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Single-embryo RNA sequencing for continuous and sex- specific gene expression analysis on Drosophila

STAR PROTOCOLS 2023年第3期4卷 102535页

作者： Perez-Mojica, J. Eduardo Enders, Lennart Lau, Kin H. Lempradl, Adelheid Van Andel Inst Dept Metab & Nutr Programming Grand Rapids MI 49503 USA Max Planck Inst Immunobiol & Epigenet Dept Epigenet D-79108 Freiburg Germany Van Andel Inst Bioinformat & Biostat Core Grand Rapids MI 49503 USA Austrian Acad Sci CeMM Res Ctr Mol Med A-1090 Vienna Austria

Exploring early embryonic gene expression is challenging due to the rate of development and the limited material available. Here, we present a protocol for ordering Drosophila embryos along a developmental pseudo-time trajectory and determining the sex of the embryos using RNA-seq data. We describe steps for sample collection, RNA isolation, RNA-seq, and RNA-seq data processing. We then detail the establishment of a continuous transcriptome dataset for assessing gene expression throughout early development and in a sex-specific manner. For complete details on the use and execution of this protocol, please refer to Perez-Mojica et al.1

关键词： Developmental Biology RNAseq Gene Expression

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Post-hoc analysis from phase III trials of human papillomavirus vaccines: considerations on impact on non-vaccine types

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EXPERT REVIEW OF VACCINES 2019年第3期18卷 309-322页

作者： Ryser, Martin Berlaimont, Valerie Karkada, Naveen Mihalyi, Attila Rappuoli, Rino van der Most, Robbert GSK Global Med Affairs Wavre Belgium GSK Biostat & Stat Programming Wavre Belgium GSK Res & Dev Siena Italy GSK Translat Sci Rixensart Belgium

Background: Substantial heterogeneity has been reported in efficacy against high-grade cervical intraepithelial neoplasia (CIN) irrespective of HPV type in phase III results for bivalent and quadrivalent human papillomavirus virus (HPV) vaccines (AS04-HPV and qHPV). Real-world data recently confirmed a very high overall impact of AS04-HPV, supporting the validity of the observed heterogeneity. To explore the reasons for heterogeneous efficacy, we assessed vaccine impact on high-grade lesions not caused by vaccine types. Research methods: We extracted case counts of CIN lesions containing (1) at least one vaccine HPV type, (2) at least one vaccine HPV type and a high-risk non-vaccine type (co-infections) and (3) no vaccine types (non-vaccine or no high-risk HPV types). Based on these, Phase III cross-protective efficacies were estimated with exclusion (3) and with inclusion (2 and 3) of co-infections. Results: Cross-protective efficacy of AS04-HPV against CIN3 lesions ranges from 81.3% (95%CI: 34.7;96.5) (excluding co-infections) to 88.5% (95%CI:62.4;97.8) (including co-infections). For qHPV the efficacy ranges from -58.7% (95%CI: -180.5;8.5) (excluding co-infections) to 13.1% (95%CI: -39.0;45.9) (including co-infections). Conclusions: Heterogenous overall efficacy against CIN3 between AS04-HPV and qHPV is driven by differential efficacy against lesions that do not contain vaccine types, which may be related to the impact of different adjuvants on the immune response.

关键词： AS04-adjuvanted HPV-16 18 vaccine cervical cancer cervical intraepithelial neoplasia cross-protection human papillomavirus

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State of the art in total pulse production in major states of India using ARIMA techniques

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CURRENT RESEARCH IN FOOD SCIENCE 2021年 4卷 800-806页

作者： Mishra, Pradeep Yonar, Aynur Yonar, Harun Kumari, Binita Abotaleb, Mostafa Das, Soumitra Sankar Patil, S. G. Jawaharlal Nehru Krishi Vishwa Vidyalaya Coll Agr Hoshangabad Madhya Pradesh India Selcuk Univ Dept Stat Fac Sci Konya Turkey Selcuk Univ Dept Biostat Fac Vet Med Konya Turkey Rashtriya Kisan PG Coll Dept Agr Econ Shamli India Chaudhary Charan Singh Univ Meerut Uttar Pradesh India South Ural State Univ Dept Syst Programming Chelyabinsk Russia Birsa Agr Univ Ranchi Jharkhand India Tamil Nadu Agr Univ Coimbatore Tamil Nadu India

Pulses are staple protein-rich food for Indian vegetarians, and India is one of the largest producers in the world. The present investigation is an attempt to study the trend in the production of total pulses in India using the autoregressive integrated moving average (ARIMA) method. For stochastic trend estimation, yearly data were used for the period from 1961 to 2019. On the basis of the performance of several goodness of model fit criteria, the most suitable ARIMA model is chosen to capture the trend of pulse production. Forecasting for the 10 years from 2020 to 2029 is done, and it is observed that India has the highest forecast value (31.03302 million tonnes) in 2029. This study will play an important role in determining the gap between production of and demand for pulses in the future.

关键词： Autoregressive integrated moving average Autocorrelation function Forecasting Modeling Production

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Phase I dose-escalation study of the safety, tolerability, and pharmacokinetics of aflibercept in combination with S-1 in Japanese patients with advanced solid malignancies

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INVESTIGATIONAL NEW DRUGS 2020年第5期38卷 1390-1399页

作者： Doi, Toshihiko Boku, Narikazu Onozawa, Yusuke Takahashi, Keishiro Kawaguchi, Osamu Ohtsu, Atsushi Natl Canc Ctr Hosp East Dept Gastrointestinal Oncol 6-5-1 Kashiwanoha Kashiwa Chiba 2778577 Japan Natl Canc Ctr Dept Gastrointestinal Med Oncol Tokyo Japan Shizuoka Canc Ctr Div Clin Oncol Shizuoka Japan Sanofi KK Res & Dev Tokyo Japan Sanofi KK Biostat & Programming Tokyo Japan

BackgroundAflibercept, a recombinant fusion protein binding VEGF-A, VEGF-B and placental growth factor, inhibits tumor growth by blocking angiogenesis. The aim of this phase I dose-escalation study was to determine the recommended phase II dose (RP2D) of aflibercept in combination with S-1 in Japanese patients with solid *** and methodsSequential cohorts of 3-6 patients with metastatic or unresectable solid tumors, who had failed at least one prior line of standard treatment or who were not suitable for such treatment, were to receive escalating doses of aflibercept every 2 weeks, starting at 2 mg/kg, combined with S-1 at 40 mg/m(2)twice daily (80 mg/m(2)/day;4 weeks on/2 weeks off). Dose-escalation was to be based on the incidence of dose-limiting toxicity (DLT). Blood samples were collected for pharmacokinetic *** the first dose level (aflibercept 2 mg/kg plus S-1) 1 of 6 patients experienced a DLT (grade 4 proteinuria). The aflibercept dose was consequently escalated to 4 mg/kg;1 of 3 patients treated at this dose level had a DLT (grade 2 pleural effusion), and another patient experienced grade 3 reversible posterior leukoencephalopathy syndrome after the DLT assessment period. Additional patients were therefore enrolled into the first dose level to explore safety and tolerability. The study was subsequently terminated prematurely. The maximum tolerated dose was not reached and the RP2D was not determined in Japanese *** tolerability and safety of aflibercept 2 mg/kg in combination with S-1 was confirmed in Japanese patients with advanced solid tumors.

关键词： Aflibercept S-1 Phase I trial Japanese VEGF trap

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Maternal intake of folate during pregnancy and risk of cerebral palsy in the MOBAND-CP cohort

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AMERICAN JOURNAL OF CLINICAL NUTRITION 2022年第2期115卷 397-406页

作者： Groot, Jonathan Petersen, Tanja G. Suren, Pal Brantsoeter, Anne Lise Uldall, Peter Martinussen, Torben Granstrom, Charlotta Olsen, Sjurdur F. Wilcox, Allen J. Strandberg-Larsen, Katrine Univ Copenhagen Fac Hlth & Med Sci Dept Publ Hlth Sect Epidemiol Copenhagen Denmark Odense Univ Hosp Open Patient Data Explorat Network Odense Denmark Norwegian Inst Publ Hlth Dept Child Hlth & Dev Div Mental & Phys Hlth Oslo Norway Norwegian Inst Publ Hlth Dept Environm Exposure & Epidemiol Div Infect Control & Environm Hlth Oslo Norway Copenhagen Univ Hosp Rigshosp Pediat Dept Copenhagen Denmark Dianalund Epilepsy Ctr Dianalund Denmark Univ Copenhagen Fac Hlth & Med Sci Dept Publ Hlth Sect Biostat Copenhagen Denmark Ctr Fetal Programming Statens Serum Inst Div Epidemiol Copenhagen Denmark Harvard Sch Publ Hlth Dept Nutr Boston MA USA NIEHS Epidemiol Branch Durham NC USA

Background Folate prevents neural tube defects and may play a role in some neurodevelopmental disorders. Objectives We investigated whether higher intakes of periconceptional or midpregnancy folate, as recommended, were associated with a reduced risk of offspring cerebral palsy (CP). Methods We included participants from the Nordic collaboration cohort consisting of mother-child dyads in the Danish National Birth Cohort and the Norwegian Mother, Father, and Child Cohort Study [combined as MOthers and BAbies in Norway and Denmark (MOBAND-CP)]. A total of 190,989 live-born children surviving the first year of life were included. Missing covariate data were multiply imputed. Our exposures were defined as any or no folic acid supplementation in gestational weeks (GWs) -4 to 8 (periconceptional), 9 to 12, and -4 to 12, and supplemental, dietary, and total folate during midpregnancy (GWs 22-25). CP overall and the unilateral and bilateral spastic subtypes, as well as CP with low or moderate/high gross motor function impairments, were our outcomes of interest. Results Periconceptional folic acid supplementation was not associated with CP [adjusted odds ratio (aOR), 1.02;95% CI: 0.82-1.28]. However, supplementation in GWs 9 to 12 was associated with a reduced risk of CP (aOR, 0.74;95% CI: 0.57-0.96), and inverse associations were indicated for both the unilateral (aOR, 0.68;95% CI: 0.46-1.02) and bilateral (aOR, 0.70;95% CI: 0.49-1.02) spastic subtypes, although the associations were not statistically significant. Supplemental or dietary folate in midpregnancy alone were not associated with CP. Strong inverse associations were observed with low gross motor function impairment (aOR, 0.49;95% CI: 0.29-0.83), while for unilateral CP the aOR was 0.63 (95% CI: 0.34-1.22) for intakes of >= 500 compared to <= 199 dietary folate equivalents/day during midpregnancy. Conclusions Our findings suggest that folate intakes in GWs 9 to 12 and midpregnancy were associated with lower risks

关键词： DNBC MoBa MOBAND-CP cerebral palsy folic acid nutrition epidemiology neurodevelopment food frequency questionnaire

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Confidence, prediction, and tolerance in linear mixed models

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STATISTICS IN MEDICINE 2019年第30期38卷 5603-5622页

作者： Francq, Bernard G. Lin, Dan Hoyer, Walter GSK TRD CMC Stat Sci B-1330 Rixensart Belgium GSK Preclin & Res Biostat & Stat Programming Rixensart Belgium GSK TRD CMC Stat Sci Marburg Germany

The literature about Prediction Interval (PI) and Tolerance Interval (TI) in linear mixed models is usually developed for specific designs, which is a main limitation to their use. This paper proposes to reformulate the two-sided PI to be generalizable under a wide variety of designs (one random factor, nested and crossed designs for multiple random factors, and balanced or unbalanced designs). This new methodology is based on the Hessian matrix, namely, the inverse of (observed) Fisher Information matrix, and is built with a cell mean model. The degrees of freedom for the total variance are calculated with the generalized Satterthwaite method and compared to the Kenward-Roger's degrees of freedom for fixed effects. Construction of two-sided TIs are also detailed with one random factor, and two nested and two crossed random variables. An extensive simulation study is carried out to compare the widths and coverage probabilities of Confidence Intervals (CI), PIs, and TIs to their nominal levels. It shows excellent coverage whatever the design and the sample size are. Finally, these CIs, PIs, and TIs are applied to two real data sets: one from orthopedic surgery study (intralesional resection risk) and the other from assay validation study during vaccine development.

关键词： assay validation and qualification generalized Satterthwaite Hessian and Fisher information matrix intralesional resection mixed model prediction interval tolerance interval

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Considerations for pediatric trial designs and analyses

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JOURNAL OF BIOPHARMACEUTICAL STATISTICS 2018年第3期28卷 413-436页

作者： Cho, Meehyung Qiu, Zhiying Ye, Jenny Quan, Hui Zhao, Peng-Liang Sanofi US Biostat & Programming Bridgewater NJ 08807 USA

There are challenges in designing pediatric trials arising from special ethical issues and the relatively small accessible patient population. The application of conventional phase 3 trial designs to pediatrics is not realistic in some therapeutic areas. To address this issue, we propose various approaches for designing pediatric trials that incorporate data available from adult studies using James-Stein shrinkage estimation, empirical shrinkage estimation, and Bayesian methods. We also apply the concept of consistency used in multi-regional trials to pediatric trials. The performance of these methods is assessed through representative scenarios and an example using actual Type 2 diabetes mellitus (T2DM) trials.

关键词： Bayesian method empirical shrinkage estimation James-Stein shrinkage estimation pediatric sample size weighted combination

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Robust designs in longitudinal studies accounting for parameter and model uncertainties - application to count data

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JOURNAL OF BIOPHARMACEUTICAL STATISTICS 2020年第1期30卷 31-45页

作者： Loingeville, Florence Thu Thuy Nguyen Riviere, Marie-Karelle Mentre, France INSERM IAME UMR 1137 F-75018 Paris France Univ Paris Diderot Sorbonne Paris Cite F-75018 Paris France Univ Lille Fac Pharm Publ Hlth Epidemiol & Healthcare Qual EA 2694 F-59000 Lille France Sanofi Aventis R&D Stat Methodol Grp Biostat & Programming Dept Chilly Mazarin France

Nonlinear mixed effect models (NLMEMs) are widely used for the analysis of longitudinal data. To design these studies, optimal designs based on the expected Fisher information matrix (FIM) can be used. A method evaluating the FIM using Monte-Carlo Hamiltonian Monte-Carlo (MC-HMC) has been proposed and implemented in the R package MIXFIM using Stan. This approach, however, requires a priori knowledge of models and parameters, which leads to locally optimal designs. The objective of this work was to extend this MC-HMC-based method to evaluate the FIM in NLMEMs accounting for uncertainty in parameters and in models. When introducing uncertainty in the population parameters, we evaluated the robust FIM as the expectation of the FIM computed by MC-HMC over the distribution of these parameters. Then, the compound D-optimality criterion (CD optimality), corresponding to a weighted product of the D-optimality criteria of several candidate models, was used to find a common CD-optimal design for the set of candidate models. Finally, a compound DE-criterion (CDE optimality), corresponding to a weighted product of the normalized determinants of the robust FIMs of all the candidate models accounting for uncertainty in parameters, was calculated to find the CDE-optimal design which was robust on both parameters and model. These methods were applied in a longitudinal Poisson count model. We assumed prior distributions on the population parameters, as well as several candidate models describing the relationship between the logarithm of the event rate parameter and the dose. We found that assuming uncertainty in parameters could lead to different optimal designs, and misspecification of models could induce designs with low efficiencies. The CD- or CDE-optimal designs therefore provided a good compromise for different candidate models. Finally, the proposed approach allows for the first time optimization of designs for repeated discrete data accounting for parameter and model uncerta

关键词： Fisher information matrix longitudinal count data Markov chain Hamiltonian Monte Carlo nonlinear mixed effect models optimal design Robust design

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Look before you leap: systematic evaluation of tree-based statistical methods in subgroup identification

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JOURNAL OF BIOPHARMACEUTICAL STATISTICS 2019年第6期29卷 1082-1102页

作者： Liu, Yang Ma, Xiwen Zhang, Donghui Geng, Lijiang Wang, Xiaojing Zheng, Wei Chen, Ming-Hui Univ Connecticut Dept Stat Storrs CT 06269 USA Karyopharm Therapeut Inc Biostat Dept Newton MA USA Sanofi US Global Biostat & Programming Bridgewater NJ USA Kehang Suzhou Informat & Technol Ltd Co Suzhou Jiangsu Peoples R China

Subgroup analysis, as the key component of personalized medicine development, has attracted a lot of interest in recent years. While a number of exploratory subgroup searching approaches have been proposed, informative evaluation criteria and scenario-based systematic comparison of these methods are still underdeveloped topics. In this article, we propose two evaluation criteria in connection with traditional type I error and power concepts, and another criterion to directly assess recovery performance of the underlying treatment effect structure. Extensive simulation studies are carried out to investigate empirical performance of a variety of tree-based exploratory subgroup methods under the proposed criteria. A real data application is also included to illustrate the necessity and importance of method evaluation.

关键词： GUIDE interaction tree qualitative interaction trees T-AIC/T-BIC virtual twins

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Burden of Herpes Zoster in the Japanese Population with Immunocompromised/Chronic Disease Conditions: Results from a Cohort Study Claims Database from 2005-2014

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DERMATOLOGY AND THERAPY 2019年第1期9卷 117-133页

作者： Imafuku, Shinichi Matsuki, Taizo Mizukami, Akiko Goto, Yasushi de Souza, Sabrina Jegou, Celine Bianco, Veronique Rosillon, Dominique Ito, Chie Curran, Desmond Holl, Katsiaryna Fukuoka Univ Dept Dermatol Sch Med Fukuoka Fukuoka Japan GSK Healthoutcomes Dept Tokyo Japan Natl Canc Ctr Dept Thorac Oncol Tokyo Japan GSK Keyrus Biopharma London England GSK Business & Decis Life Sci Wavre Belgium GSK Biostat & Stat Programming Rockville MD USA GSK Biostat & Stat Programming Wavre Belgium JMDC Co Ltd Tokyo Japan GSK Vaccines Hlth Outcomes Dept Wavre Belgium

IntroductionThe aim of this study is to describe the disease burden and costs of herpes zoster (HZ) in the general adult Japanese population or patients with immunocompromised (IC) conditions or chronic *** retrospective cohort study of individuals aged 18-74years was conducted using January 2005 to December 2014 records from the Japan Medical Data Center claims database. Twenty-eight IC conditions and chronic disorders were defined by diagnosis codes and/or procedures/treatments. HZ and its related complications were identified. Incidence rates (IR), frequency of HZ-related complications, healthcare resource utilization (HRU), and direct medical costs were estimated. HRU and costs were estimated on a subcohort of HZ cases occurring April 2012-January *** overall IR of HZ in the total cohort of 2,778,476 adults was 4.92/1000 person-years (PY) [95% confidence interval (CI): 4.86-4.98] and increased with age. The IR in the IC cohort (51,818 subjects) was 8.87/1000 PY (95% CI: 8.29-9.48), ranging from 5.55/1000 PY (95% CI: 4.26-7.09) in psoriasis to 151.68/1000 PY (95% CI: 111.45-201.71) in hematopoietic stem cell transplant recipients;most IRs were in the range 6-10/1000 PY. The IRs in individuals with chronic disorders were also relatively high, in the range 5.40-12.90/1000 PY. The frequency of postherpetic neuralgia was 4.01% (95% CI: 3.72-4.33) in the total cohort and 11.73% (95% CI: 9.01-14.93) in the IC cohort. The mean [standard deviation (SD)] number of outpatient visits was 3.4 (4.9) and 5.0 (5.7), respectively, and the proportion of HZ patients hospitalized was 2.20% and 6.70%, respectively. The mean (SD) direct medical cost per HZ episode was yen34,664 (yen54,433) and yen55,201 (yen92,642) in the total and IC cohort, *** elevated burden of HZ in Japanese individuals harboring IC conditions and chronic disorders documented in our study underlines the need for prevention of HZ in people with these conditions.F

关键词： Claims database Healthcare resource utilization Herpes zoster Immunocompromised Japan Medical cost Postherpetic neuralgia

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