cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9w0vt4bbg
title: Interaction of field realistic doses of clothianidin and Varroa destructor parasitism on adult honey bee (Apis mellifera L.) health and neural gene expression, and antagonistic effects on differentially expressed genes

description: While many studies have examined the effects of neonicotinoid insecticides
 and the parasitic mite Varroa destructor on honey bees
 (Apis mellifera), more information on the combined effects of such
 stressors on gene expression, including neural related genes, and their
 impact on biological pathways is needed. This study analyzed the effects
 of field realistic concentrations of the neonicotinoid clothianidin on
 adult bees infested and not infested
 with V. destructor over 21 consecutive days and
 then determined bee survivorship, weight, deformed wing virus (DWV) levels
 and gene expression. V. destructor parasitism
 with or without clothianidin exposure was significantly associated with
 decreased survivorship, weight loss and higher DWV levels, while
 clothianidin exposure was only associated with higher levels of DWV.
 Expression analysis of the neural
 genes AmNlg-1, BlCh and AmAChE-2 showed that V. destructor caused a significant down-regulation of all of them, whereas clothianidin caused a significant down-regulation of only AmNrx-1 and BlCh. An interaction was only detected for AmNrx-1 expression. RNAseq analysis showed that clothianidin exposure resulted in 6.5 times more up-regulated differentially expressed genes (DEGs) than V. destructor alone and 123 times more than clothianidin combined with V. destructor. Similar results were obtained with down-regulated DEGs, except for a higher number of DEGs shared between V. destructor and the combined stressors. KEGG (Kyoto Encyclopedia of Genes and Genomes) biological pathway analysis of the DEGs showed that the stressor linked to the highest number of KEGG pathways was clothianidin, followed by V. destructor, and then considerably fewer number of KEGG pathways with the combined stressors. The reduced numbers of DEGs and KEGG pathways associated with the DEGs for the combined stressors compared to the stressors alone indicates that the interaction of the stressors is not additive or synergistic, but antagonistic. The possible implications of the antagonistic effect on the number of DEGs are discussed.
description: The description of the collection of the data is described in the
 research article Morfin N, Goodwin PH, Guzman-Novoa E. Interaction of
 field realistic doses of clothianidin and <em>Varroa
 destructor</em> parasitism on adult honey bee (<em>Apis
 mellifera</em> L.) health and neural gene expression, and
 antagonistic effects on differentially expressed genes. PloS ONE. 2020 Feb
 20;15(2):e0229030.
DOI: 10.5281/zenodo.18394745
title: STUDYING THE POSITIVE AND NEGATIVE EFFECTS OF MUD AND COPPER IN COMBINATION ON THE ORGANISM AND SKIN, AS WELL AS STUDYING THE EFFECTS OF MUD SOLUTION PREPARED IN COPPER CONTAINERS ON THE ORGANISM

description: Strengthening the body as a result of external influences and their methods, as well as the widespread promotion of physiotherapeutic procedures among the population.
DOI: 10.5061/dryad.wwpzgmsg5
title: Data from: Leptin increases sympathetic nerve activity via induction of its own receptor in the paraventricular nucleus

description: Whether leptin acts in the paraventricular nucleus (PVN) to increase
 sympathetic nerve activity (SNA) is unclear, since PVN leptin receptors
 (LepR) are sparse. We show in rats that PVN leptin slowly increases SNA to
 muscle and brown adipose tissue, because it induces the expression of its
 own receptor and synergizes with local glutamatergic neurons. PVN LepR are
 not expressed in astroglia and rarely in microglia; instead, glutamatergic
 neurons express LepR, some of which project to a key presympathetic hub,
 the rostral ventrolateral medulla (RVLM). In PVN slices from mice
 expressing GCaMP6, leptin excites glutamatergic neurons. LepR are
 expressed mainly in thyrotropin-releasing hormone (TRH) neurons, some of
 which project to the RVLM. Injections of TRH into the RVLM and dorsomedial
 hypothalamus increase SNA, highlighting these nuclei as likely targets. We
 suggest that this neuropathway becomes important in obesity, in which
 elevated leptin maintains the hypothalamic pituitary thyroid axis, despite
 leptin resistance.
description: Physiological data was collected and processed using Biopac
 Systems, Inc, A-D system. Imagery was collected using
 Zen Blue and ImageJ.
DOI: 10.5281/zenodo.18394744
title: STUDYING THE POSITIVE AND NEGATIVE EFFECTS OF MUD AND COPPER IN COMBINATION ON THE ORGANISM AND SKIN, AS WELL AS STUDYING THE EFFECTS OF MUD SOLUTION PREPARED IN COPPER CONTAINERS ON THE ORGANISM

description: Strengthening the body as a result of external influences and their methods, as well as the widespread promotion of physiotherapeutic procedures among the population.
DOI: 10.7280/d19t0c
title: Ionic amplifying circuits inspired by electronics and biology

description: Integrated circuits are present in all electronic devices, and enable
 signal amplification, modulation, and relay. Nature uses another type of
 circuits composed of channels in a cell membrane, which regulate and
 amplify transport of ions, not electrons and holes as is done in
 electronic systems. Here we show an abiotic ionic circuit that is inspired
 by concepts from electronics and biology. The circuit amplifies small
 ionic signals into ionic outputs, and its operation mimics the electronic
 Darlington amplifier composed of transistors. The individual transistors
 are pores equipped with three terminals including a gate that is able to
 enrich or deplete ions in the pore. The circuits we report function at
 gate voltages &lt; 1 V, respond to sub-nA gate currents, and offer ion
 current amplification with a gain up to ~300. Ionic amplifiers are a
 logical step toward improving chemical and biochemical sensing,
 separations and amplification, among others.
description: The data sets provided in cvs files correspond to experimental
 recordings shown in the main manuscript and supporting information
 file. All recordings were performed using Keithley 6487
 picoammeter/voltage source and Keithley 2450 (Keithley Instruments,
 Cleveland, OH) as described in the Experimental Section of the
 manuscript.
description: This file was prepared by Zuzanna Siwy on July 29,
 2021. The uploaded data file correspond to experimental
 results presented in the following publication: R.A. Lucas, C.Y. Lin, Lane
 A. Baker, Z.S. Siwy, <em>Nature Comm. </em>vol. 11, article
 nr. 1568 (2020). The files Principle
 investigators: Zuzanna S. Siwy, Department of Physics
 and Astronomy, University of California, Irvine, Irvine, CA 92697, e-mail
 address: zsiwy@uci.edu Lane A. Baker, Department of
 Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN,
 47405, USA, e-mail: lanbaker@indiana.edu The data were
 recorded between winter 2019 and winter 2020.  The
 project was supported by the National Science Foundation (CBET-1803262
 & CBET-1803002).
DOI: 10.7272/q6dz06hn
title: HIV efficiently infects T cells from the endometrium and remodels them to promote systemic viral spread

description: The female reproductive tract (FRT) is the most common site of infection
 during HIV transmission to women, but viral remodeling complicates
 characterization of cells targeted for infection. Here, we report
 extensive phenotypic analyses of HIV-infected endometrial cells by CyTOF,
 and use a "nearest neighbor" bioinformatics approach to trace
 cells to their original pre-infection phenotypes. Like in blood, HIV
 preferentially targets memory CD4+ T cells in the endometrium, but these
 cells exhibit unique phenotypes and sustain much higher levels of
 infection. Genital cell remodeling by HIV includes downregulating TCR
 complex components and modulating chemokine receptor expression to promote
 dissemination of infected cells to lymphoid follicles. HIV also
 upregulates the anti-apoptotic protein BIRC5, which when blocked promotes
 death of infected endometrial cells. These results suggest that HIV
 remodels genital T cells to prolong viability and promote viral
 dissemination a nd that interfering with these processes might reduce the
 likelihood of systemic viral spread.
DOI: 10.5061/dryad.cvdncjt14
title: Overtone focusing in biphonic Tuvan throat singing

description: Khoomei is a unique singing style originating from the Central Asian
 republic of Tuva. Singers produce two pitches simultaneously: a booming
 low-frequency rumble alongside a hovering high-pitched whistle-like tone.
 The biomechanics of this biphonation are not well-understood. Here, we use
 sound analysis, dynamic magnetic resonance imaging, and vocal tract
 modeling to demonstrate how biphonation is achieved by modulating vocal
 tract morphology. Tuvan singers show remarkable control in shaping their
 vocal tract to narrowly focus the harmonics (or overtones) emanating from
 their vocal cords. The biphonic sound is a combination of the fundamental
 pitch and a focused filter state, which is at the higher pitch (1-2 kHz)
 and formed by merging two formants, thereby greatly enhancing
 sound-production in a very narrow frequency range. Most importantly, we
 demonstrate that this biphonation is a phenomenon arising from linear
 filtering rather than a nonlinear source.
description: Data is a combination of acoustical recordings, MRI data, and
 vocal tract modeling. Movie of the dynamic MRI data are also included. All
 details are included in the manuscript "Overtone focusing in biphonic
 Tuvan throat singing".
description: Data is placed in four zipped files (compression done via Mac OS
 10.12.4). The four files each contain a particular subset of the
 data: 1. Model.zip - Modeling software (Tube Talker)
 and several illustrative simulations 2.
 CroppedMRI_CB.zip - Both statis and dynamic MRI images (as .dcm files).
 Note that the DICOM files have been cropped (so to only show the relevant
 anatomical features) and metadata have been stripped.
 3. SoundboothRecordings.zip - All soundbooth recordings, saved as
 .wav files (SR 96 kHz) 4. STL.zip - Reonstruction of
 the 3-D airspace, saved as a .stl file 5. MRIaudio.zip
 - Audio files collected during the MRI runs 6.
 MRImoviesC.zip - Movies of the dynamic data (with audio).
DOI: 10.5061/dryad.jwstqjq5n
title: Evolution of altitudinal migration in passerines is linked to diet

description: Bird migration is typically associated with a latitudinal movement from
 north to south and vice versa. However, many bird species migrate
 seasonally with an upslope or downslope movement in a process termed
 altitudinal migration. Globally, 830 of the 6579 Passeriformes species are
 considered altitudinal migrants and this pattern has emerged multiple
 times across 77 families of this order. Recent work has indicated an
 association between altitudinal migration and diet, but none have looked
 at diet as a potential evolutionary driver. Here, we investigated
 potential evolutionary drivers of altitudinal migration in passerines
 around the world by using phylogenetic comparative methods. We tested for
 evolutionary associations between altitudinal migration and foraging guild
 and primary habitat preference in passerines species worldwide. Our
 results indicate that foraging guild is evolutionarily associated with
 altitudinal migration, but this relationship varies across zoogeographical
 regions. In the Nearctic, herbivorous and omnivorous species are
 associated with altitudinal migration, while only omnivorous species are
 associated with altitudinal migration in the Palearctic. Habitat was not
 strongly linked to the evolution of altitudinal migration. While our
 results point to diet as a potentially important driver of altitudinal
 migration, the evolution of this behaviour is complex and certainly driven
 by multiple factors. Altitudinal migration varies in its use (for breeding
 or moulting), within a species, population, and even at the individual
 level. As such, the evolution of altitudinal migration is likely driven by
 an ensemble of factors, but this study provides a beginning framework for
 understanding the evolution of this complex behaviour.
DOI: 10.5061/dryad.s1rn8pk4f
title: Coevolution, diversification, and alternative states in two-trophic communities

description: Single-trait eco-evolutionary models of arms races between consumers and
 their resource species often show inhibition rather than promotion of
 community diversification. In contrast, modeling arms races involving
 multiple traits, we found that arms races can promote diversification when
 trade-off costs among traits make simultaneous investment in multiple
 traits either more beneficial or more costly. Coevolution between resource
 and consumer species generates an adaptive landscape for each, with the
 configuration giving predictable suites of consumer and resource species.
 Nonetheless, the adaptive landscape contains multiple alternative stable
 states, and which stable community is reached depends on small stochastic
 differences occurring along evolutionary pathways. Our results may solve a
 puzzling conflict between eco-evolutionary theory that predicts community
 diversification via consumer-resource interactions will be rare, and
 empirical research that has uncovered real cases. Furthermore, our results
 suggest that these real cases might be just a subset of alternative stable
 communities.
description: Matlab code for the clone-based model in the text, and R code for
 the quantitative genetics model in the text.
description: Both Matlab files are needed to run the clone-based model.
DOI: 10.5061/dryad.j0zpc869n
title: Developmental changes in bone mechanics from Florida manatees (Trichechus manatus latirostris), obligate swimming mammals

description: Mammals living in aquatic environments load their axial skeletons
 differently than their terrestrial counterparts. The structure and
 mechanical behavior of trabecular bone can be especially indicative of
 varying habitual forces. Here, we investigate vertebral trabecular bone
 mechanical properties (yield strength, stiffness, and toughness)
 throughout development in Florida manatees (Trichechus manatus
 latirostris), obligate undulatory swimmers. Thoracic, lumbar, and caudal
 vertebrae were dissected from manatees (N=20) during necropsies. We
 extracted 6 mm3 samples from vertebral bodies and tested them in
 compression in three orientations (rostrocaudal, dorsoventral, and
 mediolateral) at 2 mm min-1. We determined variation in mechanical
 properties between sexes, and among developmental stages, vertebral
 regions, and testing orientations. We also investigated the relationships
 between vertebral process lengths and properties of dorsoventrally and
 mediolaterally-tested bone. Rostrocaudally-tested bone was the strongest,
 stiffest, and toughest, suggesting that this is the principle direction of
 stress. Our results showed that bone from female subadults was stronger
 and stiffer than their male counterparts; based on these data we
 hypothesize hormonal shifts at sexual maturity may partially drive these
 differences . In calves, bone from the posterior region was stronger and
 tougher than from the anterior region. We hypothesize that since animals
 grows rapidly throughout early development, bone in the posterior region
 would be the most ossified to support the rostrocaudal force propagation
 associated with undulatory swimming .
description: We
 destructively tested bone cubes (from manatee vertebrae) in compression to
 yield at a displacement rate of 2 mm min<sup>-1</sup> using an
 Instron E1000 material tester. We converted force-displacement curves to
 engineering stress-strain (σ-ε) curves, which standardizes the compressive
 load (N) by dividing the force by the cross-sectional area (width •
 height: mm<sup>2</sup>) and displacement by dividing the
 change in length (mm) by the original length (mm). Yield was defined as
 the point where the sample transitioned from elastic to plastic
 deformation, as seen on the σ-ε curve (Fig. S1). We calculated stiffness
 (<i>E</i>: Young’s Modulus), or the resistance to deformation,
 as the slope of the steepest point of the linear portion of the σ-ε curve.
 Yield strength (σ<sub>y</sub>) indicates σ when the material
 transitions from elastic to plastic deformation (stress at permanent
 deformation). Toughness (U<sub>r</sub>) is the ability to
 absorb energy and was derived as the area under the σ-ε up until a yield
 behavior. We calculated mechanical properties using Bluehill Universal
 Software v.3.67 (Instron, Norwood, MA, USA).
DOI: 10.15468/dl.637z9v
title: Occurrence Download

description: A dataset containing 756 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 2015"
 ]
}

 The dataset includes 756 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002197-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.573n5tb44
title: Data from: Entropic bonding of the type 1 pilus from experiment and simulation

description: The type 1 pilus is a bacterial filament consisting of a long coiled
 proteic chain of subunits joined together by non-covalent bonding between
 complementing β-strands. Its strength and structural stability are
 critical for its anchoring function in uropathogenic Escherichia
 coli bacteria. The pulling and unravelling of the FimG subunit of
 the pilus was recently studied by atomic force microscopy (AFM)
 experiments and steered molecular dynamics (SMD) simulations [A.
 Alonso-Caballero et al., Nature Commun. 9, 2758 (2018)]. In this work we
 perform a quantitative comparison between experiment and simulation,
 showing a good agreement in the underlying work values for the unfolding.
 The simulation results are then used to estimate the free energy
 difference for the detachment of FimG from the complementing strand of the
 neighbouring subunit in the chain, FimF. Finally, we show that the large
 free energy difference for the unravelling and detachment of the subunits
 which leads to the high stability of the chain is entirely entropic in
 nature.
DOI: 10.5061/dryad.pk0p2ngjk
title: Respiratory medium and circulatory anatomy constrain size evolution in marine macrofauna

description: The typical marine animal has increased in biovolume by more than two
 orders of magnitude since the beginning of the Cambrian, but the causes of
 this trend remain unknown. We test the hypothesis that the efficiency of
 intra-organism oxygen delivery is a major constraint on body size
 evolution in marine animals. To test this hypothesis, we compiled a
 dataset comprising 13,723 marine animal genera spanning the Phanerozoic.
 We coded each genus according to its respiratory medium, circulatory
 anatomy, and feeding mode. In extant genera, we find that respiratory
 medium and circulatory anatomy explain more of the difference in size than
 feeding modes. Likewise, we find that most of the Phanerozoic increase in
 mean biovolume is accounted for by size increase in taxa that accomplish
 oxygen delivery through closed circulatory systems. During the Cambrian,
 water-breathing animals with closed circulatory systems were smaller, on
 average, than contemporaries with open circulatory systems. However,
 genera with closed circulatory systems superseded in size genera with open
 circulatory systems by the middle Ordovician, as part of their
 Phanerozoic-long trend of increasing size. In a regression analysis,
 respiratory and circulatory anatomy explain far more size variation in the
 living fauna than do feeding modes, even after accounting for taxonomic
 affinity at the class level. These findings suggest that ecological
 drivers of the Phanerozoic increase in the mean size of marine animals
 operated within strong, anatomically determined constraints.
description: See publication for descirption of data collection and
 processing.
description: See ReadMe.txt
DOI: 10.5061/dryad.1jwstqjrb
title: Did hard substrate taxa diversify prior to the Great Ordovician Biodiversification Event?

description: The Great Ordovician Biodiversification Event (GOBE) refers to one of the
 greatest increases in biodiversity during the Phanerozoic. Recent studies
 have shown that this taxonomic increase can be attributed to elevated
 origination rates around the Dapingian-Darriwilian boundary in the Middle
 Ordovician, while extinction rates stayed relatively constant throughout
 the Ordovician. Even though this global pattern of origination and
 extinction appears similar across diverse groups and geographic areas,
 earlier studies suggested that hard substrate taxa may have diversified
 prior to the GOBE, during the Early Ordovician. Here, we quantify
 Ordovician diversification dynamics of hard substrate taxa while
 simultaneously accounting for temporally varying sampling probabilities.
 Diversification rates of hard substrate taxa, both as a whole and when
 analysed as separate groups, appear to be very similar to those of
 free-living benthic taxa. The observation that the diversification
 dynamics of many different taxonomic and ecological groups show the same
 temporal pattern, suggests a common-cause to Ordovician diversification
 dynamics.
description: Supplementary File overview for<br> Franeck and Liow
 2020<br> Did hard substrate taxa diversify prior to the Great
 Ordovician Biodiversification? Please note that all
 RCodes need the csv files<br> - PBDB_C-S_data.csv<br> -
 Rasmussen_Ord_data_stratcorrelation.csv<br> -
 Rasmussen_Ord_data_TS.csv<br> - assignments.csv<br> as input
 files. If these files are not accessible for the RCode, the code
 won't run.<br> Please specify the file locations in the code
 before running them. The RCodes and their usage for the
 manuscript are as follows:<br> - R1.covariate.modcomparison.R
 provides the RCode for the model comparison, AICc estimation and Fig.
 S6.<br> - R1.hs.ind.R provides the RCode for the individual
 parameter estimations of hard substrate taxa<br> (namely attaching
 echinoderms, bryozoans, poriferans and corals). This code is the source
 for Fig. 2 and Figs. S3 and S4.<br> - R1.hstaxa.vs.fltaxa.R provides
 the code for the comparison of hard substrate and free-living benthic
 taxa.<br> This code is the source for Fig. 1, and Fig. S2.<br>
 - R1.comp.Fig.R provides the code for Fig. S3.