199 Works

Supplementary information for: A biased fossil record can preserve reliable phylogenetic signal

C. Henrik Woolley, Jeffrey Thompson, Yun-Hsin Wu, David Bottjer & Nathan Smith
Abstract.­­––The fossil record is notoriously imperfect and biased in representation, hindering our ability to place fossil specimens into an evolutionary context. For groups with fossil records mostly consisting of disarticulated parts (e.g., vertebrates, echinoderms, plants), the limited morphological information preserved sparks concerns about whether fossils retain reliable evidence of phylogenetic relationships, and lends uncertainty to analyses of diversification, paleobiogeography, and biostratigraphy in Earth history. To address whether a fragmentary past can be trusted, we need...

A new genus of treeshrew and other micromammals from the middle Miocene hominoid locality of Ramnagar, Udhampur District, Jammu & Kashmir, India

Ramesh Sehgal, Abhishek Singh, Christopher Gilbert, Biren Patel, Christopher Campisano, Keegan Selig, Rajeev Patnaik & Ningthoujam Premjit Singh
The fossil record of treeshrews, hedgehogs, and other micromammals from the Lower Siwaliks of India is sparse. Here, we report on a new genus and species of fossil treeshrew, specimens of the hedgehog Galerix, and other micromammals from the middle Miocene (Lower Siwalik) deposits surrounding Ramnagar (Udhampur District, Jammu & Kashmir), at a fossil locality known as Dehari. The treeshrew from Dehari (Sivatupaia ramnagarensis gen. nov. et sp. nov.) currently represents the oldest record of...

Data from: Randomized phase 2 study of FcRn antagonist efgartigimod in generalized myasthenia gravis

James F. Howard, Vera Bril, Ted M. Burns, Renato Mantegazza, Malgorzata Bilinska, Andrzej Szczudlik, Said Beydoun, Francisco Javier Rodriguez De Rivera Garrido, Fredrik Piehl, Mariarosa Rottoli, Philip Van Damme, Tuan Vu, Amelia Evoli, Miriam Freimer, Tahseen Mozaffar, E. Sally Ward, Torsten Dreier, Peter Ulrichts, Katrien Verschueren, Antonio Guglietta, Hans De Haard, Nicolas Leupin & Jan J. G. M. Verschuuren
Objective: To investigate safety and explore efficacy of efgartigimod (ARGX-113), an anti-neonatal Fc receptor immunoglobulin G1 Fc fragment, in patients with generalized myasthenia gravis (gMG) with a history of anti-acetylcholine receptor (AChR) autoantibodies, who were on stable standard-of-care myasthenia gravis (MG) treatment. Methods: A phase 2, exploratory, randomized, double-blind, placebo-controlled, 15-center study is described. Eligible patients were randomly assigned (1:1) to receive 4 doses over a 3-week period of either 10 mg/kg IV efgartigimod or...

Additional file 3 of Elevated NRAS expression during DCIS is a potential driver for progression to basal-like properties and local invasiveness

Ze-Yi Zheng, Hanan Elsarraj, Jonathan T. Lei, Yan Hong, Meenakshi Anurag, Long Feng, Hilda Kennedy, Yichao Shen, Flora Lo, Zifan Zhao, Bing Zhang, Xiang H.-F. Zhang, Ossama W. Tawfik, Fariba Behbod & Eric C. Chang
Additional file 3: Table S2. NRAS-silencing induced a switch from basal to luminal gene expression pattern in SUM102PT cells as measured by RNA-seq.

Additional file 3 of Elevated NRAS expression during DCIS is a potential driver for progression to basal-like properties and local invasiveness

Ze-Yi Zheng, Hanan Elsarraj, Jonathan T. Lei, Yan Hong, Meenakshi Anurag, Long Feng, Hilda Kennedy, Yichao Shen, Flora Lo, Zifan Zhao, Bing Zhang, Xiang H.-F. Zhang, Ossama W. Tawfik, Fariba Behbod & Eric C. Chang
Additional file 3: Table S2. NRAS-silencing induced a switch from basal to luminal gene expression pattern in SUM102PT cells as measured by RNA-seq.

Additional file 1 of Elevated NRAS expression during DCIS is a potential driver for progression to basal-like properties and local invasiveness

Ze-Yi Zheng, Hanan Elsarraj, Jonathan T. Lei, Yan Hong, Meenakshi Anurag, Long Feng, Hilda Kennedy, Yichao Shen, Flora Lo, Zifan Zhao, Bing Zhang, Xiang H.-F. Zhang, Ossama W. Tawfik, Fariba Behbod & Eric C. Chang
Additional file 1: Table S1. Pathological, Biomarker and Demographic Characteristics of the patients in the TMAs.

Additional file 1 of Gene Identification, expression analysis and molecular docking of ATP sulfurylase in the selenization pathway of Cardamine hupingshanensis

Zhijing Xiao, Yanke Lu, Yi Zou, Chi Zhang, Li Ding, Kai Luo, Qiaoyu Tang & Yifeng Zhou
Supplementary Figure S1: Multiple sequence alignment of all the ChATPS proteins; Supplementary Table S1: Physicochemical properties of ATPS proteins in C. hupingshanensis. Supplementary Table S2: The gene coding sequences and protein sequences of ChATPS. Supplementary Table S3: Secondary structure analysis of the nine proteins. Supplementary Table S4: Primers used in qRT-PCR analysis for ChATPS. Table S5: The binding energy of each ligand to each protein at the catalytic site (unit: kcal mol-1). Table S6: At...

Combining metabolomics and experimental evolution reveals key mechanisms underlying longevity differences in laboratory evolved Drosophila melanogaster populations

Mark Phillips, Kenneth R. Arnold, Zer Vue, Heather K. Beasley, Edgar Garza-Lopez, Andrea G. Marshall, Derrick J. Morton, Melanie R. McReynolds, Thomas T. Barter & Antentor Hinton
Experimental evolution with Drosophila melanogaster has been used extensively for decades to study aging and longevity. In recent years, the addition of DNA and RNA sequencing to this framework has allowed researchers to leverage the statistical power inherent to experimental evolution to study the genetic basis of longevity itself. Here, we incorporated metabolomic data into to this framework to generate even deeper insights into the physiological and genetic mechanisms underlying longevity differences in three groups...

A dataset for pollinator diversity and their interactions with plants in the Pacific NorthWest

Laura Melissa Guzman, Tyler Kelly & Elizabeth Elle
Pollinator populations have declined substantially in recent years. The resulting loss in pollination services has both ecological and economic consequences including reductions in plant diversity and crop production and lower food security. Datasets that identify pollinators and their plant hosts are of utmost importance in order to understand the main causes of pollinator declines. Here we present a dataset, which contains 67,954 individual pollinator records. The data has been collected across the Pacific Northwest, primarily...

Additional file 2 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 2. Table S2: Adjuvant treatment information.

Additional file 3 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 3. Table S3: Performance of three strategies.

Additional file 3 of Changes in concentrations of cervicovaginal immune mediators across the menstrual cycle: a systematic review and meta-analysis of individual patient data

Sean M. Hughes, Claire N. Levy, Ronit Katz, Erica M. Lokken, Melis N. Anahtar, Melissa Barousse Hall, Frideborg Bradley, Philip E. Castle, Valerie Cortez, Gustavo F. Doncel, Raina Fichorova, Paul L. Fidel, Keith R. Fowke, Suzanna C. Francis, Mimi Ghosh, Loris Y. Hwang, Mariel Jais, Vicky Jespers, Vineet Joag, Rupert Kaul, Jordan Kyongo, Timothy Lahey, Huiying Li, Julia Makinde, Lyle R. McKinnon … & Florian Hladik
Additional file 3. Code and data. IPD from co-authors who agreed to share it, results of all analyses presented in the paper, and R code files necessary to reproduce the analysis and figures.

Additional file 5 of Changes in concentrations of cervicovaginal immune mediators across the menstrual cycle: a systematic review and meta-analysis of individual patient data

Sean M. Hughes, Claire N. Levy, Ronit Katz, Erica M. Lokken, Melis N. Anahtar, Melissa Barousse Hall, Frideborg Bradley, Philip E. Castle, Valerie Cortez, Gustavo F. Doncel, Raina Fichorova, Paul L. Fidel, Keith R. Fowke, Suzanna C. Francis, Mimi Ghosh, Loris Y. Hwang, Mariel Jais, Vicky Jespers, Vineet Joag, Rupert Kaul, Jordan Kyongo, Timothy Lahey, Huiying Li, Julia Makinde, Lyle R. McKinnon … & Florian Hladik
Additional file 5: Figure S1. Assessment of publication bias. A Funnel plots. Symbols show the effect of the menstrual cycle (x-axis) and the standard error of that effect (y-axis, reversed). Each symbol shows an individual study. Vertical solid line shows no effect. Vertical dashed line shows the meta-estimate of effect. Diagonal dashed lines enclose the region expected to include 95% of studies based on the estimated meta-effect and the standard errors. B Results of Egger’s...

Harmonized Mex-Cog, Version A

Sandy Chien, Codi Young, Erik Meijer, Kanghong Shao, Alden Gross, Alejandra Michaels-Obregon, Rebeca Wong & Jinkook Lee

Intentional Control of Type I Error Over Unconscious Data Distortion: A Neyman–Pearson Approach to Text Classification

Lucy Xia, Richard Zhao, Yanhui Wu & Xin Tong
This article addresses the challenges in classifying textual data obtained from open online platforms, which are vulnerable to distortion. Most existing classification methods minimize the overall classification error and may yield an undesirably large Type I error (relevant textual messages are classified as irrelevant), particularly when available data exhibit an asymmetry between relevant and irrelevant information. Data distortion exacerbates this situation and often leads to fallacious prediction. To deal with inestimable data distortion, we propose...

Additional file 15 of Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Bing Zhang, Zhuoting Chen, Qixue Sun & Jianxiu Liu
Additional file 15: Table S8: Conserved acetylated proteins and acetylated sites in three grasses.

Additional file 15 of Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Bing Zhang, Zhuoting Chen, Qixue Sun & Jianxiu Liu
Additional file 15: Table S8: Conserved acetylated proteins and acetylated sites in three grasses.

Synthetic vehicle trajectory dataset for the metropolitan city of Los Angeles using DDTG

Chrysovalantis Anastasiou
The analysis of trajectory datasets has numerous applications ranging from urban planning to human mobility understanding, but to protect the privacy of individuals trajectory datasets are rarely released to researchers. And even when they are, they are limited in size and spatio-temporal coverage. To address these issues a number of methods for generating synthetic yet realistic trajectory datasets have been proposed. These existing methods either require a lot of complex parameters to be calibrated (simulators)...

Centromere protein F (CENPF), a microtubule binding protein, modulates cancer metabolism by regulating pyruvate kinase M2 phosphorylation signaling

Muhammad Shahid, Min Young Lee, Honit Piplani, Allen M. Andres, Bo Zhou, Austin Yeon, Minjung Kim, Hyung L. Kim & Jayoung Kim
Prostate cancer (PC) is the most commonly diagnosed cancer in men and is the second leading cause of male cancer-related death in North America. Metabolic adaptations in malignant PC cells play a key role in fueling the growth and progression of the disease. Unfortunately, little is known regarding these changes in cellular metabolism. Here, we demonstrate that centromere protein F (CENPF), a protein associated with the centromere-kinetochore complex and chromosomal segregation during mitosis, is mechanically...

Data from: Testing adaptive hypotheses of convergence with functional landscapes: a case study of bone-cracking hypercarnivores

Zhijie Jack Tseng
Morphological convergence is a well documented phenomenon in mammals, and adaptive explanations are commonly employed to infer similar functions for convergent characteristics. I present a study that adopts aspects of theoretical morphology and engineering optimization to test hypotheses about adaptive convergent evolution. Bone-cracking ecomorphologies in Carnivora were used as a case study. Previous research has shown that skull deepening and widening are major evolutionary patterns in convergent bone-cracking canids and hyaenids. A simple two-dimensional design...

Data from: Recovery from hybrid breakdown in a marine invertebrate is faster, stronger and more repeatable under environmental stress

AnnMarie S. Hwang, Victoria Pritchard, Suzanne Edmands & V. L. Pritchard
Understanding how environmental stress alters the consequences of hybridization is important, because the rate of hybridization and the likelihood of hybrid speciation both appear elevated in harsh, disturbed or marginal habitats. We assessed fitness, morphometrics and molecular genetic composition over 14 generations of hybridization between two highly divergent populations of the marine copepod Tigriopus californicus. Replicated, experimental hybrid populations in both control and high salinity conditions showed a decline in fitness, followed by a recovery....

Data from: Adaptation in isolated populations: when does it happen and when can we tell?

Jessica L. Crisci, Matthew D. Dean & Peter Ralph
Isolated populations with novel phenotypes present an exciting opportunity to uncover the genetic basis of ecologically significant adaptation, and genomic scans have often, but not always, led to candidate genes directly related to an adaptive phenotype. However, in many cases these populations were established by a severe bottleneck, which can make identifying targets of selection problematic. Here, we simulate severe bottlenecks and subsequent selection on standing variation, mimicking adaptation after establishment of a new small...

Data from: Extreme QTL mapping of germination speed in Arabidopsis thaliana

Wei Yuan, Jonathan M. Flowers, Dustin J. Sahraie, Ian M. Ehrenreich & Michael D. Purugganan
Seed germination is a key life history transition for annual plants and partly determines lifetime performance and fitness. Germination speed, the elapsed time for a nondormant seed to germinate, is a poorly understood trait important for plants’ competitiveness and fitness in fluctuating environments. Germination speed varied by 30% among 18 Arabidopsis thaliana populations measured, and exhibited weak negative correlation with flowering time and seed weight, with significant genotype effect (P < 0.005). To dissect the...

Data from: GATA2 controls lymphatic endothelial cell junctional integrity and lymphovenous valve morphogenesis through miR-126

, Xin Geng, YenChun Ho, Boksik Cha, Yuenhee Kim, Jing Ma, Lijuan Chen, Greggory Myers, Sally Camper, Debbie Mustacich, Marlys Witte, Dongwon Choi, Young-Kwon Hong, Hong Chen, Gaurav Varshney, James D Engel, Shusheng Wang, Tae-Hoon Kim, Kim-Chew Lim & Sathish Srinivasan
Mutations in the transcription factor GATA2 cause lymphedema. GATA2 is necessary for the development of lymphatic valves (LVs) and lymphovenous valves (LVVs), and for the patterning of lymphatic vessels. Here, we report that GATA2 is not necessary for valvular endothelial cell (VEC) differentiation. Instead, GATA2 is required for VEC maintenance and morphogenesis. GATA2 is also necessary for the expression of cell junction molecules VE-Cadherin and Claudin5 in lymphatic vessels. We identified miR-126 as a target...

Data from: Fine-scale temporal analysis of genotype-dependent mortality at settlement in the Pacific oyster Crassostrea gigas

Louis V. Plough
Settlement and metamorphosis mark a critical transition in the life cycle of marine invertebrates, during which substantial mortality occurs in both field and laboratory settings. Previous pair-crossing experiments with the Pacific oyster Crassostrea gigas have revealed significant selective or genotype-dependent mortality around the metamorphic transition, but the fine-scale nature and timing of this mortality is not known, particularly whether it occurs before, during or after metamorphosis. In this laboratory study, microsatellite marker segregation ratios were...

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