cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cjsxksn5j
title: Data for butterfly near-infrared adaptation research

description: Climatic gradients frequently predict large-scale ecogeographical patterns
 in animal coloration, but the underlying causes are often difficult to
 disentangle. We examined ecogeographical patterns of reflectance among 343
 European butterfly species and isolated the role of selection for thermal
 benefits by comparing animal-visible and near-infrared (NIR) wavebands.
 NIR light accounts for ~50% of solar energy but cannot be seen by animals
 so functions primarily in thermal control. We found that reflectance of
 both dorsal and ventral surfaces shows thermally adaptive correlations
 with climatic factors including temperature and precipitation. This
 adaptive variation was more prominent in NIR than animal-visible wavebands
 and for body regions (thorax-abdomen and basal wings) that are most
 important for thermoregulation. Thermal environments also predicted the
 reflectance difference between dorsal and ventral surfaces, which may be
 due to modulation between requirements for heating and cooling. These
 results highlight the importance of climatic gradients in shaping the
 reflectance properties of butterflies at a continent-wide scale.
DOI: 10.5061/dryad.gb5mkkwpq
title: Data from: Black goby territorial males adjust their ejaculate’s characteristics in response to the presence of sneakers

description: In many species males can rapidly adjust their ejaculate performance in
 response to changing levels of sperm competition, an ability that is
 probably mediated by seminal fluid adaptive plasticity. In the black
 goby, Gobius niger, female spawning in the nest of a territorial
 male can last hours, and males attach a viscous ejaculate to the nest
 roof, from which sperm are slowly released. During spawning, sneaker males
 attempt to approach the nest and release their sperm, and territorial
 males intensify their defensive effort at the increasing of sneaking
 pressure. We show here that territorial males adjust the characteristics
 of their seminal fluid in response to the number of competitor sneakers.
 Territorial males produce an ejaculate from which sperm are released at a
 rate that decreases as the number of surrounding competitor sneakers
 increases. Field observations showed that multiple sneaking attempts
 occurred sequentially, forcing territorials to frequently leave the
 nest. Overall these results suggest that the adjustment of
 seminal fluid viscosity may guarantee a continuous release of sperm from
 the ejaculate, although at a lower rate, when the territorial male is
 engaged in prolonged nest defense possibly minimizing the postcopulatory
 cost of an increased precopulatory mate guarding.
DOI: 10.5061/dryad.2280gb5rq
title: Alterations of brain metabolites in adults with HIV: a systematic meta-analysis of MRS studies

description: Objective. A meta-analysis of proton magnetic resonance
 spectroscopy (MRS) studies to investigate alterations in brain metabolites
 in people with HIV (PWH), as well as their relationship with combination
 antiretroviral therapy (cART) and cognitive impairment. 
 Methods. The PubMed database was searched for studies published
 from 1997 to 2020. Twenty-seven studies were identified, which included
 1255 PWH and 633 controls. Four metabolites (N-acetyl aspartate (NAA),
 myo-Inositol (mI), choline (Cho), and glutamatergic
 metabolites (Glx) from five brain regions (basal ganglia (BG), frontal
 gray and white matter (FGM, FWM), and parietal gray and white matter (PGM,
 PWM)) were pooled separately using random-effects meta-analysis.
 Results. During early HIV infection, metabolite alterations were
 largely limited to the BG, including Cho elevation, a marker of
 inflammation. cART led to global mI and Cho normalization (i.e.,
 less elevations), but improvement in NAA was negligible. In chronic PWH on
 cART, there were consistent NAA reductions across brain regions, along
 with Cho and mI elevations in the FWM and BG, and Glx elevations in the
 FWM. Cognitive impairment was associated with NAA reduction and to a
 lesser degree, mI elevation.  Conclusions. The basal
 ganglia is the primary region affected during early infection. cART is
 successful in partially controlling neuroinflammation (global mI and
 Cho normalization). However, neuronal dysfunction (NAA
 reductions) and neuroinflammation (mI and Cho elevations) persist and
 contribute to cognitive impairment in chronic PWH. Novel compounds
 targeting NAA signal pathways, along with better neuroinflammation
 control, may help to reduce cognitive impairment in PWH. 
description: Meta-analysis
DOI: 10.5061/dryad.7sqv9s4s1
title: Allium shinasii (Amaryllidaceae), a new species from Turkey

description: Allium shinasii (Amaryllidaceae) is described here as a new species.
 Diagnostic morphological characters, a full description, and detailed
 illustrations are given herein. Allium shinasii is known from Tunceli
 province in eastern Anatolia, Turkey. According to its morphological
 features, it belongs to Allium sect. Codonoprasum. It is related to A.
 kurtzianum that belongs to the same section, A. sieheanum and A. sivasicum
 that belong to A. sect. Scorodon. However, it is easily distinguished from
 these species mainly by tepals, leaves and spathe characters.
description: Karyological studies were done on root tips were pretreated with
 0.05% 1-bromonaphthalene in water solution (Elçi 1982) at +4°C for 17 h
 and fixed in Carnoy solution (1 part glacial acetic acid: 3 parts 95% or
 absolute ethanol) 24 h. Root tips were hydrolyzed for 20–25 min in 1 N HCl
 at room temperature, then stained 30 min in 4% Hematoxilin (Guerra 1999).
 Stained meristems were squashed in a drop of 45% acetic acid.
DOI: 10.5061/dryad.ttdz08kxq
title: Molecular subtyping of alzheimer’s disease with consensus non-negative matrix factorization

description: Alzheimer’s disease (AD) is a heterogeneous disease and exhibits
 diverse clinical presentations and disease progression. Some pathological
 and anatomical subtypes have been proposed. However, these subtypes
 provide a limited mechanistic understanding for AD. Leveraging
 gene expression data of 222 AD patients from The Religious Orders Study
 and Memory and Aging Project (ROSMAP) Study, we identified two AD
 molecular subtypes (synaptic type and inflammatory type) using consensus
 non-negative matrix factorization (NMF). Synaptic type is characterized by
 disrupted synaptic vesicle priming and recycling and synaptic plasticity.
 Inflammatory type is characterized by disrupted IL2, interferon alpha and
 gamma pathways. The two AD molecular subtypes were validated using
 independent data from Gene Expression Omnibus. We further demonstrated
 that the two molecular subtypes are associated with APOE genotypes,
 with synaptic type more prevalent in AD patients with E3E4
 genotype and inflammatory type more prevalent in AD patients with E3E3
 genotype (p = 0.031). In addition, two molecular subtypes are
 differentially represented in male and female AD, with synaptic type more
 prevalent in male and inflammatory type in female patients (p =
 0.051). Identification of AD molecular subtypes has potential in
 facilitating disease mechanism understanding, clinical trial design, drug
 discovery, and precision medicine for AD.
description: ROSMAP gene expression data and corresponding metadata were downloaded from synapse.org (syn3219045). Raw count data were normalized and processed according to commonly used procedure described in edgeR (version: 3.28.0). Data were first normalized by sequencing library size. Non-expressed genes, defined as count per million less than 5 in 80% of samples, were then filtered out, resulting in 12281 genes. The number of genes were further narrowed down to 2456 using top 20% cut-off based on their interquartile range (IQR) for NMF-based clustering. 
description: Please see the readme file for the datafile description and the
 data dictionaries.
DOI: 10.5061/dryad.4qrfj6q9d
title: Fleshy-fruited invasive shrubs indirectly increase native tree seed dispersal

description: Biological invasions are one of the main threats to biodiversity and
 ecosystem functioning in the Anthropocene. Fleshy-fruited invasive plants
 establish mutualistic interactions with native seed dispersers and may
 affect the mutualisms between native partners, negatively by disrupting
 plant dispersal through competition for seed dispersers or positively by
 facilitating seed dispersal via the attraction of fruit-eating animals.
 Moreover, the invaders’ density in the neighborhood of native plants may
 modulate the direction and/or magnitude of such effects on natives. In
 mountains of central Argentina, the cessation of fruiting of the dominant
 native tree Lithraea molleoides overlaps with the beginning of the
 fruiting of invasive shrubs (Pyracantha spp.). This partial overlap allows
 for testing opposite predictions regarding the effect of invasive fruits
 on native seed dispersal. We compared frugivory by seed disperser birds on
 L. molleoides during non-overlapping and overlapping periods, at six sites
 that differed in Pyracantha shrub density (high, low, and no invasion). We
 counted frugivory during 2-hours on 15 individuals of L. molleoides at
 each site and period, totaling 360 h of observation. Frugivory on the
 native tree was similar among sites during the nonoverlapping period and
 remained constant in both periods at noninvaded sites. At invaded sites,
 frugivory increased from non-overlapping to overlapping period and was
 greater at highly invaded sites. The resource provided by Pyracantha did
 not disrupt seed dispersal of the dominant native tree. Rather, it
 facilitated frugivory by seed dispersers and this effect may be
 exacerbated with higher fruit availability of invasives. Our results
 provide a counterview to the prevailingly negative impacts of invasive
 species on the seed dispersal of native species since the fruiting of
 invasive plants facilitated the seed dispersal of native species in a
 continental region contrasts with the mutualism disruption commonly
 observed in insular environments.
DOI: 10.5061/dryad.gqnk98smt
title: Better together: 14-month-old infants expect agents to cooperate even when it’s costly

description: Humans engage in cooperative activities from early on and the breadth of
 human cooperation is unparalleled. Human preference for cooperation might
 reflect cognitive and motivational mechanisms that reinforce engagement in
 cooperative activities. We applied the naive utility calculus model to
 cooperation and investigated if 14-month-old infants expect agents to
 prefer cooperative over individual goal achievement. Two groups of infants
 saw videos of agents facing a choice between two actions that led to
 identical rewards but differed in the individual costs. First, we
 established that infants expect agents to make instrumentally rational
 choices (prefer less costly individual actions). We then demonstrated that
 when one of the action alternatives is cooperative, infants expected
 agents to choose cooperation over individual action, despite the
 cooperative action demanding more effort from each agent to achieve the
 same outcome. This supports the proposal that infants may ascribe
 additional rewards to cooperative actions that go beyond the observable
 utility of instrumental actions.
description: This repository holds 3 data files relating to the following manuscript: Vorobyova, L., Begus, K., Knoblich, G., Gergely, G., Curioni, A. (2022) Better together: 14-month-old infants expect agents to cooperate   These files are as follows:         - Exp1_data.xclx: output of participants’ looking time, coded offline from the video recordings in Experiment 1.         - Exp2_data.xclx: output of participants’ looking time, coded offline from the video recordings in Experiment 2.         - Exp3_data.xclx: output of participants’ looking time, coded offline from the video recordings in Experiment 3. The data reported in these files is described below.   Columns in the files:         Name - unique personal identifier of each participant         Trial - trial number for each looking time episode         Condition - condition for a given looking time episode: easy vs costly in Exp1_data; joint vs individual in Exp2_data         Start Looking Time - start of a looking time episode in ms, counting from the beginning of a given trial         End Looking Time - end of a looking time episode in ms, counting from the beginning of a given trial         Looking Time episode - looking time episode in ms, calculated based on the two previous variables. Multiple looking time episodes are possible in one trial, if the time a participant looked away was less than 2 seconds. The analysis was performed on the sum of looking time episodes for each trial.                  Sex - sex of a participant
DOI: 10.5061/dryad.xksn02vfz
title: Data from: Early origin of sweet perception in the songbird radiation

description: Early events in the evolutionary history of a clade can shape the sensory
 systems of descendant lineages. Although the avian ancestor may not have
 had a sweet receptor, the widespread incidence of nectar-feeding birds
 suggests multiple acquisitions of sugar detection. In this study, we
 identify a single early sensory shift of the umami receptor (the T1R1-T1R3
 heterodimer) that conferred sweet-sensing abilities in songbirds, a large
 radiation containing nearly half of all living birds. We demonstrate sugar
 responses across species with diverse diets, uncover critical sites
 underlying carbohydrate detection, and identify the molecular basis of
 sensory convergence between songbirds and nectar-specialist hummingbirds.
 This early shift shaped the sensory biology of an entire radiation,
 emphasizing the role of contingency and providing an example of the
 genetic basis of convergence in avian evolution.
DOI: 10.5061/dryad.ksn02v743
title: Flexible analysis of animal behavior via time-resolved embedding

description: Uncovering relationships between neural activity and behavior represents a
 critical challenge, one that would benefit from facile tools that can
 capture complex structures within large datasets. Here we demonstrate a
 generalizable strategy for capturing such structures across diverse
 behaviors: Time-REsolved BehavioraL Embedding (TREBLE). Using
 data from synthetic trajectories, adult and larval Drosophila, and mice we
 show how TREBLE captures both continuous and discrete behavioral dynamics,
 can uncover variation across individuals, detect the effects of
 optogenetic perturbation in unbiased fashion, and reveal structure in pose
 estimation data. By applying TREBLE to moving mice, and medial entorhinal
 cortex (MEC) recordings, we show that nearly all MEC neurons encode
 information relevant to specific movement patterns, expanding our
 understanding of how navigation is related to the execution of locomotion.
 Thus, TREBLE provides a flexible framework for describing the structure of
 complex behaviors and their relationships to neural activity.
description: <i>Drosophila</i> embryos were collected for 1 h on
 standard 3.0% agar molasses collection caps covered with a thin layer of
 wet yeast. Twenty-four hours later, hatched embryos were transferred to
 standard cornmeal fly food. After forty-eight hours (L2 larval stage),
 animals were collected and transferred to a Petri dish with1.2% agar and
 relocated to a behavioral room kept at 23°C and 60% humidity. Ten to
 fifteen minutes after acclimation to the room, groups of 5 to 10 larvae
 were transferred to a 30 x 30 cm 1.2% agar arena. After 15 to 30 seconds,
 locomotion was recorded using a FIM imaging system (https://www.uni
 muenster.de) at 10 fps for 5 minutes. The FIM system was equipped with an
 azA2040-25gm (Basler) camera and a LM16HC-SW (Kowa) lens. Individual
 larvae were then tracked using FIMtrack software.
 Collected here are primary measurements of larvae shape and
 movement that were used for downstreamn analysis: area, bending, velocity,
 spine length, head radius, midpoint radius, tail radius, perimeter, head
 angular velocity,  midpoint angular velocity, and tail angular velocity.
 Distance from origin is also included for data filtering
 purposes.
DOI: 10.5061/dryad.pzgmsbckt
title: Root influence on soil nitrogen availability and microbial community dynamics results in contrasting rhizosphere priming effects in pine and spruce soil

description: 1. The rhizosphere priming effect (RPE) is increasingly considered an
 important regulator of belowground C and N cycling, with implications for
 terrestrial ecosystem feedback to global change. Even so there is a lack
 of knowledge about the mechanisms underlying RPEs. 2. We used novel stable
 isotope probing methods to investigate RPEs in an experiment with Scots
 pine and Norway spruce seedlings, two of the most common boreal forest
 species. We determined root exudation rates, RPEs on SOM decomposition and
 gross N mineralization, and the contribution of different microbial
 functional groups to the observed RPEs. 3. Pine induced positive and
 spruce negative RPEs on SOM decomposition, while no RPE on gross N
 mineralization was observed. Negative RPEs in the spruce treatment were
 attributed to an opportunistic subset of the fungal community that was
 growing on root-derived 13C while depleting available N, thus reducing the
 activity of microbial SOM decomposers. In the pine treatment, available N
 was likely sufficient to support root induced decomposition activities of
 fungal decomposers, resulting in positive RPEs. 4. The findings suggest
 that RPEs, promoted by root stimulation of distinct subsets of the
 microbial community, can either contribute to conserving the soil C stock
 or to depleting it, depending on plant species and soil N availability.
description: Data were acquired in a greenhouse experiment performed at Lund
 University.
description: Data are provided in the Excel workbook. Variables that are not
 self explanatory are defined in the "Description" sheet of the
 excel workbook.
DOI: 10.5061/dryad.8gtht76pd
title: Find the Food First: An Omnivorous Sensory Morphotype Predates Biomechanical Specialization for Plant Based Diets in Phyllostomid Bats

description: The role of mechanical morphologies in the exploitation of novel niche
 space is well characterized. However, the role of sensory structures in
 unlocking new niches is less clear. Here we investigate the relationship
 between the evolution of sensory structures and diet during the
 diversification of noctilionoid bats. With a broad range of foraging
 ecologies and a well-supported phylogeny, noctilionoids constitute an
 ideal group for studying this relationship. We used diffusible
 iodine-based contrast enhanced computed tomography (diceCT) scans of 44
 noctilionoid species to analyze relationships between the relative volumes
 of three sensory structures (olfactory bulbs, orbits, and cochleae) and
 diet. We found a positive relationship between frugivory and both
 olfactory and orbit size. However, we also found a negative relationship
 between nectarivory and cochlea size. Ancestral state estimates suggest
 that larger orbits and olfactory bulbs were present in the common ancestor
 of family Phyllostomidae, but not in other noctilionoids. This
 constellation of traits indicates a shift toward omnivory at the base of
 Phyllostomidae, predating their radiation into an exceptionally broad
 range of dietary niches. This is consistent with a scenario in which
 changes in sensory systems associated with foraging and feeding set the
 stage for subsequent morphological innovation and diversification.
DOI: 10.7291/d1bm2p
title: Data associated with: Haze evolution in temperate exoplanet atmospheres through surface energy measurements

description: Photochemical hazes are important opacity sources in temperate exoplanet
 atmospheres, hindering current observations from characterizing exoplanet
 atmospheric compositions. The haziness of an atmosphere is determined by
 the balance between haze production and removal. However, the
 material-dependent removal physics of the haze particles is currently
 unknown under exoplanetary conditions. Here we provide
 experimentally-measured surface energies for a grid of temperate exoplanet
 hazes to characterize haze removal in exoplanetary atmospheres. We found
 large variations of surface energies for hazes produced under different
 energy sources, atmospheric compositions, and temperatures. The surface
 energies of the hazes were found to be the lowest around 400 K for the
 cold plasma samples, leading to the lowest removal rates. We show a
 suggestive correlation between haze surface energy and atmospheric
 haziness with planetary equilibrium temperature. We hypothesize that
 habitable zone exoplanets could be less hazy, as they would possess
 high-surface-energy hazes which can be removed efficiently.
description: We perform the sessile drop contact angle measurements using a
 Rame-Hart goniometer using two test liquids
 (diiodomethane, ReagentPlus Sigma-Aldrich, 99% and HPLC water, Fisher
 Chemical) on 18 exoplanet haze analog samples and two substrates (quartz
 and mica disks). Images of the droplet profile were taken by the
 goniometer software. The images are processed using the contact angle
 plugin of ImageJ to extract the contact angle values.
description: The original droplet profile images can be found in each folder
 for a specific sample named with the sample name. The extracted contact
 angle data (in excel) file using ImageJ is also included in the folder for
 each sample. The data reduction folder has all the calculated surface
 energy values and the corresponding standard deviations using
 the Owens-Wendt-Rabel-Kaelble (OWRK) method for each sample.
DOI: 10.5061/dryad.2z34tmpm9
title: Dataset for: Trade-offs between weapons and testes do not manifest at high social densities

description: Social conditions can alter the allocation of resources to reproductive
 traits. For example, an increase in social density during development is
 frequently associated with an increase in the testes mass of males. Sperm
 competition theory assumes that increased investment in testes should come
 at the expense of investing into precopulatory traits, such as sexually
 selected weaponry. However, much remains unknown about the role of the
 social context on the concurrent, relative investment in both testes and
 weapons. We found that the leaf-footed cactus bug, Narnia femorata
 (Hemiptera: Coreidae), grew nearly 20% larger testes when raised in high
 social densities. In addition to manipulating social density, we used
 autotomy (limb loss) to limit investment in their hind-limb weapon during
 development. At low densities, we found that those that lost a weapon
 during development grew larger testes by adulthood, supporting previous
 work demonstrating a weapons-testes trade-off. However, at high social
 densities, males that dropped a hind limb did not grow larger testes,
 though testes were already large at this density. These results underscore
 the importance of the social context to resource allocation patterns
 within the individual.