cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25740/kx198qv1232
title: 16S and Sanger Sequencing, and Proteomics for "Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota"

description: Efforts to probe the role of gut microbiota in disease would benefit from a system in which patient-derived bacterial communities can be studied at scale. We addressed this by validating a strategy to propagate phylogenetically complex, diverse, stable, and highly reproducible stool-derived communities in vitro. We generated hundreds of in vitro communities cultured from diverse stool samples in various media; certain media generally preserved inoculum composition, and inocula from different subjects yielded source-specific community compositions. Upon colonization of germ-free mice, community composition was maintained and host proteome resembled the host from which the community was derived. Treatment with ciprofloxacin in vivo increased susceptibility to Salmonella invasion in vitro and the in vitro response to ciprofloxacin was predictive of compositional changes observed in vivo, including the resilience and sensitivity of each Bacteroides species. These findings demonstrate that stool-derived in vitro communities can serve as a powerful system for microbiota research.
DOI: 10.3535/8ly-59m-13s
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/37j-nty-yk0
title: Tethysbaena atlantomaroccana (Boutin & Cals, 1985)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6w8-qz5-9pk
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/hn961zj6005
title: Data used in arcticle "Increases in Arctic sea ice bottom algal habitat, 1985-2018"

description: Data used in arcticle "Increases in Arctic sea ice bottom algal habitat, 1985-2018"
DOI: 10.3535/8qc-znq-zs6
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jml-00v-mlf
title: Paraeuchaeta aequatorialis Tanaka, 1958

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/ct503zg9433
title: 16S rRNA data and sample metadata for "Optimization of the 16S rRNA sequencing analysis pipeline for studying in vitro communities of gut commensals"

description: This repository contains raw data for the manuscript "Optimization of the 16S rRNA sequencing analysis pipeline for studying in vitro communities of gut commensals". 
While microbial communities inhabit a wide variety of complex natural environments, in vitro culturing enables highly controlled conditions and high-throughput interrogation for generating mechanistic insights. In vitro assemblies of gut commensals have recently been introduced as models for the intestinal microbiota, which plays fundamental roles in host health. However, a protocol for 16S rRNA sequencing and analysis of in vitro samples that optimizes financial cost, time/effort, and accuracy/reproducibility has yet to be established. Here, we systematically identify protocol elements that have significant impact, introduce bias, and/or can be simplified. Our results indicate that community diversity and composition are generally unaffected by substantial protocol streamlining. Additionally, we demonstrate that a strictly aerobic halophile is an effective spike-in for estimating absolute abundances in communities of anaerobic gut commensals. This time- and money-saving protocol should accelerate discovery by increasing 16S rRNA data reliability and comparability and through the incorporation of absolute abundance estimates.
DOI: 10.25740/gw191zv5762
title: Foreign Intelligence Surveillance Act notices and recipients, 1990-2020

description: An exhaustive collection of all Foreign Intelligence Surveillance Act (FISA) notices, 1990-2020, with enriched data on notice recipients and litigation.
DOI: 10.25740/sy352sf3635
title: Unrestricted data and statistical code for the findings presented in Hwang, J. and T. McDaniel. 2022. "Racialized Reshuffling: Urban Change and the Persistence of Segregation in the Twenty-First Century"

description: Replication material for Hwang, J. and T. McDaniel. 2022. "Racialized Reshuffling: Urban Change and the Persistence of Segregation in the Twenty-First Century". Annual Review of Sociology. 48:XX-XX.
DOI: 10.3535/bqq-vck-536
title: Paraeuchaeta aequatorialis Tanaka, 1958

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/sq515dd6404
title: Nova, N., Pagliara, R., Gordon, D. M. Individual variation does not regulate foraging response to humidity in harvester ant colonies. Frontiers Ecology and Evolution.

description: Differences among groups in collective behavior may arise from responses that all group members share, or instead from differences in the distribution of individuals of particular types. We examined whether the collective regulation of foraging behavior in colonies of the desert red harvester ant (Pogonomyrmex barbatus) depends on individual differences among foragers. Foragers lose water while searching for seeds in hot, dry conditions, so colonies regulate foraging activity in response to humidity. In the summer, foraging activity begins in the early morning when humidity is high, and ends at midday when humidity is low. We investigated whether individual foragers within a colony differ in the decision whether to leave the nest on their next foraging trip as humidity decreases, by tracking the foraging trips of marked individuals. We found that individuals did not differ in response to current humidity. No ants were consistently more likely than others to stop foraging when humidity is low. Each day there is a skewed distribution of trip number: only a few individuals make many trips, but most individuals make few trips. We found that from one day to the next, individual foragers do not show any consistent tendency to make a similar number of trips. These results suggest that the differences among colonies in response to humidity, found in previous work, are due to behavioral responses to current humidity that all workers in a colony share, rather than to the distribution within a colony of foragers that differ in response.
DOI: 10.25740/xd864rp1501
title: Critical thermal limits and temperature-dependent walking speed may mediate coexistence between the native winter ant (Prenolepis imparis) and the invasive Argentine ant (Linepithema humile)

description: The Argentine ant (Linepithema humile) is an invasive species that has spread to Mediterranean climates worldwide, where it is associated with losses in native arthropod biodiversity. In northern California, long-term surveys of ant biodiversity have shown that the winter ant (Prenolepis imparis) is the native species best able to coexist with Argentine ants. Both species tend hemipteran scales for food, and previous research suggests that these species’ coexistence may depend on seasonal partitioning: winter ants are active primarily in the colder winter months, while Argentine ants are active primarily in the warmer months in northern California.  
            We investigated the physiological basis of seasonal partitioning in Argentine and winter ants by a) testing critical thermal limits, and b) measuring the relationship of temperature and Argentine ant and winter ant walking speed. While both species respond similarly to high temperatures, we found small differences between the two species’ critical thermal minima that may allow winter ants to remain functional at ecologically relevant temperatures between 0-2.5°C. We also found that winter ants’ walking speeds are significantly less temperature-dependent than those of Argentine ants. We found that winter ants walk faster than Argentine ants at low temperatures, which may allow the winter ants to remain active and forage at lower winter temperatures. These results suggest that partitioning based on differences in temperature tolerance promotes the winter ant’s continued occupation of areas invaded by the Argentine ant.
DOI: 10.3535/60h-v11-101
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hvq-chs-9wb
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/gr652yp4782
title: Data for Nova, N., Pagliara, R., Gordon, D. M. 2022. Individual variation does not regulate foraging response to humidity in harvester ants. Frontiers Ecology and Evolution

description: Differences among groups in collective behavior may arise from responses that all group members share, or instead from differences in the distribution of individuals of particular types. We examined whether the collective regulation of foraging behavior in colonies of the desert red harvester ant (Pogonomyrmex barbatus) depends on individual differences among foragers. Foragers lose water while searching for seeds in hot, dry conditions, so colonies regulate foraging activity in response to humidity. In the summer, foraging activity begins in the early morning when humidity is high, and ends at midday when humidity is low. We investigated whether individual foragers within a colony differ in the decision whether to leave the nest on their next foraging trip as humidity decreases, by tracking the foraging trips of marked individuals. We found that individuals did not differ in response to current humidity. No ants were consistently more likely than others to stop foraging when humidity is low. Each day there is a skewed distribution of trip number: only a few individuals make many trips, but most individuals make few trips. We found that from one day to the next, individual foragers do not show any consistent tendency to make a similar number of trips. These results suggest that the differences among colonies in response to humidity, found in previous work, are due to behavioral responses to current humidity that all workers in a colony share, rather than to the distribution within a colony of foragers that differ in response.
DOI: 10.25740/hw279tj6064
title: Nutrient and Isotope data from ETNP 2016-2017, cruise SKQ201617S

description: This deposit includes the nutrient, hydrographic, and isotopic data from a 2016-2017 cruise to the Eastern Tropical North Pacific (SKQ201617S) used to analyze the sources, sinks, and cycling of nitrous oxide.
DOI: 10.25740/rh973jh7848
title: Comparison of temperature and doping dependence of nematic susceptibility near aputative nematic quantum critical point, Figures 1-4 Data

description: Strong electronic nematic fluctuations have been discovered near optimal doping for several families of Fe-based superconductors, motivating the search for a possible link between these fluctuations, nematic quantum criticality, and high temperature superconductivity. Here we probe a key prediction of quantum criticality, namely power law dependence of the associated nematic susceptibility as a function of composition and temperature approaching the compositionally-tuned putative quantum critical point. To probe the 'bare' quantum critical point requires suppression of the superconducting state, which we achieve by using large magnetic fields, up to 45 T, while performing elastoresistivity measurements to follow the nematic susceptibility. We performed these measurements for the prototypical electron-doped pnictide, Ba(Fe1−xCox)2As2, over a dense comb of dopings. We find that close to the putative quantum critical point, the nematic susceptibility appears to obey power law behavior over almost a decade of variation in composition, consistent with basic notions of nematic quantum criticality. Paradoxically, however, we also find that the temperature dependence for compositions close to the critical value cannot be described by a single power law. This is surprising as power law scaling in both doping and temperature is expected close to a quantum critical point.
DOI: 10.3535/81d-ebb-z3w
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cca-3ny-mad
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.4121/12e73a6e-10bd-4e58-b24a-4c6b1912247b
title: Supplementary Materials for the article: Multi-operating condition pattern recognition of centrifugal pump impeller hydraulic radial force based on multi-dimensional features and hierarchical clustering.

description: Supplementary data for the article: "Multi-operating condition pattern recognition of centrifugal pump impeller hydraulic radial force based on multi-dimensional features and hierarchical clustering". This dataset includes supplementary matlab source code. This article proposes an unsupervised learning framework through Pearson correlation analysis and the clustering hierarchical Clustering (AHC) algorithm, providing a data-driven approach for the hydraulic optimization and intelligent diagnosis of centrifugal pumps. It reveals the multi-condition classification mode of hydraulic radial force, which has engineering significance for improving equipment reliability and operational efficiency.
DOI: 10.3535/9a5-jta-1nn
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c0t-ngd-p29
title: Decapoda

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.4121/12e73a6e-10bd-4e58-b24a-4c6b1912247b.v1
title: Supplementary Materials for the article: Multi-operating condition pattern recognition of centrifugal pump impeller hydraulic radial force based on multi-dimensional features and hierarchical clustering.

description: Supplementary data for the article: "Multi-operating condition pattern recognition of centrifugal pump impeller hydraulic radial force based on multi-dimensional features and hierarchical clustering". This dataset includes supplementary matlab source code. This article proposes an unsupervised learning framework through Pearson correlation analysis and the clustering hierarchical Clustering (AHC) algorithm, providing a data-driven approach for the hydraulic optimization and intelligent diagnosis of centrifugal pumps. It reveals the multi-condition classification mode of hydraulic radial force, which has engineering significance for improving equipment reliability and operational efficiency.
DOI: 10.3535/f52-ywy-z7v
title: Tethysbaena tarsiensis Wagner, 1994

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hlz-51b-zme
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lr5-b22-vxg
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xlr-82e-kjb
title: Decapoda

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yj9-pfb-yft
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/e7w-axv-caq
title: Pseudochirella notacantha (Sars G.O., 1905)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zge-2l9-wbs
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/75y-e8c-qw4
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q2r-tbe-hz5
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vw8-slv-txh
title: Decapoda

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2ge-1he-tsf
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tq4-maj-g7q
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/xc612sy7581
title: Data used in arcticle: Increases in benthic particulate export and sedimentary denitrification in the northern Chukchi Sea tied to under-ice primary production

description: Data used in submitted manuscript: Increases in benthic particulate export and sedimentary denitrification in the northern Chukchi Sea tied to under-ice primary production
DOI: 10.3535/b4e-d8d-50c
title: Tethysbaena texana (Maguire, 1965)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/eeb-fq1-347
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/hs561fr5902
title: Data for Detection of SARS-CoV-2 variant Mu, Beta, Gamma, Lambda, Delta, Alpha, and Omicron in wastewater settled solids using mutation-specific assays is associated with regional detection of variants in clinical samples

description: These are the data used in our paper: Detection of SARS-CoV-2 variant Mu, Beta, Gamma, Lambda, Delta, Alpha, and Omicron in wastewater settled solids using mutation-specific assays is associated with regional detection of variants in clinical samples
DOI: 10.25740/nz800dp6262
title: Data used in article: North-south differences in under-ice primary production in the Chukchi Sea from 1988 to 2018

description: Data used in arcticle: North-south differences in under-ice primary production in the Chukchi Sea from 1988 to 2018
DOI: 10.3535/9nr-wz1-a1w
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/fp177dq8431
title: Urban Risk Factors for Human Rift Valley Fever virus exposure in Kenya

description: The Rift Valley fever virus (RVFV) is a zoonotic arbovirus that can also transmit directly to humans from livestock. Previous studies have shown consumption of sick animal products are risk factors for RVFV infection, but it is difficult to disentangle those risk factors from other livestock rearing activities. Urban areas have an increased demand for animal source foods, different vector distributions, and various arboviruses are understood to establish localized urban transmission cycles. Thus far, RVFV is an unevaluated public health risk in urban areas within endemic regions. We tested participants in our ongoing urban cohort study on dengue (DENV) and chikungunya (CHIKV) virus for RVFV exposure and found 1.6% (57/3,560) of individuals in two urban areas of Kenya had anti-RVFV IgG antibodies.  88% (50/57) of RVFV exposed participants also had co-exposure to DENV, CHIKV, or both. Although livestock ownership was very low in urban study sites, RVFV exposure was significantly associated with seeing goats and poultry around the homestead (p=0.04) and consumption of raw milk (p=0.02) in multivariate modeling. Risk of exposure to RVFV was three times higher (OR=3.3 [95%CI: 0.86-12.5], p=0.07) among those buying unpasteurized milk from milk vendors or directly from dairy owners compared to those that purchased commercialized packets of milk. In addition, lack of piped water and use of small jugs (15-20 liters) for water was associated with a higher risk of RVFV exposure (p=0.002) and may contribute to interepidemic vector-borne maintenance of RVFV. This study provides baseline evidence to guide future studies investigating the urban potential of RVFV and highlights the unexplored role of animal products in continued spread of RVFV.
DOI: 10.25740/kn066mv7984
title: Blue Whales and Lagrangian Features data archive

description: These files allow for the reproducibility of the analysis in the manuscript "Blue whales increase feeding rates at fine-scale ocean features". 
rawData.zip includes files and folders that comprise the raw data used in the manuscript 
Models.zip contains the Generalized Linear Mixed Effects Models produced in the analysis of the manuscript
DOI: 10.3535/3mv-qpk-9yp
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gwv-xra-hmr
title: Decapoda

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/mh541zb5994
title: Data and STATA code used for Luo et al. (2022) in JPART

description: This is a dataset underlying article "Relational Work and Its Pitfalls: 
Nonprofits’ Participation in Government-Sponsored Voluntary Accreditation" published by Journal of Public Administration Research and Theory
DOI: 10.25740/tv301yr5579
title: GEOTRACES GP15 Water Mass Analysis

description: A water mass analysis is a tool for interpreting the effect of ocean mixing on the distributions of trace elements and isotopes (TEIs) along an oceanographic transect. The GEOTRACES GP15 transect along 152°W covers a wide range in latitude from Alaska to Tahiti. We used a modified Optimum Multiparameter (OMP) analysis to determine the distributions of water masses with high importance to nutrient and hydrographic features on GEOTRACES GP15. In the thermocline, our results indicated the dominance of Pacific Subarctic Upper Water (PSUW) in the subpolar gyre, Eastern North Pacific Central Water (ENPCW) in the northern subpolar gyre, and Equatorial Subsurface Water (ESSW) in the equatorial region. South Pacific Subtropical Water (SPSTW) dominated the top of the thermocline in the southern subtropical gyre, while South Pacific Central Water (SPCW) dominated the lower thermocline. Antarctic Intermediate Water (AAIW), Equatorial Intermediate Water (EqIW), and North Pacific Intermediate Water (NPIW) in the southern hemisphere, equatorial region, and northern hemisphere, respectively, occupied waters just below the thermocline. Dominant water masses in the deep waters of the southern hemisphere include Upper Circumpolar Deep Water (UCDW) and Lower Circumpolar Deep Water (LCDW) with minimal contributions from Antarctic Bottom Water (AABW). Pacific Deep Water (PDW) dominated the deep water in the northern hemisphere. Our results align well with literature descriptions of these water masses and related circulation patterns.
DOI: 10.3535/62t-l63-7xq
title: Tethysbaena coqui Wagner, 1994

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9q3-8fr-ppr
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/vm787sj6177
title: Data on SARS-CoV-2 RNA and N protein quantification via wastewater at campus level, building cluster level and individual building level

description: Measured concentrations of SARS-CoV-2 RNA and N protein in wastewater
DOI: 10.3535/7zk-32w-r0r
title: Tethysbaena texana (Maguire, 1965)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8xk-lbz-dqa
title: Decapoda

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/gg221yy5416
title: SARS-CoV-2 RNA concentrations from 8 wastewater plants April - Sept 2021

description: SARS-CoV-2 N gene and PMMoV RNA gene concentrations from wastewater settled solids
DOI: 10.25740/zf704jg7109
title: Antarctic Seawater d18O isotope data and calculated glacial melt (meteoric), sea ice melt, and circumpolar deep water (CDW) water mass fractions from SE Amundsen Sea: 1994, 200, 2007, 2009, 2014, 2019, 2020

description: Antarctic Seawater d18O isotope data and calculated glacial melt (meteoric), sea ice melt, and circumpolar deep water (CDW) water mass fractions from SE Amundsen Sea: 1994, 200, 2007, 2009, 2014, 2019, 2020
DOI: 10.3535/am6-4bp-leq
title: Amallothrix robusta (Scott T., 1894)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.