22 Works

Data from: Strong effects of lab-to-field environmental transitions on the bacterial intestinal microbiota of Mus musculus are modulated by Trichuris muris infection

Julian Bär, Jacqueline Leung, Christina Hansen, P'ng Loke, Alex Hall, Laura Conour & Andrea Graham
Studies of controlled lab animals and natural populations represent two insightful extremes of microbiota research. We bridged these two approaches by transferring lab-bred female C57BL/6 mice from a conventional mouse facility to an acclimation room and then to an outdoor enclosure, to investigate how the gut microbiota changes with environment. Mice residing under constant conditions served as controls. Using 16S rRNA sequencing of fecal samples, we found that the shift in temperature and humidity, as...

Anonymized source data files for figures in: Recurrent processes support a cascade of hierarchical decisions

Laura Gwilliams & Jean-Remi King
Perception depends on a complex interplay between feedforward and recurrent processing. Yet, while the former has been extensively characterized, the computational organization of the latter remains largely unknown. Here, we use magneto-encephalography to localize, track and decode the feedforward and recurrent processes of reading, as elicited by letters and digits whose level of ambiguity was parametrically manipulated. We first confirm that a feedforward response propagates through the ventral and dorsal pathways within the first 200...

US and Canada Public Pension System Data 2008-2018

Ingo Walter, Clive Lipshitz, Fernando Falbo, Patricio Cox & Lebogang Mahlare
This dataset comprises eleven years of historical data (2008 through 2018) for the 25 largest U.S. public pension plans and the ten largest Canadian public pension plans.

Modeling Morphological Processing in Human Magnetoencephalography

Yohei Oseki & Alec Marantz

BLiMP: A Benchmark of Linguistic Minimal Pairs for English

Alex Warstadt, Alicia Parrish, Haokun Liu, Anhad Mohananey, Wei Peng, Sheng-Fu Wang & Samuel R. Bowman

Awareness and empowerment in document production and distribution as a “must” for open access: experiences from the “Nancy style” to guarantee quality

Paola De Castro, Sandra Salinetti & Marcus Banks
Co-authored together with Sandra Salinetti and Marcus Banks. - The debate on Grey Literature (GL) has now a very long tradition going from uncertainty and confusion, in the last century, to new certainties and appraisal in the open access era. This implies the general acquisition of the awareness of the importance of GL as a fundamental primary source of information, hence the necessity to empower authors and issuing organization to guarantee quality in both production...

Implications of copyright evolution for the future of scholarly communication and grey literature

Marcus Banks & Cees De Blaaij
Traditional practices regarding copyright are undergoing transformation. Although it is still common for scholars to give up their rights to their articles so that they will be published, this happens less frequently than it once did. Our analysis of the RoMEO database [1] shows that 75% of publishers allow authors to post their work in an online repository, whether that repository is hosted by their institution or on a personal web page. Whatever becomes of...

Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features

Charles Roseman, Terrence Capellini, Evelyn Jagoda, Scott Williams, Mark Grabowski, Christine O'Connor, John Polk & James Cheverud
Variation in pelvic morphology has a complex genetic basis and its patterning and specification is governed by conserved developmental pathways. Whether the mechanisms underlying the differentiation and specification of the pelvis also produce the morphological covariation on which natural selection may act is still an open question in evolutionary developmental biology. We use high-resolution Quantitative Trait Locus (QTL) mapping in the F34 generation of an advanced intercross experiment (LG,SM-G34) to characterize the genetic architecture of...

Archives and Special Collections Linked Data: Navigating between Notes and Nodes

Erin Blake, Itza A. Carbajal, Regine Heberlein, Sarah Horowitz, Jason Kovari, VANESSA LACEY, Cory Lampert, Holly Mengel, Cory Nimer, Maria Oldal, Merrilee Proffitt, Nathan Putnam, Arielle Rambo, Elizabeth Roke, Eric de Ruijter, Dan Santamaria, Karen Smith-Yoshimura, Weatherly Stephan, Bruce Washburn & Chela Weber

Dataset for the transcriptome analysis of hippocampal subfields identifies gene expression profiles associated with long-term active place avoidance memory

Rayna Harris, Hsin-Yi Kao, Juan Marcos Alarcon, André Fenton & Hans Hofmann
The hippocampus plays a critical role in storing and retrieving spatial information. By targeting the dorsal hippocampus and manipulating specific “candidate” molecules using pharmacological and genetic manipulations, we have previously discovered that long-term active place avoidance memory requires transient activation of particular molecules in dorsal hippocampus. These molecules include amongst others, the persistent kinases Ca-calmodulin kinase II (CaMKII) and the atypical protein kinase C isoform PKC iota/lambda for acquisition of the conditioned behavior, whereas persistent...

Acquisition of Inflectional Morphology in Artificial Neural Networks With Prior Knowledge

Katharina Kann

Disentangling ecological and taphonomic signals in ancient food webs

Jack Shaw, Emily Coco, Kate Wootton, Dries Daems, Andrew Gillreath-Brown, Anshuman Swain & Jennifer Dunne
Analyses of ancient food webs reveal important paleoecological processes and responses to a range of perturbations throughout Earth’s history, such as climate change. These responses can inform our forecasts of future biotic responses to similar perturbations. However, previous analyses of ancient food webs rarely accounted for key differences between modern and ancient community data, particularly selective loss of soft-bodied taxa during fossilization. To consider how fossilization impacts inferences of ancient community structure we (1) analyzed...

Female ornaments: is red skin color attractive to males and related to condition in rhesus macaques?

James Higham, Clare Kimock, Tara Mandalaywala, Michael Heistermann, Julie Cascio, Megan Petersdorf, Sandra Winters, Will Allen & Constance Dubuc
Sexual selection produces extravagant male traits, such as colorful ornaments, via female mate choice. More rarely, in mating systems in which males allocate mating effort between multiple females, female ornaments may evolve via male mate choice. Females of many anthropoid primates exhibit ornaments that indicate intra-individual cyclical fertility, but which have also been proposed to function as inter-individual quality signals. Rhesus macaque females are one such species, exhibiting cyclical facial color variation that indicates ovulatory...

Domestication phenotype linked to vocal behavior in marmoset monkeys

Asif Ghazanfar, Lauren Kelly, Daniel Takahashi, Sandra Winters, Rebecca Terrett & James Higham
The domestication syndrome refers to a set of traits that are the incidental by-products of artificial selection for increased tolerance towards humans. One hypothesis is that some species like humans and bonobos “self domesticated”, that they have been under selection for that same suite of domesticated phenotypes. However, the evidence for this has been largely circumstantial. Here, we provide evidence that in marmoset monkeys, the size of a domestication phenotype—a white facial fur patch—is linked...

Data from: Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction

Anand Ranjan, Vu Q. Nguyen, Sheng Liu, Jan Wisniewski, Kim Jee Min, Xiaona Tang, Gaku Mizuguchi, Vivian Jou, Timothy J. Nickels, Brian P. English, Qinsi Zheng, Ed Luk, Timothee Lionnet, Luke D. Lavis, Carl Wu & Ejlal Elalaoui
The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. H2A.Z is deposited by the SWR1 chromatin remodeler and evicted by unclear mechanisms. We tracked H2A.Z in living yeast at single-molecule resolution, and found that H2A.Z eviction is dependent on RNA Polymerase II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of heptapeptide repeats on the carboxy-terminal domain of the largest Pol II subunit...

SARS-CoV-2 Hotspots in NYC: Risk of City-Wide Resurgence and Impact of Policies

Hae-Young Kim, Anna Bershteyn, Jessica McGillen & Ronald Scott Braithwaite

Could a Mass Testing Campaign or a Brief Shutdown Avoid a Second SARS-CoV-2 Wave in NYC?

Anna Bershteyn, Hae-Young Kim, Jessica McGillen & Ronald Scott Braithwaite

Urinary suPAR: a non-invasive biomarker of infection and tissue inflammation for use in studies of large free-ranging mammals

James Higham, Christiane Stahl-Hennig & Michael Heistermann
Studies of large free-ranging mammals incorporating physiological measurements typically require the collection of urine or faecal samples, due to ethical and practical concerns over trapping or darting animals. However, there is a dearth of validated biomarkers of immune activation and inflammation that can be measured non-invasively. We here evaluate the utility of urinary measurements of the soluble form of the urokinase plasminogen activator receptor (suPAR), for use as a health marker in studies of wild...

Dynamic expression of MMP28 during cranial morphogenesis

Nadege Gouignard
Matrix metalloproteinases (MMP) are a large family of proteases comprising 24 members in vertebrates. They are well known for their extracellular matrix remodelling activity. MMP28 is the last member of the family to be discovered. It is a secreted MMP involved in wound healing, immune system maturation, cell survival and migration. MMP28 is also expressed during embryogenesis in human and mouse. Here we describe the detailed expression profile of MMP28 in Xenopus laevis embryos. We...

Movement Tracing of Patients Recovering from COVID in New York City, 2020

Debra Laefer
This shapefile layer and associated datasets represent the movements of patients after they had been released from various healthcare facilities in New York during the onset of the COVID-19 outbreak in New York City during late-March and early-April, 2020. A team of field researchers recorded movements and observations, which have been aggregated to a shapefile layer for analysis. This data is released with an Attribution 4.0 International (CC BY 4.0) license. Please consult the documentation...

Effects of tidal influence on the structure and function of prokaryotic communities in the sediments of a pristine Brazilian mangrove

Pieter Spealman, Carolina Santana, David Gresham, Vânia Maria Maciel Melo, Taíse Bomfim De Jesus & Fabio Alexandre Chinalia
Mangrove forests are ecosystems that constitute a large portion of the world’s coastline and span tidal zones below, between, and above the waterline, while the ecosystem as a whole is defined by the health of these tidal microhabitats. However, we are only beginning to understand tidal zone microbial biodiversity and the role of these microbiomes in nutrient cycling. While extensive research has characterized microbiomes in pristine versus anthropogenically impacted mangroves these have, largely, overlooked differences...

Cortical encoding of melodic expectations in human temporal cortex

Giovanni Di Liberto, Claire Pelofi, Roberta Bianco, Prachi Patel, Ashesh D Mehta, Jose L Herrero, Alain De Cheveigné, Shihab A Shamme & Nima Mesgarani
Humans engagement in music rests on underlying elements such as the listeners’ cultural background and interest in music. These factors modulate how listeners anticipate musical events, a process inducing instantaneous neural responses as the music confronts these expectations. Measuring such neural correlates would represent a direct window into high-level brain processing. Here we recorded cortical signals as participants listened to Bach melodies. We assessed the relative contributions of acoustic versus melodic components of the music...

Registration Year

  • 2020
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Affiliations

  • New York University
    22
  • Princeton University
    3
  • The University of Texas at Austin
    2
  • Columbia University
    2
  • University of Maryland, Baltimore
    2
  • SUNY Downstate Medical Center
    1
  • Howard Hughes Medical Institute
    1
  • University of Massachusetts Amherst
    1
  • University of Pennsylvania
    1
  • Waseda University
    1