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Comparison of aerobic conjunctival bacterial flora in pregnant, reproductive-aged and postmenopausal women

International Journal of Ophthalmology(English edition) 2012年第6期5卷 731-736页

作者： Melike Balikoglu-Yilmaz Emine Sen Osman Sevket Yusuf Polat Aysun Karabulut Omer Uysal Department of Ophthalmology Denizli State Hospital Ulucanlar Eye Education and Research Hospital Department of Obstetrics and Gynecology Denizli State Hospital Department of Microbiology and Clinic Microbiology Denizli State Hospital Department of biostatistics and medical informatics Bezmi Alem Vakif University

AIM: To evaluate the effect of hormonal status on aerobic conjunctival flora in women. METHODS: One hundred fifty-eight women [reproductive-aged (n=55), pregnant (n=51), and postmenopausal (n=52)] who admitted to outpatient clinic of Obstetrics and Gynecology Department of Denizli State Hospital were enrolled. Age, body-mass index (BMI), obstetric history, cigarette smoking, drug usage, presence of systemic disease, and intraocular pressure (IOP) were recorded for each patient. The samples were taken from the lower fornix with two culture swabs and directly incubated in culture containing 5% sheep blood, eosin-methylene blue and chocolate agar. The other swab specimen was Gram stained. All growths and microscopic results were analyzed. RESULTS: The coagulase-negative Staphylococcus was the predominant organism isolated in the conjunctival samples in both three groups. The aerobic microorganism growth rate for all isolated aerobic organisms revealed no significant change in the three groups (P>0.05). The conjunctival culture positivity rates were similar in the three groups (49% in reproductive-aged, 57% in pregnant and 58% in postmenopausal women) (P>0.05). Age, IOP, BMI, gravidity, parity, cigarette smoking, drug usage, and presence of systemic diseases did not have an effect on culture positivity in three groups. CONCLUSION: Results of this study showed that conjunctival aerobic flora and bacterial colonization did not differ between reproductive-aged, pregnant and postmenopausal women.

关键词： aerobic conjunctival flora coagulase-negative Staphylococcus menopause pregnancy reproductive-aged

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Personalised treatment assignment maximising expected benefit with smooth hinge loss

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Statistical Theory and Related Fields 2017年第1期1卷 37-47页

作者： Shixue Liu Jun Shao Menggang Yu Department of Statistics University ofWisconsinMadisonWIUSA School of Statistics East China Normal UniversityShanghaiChina Department of biostatistics and medical informatics University ofWisconsinMadisonWIUSA

In personalised medicine,the goal is tomake a treatment recommendation for each patient with a given set of covariates tomaximise the treatment benefitmeasured by patient’s response to the *** application,such a treatment assignment rule is constructed using a sample training data consisting of patients’responses and *** of modelling responses using treatments and covariates,an alternative approach is maximising a response-weighted target function whose value directly reflects the effectiveness of treatment *** the target function involves a loss function,efforts have been made recently on the choice of the loss function to ensure a computationally feasible and theoretically sound *** propose to use a smooth hinge loss function so that the target function is convex and differentiable,which possesses good asymptotic properties and numerical *** further simplify the computation and interpretability,we focus on the rules that are linear functions of covariates and discuss their asymptotic *** also examine the performances of our method with simulation studies and real data analysis.

关键词： Convex loss linear rules oracle property subgroup identification weighted outcome learning

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Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from A Data-driven Perspective

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Genomics, Proteomics & Bioinformatics 2023年第1期21卷 164-176页

作者： Jianlei Gu Jiawei Dai Hui Lu Hongyu Zhao SJTU-Yale Joint Center for biostatistics and Data Science Department of Bioinformatics and BiostatisticsSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Center for Biomedical informatics Shanghai Engineering Research Center for Big Data in Pediatric Precision MedicineShanghai Children’s HospitalShanghai 200040China Department of biostatistics Yale UniversityNew HavenCT 06511USA

Comprehensive characterization of spatial and temporal gene expression patterns in humans is critical for uncovering the regulatory codes of the human genome and understanding the molecular mechanisms of human *** expressed genes(UEGs)refer to the genes expressed across a majority of,if not all,phenotypic and physiological conditions of an *** is known that many human genes are broadly expressed across ***,most previous UEG studies have only focused on providing a list of UEGs without capturing their global expression patterns,thus limiting the potential use of UEG *** this study,we proposed a novel data-driven framework to leverage the extensive collection of40,000 human transcriptomes to derive a list of UEGs and their corresponding global expression patterns,which offers a valuable resource to further characterize human *** results suggest that about half(12,234;49.01%)of the human genes are expressed in at least 80%of human transcriptomes,and the median size of the human transcriptome is 16,342 genes(65.44%).Through gene clustering,we identified a set of UEGs,named LoVarUEGs,which have stable expression across human transcriptomes and can be used as internal reference genes for expression *** further demonstrate the usefulness of this resource,we evaluated the global expression patterns for 16 previously predicted disallowed genes in islet beta cells and found that seven of these genes showed relatively more varied expression patterns,suggesting that the repression of these genes may not be unique to islet beta cells.

关键词： Ubiquitous expression Housekeeping gene Disallowed gene Expression specificity Expression variability

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A comprehensive evaluation of large language models in mining gene relations and pathway knowledge

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Quantitative Biology 2024年第4期12卷 360-374页

作者： Muhammad Azam Yibo Chen Micheal Olaolu Arowolo Haowang Liu Mihail Popescu Dong Xu Department of Electrical Engineering and Computer Science University of MissouriColumbiaMissouriUSA Bond Life Sciences Center University of MissouriColumbiaMissouriUSA Institute for Data Science and informatics University of MissouriColumbiaMissouriUSA Department of Biomedical informatics Biostatistics and Medical EpidemiologyUniversity of MissouriColumbiaMissouriUSA

Understanding complex biological pathways,including gene–gene interactions and gene regulatory networks,is critical for exploring disease mechanisms and drug *** literature curation of biological pathways cannot keep up with the exponential growth of new discoveries in the ***-scale language models(LLMs)trained on extensive text corpora contain rich biological information,and they can be mined as a biological knowledge *** study assesses 21 LLMs,including both application programming interface(API)-based models and open-source models in their capacities of retrieving biological *** evaluation focuses on predicting gene regulatory relations(activation,inhibition,and phosphorylation)and the Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway *** indicated a significant disparity in model ***-based models GPT-4 and Claude-Pro showed superior performance,with an F1 score of 0.4448 and 0.4386 for the gene regulatory relation prediction,and a Jaccard similarity index of 0.2778 and 0.2657 for the KEGG pathway prediction,***-source models lagged behind their API-based counterparts,whereas Falcon-180b and llama2-7b had the highest F1 scores of 0.2787 and 0.1923 in gene regulatory relations,*** KEGG pathway recognition had a Jaccard similarity index of 0.2237 for Falcon-180b and 0.2207 for *** study suggests that LLMs are informative in gene network analysis and pathway mapping,but their effectiveness varies,necessitating careful model *** work also provides a case study and insight into using LLMs das knowledge *** code is publicly available at the website of GitHub(Muh-aza).

关键词： biomedical text mining gene-gene interaction KEGG pathway large language model

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Treatment recommendation and parameter estimation under single-index contrast function

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Statistical Theory and Related Fields 2017年第2期1卷 171-181页

作者： Cui Xiong Menggang Yu Jun Shao School of Statistics East China Normal UniversityShanghaiChina Department of biostatistics and medical informatics University of Wisconsin-MadisonMadisonWIUSA Department of Statistics University of Wisconsin-MadisonMadisonWIUSA

In this article, we consider a semiparametric model for contrast function which is defined asthe conditional expected outcome difference under comparative treatments. The contrast function can be used to recommend treatment for better average outcomes. Existing approachesmodel the contrast function either parametrically or nonparametrically. We believe our approachimproves interpretability over the non-parametric approach while enhancing robustness overthe parametric approach. Without explicit estimation of the nonparametric part of our model,we show that a kernel-based method can identify the parametric part up to a multiplying constant. Such identification suffices for treatment recommendation. Our method is also extendedto high-dimensional settings. We study the asymptotics of the resulting estimation procedure inboth low- and high-dimensional cases. We also evaluate our method in simulation studies andreal data analyses.

关键词： Kernel weighting LASSO penalty personalised medicine semiparametric model

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Incidence and consequences of varicella in children treated for cancer in Guatemala

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World Journal of Pediatrics 2016年第3期12卷 320-326页

作者： Amy E.Caruso Brown Edwin J.Asturias Mario Melgar Federico A.Antillon-Klussmann Pamela Mettler Myron J.Levin Center for Bioethics and Humanities and Department of Pediatrics SUNY Upstate Medical University Center for Global Health and Department of Epidemiology Colorado School of Public HealthAuroraColoradoUSA National Unit of Pediatric Oncology Guatemala CityGuatemala Department of biostatistics and informatics Colorado Biostatistics ConsortiumColorado School of Public HealthAuroraColoradoUSA Section of Pediatric Infectious Diseases Department of PediatricsUniversity of Colorado Denver Anschutz Medical CampusAuroraColoradoUSA

Background:Varicella-zoster virus infection is associated with significant morbidity and mortality in immune-compromised children,despite treatment with antiviral *** varicella vaccine programs have significantly decreased this risk in many highincome countries,but in most low-income and middleincome countries,the burden of varicella in children treated for malignancy is poorly defi ***:We retrospectively reviewed records of children at the National Unit of Pediatric Oncology(UNOP)in Guatemala diagnosed with varicella between January 2009 and March 2013 in order to calculate incidence of varicella and evaluate morbidity,mortality,treatment interruption,and ***:Fifty-nine cases of varicella were *** was 23.4 cases per 1000 person-years(p-y).66.1%of cases occurred in children with leukemia(median age 5.2 years;interquantile range 3.4-7 years)and 41.0%of these occurred during maintenance *** of exposure was identified for 14/59(23.7%)*** were hospitalized(71.2%)and given intravenous acyclovir(64.4%).Eight(13.6%)children required critical care,and two(3.4%)died from disseminated varicella with multiorgan *** was delayed or omitted due to varicella in 50%.No signifi cant differences in outcomes based on nutritional and immunologic status were *** minimum average cost of treatment per episode was 598.75 ***:Varicella is a significant problem in children treated for cancer in Guatemala,where effective post-exposure prophylaxis is *** the absence of universal varicella vaccination,strategies to improve recognition of exposure and the future use of novel inactivated vaccines currently under investigation in clinical trials could mitigate this burden.

关键词： cancer developing countries immunocompromised host oncology varicella

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Geospatial and clinical analyses on pediatric related road traffic injury in Malaysia

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World Journal of Emergency Medicine 2016年第3期7卷 213-220页

作者： Nik Hisamuddin Rahman Ruslan Rainis Syed Hatim Noor Sharifah Mastura Syed Mohamad Department of Emergency Medicine School of Medical Sciences USM Kota Bharu 16150 Malaysia School of Humanity USM Penang Malaysia Unit of biostatistics School of Medical Sciences USM Kota Bharu 16150 Malaysia Unit of Health informatics School of Health Sciences USM Kota Bharu 16150 Malaysia

BACKGROUND: The main aim of this study is to utilize the geographical information system(GIS) software and perform the spatial analysis in relation to clinical data for road traffi c injury(RTI) pediatric cases attending the emergency ***: The study sample included pediatric patients(age less than 18 years) with roadrelated injuries within a district in Malaysia who attended emergency departments of two tertiary hospitals within the district. In addition to injury, pre-hospital care and outcome data, the coordinate of the locations were obtained by the ambulance paramedics by using portable handheld GPS unit brand Garmin? model GPS 72 H. The data was transferred into the excel format which in turn underwent GIS analysis by using ARCGIS?(by ESRI) software version 10.1 licensed to the study ***: A total of 102(24.8%) of all motor vehicle crash(MVC) victims involved the pediatric age group(age 18 years and below). The mean(SD) age of the pediatric victims was 14.30 years(SD 3.830). Male comprised of 68(66.7%) of the cases. Motorcyclists [88(88.0%)] were the most common type of victims involved. Interestingly, the majority of the severely injured victims [75(73%)] sustained the RTI on roads with maximum speed limit of 60 km/hour. The mean(SD) length of hospital stay was 7.83 days(5.59).CONCLUSION: The pediatric related road traffic injury in Malaysia causes significant health and social burden in the country. This study showed both important clinical and geographical factors that need to be taken into consideration for future preventive action.

关键词： Pediatric Injury Road safety Geospatial Geographical information system

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Polygenic risk scores: effect estimation and model optimization

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Quantitative Biology 2021年第2期9卷 133-140页

作者： Zijie Zhao Jie Song Tuo Wang Qiongshi Lu Department of biostatistics and medical informatics University of Wisconsin-MadisonMadison Wl 53726USA Department of Statistics University of Wisconsin-MadisonMadison Wl 53726USA Center for Demography of Health and Aging University of Wisconsin-MadisonMadison Wl 53726USA

Background:Polygenic risk score(PRS)derived from summary statistics of genome-wide association studies(GWAS)is a useful tool to infer an individuaPs genetic risk for health outcomes and has gained increasing popularity in human genetics *** in its simplest form enjoys both computational efficiency and easy accessibility,yet the predictive performance of PRS remains moderate for diseases and ***:We provide an overview of recent advances in statistical methods to improve PRS's performance by incorporating information from linkage disequilibrium,functional annotation,and *** also introduce model validation methods that fine-tune PRS using GWAS summary ***:In this review,we showcase methodological advances and current limitations of PRS,and discuss several emerging issues in risk prediction research.

关键词： GWAS polygenic risk score summary statistics model selection

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Prognostic factors of response to endoscopic treatment in painful chronic pancreatitis

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World Journal of Gastroenterology 2017年第37期23卷 6884-6893页

作者： Alina Tantau Alina Mandrutiu Daniel-Corneliu Leucuta Lidia Ciobanu Marcel Tantau Department of Internal Medicine and Gastroenterology “Iuliu Hatieganu”University of Medicine and Pharmacy Department of Internal Medicine and Gastr-oenterology 4th medical Clinic Department of Gastroenterology Gastr-oenterology and Hepatology medical Center medical informatics and biostatistics Department “Iuliu Hatieganu”University of Medicine and Pharmacy Department of Internal Medicine and Gastroenterology “Prof.Dr.Octavian Fodor“Regional Institute of Gastroenterology and Hepatology

AIM To evaluate the endoscopic treatment efficacy and prognostic factors of long-term response to treatment for painful chronic *** This retrospective analysis identified 168 patients with painful chronic pancreatitis hospitalized during January 2010-January 2015 in a Romanian tertiary referral center. Data on demographics, medical history, alcohol consumption, smoking habit, clinical parameters, type and number of endoscopic procedures and hospital admissions number were collected from the medical charts and analyzed. The absence or substantial reduction of pain(mild pain) at the end of the follow-up associated with the technical success of endotherapy was considered as clinical success. RESULTS Among the 168 patients with painful chronic pancreatitis admitted to our department during the study period, 39(23.21%) had optimal response to the medical therapy. One hundred and twenty-nine patients required endoscopic treatment. The median follow-up period was 15 mo(range, 0-60 mo). Overall, technical success of endotherapy was achieved in 105 patients(81.39%). More than two-thirds of patients(82.78%) had substantial improvement of pain after the endoscopic treatment, including frequency and severity of the pain attacks. Patients younger than 40 years had significantly more successful endoscopic procedures(P = 0.041). Clinical success was higher in non-smoking patients(P = 0.003). The hospital admission rate was higher in patients with recognized alcohol consumption(P = 0.03) and in smokers(P = 0.027). The number and location of pancreatic stones and locations of strictures did not significantly influence the technical success(P > 0.05) or the clinical success(P > 0.05).CONCLUSION Younger age than 40 years can be considered an important factor positively influencing endoscopic treatment outcome in patients with painful chronic pancreatitis.

关键词： Pain Chronic pancreatitis Endoscopicprocedures Alcohol Smoking Hospital admission Technical success Clinical success

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Treatment and prognosis of hepatic epithelioid hemangioendothelioma based on SEER data analysis from 1973 to 2014

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Hepatobiliary & Pancreatic Diseases International 2020年第1期19卷 29-35页

作者： O Kyu Noh Soon Sun Kim Min Jae Yang Sun Gyo Lim Jae Chul Hwang Hyo Jung Cho Jae Youn Cheong Sung Won Cho Department of Radiation Oncology Ajou University School of MedicineSuwonKorea Department of Biomedical informatics Ajou University School of MedicineSuwonKorea Office of biostatistics Ajou Research Institute for Innovative MedicineAjou University Medical CenterSuwonKorea Department of Gastroenterology Ajou University School of MedicineSuwonKorea

Background: Hepatic epithelioid hemangioendothelioma (HEH) is a rare tumor of vascular origin with an unknown etiology, a low incidence, and a variable natural course. We evaluated the management and prognosis of HEH from the Surveillance, Epidemiology and End Results (SEER) program and changes in treatment modalities of HEH over 30 years. Methods: From 1973 to 2014 in the SEER database, we selected patients diagnosed with HEH. We analyzed the clinical characteristics, patterns of management, and clinical outcomes of patients with HEH. Results: We identi ed 79 patients with HEH (median age: 54.0 years;male to female ratio: 1:2.6). The initial extent of disease was local in 22 (27.8%) patients, regional metastasis in 22 (27.8%), distant metas-tasis in 31 (39.2%) and unknown in 4 (5.1%). The median size of primary tumor was 3.85 cm (interquartile range, 2.50 7.93 cm). Among 74 patients with available management data, the most common manage-ment was no treatment (29/74, 39.2%), followed by chemotherapy only (22/74, 29.7%), liver resection-based (13/74, 17.6%), and transplantation-based therapy (6/74, 8.1%). The 5-year cancer-speci c survival rate was 57.8%. Patients who underwent surgical treatment had signi cantly higher survival than those who underwent non-surgical treatment (5-year survival;88% vs. 49%, P=0.019). Multivariate analysis revealed that surgical therapy was the only independent prognostic factor for survival (hazard ratio: 0.20, P=0.040). Conclusions: Resection or liver transplantation is worth considering for treatment of patients with HEH.

关键词： Hemangioendothelioma Epithelioid SEER program Liver transplantation Hepatectomy Liver neoplasms

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