146 Works

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...

B7 family member H4 induces epithelial-mesenchymal transition and promotes the proliferation, migration and invasion of colorectal cancer cells

Yuzhen Yin, Lili Shi, Jing Yang, Hui Wang, Hang Yang & Qiang Wang
Colorectal cancer (CRC) is a common malignancy of the gastrointestinal tract, which has the second highest incidence among gastrointestinal tumors. At present, due to the limitations of current CRC treatment strategies, there is an urgent need for developing more effective therapies. B7 family member H4 (B7-H4) is associated with the progression of a wide spectrum of cancers, but its functional role in CRC is unknown. The purpose of this study is to clarify the role...

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...

Projected climate risk of aquatic food system benefits

Michelle Tigchelaar, William Cheung, Essam Mohammed, Michael Phillips, Hanna Payne, Elizabeth Selig, Colette Wabnitz, Muhammed Oyinlola, Thomas Frölicher, Jessica Gephart, Christopher Golden, Edward Allison, Abigail Bennett, Ling Cao, Jessica Fanzo, Benjamin Halpern, Fiorenza Micheli, Rosamond Naylor, Rashid Sumaila, Alessandro Tagliabue & Max Troell
Aquatic foods from marine and freshwater systems are critical to the nutrition, health, livelihoods, economies and culture of billions of people worldwide – but climate-related hazards may compromise their ability to provide these benefits. This analysis estimates national-level aquatic food system climate risk using a fuzzy logic modeling approach that connects climate hazards impacting marine and freshwater capture fisheries and aquaculture to their contributions to sustainable food system outcomes, and vulnerability to losing those contributions....

Anti-neoplastic characteristics and potential targets of calycosin against bisphenol A-related osteosarcoma: bioinformatics analysis

Qijin Pan, Ka Wu, Jiachang Tan, Yu Li, Xiao Liang & Min Su
Environmentally, bisphenol A (BPA) is a well-known pollutant caused human health risk, including osteosarcoma (OS). OS, a deadly bone neoplasia, may occur in children and adults. However, the anti-OS pharmacotherapy prescribes limitedly in clinical practice. Interestingly, previous experimental evidences indicate calycosin-exerting potential anti-OS actions. Thus, in this report, we aimed to further characterize and detail the therapeutic targets and molecular mechanisms of calycosin-anti-BPA-related OS by using network pharmacology and molecular docking analyses. In results, the...

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...

Drainage Canals in Southeast Asian Peatland

Nathan Dadap, Alison M Hoyt, Alexander R Cobb, Doruk Oner, Mateusz Kozinski, Pascal V Fua, Krishna Rao, Charles F Harvey & Alexandra G Konings
These images depict drainage canals and roads in peatlands in Borneo, Sumatra, and Peninsular Malaysia at 5 meter resolution. These canals were detected from July-September 2017 Planet Basemaps satellite imagery using a convolutional neural network. Please contact Nathan Dadap (ndadap@stanford.edu) with any questions.

How adaptive capacity shapes the Adapt, React, Cope Response to climate impacts: insights from small-scale fisheries

Jennifer Selgrath & Kristen Green
As the impacts of climate change on human society accelerate, coastal communities are vulnerable to changing environmental conditions. The capacity of communities and households to respond to these changes (i.e., their adaptive capacity) will determine the impacts of climate and co-occurring stressors. To date, empirical evidence linking theoretical measures of adaptive capacity to community and household responses remains limited. Here we conduct a global meta-analysis examining how metrics of adaptive capacity translate to human responses...

Modeling cross-linguistic production of referring expressions

Brandon Waldon & Judith Degen

Data from: Broad geographic sampling reveals predictable, pervasive, and strong seasonal adaptation in Drosophila

Heather E. Machado, Alan O. Bergland, Ryan Taylor, Susanne Tilk, Emily Behrman, Kelly Dyer, Daniel K. Fabian, Thomas Flatt, Josefa González, Talia L. Karasov, Iryna Kozeretska, Brian P. Lazzaro, Thomas JS Merritt, John E. Pool, Katherine O’Brien, Subhash Rajpurohit, Paula R. Roy, Stephen W. Schaeffer, Svitlana Serga, Paul Schmidt, Dmitri Petrov & Bernard Kim
To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identified parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. Seasonally fluctuating polymorphisms are enriched at...

Pragmatically Informative Color Generation by Grounding Contextual Modifiers

Zhengxuan Wu & Desmond C. Ong

Multilingual BERT, Ergativity, and Grammatical Subjecthood

Isabel Papadimitriou, Ethan A. Chi, Richard Futrell & Kyle Mahowald

Data: Avian cultural services peak in tropical wet forests

Alejandra Echeverri, Daniel Karp, Luke Frishkoff, Jaya Krishnan, Robin Naidoo, Jiaying Zhao, Jim Zook & Kai Chan
The current biodiversity crisis involves major shifts in biological communities at local and regional scales. The consequences for Earth’s life-support systems are increasingly well-studied, but knowledge of how community shifts affect cultural services associated with wildlife lags behind. We integrated bird census data (three years across 150 point-count locations) with questionnaire surveys (>400 people) to evaluate changes in culturally important species across climate and land-use gradients in Costa Rica. For farmers, urbanites, and birdwatchers alike,...

Predicting Scalar Inferences From \"Or\" to \"Not Both\" Using Neural Sentence Encoders

Elissa Li, Sebastian Schuster & Judith Degen

Data from: High-performance brain-to-text communication via handwriting

Francis Willett, Donald Avansino, Leigh Hochberg, Jaimie Henderson & Krishna Shenoy
Brain-computer interfaces (BCIs) can restore communication to people who have lost the ability to move or speak. In this study, we demonstrated an intracortical BCI that decodes attempted handwriting movements from neural activity in motor cortex and translates it to text in real-time, using a recurrent neural network decoding approach. With this BCI, our study participant, whose hand was paralyzed from spinal cord injury, achieved typing speeds that exceed those of any other BCI yet...

Phenotypic plasticity in plant defense across life stages: inducibility, transgenerational induction, and transgenerational priming in wild radish

Mar Sobral & Rodolfo Dirzo
As they develop, many plants deploy shifts in anti-herbivore defense allocation due to changing costs and benefits of their defensive traits. Plant defenses are known to be primed or directly induced by herbivore damage within generations, and across generations by long-lasting epigenetic mechanisms. However, little is known about the ontogenetic trajectories of epigenetically inducible defensive traits across generations and their consequences. To help fill this knowledge gap, we conducted a multigenerational experiment to determine whether...

Dataset: Charge order textures induced by non-linear couplings in a half-doped manganite

Ismail El Baggari, David Baek, Michael Zachman, Di Lu, Yasuyuki Hikita, Harold Hwang, Elizabeth Nowadnick & Lena Kourkoutis
Raw data associated with publication. The self-organization of strongly interacting electrons into superlattice structures underlies the properties of many quantum materials. How these electrons arrange within the superlattice dictates what symmetries are broken and what ground states are stabilized. Here we show that cryogenic scanning transmission electron microscopy (cryo-STEM) enables direct mapping of local symmetries and order at the intra-unit-cell level in the model charge-ordered system Nd1/2Sr1/2MnO3. In addition to imaging the prototypical site-centered charge...

Biological and chemical quantification of tadpole nurseries (phytotelmata)

Chloe Fouilloux, Shirley Jennifer Serrano-Rojas, Juan David Carvajal-Castro, Janne K. Valkonen, Philippe Gaucher, Marie-Therese Fischer, Andrius Pašukonis & Bibiana Rojas
Many species of Neotropical frogs have evolved to deposit their tadpoles in small water bodies inside plant structures called phytotelmata. These pools are small enough to exclude large predators but have limited nutrients and high desiccation risk. Here, we explore phytotelm use by three common Neotropical species: Osteocephalus oophagus, an arboreal frog that periodically feeds eggs to its tadpoles; Dendrobates tinctorius, a tadpole-transporting poison frog with cannibalistic tadpoles; and Allobates femoralis, a terrestrial tadpole-transporting poison...

Canadian university syllabuses with academic and non-academic assigned readings identified.

John Willinsky & Catherine Baron
In the context of the significant court battles that are being fought over the potential copyright infringement involved in distributing the articles and excerpts assigned to students in university courses, this study analyzes 3,391 course syllabuses (2015-2020) from nine provinces and 34 universities across Canada. It identifies the types and proportions of required readings among academic and non-academic sources. Academic readings are assigned on 26.6 percent of the syllabuses, compared to 8.3 percent of syllabuses...

Climate-driven limits to future carbon storage in California's wildland ecosystems

Shane Coffield, Kyle Hemes, Charles Koven, Michael Goulden & James Randerson
Enhanced ecosystem carbon storage is a key component of many climate mitigation pathways. The State of California has set an ambitious goal of carbon neutrality by 2045, relying in part on enhanced carbon sequestration in natural and working lands. We used statistical modeling, including random forests and climate analogues, to explore the climate-driven challenges and uncertainties associated with the goal of long-term carbon sequestration in forests and shrublands. We found that seasonal patterns of temperature...

Data: Similar neural and perceptual masking effects of low-power optogenetic stimulation in primate V1

Spencer Chen, Giacomo Benvenuti, Yuzhi Chen, Satwant Kumar, Charu Ramakrishnan, Karl Deisseroth, Wilson Geisler & Eyal Seidemann
Can direct stimulation of primate V1 substitute for a visual stimulus and mimic its perceptual effect? To address this question, we developed an optical-genetic toolkit to “read” neural population responses using widefield calcium imaging, while simultaneously using optogenetics to “write” neural responses into V1 of behaving macaques. We focused on the phenomenon of visual masking, where detection of a dim target is significantly reduced by a co-localized medium-brightness pedestal. Using our toolkit, we tested whether...

High-resolution mapping of the period landscape reveals polymorphism in cell cycle frequency tuning

Zhengda Li, Shiyuan Wang, Meng Sun, Minjun Jin, Daniel Khain & Qiong Yang
Biological oscillators adapt to environmental changes with widely tunable frequencies, a property theoretical studies attributed to positive feedbacks. However, no experiments have tested this theory. Here, we created synthetic cells to independently tune the frequency and feedback strength of a cell-cycle oscillator, enabling continuous mapping of period landscape in response to network perturbations. We found that although inhibiting positive feedback of cyclin-dependent kinase (Cdk1) reduces the tunability, the reduction is not as significant as theoretically...

Plasmodium infection is associated with cross-reactive antibodies to carbohydrate epitopes on the SARS-CoV-2 Spike protein

Sarah Lapidus, Feimei Liu, Arnau Casanovas-Massana, Yile Dai, John D. Huck, Carolina Lucas, Jon Klein, Renata B. Filler, Madison S. Strine, Mouhamad Sy, Awa B. Deme, Aida S. Badiane, Baba Dieye, Ibrahima Mbaye Ndiaye, Younous Diedhiou, Amadou Moctar Mbaye, Cheikh Tidiane Diagne, Inés Vigan-Womas, Alassane Mbengue, Bacary D. Sadio, Moussa M. Diagne, Adam J. Moore, Khadidiatou Mangou, Fatoumata Diallo, Seynabou D. Sene … & Amy K. Bei
Sero-surveillance can monitor and project disease burden and risk. However, SARS-CoV-2 antibody test results can produce false positive results, limiting their efficacy as a sero-surveillance tool to estimate population-level SARS-CoV-2 exposure. False positive SARS-CoV-2 antibody results have been associated with malaria exposure, and understanding this association is essential to interpret sero-surveillance results from malaria-endemic countries. Here, pre-pandemic samples from eight malaria endemic and non-endemic countries and four continents were tested by ELISA to measure SARS-CoV-2...

Predictability and parallelism in the contemporary evolution of hybrid genomes

Quinn K. Langdon, Daniel L. Powell, Bernard Kim, Shreya M. Banerjee, Cheyenne Payne, Tristram O. Dodge, Ben Moran, Paola Fascinetto-Zago & Molly Schumer
Hybridization between species is widespread across the tree of life. As a result, many species, including our own, harbor regions of their genome derived from hybridization. Despite the recognition that this process is widespread, we understand little about how the genome stabilizes following hybridization, and whether the mechanisms driving this stabilization tend to be shared across species. Here, we dissect the drivers of variation in local ancestry across the genome in replicated hybridization events between...

Registration Year

  • 2021
    146

Resource Types

  • Dataset
    104
  • Text
    32
  • Image
    4
  • Collection
    2
  • Interactive Resource
    2
  • Journal Article
    1
  • Software
    1

Affiliations

  • Stanford University
    146
  • Chinese Academy of Sciences
    31
  • Huazhong University of Science and Technology
    30
  • Capital Medical University
    30
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    30
  • Sichuan University
    28
  • Fudan University
    24
  • University of Chinese Academy of Sciences
    24
  • Shanghai Jiao Tong University
    23
  • Chinese PLA General Hospital
    23