cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2v6wwpzp2
title: The new normal? Redaction bias in biomedical science

description: A concerning amount of biomedical research is not reproducible. Unreliable
 results impede empirical progress in medical science, ultimately putting
 patients at risk. Many proximal causes of this irreproducibility have been
 identified, a major one being inappropriate statistical methods and
 analytical choices by investigators. Within this, we formally quantify the
 impact inappropriate redaction beyond a threshold value in biomedical
 science. This is effectively truncation of a data-set by removing extreme
 data points, and we elucidate its potential to accidentally or
 deliberately engineer a spurious result in significance testing. We
 demonstrate that the removal of a surprisingly small number of data points
 can be used to dramatically alter a result. It is unknown how often
 redaction bias occurs in the broader literature, but given the risk of
 distortion to the literature involved, we suggest that it must be
 studiously avoided, and mitigated with approaches to counteract any
 potential malign effects to the research quality of medical science.
description: The code herein consists of the Mathematica notebook file that
 faciliates direct derivation of the equations employed in the manuscript,
 and the raw data used to generate the illustrative examples (MATLAB /
 OCTAVE code).
description: Notebook can be executed as in inside Mathematica, or using
 Mathematica's stand alone player. The MATLAB .m files can be deployed
 in MATLAB or in OCTAVE.
DOI: 10.5061/dryad.931zcrjks
title: Green spectrophotometric analysis data for the assay of betrixaban and lercanidipine

description: Three facile, accurate, and eco-friendly spectrophotometric methods were
 developed for determination of the novel anticoagulant drug, betrixaban
 (BTX). The first method (method A) was based on the unique UV absorption
 spectrum of BTX, where direct analysis of BTX was performed at 229.4nm on
 the recorded zero order spectrum using methanol as the optimum solvent.
 While the second method(method B) was based on measuring difference
 absorption value(DA) of BTX at 335nm, which was obtained from pH-induced
 spectral difference (Difference spectra of BTX in 0.1M NaOH versus 0.1M
 HCl). The third mathematical spectrophotometric method (method C) was
 established for simultaneous analysis of BTX with the co-administered Ca
 channel blocker lercanidipine (LER). In this method, the first order
 derivative technique was utilized to resolve the overlapping UV spectra of
 both drugs. The first derivative amplitudes at 206nm and 229nm were used
 for quantitative assay of BTX and LER, respectively. All methods obeyed
 Beer’s law in the concentration ranges of 1.0–20.0µg.mL-1 and 8.0–80.0
 µg.mL-1 for BTX in methods A and B, respectively, and of 1.0–20.0 µg.mL-1
 and 1.0–25.0µg.mL-1 for BTX and LER, respectively in method C. The three
 methods were fully validated, and the results showed good agreement with
 the other compared ones where high %recoveries and low values of RSD
 (&lt;1.5%) were obtained. Moreover, the green profile of the proposed
 methods was assessed by using two approaches: analytical eco-scale and
 green analytical procedure index. The results indicated that method B was
 the greenest one because hazardous organic solvents were avoided. Both
 methods A and C have analytical eco-scale scores of 85 which indicated the
 greenness of these methods as well. The absence of interferences
 that could be produced from encountered additives, excipients, or
 degradation products ensured the high specificity of the proposed methods
 and supported their applicability in quality control laboratories.
DOI: 10.5061/dryad.wstqjq2n2
title: Out from under the wing: reconceptualizing the insect wing gene regulatory network as a versatile, general module for body-wall lobes in arthropods

description: Body plan evolution often occurs through the differentiation of serially
 homologous body parts, particularly in the evolution of arthropod body
 plans. Recently, homeotic transformations resulting from experimental
 manipulation of gene expression have been interpreted as evidence that
 portions of dorsal and lateral arthropod body-wall are serially homologous
 to wings. These results, along with comparative data on the expression and
 function of genes in the wing regulatory network, provided a new
 perspective on an old question in insect evolution—how did the insect
 wing, evolve? A proposed ancestral role for the wing regulatory network in
 patterning body-wall margins motivated a broader comparison of gene
 function in wings and body-wall. We investigated the roles of a suite of
 ten wing- and body-wall related genes in a hemimetabolous insect,
 Oncopeltus fasciatus. Our results indicate that genes involved in wing
 development in O. fasciatus play similar roles in the development of adult
 body-wall flattened cuticular evaginations. We found extensive functional
 similarity between the development of wings and other bilayered
 evaginations of the body wall. Overall, our results support the existence
 of a versatile development module for building bilayered cuticular
 epithelial structures, which may have played a central role in the
 evolution of wings.
description: Data were collected by scoring emerged adults and pharate nymphs
 across a matrix of characters. Scoring was binary - 1 = affected and 0 =
 wild-type. Scoring was performed by two researchers. After scoring was
 completed, an R script was used to filter down to "informative"
 individuals -- those that presented at least one relevant character as
 scoreable -- and to aggregate information across different characters that
 were subparts of larger relevant characters. The raw data, Rscript, R
 session info, and processed data are provided along with subsets of the
 raw data that made up the "informative" data sets for each
 relevant character.
description: A markdown README file is provided. It details the full file
 manifest available at the github repository, https://github.com/fishercera/oncopeltus_RNAI
DOI: 10.5061/dryad.547d7wm8q
title: Data from: Using singleton densities to detect recent selection in Bos taurus

description: Many quantitative traits are subject to polygenic selection, where several
 genomic regions undergo small, simultaneous changes in allele frequency
 that collectively alter a phenotype. The widespread availability of genome
 data, along with novel statistical techniques, has made it easier to
 detect these changes. We apply one such method, the ‘Singleton Density
 Score’, to the Holstein breed of Bos taurus to detect recent selection
 (arising up to around 740 years ago). We identify several genes as
 candidates for targets of recent selection, including some relating to
 cell regulation, catabolic processes, neural-cell adhesion and immunity.
 We do not find strong evidence that three traits that are important to
 humans – milk protein content, milk fat content, and stature ­– have been
 subject to directional selection. Simulations demonstrate that since B.
 taurus recently experienced a population bottleneck, singleton numbers are
 reduced limiting the power of SDS methods. These results inform on which
 genes underlie recent genetic change in B. taurus, while providing
 information on how polygenic selection can be best investigated in future
 studies.
description: This depository contains (i) SDS scores for Bos taurus, Holstein
 breed autosomes, excluding Chromosome 25; (ii) polarisation information
 for Bos taurus SNPs. Further details on the methods are available in the
 publication.
description: This depository contains the raw data only. Scripts for analysing
 the data are available from
 https://github.com/MattHartfield/CattleSDS.
DOI: 10.5061/dryad.dz08kprz7
title: Data for: Inhibition of Ca2+-triggered secretion by hydrocarbon-stapled peptides

description: Ca2+-triggered membrane fusion is orchestrated by a conserved set of
 proteins to mediate synaptic neurotransmitter release, mucin secretion,
 and other regulated exocytic processes. For neurotransmitter release, the
 Ca2+ sensitivity is introduced by interactions between the
 Ca2+ sensor synaptotagmin and the SNARE complex, and sequence
 conservation and functional studies suggest this mechanism is also
 conserved for mucin secretion. Disruption of Ca2+-triggered membrane
 fusion by a pharmacologic agent would have therapeutic value for mucus
 hypersecretion since it is the major cause of airway obstruction in the
 pathophysiology of respiratory viral infection, asthma, COPD and cystic
 fibrosis. We designed a hydrocarbon-stapled peptide that specifically
 disrupts Ca2+-triggered membrane fusion by interfering with the so-called
 primary interface between the neuronal SNARE complex and
 Ca2+ binding C2B domain of synaptotagmin-1. In reconstituted
 systems with these neuronal synaptic proteins or with their airway
 homologues syntaxin-3, SNAP-23, VAMP8, synaptotagmin-2, along with
 Munc13-2 and Munc18-2, the stapled peptide strongly suppressed
 Ca2+-triggered fusion at physiological Ca2+ concentrations.
 Conjugation of cell penetrating peptides to the stapled peptide resulted
 in efficient delivery into cultured human airway epithelial cells and
 mouse airway epithelium, where it markedly and specifically reduced
 stimulated mucin secretion in both systems, and substantially attenuated
 mucus occlusion of mouse airways. Taken together, peptides that disrupt
 Ca2+-triggered membrane fusion may allow therapeutic modulation of mucin
 secretory pathways. This data set contains the imaging data for the
 studies of primary human airway epithelial cells (HAECs), for the mucin
 secretion and airway mucus occlusion studies in mice, and the NAMD input
 files and trajectories of the molecular dynamics simulations.
description: There are individual README files in each of the
 directories.
DOI: 10.5061/dryad.mkkwh7116
title: Disparities in pediatric patient portal adoption and feature use

description: Objective: Disparities in adult patient portal adoption are
 well-documented; however, less is known about disparities in portal
 adoption in pediatrics. This study examines the prevalence and factors
 associated with patient portal activation and use of specific portal
 features in general pediatrics. Materials and Methods: We analyzed
 electronic health record (EHR) data from 2012-2020 in a large academic
 medical center that offers both parent and adolescent portals. We
 summarized portal activation and use of select portal features (messaging,
 records access and management, appointment management, visit/admissions
 summaries, and interactive feature use). We used logistic regression to
 model factors associated with patient portal activation among all patients
 along with feature use and frequent feature use among ever users (i.e., ≥1
 portal use). Results: Among 52,713 unique patients, 39% had activated the
 patient portal, including 36% of patients aged 0-11, 41% of patients aged
 12-17 and 62% of patients aged 18-21 years. Among activated accounts, ever
 use of specific features ranged from 28% for visit/admission summaries to
 92% for records access and management. Adjusted analyses showed patients
 with activated accounts were more likely to be adolescents or young
 adults, white, female, privately insured, and less socioeconomically
 vulnerable. Individual feature use among ever users generally followed the
 same pattern. Conclusions: Our findings demonstrate that important
 disparities persist in portal adoption in pediatric populations,
 highlighting the need for strategies to promote equitable access to
 patient portals.
description: We obtained patient-level data from the electronic health record
 (EHR) for all general pediatric patient visits between September 1, 2012
 and July 30, 2020. General pediatrics clinics included primary care and
 associated outpatient clinics. We geocoded patient addresses to identify
 residential census tract, which was linked to the socioeconomic
 vulnerability (SEV) measure. All variables were assessed at the time of
 the most recent visit.
description: No more than 3% of the data had missing values for race and
 ethnicity. A total of 2.2% of patients lived outside of Florida and were
 not geocoded. Among Florida residents, 1,679 gave a postal office box and
 31 declined to give a residential address. These records could not be
 assigned to a census tract or SEV value. The remaining 43,221 records with
 residential addresses were geocoded to residential street and census
 tract.
DOI: 10.5061/dryad.3ffbg79jf
title: Data from: Monitoring soil moisture at the catchment scale – A novel approach combining antecedent precipitation index and radar-derived rainfall data

description: Knowledge about soil moisture is important for event-based rainfall-runoff
 models but monitoring conditions at the catchment scale is not a trivial
 task. Soil moisture is highly variable in space and time, particularly in
 dry climates with seasonal and spatially heterogeneous rainfall. Point
 measurements are difficult to upscale, and remotely sensed (RS) data often
 lack in spatial or temporal resolution for local or regional studies.
 Longer latency periods – the time required before data becomes available –
 of some RS data make them less applicable to time-sensitive analyses such
 as flash flood forecasting. This study evaluated a novel approach for
 estimating catchment-scale volumetric soil moisture using an antecedent
 precipitation index (API) -based model. The model was trained and tested
 using in-situ soil moisture measurements collected during a 3-month field
 sampling campaign in a 142 km2 study area in central New
 Mexico. The calibrated model was applied at the catchment scale to produce
 soil moisture grids from radar-derived rainfall estimates. Model
 performance, resolution and latency were compared to satellite-based soil
 moisture estimates. Benefits of the proposed new method include high
 spatial resolution (1 × 1 km or less depending
 on the precipitation data source) and high prediction accuracy (root mean
 square errors 0.014–0.018 m3/m3). Given the short latency period
 for radar-derived rainfall data, the method has potential for use in
 operational flood risk assessment and forecasting.
description: This dataset contains soil moisture measurements collected at 25
 locations in central New Mexico on 15 separate sampling days between June
 25 and October 7, 2019. Volumetric moisture content
 (m<sup>3</sup>/m<sup>3</sup>) was measured for
 depths of 0-7.5 cm and 7.5-15 cm using a portable time-domain
 reflectometer calibrated to in-situ soil conditions.
DOI: 10.15468/dl.4yt4jn
title: Occurrence Download

description: A dataset containing 12466 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Platalea minor",
 "Year 2021-2026"
 ]
}

 The dataset includes 12466 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002924-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hhmgqnkhd
title: Capture-recapture dataset of Svalbard voles (1990-2007) with trap locations and rain-on-snow measurements

description: Ecologists are still puzzled by the diverse population dynamics of
 herbivorous small mammals that range from high-amplitude, multi-annual
 cycles to stable dynamics. Theory predicts that this diversity results
 from combinations of climatic seasonality, weather stochasticity and
 density-dependent food web interactions. The almost ubiquitous 3-5-yr
 cycles in boreal and arctic climates may theoretically result from
 bottom-up (plant-herbivore) and top-down (predator-prey) interactions.
 Assessing empirically the roles of such interactions, and how they are
 influenced by environmental stochasticity, has been hampered by food web
 complexity. Here, we take advantage of a uniquely simple High-Arctic food
 web, which allowed us to analyze dynamics of a graminivorous vole
 population not subjected to top-down regulation. This population exhibited
 high-amplitude, non-cyclic fluctuations - partly driven by weather
 stochasticity.  However, the predominant driver of the dynamics
 was overcompensatory density dependence in winter that caused the
 population to frequently crash. Model simulations showed that the seasonal
 pattern of density dependence would yield regular 2-year cycles in absence
 of stochasticity. While such short cycles have not yet been observed in
 mammals, they are theoretically plausible if graminivorous vole
 populations are deterministically bottom-up regulated. When incorporating
 weather stochasticity in the model simulations, cyclicity became disrupted
 and the amplitude was increased - akin to the observed
 dynamics. Our findings contrast with the 3-5-yr population cycles
 that are typical of graminivorous small mammals in more complex food webs,
 suggesting that top-down regulation is normally an important component of
 such dynamics.
description: This capture-recapture dataset of Sibling voles was collected
 near Grumant, Svalbard from 1990 to 2007. For more details, please consult
 the associated article published in Proceedings of the National Academy of
 Science of the United-States.
DOI: 10.5061/dryad.ncjsxksvt
title: Marbled Murrelets prefer stratified waters close to freshwater inputs in Haida Gwaii, BC, Canada

description: The Marbled Murrelet (Brachyramphus marmoratus) is a small seabird that is
 currently listed as threatened in Canada. Understanding this species’
 marine habitat preferences plays a vital role in our ability to focus
 conservation planning. We used the longest-running at-sea survey dataset
 available in British Columbia to examine hotspot persistence and habitat
 use at Laskeek Bay, Haida Gwaii, BC. The Laskeek Bay Conservation Society
 has been conducting spring and summer surveys along fixed transect routes
 in open and shoreline waters from 1997‒2018. Along with analyzing this
 long-term dataset, we conducted surveys to measure oceanographic variables
 (2018–2019) and tested whether murrelets in the same area used prey and
 oceanographic information to select marine habitat in conjunction with
 physical habitat features. Our hotspot persistence map, defined as areas
 that repeatedly had counts above a 75% threshold relative to other areas
 during a given survey, showed that murrelets consistently preferred
 shoreline transects. Murrelets also preferred shallow marine areas closer
 to streams, above higher proportions of sandy substrate and closer
 proximity to abundant nesting habitat. Modeling weather and time variables
 contributed little additional predictive power. Nonetheless, models that
 included physical environmental, oceanographic, and prey variables
 outperformed those with only physical environmental variables. Stratified
 water was the oceanographic variable most strongly related to higher
 counts. Our study suggests that stratified waters could work with stream
 systems to create productive zones for foraging murrelets, and highlights
 the importance of murrelets having access to marine areas with the
 preferred physical features.
DOI: 10.25338/b83g9n
title: Implementing social network analysis to understand the socio-ecology of wildlife co-occurrence and joint interactions with humans in anthropogenic environments

description: 1. Human population expansion into wildlife habitats has increased
 interest in the behavioral ecology of human-wildlife interactions. To
 date, however, the socio-ecological factors that determine whether, when
 or where wild animals take risks by interacting with humans and
 anthropogenic factors still remains unclear. 2. We adopt a comparative
 approach to address this gap, using social network analysis (SNA). SNA,
 increasingly implemented to determine human impact on wildlife ecology,
 can be a powerful tool to understand how animal socioecology influences
 the spatiotemporal distribution of human-wildlife interactions. 3. For 10
 groups of rhesus, long-tailed, and bonnet macaques (Macaca spp.) living in
 anthropogenically-impacted environments in Asia, we collected data on
 human-macaque interactions, animal demographics, and macaque-macaque
 agonistic and affiliative social interactions. We constructed ‘human
 co-interaction networks’ based on associations between macaques that
 interacted with humans within the same time and spatial locations, and
 social networks based on macaque-macaque allogrooming behavior,
 affiliative behaviors of short duration (agonistic support, lip-smacking,
 silent bare-teeth displays, and non-sexual mounting), and proximity. 4.
 Pre-network permutation tests revealed that, within all macaque groups,
 specific individuals jointly took risks by repeatedly, consistently
 co-interacting with humans within and across time and space. GLMMs
 revealed that macaques’ tendencies to co-interact with humans was
 positively predicted by their tendencies to engage in short-duration
 affiliative interactions and tolerance of conspecifics, although the
 latter varied across species (bonnets&gt;rhesus&gt;long-tailed).
 Male macaques were more likely to co-interact with humans than females.
 Neither macaques’ grooming relationships nor their dominance ranks
 predicted their tendencies to co-interact with humans. 5. Our findings
 suggest that, in challenging anthropogenic environments, less (compared to
 more) time-consuming forms of affiliation, and additionally greater social
 tolerance in less ecologically flexible species with a shorter history of
 exposure to humans, may be key to animals’ joint propensities to take
 risks to gain access to resources. For males, greater exploratory
 tendencies and less energetically demanding long-term life-history
 strategies (compared to females), may also influence such joint
 risk-taking. From conservation and public health perspectives, wildlife
 connectedness within such co-interaction networks may inform interventions
 to mitigate zoonosis, and move human-wildlife interactions from conflict
 towards co-existence.
DOI: 10.5061/dryad.vhhmgqnv5
title: Targeting metabotropic glutamate receptor 4 for cancer immunotherapy

description: The complex mechanism regulating the immunosuppressive tumor
 microenvironment (TME) remains poorly understood. Here,
 we reported a novel role of the metabotropic glutamate
 receptor-4 (GRM4) in suppressing the anti-tumor immunity. We revealed in
 three murine syngeneic tumor models (B16, MC38, and 3LL) that either
 genetic knockout (Grm4−/−) or pharmacological inhibition led to
 significant delay in tumor growth and synergized with immune checkpoint
 inhibitors in male mice. Mechanistically, perturbation of GRM4 resulted in
 a strong anti-tumor immunity by promoting nature killer (NK),
 CD4+ and CD8+ T cells towards an activated,
 proliferative, and functional phenotype. Single-cell RNA-sequencing and T
 Cell Receptor (TCR) profiling further defined the clonal expansion and
 immune landscape changes in CD8+ T cells.
 Mechanistically, Grm4-/- intrinsically activated
 IFN-g production in CD8+ T cells through
 cAMP/CREB-mediated pathway. Our study appears to be of clinical
 significance as a signature of NKhigh-GRM4low and
 CD8high-GRM4low correlated with improved survival in melanoma
 patients. Therefore, targeting GRM4 could be exploited as a new approach
 for cancer immunotherapy. 
description: KO refers to Grm4<sup>-/- </sup>Mice