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Marx-Stoelting P, Rivière G, Luijten M, Aiello-Holden K, Bandow N, Baken K, Cañas A, Castano A, Denys S, Fillol C, Herzler M, Iavicoli I, Karakitsios S, Klanova J, Kolossa-Gehring M, Koutsodimou A, Vicente JL, Lynch I, Namorado S, Norager S, Pittman A, Rotter S, Sarigiannis D, Silva MJ, Theunis J, Tralau T, Uhl M, van Klaveren J, Wendt-Rasch L, Westerholm E, Rousselle C, Sanders P. A walk in the PARC: developing and implementing 21st century chemical risk assessment in Europe. Arch Toxicol 2023; 97:893-908. [PMID: 36645448 PMCID: PMC9968685 DOI: 10.1007/s00204-022-03435-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [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] [Received: 12/08/2022] [Accepted: 12/14/2022] [Indexed: 01/17/2023]
Abstract
Current approaches for the assessment of environmental and human health risks due to exposure to chemical substances have served their purpose reasonably well. Nevertheless, the systems in place for different uses of chemicals are faced with various challenges, ranging from a growing number of chemicals to changes in the types of chemicals and materials produced. This has triggered global awareness of the need for a paradigm shift, which in turn has led to the publication of new concepts for chemical risk assessment and explorations of how to translate these concepts into pragmatic approaches. As a result, next-generation risk assessment (NGRA) is generally seen as the way forward. However, incorporating new scientific insights and innovative approaches into hazard and exposure assessments in such a way that regulatory needs are adequately met has appeared to be challenging. The European Partnership for the Assessment of Risks from Chemicals (PARC) has been designed to address various challenges associated with innovating chemical risk assessment. Its overall goal is to consolidate and strengthen the European research and innovation capacity for chemical risk assessment to protect human health and the environment. With around 200 participating organisations from all over Europe, including three European agencies, and a total budget of over 400 million euro, PARC is one of the largest projects of its kind. It has a duration of seven years and is coordinated by ANSES, the French Agency for Food, Environmental and Occupational Health & Safety.
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Affiliation(s)
- P. Marx-Stoelting
- grid.417830.90000 0000 8852 3623German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - G. Rivière
- grid.15540.350000 0001 0584 7022French Agency for Food, Environmental and Occupational Health and Safety (ANSES), 94701 Maisons-Alfort, France
| | - M. Luijten
- National Institute for Health and Environment (RIVM), Bilthoven, The Netherlands
| | - K. Aiello-Holden
- grid.417830.90000 0000 8852 3623German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - N. Bandow
- grid.425100.20000 0004 0554 9748German Environment Agency (UBA), Wörlitzer Platz 1, 06844 Dessau, Germany
| | - K. Baken
- grid.6717.70000000120341548VITO (Flemish Institute for Technological Research), Boeretang 200, 2400 Mol, Belgium
| | - A. Cañas
- grid.413448.e0000 0000 9314 1427National Centre for Environmental Health, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - A. Castano
- grid.413448.e0000 0000 9314 1427National Centre for Environmental Health, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - S. Denys
- grid.493975.50000 0004 5948 8741Santé Publique France (SpFrance), 12, Rue du Val D’Osne, 94415 St. Maurice, France
| | - C. Fillol
- grid.493975.50000 0004 5948 8741Santé Publique France (SpFrance), 12, Rue du Val D’Osne, 94415 St. Maurice, France
| | - M. Herzler
- grid.417830.90000 0000 8852 3623German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - I. Iavicoli
- grid.4691.a0000 0001 0790 385XDepartment of Public Health, University of Naples Federico II (UNINA), Naples, Italy
| | - S. Karakitsios
- grid.4793.90000000109457005Aristoteles University Thessaloniki (AUTH), Thessaloniki, Greece
| | - J. Klanova
- Masaryk Uinversity, Recetox, Kotlarska 2, 61137 Brno, Czechia
| | - M. Kolossa-Gehring
- grid.425100.20000 0004 0554 9748German Environment Agency (UBA), Wörlitzer Platz 1, 06844 Dessau, Germany
| | - A. Koutsodimou
- General Chemical State Laboratory of Greece, Athens, Greece
| | - J. Lobo Vicente
- grid.453985.60000 0004 0619 3405European Environment Agency, Kongens Nytorv 6, 1050 Copenhagen K, Denmark
| | - I. Lynch
- grid.6572.60000 0004 1936 7486School of Geography, Earth and Environmental Sciences, University of Birmingham (UoB), Edgbaston, Birmingham, B15 2TT UK
| | - S. Namorado
- grid.422270.10000 0001 2287 695XNational Institute of Health Dr. Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - S. Norager
- grid.270680.bEuropean Commission, DG Research and Innovation, Orban 09/199, 1049 Brussels, Belgium
| | - A. Pittman
- grid.15540.350000 0001 0584 7022French Agency for Food, Environmental and Occupational Health and Safety (ANSES), 94701 Maisons-Alfort, France
| | - S. Rotter
- grid.417830.90000 0000 8852 3623German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - D. Sarigiannis
- grid.4793.90000000109457005Aristoteles University Thessaloniki (AUTH), Thessaloniki, Greece
| | - M. J. Silva
- grid.422270.10000 0001 2287 695XNational Institute of Health Dr. Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - J. Theunis
- grid.6717.70000000120341548VITO (Flemish Institute for Technological Research), Boeretang 200, 2400 Mol, Belgium
| | - T. Tralau
- grid.417830.90000 0000 8852 3623German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - M. Uhl
- Austrian Federal Environments Agency, Vienna, Austria
| | - J. van Klaveren
- National Institute for Health and Environment (RIVM), Bilthoven, The Netherlands
| | - L. Wendt-Rasch
- grid.437386.d0000 0001 1523 2072Swedish Chemicals Agency (KemI), Vasagatan 12D, 172 67 Sundbyberg, Sweden
| | - E. Westerholm
- grid.437386.d0000 0001 1523 2072Swedish Chemicals Agency (KemI), Vasagatan 12D, 172 67 Sundbyberg, Sweden
| | - C. Rousselle
- grid.15540.350000 0001 0584 7022French Agency for Food, Environmental and Occupational Health and Safety (ANSES), 94701 Maisons-Alfort, France
| | - P. Sanders
- grid.15540.350000 0001 0584 7022French Agency for Food, Environmental and Occupational Health and Safety (ANSES), 94701 Maisons-Alfort, France
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Lew MV, Ren Y, Lowder YP, Siamakpour-Reihani S, Ramalingam S, Romero KM, Thompson JC, Bohannon LM, McIntyre J, Tang H, Van Opstal J, Johnson E, Cohen HJ, Bartlett DB, Pastva AM, Morey M, Hall KS, Smith P, Peters KB, Somers TJ, Kelleher S, Smith SK, Wischmeyer PE, Lin PH, Wood WA, Thorpe G, Minor K, Wiggins K, Hennig T, Helms T, Welch R, Matthews B, Liu J, Burleson J, Aberant T, Engemann AK, Henshall B, Darby M, Proch C, Dellascio M, Pittman A, Suminguit J, Choi T, Gasparetto C, Long GD, Lopez RD, Sarantopoulos S, Horwitz ME, Chao NJ, Sung AD. Geriatric Assessment Reveals Actionable Impairments in Hematopoietic Stem Cell Transplantation Candidates Age 18 to 80 Years. Transplant Cell Ther 2022; 28:498.e1-498.e9. [PMID: 35595226 PMCID: PMC10042624 DOI: 10.1016/j.jtct.2022.05.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 02/23/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 10/18/2022]
Abstract
Allogeneic hematopoietic stem cell transplantation (HCT) is a potentially curative treatment for both malignant and nonmalignant hematologic diseases; however, reported rates of treatment-related mortality approach 30%. Outcomes are worse in patients who begin HCT with functional impairments. To detect such impairments, a geriatric assessment (GA) is recommended in adults age ≥65 years. Younger HCT candidates also may be impaired because of chemotherapy regimens pre-HCT. Therefore, we hypothesized that GA can be beneficial for adult patients of all ages and subsequently created a clinical pretransplantation optimization program to assess all HCT candidates using a modified GA. One-hundred fifty-seven patients were evaluated in 4 functional domains- physical, cognitive, nutritional, and psychological-at 2 time points prior to HCT-new patient evaluation (NPE) and sign-off (SO)-between October 2017 and January 2020. At NPE, 80.9% of the patients had at least 1 domain with a functional impairment, and physical (P = .006), cognitive (P = .04), and psychological (P = .04) impairments were associated with an increased likelihood of not proceeding to HCT. In addition, patients age 18 to 39 years were more likely than older patients to have a physical function impairment (P = .001). Between NPE and SO, 51.9% of the patients had resolution of 1 or more impairments, and nutritional impairment at SO was predictive of worse overall survival (P = .01). Our study shows that GA can identify functional impairments in patients of all ages. Early identification of impairments could facilitate referrals to supportive care and resolution of impairments prior to HCT, suggesting that GA could be recommended for HCT candidates of all ages.
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Affiliation(s)
- Meagan V Lew
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Yi Ren
- Duke Cancer Institute Biostatistics Shared Resources, Durham, North Carolina
| | - Yen P Lowder
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Sharareh Siamakpour-Reihani
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Sendhilnathan Ramalingam
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | | | - Jillian C Thompson
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Lauren M Bohannon
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Jackie McIntyre
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Helen Tang
- Duke University School of Medicine, Durham, North Carolina
| | - Jolien Van Opstal
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina; Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Ernaya Johnson
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Harvey Jay Cohen
- Claude D. Pepper Older Americans Independence Center, Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, North Carolina
| | - David B Bartlett
- Claude D. Pepper Older Americans Independence Center, Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, North Carolina; School of Biosciences and Medicine, University of Surrey, Surrey, United Kingdom
| | - Amy M Pastva
- Claude D. Pepper Older Americans Independence Center, Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, North Carolina; Department of Orthopedic Surgery, Division of Physical Therapy, Duke University Medical Center, Durham, North Carolina
| | - Miriam Morey
- Claude D. Pepper Older Americans Independence Center, Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, North Carolina; Geriatric Research, Education and Clinical Center, Durham VA Healthcare System, Durham, North Carolina
| | - Katherine S Hall
- Claude D. Pepper Older Americans Independence Center, Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, North Carolina; Geriatric Research, Education and Clinical Center, Durham VA Healthcare System, Durham, North Carolina
| | - Patrick Smith
- Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina
| | - Katherine B Peters
- Departments of Neurology and Neurosurgery, The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina
| | - Tamara J Somers
- Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina
| | - Sarah Kelleher
- Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina
| | - Sophia K Smith
- School of Nursing, Duke University Medical Center, Durham, North Carolina
| | - Paul E Wischmeyer
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina
| | - Pao-Hwa Lin
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina
| | - William A Wood
- Division of Hematology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Glynnis Thorpe
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Kerry Minor
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Kristi Wiggins
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Therese Hennig
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Tanya Helms
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Renee Welch
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Brittany Matthews
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - JoAnn Liu
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Jill Burleson
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Thomas Aberant
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Ashley K Engemann
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Bethany Henshall
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Maurisa Darby
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Christina Proch
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Michelle Dellascio
- Duke Health Department of Physical Therapy and Occupational Therapy, Durham, North Carolina
| | - Alyssa Pittman
- Duke Health Department of Physical Therapy and Occupational Therapy, Durham, North Carolina
| | - Jacob Suminguit
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Taewoong Choi
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Cristina Gasparetto
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Gwynn D Long
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Richard D Lopez
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Stefanie Sarantopoulos
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina
| | - Mitchell E Horwitz
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Nelson J Chao
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Anthony D Sung
- Division of Hematologic Malignancies and Cellular Therapy, Duke University Medical Center, Durham, North Carolina; Claude D. Pepper Older Americans Independence Center, Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, North Carolina.
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3
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Smith PJ, Lew M, Lowder Y, Romero K, Thompson JC, Bohannon L, Pittman A, Artica A, Ramalingam S, Choi T, Gasparetto C, Horwitz M, Long G, Lopez R, Rizzieri D, Sarantopoulos S, Sullivan K, Chao N, Sung AD. Cognitive impairment in candidates for allogeneic hematopoietic stem cell transplantation. Bone Marrow Transplant 2022; 57:89-94. [PMID: 34667271 PMCID: PMC10037500 DOI: 10.1038/s41409-021-01470-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 07/16/2021] [Accepted: 09/13/2021] [Indexed: 02/06/2023]
Abstract
Hematopoietic cell transplant (HCT) is an increasingly common and curative treatment strategy to improve survival among individuals with malignant and nonmalignant diseases, with over one million HCTs having been performed worldwide. Neurocognitive dysfunction is a common and untoward consequence of HCT for many recipients, although few studies have examined the profile of neurocognitive impairments in HCT or their association with clinical features, such as frailty, or the incidence of pre-HCT neurocognitive impairments across all ages, which may influence post-HCT neurocognitive impairments. We examined the pattern and correlates of pre-transplant neurocognitive dysfunction in a prospective sample of adults undergoing HCT. Neurocognition was assessed using the Montreal Cognitive Assessment Battery. Frailty was assessed using the Short Physical Performance Battery. Linear regression analysis was used to examine the associations between neurocognitive performance and frailty. Neurocognitive screening profiles were also examined by partitioning MoCA into domain scores, including Executive Function and Memory. We also examined the associations between neurocognition, frailty, and clinical outcomes, including length of transplant hospitalization and survival. One hundred and ten adults were evaluated across a wide age range (range: 19-75; mean age = 54.7 [SD = 14.1]). Neurocognitive performance tended to fall below published normative levels (mean MoCA = 25.5 [SD = 4.1]), with 17% of participants demonstrating impaired performance compared with medical normative data (MoCA ≤ 22) and 34% exhibiting impaired performance relative to healthy samples (MoCA ≤ 25). Mild impairments (MoCA ≤ 25) were common across age ranges, including middle-aged patients (23% for age < 50; 35% for age 50-60, 41% for age ≥ 60), particularly for items assessing Executive Function. Greater levels of frailty associated with lower neurocognitive screening scores (r = -0.29, P < 0.01) and Executive Functioning (r = -0.24, P < 0.01), whereas greater age was associated with poorer Memory performance only (r = -0.33, P < 0.01). Greater levels of frailty prior to transplant associated with longer length of stay (β = 0.10, P = 0.046), but were not associated with survival. Neurocognitive impairments are common among adults undergoing HCT and the pattern of performance varies by age. Pre-transplant frailty is associated with neurocognitive functioning and may portend worse post-transplant early clinical outcomes.
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Affiliation(s)
- Patrick J Smith
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC, USA.
| | - Meagan Lew
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Yen Lowder
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Kristi Romero
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Jillian C Thompson
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Lauren Bohannon
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Alyssa Pittman
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Alexandra Artica
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Sendhilnathan Ramalingam
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Taewoong Choi
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Cristina Gasparetto
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Mitchell Horwitz
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Gwynn Long
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Richard Lopez
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - David Rizzieri
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Stefanie Sarantopoulos
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Keith Sullivan
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Nelson Chao
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Anthony D Sung
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
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Smith PJ, Lew M, Lowder YP, Romero K, Thompson J, Bohannen L, Pittman A, Sullivan K, Choi T, Gasparetto C, Horwitz ME, Long GD, Lopez R, Rizzieri DA, Sarantopoulos S, Chao NJ, Sung AD. Cognitive Impairment in Candidates for Allogeneic Hematopoietic Stem Cell Transplantation. Biol Blood Marrow Transplant 2020. [DOI: 10.1016/j.bbmt.2019.12.487] [Citation(s) in RCA: 1] [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]
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Bugiardini E, Khan A, Phadke R, Lynch D, Cortese A, Feng L, Gang Q, Pittman A, Morrow J, Turner C, Carr A, Quinlivan R, Rossor A, Holton J, Parton M, Blake J, Reilly M, Houlden H, Matthews E, Hanna M. EP.103Genetic and phenotypic characterisation of inherited myopathies in a tertiary neuromuscular centre. Neuromuscul Disord 2019. [DOI: 10.1016/j.nmd.2019.06.509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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King R, Greene E, Pittman A, Spratley D, Matthiesen M. Evaluation of Registered Dietitians’ Interest and Involvement in Nutrition-Related Public Policy. J Acad Nutr Diet 2019. [DOI: 10.1016/j.jand.2019.06.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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7
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Iacoangeli A, Al Khleifat A, Sproviero W, Shatunov A, Jones AR, Morgan SL, Pittman A, Dobson RJ, Newhouse SJ, Al-Chalabi A. DNAscan: personal computer compatible NGS analysis, annotation and visualisation. BMC Bioinformatics 2019; 20:213. [PMID: 31029080 PMCID: PMC6487045 DOI: 10.1186/s12859-019-2791-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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] [Received: 10/02/2018] [Accepted: 04/02/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Next Generation Sequencing (NGS) is a commonly used technology for studying the genetic basis of biological processes and it underpins the aspirations of precision medicine. However, there are significant challenges when dealing with NGS data. Firstly, a huge number of bioinformatics tools for a wide range of uses exist, therefore it is challenging to design an analysis pipeline. Secondly, NGS analysis is computationally intensive, requiring expensive infrastructure, and many medical and research centres do not have adequate high performance computing facilities and cloud computing is not always an option due to privacy and ownership issues. Finally, the interpretation of the results is not trivial and most available pipelines lack the utilities to favour this crucial step. RESULTS We have therefore developed a fast and efficient bioinformatics pipeline that allows for the analysis of DNA sequencing data, while requiring little computational effort and memory usage. DNAscan can analyse a whole exome sequencing sample in 1 h and a 40x whole genome sequencing sample in 13 h, on a midrange computer. The pipeline can look for single nucleotide variants, small indels, structural variants, repeat expansions and viral genetic material (or any other organism). Its results are annotated using a customisable variety of databases and are available for an on-the-fly visualisation with a local deployment of the gene.iobio platform. DNAscan is implemented in Python. Its code and documentation are available on GitHub: https://github.com/KHP-Informatics/DNAscan . Instructions for an easy and fast deployment with Docker and Singularity are also provided on GitHub. CONCLUSIONS DNAscan is an extremely fast and computationally efficient pipeline for analysis, visualization and interpretation of NGS data. It is designed to provide a powerful and easy-to-use tool for applications in biomedical research and diagnostic medicine, at minimal computational cost. Its comprehensive approach will maximise the potential audience of users, bringing such analyses within the reach of non-specialist laboratories, and those from centres with limited funding available.
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Affiliation(s)
- A Iacoangeli
- Department of Biostatistics and Health Informatics, King's College London, London, UK. .,Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.
| | - A Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - W Sproviero
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - A Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - A R Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - S L Morgan
- Department of Molecular Neuroscience, UCL, Institute of Neurology, London, UK
| | - A Pittman
- Department of Molecular Neuroscience, UCL, Institute of Neurology, London, UK
| | - R J Dobson
- Department of Biostatistics and Health Informatics, King's College London, London, UK.,Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, UK.,National Institute for Health Research (NIHR) Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King's College London, London, UK
| | - S J Newhouse
- Department of Biostatistics and Health Informatics, King's College London, London, UK.,Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, UK.,National Institute for Health Research (NIHR) Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King's College London, London, UK
| | - A Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.,King's College Hospital, Bessemer Road, London, SE5 9RS, UK
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Bugiardini E, Phadke R, Maas R, Pittman A, Kusters B, Morrow J, Parton M, Nunes A, Akhtar M, Syrris P, Lopes L, Fotelonga T, Houlden H, Elliott P, Hanna M, Raaphorst J, Burkin D, Matthews E. CONGENITAL MUSCULAR DYSTROPHIES. Neuromuscul Disord 2018. [DOI: 10.1016/j.nmd.2018.06.382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Bugiardini E, Poole O, Pittman A, Woodward C, Sweeney M, Heales S, Houlden H, Hanna M, Pitceathly R. TPK1 mutations: unmasking a potentially treatable cause of Leigh-like syndrome. Neuromuscul Disord 2017. [DOI: 10.1016/s0960-8966(17)30285-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Petrisor D, Pittman A, Wax M, Steele E, Chamberlain W. Submandibular Gland Transfer in the Treatment of Severe Dry Eye Syndrome. J Oral Maxillofac Surg 2013. [DOI: 10.1016/j.joms.2013.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Pittman K, Pittman A, Karlson S, Cieplinska T, Sourd P, Redmond K, Ravnøy B, Sweetman E. Body site matters: an evaluation and application of a novel histological methodology on the quantification of mucous cells in the skin of Atlantic salmon, Salmo salar L. J Fish Dis 2013; 36:115-127. [PMID: 23009125 DOI: 10.1111/jfd.12002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/30/2012] [Accepted: 08/04/2012] [Indexed: 06/01/2023]
Abstract
Mucous cell size and distribution were investigated in the skin of five salmon using a novel stereology-based methodology: one (48 cm) fish to test 15 tissue treatment combinations on measures of cell area and density on the dorsolateral region and, using the most suitable treatment, we mapped mucous cell differences between body regions on four (52 cm) salmon, comprising a male and a female on each of two diets. The section site, decalcification, embedding medium and plane of sectioning all impacted significantly on mucous cell size, whereas mucous cell density is more robust. There were highly significant differences in both mucosal density and mean mucous cell size depending on body site: the dorsolateral skin of the four salmon had significantly denser (about 8% of skin area) and larger (mean about 160 μm(2)) mucous cells, whereas the lowest mean density (about 4%) and smallest mean area (115 μm(2)) were found on the head. We found that 100 random measurements may be sufficient to distinguish differences >7 μm(2) in mean mucous cell areas. The results further suggest that salmon exhibit a dynamic repeatable pattern of mucous cell development influenced by sex, diet and possibly strain and season.
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Affiliation(s)
- K Pittman
- Department of Biology, University of Bergen, Bergen, Norway.
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12
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Pittman K, Sourd P, Ravnøy B, Espeland O, Fiksdal IU, Oen T, Pittman A, Redmond K, Sweetman J. Novel method for quantifying salmonid mucous cells. J Fish Dis 2011; 34:931-936. [PMID: 22004586 DOI: 10.1111/j.1365-2761.2011.01308.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- K Pittman
- Department of Biology, University of Bergen, Bergen, Norway.
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13
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Hardy J, Pittman A, Myers A, Gwinn-Hardy K, Fung HC, de Silva R, Hutton M, Duckworth J. Evidence suggesting that Homo neanderthalensis contributed the H2 MAPT haplotype to Homo sapiens. Biochem Soc Trans 2005; 33:582-5. [PMID: 16042549 DOI: 10.1042/bst0330582] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The tau (MAPT) locus exists as two distinct clades, H1 and H2. The H1 clade has a normal linkage disequilibrium structure and is the only haplotype found in all populations except those derived from Caucasians. The H2 haplotype is the minor haplotype in Caucasian populations and is not found in other populations. It shows no recombination over a region of 2 Mb with the more common H1 haplotype. The distribution of the haplotype and analysis of the slippage of dinucleotide repeat markers within the haplotype suggest that it entered Homo sapiens populations between approx. 10000 and 30000 years ago. However, sequence comparison of the H2 haplotype with the H1 haplotype and with the chimp sequence suggests that the common founder of the H1 and H2 haplotypes was far earlier than this. We suggest that the H2 haplotype is derived from Homo neanderthalensis and entered H. sapiens populations during the co-existence of these species in Europe from approx. 45000 to 18000 years ago and that the H2 haplotype has been under selection pressure since that time, possibly because of the role of this H1 haplotype in neurodegenerative disease.
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Affiliation(s)
- J Hardy
- Laboratory of Neurogenetics, National Institutes on Aging and National Institutes of Neurological Diseases and Stroke, National Institutes of Health, 35 Convent Drive, Bethesda, MD 20892, USA.
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14
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de Silva R, Hope A, Pittman A, Weale ME, Morris HR, Wood NW, Lees AJ. Strong association of the Saitohin gene Q7 variant with progressive supranuclear palsy. Neurology 2003; 61:407-9. [PMID: 12913211 DOI: 10.1212/01.wnl.0000073140.25533.90] [Citation(s) in RCA: 22] [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: 11/15/2022] Open
Abstract
Recent reports are inconclusive in showing that the Q7R polymorphism of the novel Saitohin gene, nested in intron 9 of the tau gene, is associated with AD. The authors show that this polymorphism is in complete linkage disequilibrium with the extended tau H1/H2 haplotype and that the Q variant and QQ genotype of Q7R are strongly associated with progressive supranuclear palsy, implicating it as a possibly important pathogenic candidate.
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Affiliation(s)
- R de Silva
- Reta Lila Weston Institute of Neurological Studies, University College London, Windeyer Building, 46 Cleveland Street, London, W1T 4JF, UK.
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Lochte H, Pittman A. Notes- The Nitrogen Compounds of Petroleum Distillates. XXIX. Identification of 5-Methyl-6,7-dihydro-1,5-pyridine. J Org Chem 2003. [DOI: 10.1021/jo01078a620] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Vistica DT, Skehan P, Scudiero D, Monks A, Pittman A, Boyd MR. Tetrazolium-based assays for cellular viability: a critical examination of selected parameters affecting formazan production. Cancer Res 1991; 51:2515-20. [PMID: 2021931] [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: 12/29/2022]
Abstract
The hydrogen acceptor 3-(4,5-dimethylthiazol-2-yl)-2,5 diphenyltetrazolium bromide (MTT) is commonly utilized to estimate cellular viability in drug screening protocols. The present investigation was prompted, in part, by observations that reduction of MTT to its colored reaction product, MTT formazan, varied between cell lines and with culture age. A correlation was established between the D-glucose concentration of the culture medium at the time of assay and the production of MTT formazan for cell lines representing seven tumor histologies. A decrease in the concentration of D-glucose from culture medium was accompanied by a decrease in MTT specific activity (MTT formazan/microgram cell protein) for a number of cell lines. Cells which extensively metabolized D-glucose exhibited the greatest reduction in MTT specific activity. Further evidence that the D-glucose concentration of the culture medium played an important role in MTT reduction was provided by experiments which demonstrated that transfer of cells to a glucose-free medium (L-15) was accompanied by an immediate decrease in MTT reduction which was pH independent. These studies suggested that cellular transport and constant metabolism of glucose were required for maximum MTT reduction. Decreases in the cellular concentration of the reduced pyridine nucleotides NADH and NADPH were accompanied by concomitant decreases in MTT formazan production. MTT formazan varied significantly among cell lines in both the kinetics of its formation and the degree of saturability exhibited. Apparent IC50 values for Adriamycin varied, in a cell line-specific manner, with MTT exposure time. These results indicate that MTT specific activity is significantly influenced by a number of parameters and suggest that assay conditions should be established which minimize their effects.
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Affiliation(s)
- D T Vistica
- Laboratory of Drug Discovery Research and Development, National Cancer Institute, Frederick, Maryland 21702-1201
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