16 Works

F2R polymorphisms and clopidogrel efficacy and safety in patients with minor stroke or TIA: supplemental figures and tables

Yuesong Pan, Runqi Wangqin, Hao Li, Yilong Wang, Xia Meng, S. Claiborne Johnston, Tabassome Simon, Jinxi Lin, Xingquan Zhao, Liping Liu, David Wang & Yongjun Wang
Objective: To investigate the association between protease-activated receptors-1 (PAR-1) gene F2R polymorphisms and efficacy of clopidogrel for minor stroke or transient ischemic attack (TIA). Methods: Three single-nucleotide polymorphisms (CYP2C19*2 [681G>A, rs4244285], CYP2C19*3 [636G>A, rs4986893] and F2R [IVSn-14 A/T, rs168753] were genotyped among 2,924 patients randomized to clopidogrel plus aspirin (n=1461) or aspirin alone (n=1463). The primary efficacy outcome was new stroke (ischemic or hemorrhagic) and the safety outcome was any bleeding. Results: Overall, 859(29.4%) were...

Additional file 2 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Additional file 2: Supplementary Table 1. TOGA status of 18430 ancestral placental mammal genes in muroid rodent genome assemblies. Supplementary Table 2. Positively selected genes and their mutation tolerance in humans according to gnomAD.

Data from: Clustering Deviation Index (CDI): A robust and accurate internal measure for evaluating scRNA-seq data clustering

Jiyuan Fang, Cliburn Chan, Kouros Owzar, Liuyang Wang, Diyuan Qin, Qi-Jing Li & Jichun Xie
The clustering of cells has been widely used to explore the heterogeneity of cell populations in single-cell RNA-sequencing (scRNA-seq). We proposed a parametric model for monoclonal and polyclonal scRNA-seq data to evaluate clustering results. Based on the parametric model, we proposed a metric (CDI) to quantify the goodness-of-fit of cell clustering to the data. Here we presented CT26.WT and T-CELL as two datasets to examine the performance of our model and metric. CT26.WT contains wild-type...

sj-docx-1-tva-10.1177_15248380221129575 – Supplemental material for Teaching Trauma Content in Higher Education: A Systematic Literature Review

Jessica Gladden, Bridget E. Weller, Adrian Hernandez & Andrea Hopkins
Supplemental material, sj-docx-1-tva-10.1177_15248380221129575 for Teaching Trauma Content in Higher Education: A Systematic Literature Review by Jessica Gladden, Bridget E. Weller, Adrian Hernandez and Andrea Hopkins in Trauma, Violence, & Abuse

Additional file 1 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Additional file 1: Figure S1. Venn diagram of gene lists linked to type 2 diabetes by different types of evidence. Figure S2. Heterozygosity inferred by comparing the paternal and maternal scaffolded contigs, shown on the paternal scaffolds. Figure S3. Length distributions of structural variants. Figure S4. Functional classification of duplicated genes. Figure S5. Sequence alignment of Nile rat Gckr proteins to 113 mammalian orthologs. Figure S6. Missing Nile rat Hadh gene present in alternate haplotype...

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Abstract Background The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic. Results We report a 2.5 Gb, chromosome-level reference genome assembly with...

Additional file 1 of Estimating the optimal linear combination of predictors using spherically constrained optimization

Priyam Das, Debsurya De, Raju Maiti, Mona Kamal, Katherine A. Hutcheson, Clifton D. Fuller, Bibhas Chakraborty & Christine B. Peterson
Additional file 1. This file contains a brief description about the literature on existing global optimization techniques, existing techniques alternative to SCOR, theoretical properties and optimization performance evaluation of SCOR, additional simulation results, and an application of SCOR to Alzheimer's disease data. Table S1. Tuning parameters, their roles and default values in the SCOR algorithm. Table S2. Comparison of minimum value achieved and average computation time (in seconds) for solving the transformed d-dimensional negative log-product...

Additional file 1 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Additional file 1: Figure S1. Venn diagram of gene lists linked to type 2 diabetes by different types of evidence. Figure S2. Heterozygosity inferred by comparing the paternal and maternal scaffolded contigs, shown on the paternal scaffolds. Figure S3. Length distributions of structural variants. Figure S4. Functional classification of duplicated genes. Figure S5. Sequence alignment of Nile rat Gckr proteins to 113 mammalian orthologs. Figure S6. Missing Nile rat Hadh gene present in alternate haplotype...

sj-docx-1-tva-10.1177_15248380221129575 – Supplemental material for Teaching Trauma Content in Higher Education: A Systematic Literature Review

Jessica Gladden, Bridget E. Weller, Adrian Hernandez & Andrea Hopkins
Supplemental material, sj-docx-1-tva-10.1177_15248380221129575 for Teaching Trauma Content in Higher Education: A Systematic Literature Review by Jessica Gladden, Bridget E. Weller, Adrian Hernandez and Andrea Hopkins in Trauma, Violence, & Abuse

Teaching Trauma Content in Higher Education: A Systematic Literature Review

Jessica Gladden, Bridget E. Weller, Adrian Hernandez & Andrea Hopkins
Higher education must prepare future mental health providers to work with individuals who have been exposed to trauma. This is vital to the success of students’ practice, many of whom would benefit from trauma reduction strategies in their own lives. The purpose of this systematic review is to summarize the knowledge base on teaching methods that may reduce the potential that trauma content in the classroom could cause: (a) re-traumatization; (b) vicarious traumatization; or (c)...

Additional file 1 of Estimating the optimal linear combination of predictors using spherically constrained optimization

Priyam Das, Debsurya De, Raju Maiti, Mona Kamal, Katherine A. Hutcheson, Clifton D. Fuller, Bibhas Chakraborty & Christine B. Peterson
Additional file 1. This file contains a brief description about the literature on existing global optimization techniques, existing techniques alternative to SCOR, theoretical properties and optimization performance evaluation of SCOR, additional simulation results, and an application of SCOR to Alzheimer's disease data. Table S1. Tuning parameters, their roles and default values in the SCOR algorithm. Table S2. Comparison of minimum value achieved and average computation time (in seconds) for solving the transformed d-dimensional negative log-product...

Estimating the optimal linear combination of predictors using spherically constrained optimization

Priyam Das, Debsurya De, Raju Maiti, Mona Kamal, Katherine A. Hutcheson, Clifton D. Fuller, Bibhas Chakraborty & Christine B. Peterson
Abstract Background In the context of a binary classification problem, the optimal linear combination of continuous predictors can be estimated by maximizing the area under the receiver operating characteristic curve. For ordinal responses, the optimal predictor combination can similarly be obtained by maximization of the hypervolume under the manifold (HUM). Since the empirical HUM is discontinuous, non-differentiable, and possibly multi-modal, solving this maximization problem requires a global optimization technique. Estimation of the optimal coefficient vector...

Estimating the optimal linear combination of predictors using spherically constrained optimization

Priyam Das, Debsurya De, Raju Maiti, Mona Kamal, Katherine A. Hutcheson, Clifton D. Fuller, Bibhas Chakraborty & Christine B. Peterson
Abstract Background In the context of a binary classification problem, the optimal linear combination of continuous predictors can be estimated by maximizing the area under the receiver operating characteristic curve. For ordinal responses, the optimal predictor combination can similarly be obtained by maximization of the hypervolume under the manifold (HUM). Since the empirical HUM is discontinuous, non-differentiable, and possibly multi-modal, solving this maximization problem requires a global optimization technique. Estimation of the optimal coefficient vector...

Teaching Trauma Content in Higher Education: A Systematic Literature Review

Jessica Gladden, Bridget E. Weller, Adrian Hernandez & Andrea Hopkins
Higher education must prepare future mental health providers to work with individuals who have been exposed to trauma. This is vital to the success of students’ practice, many of whom would benefit from trauma reduction strategies in their own lives. The purpose of this systematic review is to summarize the knowledge base on teaching methods that may reduce the potential that trauma content in the classroom could cause: (a) re-traumatization; (b) vicarious traumatization; or (c)...

Additional file 2 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Additional file 2: Supplementary Table 1. TOGA status of 18430 ancestral placental mammal genes in muroid rodent genome assemblies. Supplementary Table 2. Positively selected genes and their mutation tolerance in humans according to gnomAD.

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Abstract Background The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic. Results We report a 2.5 Gb, chromosome-level reference genome assembly with...

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