146 Works

Neferine hinders choriocarcinoma cell proliferation, migration and invasion through repression of long noncoding RNA-CHRF

Gang Wang, Ping Wang, Xiaojun Yan & Jing Liu
The comprehensive pathological peculiarities of Neferine (NEF) have been testified in disparate diseases. But, the functions of NEF in choriocarcinoma progression remain unexplored. The research endeavoured to uncover the anti-tumour action of NEF in choriocarcinoma cells. NEF at diverse doses was employed to dispose JEG-3 and HTR-8 cells, and cell viability assessment adopted CCK-8 assay. After 60 μg/mL NEF management, BrdU-positive cells, apoptosis, migration, invasion and correlative factors were assessed. CHRF expression in choriocarcinoma tumour...

Identification and validation of potential mRNA- microRNA- long-noncoding RNA (mRNA-miRNA-lncRNA) prognostic signature for cervical cancer

Jie Wang & Chen Zhang
Cervical cancer is one of the most common causes of cancer deaths in women due to poor prognosis and high mortality rates. A novel mRNA-miRNA-lncRNA signature linked to prognosis of cervical cancer is needed to help clinicians judge the prognosis of individual patients more accurately. On the basis of GEO datasets, a total of 161 upregulated and 242 downregulated DE-mRNAs were identified firstly. Among them, eight potential biomarkers were found to have prognostic values with...

Identification of hepatocellular carcinoma-related genes associated with macrophage differentiation based on bioinformatics analyses

Jun Cao, Chi Zhang, Guo-Qing Jiang, Sheng-Jie Jin, Qian Wang, Ao-Qing Wang & Dou-Sheng Bai
Macrophage differentiation is associated with tumorigenesis, including the tumorigenesis of hepatocellular carcinoma (HCC). Herein, we explored the value of macrophage differentiation-associated genes (MDGs) in the prognosis of HCC using data from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) databases. We performed multivariate Cox regression analyses to identify the hub genes affecting HCC patient prognoses. The correlations between hub genes and macrophage differentiation and immune checkpoint inhibitors (PD-1, PD-L1, and CTLA4)...

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....

Comprehensive analysis of pivotal biomarkers, immune cell infiltration and therapeutic drugs for steroid-induced osteonecrosis of the femoral head

Bo Wang, Song Gong, Wenkai Shao, Lizhi Han, Zilin Li, Zhichao Zhang, Yang Zheng, Fang Ouyang, Yan Ma, Weihua Xu & Yong Feng
Steroid-induced osteonecrosis of the femoral head (SONFH) is a progressive disease that leads to an increased disability rate. This study aimed to ascertain biomarkers, infiltrating immune cells, and therapeutic drugs for SONFH. The gene expression profile of the GSE123568 dataset was downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using the NetworkAnalyst platform. Functional enrichment, protein-protein interaction network (PPI), and module analyses were performed using Metascape tools. An...

Data from: Reverse diel vertical movements of oceanic manta rays off the northern coast of Peru and implications for conservation

Samantha Andrzejaczek, Robert Schallert, Kerstin Forsberg, Natalie Arnoldi, Mariano Cabanillas, Wilmer Purizaca & Barbara Block
An understanding of the vertical movements of elasmobranchs across their range is crucial to defining critical habitat use, its overlap with anthropogenic activities, and subsequently managing such interactions. In this study, satellite telemetry was used to investigate the vertical habitat use of three oceanic manta rays (Mobula birostris) tagged on the northern coast of Peru. All three oceanic mantas exhibited patterns of reverse diel vertical migration, where vertical movements were significantly deeper at night than...

Data Supplement for Digital Atlas of Dioceses and Ecclesiastical Provinces in Late Medieval Europe (1200-1500)

Rowan Dorin, Clara Romani, Lauren Schlansky & Claire Womack
This data supplement includes shapefiles and GeoJSON documents for the Digital Atlas of Dioceses and Ecclesiastical Provinces in Late Medieval Europe (1200-1500) Collection. Also included with this supplement is a list of contributors, map sources, a README file, and tabular metadata describing dioceses and provinces.

Land use impacts on parasitic infection: A cross-sectional epidemiological study on the role of irrigated agriculture in schistosome infection in a dammed landscape

Andrea Lund, David Rehkopf, Susanne Sokolow, M. Moustapha Sam, Nicolas Jouanard, Anne-Marie Schacht, Simon Senghor, Assane Fall, Gilles Riveau, Giulio De Leo & David Lopez-Carr
Background: Water resources development promotes agricultural expansion and food security. But are these benefits offset by increased infectious disease risk? Dam construction on the Senegal River in 1986 was followed by agricultural expansion and increased transmission of human schistosomes. Yet the mechanisms linking these processes at the individual and household levels remain unclear. We investigated the association between household land use and schistosome infection in children. Methods: We analyzed cross-sectional household survey data (n =...

Data from: Gene expression plasticity and desert adaptation in house mice

Noelle Bittner, Katya Mack & Michael Nachman
Understanding how organisms adapt to new environments is a key problem in evolution, yet it remains unclear whether phenotypic plasticity generally facilitates or hinders this process. Here we studied evolved and plastic responses to water-stress in lab-born descendants of wild house mice (Mus musculus domesticus) collected from desert and non-desert environments and measured gene expression and organismal phenotypes under control and water-stressed conditions. After many generations in the lab, desert mice consumed significantly less water...

Contrasting fungal responses to wildfire across different ecosystem types

Gabriel Smith, Lucy Edy & Kabir Peay
We took topsoil samples in burned and unburned areas across two California ecosystem types (Sonoma, California, United States) with differing fire ecologies in the immediate aftermath of a damaging wildfire in 2017. From our soil samples, we extracted DNA, amplified and sequenced fungal communities, and also measured chemistry (C%, N% and pH). Soil fungal communities of fire‐dependent oak woodlands differ from those of neighbouring mixed evergreen forests. The latter are more strongly altered compositionally by...

Quantum mechanical double slit for molecular scattering

Haowen Zhou, William E. Perreault, Nandini Mukherjee & Richard N. Zare
Interference observed in a double-slit experiment most conclusively demonstrates the wave properties of particles. We construct a quantum mechanical double-slit interferometer by rovibrationally exciting D2 (v=2, j=2) molecules in a biaxial state using Stark-induced adiabatic Raman passage. In D2(v=2, j=2)→D2(v=2, j'=0) rotational relaxation via a cold collision with ground state He, the entangled bond axis orientations in the biaxial state act as two slits generating two indistinguishable quantum mechanical pathways connecting initial and final states...

OpenSense: Validation of IMU-based estimates of kinematics over long durations

Johanna O'Day, Scott Delp, Mazen Al Borno, Vanessa Ibarra, James Dunne, Ajay Seth, Ayman Habib, Carmichael Ong, Jennifer Hicks & Scott Uhlrich
Here we provide the dataset for validation of OpenSense, an open-source toolbox for Inertial-Measurement-Unit-based measurement of lower extremity kinematics over long durations (10 minutes). We computed IMU-based estimates of kinematics using sensor fusion and an inverse kinematics approach with a constrained biomechanical model. We measured kinematics for 11 subjects as they performed two 10-minute trials: (1) walking and turning, and (2) a repeated sequence of varied lower-extremity movements (sitting, standing, stair-climbing, side-stepping, walking, running). Subjects...

OpenSenseRT Raspberry Pi Image

Patrick Slade, Ayman Habib, Jennifer Hicks & Scott Delp
The Raspberry Pi image replicates the OpenSenseRT, a real-time and wearable system for motion capture.

Data for: Successful management of invasive rats across a fragmented landscape

Erin Rankin, Sarah Barney, Devin Leopold, Kainana Francisco, David Flaspohler, Tad Fukami, Christian Giardina, Daniel Gruner, Jessie Knowlton & William Pitt
This dataset is from the manuscript "Successful management of invasive rats across a fragmented landscape" and provides the details on snap trap and tracking card data in a broadscale rat removal effort 2011-2015 in the Upper Waiakea Forest Reserve on the Island of Hawai‘i. It describes the successful trapping efforts as well as long term tracking data, which allow us to describe patterns of habitat use of non-native vertebrate species in these naturally fragmented forests...

Growth rates of populations evolved and assayed at two temperatures for 6500 generations

Jason Tarkington & Rebecca Zufall
Evolutionary biologists have long sought to understand what factors affect the repeatability of adaptive outcomes. To better understand the role of temperature in determining the repeatability of adaptive trajectories, we evolved populations of different genotypes of the ciliate Tetrahymena thermophila at low and high temperatures and followed changes in growth rate over 6,500 generations. As expected, growth rate increased with a decelerating rate for all populations; however, there were differences in the patterns of evolution...

The influence of climate and paleoclimate on distributions of global conifer clades depends on geographic range size

Mekala Sundaram & Andrew Leslie
Aim: We investigate how plant distributions are shaped by current and paleoclimate regimes. We specifically use global conifer biodiversity to test if paleoclimatic signatures are stronger in range-restricted taxa compared to widespread taxa. Location: Global Taxon: Coniferales Methods: We combine global geographic occurrences for 606 conifer species and 69 conifer genera with climate information (modern day and paleoclimate) to examine predictors of current conifer distribution. We test how climate predicts richness of range-restricted taxa and...

A Q-Theory of Banks

Juliane Beganau, Saki Bigio, Jeremy Majerovitz & Matías Vieyra
"The Great Recession in 2009 forced researchers and policy-makers to rethink regulations of the financial system. There has been a renewed effort to understand the behaviour of banks, their objectives and constraints, and their role in the economy. This paper contributes to that end by studying how banks react to changes in the value of their assets (generated, for example, by defaults on their loans). We argue that it is important to distinguish between the...

Decrypting cryptic crosswords: Semantically complex wordplay puzzles as a target for NLP

Joshua Rozner, Christopher Potts & Kyle Mahowald
Cryptic crosswords, the dominant crossword variety in the UK, are a promising target for advancing NLP systems that seek to process semantically complex, highly compositional language. Cryptic clues read like fluent natural language but are adversarially composed of two parts: a definition and a wordplay cipher requiring character-level manipulations. Expert humans use creative intelligence to solve cryptics, flexibly combining linguistic, world, and domain knowledge. In this paper, we make two main contributions. First, we present...

Stanford Geophysics Donor Data Collection

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Data for: Imaging the short-lived hydroxyl-hydronium pair in ionized liquid water

Ming-Fu Lin, Narendra Singh, Shujia Liang, Mianzhen Mo, Joao Pedro Figueira Nunes, Kathryn Ledbetter, Jie Yang, Michael Kozina, Stephen Weathersby, Xiaozhe Shen, Amy Cordones, Thomas Wolf, Sri Chaitanya Das Pemmaraju, Matthias Ihme & Xijie Wang
The radiolysis of water is ubiquitous in nature and plays a critical role in numerous biochemical and technological applications. Although the elementary reaction pathways for the ionized water have been studied, the short-lived intermediate complex and structural dynamic response after the proton transfer reaction remain poorly understood. Using liquid-phase ultrafast electron diffraction technique to measure the intermolecular O··O and O··H bonds, we captured the short-lived radical-cation complex OH(H3O+) that was formed within 140 femtoseconds through...

Macrophage-derived IL-6 trans-signaling as a novel target in the pathogenesis of bronchopulmonary dysplasia (RNA-seq-P14-HYXvsNOX)

Dharmesh Hirani & Cristina Alvira
Rationale: Premature infants exposed to oxygen are at risk for bronchopulmonary dysplasia (BPD), which is characterized by lung growth arrest. Inflammation is important, but the mechanisms remain elusive. Here, we investigated inflammatory pathways and therapeutic targets in severe clinical and experimental BPD. Methods and Results: First, transcriptomic analysis with in-silico cellular deconvolution identified a lung-intrinsic M1-like-driven cytokine pattern in newborn mice after hyperoxia. These findings were confirmed by gene expression of macrophage-regulating chemokines (Ccl2, Ccl7,...

Huge sedimentary hiatus in the southern margin of the North China Craton from mid-Mesoproterozoic to Neoproterozoic

Pengfei Zuo, Yu Li, Haihua Cheng, Christopher J. Spencer, Fengbo Sun, Shiyan Wang & Deshun Zheng
The Meso- to Neoproterozoic Eras were characterized by environmental, evolutionary, and lithospheric stability in the North China Craton (NCC). It is controversial that huge uplift(s) occurred in the North China Craton during this period. The southern NCC developed early terrestrial deposition in the late-Paleoproterozoic and glacial sequence in the late Neoproterozoic record integrated geological history of the NCC in the intervening interval. Geochemistry compositions of mid-Mesoproterozoic carbonaceous slates (ca. 1330 Ma) show similar provenances to...

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...

Cell type labels for all clustering and normalization combinations compared for CODEX multiplexed imaging

John Hickey
We performed CODEX (co-detection by indexing) multiplexed imaging on four sections of the human colon (ascending, transverse, descending, and sigmoid) using a panel of 47 oligonucleotide-barcoded antibodies. Subsequently images underwent standard CODEX image processing (tile stitching, drift compensation, cycle concatenation, background subtraction, deconvolution, and determination of best focal plane), and single cell segmentation. Output of this process was a dataframe of nearly 130,000 cells with fluorescence values quantified from each marker. We used this dataframe...

Data for: Cdt1 inhibits CMG helicase in early S phase to separate origin licensing from DNA synthesis

Nalin Ratnayeke, Yasemin Baris, Mingyu Chung, Joseph Yeeles & Tobias Meyer
Human cells license tens of thousands of origins of replication in G1 and then must stop all licensing before DNA synthesis in S phase to prevent re-replication and genome instability that ensue when an origin is licensed on replicated DNA. However, the E3 ubiquitin ligase CRL4Cdt2 only starts to degrade the licensing factor Cdt1 after origin firing, raising the question of how cells prevent re-replication before Cdt1 is fully degraded. Here, using quantitative microscopy and...

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