without prohibitively increasing the search time by docking ensembles of precomputed conformers from a conformationally expanded database. A pharmacophore-based docking method whereby conformers of the same or different molecules are overlaid by their largest 3D pharmacophore and simultaneously docked by partial matches to that pharmacophore is presented. The method is implemented in DOCK 4.0.
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Affiliation(s)
- Diane Joseph-McCarthy
- Wyeth Research, Biological Chemistry Department, Cambridge, Massachusetts 02140, USA.
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41
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Abstract
All docking methods employ some sort of heuristic to orient the ligand molecules into the binding site of the target structure. An automated method, MCSS2SPTS, for generating chemically labeled site points for docking is presented. MCSS2SPTS employs the program Multiple Copy Simultaneous Search (MCSS) to determine target-based theoretical pharmacophores. More specifically, chemically labeled site points are automatically extracted from selected low-energy functional-group minima and clustered together. These pharmacophoric site points can then be directly matched to the pharmacophoric features of database molecules with the use of either DOCK or PhDOCK to place the small molecules into the binding site. Several examples of the ability of MCSS2SPTS to reproduce the three-dimensional pharmacophoric features of ligands from known ligand-protein complex structures are discussed. In addition, a site-point set calculated for one human immunodeficiency virus 1 (HIV1) protease structure is used with PhDOCK to dock a set of HIV1 protease ligands; the docked poses are compared to the corresponding complex structures of the ligands. Finally, the use of an MCSS2SPTS-derived site-point set for acyl carrier protein synthase is compared to the use of atomic positions from a bound ligand as site points for a large-scale DOCK search. In general, MCSS2SPTS-generated site points focus the search on the more relevant areas and thereby allow for more effective sampling of the target site.
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42
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Santiveri X, Mansilla R, Pardina B, Navarro J, Alvarez JC, Castillo J. [Ephedrine shortens the onset of action of rocuronium but not atracurium]. Rev Esp Anestesiol Reanim 2003; 50:176-81. [PMID: 12825305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
HYPOTHESIS Ephedrine increases blood flow to muscles and may shorten the onset of action of rocuronium and atracurium. MATERIAL AND METHODS A prospective study of 80 ASA I-III patients undergoing surgery under general anesthesia and randomized to 4 groups: ephedrine-rocuronium, placebo-rocuronium, ephedrine-atracurium and placebo-atracurium. Atracurium or rocuronium was administered at a dose of 0.04 mg.Kg-1. We monitored neuromuscular function by acceleromyography, ECG and pulse oxymetry, arterial blood pressure (ABP) using an intra-arterial catheter (AT), heart rate (HR) and carbon dioxide pressure. Patient characteristics, time to onset, duration and recovery from the neuromuscular block were recorded. HR and ABP were measured at baseline, 3 minutes after ephedrine dosing, 1 minute after induction, immediately after intubation and 5, 10 and 20 minutes after intubation. RESULTS Patient characteristics were similar in all groups. The time to onset of neuromuscular block was significantly shorter in the rocuronium and rocuronium-ephedrine groups than in the atracurium groups. Duration and recovery were similar in all groups. Patients premedicated with ephedrine experienced a significant increase in HR for 20 minutes. The only complications were 2 cases of self-limiting sinus tachycardia of less than 130 beats.min-1 in the ephedrine group. CONCLUSIONS Premeditation with 10 mg of ephedrine decreases the time until onset of action of rocuronium but does not affect the timing of atracurium.
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Affiliation(s)
- X Santiveri
- Servicio de Anestesiología, Reanimación y Terapéutica del Dolor, Hospital Universitario Mar-Esperança, IMAS, C/Passeig Maritim, 25 08003 Barcelona.
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Martinez-Espin E, Fernández-Rosado F, Alvarez JC, Entrala C, Lorente JA, Oviedo de Duarte M, Villanueva E, Budowle B. Paraguayan population data on the fifteen STR loci included in the PowerPlex 16 kit. J Forensic Sci 2003; 48:253-5. [PMID: 12570248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Affiliation(s)
- E Martinez-Espin
- Laboratory of Genetic Identification, Dept de Medicina Legal, Facultad de Medicina, Universidad de Granada, E-18012 Granada, Spain
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Fenández-Rosado F, Martinez-Espin E, Rodríguez T, Entrala C, Alvarez JC, Lorente JA, Lorente M, Budowle B, Villanueva E. Population data of Ecuador for fifteen STR loci (PowerPlex 16). J Forensic Sci 2003; 48:224-6. [PMID: 12570242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Affiliation(s)
- F Fenández-Rosado
- Laboratory of Genetic Identification, Dept de Medicina Legal, Facultad de Medicina, Universidad de Granada, E-18012 Granada, Spain
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45
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Morales JA, Monterrosa JC, Alvarez JC, Entrala C, Lorente JA, Lorente M, Budowle B, Villanueva E. Population data on nine STR loci in an El Salvadoran (Central American) sample population. J Forensic Sci 2002; 47:900-1. [PMID: 12137005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- J A Morales
- Laboratory of DNA, Instituto de Medicina Legal Roberto Masferrei, Corte Suprema de Justicia, San Salvador, El Salvador
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Lorente JA, Entrala C, Alvarez JC, Lorente M, Arce B, Heinrich B, Carrasco F, Budowle B, Villanueva E. Social benefits of non-criminal genetic databases: missing persons and human remains identification. Int J Legal Med 2002; 116:187-90. [PMID: 12111326 DOI: 10.1007/s004140100255] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A Missing Persons Genetic Identification Program (Phoenix Program) was implemented in Spain in order to try to identify cadavers and human remains that could not be identified using traditional forensic approaches; to our knowledge, this is the first database ever implemented and in function in the world. Two separate mitochondrial DNA (mtDNA) databases have been generated and comparisons can be made automatically to match identical or similar sequences contained in both databases. One database is called the Reference Database (RD), which contains mtDNA sequences from maternal relatives of missing persons that provide the samples voluntarily after informed consent. The other database is called the Questioned Database (QD) and is comprised of mtDNA data on unknown remains and cadavers that could not be unequivocally identified. The combined database is a civil database designed solely for human identification and because of the informed consent and voluntary donation of reference samples is different from other databases now used to solve criminal cases. It is timely and incumbent on other willing countries to begin an international collaboration so compatibility and full utility can be enjoyed with this kind of non-criminal database.
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Affiliation(s)
- J A Lorente
- Department of Legal Medicine, University of Granada, Av. Madrid 11, 18012 Granada, Spain.
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Abstract
Potential E- and P-selectin inhibitors were synthesized to explore a hydrophobic area on the E-selectin surface and the PSGL-1 protein binding site on the P-selectin surface that was recently defined by crystallography. Three series of mannose-based compounds (libraries A, B, and C) were synthesized using solution phase parallel synthesis. Biological evaluation of these compounds was done using two ELISA-based assays and transferred NOE (trNOE) experiments. Some of the compounds showed better activity than sLe(x) in the P-selectin assay.
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Affiliation(s)
- Neelu Kaila
- Department of Chemical Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, USA.
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Mathonnet F, Peltier JY, Detruit H, de Raucourt E, Alvarez JC, Mazmanian GM, de Mazancourt P. Fibrinogen Saint-Germain I: a case of the heterozygous Aalpha GLY 12 --> VAL fibrinogen variant. Blood Coagul Fibrinolysis 2002; 13:149-53. [PMID: 11914657 DOI: 10.1097/00001721-200203000-00010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A fibrinogen variant was suspected based on the results of routine coagulation tests in a 2-year-old asymptomatic child. Coagulation studies showed marked prolongation of both the thrombin and reptilase times, and discrepancy was noted between the level of plasma fibrinogen as measured by a kinetic versus immunological determination. Family studies revealed that the father beared the same abnormality. Studies of purified fibrinogen revealed an impaired release of both fibrinopeptides by thrombin. Fibrin monomer polymerization and fibrin stabilization were normal. DNA sequencing revealed a heterozygous G --> T point mutation in exon 2 of the gene coding for the Aalpha chain, which substituted a Gly for Val at position 12. Although the mutation is the same as in fibrinogen Rouen, fibrinogen Saint-Germain I shows a different fibrinopeptide release pattern and a mild factor V deficiency.
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Affiliation(s)
- F Mathonnet
- Laboratoire de biochimie et biologie moléculaire, Hôpital R Poincaré, Garches, France
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Multhaupt HA, Alvarez JC, Rafferty PA, Warhol MJ, Lackman RD. Fluoroquinolone's effect on growth of human chondrocytes and chondrosarcomas. In vitro and in vivo correlation. J Bone Joint Surg Am 2002; 83-A Suppl 2:56-61. [PMID: 11685846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Clinical and in vitro studies have demonstrated that fluoroquinolones are toxic to chondrocytes; however, the exact mechanism of fluoroquinolone arthropathy is unknown. We investigated the toxicity of ciprofloxacin on normal cartilage and on cartilaginous tumors. Normal human cartilage, enchondroma, and chondrosarcoma explants were cultured either alone or with the addition of ciprofloxacin at 1, 10, or 20 mg/L of medium. Samples were collected up to twenty-one days after treatment and were processed for electron microscopy and conventional light microscopy. The specimens were characterized morphologically with use of conventional light microscopy, electron microscopy, and immunohistochemistry to identify extracellular matrix, cell proliferation, and apoptosis. Cultures of normal chondrocytes expressed type-II collagen. Electron microscopy revealed a large amount of glycogen in the cells; the presence of fat droplets, rough endoplasmic reticulum, and prominent Golgi apparatus; and a proteoglycan layer surrounding the cells. With prolonged ciprofloxacin treatment and with increased doses, there was an increase in dilated rough endoplasmic reticulum, the appearance of phagosomes, and disintegrated bundles of vimentin filaments. The treated chondrocytes showed a decrease in cell proliferation, but there was no induction of apoptosis or effect on the expression of extracellular matrix proteins. Ciprofloxacin-treated chondrosarcoma cultures and tissue samples showed changes in cartilage matrix composition. Ultrastructural analysis demonstrated clumped glycogen, dilation of endoplasmic reticulum, numerous abnormal lysosomes containing degeneration products, and a decreased proteoglycan deposit surrounding the tumor cells. Treated chondrosarcoma cells and tissue specimens did not proliferate, and apoptosis was induced. In contrast, the in vitro growth of other noncartilaginous malignant tumors like osteosarcoma and liposarcoma was unaffected by ciprofloxacin. Our results indicate that ciprofloxacin is toxic to chondrocytes. In vitro and in vivo treated chondrosarcomas are the most affected.
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Affiliation(s)
- H A Multhaupt
- Division of Biomedical Sciences, Imperial College of Science Technology and Medicine, Sir Alexander Fleming Building, Exhibition Hall, London SW7 2AZ, England
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Quintin P, Benkelfat C, Launay JM, Arnulf I, Pointereau-Bellenger A, Barbault S, Alvarez JC, Varoquaux O, Perez-Diaz F, Jouvent R, Leboyer M. Clinical and neurochemical effect of acute tryptophan depletion in unaffected relatives of patients with bipolar affective disorder. Biol Psychiatry 2001; 50:184-90. [PMID: 11513817 DOI: 10.1016/s0006-3223(01)01140-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND The lowering of mood induced by an acute tryptophan depletion (ATD) has been proposed as a candidate endophenotype for the vulnerability to manic-depressive illness. This study tests this hypothesis in relatives of probands from well-characterized multiplex families affected with bipolar affective disorder (BAD). METHODS In a double-blind, crossover design, 20 unaffected relatives (URs) and 19 control subjects received either a 100-g amino acid (AA) drink devoid of tryptophan or a placebo, respectively. Clinical and biochemical effects of ATD were compared between unaffected relatives of BAD probands and age- and sex-matched control subjects. RESULTS At 5 hours after AA drink ingestion, relative to the placebo, ATD resulted in 74% and 84% decreases in total plasma tryptophan concentrations in control subjects and relatives of patients with BAD, respectively. Unlike control subjects unaffected relatives experienced a lowering of mood during ATD but not with the placebo. Furthermore, URs tended to show increased impulsivity in the ATD condition. Measurements obtained before ingestion of the AA drink indicated that, relative to control subjects URs exhibited lower serotonin platelet concentrations, lower affinity, and fewer binding sites of the serotonin transporter for imipramine; these differences were unaffected by ATD. CONCLUSION These results replicate and extend previous findings suggesting that URs of patients with BAD are more susceptible to low tryptophan availability. This finding may bear significance in the purported role of serotonergic mechanisms in the vulnerability to depressive syndrome and/or illness.
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Affiliation(s)
- P Quintin
- Service de Psychiatrie, Hôpital Albert Chenevier et Henri Mondor, AP-HP, Creteil, France
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