cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jm63xsj99
title: Towards a stable global Noctuidae (Lepidoptera) taxonomy

description: The family Noctuidae is one of the world’s most diverse, ecologically
 successful, and economically important animal lineages; with over 12,000
 species in ~1150 genera. We inferred a phylogeny based on eight
 protein-coding genes (&gt;6,400 base pairs) for the global fauna,
 greatly expanding upon previous attempts to stabilize the higher
 classification of Noctuidae by sampling 70 of the 76 widely recognized
 family-group taxa: 20 of the 21 subfamilies, 32 of the 35 tribes, and 18
 of the 20 subtribes. For nearly half of the 341 genera included we sampled
 their type species. We evaluated seventeen subfamily-level taxa in detail;
 discussing adult and larval morphology, life history data, and taxonomic
 implications of our results. We significantly alter current concepts of
 Acontiinae, Condicinae, Eustrotiinae, Metoponiinae, and Stiriinae. We
 lowered Bryophilinae and Eriopinae to Bryophilini stat. rev. and Eriopini
 stat. rev. within Noctuinae. Our results also supported recognition of
 Cropiinae Keegan and Wagner subf. nov. Other nomenclatural changes we made
 are as follows. We moved “Acontia” viridifera (Hampson, 1910); “Azenia”
 virida Barnes and McDunnough, 1916; Aleptinoides; Austrazenia; Chalcoecia;
 Megalodes; and Trogotorna to Chamaecleini in Acontiinae. We moved Apaustis
 to Acontiinae and reinstated Emmelia as a valid genus in Acontiinae. We
 moved Allophyes and Meganephria to Cuculliinae. We moved “Plagiomimicus”
 navia (Harvey, 1875); Airamia; Alvaradoia; Hypoperigea; Neotarache; and
 Mesotrosta to Condicinae. We moved Axenus, Azenia, Metaponpneumata,
 Sexserrata, and Tristyla to Metoponiinae. We moved Pachythrix and
 “Paramiana” canoa (Barnes, 1907) to Noctuinae. Finally, we moved
 Cobubatha, Copibryophila, Homolagoa, Tripudia, and Tyta to Noctuidae
 incertae sedis.
DOI: 10.5061/dryad.mkkwh70zr
title: Morphometric materials for analyzing Eulipotyphlans across the Paleocene-Eocene-Thermal Maximum

description: Interpreting the impact of climate change on vertebrates in the fossil
 record can be complicated by the effects of potential biotic drivers on
 morphological patterns observed in taxa. One promising area where this
 impact can be assessed is a high-resolution terrestrial record from the
 Bighorn Basin, Wyoming, that corresponds to the Paleocene-Eocene Thermal
 Maximum (PETM), a geologically rapid (~170 ky) interval of sustained
 temperature and aridity shifts about 56 million years ago. The PETM has
 been extensively studied, but different lines of research have not yet
 been brought together to compare the timing of shifts in abiotic drivers
 that include temperature and aridity proxies, and those of biotic drivers,
 measured through changes in floral and faunal assemblages, to the timing
 of morphological change within mammalian species lineages. We used a suite
 of morphometric tools to document morphological changes in molar-crown
 morphology of three lineages of stem erinaceid eulipotyphlans. We then
 compared the timing of morphological change to that of both abiotic and
 other biotic records through the PETM. In all three species lineages, we
 failed to recover any significant changes in tooth crown shape or size
 within the PETM. These results contrast with those documented previously
 for lineages of medium-sized mammals, which show significant dwarfing
 within the PETM. Our results suggest that biotic drivers such as shifts in
 community composition may have also played an important role in shaping
 species-level patterns during this dynamic interval in earth history.
description: Please see materials and methods of the associated manuscript for
 more information on data collection and processing.
DOI: 10.5061/dryad.8pk0p2nmh
title: Large mitochondrial DNA deletions in HIV sensory neuropathy

description: Objective: The primary objective of this study was to evaluate the
 correlation of large mitochondrial DNA deletions in skin samples of people
 with HIV with measure of neuropathy and prior exposure to therapy. We
 hypothesized that deletions would be associated with the presence of
 neuropathy. As secondary objectives we determined the correlation of
 deletion burden with demographic data and neuropathy measures. Methods: In
 this retrospective cohort study we measured the accumulation of large
 mtDNA deletions in skin biopsies from PWH recruited as part of the ACTG.
 Our cohort includes individuals with and without sensory neuropathy, as
 well as individuals with normal or abnormal skin biopsies. Skin biopsies,
 sural and peroneal nerve conduction studies, Total Neuropathy Score and
 deletion burden scores were measured along with baseline demographic data
 such as age, CD+4 cell count, viral counts and prior dNRTI exposures.
 Results: Sixty-seven PWH were enrolled in the study. The mean age of the
 cohort (n=67) was 44 years (SD 6.8, range 32-65 years) and 9 were female.
 The mean CD4+ T-cell count was 168 cells/mm3 (SD 97, range 1 – 416) and
 mean viral load was 51129 copies/mL (SD 114586, range 147 – 657775). We
 determined that there was a correlation between the total mtDNA deletion
 and IENFD (r=-0.344, p=0.04) and sural nerve amplitude (r=-0.359,
 p=0.004). Conclusions: IENFD and sural nerve amplitude both statistically
 correlate with mitochondrial mutation burden in PWH, specifically in those
 with HIV-SN as assessed by skin biopsy.
DOI: 10.5061/dryad.3j9kd51h2
title: Data from: Association of venous outflow profiles and successful vessel reperfusion after thrombectomy

description: Background and Purpose: Robust arterial collaterals are associated with
 successful reperfusion after thrombectomy treatment of acute ischemic
 stroke due to large vessel occlusion (AIS-LVO). Excellent venous outflow
 (VO) reflects excellent tissue perfusion and collateral status in AIS-LVO
 patients. Objective: To determine whether favorable VO profiles assessed
 on pre-treatment CT angiography (CTA) images correlate with successful
 vessel reperfusion after thrombectomy in AIS-LVO patients. Materials and
 Methods: Multicenter retrospective cohort study of consecutive AIS-LVO
 patients treated by thrombectomy. Baseline CTA was used to assess
 collateral status (Tan scale) and VO using the cortical vein opacification
 score (COVES). Favorable VO was defined as COVES ≥3. Primary outcome was
 excellent vessel reperfusion status (modified Thrombolysis In Cerebral
 Infarction [TICI] 2c-3). Secondary outcome was good functional outcome
 defined as 0-2 on the Modified Ranking Scale (mRS) after 90 days. Results:
 565 patients met inclusion criteria. Multivariable logistic regression
 analysis showed that favorable VO (OR= 2.10 [95% CI 1.39-3.16];
 p&lt;0.001) was associated with excellent vessel reperfusion during
 thrombectomy, regardless of good CTA collateral status (OR= 0.87 [95%CI
 0.58-1.34]; p=0.48). A favorable VO profile (OR= 8.9 [95%CI 5.3-14.9];
 p&lt;0.001) and excellent vessel reperfusion status (OR = 2.7 [95%CI
 1.7-4.4]; p&lt;0.001) were independently associated with good
 functional outcome adjusted for age, sex, glucose, tPA administration,
 good CTA collateral status and presentation NIHSS. Conclusion: A favorable
 VO profile is associated with reperfusion success and good functional
 outcomes in patients with AIS-LVO treated by endovascular thrombectomy.
DOI: 10.15468/dl.6tv76g
title: Occurrence Download

description: A dataset containing 392 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Fagus hayatae"
 ]
}

 The dataset includes 392 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002767-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.x95x69ph9
title: First Atlantic satellite tracks of lost years green turtles support the importance of the Sargasso Sea as a sea turtle nursery

description: In-water behaviour and long-term movements of oceanic-stage juvenile sea
 turtles are not well described or quantified. This is due to technological
 or logistical limitations of tracking small, fast-growing animals across
 long distances and time-periods within marine habitats. Here we present
 the first long-term offshore tracks of oceanic green turtles (Chelonia
 mydas) in western North Atlantic waters. Using a tag attachment technique
 developed specifically for young (&lt;1 year old) green turtles, we
 satellite tracked 21 oceanic-stage green turtles (&lt;19 cm straight
 carapace length) up to 152 days using small, solar-powered transmitters.
 We verify that oceanic-stage green turtles: (i) travel to and remain
 within oceanic waters; (ii) often depart the Gulf Stream and North
 Atlantic Subtropical Gyre currents, orienting toward waters associated
 with the Sargasso Sea; (iii) remain at the sea surface, using
 thermally-beneficial habitats that promote growth and survival of young
 turtles; and (iv) green turtles orient differently compared to same stage
 loggerhead turtles (Caretta caretta). Combined with satellite tracks of
 oceanic-stage loggerhead turtles, our work identifies the Sargasso Sea as
 an important nursery habitat for North Atlantic sea turtles, supporting a
 growing body of research that suggests oceanic-stage sea turtles are
 behaviourally more complex than previously assumed.
description: Please contact data owner for additional details or refer to the
 published article. Data collected via ARGOS satellites and small
 solar-powered satellite tags. 
description: Please contact data owner for additional details if
 needed.  Loggerhead file: Turtle ID
 refers to the unique tag identifying number assigned to indivirual
 turtles GMT: Greenwich Mean Time
 Local: Greenwich Mean Time converted to local time (local meaning
 the location of the turtle at the time the latitude and longitude was
 received).   Green turtle
 file: tag_id: refers to the unique tag identifying
 number assigned to indivirual turtles UTC: refers to
 Coordinated Universal Time (and date) for each location (latitude and
 longitude) received by the tags. lc: refers to
 ARGOS/CLS America location codes for each loccation receoved (Codes range
 from 0-3, A, B, and Z). Dir 1: refers to the direction
 relative to the Equator for each location. This is associated with the
 longitude; all locations are  within the northern hemisphere or
 N) Dir 2:  refers to the direction relative to the
 Prime Meridian in Greenwich, UK for each transmitter locatoin. This
 is associated with the latitude; all locations are  west of the Greenwish
 Prime Meridian, therefore W.
DOI: 10.5061/dryad.xsj3tx9dq
title: Influence of YES1 kinase and tyrosine phosphorylation on the activity of OCT1

description: Organic cation transporter 1 (OCT1) is a transporter that regulates the
 hepatic uptake and subsequent elimination of diverse cationic compounds.
 Although OCT1 has been involved in drug-drug interactions and causes
 pharmacokinetic variability of many prescription drugs, details of the
 molecular mechanisms that regulate the activity of OCT1 remain
 incompletely understood. Based on an unbiased phospho-proteomics screen,
 we identified OCT1 as a tyrosine-phosphorylated transporter, and
 functional validation studies using genetic and pharmacological approaches
 revealed that OCT1 is highly sensitive to small molecules that target the
 protein kinase YES1, such as dasatinib. In addition, we found that
 dasatinib can inhibit hepatic OCT1 function in mice as evidenced from its
 ability to modulate levels of isobutyryl L-carnitine, a hepatic OCT1
 biomarker identified from a targeted metabolomics analysis. These findings
 provide novel insight into the post-translational regulation of OCT1 and
 suggest that caution is warranted with polypharmacy regimes involving the
 combined use of OCT1 substrates and kinase inhibitors that target YES1.
description: The tyrosine-phosphorylation landscape of ADME proteins was
 evaluated in FVB mice with the genetic deletion of OCT1/2 transporters
 using LC-MS/MS.
description: The dataset contains both liver metabolomics (males and females),
 and phosphotyrosine proteomics data from kidney samples. In the liver
 metabolic data, certain cells are marked as red color which represents
 p-values &lt;0.05.
DOI: 10.5061/dryad.z08kprrc0
title: Canalization of seasonal phenology in the presence of developmental variation: seed dormancy cycling in an annual weed

description: Variation in the developmental timing in one life stage may ramify within
 and across generations to disrupt optimal phenology of other life stages.
 By focusing on a common mechanism of developmental arrest in plants-seed
 dormancy-we investigated how variation in flowering time influenced seed
 germination behavior and identified potential processes that can lead to
 canalized germination behavior despite variation in reproductive timing.
 We quantified effects of reproductive timing on dormancy cycling by
 experimentally manipulating the temperature during seed maturation and the
 seasonal timing of seed dispersal/burial, and by assessing
 temperature-dependent germination of un-earthed seeds over a seasonal
 cycle. We found that reproductive timing, via both seed-maturation
 temperature and the timing of dispersal, strongly influenced germination
 behavior in the weeks immediately following seed burial. However, buried
 seeds subsequently canalized their germination behavior, after losing
 primary dormancy and experiencing natural temperature and moisture
 conditions in the field. After the complete loss of primary dormancy,
 germination behavior was similar across seed-maturation and dispersal
 treatments, even when secondary dormancy was induced. Maternal effects
 themselves may contribute to the canalization of germination: first, by
 inducing stronger dormancy in autumn-matured seeds, and second by
 modifying the responses of those seeds to their ambient environment.
 Genotypes differed in dormancy cycling, with functional alleles of known
 dormancy genes necessary for the suppression of germination at warm
 temperatures in autumn through spring across multiple years. Loss of
 function of dormancy genes abolished almost all dormancy cycling. In
 summary, effects of reproductive phenology on dormancy cycling of buried
 seeds were apparent only as long as seeds retained primary dormancy, and a
 combination of genetically imposed seed dormancy, maternally induced seed
 dormancy, and secondary dormancy can mitigate variation in germination
 behavior imposed by variation in reproductive phenology.
description: Regular censuses of phenological stages in the field
DOI: 10.5061/dryad.9w0vt4bds
title: Cnidocyte discharge analysis

description: Complex biological traits often originate by integrating previously
 separate parts, but the organismal functions of these precursors are
 challenging to infer. If we can understand the ancestral functions of
 these precursors, it could help explain how they persisted and how they
 facilitated the origins of complex traits. Animal eyes are some of the
 best studied complex traits, and they include many parts, such as
 opsin-based photoreceptor cells, pigment cells, and lens cells. Eye
 evolution is understood through conceptual models that argue these parts
 gradually came together to support increasingly sophisticated visual
 functions. Despite the well accepted logic of these conceptual models,
 explicit comparative studies to identify organismal functions of
 eye-precursors are lacking. Here, we investigate how precursors functioned
 before they became part of eyes in Cnidaria, a group formed by sea
 anemones, corals and jellyfish. Specifically, we test whether ancestral
 photoreceptor cells regulated the discharge of cnidocytes, the expensive
 single-use cells with various uses including prey capture, locomotion, and
 protection. Similar to a previous study of Hydra, we show an
 additional four distantly related cnidarian groups discharge significantly
 more cnidocytes when exposed to dim blue light compared to bright blue
 light. Our comparative analyses support the hypothesis that the cnidarian
 ancestor was capable of modulating cnidocyte discharge with light, which
 we speculate uses an opsin-based phototransduction pathway homologous to
 that previously described in Hydra. Although eye precursors might
 have had other functions like regulating timing of spawning, our findings
 are consistent with the hypothesis that photoreceptor cells which mediate
 cnidocyte discharge predated eyes, perhaps facilitating the prolific
 origination of eyes in Cnidaria.
DOI: 10.5061/dryad.c59zw3r6p
title: Shorter distal forelimbs benefit bipedal walking and running mechanics: implications for hominin forelimb evolution

description: This file provides the data from the manuscript "Shorter distal
 forelimbs benefit bipedal walking and running mechanics: implications for
 hominin forelimb evolution" sin the American Journal of Physical
 Anthropology. Objectives: Brachial index is a skeletal ratio that
 describes the relative length of the distal forelimb. Over the course of
 hominin evolution, a shift towards smaller brachial
 indices occurred. First,
 Pleistocene australopiths yield values between
 extant chimpanzees and humans, with further evolution
 in Pliocene Homo to the modern human
 range. We hypothesized that shorter distal forelimbs benefit
 walking and running performance, notably elbow and
 shoulder joint torques, and predicted that the benefit would be
 greater in running compared to walking. Materials and Methods: We
 tested our hypothesis in a modern
 human sample walking and running while carrying hand
 weights, which increase the inertia (mass
 and effective length) of the distal forelimb, simulating
 a larger brachial index. Results: We found longer distal
 forelimbs and the added mass increased
 elbow muscle torque by 98% while walking and 70% in running, confirming
 our hypothesis that shorter distal forelimbs benefit walking and
 running performance. Shoulder muscle torque similarly increased
 in both gaits with the addition of hand weights due to elongation of the
 effective forelimb length. Normalized elbow torque, which accounted for
 the effect on shoulder torque caused by the experimental manipulation,
 increased by 16% while walking but 52% while running, indicating that
 shorter distal forelimbs provide a greater benefit for running by
 approximately three-fold. Discussion: Selection for
 economical bipedal walking
 in Australopithecus and endurance running
 in Homo likely contributed to the shift towards
 relatively smaller distal forelimbs across hominin
 evolution, with modern human proportions attained in
 Pleistocene Homo erectus and retained in later
 species.
description: The data contained here represent intersubject means and standard
 errors. The underlying data were collected using motion capture (Qualysys
 AB, Goteborg, Sweden) while subjects walked and ran on an instrumented
 (Bertec Corp., Columbus OH, USA). The subjects walked and ran normally and
 holding extra mass in their hands.
description: The data contained here represent intersubject means and standard
 errors, and are presented graphically in the main paper. Elbow angle and
 torque, as well as shoulder angle and torque, are given as time series.
 The x-axis is percent of the stride cycle, and therefore is
 time-normalized. Note that statistical comparisons between data from the
 normal and added mass conditions must account for repeated measures, as
 each subject participated in all conditions.
DOI: 10.5061/dryad.6wwpzgmxr
title: Spatial patterns and ecological drivers of soil nematode β-diversity in natural grasslands vary among vegetation types and trophic position

description: 1. Understanding biogeographic patterns of community assemblages is a core
 objective in ecology, but for soil communities these patterns are poorly
 understood. To understand the spatial patterns and underlying mechanisms
 of β-diversity in soil communities, we investigated the β-diversity of
 soil nematode communities along a 3200 km transect across semi-arid and
 arid grasslands. 2. Spatial turnover and nested-resultant are the two
 fundamental components of β-diversity, which have been attributed to
 various processes of community assembly. We calculated the spatial
 turnover and nested-resultant components of soil nematode β-diversity
 based on the β-partitioning framework. Distance matrices for the
 dissimilarity of soil nematode communities were computed using the
 “Sørensen” method. We fitted negative exponential models to compare the
 distance decay patterns in nematode community similarity with geographic
 distance and plant community distance in three vegetation types (desert,
 desert steppe, and typical steppe) and along the whole transect. Variation
 partitioning was used to distinguish the contribution of geographic
 distance and environmental variables to β-diversity and the partitioned
 components. 3. Geographic distance and environmental filtering jointly
 drove the β-diversity patterns of nematode community, but environmental
 filtering explained more of the variation in β-diversity in the desert and
 typical steppe, whereas geographic distance was important in the desert
 steppe. Nematode community assembly was explained more by the spatial
 turnover component than by the nested-resultant component. For nematode
 feeding groups, the β-diversity in different vegetation types increased
 with geographic distance and plant community distance, but the
 nested-resultant component in the desert ecosystem decreased with
 geographic distance and plant community distance. 4. Our findings show
 that spatial variation in soil nematode communities is regulated by
 environmental processes at the vegetation type scale, while spatial
 processes mainly work on the regional scale, and emphasize that the
 spatial patterns and drivers of nematode β-diversity differ among trophic
 levels. Our study provides insight into the ecological processes that
 maintain soil biodiversity and biogeographic patterns of soil community
 assemblage at large spatial scales. 28-Jan-2021
DOI: 10.5061/dryad.0rxwdbrzj
title: Supplementary data to the paper: Causal association between serum thyroid-stimulating hormone and obesity: A bidirectional Mendelian randomization study

description: Context The association between serum thyroid-stimulating hormone (TSH)
 and obesity traits has been investigated previously in several
 epidemiological studies. However, the underlying causal association has
 not been established. Objective To determine and analyze the causal
 association between serum TSH level and obesity-related traits (BMI and
 obesity). Design, Setting, Participants The latest genome-wide association
 studies (GWASs) on TSH, BMI and obesity were searched to obtain full
 statistics. Bidirectional two-sample Mendelian randomization (MR) was
 performed to explore the causal relationship between serum TSH and BMI and
 obesity. The inverse variance-weighted (IVW) and MR-Egger methods were
 used to combine the estimation for each SNP. Based on the preliminary MR
 results, free thyroxine (fT4) and free triiodothyronine (fT3) levels were
 also set as outcomes to further analyze the impact of BMI on them. Main
 Outcome Measures BMI and obesity were treated as the outcomes to evaluate
 the effect of serum TSH on them, and TSH was set as the outcome to
 estimate the effect of BMI and obesity on it. Results Both IVW and
 MR-Egger results indicated that genetically driven serum TSH did not
 causally lead to changes in BMI or obesity. Moreover, the IVW method
 showed that the TSH level could be significantly elevated by genetically
 predicted high BMI (β=0.038, se=0.013, p=0.004). In further MR analysis,
 the IVW method indicated that BMI could causally increase the fT3
 (β=10.123, se=2.523, p&lt;0.001) while not significantly affecting the
 fT4 level. Conclusion Together with fT3, TSH can be significantly elevated
 by an increase in genetically driven BMI.