cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c866t1g36
title: Data from: External temperature and distance from nearest entrance influence microclimates of cave and culvert roosting tri-colored bats Perimyotis subflavus

description: Many North American bat species hibernate in both natural and artificial
 roosts. Although hibernacula can have high internal climate stability,
 they still retain spatial variability in their thermal regimes, resulting
 in various ‘microclimates’ throughout the roost that differ in their
 characteristics (e.g., temperature, air moisture). These microclimate
 components can be influenced by factors such as the number of entrances,
 the depth of the roost, and distance to the nearest entrance of the roost.
 Tri-colored bats are commonly found roosting in caves in winter, but they
 can also be found roosting in large numbers in culverts, providing the
 unique opportunity to investigate factors influencing microclimates of
 bats in both natural and artificial roost sites. As tri-colored bats are
 currently under consideration for federal listing, information of this
 type could be useful in aiding in the conservation and management of this
 species through a better understanding of what factors affect the
 microclimate near roosting bats. We collected data on microclimate
 temperature and microclimate actual water vapor pressure (AWVP) from a
 total of 760 overwintering tri-colored bats at 18 caves and 44 culverts.
  Using linear mixed models analysis, we found that variation in
 bat microclimate temperatures was best explained by external temperature
 and distance from nearest entrance in both caves and culverts. External
 temperature had a greater influence on microclimate temperatures in
 culverts than caves. We found that variation in microclimate AWVP was best
 explained by external temperature, distance from nearest entrance and
 proportion from entrance (proportion of the total length of the roost from
 the nearest entrance) in culvert roosting bats. Variation in microclimate
 AWVP was best explained by external temperature and proportion from
 entrance in cave roosting bats. Our results suggest that bat microclimate
 temperature and AWVP are influenced by the similar factors in both
 artificial and natural roosts, although the relative contribution of these
 factors differ between roost types.
DOI: 10.5061/dryad.3bk3j9kdw
title: Host heterogeneity mitigates virulence evolution

description: Parasites often infect genetically diverse host populations, and the
 evolutionary trajectories of parasite populations may be shaped by levels
 of host heterogeneity. Mixed genotype host populations, compared to
 homogeneous host populations, can reduce parasite prevalence and
 potentially reduce rates of parasite adaptation due to tradeoffs
 associated with adapting to specific host genotypes. Here, we used
 experimental evolution to select for increased virulence in populations of
 the bacterial parasite Serratia marcescens exposed to either heterogenous
 or homogenous populations of Caenorhabditis elegans. We found that
 parasites exposed to heterogenous host populations evolved significantly
 less virulence than parasites exposed to homogeneous host populations over
 several hundred bacterial generations. Thus, host heterogeneity impeded
 parasite adaptation to host populations. While we detected tradeoffs in
 virulence evolution, parasite adaptation to two specific host genotypes
 also resulted in modestly increased virulence against the reciprocal host
 genotypes. These results suggest that parasite adaptation to heterogenous
 host populations may be impeded by both tradeoffs and a reduction in the
 efficacy of selection as different host genotypes exert different
 selective pressures on a parasite population.
description: The raw data was collected by methods outlined in the methods
 section (2. Methods). Data was recorded into an Excel spreadsheet,
 cleaned, then uploaded into JMP Pro 14 and Prism for statistical analysis
 and figure creation.
DOI: 10.25338/b8x318
title: Data from: What is in a general plan? using natural language processing to read 461 California city general plans

description: This repository contains all data outputs related to reasearch
 that analyzed General Plans from cities across the state of
 California to understand what topics are adressed and the spacial
 distribution of topic rerpresentation.  We assembles a database
 of 421 California city-level General Plans and used Natural Language
 Processing to read their contents.  The plans contained over 60
 discrete topics and wer generally optimistic in sentiment.  A
 quarter of the topics were reagionally specific.  Housing is a
 unique subset of planning topics, and plans for affordable housing are not
 evenly shared across sites.
DOI: 10.5061/dryad.r7sqv9s7k
title: Genetic diversity and the origin of commercial plantation of Indonesian teak on Java Island

description: Teak (Tectona grandis) has been widely planted in 70 tropical countries
 because of the utility and value of its wood. This species was introduced
 to Indonesia more than 100 years ago, and large plantations - covering 1.2
 million ha – can be found on Java Island. However, little information
 currently exists about the genetic diversity and origin of these trees. We
 collected plant materials from three regions across Java Island (east,
 central, and west), and sampled trees spanning three age classes in each
 region, to clarify the genetic diversity and structure of teak plantations
 on Java Island. We investigated teak plantation and clonal experiment
 populations using multiplexed ISSR genotyping by sequencing (MIG-seq), and
 compared the genetic diversity and structure with the provenance test
 populations derived from natural teak forest in India, Myanmar, Thailand
 and Laos. Analyses using 459 single-nucleotide polymorphism (SNP) loci
 revealed that native provenances had higher genetic diversity than the
 Indonesian teak plantations. Moreover, old teak plantations demonstrated
 lower genetic diversity than young plantations. Further analyses showed
 that most Indonesian teak plantations are genetically related to Laos,
 Thailand and Myanmar provenances. We conclude that there is a weak genetic
 structure on teak plantations among the regions, which indicates that most
 plantations were established using plant materials from a specific part of
 the natural teak distribution. Information regarding the genetic diversity
 and structure of plantation forests should be taken into account when
 making future plantation programs.
DOI: 10.5061/dryad.fn2z34tpt
title: Dataset for: Image-based screen capturing misfolding status of Niemann-Pick type C1 identifies potential candidates for chaperone drugs

description: Niemann-Pick disease type C is a rare, fatal neurodegenerative disorder
 characterized by massive intracellular accumulation of cholesterol. In
 most cases, loss-of-function mutations in NPC1 gene that encodes for a
 lysosomal cholesterol transporter NPC1 are responsible for the disease,
 and more than half of the mutations are considered to interfere with
 biogenesis or folding of the protein. Previously we have identified a
 series of oxysterol derivatives and phenanthridine-6-one derivatives as
 pharmacological chaperones, small molecules that rescue folding defective
 phenotypes of a mutated NPC1, and opened an avenue to develop chaperone
 therapy for Niemann-Pick disease type C. Here, we established an improved
 image-based screen for NPC1 chaperones and performed drug-repurposing
 screening to identify some azole antifungals, including itraconazole and
 posaconazole, and a kinase inhibitor lapatinib as probable pharmacological
 chaperones. Photo-crosslinking probes of the compounds allowed us to
 detect direct binding of itraconazole to a representative
 folding-defective mutant, NPC1-I1061T. Competitive photo-crosslinking
 experiments suggested that oxysterol-based chaperones and itraconazole
 share the same or nearby binding site(s), and sensitivity of the
 crosslinking to P691S mutation on the sterol-sensing domain supported
 currently proposed hypothesis that their binding sites are located near
 the domain. Although the azoles were less effective in reducing
 cholesterol accumulation than the oxysterol-derived chaperone or an HDAC
 inhibitor LBH-589, our findings should offer new starting points for
 developing better pharmacological chaperones for NPC1 through medicinal
 chemistry efforts.
description: Methods HEK293 cells stably expressing
 NPC1-I1061T-GFP (under CMV promoter) were treated with a library of
 compounds (an FDA-approved drug library obtained from Enzo Life Sciences)
 for 20-21 h at 10 µM concentration, and cells were fixed with
 formaline-PBS containing Hoechst 33342. Images for NPC1-I1061T-GFP and
 nuclei were acquired on an IN Cell Analyzer 2000 with 60x objective lens.
 For more detail, see the accompanying manuscript.
 Format of the screen data This dataset
 contains 11 zipped directory containing screening data.
 Each of the zipped directory corresponds to one of the library
 plate (total 11 96-well plates of compounds), and 16-bit TIFF images are
 stored. For each well, 6 fields of images were acquired with two channels
 (FITC filter set for GFP detection and DAPI filter set for Hoechst
 detection). File naming convention
 For each zipped directory: A - 1(fld 1 wv DAPI
 - DAPI).tif<br> A - 1(fld 1 wv FITC - FITC).tif<br> A - 1(fld
 2 wv DAPI - DAPI).tif<br> A - 1(fld 2 wv FITC - FITC).tif<br>
 ...<br> H - 12(fld 6 wv DAPI - DAPI).tif<br> H - 12(fld 6 wv
 FITC - FITC).tif
DOI: 10.5061/dryad.nzs7h44mq
title: Effect of participation in commercial production of medicinal plants through community-based conservation groups on farm income at Kakamega forest, Kenya

description: Forest conservation by peripheral communities is one of the most advocated
 strategies for ensuring sustainable supply of forest goods and services.
 In Kenya, although conservation activities generate considerable
 environmental improvements, studies evaluating the economic benefits are
 very limited. This study aimed at assessing the impact of participating in
 the commercialization training program by forest adjacent communities on
 farm income. Utilizing matching techniques, the analysis is based on the
 data collected from a randomly selected sample of farm households around
 Kakamega forest in Kenya. The results show that age, forest distance,
 forest benefit, market distance and farming experience are the main
 factors that influence the participation in the commercialization program.
 Also, participating in commercial production of medicinal plants has a
 positive and significant effect on farmers’ income. The average treatment
 effect on the treated (ATT), based on three estimation algorithms, ranges
 from KSH. 80,047 to KSH. 176,788 per hectare, per year, implying that
 policy efforts that focus on the participation in the commercialization
 program of medicinal plants can enhance incomes among farm-dependent
 households. The findings from this study suggest that upscaling the
 participation in the commercialization program to other areas.
description: A two-stage stratified random sampling technique was employed to
 identify the household level sample units. First, five major medicinal
 plant producer groups involved in the <i>icipe</i> project
 were selected purposively with the help of agricultural experts in the
 area. Second, 5 farmers from each group were randomly selected from the
 list of members summing up to 25 households. An additional 25 households
 were randomly selected among households that were not participating in the
 commercial production of MPs program but living in the same locality with
 those who were participating in the project. Data was collected from the
 selected households using pre-tested semi-structured questionnaires by
 trained and experienced enumerators who understood the local language.
 Data collected included information on household demographic
 characteristics, household monthly expenditure, access to training, the
 perceived value of the forest including source of medicinal plants,
 availability of timber and fire wood and livestock grazing, production and
 marketing of MPs and other farm crops and returns generated from
 sales. Given the cross-sectional nature of our dataset,
 we employed matching methods in estimating the observed mean outcome
 differences between the treatment and control groups.
description: No missing values
DOI: 10.5061/dryad.98sf7m0dt
title: Data from: A multilocus analysis of Epicopeiidae (Lepidoptera, Geometroidea) provides new insights into their relationships and the evolutionary history of mimicry

description: The family Epicopeiidae is a small group of day-flying moths, known for
 mimicking many different groups of butterflies and moths. So far, there
 still lacks a reliable phylogenetic framework of Epicopeiidae that is
 necessary to our understanding of the evolutionary process of their
 mimicry. In this study, we sequenced 94 nuclear protein-coding markers for
 56 epicopeiid samples and 11 outgroups, covering all ten genera of
 Epicopeiidae. We used homemade PCR-generated baits to capture target
 sequences, which allowed us to utilize old and dried specimens that were
 difficult to handle by conventional PCR + Sanger
 sequencing. Maximum likelihood and Bayesian analyses of the newly obtained
 dataset (86,388 bp) at both DNA and protein levels produced
 identical phylogenies with strong support. The non-mimicry
 genus Deuveia is the sister group of other epicopeiid
 genera. Epicopeia and Nossa are not
 monophyletic, and these two genera nest together to form a clade. We also
 estimated divergence times of Epicopeiidae and found that their initial
 diversification happened in Eocene about 41 million years ago. The
 ancestral state reconstruction of mimicry type for this family suggested
 that the last common ancestor of epicopeiid moths is non-mimetic,
 and the Riodinidae-mimicry type evolved first. In summary, our work
 provides a comprehensive and robust time-calibrated phylogeny of
 Epicopeiidae that provides a sound framework for revising their
 classification and interpreting character evolution.
description: Sequence capture experiment following the method of Zhang, Y.,
 Deng, S., Liang, D., Zhang, P., 2019. Sequence capture across large
 phylogenetic scales by using pooled PCR-generated baits: A case study of
 Lepidoptera. <i>Molecular ecology
 resources</i>,<i> </i>00, 1–15. doi:
 10.1111/1755-0998.13026
DOI: 10.5061/dryad.2v6wwpzh9
title: Assessment of appropriateness of hospitalizations in Ukraine: analytical framework, method, and findings

description: Objectives: This article reviews the applicability of a customized version
 of the Appropriateness Evaluation Protocol (AEP) to evaluate the magnitude
 of inappropriate hospitalizations in two regions of Ukraine. Data and
 methods: The original AEP was modified to develop a customized tool, which
 included criteria for the appropriateness of hospitalization and duration
 of inpatient stay. The customization of the tool followed the Delphi
 procedure. We randomly selected 381 medical records to test the
 feasibility and reliability of the method and 800 medical records to
 evaluate the scope of inappropriate hospitalizations. We used descriptive
 and analytical statistics, ROC analysis, and Cohen's kappa to check
 the consistency between the findings of primary reviewers and experts.
 Result: We observed high levels of agreement in conclusions of primary
 reviewers (reference standard) and experts during testing of the
 reliability and validity of the method. The external validity check showed
 that the use of the tool by different experts provided high accuracy: 95.1
 sensitivity, 76.6 specificity, and AUC=0.948 (р&lt;0.001) for analysis
 of the appropriateness of admissions; 95.3 sensitivity, 84.7 specificity,
 and AUC=0.900 (р=0.001) for the duration of hospitalizations. Cohen's
 kappa coefficient (κ) indicated agreement in expert evaluations of 0.915
 (95% СІ 0.799 to 1.000) and 0.812 (95% СІ 0.749 to 0.875), respectively.
 We found that over one-third of admissions (38.1%; 95% СІ 33.9 to 43.5)
 and over half of total bed-days were unnecessary (57.4%; 95% СІ 56.4 to
 58.5). The highest levels of stay were observed in hospitals’ general
 medicine departments (64.6%; 95% СІ 63.0 to 66.3) compared to other
 departments included in the analysis. Conclusion: The proposed method is
 robust in assessing the appropriateness of hospitalizations and duration
 of inpatient stays. The quantified levels of unnecessary hospital care
 indicate the need for improving efficiency and quality of care and
 optimizing the excessive hospital capacities in Ukraine.
description: The original AEP
 was modified to develop a customized tool, which included criteria for the
 appropriateness of hospitalization and duration of inpatient stay. The
 customization of the tool followed the Delphi procedure. We randomly
 selected 381 medical records to test the feasibility and reliability of
 the method and 800 medical records to evaluate the scope of
 inappropriate hospitalizations. We used
 descriptive and analytical statistics, ROC analysis, and Cohen's
 kappa to check the consistency between the findings of primary reviewers
 and experts.
description: In addition to the dataset, we included the table with the
 description of variables, and the questionnaires used for data
 collection
DOI: 10.24342/e0cf3b6b-edd3-4e85-849f-caf19c9749b9
title: Demo of wireless HD-video transfer from inside a human-body-phantom to an on-body receiver

description: This video demostrates wireless HD video transmission from a capsule placed inside a liquid human-body-phantom to a receiver located outside of this phantom. We show and discuss how different parameters affect link quality.
We designed the antenna system as well as the test setup, in order to enable transmitting HD video data from a capsule embedded inside the the human body, wirelessly to a receiver placed outside the body. The wireless link in this test setup is realised with software-defined-radios handling the video transmission and reception, and especially designed antennas for the capsule transmitter and for the on-body receiver. The target application is wireless gastroendoscopy, i.e. medical applications that require high-resolution video images from inside the gastrointestinal tract of a patient. We hence demonstrate one promising practical implementation of an antenna system that enables very high data rates needed to ensure HD video transmission.
DOI: 10.5061/dryad.2fqz612k4
title: Metabolomics signatures in type 2 diabetes: a systematic review and integrative analysis

description: Objective Metabolic signatures have emerged as valuable signaling
 molecules in the biochemical process of type 2 diabetes (T2D). To
 summarize and identify metabolic biomarkers in T2D, we performed a
 systematic review and meta-analysis of the associations between
 metabolites and T2D using high-throughput metabolomics techniques. Methods
 We searched relevant studies from MEDLINE (PubMed), Embase, Web of
 Science, and Cochrane Library as well as Chinese databases (Wanfang, Vip,
 and CNKI) inception through 31 December 2018. Meta-analysis was conducted
 using STATA 14.0 under random effect. Besides, bioinformatic analysis was
 performed to explore molecule mechanism by MetaboAnalyst and R 3.5.2.
 Results Finally, 46 articles were included in this review on metabolites
 involved amino acids, acylcarnitines, lipids, carbohydrates, organic
 acids, and others. Results of meta-analysis in prospective studies
 indicated that isoleucine, leucine, valine, tyrosine, phenylalanine,
 glutamate, alanine, valerylcarnitine (C5), palmitoylcarnitine (C16),
 palmitic acid, and linoleic acid were associated with higher T2D risk.
 Conversely, serine, glutamine, and lysophosphatidylcholine C18:2 decreased
 risk of T2D. Arginine and glycine increased risk of T2D in the Western
 countries subgroup, and betaine was negatively correlated with T2D in
 nested case-control subgroup. In addition, slight improvements in T2D
 prediction beyond traditional risk factors were observed when adding these
 metabolites in predictive analysis. Pathway analysis identified 17
 metabolic pathways may alter in the process of T2D and metabolite-related
 genes were also enriched in functions and pathways associated with T2D.
 Conclusions Several metabolites and metabolic pathways associated with T2D
 have been identified, which provide valuable biomarkers and novel targets
 for prevention and drug therapy.
description: Supplementary materials for a systematic review and integrative
 analysis of the associations between metabolites and T2D using
 high-throughput metabolomics techniques.
DOI: 10.5061/dryad.v9s4mw6qt
title: Data from: Live, dead, and fossil mollusks in Florida freshwater springs and spring-fed rivers: taphonomic pathways and the formation of multi-sourced, time-averaged death assemblages

description: Taphonomic processes are informative about the magnitude and timing of
 paleoecological changes but remain poorly understood with respect to
 freshwater invertebrates in spring-fed rivers and streams. We compared
 taphonomic alteration among freshwater gastropods in live, dead (surficial
 shell accumulations), and fossil (late Pleistocene-early Holocene in situ
 sediments) assemblages from two Florida spring-fed systems, the Wakulla
 and Silver/Ocklawaha Rivers. We assessed taphonomy of two gastropod
 species: the native Elimia floridensis (n=2504) and introduced Melanoides
 tuberculata (n=168). We quantified seven taphonomic attributes (aperture
 condition, color, fragmentation, abrasion, juvenile spire condition,
 dissolution, and exterior luster) and combined those attributes into a
 total taphonomic score (TT). Fossil E. floridensis specimens exhibited the
 greatest degradation (highest TT scores), whereas live specimens of both
 species were least degraded. Specimens of E. floridensis from death
 assemblages were less altered than fossil specimens of the same species.
 Within death assemblages, specimens of M. tuberculata were significantly
 less altered than specimens of E. floridensis, but highly degraded
 specimens dominated in both species. Radiocarbon dates on fossils
 clustered between 9792 and 7087 cal. BP, whereas death assemblage ages
 ranged from 10,692 to 1173 cal. BP. Possible explanations for the observed
 taphonomic patterns include: (1) rapid taphonomic shell alteration, (2)
 prolonged near-surface exposure to moderate alteration rates, and/or (3)
 introduction of reworked fossil shells into surficial assemblages.
 Combined radiocarbon dates and taphonomic analyses suggest that all these
 processes may have played a role in death assemblage formation. In these
 fluvial settings, shell accumulations develop as a complex mixture of
 specimens derived from multiple sources and characterized by
 multi-millennial time averaging. These findings suggest that, when
 available, fossil assemblages may be more appropriate than death
 assemblages for assessing pre-industrial faunal associations and recent
 anthropogenic changes in freshwater ecosystems.