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APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control

GENOMICS PROTEOMICS & BIOINFORMATICS 2024年第2期22卷 qzae042页

作者： Chen, Yiling Elaine Ge, Xinzhou Woyshner, Kyla McDermott, Meilu Manousopoulou, Antigoni Ficarro, Scott B. Marto, Jarrod A. li, Kexin Wang, Leo David li, jingyi jessica Univ Calif Los Angeles Dept Stat & Data Sci Los Angeles CA 90095 USA Univ Calif Los Angeles Bioinformat Interdept Program Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Human Genet Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Computat Med Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Biostat Los Angeles CA 90095 USA City Hope Natl Med Ctr Beckman Res Inst Dept Immuno Oncol Duarte CA 91010 USA Univ Southern Calif Dept Quantitat & Computat Biol Los Angeles CA 90007 USA City Hope Natl Med Ctr Dept Pediat Duarte CA 91010 USA Brigham & Womens Hosp Dept Canc Biol Boston MA 02215 USA Brigham & Womens Hosp Dana Farber Canc Inst Blais Prote Ctr Dept Pathol Boston MA 02215 USA Harvard Med Sch Boston MA 02215 USA

Advances in mass spectrometry (MS) have enabled high-throughput analysis of proteomes in biological systems. The 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 sequences. Different database search algorithms use distinct search strategies and thus may identify unique PSMs. However, 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 algorithms. Notably, under an FDR threshold, APIR is guaranteed to identify at least as many, if not more, peptides as individual database search algorithms do. Evaluation of APIR on a complex proteomics standard dataset showed that APIR outpowers individual database search algorithms and empirically controls the FDR. Real data studies showed that APIR can identify disease-related proteins and post-translational modifications missed by some individual database search algorithms. The 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 data. The APIR R package is available at https://***/yiling0210/APIR.

关键词： Shotgun proteomics Peptide-spectrum match Peptide identification Aggregation of lists FDR control PROTEIN IDENTIFICATION BRCA2 MUTATIONS CELL-CYCLE TANDEM TARGET CANCER PREVALENCE EXPRESSION GENE APOPTOSIS

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Working toward an integrated plasticity/network framework for repetitive transcranial magnetic stimulation to inform tailored treatments

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Neural Regeneration Research 2024年第7期19卷 1423-1424页

作者： jessica Moretti Jennifer Rodger Experimental and Regenerative Neurosciences School of Biological SciencesUniversity of Western AustraliaCrawleyWAAustralia Brain Plasticity Lab Perron Institute for Neurological and Translational ScienceNedlandsWAAustralia

Non-invasive brain stimulation techniques(NIBS),including repetitive transcranial magnetic stimulation(rTMS) and transcranial electric stim ulation(tES),are increasingly being adopted clinically for treatment of neuropsychiatric and neurological disorders,albeit with varying *** rationale behind the use of NIBS has historically been that stim ulation techniques modulate neuronal activity in the targeted region and consequently induce plasticity which can lead to therapeutic outcomes.

关键词： stimulation transcranial treatment

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Vonoprazan-amoxicillin dual regimen with Saccharomyces boulardii as a rescue therapy for Helicobacter pylori:Current perspectives and implications

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World Journal of Gastroenterology 2024年第10期30卷 1280-1286页

作者： Valerie Josephine Dirjayanto jessica Audrey Daniel Martin Simadibrata Faculty of Medicine Universitas IndonesiaJakarta Pusat 10430DKI JakartaIndonesia Division of Gastroenterology and Hepatology Mayo ClinicRochesterMinnesota 55905United States Nuffield Department of Population Health University of OxfordOxford OX37LFUnited Kingdom

Yu et al’s study in the World Journal of Gastroenterology(2023)introduced a novel regimen of Vonoprazan-amoxicillin dual therapy combined with Saccharomyces boulardii(***)for the rescue therapy against Helicobacter pylori(***),a pathogen responsible for peptic ulcers and gastric *** is a potassium-competitive acid blocker renowned for its rapid and long-lasting acid suppression,which is minimally affected by *** to proton pump inhibitors,which bind irreversibly to cysteine residues in the H+/K+-ATPase pump,Vonoprazan competes with the K+ions,prevents the ions from binding to the pump and blocks acid *** with increasing antibiotic resistance,effects on the gut microbiota,patient compliance,and side effects have led to the advent of a dual regimen for *** studies suggested that *** plays a role in stabilizing the gut barrier which improves *** eradication *** an acceptable safety profile,the dual-adjunct regimen was effective regardless of prior treatment failure and antibiotic resistance profile,thereby strengthening the applicability in clinical ***,*** comes in various formulations and dosages,warranting further exploration into the optimal dosage for supplementation in rescue ***,larger,randomized,double-blinded controlled trials are warranted to confirm these promising results.

关键词： Vonoprazan Saccharomyces boulardii Helicobacter pylori Rescue therapy Eradication rate

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Vonoprazan 10 mg or 20 mg *** 15 mg as maintenance therapy in Asian patients with healed erosive esophagitis:A randomized controlled trial

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Chinese Medical Journal 2024年第8期137卷 962-971页

作者： Yinglian Xiao Jiaming Qian Shutian Zhang Ning Dai Hoon Jai Chun Chengtang Chiu Chui Fung Chong Nobuo Funao Yuuichi Sakurai jessica D.Eisner li Xie Minhu Chen Department of Gastroenterology The First Affiliated HospitalSun Yat-sen UniversityGuangzhouGuangdong 510062China Department of Gastroenterology Peking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijing 100006China Department of Gastroenterology Beijing Friendship HospitalCapital Medical UniversityBeijing 100050China Department of Gastroenterology Sir Run Run Shaw HospitalSchool of Medicine Zhejiang UniversityHangzhouZhejiang 310020China Department of Internal Medicine Korea University Anam HospitalKorea University College of Medicine73 Goryeodae-roSeongbuk-guSeoul 02841Republic of Korea Department of Gastroenterology&Hepatology Linkou Medical CenterChang Gung Memorial HospitalTaoyuanTaiwan 33353China College of Medicine Chang Gung UniversityTaoyuanTaiwan 33353China Takeda Development Center Asia Singapore 018981Singapore Takeda Pharmaceutical Company Chuo-kuOsaka 540-8645Japan Takeda Pharmaceuticals International Company CambridgeMA02142 USA China Medical Team Takeda ChinaBeijing 100027China Hoffmann-La Roche Basel4070 Switzerland Abbott Laboratories Lake ForestIL 60045USA

Background:Erosive esophagitis(EE)is a gastroesophageal reflux disease characterized by mucosal breaks in the *** pump inhibitors are widely used as maintenance therapy for EE,but many patients still *** this trial,we evaluated the noninferiority of vonoprazan *** as maintenance therapy in patients with healed ***:We performed a double-blind,double-dummy,multicenter,phase 3 clinical trial among non-Japanese Asian adults with endoscopically confirmed healed EE from April 2015 to February *** from China,South Korea,and Malaysia were randomized to vonoprazan 10 mg or 20 mg once daily or lansoprazole 15 mg once daily for 24 *** primary endpoint was endoscopically confirmed EE recurrence rate over 24 weeks with a noninferiority margin of 10%using a two-sided 95%confidence interval(CI).Treatment-emergent adverse events(TEAEs)were ***:Among 703 patients,EE recurrence was observed in 24/181(13.3%)and 21/171(12.3%)patients receiving vonoprazan 10 mg or 20 mg,respectively,and 47/184(25.5%)patients receiving lansoprazole(differences:-12.3%[95%CI,-20.3%to-4.3%]and-13.3%[95%CI,-21.3%to-5.3%],respectively),meeting the primary endpoint of noninferiority to lansoprazole in preventing EE recurrence at 24 *** of superiority(upper bound of 95%CI<0%)was also *** 12 weeks,endoscopically confirmed EE recurrence was observed in 5/18,2/20,and 7/20 of patients receiving vonoprazan 10 mg,vonoprazan 20 mg,and lansoprazole,*** were experienced by 66.8%(157/235),69.0%(156/226),and 65.3%(158/242)of patients receiving vonoprazan 10 mg,vonoprazan 20 mg,and lansoprazole,*** most common TEAE was upper respiratory tract infection in 12.8%(30/235)and 12.8%(29/226)patients in vonoprazan 10 mg and 20 mg groups,respectively and 8.7%(21/242)patients in lansoprazole ***:Vonoprazan maintenance therapy was well-tolerated and noninferior to lansoprazole for preventing EE recurrence i

关键词： Erosive esophagitis Lansoprazole Maintenance therapy Potassium-competitive acid blockers Vonoprazan

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A new bioinformatics tool to recover missing gene expression in single-cell RNA sequencing data

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Journal of Molecular Cell Biology 2021年第1期13卷 1-2页

作者： jingyi jessica li Department of Statistics University of CaliforniaLos AngelesCA 90095-1554USA

Single-cell RNA sequencing (ScRNA-seq) is a burgeoning field where experi-mental techniques and computationalmethods have been under rapid evolution in the past 6 *** techno-logicaladvances haveallowedbiomedical researchers to identify newcell types, delineate cell sub-populations, and infer cell differentiationtrajectories in various tissue *** the important features extract-able from scRNA-seq data, the predomi-nant onesare individualgenes'expression levels in single cells.

关键词： cell allowed advances

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Orchard Sports Injury and Illness Classification System (OSIICS) Version 15

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Journal of Sport and Health Science 2024年第4期13卷 599-604页

作者： John W.Orchard Ebonie Rio Kay M.Crossley jessica J.Orchard Margo Mountjoy School of Public Health University of SydneySydneyNSW 2006Australia La Trobe Sport and Exercise Medicine Research Centre La Trobe UniversityMelbourneVIC 3083Australia Department of Family Medicine McMaster UniversityHamilton L8S 4L8Canada

Background:Sports medicine(injury and illnesses)requires distinct coding systems because the International Classification of Diseases is insuf-ficient for sports medicine *** Orchard Sports Injury and Illness Classification System(OSIICS)is one of two sports medicine coding systems recommended by the International Olympic *** updates of coding systems are ***:For Version 15,updates for mental health conditions in athletes,sports cardiology,concussion sub-types,infectious diseases,and skin and eye conditions were considered particularly ***:Recommended codes were added from a recent International Olympic Committee consensus statement on mental health conditions in *** landmark sports cardiology papers were used to update a more comprehensive list of sports cardiology *** union protocols on head injury assessment were used to create additional concussion ***:It is planned that OSIICS Version 15 will be translated into multiple new languages in a timely fashion to facilitate international *** large number of recently published sport-specific and discipline-specific consensus statements on athlete surveillance warrant regular updating of OSIICS.

关键词： Sports cardiology Dermatology Eye injuries Concussion Infectious diseases Sports injury classification

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Advances in teleophthalmology and artificial intelligence for diabetic retinopathy screening:a narrative review

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Annals of Eye Science 2024年第2期9卷 24-37页

作者： Tanvi Chokshi Maria jessica Cruz Jonathon Ross Glenn Yiu Tschannen Eye Institute Department of OphthalmologyUniversity of CaliforniaDavis HealthSacramentoCAUSA Department of Research College of MedicineCalifornia Northstate UniversityElk GroveCAUSA

Background and Objective:Advances in teleophthalmology and artificial intelligence(AI)for diabetic retinal screening is of growing public health ***,only 30–40%of patients with diabetes adhere to recommended diabetes screening *** enhance early detection and reduce vision threatening complications,there has been a growing number of teleophthalmology programs and novel AI algorithms with the aim to improve eye care *** purpose of this review is to assess current literature on teleophthalmology and AI for use in diabetic retinopathy(DR)screening,and to discuss advances and barriers to these innovative ***:literature review involving teleophthalmology and AI for DR screening,with focus on the past *** Content and Findings:Teleophthalmology has demonstrated the ability to increase DR screening rates,enable earlier eye care access,and reduce healthcare *** AI-based DR screening programs appear accurate and effective,but detection of other ocular pathologies is still under development and not yet approved in the United ***,technological,financial,and legal barriers limit widespread adoption and long-term sustainability of teleophthalmology ***:The use of teleophthalmology and AI algorithms expands eye care access and helps prevent vision loss from DR and potentially other sight threatening *** in the process utilized for arriving at a particular diagnosis or decision to refer,often referred to as the“black box”,remains a multifaceted issue within the field of telemedicine for developing trust and improving patient-centered outcomes.

关键词： Teleophthalmology artificial intelligence(AI) diabetic retinopathy(DR) screening public health

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Multiple sclerosis is at a checkpoint: advancing the program

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Neural Regeneration Research 2025年第3期20卷 811-812页

作者： Brandon C.Smith jessica L.Williams Department of Neurosciences Lerner Research InstituteCleveland ClinicClevelandOHUSA Department of Biological Geologicaland Environmental SciencesCleveland State UniversityClevelandOHUSA

Multiple sclerosis(MS) is a chronic inflammatory and demyelinating disease of the central nervous system(CNS). Patients with MS experience sensory and motor function loss due to myelin and/or axon damage perpetuated b... 详细信息

关键词： Hauser sclerosis damage

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Bedtime Stories Aren't Just for Kids--Tell yourself a bedtime story to fall asleep faster

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空中英语教室（高级版．彭蒙惠英语） 2024年第9期 32-33,48页

作者： jessica Stillman 不详

Nearly every night for the past nine years,my husband and I have cajoled our daughter into a bath and PJs,read her a bedtime story and tucked her into bed.A few nights of struggle and exhaustion aside,this has mostly ... 详细信息

关键词： yourself Just daughter

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Modeling and analysis of RNA-seq data： a review from a statistical perspective

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Frontiers of Electrical and Electronic Engineering in China 2018年第3期6卷 195-209页

作者： Wei Vivian li jingyi jessica li Department of Statistics University of CaliforniaLos AngelesLos AngelesCA 90095-1554USA Department of Human Genetics University of CaliforniaLos AngelesLos AngelesCA 90095-088USA

Background： Since the invention of next-generation RNA sequencing （RNA-seq） technologies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic studies. The analysis of RNA-seq data at four different levels （samples, genes, transcripts, and exons） involve multiple statistical and computational questions, some of which remain challenging up to date. Results： We review RNA-seq analysis tools at the sample, gene, transcript, and exon levels from a statistical perspective. We also highlight the biological and statistical questions of most practical considerations. Conclusions： The development of statistical and computational methods for analyzing RNA-seq data has made significant advances in the past decade. However, methods developed to answer the same biological question often rely on diverse statistical models and exhibit different performance under different scenarios. This review discusses and compares multiple commonly used statistical models regarding their assumptions, in the hope of helping users select appropriate methods as needed, as well as assisting developers for future method development.

关键词： RNA-seq statistical modeling differentially expressed genes alternatively spliced exons isoformreconstruction and quantification

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