cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8t8s248
title: Data from: Molecular, spatial and functional single-cell profiling of the hypothalamic preoptic region

description: The hypothalamus controls essential social behaviors and homeostatic
 functions. However, the cellular architecture of hypothalamic nuclei,
 including the molecular identity, spatial organization, and function of
 distinct cell types, is poorly understood. Here, we developed an
 imaging-based cell type identification and mapping method and combined it
 with single-cell RNA-sequencing to create a molecularly annotated and
 spatially resolved cell atlas of the mouse hypothalamic preoptic region.
 We profiled ~1 million cells, identified ~70 neuronal populations
 characterized by distinct neuromodulatory signatures and spatial
 organizations, and defined specific neuronal populations activated during
 key social behaviors in male and female mice, providing a high-resolution
 framework for mechanistic investigation of behavior circuits. The approach
 described here opens a new avenue for the construction of cell atlases in
 diverse tissues and organisms.
description: Properties of cells
 measured with MERFISHProperties of all cells
 measured with MERFISH provided as a csv file. “Cell ID” is a unique ID
 associated with each cell. “Animal ID” is a unique ID associated with
 animal. “Animal sex” is the gender of the animal in which the cell was
 imaged. “Behavior” describes the behavioral treatment of the animal.
 ‘Naïve’ indicates that no treatment was performed. “Bregma” indicates the
 approximate location of the slice in bregma coordinates. “Centroid X” is
 the x coordinate of the centroid position for the cell in µm. “Centroid Y”
 is the y coordinate of the centroid position for the cell in µm. “Cell
 class” lists the major cell class to which a cell was assigned. A value of
 'Ambiguous' represents cells that were identified as putative
 doublets and were not further analyzed. “Neuron cluster_ID” represents the
 neuronal cluster to which a cell was assigned. This field is empty if the
 cell was not a neuron. Columns with a gene name, e.g. ‘Ace2’, contain the
 expression values for that gene in that cell. Expression values for the
 135 genes measured in the combinatorial smFISH run were determined as the
 total counts per cell divided by the cell volume and scaled by 1000.
 Expression values for the 21 genes (including Fos) measured in the
 non-combinatorial, sequential FISH rounds were arbitrary fluorescence
 units per µm^3, but the same scale is used for all cells. A value of
 'NaN' for Fos indicates that this gene was not measured in this
 animal. These 21 genes are the final genes in the listed genes. Genes
 named 'Blank-' represent the measurement of barcodes not
 assigned to any RNA and which serve as blank controls. There are five
 blank controls.Moffitt_and_Bambah-Mukku_et_al_merfish_all_cells.csv
DOI: 10.5061/dryad.94t53
title: Data from: A functional cartography of cognitive systems

description: One of the most remarkable features of the human brain is its ability to
 adapt rapidly and efficiently to external task demands. Novel and
 non-routine tasks, for example, are implemented faster than structural
 connections can be formed. The neural underpinnings of these dynamics are
 far from understood. Here we develop and apply novel methods in network
 science to quantify how patterns of functional connectivity between brain
 regions reconfigure as human subjects perform 64 different tasks. By
 applying dynamic community detection algorithms, we identify groups of
 brain regions that form putative functional communities, and we uncover
 changes in these groups across the 64-task battery. We summarize these
 reconfiguration patterns by quantifying the probability that two brain
 regions engage in the same network community (or putative functional
 module) across tasks. These tools enable us to demonstrate that
 classically defined cognitive systems—including visual, sensorimotor,
 auditory, default mode, fronto-parietal, cingulo-opercular and salience
 systems—engage dynamically in cohesive network communities across tasks.
 We define the network role that a cognitive system plays in these dynamics
 along the following two dimensions: (i) stability vs. flexibility and (ii)
 connected vs. isolated. The role of each system is therefore summarized by
 how stably that system is recruited over the 64 tasks, and how
 consistently that system interacts with other systems. Using this
 cartography, classically defined cognitive systems can be categorized as
 ephemeral integrators, stable loners, and anything in between. Our results
 provide a new conceptual framework for understanding the dynamic
 integration and recruitment of cognitive systems in enabling behavioral
 adaptability across both task and rest conditions. This work has important
 implications for understanding cognitive network reconfiguration during
 different task sets and its relationship to cognitive effort, individual
 variation in cognitive performance, and fatigue.
description: Task-based functional
 connectivity matricesTask-based functional
 connectivity matrices, in MATLAB data format (.mat).taskFC_Corr_EmpirHRF_v2a_27-Jun-2013.matResting-state functional connectivity matricesResting-state functional connectivity matrices, in MATLAB data format (.mat).restFC_CorrConcat_saveData_v1a_25-Feb-2014.mat
DOI: 10.5061/dryad.gk04t
title: Data from: Short term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes

description: The short-term variation in the community structure of freshwater small
 eukaryotes (0.2-5 μm) was investigated in a mesotrophic lake every 2-3
 days over one summer by coupling three molecular methods: 454 amplicon
 pyrosequencing, qPCR and TSA-FISH. The pyrosequencing approach unveiled a
 much more extensive small-eukaryotic diversity (991 OTUs) than has been
 described previously. The vast majority of the diversity described was
 represented by rare OTUs (≤ 0.01% of reads) belonging primarily to
 Cryptomycota, Dikarya and photosynthetic organisms, which were never
 detected as abundant in any of the samples. The small eukaryote community
 was characterized by a continual and important reassembly. These
 rearrangements involved the 20 “core taxa” (≥ 1% of reads), and, were
 essentially due to a handful of OTUs that were detected in intermediate
 abundance (0.01-1% of reads) and sporadically in dominant taxa. Putative
 bacterivorous (Ciliophora and Cercozoa) as well as parasitic and
 saprotrophic taxa (Perkinsozoa and Cryptomycota) were involved in these
 changes of diversity. A putative infection of microalgae by a lacustrine
 perkinsozoan was also reported for the first time in this study. Open
 questions regarding both the patterns that govern the rapid small
 eukaryote reassemblies and the possible biogeography of these organisms
 arise from this study.
description: NG-5612_LEM_sequencePhylogeniesPhylogeny.tar.gz
DOI: 10.5061/dryad.md2n292
title: Data from: Faster processing of moving compared to flashed bars in awake macaque V1 provides a neural correlate of the flash lag illusion

description: When the brain has determined the position of a moving object, due to
 anatomical and processing delays, the object will have already moved to a
 new location. Given the statistical regularities present in natural
 motion, the brain may have acquired compensatory mechanisms to minimize
 the mismatch between the perceived and the real position of moving
 objects. A well-known visual illusion — the flash lag effect — points
 towards such a possibility. Although many psychophysical models have been
 suggested to explain this illusion, their predictions have not been tested
 at the neural level, particularly in a species of animal known to perceive
 the illusion. Towards this, we recorded neural responses to flashed and
 moving bars from primary visual cortex (V1) of awake, fixating macaque
 monkeys. We found that the response latency to moving bars of varying
 speed, motion direction and luminance was shorter than that to flashes, in
 a manner that is consistent with psychophysical results. At the level of
 V1, our results support the differential latency model positing that
 flashed and moving bars have different latencies. As we found a neural
 correlate of the illusion in passively fixating monkeys, our results also
 suggest that judging the instantaneous position of the moving bar at the
 time of flash — as required by the postdiction/motion-biasing model — may
 not be necessary for observing a neural correlate of the illusion. Our
 results also suggest that the brain may have evolved mechanisms to process
 moving stimuli faster and closer to real time compared with briefly
 appearing stationary stimuli.
description: all_data_zippedThis zipped folder contains subfolders raw_data and processed_data. Inside raw_data, there are separate folders for each monkey. Check the README file for full details.data.zip
DOI: 10.5061/dryad.10hq7
title: Data from: Using terrestrial laser scanning data to estimate large tropical trees biomass and calibrate allometric models: a comparison with traditional destructive approach

description: 1. Calibration of local, regional or global allometric equations to
 estimate biomass at the tree level constitutes a significant burden on
 projects aiming at reducing Carbon emissions from forest degradation and
 deforestation. The objective of this contribution is to assess the
 precision and accuracy of Terrestrial Laser Scanning (TLS) for estimating
 volumes and above-ground biomass (AGB) of the woody parts of tropical
 trees, and for the calibration of allometric models. 2. We used a
 destructive dataset of 61 trees, with diameters and AGB of up to 186.6 cm
 and 60 Mg respectively, which were scanned, felled and weighed in the
 semi-deciduous forests of eastern Cameroon. We present an operational
 approach based on available software allowing the retrieving of TLS volume
 with low bias and high accuracy for large tropical trees. Edition of the
 obtained models proved necessary, mainly to account for the complexity of
 buttressed parts of tree trunks, which were separately modelled through a
 meshing approach, and to bring a few corrections in the topology and
 geometry of branches, thanks to the amapstudio-scan software. 3. Over the
 entire dataset, TLS-derived volumes proved highly reliable for branches
 larger than 5 cm in diameter. The volumes of the remaining woody parts
 estimated for stumps, stems and crowns as well as for the whole tree
 proved very accurate (RMSE below 2.81% and R² above of .98) and unbiased.
 Once converted into AGB using mean local-specific wood density values, TLS
 estimates allowed calibrating a biomass allometric model with coefficients
 statistically undistinguishable from those of a model based on destructive
 data. The Unedited Quantitative Structure Model (QSM) however leads to
 systematic overestimations of woody volumes and subsequently to
 significantly different allometric parameters. 4. We can therefore
 conclude that a non-destructive TLS approach can now be used as an
 operational alternative to traditional destructive sampling to build the
 allometric equations, although attention must be paid to the quality of
 QSM model adjustments to avoid systematic bias.
description: Trees database (Momo et
 al)Trees.rar
DOI: 10.5061/dryad.t7ck5
title: Data from: Predicting animal behaviour using deep learning: GPS data alone accurately predict diving in seabirds

description: 1.In order to prevent further global declines in biodiversity, identifying
 and understanding key habitats is crucial for successful conservation
 strategies. For example, globally, seabird populations are under threat
 and animal movement data can identify key at-sea areas and provide
 valuable information on the state of marine ecosystems. To date, in order
 to locate these areas, studies have used Global Positioning System (GPS)
 to record position and are sometimes combined with Time Depth Recorder
 (TDR) devices to identify diving activity associated with foraging, a
 crucial aspect of at-sea behaviour. However, the use of additional devices
 such as TDRs can be expensive, logistically difficult, and may adversely
 affect the animal. Alternatively, behaviours may be resolved from
 measurements derived from the movement data alone. However, this
 behavioural analysis frequently lacks validation data for locations
 predicted as foraging (or other behaviours). 2.Here, we address these
 issues using a combined GPS and TDR dataset from 108 individuals by
 training deep learning models to predict diving in European shags, common
 guillemots and razorbills. We validate our predictions using withheld
 data, producing quantitative assessment of predictive accuracy. The
 variables used to train these models are those recorded solely by the GPS
 device: variation in longitude and latitude, altitude, and coverage ratio
 (proportion of possible fixes acquired within a set window of time).
 3.Different combinations of these variables were used to explore the
 qualities of different models, with the optimum models for all species
 predicting non-diving and diving behaviour correctly over 94% and 80% of
 the time, respectively. We also demonstrate the superior predictive
 ability of these supervised deep-learning models over other commonly used
 behavioural prediction methods such as hidden Markov models. 4.Mapping
 these predictions provides useful insights into the foraging activity of a
 range of seabird species, highlighting important at sea locations. These
 models have the potential to be used to analyse historic GPS datasets and
 further our understanding of how environmental changes have affected these
 seabirds over time.
description: GPS dive
 dataFile containing the GPS
 dive data, with lon/lat centred around each colony for anonymity. Dive
 data is included at the true/false level depending on classification and
 the maximum dive recorded in a 100 second window is also
 included.gps.zipMatricesThis file contains the matrices used for the main analyses and matrices used for the analyses in SI appendix S4.
DOI: 10.5061/dryad.50s1g
title: Data from: Description of a soft-bodied invertebrate with microcomputed tomography and revision of the genus Chtonobdella (Hirudinea: Haemadipsidae)

description: Two-jawed (duognathous) terrestrial leeches in the Haemadipsidae are major
 pests across their wide geographic range, represented by numerous endemic
 species in Australia and across many islands in the Indian and Pacific
 Oceans. However, haemadipsid taxonomy, based largely on externally visible
 characters, remains in conflict with phylogenetic relationships. We
 capitalize on the power of microcomputed tomography (μCT), allowing for
 the first description of an extant soft-bodied species – Chtonobdella
 tanae sp. n. – using this technology. Several fixation strategies for
 soft-bodied invertebrates in μCT scanning applications are also evaluated.
 Expanding on prior work, higher taxonomy of duognathous haemadipsids also
 was evaluated with phylogenetic analyses of DNA sequence data. Whereas
 monophyly of duognathous leeches was supported, substantial conflict
 remained with respect to named genera. Consequently, the genus
 Chtonobdella was revised to include all duognathous leech species
 previously distributed in 31, mostly monotypic genera.
description: Chtonobdella tanae sp.
 n. holotype (AU81) from Queensland Australia, μCT volumetric video
 rendering of external and internal features.Video starts with
 whole-body (anterior to the right) external feature rendering viewed
 dorsally, laterally, and then ventrally, followed by whole-body internal
 feature rendering viewed dorsally, laterally, and then ventrally. Video
 zooms in on eyespots (green), jaws (magenta), ganglia (yellow), and
 gastric tissue (grey) viewed dorsally, laterally, and then ventrally.
 Video moves posteriorly, focusing on male median reproductive tissues
 (shades of blue), female median reproductive tissues (pink), and testisacs
 (red) viewed dorsally, laterally, and then ventrally. Video goes to the
 posterior focusing on intestinal tissue (pale green) viewed dorsally,
 laterally, and then ventrally. Video then focuses on the auricle cavities
 (blue), finishing on the dorsal view of whole-body internal
 feature.Chtonobdella_tanae_AU81_virtual_dissection.mp4Chtonobdella tanae sp. n. holotype (AU81) from Queensland Australia, μCT projections.Specimen fixed in 10% formalin and 70% ethanol for over a decade was refixed with AFA, stained in osmium tetroxide, and then scanned in a GE v|tome|x s240.Chtonobdella_tanae_AU81_tiff_stacks.zipJuvenile Macrobdella decora, μCT projections.Specimens were fixed first with either ethanol (small sized specimen on left), glutaraldehyde (large sized specimen in middle), or AFA (medium sized specimen on right); stained in osmium tetroxide; and then scanned in a GE v|tome|x s240.Macrobdella_decora_juveniles_LeftEthanol_MiddleGlutaraldehyde_RightAFA_tiff_stacks.zip
DOI: 10.5061/dryad.5pd17
title: Data from: The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts of tiger salamanders (Ambystoma tigrinum)

description: BACKGROUND: Next-generation sequencing methods have contributed to rapid
 progress in the fields of genomics and population genetics. Using this
 high-throughput and cost-effective technology, a number of studies have
 estimated single nucleotide polymorphism (SNP) frequency by calculating
 the mean number of SNPs per unit sequence length (e.g., mean SNPs/kb).
 However, both read length and contig depth are highly variable and thus
 raise doubt about simple methods of SNP frequency estimation. RESULTS: We
 used 454 pyrosequencing to identify 2,980 putative SNPs in the eastern
 tiger salamander (Ambystoma tigrinum tigrinum) transcriptome, then
 constructed analytical models to estimate SNP frequency. The model which
 considered only contig length (i.e., the method employed in most published
 papers) was evaluated with very poor likelihood. Our most robust model
 considered read depth as well as contig length, and was 7.5 × 1055 times
 more likely than the length-only model. Using this novel modeling
 approach, we estimated SNP frequency in protein-coding (mRNA) and
 non-coding transcripts (e.g., small RNAs). We found little difference in
 SNP frequency in the contigs, but we found a trend of a higher frequency
 of SNPs in long contigs representing non-coding transcripts relative to
 protein-coding transcripts. These results support the hypothesis that long
 non-coding transcripts are less conserved than long protein-coding
 transcripts. CONCLUSIONS: A modeling approach (i.e., using multiple model
 construction and model selection approaches) can be a powerful tool for
 identifying selection on specific functional sequence groups by comparing
 the frequency and distribution of polymorphisms.
description: AllTigerSalamander
DOI: 10.5061/dryad.8q0s4
title: Data from: A curated and standardized adverse drug event resource to accelerate drug safety research

description: Identification of adverse drug reactions (ADRs) during the post-marketing
 phase is one of the most important goals of drug safety surveillance.
 Spontaneous reporting systems (SRS) data, which are the mainstay of
 traditional drug safety surveillance, are used for hypothesis generation
 and to validate the newer approaches. The publicly available US Food and
 Drug Administration (FDA) Adverse Event Reporting System (FAERS) data
 requires substantial curation before they can be used appropriately, and
 applying different strategies for data cleaning and normalization can have
 material impact on analysis results. We provide a curated and standardized
 version of FAERS removing duplicate case records, applying standardized
 vocabularies with drug names mapped to RxNorm concepts and outcomes mapped
 to SNOMED-CT concepts, and pre-computed summary statistics about
 drug-outcome relationships for general consumption. This publicly
 available resource, along with the source code, will accelerate drug
 safety research by reducing the amount of time spent performing data
 management on the source FAERS reports, improving the quality of the
 underlying data, and enabling standardized analyses using common
 vocabularies.
description: AEOLUS master
 fileThis zipped file
 includes all the files needed to load a copy of AEOLUS into a
 RDBMSaeolus_v1.zip
DOI: 10.5061/dryad.34f4q
title: Data from: Effects of sea ice cover on satellite-detected primary production in the Arctic Ocean

description: The influence of decreasing Arctic sea ice on net primary production (NPP)
 in the Arctic Ocean has been considered in multiple publications but is
 not well constrained owing to the potentially large errors in satellite
 algorithms. In particular, the Arctic Ocean is rich in coloured dissolved
 organic matter (CDOM) that interferes in the detection of chlorophyll a
 concentration of the standard algorithm, which is the primary input to NPP
 models. We used the quasi-analytic algorithm (Lee et al. 2002 Appl. Opti.
 41, 5755−5772. (doi:10.1364/AO.41.005755)) that separates absorption by
 phytoplankton from absorption by CDOM and detrital matter. We merged
 satellite data from multiple satellite sensors and created a 19 year time
 series (1997–2015) of NPP. During this period, both the estimated annual
 total and the summer monthly maximum pan-Arctic NPP increased by about
 47%. Positive monthly anomalies in NPP are highly correlated with positive
 anomalies in open water area during the summer months. Following the
 earlier ice retreat, the start of the high-productivity season has become
 earlier, e.g. at a mean rate of −3.0 d yr−1 in the northern Barents Sea,
 and the length of the high-productivity period has increased from 15 days
 in 1998 to 62 days in 2015. While in some areas, the termination of the
 productive season has been extended, owing to delayed ice formation, the
 termination has also become earlier in other areas, likely owing to
 limited nutrients.
description: NPP_VgpmFromQaa_25_2.0_1997-2012Series of 5-day NPP for period 1997-2012 in HDF4 filesNPP_VgpmFromQaa_25_2.0_2013-2015
DOI: 10.5061/dryad.81h12
title: Data from: Bile diversion to the distal small intestine has comparable metabolic benefits to bariatric surgery

description: Roux-en-Y gastric bypass (RYGB) is highly effective in reversing obesity
 and associated diabetes. Recent observations in humans suggest a
 contributing role of increased circulating bile acids in mediating such
 effects. Here we use a diet-induced obesity (DIO) mouse model and compare
 metabolic remission when bile flow is diverted through a gallbladder
 anastomosis to jejunum, ileum or duodenum (sham control). We find that
 only bile diversion to the ileum results in physiologic changes similar to
 RYGB, including sustained improvements in weight, glucose tolerance and
 hepatic steatosis despite differential effects on hepatic gene expression.
 Circulating free fatty acids and triglycerides decrease while bile acids
 increase, particularly conjugated tauro-β-muricholic acid, an FXR
 antagonist. Activity of the hepatic FXR/FGF15 signalling axis is reduced
 and associated with altered gut microbiota. Thus bile diversion,
 independent of surgical rearrangement of the gastrointestinal tract,
 imparts significant weight loss accompanied by improved glucose and lipid
 homeostasis that are hallmarks of RYGB.
description: Raw
 dataRaw Data for microbiome
 sequences052913SA27F.zipAnalysis resultAnalysis resultanalysis.zip