Fitting Linear Mixed-Effects Models Using lme4
TLDR
In this article, a model is described in an lmer call by a formula, in this case including both fixed-and random-effects terms, and the formula and data together determine a numerical representation of the model from which the profiled deviance or the profeatured REML criterion can be evaluated as a function of some of model parameters.Abstract:
Maximum likelihood or restricted maximum likelihood (REML) estimates of the parameters in linear mixed-effects models can be determined using the lmer function in the lme4 package for R. As for most model-fitting functions in R, the model is described in an lmer call by a formula, in this case including both fixed- and random-effects terms. The formula and data together determine a numerical representation of the model from which the profiled deviance or the profiled REML criterion can be evaluated as a function of some of the model parameters. The appropriate criterion is optimized, using one of the constrained optimization functions in R, to provide the parameter estimates. We describe the structure of the model, the steps in evaluating the profiled deviance or REML criterion, and the structure of classes or types that represents such a model. Sufficient detail is included to allow specialization of these structures by users who wish to write functions to fit specialized linear mixed models, such as models incorporating pedigrees or smoothing splines, that are not easily expressible in the formula language used by lmer.read more
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Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases.
Mineto Ota,Yasuo Nagafuchi,Hiroaki Hatano,Kazuyoshi Ishigaki,Chikashi Terao,Yusuke Takeshima,Haruyuki Yanaoka,Satomi Kobayashi,Mai Okubo,Harumi Shirai,Yusuke Sugimori,Junko Maeda,Masahiro Nakano,Saeko Yamada,Ryochi Yoshida,Haruka Tsuchiya,Yumi Tsuchida,Shuji Akizuki,Hajime Yoshifuji,Koichiro Ohmura,Tsuneyo Mimori,Ken Yoshida,Daitaro Kurosaka,Masato Okada,Keigo Setoguchi,Hiroshi Kaneko,Nobuhiro Ban,Nami Yabuki,Kosuke Matsuki,Hironori Mutoh,Sohei Oyama,Makoto Okazaki,Hiroyuki Tsunoda,Yukiko Iwasaki,Shuji Sumitomo,Hirofumi Shoda,Yuta Kochi,Yukinori Okada,Kazuhiko Yamamoto,Tomohisa Okamura,Keishi Fujio +40 more
TL;DR: In this article, a large-scale immune cell gene-expression analysis, together with whole-genome sequence analysis, was performed to understand the function of these variants, especially under disease-associated conditions.
Journal ArticleDOI
Do sown flower strips boost wild pollinator abundance and pollination services in a spring-flowering crop? A case study from UK cider apple orchards
TL;DR: Positive effects of ground flora on wild insect abundance in orchards suggest that flower mixtures or orchard management could be optimised for andrenid bees, the single most important pollinator taxa, by increasing the availability of early-flowering plants in Orchards.
Journal ArticleDOI
Same-sex marriage legalization associated with reduced implicit and explicit antigay bias
TL;DR: While antigay bias had been decreasing over time, following local same-sex marriage legalization antIGay bias decreased at roughly double the rate, indicating that government legislation can inform attitudes even on religiously and politically entrenched positions.
Journal ArticleDOI
Bayesian data analysis in the phonetic sciences: A tutorial introduction
TL;DR: This tutorial analyzes voice onset time (VOT) data from Dongbei (Northeastern) Mandarin Chinese and North American English to demonstrate how Bayesian linear mixed models can be fit using the programming language Stan via the R package brms.
Journal ArticleDOI
PSMA-targeting TGFβ-insensitive armored CAR T cells in metastatic castration-resistant prostate cancer: a phase 1 trial
Vivek Narayan,Julie S. Barber-Rotenberg,In-Young Jung,Simon F. Lacey,Andrew J. Rech,Megan M. Davis,Wei-Ting Hwang,Priti Lal,Erica L. Carpenter,Shannon L. Maude,Gabriela Plesa,Neha Vapiwala,Anne Chew,Michael Moniak,Ronnie Sebro,Michael D. Farwell,Amy D. Marshall,Joan Gilmore,Lester Lledo,Karen Dengel,Sarah E. Church,Tyler Hether,Jun Xu,Mercy Gohil,Thomas H. Buckingham,Stephanie S. Yee,Vanessa E. Gonzalez,Irina Kulikovskaya,Fang Chen,Lifeng Tian,Kyle Tien,Whitney L. Gladney,Christopher L. Nobles,Hayley Raymond,Diane Frazee,Mary Truran,Elizabeth Veloso,Holly McConville,Jonathan Aguedelo,S.M. Hower,Sophia Ngo,Julie K. Jadlowsky,J. Joseph Melenhorst,Aoife M. Roche,A. Everett,Minnal Gupta,Farzana Nazimuddin,Chelsie Bartoszek,Natalka Koterba,Rachael Reynolds,F. H. Ellington,Christopher C. Kloss,Jihyun Lee,Yangbing Zhao,John Scholler,James L. Riley,Christina Bailey,Andrew White,Brian Hudson,Pearlly Chang,Marcela V. Maus,Bruce L. Levine,Elizabeth O. Hexner,Don L. Siegel,Frederic D. Bushman,Carl H. June,Joseph A. Fraietta,Naomi B. Haas +67 more
TL;DR: Clinical application of TGF-β-resistant CAR T’cells is feasible and generally safe, and future studies should use superior multipronged approaches against the TME to improve outcomes.
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