146 Works

T cell characteristics associated with toxicity to immune checkpoint blockade

Alexander X Lozano, Aadel A Chaudhuri, Aishwarya Nene & Aaron M Newman
A supplementary resource for “T cell characteristics associated with toxicity to immune checkpoint blockade in patients with melanoma”.

Data from: Opportunities to catalyze improved healthcare access in pluralistic systems: a cross-sectional study in Haiti

Molly Klarman, Justin Schon, Youseline Cajusma, Stacey Maples, Valery M Beau De Rochars, Chantale Baril & Eric J Nelson
Introduction. Gains to ensure global healthcare access are at risk of stalling because some old resilient challenges require new solutions. Our objective was to identify determinants of intended versus actual care-seeking behaviors in a pluralistic healthcare system that is reliant on both conventional and non-conventional providers and discover opportunities to catalyze improved healthcare access. Methods. A cross-sectional study was conducted among households with children less than 5 years of age in Haiti. Households were randomly...

Centralizing Over-the-Counter Markets?

Jason Allen & Milena Wittwer
Would a shift in trading in fixed-income markets—from over the counter (bilateral trading) to a centralized electronic platform—improve welfare? We use trade-level data on the secondary market for Government of Canada debt to answer this question.

Seasonal particle responses to near-bed shear stress in a shallow, wave- and current-driven environment

Grace Chang, Galen Egan, Frank Spada, Craig Jones, Stephen Monismith & Oliver Fringer
Novel analysis of in-situ acoustic and optical data collected in a shallow, wave- and current-driven environment enabled determination of: (1) particle characteristics that were most affected by near-bed physical forcing over seasonal scales, and (2) characteristic shear stress, tchar, at which the rate of change to particle characteristics was most pronounced. Near-bed forcing and particle responses varied by season. Results indicated that moderate tchar values of 0.125 Pa drove changes in particle composition during summer....

Transcriptional acclimation and spatial differentiation characterize drought response by the ectomycorrhizal fungus Suillus pungens

Kabir Peay
Changing precipitation regimes are a challenge for forest health under future climate scenarios. If belowground symbionts can acclimate to changing moisture regimes it may buffer forest trees from these changes. In this study we exposed the ectomycorrhizal fungus Suillus pungens to acute and chronic drought stress and used RNASeq of both ectomycorrhizal roots and extraradical mycelium to gauge the magnitude of stress, identify key genes involved in drought response, and gauge potential ecosystem consequences of...

Spore size data for free-sporing extant and fossil plants

Andrew Leslie
The evolution of different spore size classes, or heterospory, is a fundamental reproductive innovation in land plants. The appearance of heterospory is particularly notable during the Devonian, when most known origins of the trait occur. Here we provide a perspective on the evolution of heterospory during this time interval, particularly from the late Early Devonian through the Middle Devonian (Emsian to Givetian stages; 408-383 Ma), which shows an unusually high concentration of heterospory origins. We...

Transmission electron micrographs of AMPAR containing vesicles

John Peters, Jeremy Leitz, Juan Oses-Prieto, Alma Burlingame & Axel Brunger
Here we present transmission electron micrographs of AMPAR containing vesicles. AMPAR containing vesicles were purified from whole mouse brain via immunoisolation, applied to a copper electron microscopy grid, and stained with uranyl acetate. Vesicles were imaged at a range of magnifications from 4,000 to 15,000. Included in these data are immunoelectron micrographs where we probed for synaptobrevin-2, synaptophysin-1, GluA2, and GluA3.

The predictive value of diabetic retinopathy on subsequent diabetic nephropathy in patients with type 2 diabetes: a systematic review and meta-analysis of prospective studies

Yu Li, Xiaoxuan Su, Qing Ye, Xiaodan Guo, Bo Xu, Tianjun Guan & Anqun Chen
This systematic review and meta-analysis aimed to assess the predictive value of diabetic retinopathy (DR) on further diabetic nephropathy (DN) risk in patients with type 2 diabetes (T2D) based on the prospective cohort studies. PubMed, Embase, and the Cochrane Library were systematically searched for eligible prospective cohort studies through March 2020. The predictive value of DR was assessed using sensitivity, specificity, positive likelihood ratio (PLR) and negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and...

In-hospital acute kidney injury and atrial fibrillation: incidence, risk factors, and outcome

Guoqin Wang, Lijiao Yang, Nan Ye, Weijing Bian, Changsheng Ma, Dong Zhao, Jing Liu, Yongchen Hao, Na Yang & Hong Cheng
The incidence and the risk factors of in-hospitalized acute kidney injury (AKI) in patients hospitalized for atrial fibrillation (AF) were unclear. The Improving Care for Cardiovascular Disease in China-AF (CCC-AF) project is an ongoing registry and quality improvement project, with 240 hospitals recruited across China. We selected 4527 patients hospitalized for AF registered in the CCC-AF from January 2015 to January 2019. Patients were divided into the AKI and non-AKI groups according to the changes...

Optimization of the extraction conditions and dermal toxicity of oil body fused with acidic fibroblast growth factor (OLAF)

Yongxin Guo, Yaying Li, Qian Wu, Xinxin Lan, Guodong Chu, Weidong Qiang, Muhammad Noman, Tingting Gao, Jinnan Guo, Long Han, Jing Yang, Xiaokun Li & Linna Du
Oil body (OB), a subcellular organelle that stores oil in plant seeds, is considered a new transdermal drug delivery system. With the increasing understanding of the OB and its main protein (oleosin), numerous studies have been conducted on OB as “carrier” for the expression of exogenous proteins. In our previous study, oil body fused with aFGF (OLAF) was obtained using a plant oil body expression system that had been preliminarily proven to be effective in...

Optimization of the extraction conditions and dermal toxicity of oil body fused with acidic fibroblast growth factor (OLAF)

Yongxin Guo, Yaying Li, Qian Wu, Xinxin Lan, Guodong Chu, Weidong Qiang, Muhammad Noman, Tingting Gao, Jinnan Guo, Long Han, Jing Yang, Xiaokun Li & Linna Du
Oil body (OB), a subcellular organelle that stores oil in plant seeds, is considered a new transdermal drug delivery system. With the increasing understanding of the OB and its main protein (oleosin), numerous studies have been conducted on OB as “carrier” for the expression of exogenous proteins. In our previous study, oil body fused with aFGF (OLAF) was obtained using a plant oil body expression system that had been preliminarily proven to be effective in...

Three periods of gold mineralization in the Liaodong Peninsula, North China Craton

Peng Zhang, Linlin Kou & Yang Zhao
The Liaodong gold province includes voluminous gold deposits, which occur in an Archean gneiss complex, Paleoproterozoic metamorphic rocks, and Mesozoic granite. However, the ore-forming age, the genesis, and the geodynamic setting of the gold deposits are not well constrained. In this study, we have summarized previous geochronology data, H-O-S-Pb isotopes, and He-Ar isotopic compositions of the gold deposits. Based on geochronology data, the gold mineralization was divided into Late Triassic, Early Jurassic, and Early Cretaceous....

Gestational hypertensive disease and birthweight discordance in twin pregnancies: a systematic review and meta-analysis

Yuan Wang, Hongying Zeng, Jing Liu & Feng Zhang
The objective of this systematic review was to explore the association between gestational hypertensive disease (GHD) and birthweight discordance in twin pregnancies. PubMed, Embase, Web of Science and Cochrane Library were systematically searched for studies reporting the risk of birthweight discordance in twin pregnancies complicated compared with those not complicated by GHD from establishment until July 2021. Risk of bias was assessed with the Newcastle-Ottawa Scale. According to the classification of GHD, sub-group analyses reporting...

Investigating genetic diversity and population phylogeny of five Chongqing local chicken populations autosomal using microsatellites

Xue Yang, Cheng-Li Liu, Bai-Gao Yang, Hai-Qiang Hu, Gong Ying, Guo Yi, Bo-Er Chen, Ying Yuan, He Yong-Meng, Wei-Yi Zhang, Dan-Ping Zhang, Guang-Xin E. & Ming-Hui Li
The genetic diversity and population structures of five Chongqing local chicken populations were investigated using by 24 microsatellite markers. Results revealed that the mean number of alleles (NA) ranged from 7.08 (Daninghe chicken, DN) to 8.46 (Nanchuan chicken, NC). The highest observed heterozygosity (HO) and expected heterozygosity (HE) were observed in DN (HO = 0.7252; HE = 0.7409) and the lowest HO and HE were observed in XS (Xiushan native chicken [XS], HO = 0.5910...

Azilsartan protects against hyperglycemia-induced hyperpermeability of the blood-brain barrier

Jing Han, Hua Tang, Longfei Yao, Erliang Jin, Wanxi Pan & Shaojun Chen
Diabetes mellitus (DM) is a complex metabolic disease with significant neurological complications and is reported to be closely related to the blood-brain barrier (BBB) disruption. Azilsartan is an antagonist of the Angiotensin II receptor developed for the treatment of hypertension, and it has been recently reported to have neuroprotective effects. The present study aims to investigate the protective effect of Azilsartan against hyperglycemia-induced BBB disruption and its underlying mechanism. Male db/db mice were treated with...

Whole-transcriptome analysis of rat cavernosum and identification of circRNA-miRNA-mRNA networks to investigate nerve injury erectile dysfunction pathogenesis

Jie Huang, Jianxiong Ma, Jie Wang, Ke Ma, Kang Zhou, Wenjie Huang, Fan Zhao, Bodong Lv & Qing Hu
There is growing evidence that circular RNAs (circRNAs) play a vital role in many kinds of diseases, including erectile dysfunction (ED). Nevertheless, the role of circRNAs in cavernous nerve-damaging ED (CNI-ED) is unknown. Here, we aimed to discover novel circRNAs, probed their potential role in the CNI-ED, and construct a ceRNA network of circRNAs. Twelve male Sprague Dawley rats were randomly divided into 2 groups by us: bilateral cavernous nerve crush (BCNC) and control groups....

Bioinformatics analysis reveals the competing endogenous RNA (ceRNA) coexpression network in the tumor microenvironment and prognostic biomarkers in soft tissue sarcomas

Dandan Zou, Yang Wang, Meng Wang, Bo Zhao, Fei Hu, Yanguo Li & Bingming Zhang
Soft tissue sarcomas (STSs) are rare, heterogeneous mesenchymal neoplasias. Understanding the tumor microenvironment (TME) and identifying potential biomarkers for prognosis associated with the TME of STS might provide effective clues for immune therapy. We evaluated the immune scores and stromal scores of STS patients by using the RNA sequencing dataset from The Cancer Genome Atlas (TCGA) database and the ESTIMATE algorithm. Then, the differentially expressed mRNAs (DEGs), miRNAs (DEMs) and lncRNAs (DELs) were identified after...

Data from: Non-invasive stratification of non-alcoholic fatty liver disease by whole-transcriptome cell-free mRNA characterization

Naga Chalsani, Shusuke Toden, John Sninsky, Richard Rava, Jerome Braun, Samer Gawrieh, Jiali Zhuang, Michael Nerenberg, Stephen Quake & Tara Maddala
Hepatic fibrosis stage is the most important determinant of outcomes in patients with non-alcoholic fatty liver disease (NAFLD). There is an urgent need for non-invasive tests that can accurately stage fibrosis and determine efficacy of interventions. Here we describe a novel cf-mRNA-Sequencing approach that can accurately and reproducibly profile low levels of circulating mRNAs and evaluate the feasibility of developing a cf-mRNA-based NAFLD fibrosis classifier. Using separate discovery and validation cohorts with biopsy-confirmed NAFLD (n=176...

Data from: Facilitation and biodiversity jointly drive mutualistic networks

Gianalberto Losapio, Elizabeth Norton Hasday, Xavier Espadaler, Christoph Germann, Francisco Javier Ortiz-Sánchez, Adrian Pont, Daniele Sommaggio & Christian Schöb
1. Facilitation by nurse plants increases understorey diversity and supports ecological communities. In turn, biodiversity shapes ecological networks and enhances ecosystem functioning. However, whether and how facilitation and increased biodiversity jointly influence community structure and ecosystem functioning remains unclear. 2. We performed a field experiment disentangling the relative contribution of nurse plants and increasing understorey plant diversity in driving pollination interactions. Both the presence of nurse shrubs as well as increased understorey plant diversity increased...

Flexible analysis of animal behavior via time-resolved embedding

Ryan York
Uncovering relationships between neural activity and behavior represents a critical challenge, one that would benefit from facile tools that can capture complex structures within large datasets. Here we demonstrate a generalizable strategy for capturing such structures across diverse behaviors: Time-REsolved BehavioraL Embedding (TREBLE). Using data from synthetic trajectories, adult and larval Drosophila, and mice we show how TREBLE captures both continuous and discrete behavioral dynamics, can uncover variation across individuals, detect the effects of optogenetic...

Two new hybrid populations expand the swordtail hybridization model system

Daniel Powell, Ben Moran, Bernard Kim, Shreya Banerjee, Stepfanie Aguillon, Paola Fascinetto-Zago, Quinn Langdon & Molly Schumer
Natural hybridization events provide unique windows into the barriers that keep species apart as well as the consequences of their breakdown. Here we characterize hybrid populations formed between the northern swordtail fish Xiphophorus cortezi and X. birchmanni from collection sites on two rivers. We use simulations and new genetic reference panels to develop sensitive and accurate local ancestry calling in this novel system. Strikingly, we find that hybrid populations on both rivers consist of two...

EcoTyper: a machine learning framework for large-scale identification of cell type-specific transcriptional states and cellular ecosystems

Bogdan-Alexandru Luca, Chloé Steen, Armon Azizi, Andrew Gentles, Arash Ash Alizadeh & Aaron Newman
EcoTyper is a machine learning framework for large-scale identification of cell type-specific transcriptional states and their co-association patterns from bulk, single-cell, and spatially resolved gene expression data. EcoTyper performs the following major steps: 1) In silico purification: This step enables imputation of cell type-specific gene expression profiles from bulk tissue transcriptomes, using CIBERSORTx (Newman et al., Nature Biotechnology 2019). 2) Cell state discovery: This step enables identification and quantitation of cell type-specific transcriptional states. 3)...

Data for: Modeling short-term energetic costs of sonar disturbance to cetaceans using high resolution foraging data

Max Czapanskiy, Matthew Savoca, William Gough, Paolo Segre, Danuta Wisniewska, David Cade & Jeremy Goldbogen
Anthropogenic noise is a pervasive and increasing source of disturbance to wildlife. Marine mammals exhibit behavioral and physiological responses to naval sonar and other sound sources. The lost foraging opportunities and elevated locomotor effort associated with sonar disturbance likely carry energetic costs, which may lead to population-level consequences. We modeled the energetic costs associated with behavioral responses using (1) empirical datasets of cetacean feeding rates and prey characteristics and (2) allometry of swimming performance and...

WaveMAP analysis of extracellular waveforms from monkey premotor cortex during decision-making

Eric Lee, Hymavathy Balasubramanian, Alexandra Tsolias, Stephanie Anakwe, Maria Medalla, Krishna Shenoy & Chandramouli Chandrasekaran
Cortical circuits are thought to contain a large number of cell types that coordinate to produce behavior. Current in vivo methods rely on clustering of specified features of extracellular waveforms to identify putative cell types, but these capture only a small amount of variation. Here, we develop a new method (WaveMAP) that combines non-linear dimensionality reduction with graph clustering to identify putative cell types. We apply WaveMAP to extracellular waveforms recorded from dorsal premotor cortex...

Dendritic calcium signals in rhesus macaque motor cortex drive an optical brain-computer interface

Daniel J O'Shea, Eric Trautmann, Xulu Sun, Karl Deisseroth & Krishna Shenoy
Calcium imaging has rapidly developed into a powerful tool for recording from large populations of neurons in vivo. Imaging in rhesus macaque motor cortex can enable the discovery of new principles of motor cortical function and can inform the design of next generation brain-computer interfaces (BCIs). Surface two-photon (2P) imaging, however, cannot presently access somatic calcium signals of neurons from all layers of macaque motor cortex due to photon scattering. Here, we demonstrate an implant...

Registration Year

  • 2021

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  • Stanford University
  • Chinese Academy of Sciences
  • Huazhong University of Science and Technology
  • Capital Medical University
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • Sichuan University
  • Fudan University
  • University of Chinese Academy of Sciences
  • Shanghai Jiao Tong University
  • Chinese PLA General Hospital