cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bzkh1894d
title: Data from: Comparative genomic analysis of the pheromone receptor Class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and a chromosomal hotspot across mammals

description: Sensory gene families are of special interest, both for what they can tell
 us about molecular evolution, and for what they imply as mediators of
 social communication. The vomeronasal type-1 receptors (V1Rs) have often
 been hypothesized as playing a fundamental role in driving or maintaining
 species boundaries given their likely function as mediators of
 intraspecific mate choice, particularly in nocturnal mammals. Here, we
 employ a comparative genomic approach for revealing patterns of V1R
 evolution within primates, with a special focus on the small-bodied
 nocturnal mouse and dwarf lemurs of Madagascar (genera Microcebus and
 Cheirogaleus, respectively). By doubling the existing genomic resources
 for strepsirrhine primates (i.e., the lemurs and lorises), we find that
 the highly speciose and morphologically cryptic mouse lemurs have
 experienced an elaborate proliferation of V1Rs that we argue is
 functionally related to their capacity for rapid lineage diversification.
 Contrary to a previous study that found equivalent degrees of V1R
 diversity in diurnal and nocturnal lemurs, our study finds a strong
 correlation between nocturnality and V1R elaboration, with nocturnal
 lemurs showing elaborate V1R repertoires and diurnal lemurs showing less
 diverse repertoires. Recognized subfamilies among V1Rs show unique
 signatures of diversifying positive selection, as might be expected if
 they have each evolved to respond to specific stimuli. Further, a detailed
 syntenic comparison of mouse lemurs with mouse (genus Mus) and other
 mammalian outgroups shows that orthologous mammalian subfamilies,
 predicted to be of ancient origin, tend to cluster in a densely populated
 region across syntenic chromosomes that we refer to as a V1R “hotspot.”
description: Genomes were assembled de novo using a combination of standard
 Illumina library prep and 10X Genomics Chromium library preps with MASURCA
 and SUPERNOVA respectively. Annotations were made with MAKER. V1R gene
 sequences were annotated independently using BLAST. Alignment of V1R
 sequences was performed with MAFFT and a phylogeny estimated with RAXML.
 The resulting alignment and phylogeny are provided here. Subfamilies were
 circumscribed based on the phylogeny and previously recognized subfamiles.
 Individual phylogenies and alignments for all subfamilies were extracted
 for tests of positive selection and provided here too.
DOI: 10.5061/dryad.tmpg4f4ts
title: Assembly and origin of the flora of the Chihuahuan Desert: the case of sclerophyllous Rosaceae

description: Aim To test hypotheses on the origin and assembly of the flora of the
 Chihuahuan Desert using as a system the hard-leaved shrubby lineages of
 the Rosaceae distributed in North American Deserts. Location North
 American Deserts, Chihuahuan Desert, Mexican Plateau, Tehuacán Valley.
 Methods Phylogenetic analyses were conducted based on nine chloroplast and
 nuclear molecular markers of eleven newly sequenced species of Rosaceae
 distributed in the Chihuahuan Desert along with previous sequences of 41
 species in 25 genera representative of the major clades in the family.
 Based on phylogeny, divergence times, migration, vicariance events and
 ancestral biogeographic areas were determined. Ecological niche-based
 modeling will predict changes in distribution during Pleistocene climate
 oscillations. Traitgrams were constructted to visualize departure among
 lineages in the most significant climate variables. Results The lineages
 studied diverged during the Eocene-Oligocene (53 – 33Mya). The ancestral
 area for most of the taxa was in the Mojave and Chihuahuan Deserts. Most
 dispersal events occurred from the Mojave Desert to the central area of
 the Chihuahuan Desert on the Mexican Plateau. Ecological niche-based
 modeling suggests a contraction of suitable habitat during the Last
 Interglacial period (~120,000 - 140,000 years), followed by expansion
 during the Last Glacial Maximum (~ 22,000 years) and the Middle Holocene
 (~ 6000 years). Main conclusions Our results confirm the Axelrod’s
 hypothesis of an origin of the flora of the Chihuahuan Desert in SW North
 America migrating to occupy North American arid lands. Vicariance and the
 expansion of arid lands allowed divergence, migration and permanence of
 the lineages studied on the Mexican Plateau. Divergence occurred prior to
 the onset of aridification. The Mexican Plateau acted as a refuge for
 hard-leaved lineages during the Miocene. Shifts in ecological niches of
 related species allowed them to colonize new areas with different
 temperatures and precipitation. Current distribution of lineages is the
 most limited.
description: Eleven species of Rosaceae distributed in the Chihuahuan Desert
 were newly sequenced. Samples were collected taking into account their
 entire range in this arid land  including the Tehuacán Valley. Samples
 were obtained either from the field or from herbarium specimens (HGOM,
 SLPM, MEXU, and XAL). In total, sequences from 9 molecular markers: one
 nuclear ribosomal (ITS) and eight plastid markers
 (<i>atpB-rbcL</i>, <i>matK</i>,
 <i>psbA</i>-<i>trnH</i>, <i>rpL16</i>,
 <i>rps16</i>, <i>trnH</i>-<i>rpl2</i>,
 <i>trnL</i>-<i>trnF</i>, <i>trnS</i>-
 <i>trnG</i>) were analized.
description: Sequence file: atpB-rbcL Sequence file:
 ITS Sequence file: matK Sequence
 file: psbA-trnH Sequence file: rpL16
 Sequence file: rpS16 Sequence file:
 trnH-rpl2 Sequence file:trnL-trnH
 Sequence file: trnS-trnG
DOI: 10.34740/kaggle/dsv/14642671
title: Market Prices of Commodities in South Tangerang
DOI: 10.5061/dryad.9cnp5hqd4
title: Databank floristics, phytogeography and environmental factors of the Brazilian Middle North Savannas

description: Neotropical savannas are distributed in the Brazilian territory under
 different phytophysiognomies. The richness of these landscapes is so
 variable that less than 15% of the diversity is maintained throughout its
 range. In order to understand the distribution patterns of Cerrado
 vegetation and the differentiation of northern ecotonal communities, we
 used a database of 482 communities, with accumulation of 1221 woody
 species. Similar composition patterns were calculated between “areal”
 floras (typical of each area), where the northern floristic concentrations
 stood out and a high β-diversity was evidenced by the formation of nine
 synareal floras. High turnover rates attest that a great number of
 protected areas in different regions are necessary for a comprehensive
 protection of species diversity, physiognomies and functionalities of
 cerrados. Environmental data were recorded from the investigated areas of
 the North and Northeast of Brazil. The results provide updated and
 complementary scientific evidence to aid national decision makers
 contextualize the mesologic relevance of Brazilian savannas as
 environmental drivers connected to a larger system.
DOI: 10.5061/dryad.4mw6m906b
title: Data from: The Moorfields AMD database report 2 - fellow eye involvement with neovascular age-related macular degeneration

description: Background/Aims: Neovascular age-related macular degeneration (nAMD) is
 frequently bilateral, and previous reports on ‘fellow eyes’’ have assumed
 sequential treatment after a period of treatment of the first eye only.
 The aim of our study was to analyse baseline characteristics and visual
 acuity (VA) outcomes of fellow eye involvement with nAMD, specifically
 differentiating between sequential and non-sequential (due to macular
 scarring in the first eye) anti-vascular endothelial growth factor
 treatment and timelines for fellow eye involvement. Methods:
 Retrospective, electronic medical record database study of the Moorfields
 AMD database of 6265 patients /120,286 single entries with data extracted
 between October 21, 2008 and August 9, 2018. The dataset for analysis
 consisted of 1180 sequential, 807 nonsequential, and 3410 unilateral eyes.
 Results: Mean VA (Early Treatment Diabetic Retinopathy Study letters±SD)
 of sequentially treated fellow eyes at baseline was significantly higher
 (63±13), VA gain over two years lower (0.37±14), and proportion of eyes
 with good VA (≥70 letters) higher (46%) than the respective first eyes
 (baseline VA 54±16, VA gain at two years 5.6±15, percentage of eyes with
 good VA 39%). Non-sequential fellow eyes showed baseline characteristics
 and VA outcomes similar to first eyes. Fellow eye involvement rate was 32%
 at two years, and median time interval to fellow eye involvement was 71
 (IQR 27-147) weeks. Conclusion: This report shows sequentially treated
 nAMD fellow eyes have better baseline and final VA than non-sequentially
 treated eyes after 2 years of treatment. Sequentially treated eyes also
 had a greater proportion with good VA after 2 years.
DOI: 10.15468/dl.2rzbaj
title: Occurrence Download

description: A dataset containing 915 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "NetworkKey is 99d66b6c-9087-452f-a9d4-f15f2c2d0e7e",
 "TaxonKey is Chordata"
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Ambystoma tigrinum [GBIF Backbone Taxonomy])",
 "StateProvince is one of (Texas)",
 "Country is one of (United States of America)"
 ]
 }
 ]
}

 The dataset includes 915 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001920-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7272/q6pz5715
title: Utility of routinely collected electronic health records data to support effectiveness evaluations in Inflammatory Bowel Disease: A pilot study of Tofacitinib

description: Objectives: Electronic health records (EHR) are receiving growing
 attention from regulators, biopharmaceuticals, and payors as a potential
 source of real-world evidence. However, their suitability for the study of
 diseases with complex activity measures is unclear. We sought to evaluate
 the use of EHR data for estimating treatment effectiveness in inflammatory
 bowel disease (IBD), using tofacitinib as a use case. Methods: Records
 from the University of California, San Francisco (6/2012-4/2019) were
 queried to identify tofacitinib-treated IBD patients. Disease activity
 variables at baseline and follow-up were manually abstracted according to
 a pre-registered protocol. The proportion of patients meeting the
 endpoints of recent randomized trials in ulcerative colitis (UC) and
 Crohn’s disease (CD) was assessed. Results: 86 patients initiated
 tofacitinib. Baseline characteristics of the real-world and trial cohorts
 were similar, except for universal failure of TNF-inhibitors in the
 former. 54% (UC) and 62% (CD) of patients had complete capture of disease
 activity at baseline (month -6 to 0), while only 32% (UC) and 69% (CD) of
 patients had complete follow-up data (month 2 to 8). Using data
 imputation, we estimated the proportion achieving the trial primary
 endpoints as being similar to the published estimates for both UC (16%,
 p-value=0.5) and CD (38%, p-value=0.8). Discussion/Conclusions: This pilot
 study reproduced trial-based estimates of tofacitinib efficacy despite its
 use in a different cohort but revealed substantial missingness in
 routinely collected data. Future work is needed to strengthen EHR data and
 enable real-world evidence in complex diseases like IBD.
description: This data was primarily collected by manual review of the
 electronic health records according to the following protocol: dx.doi.org/10.17504/protocols.io.2bqgamw It was subsequently de-identified and certified as such by the UCSF CTSI prior to broad release.
description: There are missing values in this dataset. These correspond to
 data that were not documented in the setting of routinely collected
 clinical data. The dataset file is accompanied by a R markdown file which
 takes the user through the end-to-end analytic pipeline that reproduce all
 of the results of the accompanying work.
DOI: 10.15468/dl.v5pt9q
title: Occurrence Download

description: A dataset containing 6377 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Krefftichthys anderssoni",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 6377 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001916-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tqjq2bvt9
title: Patterns of thermal sensitivity and sex-specificity of courtship behavior differs between two sympatric species of Enchenopa treehopper

description: Predicting how insects will react to future thermal conditions requires
 understanding how temperature currently affects insect behavior, from
 performance traits to those involved in mating and reproduction. Many
 reproductive behaviors are thermally-sensitive, but little is known how
 temperature affects the behaviors used to find mates and coordinate
 mating. Here, we investigate how temperature influences courtship activity
 in two sympatric species of Enchenopa treehoppers (Hemiptera:
 Membracidae). Enchenopa use substrate-borne vibrational signals
 exchanged in male-female duets to facilitate pair formation prior to
 mating. In a controlled laboratory setting, we assessed the likelihood of
 males and females to produce courtship signals across a range of
 ecologically relevant temperatures. We found that changes in courtship
 activity across temperatures differed between the two species. We
 also found sex differences within species: in one species males were more
 likely to signal at higher temperatures, while in the other species
 females were more likely to signal at higher temperatures. Our results
 suggest that sex-specific responses to temperature may constrain mating to
 narrower ranges of temperatures. Furthermore, sympatric species may
 respond differently to changes in thermal variation despite sharing
 similar climactic history.
DOI: 10.5061/dryad.xgxd254bs
title: λ/4 Retarder Film Measurement from: Polarization of foliar reflectance – novel host plant cue for insect herbivores

description: Insect herbivores exploit plant cues to discern host and non-host plants.
 Studies of visual plant cues have focused on color despite the inherent
 polarization sensitivity of insect photoreceptors  and the
 information carried by polarization of foliar reflectance, most notably
 the degree of linear polarization (DoLP; 0-100%). The DoLP of foliar
 reflection was hypothesized to be a host plant cue for insects but was
 never experimentally tested. Here we show that cabbage white butterflies,
 Pieris rapae (Pieridae), exploit the DoLP of foliar reflection to
 discriminate among plants. In experiments with paired digital plant
 images, P. rapae females preferred images of the host plant cabbage with a
 low DoLP (31%) characteristic of cabbage foliage over images of a non-host
 potato plant with a higher DoLP (50%). By reversing the DoLP of these
 images, we were able to shift the butterflies’ preference for the cabbage
 host plant image to the potato non-host plant image, indicating that the
 DoLP had a greater effect on foraging decisions than the differential
 color, intensity or shape of the two plant images. Although previously not
 recognized, the DoLP of foliar reflection is an essential plant cue that
 may commonly be exploited by foraging insect herbivores.
description: <strong>λ/4 retarder film
 measurements, description</strong>
 Description of methods used to measure the wavelength-specific
 effects of the λ/4 retarder film (#88-253, Edmund Optics) on degree of
 linear polarization (<em>DoLP</em>) and axis of polarization
 (<em>AoP</em>). Includes figures, created with the R code in
 <strong>QWP_Retarder_Film_Measurement_R_code.R,</strong>
 showing the effect of rotation of λ/4 retarder film on the
 <em>AoP</em> and <em>DoLP</em> across different
 wavelengths of light.
 QWP_Retarder_Film_Measurement_description.pdf
   <strong>λ/4 retarder film measurements, raw
 data</strong> 136 transmission
 measurements taken through a λ/4 retarder film sandwiched between two
 polarizers. The measurements were taken at different rotations of the λ/4
 retarder film (97°, 93°, 91°, 90°, 89°, 85°, 81°, 77°, 73°, 69°, 65°, 61°,
 57°, 53°, 49°, 46°, 45°, 44°, 43°, 41°, 39°, 35°, 31°, 27°, 23°, 19°, 15°,
 11°, 7°, 3°, 1°, 0°, -1°, -5°), and different angles between the axes of
 the two polarizers (0°, 45°, 90°, 135°).
 QWP_Retarder_Film_Measurement_data.csv
   <strong>λ/4 retarder film measurements, R
 code</strong> The R code necessary
 to calculate the wavelength-specific effects of different rotations of the
 λ/4 retarder film on the <em>AoP</em> and
 <em>DoLP</em>, using the raw data contained in
 <strong>QWP_Retarder_Film_Measurement_data.csv</strong>. This
 code can also generate Figs. S5-7 in
 <strong>QWP_Retarder_Film_Measurement_description.pdf</strong>. QWP_Retarder_Film_Measurement_R_code.R
DOI: 10.15468/dl.nrn4vz
title: Occurrence Download

description: A dataset containing 150 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingOrg is 610414e0-8040-11d9-8294-b8a03c50a862",
 "TaxonKey is Oxymycterus rufus"
 ]
}

 The dataset includes 150 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001922-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3j9kd51cn
title: Data from: Contingent negative variation during a modified cueing task in simulated driving

description: The obscured pedestrian-motor vehicle crash has become a serious danger to
 driving safety. The present study aims to investigate the contingent
 negative variation (CNV) during the anticipation of an obscured
 pedestrian-motor vehicle crash in simulated driving. We adopted two cueing
 tasks: (i) a traditional cognitive paradigm of cueing task that has been
 widely used to study anticipatory process, and (ii) a modified cueing task
 in simulated driving scenes, in which Electroencephalogram (EEG) signals
 of 32 participants were recorded to detect the CNV. Simulated car
 following and pedestrian crossing tasks were designed to measure
 anticipation-related driving behaviors. The results showed that both early
 and late CNVs were observed in two cueing tasks. The mean amplitude of the
 late CNV during a modified cueing task in simulated driving was
 significantly larger than that in a traditional cueing task, which was not
 the case for the early CNV potentials. In addition, both early and late
 CNVs elicited in simulated driving were significantly correlated with
 anticipatory driving behaviors (e.g., the minimum time to collision).
 These findings show that CNV potentials during the anticipation of an
 obscured pedestrian-motor vehicle crash might predict anticipation-related
 risky driving behaviors.
description: All anonymized data necessary to replicate our study findings
 have been uploaded to Dryad Digital Repository. There are four data
 sheets: demographic variables, the amplitude of early CNV, the amplitude
 of late CNV, and simulated driving behaviors.
DOI: 10.5061/dryad.gxd2547g4
title: Bandicoots return to Booderee: initial survival, dispersal, home range and habitat preferences of reintroduced southern brown bandicoots (eastern sub species; Isoodon obesulus obesulus)

description: Context Reintroductions can be an effective means of re-establishing
 locally extinct or declining faunal populations. However, incomplete
 knowledge of variables influencing survival and establishment can limit
 successful outcomes. Aim We aimed to examine the factors (e.g. sex, body
 mass, release order) influencing the survival, dispersal, home range and
 habitat selection of reintroduced southern brown bandicoots (eastern
 subspecies; Isoodon obesulus obesulus) into an unfenced, predator-managed
 environment in south-eastern Australia (Booderee National Park). Methods
 Over 2 weeks in May 2016, six female and five male bandicoots were
 wild-caught in state forest and hard released into the park. Release
 locations were approximately evenly distributed between three primary
 vegetation types assessed as suitable habitat: heath, woodland and forest.
 Bandicoots were radio-tracked day and night for 4 weeks from the initial
 release date. Key results No mortality was detected. Males dispersed more
 than twice as far as females (male 704 m, female 332 m), but there was no
 significant sex bias in home range size. At the landscape scale,
 bandicoots preferentially selected home ranges that contained heath and
 avoided forest. Within home ranges, heath and woodland were both favoured
 over forest. Conclusions Post-release dispersal is sex-biased, but more
 data are required to determine the influence of other predictors such as
 body mass and release order. Within the release area, bandicoots favoured
 non-forest vegetation types. Implications Our study outlines factors
 influencing the establishment of reintroduced bandicoots. We recommend
 that future bandicoot reintroductions to Booderee National Park occur
 within areas of heath and woodland, and that subsequent releases consider
 the potentially larger spatial requirements and conspecific avoidance
 among male bandicoots. Our findings contribute new knowledge for improving
 translocation methods of a nationally endangered medium-sized mammal.
DOI: 10.5061/dryad.7m0cfxppt
title: Data from: Influence of intra- and interspecific variation in predator-prey body size ratios on trophic interaction strengths

description: 1. Predation is a pervasive force that structures food webs and directly
 influences ecosystem functioning. The relative body sizes of predators and
 prey may be an important determinant of interaction strengths. However,
 studies quantifying the combined influence of intra- and interspecific
 variation in predator-prey body size ratios are lacking. 2. We use a
 comparative functional response approach to examine interaction strengths
 between three size classes of invasive bluegill and largemouth bass
 towards three scaled size classes of their tilapia prey. We then quantify
 the influence of intra- and interspecific predator-prey body mass ratios
 on the scaling of attack rates and handling times. 3. Type II functional
 responses were displayed by both predators across all predator and prey
 size classes. Largemouth bass consumed more than bluegill at small and
 intermediate predator size classes, whilst large predators of both species
 were more similar. Small prey were most vulnerable overall, however
 differential attack rates among prey were emergent across predator sizes.
 For both bluegill and largemouth bass, small predators exhibited higher
 attack rates towards small and intermediate prey sizes, whilst larger
 predators exhibited greater attack rates towards large prey. Conversely,
 handling times increased with prey size, with small bluegill exhibiting
 particularly low feeding rates towards medium-large prey types. Attack
 rates for both predators peaked unimodally at intermediate predator-prey
 body mass ratios, whilst handling times generally shortened across
 increasing body mass ratios. 4. We thus demonstrate effects of body size
 ratios on predator-prey interaction strengths between key fish species,
 with attack rates and handling times dependent on the relative sizes of
 predator-prey participants. 5. Considerations for intra- and interspecific
 body size ratio effects are critical for predicting the strengths of
 interactions within ecosystems and may drive differential ecological
 impacts among invasive species as size ratios shift.