208 Works

Additional file 2 of Proteomic alterations associated with residual disease in neoadjuvant chemotherapy treated ovarian cancer tissues

Emily R. Penick, Nicholas W. Bateman, Christine Rojas, Cuauhtemoc Magana, Kelly Conrads, Ming Zhou, Brian L. Hood, Guisong Wang, Niyati Parikh, Ying Huang, Kathleen M. Darcy, Yovanni Casablanca, Paulette Mhawech-Fauceglia, Thomas P. Conrads & G. Larry Maxwell
Additional file 2: Table S1. Proteins significantly altered between post versus pre-NACT tissues (LIMMA p-value<0.01). Table S2. Proteins significantly altered between R1 versus R0 patients in pre-NACT tissues (LIMMA p-value<0.05). Table S3. Significantly (LIMMA p<0.05) co-altered proteins between pre-NACT tumors from patients with any level of residual disease vs R0 patients from an independent ovarian cancer cohort (CPTAC 2016) that exhibit highly correlated abundance trends with the present ovarian cancer cohort. Table S4. Diseases and...

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...

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.

sj-xlsx-2-cix-10.1177_11769351221136056 – Supplemental material for Optimizing Drug Response Study Design in Patient-Derived Tumor Xenografts

Jessica Weiss, Nhu-An Pham, Melania Pintilie, Ming Li, Geoffrey Liu, Frances A Shepherd, Ming-Sound Tsao & Wei Xu
Supplemental material, sj-xlsx-2-cix-10.1177_11769351221136056 for Optimizing Drug Response Study Design in Patient-Derived Tumor Xenografts by Jessica Weiss, Nhu-An Pham, Melania Pintilie, Ming Li, Geoffrey Liu, Frances A Shepherd, Ming-Sound Tsao and Wei Xu in Cancer Informatics

Classification of Type 2 Diabetes Genetic Variants and a Novel Genetic Risk Score Association with Insulin Clearance

Mark Goodarzi, Nicholette D Palmer, Jinrui Cui, Xiuqing Guo, Yii-Der I Chen, Kent D Taylor, Leslie J Raffel, Lynne E Wagenknecht, Thomas A Buchanan, Willa A Hsueh & Jerome I Rotter
Abstract Context Genome-wide association studies have identified >450 single nucleotide polymorphisms (SNPs) for type 2 diabetes (T2D). Objective To facilitate use of these SNPs in future genetic risk score (GRS)-based analyses, we aimed to classify the SNPs based on physiology. We also sought to validate GRS associations with insulin-related traits in deeply-phenotyped Mexican Americans. Design, Setting, and Participants 457 T2D SNPs from the literature were assigned physiologic function based on association studies and cluster analyses....

Data from: Elovanoids counteract oligomeric β-Amyloid-induced gene expression and protect photoreceptors

Nicolas Bazan, Khanh Do, Marie-Audrey Kautzmann, Bokkyoo Jun, William Gordon, Robert Nshimiyimana, Rong Yang & Nicos Petasis
The onset of neurodegenerative diseases activates inflammation that leads to progressive neuronal cell death and impairments in cognition (Alzheimer’s disease, AD) and sight (age-related macular degeneration, AMD). How neuroinflammation can be counteracted is not known. In AMD, amyloid β-peptide (Aβ) accumulates in subretinal drusen. In the 5xFAD retina, we found early functional deficiencies (ERG) without photoreceptor cell (PRC) death and identified early insufficiency in biosynthetic pathways of pro-homeostatic/neuroprotective mediators, neuroprotectin D1 (NPD1) and elovanoids (ELVs)....

Data from: A parapithecid stem anthropoid of African origin in the Paleogene of South America

Erik Seiffert, Marcelo Tejedor, John Fleagle, Nelson Novo, Fanny Cornejo, Mariano Bond, Dorien De Vries & Kenneth Campbell
Phylogenetic evidence suggests that platyrrhine (or New World) monkeys and caviomorph rodents of the Western Hemisphere derive from source groups from the Eocene of Afro-Arabia, a landmass that was ~1500 to 2000 kilometers east of South America during the late Paleogene. Here, we report evidence for a third mammalian lineage of African origin in the Paleogene of South America—a newly discovered genus and species of parapithecid anthropoid primate from Santa Rosa in Amazonian Perú. Bayesian...

Data from: The wings before the bird: an evaluation of flapping-based locomotory hypotheses in bird antecedents

T. Alexander Dececchi, Hans C.E. Larsson & Michael B. Habib
Background. Powered flight is implicated as a major driver for the success of birds. Here we examine the effectiveness of three hypothesized pathways for the evolution of the flight stroke, the forelimb motion that powers aerial locomotion, in a terrestrial setting across a range of stem and basal avians: flap running, Wing Assisted Incline Running (WAIR), and wing-assisted leaping. Methods. Using biomechanical mathematical models based on known aerodynamic principals and in vivo experiments and ground...

Subducted lithospheric boundary tomographically imaged beneath arc-continent collision in Eastern Indonesia

Cooper Harris
We use travel-times from a temporary seismic deployment of 30 broadband seismometers and a national catalog of arrival times to construct a finite frequency teleseismic P-wave tomographic model of the upper mantle beneath astern Indonesia, where subduction of the Indo-Australian plate beneath the Banda Arc transitions to arc-continent collision. The change in tectonics is due to a change from oceanic to continental lithosphere in the lower plate as inferred from geologic mapping and geophysical, geochemical,...

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...

Data from: Fossil lemurs from Egypt and Kenya suggest an African origin for Madagascar’s aye-aye

Gregg F. Gunnell, Doug M. Boyer, Anthony F. Friscia, Steven Heritage, Fredrick K. Manthi, Ellen R. Miller, Hesham M. Sallam, Nancy B. Simmons, Nancy J. Stevens & Erik R. Seiffert
In 1967 G.G. Simpson described three partial mandibles from early Miocene deposits in Kenya that he interpreted as belonging to a new strepsirrhine primate, Propotto. This interpretation was quickly challenged, with the assertion that Propotto was not a primate, but rather a pteropodid fruit bat. The latter interpretation has not been questioned for almost half a century. Here we re-evaluate the affinities of Propotto, drawing upon diverse lines of evidence to establish that this strange...

Data from: Functional genomic analysis of corals from natural CO2-seeps reveals core molecular responses involved in acclimatization to ocean acidification

Carly D. Kenkel, Aurelie Moya, Julia Strahl, Craig Humphrey & Line K. Bay
Little is known about the potential for acclimatization or adaptation of corals to ocean acidification and even less about the molecular mechanisms underpinning these processes. Here we examine global gene expression patterns in corals and their intracellular algal symbionts from two replicate population pairs in Papua New Guinea that have undergone long-term acclimatization to natural variation in pCO2. In the coral host, only 61 genes were differentially expressed in response to pCO2 environment, but the...

Data from: Comparative dynamics of microglialand glioma cell motility at the infiltrative margin of brain tumours

Joseph Juliano, Orlando Gil, Andrea Hawkins-Daarud, Sonal Noticewala, Russell C. Rockne, Jill Gallaher, Susan C. Massey, Peter A. Sims, Alexander R. A. Anderson, Kristin R. Swanson & Peter Canoll
Microglia are a major cellular component of gliomas, and abundant in the centre of the tumour and at the infiltrative margins. While glioma is a notoriously infiltrative disease, the dynamics of microglia and glioma migratory patterns have not been well characterized. To investigate the migratory behaviour of microglia and glioma cells at the infiltrative edge, we performed two-colour time-lapse fluorescence microscopy of brain slices generated from a platelet-derived growth factor-B (PDGFB)-driven rat model of glioma,...

Detrital magnetite grains scanned to detect inclusions for cosmogenic 3He exposure dating

Florian Hofmann & Emily Cooperdock
More than 3000 individual detrital magnetite grains from a fanglomerate near Whitewater (California, USA) were scanned using microCT. These data were used to detect mineral inclusion in these magnetite grains, which can contribute significant amounts of 3He. Grains without inclusions were then picked from these analyzed grains and used to calibrate the cosmogenic 3He production rate in magnetite (manuscript submitted to GChron).

Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity

Feng Yang, Jinghao Zhang, Su Wang, Zhaoyang Sun, Jun Zhou, Feng Li, Yue Liu, Li Ding, Yixin Liu, Wenjing Chi, Tao Liu, Yongqun He, Ping Xiang, Zhijun Bao, Michal A. Olszewski, Hu Zhao & Yanmei Zhang
Severe Helicobacter pylori-linked gastric disorders are especially prevalent in the East Asia region. The ability of H. pylori to cause different clinical outcomes is thought to be associated with unique sets of its genetic features. However, only few genetic features have been definitively linked to specific gastrointestinal pathologies. Genome heterogeneity of clinical H. pylori strains from patients with four different gastric disorders was studied to explore the population structure and molecular genomic features and their...

Data from: Differential responses to ocean acidification between populations of Balanophyllia elegans corals from high and low upwelling environments

Joanna S. Griffiths, Francis T. Pan & Morgan W. Kelly
Ocean acidification (OA), the global decrease in surface water pH from absorption of anthropogenic CO2, may put many marine taxa at risk. However, populations that experience extreme localized conditions, and are adapted to these conditions predicted in the global ocean in 2100, may be more tolerant to future OA. By identifying locally adapted populations, researchers can examine the mechanisms used to cope with decreasing pH. One oceanographic process that influences pH, is wind driven upwelling....

Data from: Dynamic relocalization of replication origins by Fkh1 requires execution of DDK function and Cdc45 loading at origins

Haiyang Zhang, Meghan V Petrie, Yiwei He, Jared M Peace, Irene E Chiolo & Oscar M Aparicio
Chromosomal DNA elements are organized into spatial domains within the eukaryotic nucleus. For example, sites actively undergoing DNA replication, high-level transcription, and repair of double-strand breaks coalesce into foci, although the significance and mechanisms giving rise to these dynamic structures are poorly understood. In S. cerevisiae, replication origins exhibit characteristic subnuclear localizations prior to S phase that anticipate their initiation timing and/or efficiency during S phase: origins found within the nuclear interior in G1 phase...

BAF155 Methylation Drives Metastasis By Hijacking Super-enhancers and Subverting Anti-tumor Immunity

Eui-Jun Kim, Peng Liu, Shengjie Zhang, Kristine Donahue, Yidan Wang, Jennifer Schehr, Serena Wolfe, Amber Dickerson, Li Lu, Lixin Rui, Xuehua Zhong, Kari Wisinski, Min Yu, Aussie Suzuki, Joshua Lang, Irene Ong & Wei Xu
Subunits of the chromatin remodeler SWI/SNF are the most frequently disrupted genes in cancer. However, how post-translational modifications (PTM) of SWI/SNF subunits elicit epigenetic dysfunction remains unknown. Arginine-methylation of BAF155 by coactivator-associated arginine methyltransferase 1 (CARM1) promotes triple negative breast cancer (TNBC) metastasis. Herein, we discovered the dual roles of methylated-BAF155 (me-BAF155) in promoting tumor metastasis: activation of super-enhanceraddicted oncogenes by recruiting BRD4, and repression of interferon / pathway genes to suppress host immune response....

Data from: Widespread loss of mammalian lineage and dietary diversity in the early Oligocene of Afro-Arabia

Dorien De Vries, Steven Heritage, Matthew Borths, Hesham Sallam & Erik Seiffert
Diverse lines of geological and geochemical evidence indicate that the Eocene-Oligocene transition (EOT) marked the onset of a global cooling phase, rapid growth of the Antarctic ice sheet, and a worldwide drop in sea level. Paleontologists have established that shifts in mammalian community structure in Europe and Asia were broadly coincident with these events, but the potential impact of early Oligocene climate change on the mammalian communities of Afro-Arabia has long been unclear. Here we...

Fitness of gnotobiotic Rhodnius prolixus nymphs

Kevin Vogel, Carissa Gilliland, Vilas Patel, Ashley Dombrowski & Bradley Mackett
Kissing bugs (Hempitera: Reduviidae) are obligately and exclusively blood feeding insects. Vertebrate blood is thought to provide insufficient B vitamins to insects, which rely on obligate symbiotic relationships with bacteria that provision these nutrients. Kissing bugs harbor environmentally acquired bacteria in their gut lumen, without which they are unable to develop to adulthood. Early experiments identified a single bacterial species, Rhodococcus rhodnii, as a symbiont of Rhodnius prolixus, but modern studies of the kissing bug...

Cannabidiol attenuates methamphetamine-induced conditioned place preference in male rats and viability in PC12 cells through the Sigma1R/AKT/GSK3β/CREB signaling pathway

Liu Liu, Juan Li, Chan Wang, Yue Xu, Chi-Kwan Leung, Genmeng Yang, Shucheng Lin, Shuwei Zhang, Yi Tan, Huijie Zhang, Haowei Wang, Jianxing Liu, Ming Li & Xiaofeng Zeng
Background: Methamphetamine use is associated with several negative consequences, including neurotoxicity and greater probability of exhibiting a substance use disorder. Sigma1 receptor is involved in the neurobiological basis of several drug use disorders. Cannabidiol has received attention in the treatment of drug use disorders and neurotoxicity. Objectives: To investigate the effects of cannabidiol on methamphetamine-induced conditioned place preference (CPP) and the viability of PC12 cells. Methods: Adult male rats (n = 70) underwent methamphetamine (2...

Additional file 11 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 11: Table S4: Proteins with both acetylation and succinylation modifications.

Additional file 4 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 4: Table S3. NRAS overexpression induces basal-like features in a human luminal DCIS model SUM225 cells.

Additional file 1 of Neoplastic cell enrichment of tumor tissues using coring and laser microdissection for proteomic and genomic analyses of pancreatic ductal adenocarcinoma

Qing Kay Li, Yingwei Hu, Lijun Chen, Michael Schnaubelt, Daniel Cui Zhou, Yize Li, Rita Jui-Hsien Lu, Mathangi Thiagarajan, Galen Hostetter, Chelsea J. Newton, Scott D. Jewell, Gil Omenn, Ana I. Robles, Mehdi Mesri, Oliver F. Bathe, Bing Zhang, Li Ding, Ralph H. Hruban, Daniel W. Chan & Hui Zhang
Additional file 1: Table S1. Clinical information of study cases. Table S2. Expression of proteins from the PDAC tumors and NATs

In silico package models for deriving values of solute parameters in linear solvation energy relationships

Z.J. Xiao, J.W. Chen, Y. Wang & Z.Y. Wang
Environmental partitioning influences fate, exposure and ecological risks of chemicals. Linear solvation energy relationship (LSER) models may serve as efficient tools for estimating environmental partitioning parameter values that are commonly deficient for many chemicals. Nonetheless, scarcities of empirical solute parameter values of LSER models restricted the application. This study developed and evaluated in silico methods and models to derive the values, in which excess molar refraction, molar volume and logarithm of hexadecane/air partition coefficient were...

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  • University of Southern California
  • Chinese Academy of Sciences
  • Fudan University
  • Sun Yat-sen University
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • China Agricultural University
  • Shanghai Jiao Tong University
  • Tianjin University of Traditional Chinese Medicine
  • University of Michigan–Ann Arbor
  • Zhejiang University