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Application of VirCapSeq-VERT and BacCapSeq in the diagnosis of presumed and definitive neuroinfectious diseases. J Neurovirol 2023; 29:678-691. [PMID: 37851324 DOI: 10.1007/s13365-023-01172-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/09/2023] [Accepted: 08/28/2023] [Indexed: 10/19/2023]
Abstract
Unbiased high-throughput sequencing (HTS) has enabled new insights into the diversity of agents implicated in central nervous system (CNS) infections. The addition of positive selection capture methods to HTS has enhanced the sensitivity while reducing sequencing costs and the complexity of bioinformatic analysis. Here we report the use of virus capture-based sequencing for vertebrate viruses (VirCapSeq-VERT) and bacterial capture sequencing (BacCapSeq) in investigating CNS infections. Thirty-four samples were categorized: (1) patients with definitive CNS infection by routine testing; (2) patients meeting clinically the Brighton criteria (BC) for meningoencephalitis; (3) patients with presumptive infectious etiology highest on the differential. RNA extracts from cerebrospinal fluid (CSF) were used for VirCapSeq-VERT, and DNA extracts were used for BacCapSeq analysis. Among 8 samples from known CNS infections in group 1, VirCapSeq and BacCapSeq confirmed 3 expected diagnoses (42.8%), were negative in 2 (25%), yielded an alternative result in 1 (11.1%), and did not detect 2 expected negative pathogens. The confirmed cases identified HHV-6, HSV-2, and VZV while the negative samples included JCV and HSV-2. In groups 2 and 3, 11/26 samples (42%) were positive for at least one pathogen; however, 27% of the total samples (7/26) were positive for commensal organisms. No microbial nucleic acids were detected in negative control samples. HTS showed limited promise for pathogen identification in presumed CNS infectious diseases in our small sample. Before conducting larger-scale prospective studies to assess the clinical value of this novel technique, clinicians should understand the benefits and limitations of using this modality.
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Application of VirCapSeq-VERT and BacCapSeq In the Diagnosis of Presumed and Definitive Neuroinfectious Diseases. RESEARCH SQUARE 2023:rs.3.rs-2675665. [PMID: 37502953 PMCID: PMC10371130 DOI: 10.21203/rs.3.rs-2675665/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Background Unbiased high-throughput sequencing (HTS) has enabled new insights into the diversity of agents implicated in central nervous system (CNS) infections. The addition of positive selection capture methods to HTS has enhanced the sensitivity while reducing sequencing costs and complexity of bioinformatic analysis. Here we report the use of virus capture based sequencing for vertebrate viruses (VirCapSeq-VERT) and bacterial capture sequencing (BacCapSeq) in investigating CNS infections. Design/Methods Thirty-four samples were categorized: (1) Patients with definitive CNS infection by routine testing; (2) Patients meeting clinically Brighton Criteria (BC) for meningoencephalitis (3) Patients with presumptive infectious etiology highest on the differential. RNA extracts from cerebrospinal fluid (CSF) were used for VirCapSeq-VERT and DNA extracts were used for BacCapSeq analysis. Results Among 8 samples from known CNS infections in group 1, VirCapSeq and BacCapSeq confirmed 3 expected diagnoses (42.8%), were negative in 2 (25%), yielded an alternative result in 1 (11.1%), and did not detect 2 expected negative pathogens. The confirmed cases identified HHV-6, HSV-2, and VZV while the negative samples included JCV and HSV-2. In groups 2 and 3,11/26 samples (42%) were positive for at least one pathogen, however 27% of the total samples (7/26) were positive for commensal organisms. No microbial nucleic acids were detected in negative control samples. Conclusions HTS showed limited promise for pathogen identification in presumed CNS infectious diseases in our small sample. Before conducting larger-scale prospective studies to assess clinical value of this novel technique, clinicians should understand benefits and limitations of using this modality.
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Kinetic investigation of the thermal decomposition of both NTO, and nNTO in the presence of Nickel-Zinc-Copper ferrite. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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4
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Thermal Decomposition of 3-Nitro-1,2,4-Triazole-5-One (NTO) and Nanosize NTO Catalyzed by NiFe2O4. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2022. [DOI: 10.1007/s13369-022-07208-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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1012 A Close Loop Audit of Acute Food Bolus Obstruction at a District General Hospital. Br J Surg 2022. [DOI: 10.1093/bjs/znac269.198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Aim
The British Society of Gastroenterology (BSG) recommends biopsies from two different regions in the oesophagus. A close loop audit was undertaken to assess performance at a district general hospital, against these guidelines and following newly agreed trust guidelines after the first audit cycle of a follow up OGD within 6 weeks of the presentation.
Method
Data was collected of patients admitted with a food bolus over the first cycle (March2019 to February 2021) and the second cycle (1/10/21 to 14/10/21). Exclusion criteria were age of less than 18 and sharp food bolus.
Results
69 patients were identified. Average age was 60 years. There were 67% male patients and 33% female. 20% of patients underwent a follow up OGD in the first cycle and 45%underwent a follow up OGD within six weeks. 7% had two regions biopsy in the first cycle and21% in the second cycle. Average OGD follow up time was 92 days in the first cycle and 59days in the second cycle. Commonest findings on histology results were eosinophilic oesophagitis and Barrett's oesophagus (22% each), GORD (15%) and carcinoma (7%).
Discussion
Food bolus obstruction indicates the presence of pathology of the oesophagus and should be investigated as so, even despite spontaneous recovery from the acute event. Number of patients undergoing OGD within six weeks and a two regions biopsy improved through this audit by implementing the new trust guidelines.
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1001 Surgical Escape Rooms: A Novel Approach for Teaching Surgical Skills. Br J Surg 2022. [DOI: 10.1093/bjs/znac269.415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Abstract
Aim
Traditional classroom-based teaching of surgical skills has been used commonly in the past. Although, use of an escape room is a new form of a practical teaching method to deliver surgical skills teaching. We compared and assessed effectiveness of the traditional classroom teaching versus practical escape room teaching of the basic surgical skills.
Method
Two teaching sessions were delivered to third year medical students. Each session consisted of two groups and two sessions. Each group received either the classroom-based teaching or the escape room teaching, then switching over to the other teaching. Each student was asked to complete a questionnaire before the session, after the first and the second teaching session. Teaching covered interrupted suturing, wound management, and administration of local aesthetic. Likert scores were used to collect feedback.
Results
Total 24 third year medical students attended the two teaching sessions. 100% either agreed or strongly agreed the classroom teaching was useful, compared to 75% for the escape room. 67% either agreed or strongly agreed that escape room style teaching is a better learning method than traditional teaching. Although, 79% either agree or strongly agree that escape room style teaching is a useful adjunct to the traditional teaching. 100% either agree or strongly agree that this teaching will improve their clinical practice.
Conclusions
Traditional classroom-based teaching is a more useful form of teaching compared to the escape room. Although escape room teaching is a useful adjunct to the current common form of classroom based surgical teaching.
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Effect of rGO with BaCuO 3 perovskite on the thermal decomposition of AP and NTO. RSC Adv 2022; 12:19101-19107. [PMID: 35865610 PMCID: PMC9244895 DOI: 10.1039/d2ra00953f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 06/06/2022] [Indexed: 11/21/2022] Open
Abstract
In this study, the syntheses of a BaCuO3 perovskite-structured oxide and rGO were conducted using a sol-gel method and ultrasonication process, respectively. Their physico-chemical characteristics were studied by powder X-ray diffraction (PXRD), Raman spectroscopy, and ultraviolet-visible (UV-vis) spectroscopy analyses. The perovskite type particles were found to present as a cubic crystal system with a crystal size in the range of 10-60 nm. Their catalytic performance was investigated using differential thermal analysis (DTA) measurements at varying heating rates via the thermal decomposition of ammonium perchlorate (AP) and 3-nitro-1,2,4-triazol-5-one (NTO). The kinetics and thermodynamics parameters, such as the average activation energy, pre-exponential factor, entropy, and Gibbs free energy, were also investigated, which showed a decrease in the decomposition peak temperature of AP and NTO in the presence of the catalysts rGO, BaCuO3, and rGO + BaCuO3 compared to pure AP and NTO.
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Augmented catalytic effect of nano‐bi‐transition metal ferrite NiZnFe
2
O
4
for nano‐nitrotriazolone thermolysis. Appl Organomet Chem 2022. [DOI: 10.1002/aoc.6773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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A Short Series of Case Reports of COVID-19 in Immunocompromised Patients. Viruses 2022; 14:v14050934. [PMID: 35632677 PMCID: PMC9145915 DOI: 10.3390/v14050934] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/13/2022] [Accepted: 04/26/2022] [Indexed: 01/08/2023] Open
Abstract
Immunocompromised individuals are at risk of prolonged SARS-CoV-2 infection due to weaker immunity, co-morbidities, and lowered vaccine effectiveness, which may evolve highly mutated variants of SARS-CoV-2. Nonetheless, limited data are available on the immune responses elicited by SARS-CoV-2 infection, reinfections, and vaccinations with emerging variants in immunocompromised patients. We analyzed clinical samples that were opportunistically collected from eight immunocompromised individuals for mutations in SARS-CoV-2 genomes, neutralizing antibody (NAb) titers against different SARS-CoV-2 variants, and the identification of immunoreactive epitopes using a high-throughput coronavirus peptide array. The viral genome analysis revealed two SARS-CoV-2 variants (20A from a deceased patient and an Alpha variant from a recovered patient) with an eight amino-acid (aa) deletion within the N-terminal domain (NTD) of the surface glycoprotein. A higher NAb titer was present against the prototypic USA/WA1/2020 strain in vaccinated immunocompromised patients. NAb titer was absent against the Omicron variant and the cultured virus of the 20A variant with eight aa deletions in non-vaccinated patients. Our data suggest that fatal SARS-CoV-2 infections may occur in immunocompromised individuals even with high titers of NAb post-vaccination. Moreover, persistent SARS-CoV-2 infection may lead to the emergence of newer variants with additional mutations favoring the survival and fitness of the pathogen that include deletions in NAb binding sites in the SARS-CoV-2 surface glycoprotein.
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Human Polyomavirus 9-An Emerging Cutaneous and Pulmonary Pathogen in Solid Organ Transplant Recipients. JAMA Dermatol 2022; 158:293-298. [PMID: 35138364 PMCID: PMC8829745 DOI: 10.1001/jamadermatol.2021.5853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
IMPORTANCE We describe the first report to our knowledge of cutaneous and systemic pathogenicity of human polyomavirus 9 in solid organ transplant recipients. OBJECTIVE Three solid organ transplant recipients developed a widespread, progressive, violaceous, and hyperkeratotic skin eruption. All died from pulmonary and multiorgan failure around 1 year from onset of the rash. Routine clinical diagnostic testing could not identify any causative agent; therefore, samples and autopsies were investigated for novel pathogens using high-throughput sequencing. DESIGN, SETTING, AND PARTICIPANTS This case series, including 3 solid organ transplant recipients who developed characteristic pink, violaceous, or brown hyperkeratotic papules and plaques throughout the body, was conducted at the Columbia University Medical Center. Lesional skin biopsies were collected from all 3 patients and subjected to high-throughput illumina sequencing for identification of microbial pathogens. Human polyomavirus 9 was identified in lesional skin biopsies. We subsequently collected ocular swabs, oral swabs, urine samples, and blood samples from patients, and organ tissues at autopsy in 1 patient. We investigated these samples for the presence of human polyomavirus 9 using in situ hybridization and quantitative polymerase chain reaction (PCR) assays. MAIN OUTCOMES AND MEASURES A description of the clinical and pathologic findings of 3 patients. RESULTS This case series study found that human polyomavirus 9 was detected in the skin biopsies of all 3 patients by a capture-based high-throughput sequencing method platform (VirCapSeq-VERT). Human polyomavirus 9 was also detected in blood, oral, ocular swabs, and urine by real-time polymerase chain reaction (PCR) assay. In situ hybridization and quantitative PCR assays were performed on the skin biopsies from 3 patients and lung autopsy of 1 patient, which showed the presence of human polyomavirus 9 messenger RNA transcripts, indicating active viral replication and pathogenesis in the skin and lungs. CONCLUSIONS AND RELEVANCE Human polyomavirus 9 was associated with the widespread cutaneous eruption. All 3 patients had progression of cutaneous disease, accompanied by clinical deterioration, pulmonary failure, and death. One patient underwent autopsy and human polyomavirus 9 was identified in the lungs and paratracheal soft tissue. These findings suggest that human polyomavirus 9 may be associated with cutaneous and possibly pulmonary infection and death in solid organ transplant recipients.
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Nano Size NiCuZnFe
2
O
4
Tri Metal Spinel Ferrite: Synthesis, Characterizations and Additive for Thermolysis of Ammonium Perchlorate. ChemistrySelect 2022. [DOI: 10.1002/slct.202103846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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448 Foundation Doctor Local Peer-Led and Organised Basic Surgical Skills in General Surgery and Plastic Surgery. Br J Surg 2021. [DOI: 10.1093/bjs/znab259.853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Aim
Foundation doctors are under pressure early in their careers to attend highly subscribed and expensive surgical courses. We assessed the feasibility of a foundation doctor led and locally organised basic surgical skills introduction.
Method
The lead foundation doctor organised a basic surgical skills introduction for foundation year doctors at Salisbury District Hospital liaising with the postgraduate centre and local surgical consultants. This training was supervised by local consultants and registrars. This teaching delivered theory and practise in suturing, knot tying and laparoscopy by local and familiar trainers. Feedback was collected using the Likert scale.
Results
12 foundation doctors attended. 100% either agreed or strongly agreed the introduction was helpful and well organised. 25% either agreed or strongly agreed feeling confident with suturing and knot tying before the teaching which increased to 92% after teaching. Only 8.3% either agreed or strongly agreed feeling confident with the principles of basic laparoscopy before teaching which increased to 83% after teaching. 100% either agreed or strongly agreed the teaching will improve their clinical practise and enhance their interest in surgery. 92% strongly agreed or agreed that the teaching improved their knowledge in basic surgical skills, and the peer led and organised structure was an effective teaching method.
Conclusions
Foundation doctor locally peer led teaching organised with supervision by local consultants is an effective method of delivering basic surgical skills with improvement especially marked in basic laparoscopy and help enhance interest in surgical training.
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Evaluation of Sealing Ability of Biodentine to Root-End Cavities Irrigated either with Maleic Acid or Irritrol Using Glucose Filtration Model. PESQUISA BRASILEIRA EM ODONTOPEDIATRIA E CLÍNICA INTEGRADA 2021. [DOI: 10.1590/pboci.2021.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Robotic-assisted partial nephrectomy (RAPN) and standardization of outcome reporting: a prospective, observational study on reaching the "Trifecta and Pentafecta". J Robot Surg 2020; 15:571-577. [PMID: 32885379 PMCID: PMC8295154 DOI: 10.1007/s11701-020-01141-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/17/2020] [Indexed: 12/29/2022]
Abstract
Partial nephrectomy (PN) for small renal masses is common, but outcomes are not reported in a standard manner. Traditionally, parameters such as 90-day mortality, blood loss, transfusion rates, length of stay, nephrometry scoring and complications are published but their collective impact on warm ischemia time (WIT) and post-surgery GFR is rarely determined. Thus, our aim was to assess if “Trifecta” and “Pentafecta” outcomes could be used as useful surgical outcome markers. A prospective database of 252 Robotic-Assisted PN (RAPN) cases (2008–2019) was analysed. “Pentafecta” was defined as achievement of “Trifecta” (negative surgical margin, no postoperative complications and WIT of < 25 min) plus over 90% estimated GFR preservation and no CKD stage upgrading at 1 year. Binary logistic regression analysis was conducted to predict factors which may prevent achieving a Trifecta/Pentafecta. Median tumour size was 3 cm and mean WIT was 15 min. Positive surgical margins (PSM) occurred in 2 cases. Overall, the intra-operative complication rate was 7%. One recurrence conferred 5-year cancer-free survival of 97%. Trifecta outcome was achieved in 169 (67%) and Pentafecta in 141 (56%) of cases. At logistic regression analysis, intraoperative blood loss was the only factor to affect Trifecta achievement (p = 0.018). Advanced patient age negatively impacted Pentafecta achievement (p = 0.010). The Trifecta and Pentafecta outcomes are easily applicable to PN data, and offer an internationally comparable PN outcome, quality measure. We recommend applying this standardization to national data collection to improve the quality of reporting and ease of interpretation of surgeon/centres’ outcomes.
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Abstract No. 644 Characterizing renal and hepatic function markers in patients who receive transjugular portosystemic shunt for refractory ascites. J Vasc Interv Radiol 2020. [DOI: 10.1016/j.jvir.2019.12.705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Zika Virus Peptide ELISA (ZIKV-NS2B-Concat ELISA) for Detection of IgG Antibodies to Zika Virus Infection. Methods Mol Biol 2020; 2142:113-122. [PMID: 32367363 DOI: 10.1007/978-1-0716-0581-3_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Maternal Zika virus (ZIKV) infection during pregnancy can have profound teratogenic effects including microcephaly and intracranial calcification. In adults, infection may cause acute inflammatory polyneuropathy. These complications appear after resolution of viremia. Thus, molecular assays of blood are typically insufficient to make the link between ZIKV infection and disease. An alternative approach to testing for ZIKV exposure is serology. However, specific serological implication of ZIKV can be confounded by cross-reactivity with closely related flaviviruses. We used high-density peptide arrays that tile the proteomes of a selection of arboviruses to search for ZIKV-specific linear epitopes that would enable the development of accurate serological tests. We identified a 20-amino-acid-long diagnostic peptide sequence in the NS2B protein of ZIKV that was immunoreactive with sera from patients with a confirmed history of infection with ZIKV but not other flaviviruses. We then established a ZIKV peptide ELISA (ZIKV-NS2B-concat ELISA) that enables sensitive and specific diagnosis of exposure to ZIKV.
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Spillover of ebolaviruses into people in eastern Democratic Republic of Congo prior to the 2018 Ebola virus disease outbreak. ONE HEALTH OUTLOOK 2020; 2:21. [PMID: 33169111 PMCID: PMC7609368 DOI: 10.1186/s42522-020-00028-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 09/28/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND The second largest Ebola virus disease (EVD) outbreak began in the Democratic Republic of Congo in July 2018 in North Kivu Province. Data suggest the outbreak is not epidemiologically linked to the 2018 outbreak in Equateur Province, and that independent introduction of Ebola virus (EBOV) into humans occurred. We tested for antibodies to ebolaviruses in febrile patients seeking care in North Kivu Province prior to the EVD outbreak. METHODS Patients were enrolled between May 2017 and April 2018, before the declared start of the outbreak in eastern DRC. Questionnaires were administered to collect demographic and behavioural information to identify risk factors for exposure. Biological samples were evaluated for ebolavirus nucleic acid, and for antibodies to ebolaviruses. Prevalence of exposure was calculated, and demographic factors evaluated for associations with ebolavirus serostatus. RESULTS Samples were collected and tested from 272 people seeking care in the Rutshuru Health Zone in North Kivu Province. All patients were negative for filoviruses by PCR. Intial screening by indirect ELISA found that 30 people were reactive to EBOV-rGP. Results were supported by detection of ebolavirus reactive linear peptides using the Serochip platform. Differential screening of all reactive serum samples against the rGP of all six ebolaviruses and Marburg virus (MARV) showed that 29 people exhibited the strongest reactivity to EBOV and one to Bombali virus (BOMV), and western blotting confirmed results. Titers ranged from 1:100 to 1:12,800. Although both sexes and all ages tested positive for antibodies, women were significantly more likely to be positive and the majority of positives were in February 2018. CONCLUSIONS We provide the first documented evidence of exposure to Ebola virus in people in eastern DRC. We detected antibodies to EBOV in 10% of febrile patients seeking healthcare prior to the declaration of the 2018-2020 outbreak, suggesting early cases may have been missed or exposure ocurred without associated illness. We also report the first known detection of antibodies to BOMV, previously detected in bats in West and East Africa, and show that human exposure to BOMV has occurred. Our data suggest human exposure to ebolaviruses may be more frequent and geographically widespread.
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Identification of immunoreactive linear epitopes of Borrelia miyamotoi. Ticks Tick Borne Dis 2019; 11:101314. [PMID: 31636001 DOI: 10.1016/j.ttbdis.2019.101314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/30/2019] [Accepted: 10/13/2019] [Indexed: 11/19/2022]
Abstract
Borrelia miyamotoi is an emerging tick-borne spirochete transmitted by ixodid ticks. Current serologic assays for B. miyamotoi are impacted by genetic similarities to other Borrelia and limited understanding of optimal antigenic targets. In this study, we employed the TBD-Serochip, a peptide array platform, to identify new linear targets for serologic detection of B. miyamotoi. We examined a wide range of suspected B. miyamotoi antigens and identified 352 IgM and 91 IgG reactive peptides, with the majority mapping to variable membrane proteins. These included peptides within conserved fragments of variable membrane proteins that may have greater potential for differential diagnosis. We also identified reactive regions on FlaB, and demonstrate crossreactivity of B. burgdorferi s.l. C6 with a B. miyamotoi C6-like peptide. The panel of linear peptides identified in this study can be used to enhance serodiagnosis of B. miyamotoi.
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One-step pentaplex real-time polymerase chain reaction assay for detection of zika, dengue, chikungunya, West nile viruses and a human housekeeping gene. J Clin Virol 2019; 120:44-50. [PMID: 31557664 DOI: 10.1016/j.jcv.2019.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/19/2019] [Accepted: 08/23/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND Recent emergence of Zika virus (ZIKV), and the global spread of dengue (DENV), chikungunya (CHIKV) and West Nile viruses (WNV) raised urgent need of accurate and affordable molecular diagnosis of these clinically indistinguishable arboviral infections. OBJECTIVES We established a pentaplex real-time reverse transcription PCR (rRT-PCR) assay (CII-ArboViroPlex rRT-PCR) for specific and sensitive detection of the African and American genotypes of ZIKV, all four serotypes of DENV, CHIKV, WNV and a housekeeping gene as internal control in single reaction. STUDY DESIGN Specific primers and probe sets were designed for ZIKV, DENV, CHIKV, WNV and RNase P (housekeeping gene) and tested for in-vitro transcribed RNA standards, virus cultures, clinical samples positive for ZIKV, DENV, CHIKV and WNV and limit of detection (LOD) were determined for each. Results Using ten-fold serially diluted in-vitro transcribed RNA, CII- ArboViroPlex rRT-PCR assay has LOD of 100 RNA copies/reaction (Rn) for ZIKV in serum or urine, 100 RNA copies/Rn for DENV in serum, and 10 RNA copies/Rn for CHIKV and WNV in serum. LODs from sera spiked with quantitated viral stocks were 2.6 × 102 GEQ/Rn for ZIKV, 2.2 × 101 GEQ/Rn for DENV-1, 9.4 × 100 GEQ/Rn for DENV-2, 2.3 × 102 GEQ/Rn for DENV-3, 1.4 × 103 GEQ/Rn for DENV-4, 2.7 × 102 GEQ/Rn for CHIKV, and 1.05 × 101 GEQ/Rn for WNV. CONCLUSIONS The CII-ArboViroPlex rRT-PCR assay is a quantitative one-step pentaplex rRT-PCR assay for the molecular detection and differential diagnosis of ZIKV, DENV, CHIKV, WNV and a human housekeeping gene control in a single- PCR reaction.
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Antibodies to Enteroviruses in Cerebrospinal Fluid of Patients with Acute Flaccid Myelitis. mBio 2019; 10:e01903-19. [PMID: 31409689 PMCID: PMC6692520 DOI: 10.1128/mbio.01903-19] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 01/05/2023] Open
Abstract
Acute flaccid myelitis (AFM) has caused motor paralysis in >560 children in the United States since 2014. The temporal association of enterovirus (EV) outbreaks with increases in AFM cases and reports of fever, respiratory, or gastrointestinal illness prior to AFM in >90% of cases suggest a role for infectious agents. Cerebrospinal fluid (CSF) from 14 AFM and 5 non-AFM patients with central nervous system (CNS) diseases in 2018 were investigated by viral-capture high-throughput sequencing (VirCapSeq-VERT system). These CSF and serum samples, as well as multiple controls, were tested for antibodies to human EVs using peptide microarrays. EV RNA was confirmed in CSF from only 1 adult AFM case and 1 non-AFM case. In contrast, antibodies to EV peptides were present in CSF of 11 of 14 AFM patients (79%), significantly higher than controls, including non-AFM patients (1/5 [20%]), children with Kawasaki disease (0/10), and adults with non-AFM CNS diseases (2/11 [18%]) (P = 0.023, 0.0001, and 0.0028, respectively). Six of 14 CSF samples (43%) and 8 of 11 sera (73%) from AFM patients were immunoreactive to an EV-D68-specific peptide, whereas the three control groups were not immunoreactive in either CSF (0/5, 0/10, and 0/11; P = 0.008, 0.0003, and 0.035, respectively) or sera (0/2, 0/8, and 0/5; P = 0.139, 0.002, and 0.009, respectively).IMPORTANCE The presence in cerebrospinal fluid of antibodies to EV peptides at higher levels than non-AFM controls supports the plausibility of a link between EV infection and AFM that warrants further investigation and has the potential to lead to strategies for diagnosis and prevention of disease.
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MESH Headings
- Adolescent
- Adult
- Antibodies, Viral/blood
- Antibodies, Viral/cerebrospinal fluid
- Antibodies, Viral/immunology
- Antigens, Viral/immunology
- Central Nervous System Viral Diseases/blood
- Central Nervous System Viral Diseases/cerebrospinal fluid
- Child
- Enterovirus D, Human/genetics
- Enterovirus D, Human/immunology
- Enterovirus D, Human/isolation & purification
- Enterovirus Infections/blood
- Enterovirus Infections/cerebrospinal fluid
- Female
- High-Throughput Nucleotide Sequencing
- Humans
- Male
- Middle Aged
- Myelitis/blood
- Myelitis/cerebrospinal fluid
- Neuromuscular Diseases/blood
- Neuromuscular Diseases/cerebrospinal fluid
- Protein Array Analysis
- RNA, Viral/blood
- RNA, Viral/cerebrospinal fluid
- RNA, Viral/genetics
- Young Adult
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298 The Pediatric Injury Quality Improvement Collaborative (PIQIC): A Quality Improvement Initiative between Five Pediatric Burn Centers. J Burn Care Res 2019. [DOI: 10.1093/jbcr/irz013.214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Comparative Evaluation of Shear Bond Strength of Resin Modified Glass Ionomer Cement and Biodentine as Dentin Substitutes to Bonded Silver Amalgam and Composite Resin. J Clin Diagn Res 2018. [DOI: 10.7860/jcdr/2018/37080.12279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Population-based cohort study of variation in the use of emergency cholecystectomy for benign gallbladder diseases. Br J Surg 2016; 103:1716-1726. [PMID: 27748962 DOI: 10.1002/bjs.10288] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/21/2016] [Accepted: 07/06/2016] [Indexed: 01/05/2023]
Abstract
Abstract
Background
The aims of this prospective population-based cohort study were to identify the patient and hospital characteristics associated with emergency cholecystectomy, and the influences of these in determining variations between hospitals.
Methods
Data were collected for consecutive patients undergoing cholecystectomy in acute UK and Irish hospitals between 1 March and 1 May 2014. Potential explanatory variables influencing the performance of emergency cholecystectomy were analysed by means of multilevel, multivariable logistic regression modelling using a two-level hierarchical structure with patients (level 1) nested within hospitals (level 2).
Results
Data were collected on 4744 cholecystectomies from 165 hospitals. Increasing age, lower ASA fitness grade, biliary colic, the need for further imaging (magnetic retrograde cholangiopancreatography), endoscopic interventions (endoscopic retrograde cholangiopancreatography) and admission to a non-biliary centre significantly reduced the likelihood of an emergency cholecystectomy being performed. The multilevel model was used to calculate the probability of receiving an emergency cholecystectomy for a woman aged 40 years or over with an ASA grade of I or II and a BMI of at least 25·0 kg/m2, who presented with acute cholecystitis with an ultrasound scan showing a thick-walled gallbladder and a normal common bile duct. The mean predicted probability of receiving an emergency cholecystectomy was 0·52 (95 per cent c.i. 0·45 to 0·57). The predicted probabilities ranged from 0·02 to 0·95 across the 165 hospitals, demonstrating significant variation between hospitals.
Conclusion
Patients with similar characteristics presenting to different hospitals with acute gallbladder pathology do not receive comparable care.
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Crooke′s cell adenoma of the pituitary: A histological, immunocytochemical, and electron microscopic study of a rare case. Neurol India 2014; 62:216-7. [DOI: 10.4103/0028-3886.132435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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One-year maintenance outcomes among patients with moderately-to-severely active ulcerative colitis who responded to induction therapy with adalimumab: subgroup analyses from ULTRA 2. Aliment Pharmacol Ther 2013; 37:204-13. [PMID: 23173821 DOI: 10.1111/apt.12145] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 10/03/2012] [Accepted: 10/27/2012] [Indexed: 12/27/2022]
Abstract
BACKGROUND Patients with moderately-to-severely active ulcerative colitis (UC) are unlikely to continue anti-TNF therapy in the absence of early therapeutic response. AIM To assess week 52 efficacy, safety and benefit/risk balance of adalimumab treatment in patients with moderately-to-severely active UC failing conventional therapy who achieved clinical response at week 8 in the 52-week ULTRA 2 trial. METHODS Patients randomised to adalimumab (160/80 mg, week 0/2; 40 mg, every other week thereafter) in ULTRA 2 who achieved clinical response at week 8 per partial Mayo score (Mayo score without endoscopy subscore) were assessed for week 52 clinical remission, clinical response, mucosal healing, steroid-free remission and steroid discontinuation rates, overall and by prior anti-TNF use. Benefit/risk balance for the overall ITT population (regardless of week 8 responder status) was assessed using 'net efficacy adjusted for risk' (NEAR) odds ratios. Safety was assessed using adverse event rates. RESULTS Of 248 adalimumab-treated patients, 123 (49.6%) achieved clinical response at week 8. Of these, 30.9%, 49.6%, and 43.1% achieved clinical remission, clinical response, and mucosal healing, respectively, at week 52. Of the week 8 responders using corticosteroids at baseline (N = 90), 21.1% achieved steroid-free remission and 37.8% were steroid-free at week 52. NEAR odds ratios indicated a positive benefit/risk balance for achievement of week 8 and week 52 response or remission without serious adverse events or serious infections. No safety concerns were identified. CONCLUSIONS Adalimumab treatment was associated with a positive benefit/risk balance in the overall population of patients with moderately-to-severely active ulcerative colitis in ULTRA 2; early response was predictive of a positive outcome at 1 year (NCT00408629).
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Abstract: P1444 ASPIRIN IN ADDITION TO NIACIN PROMOTES A MORE RAPID TOLERANCE TO FLUSHING. ATHEROSCLEROSIS SUPP 2009. [DOI: 10.1016/s1567-5688(09)71452-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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QS227. The Super-Elderly (>80 Years Old) Suffer Devastating Head Injury Outcomes Following Minor Trauma When Compared With Their Elderly Counterparts (65 to 79 Years Old). J Surg Res 2009. [DOI: 10.1016/j.jss.2008.11.529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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The ADHERE classification and regression tree model overestimates mortality rates in clinical trials: results from REVIVE I & II. Crit Care 2007. [PMCID: PMC4095277 DOI: 10.1186/cc5383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Intradermal route for prophylaxis against hepatitis B: loss of potency in relation to time. Indian J Gastroenterol 1988; 7:109-10. [PMID: 2966111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Surgery for stroke. J R Soc Med 1981; 74:330-2. [PMID: 7241482 PMCID: PMC1438829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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