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APIR:Aggregating Universal Proteomics database Search Algorithms for Peptide Identification with FdR Control

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Genomics, Proteomics & Bioinformatics 2024年第2期22卷 171-187页

作者： Yiling Elaine Chen Xinzhou Ge kyla Woyshner MeiLu Mcdermott Antigoni Manousopoulou Scott B.Ficarro Jarrod A.Marto Kexin Li Leo david Wang Jingyi Jessica Li department of Statistics and data Science University of CaliforniaLos AngelesCA 90095USA department of Immuno-Oncology Beckman Research InstituteCity of Hope National Medical CenterDuarteCA 91010USA department of Quantitative and Computational Biology University of Southern CaliforniaLos AngelesCA 90089USA department of Cancer Biology and Blais Proteomics Center Dana-Farber Cancer InstituteDepartment of PathologyBrigham and Women’s Hospital and Harvard Medical SchoolBostonMA 02215USA department of Pediatrics City of Hope National Medical CenterDuarteCA 91010USA Bioinformatics Interdepartmental Program University of CaliforniaLos AngelesCA 90095USA department of Human Genetics University of CaliforniaLos AngelesCA 90095USA department of Computational Medicine University of CaliforniaLos AngelesCA 90095USA department of Biostatistics University of CaliforniaLos AngelesCA 90095USA

Advances in mass spectrometry(MS)have enabled high-throughput analysis of proteomes in biological *** state-of-the-art MS data analysis relies on database search algorithms to quantify proteins by identifying peptide–spectrum matches(PSMs),which convert mass spectra to peptide *** database search algorithms use distinct search strategies and thus may identify unique ***,no existing approaches can aggregate all user-specified database search algorithms with a guaranteed increase in the number of identified peptides and a control on the false discovery rate(FdR).To fill in this gap,we proposed a statistical framework,Aggregation of Peptide Identification Results(APIR),that is universally compatible with all database search ***,under an FdR threshold,APIR is guaranteed to identify at least as many,if not more,peptides as individual database search algorithms *** of APIR on a complex proteomics standard dataset showed that APIR outpowers individual database search algorithms and empirically controls the *** data studies showed that APIR can identify disease-related proteins and post-translational modifications missed by some individual database search *** APIR framework is easily extendable to aggregating discoveries made by multiple algorithms in other high-throughput biomedical data analysis,e.g.,differential gene expression analysis on RNA sequencing *** APIR R package is available at https://***/yiling0210/APIR.

关键词： Shotgun proteomics Peptide–spectrum match Peptide identification Aggregation of lists FdR control

Impact of cardiologist intervention on guideline-directed use of statin therapy

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World Journal of Cardiology 2020年第8期12卷 419-426页

作者： Manouchkathe Cassagnol Ofek Hai Shaqeel A Sherali kyla d’Angelo david Bass Roman Zeltser Amgad N Makaryus department of Cardiology NuHealth/Nassau University Medical CenterEast MeadowNY 11554United States department of Clinical Health Professions College of Pharmacy and Health SciencesSt.John’s UniversityQueensNY 11430United States donald and Barbara Zucker School of Medicine at Hofstra/Northwell HempsteadNY 11549United States St.Lawrence Health System PotsdamNY 13676United States

BACKGROUNd Statins have an important and well-established role in the prevention of atherosclerotic cardiovascular disease(ASCVd).However,several studies have reported widespread underuse of statins in various practice settings and *** of relevant literature reveals opportunities for improvement in the implementation of guideline-directed statin therapy(GdST).AIM To examine the impact of cardiologist intervention on the use of GdST in the ambulatory *** Patients with at least one encounter at the adult Internal Medicine Clinic(IMC)and/or Cardiology Clinic(CC),who had an available serum cholesterol test performed,were *** 2 comparison groups were defined as:(1)Patients only seen by IMC;and(2)Patients seen by both IMC and *** were excluded if variables needed for calculation of ASCVd risk scores were lacking,and if demographic information lacked guideline-directed treatment *** were analyzed using student t-tests or χ^2,as *** of Variance was used to compare rates of adherence to *** A total of 268 patients met the inclusion criteria for this study;211 in the IMC group and 57 in the IMC-CC ***,56%of patients were female,mean age 56 years(±10.65,Sd),22%Black or African American,56%Hispanic/Latino,14%had clinical ASCVd,13%current smokers,66%diabetic and 63%*** use was observed in 55%(n=147/268)of the entire patient *** the IMC-CC group,73.6%(n=42/57)of patients were prescribed statin therapy compared to 50.7%(n=107/211)of patients in the IMC group(P=0.002).In terms of appropriate statin use based on guidelines,there was no statistical difference between groups[IMC-CC group 61.4%(n=35/57)vs IMC group,55.5%(n=117/211),P=0.421].Patients in the IMC-CC group were older,had more cardiac risk factors and had higher proportions of non-white patients compared to the IMC group(PdST was suboptimal,there was no statis

关键词： Statin use Guideline directed statin therapy Cardiologist Ambulatory care Adherence

Evaluation of the Antimicrobial Activity of Endophytic Fungus Isolated from <i>Cocos nucifera</i>(L.) Cotyledon against Medically-Important Pathogens

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Journal of Biosciences and Medicines 2021年第1期9卷 86-97页

作者： Byran N. Fuego kyla G. Romano Charlmaine d. Pinlac Gary Antonio C. Lirio Major in Science Department of Elementary and Secondary Education College of Education Polytechnic University of the Philippines Manila Philippines Institute for Science and Technology Research Center for Life Sciences Research Polytechnic University of the Philippines Manila Philippines

The study aimed to evaluate the endophytic fungi isolated from Cocos nucifera (L.) cotyledon for their possible antimicrobial activity. A total of twelve endophytic fungal species were successfully isolated, from which five were selected and presumptively identified, including Aspergillus niger, Raffaelea sp., Aspergillus flavus, Cladosporium sp. and Pseudallescheria spp. based on their macro and microscopic characters. The agar blocks of actively growing pure culture were assessed for antibacterial activity against five human pathogenic bacterial and fungal strains: Escherichia coli (BIOTECH 1634), Bacillus subtilis (BIOTECH 1697), Staphylococcus aureus (BIOTECH 1592), Serratia marcescens (BIOTECH 1748), and Candida tropicalis (BIOTECH 2085). Among the selected five endophytic used for antimicrobial activity screening, the Raffaelea sp. (CN-EF 2) has shown a high zone of inhibition of 11 mm against Bacillus subtilis, 18 mm against Escherichia coli, 15 mm against Staphylococcus aureus, and 11 mm against Candida tropicalis. Correspondingly, Aspergillus niger (CN-EF 1) has shown a zone of inhibition of 16 mm against C. tropicalis. The endophytic fungus Raffaelea sp. was effective against all test organisms except for Serratia marcescens, while Aspergillus niger was only effective for pathogenic fungi C. albicans. Hence, further in-depth studies of the isolated endophytic fungi are needed to determine the mechanisms behind the endophytes’ inhibitory effects.

关键词： Endophytic Fungi Antimicrobial Activity Cocos nucifera L. Natural Product Agar Plug diffusion Medically-Important Pathogens

Risk factors for fracture in adult kidney transplant recipients

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World Journal of Transplantation 2016年第2期6卷 370-379页

作者： kyla L Naylor Guangyong Zou William d Leslie Anthony B Hodsman Ngan N Lam Eric McArthur Lisa-Ann Fraser Gregory A Knoll Jonathan d Adachi S Joseph Kim Amit X Garg Institute for Clinical Evaluative Sciences 2nd Institute of Health Policy Management and EvaluationUniversity of Toronto department of Epidemiology and Biostatistics Western University department of Medicine University of Manitoba division of Nephrology Western University division of Nephrology University of Alberta division of Endocrinology Western University division of Nephrology Kidney Research CentreOttawa Hospital Research InstituteUniversity of Ottawa division of Rheumatology McMaster University division of Nephrology University Health NetworkUniversity of Toronto

AIM: To determine the general and transplant-specific risk factors for fractures in kidney transplant ***: We conducted a cohort study of all adults who received a kidney-only transplant(n = 2723) in Ontario, Canada between 2002 and 2009. We used multivariable Cox proportional hazards regression to determine general and transplant-specific risk factors for major fractures(proximal humerus, forearm, hip, and clinical vertebral). The final model was established using the backward elimination strategy, selecting risk factors with a P-value ≤ 0.2 and forcing recipient age and sex into the model. We also assessed risk factors for other fracture locations(excluding major fractures, and fractures involving the skull, hands or feet). RESULTS: There were 132 major fractures in the follow-up(8.1 fractures per 1000 person-years). General risk factors associated with a greater risk of major fracture were older recipient age [adjusted hazard ratio(a HR) per 5-year increase 1.11, 95%CI: 1.03-1.19] and female sex(a HR = 1.81, 95%CI: 1.28-2.57). Transplant-specific risk factors associated with a greater risk of fracture included older donor age(5-year increase)(a HR = 1.09, 95%CI: 1.02-1.17) and end-stage renal disease(ESRd) caused by diabetes(a HR = 1.72, 95%CI: 1.09-2.72) or cystic kidney disease(a HR = 1.73, 95%CI: 1.08-2.78)(compared to glomerulonephritis as the reference cause). Risk factors across the two fracture locations were not consistent(major fracture locations vs other). Specifically, general risk factors associated with an increased risk of other fractures were diabetes and a fall with hospitalization prior to transplantation, while length of time on dialysis, and renal vascular disease and other causes of ESRd were the transplant-specific risk factors associated with a greater risk of other ***: Both general and transplant-specific risk factors were associated with a higher risk of fractures in kidney transplant recipients. Results ca

关键词： Fracture Risk factors Kidney transplant recipient Prognostication Cohort study