cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c73q1
title: Data from: Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting

description: Computational neutralization fingerprinting, NFP, is an efficient and
 accurate method for predicting the epitope specificities of polyclonal
 antibody responses to HIV-1 infection. Here, we present next-generation
 NFP algorithms that substantially improve prediction accuracy for
 individual donors and enable serologic analysis for entire cohorts.
 Specifically, we developed algorithms for: (a) selection of optimized
 virus neutralization panels for NFP analysis, (b) estimation of NFP
 prediction confidence for each serum sample, and (c) identification of
 sera with potentially novel epitope specificities. At the individual donor
 level, the next-generation NFP algorithms particularly improved the
 ability to detect multiple epitope specificities in a sample, as confirmed
 both for computationally simulated polyclonal sera and for samples from
 HIV-infected donors. Specifically, the next-generation NFP algorithms
 detected multiple specificities in twice as many samples of simulated
 sera. Further, unlike the first-generation NFP, the new algorithms were
 able to detect both of the previously confirmed antibody specificities,
 VRC01-like and PG9-like, in donor CHAVI 0219. At the cohort level,
 analysis of ~150 broadly neutralizing HIV-infected donor samples suggested
 a potential connection between clade of infection and types of elicited
 epitope specificities. Most notably, while 10E8-like antibodies were
 observed in infections from different clades, an enrichment of such
 antibodies was predicted for clade B samples. Ultimately, such large-scale
 analyses of antibody responses to HIV-1 infection can help guide the
 design of epitope-specific vaccines that are tailored to take into account
 the prevalence of infecting clades within a specific geographic region.
 Overall, the next-generation NFP technology will be an important tool for
 the analysis of broadly neutralizing polyclonal antibody responses against
 HIV-1.
description: READMEInstructions for
 supplementary data/source codeArchive of
 datadata_distribution_28-Dec-2016.zip
DOI: 10.5061/dryad.km540
title: Data from: Improving transcriptome assembly through error correction of high-throughput sequence reads

description: The study of functional genomics, particularly in non-model organisms, has
 been dramatically improved over the last few years by the use of
 transcriptomes and RNAseq. While these studies are potentially extremely
 powerful, a computationally intensive procedure, the de novo construction
 of a reference transcriptome must be completed as a prerequisite to
 further analyses. The accurate reference is critically important as all
 downstream steps, including estimating transcript abundance are critically
 dependent on the construction of an accurate reference. Though a
 substantial amount of research has been done on assembly, only recently
 have the pre-assembly procedures been studied in detail. Specifically,
 several stand-alone error correction modules have been reported on and,
 while they have shown to be effective in reducing errors at the level of
 sequencing reads, how error correction impacts assembly accuracy is
 largely unknown. Here, we show via use of a simulated and empiric dataset,
 that applying error correction to sequencing reads has significant
 positive effects on assembly accuracy, and should be applied to all
 datasets. A complete collection of commands which will allow for the
 production of Reptile corrected reads is available at
 https://github.com/macmanes/error_correction/tree/master/scripts
description: Simulated Illumina
 Reads30 million 100nt PE
 reads. These are the _2 reads.sim.reads.right.fq.gzSimulated Illumina Reads30 million PE 100nt simulated Illumina reads. These are the _1 files.sim.reads.left.fq.gz
DOI: 10.5061/dryad.mv34v
title: Data from: Identification of genes important for cutaneous function revealed by a large scale reverse genetic screen in the mouse

description: The skin is a highly regenerative organ which plays critical roles in
 protecting the body and sensing its environment. Consequently, morbidity
 and mortality associated with skin defects represent a significant health
 issue. To identify genes important in skin development and homeostasis, we
 have applied a high throughput, multi-parameter phenotype screen to the
 conditional targeted mutant mice generated by the Wellcome Trust Sanger
 Institute's Mouse Genetics Project (Sanger-MGP). A total of 562
 different mouse lines were subjected to a variety of tests assessing
 cutaneous expression, macroscopic clinical disease, histological change,
 hair follicle cycling, and aberrant marker expression. Cutaneous lesions
 were associated with mutations in 23 different genes. Many of these were
 not previously associated with skin disease in the organ (Mysm1, Vangl1,
 Trpc4ap, Nom1, Sparc, Farp2, and Prkab1), while others were ascribed new
 cutaneous functions on the basis of the screening approach (Krt76, Lrig1,
 Myo5a, Nsun2, and Nf1). The integration of these skin specific screening
 protocols into the Sanger-MGP primary phenotyping pipelines marks the
 largest reported reverse genetic screen undertaken in any organ and
 defines approaches to maximise the productivity of future projects of this
 nature, while flagging genes for further characterisation.
description: Gene-FileHeader-Genotype-Phenotype Reference ListMaster reference file to link Gene to Files and Noted Phenotypes.Gene-File-Genotype-Phenotype Reference List.xlsxHEpart1Num-A-DPackage contains HE images of genes from A-D and numerical namesHE upload-1Num-A-D.rarHEpart3O-SPackage contains HE images of genes from O-SHE upload-3O-S.rarHEpart4T-Z-incWTsPackage contains HE images of genes from T-Z including Wildtype animalsHE upload-4T-Z-incWTs.rarHEpart2E-NPackage contains HE images of genes from E-NHE upload-2E-N.rar
DOI: 10.5061/dryad.qh1pg
title: Data from: Differential Expression Analysis for Pathways

description: Life science technologies generate a deluge of data that hold the keys to
 unlocking the secrets of important biological functions and disease
 mechanisms. We present DEAP, Differential Expression Analysis for
 Pathways, which capitalizes on information about biological pathways to
 identify important regulatory patterns from differential expression data.
 DEAP makes significant improvements over existing approaches by including
 information about pathway structure and discovering the most
 differentially expressed portion of the pathway. On simulated data, DEAP
 significantly outperformed traditional methods: with high differential
 expression, DEAP increased power by two orders of magnitude; with very low
 differential expression, DEAP doubled the power. DEAP performance was
 illustrated on two different gene and protein expression studies. DEAP
 discovered fourteen important pathways related to chronic obstructive
 pulmonary disease and interferon treatment that existing approaches
 omitted. On the interferon study, DEAP guided focus towards a four protein
 path within the 26 protein Notch signalling pathway.
description: DEAP Validation 1:
 Pathway DataRepresentations of the
 simulated pathways from the section "DEAP Validation 1: Simulated
 Data on Simulated Pathways" in the *.edg format utilized for input
 into the DEAP algorithm.Validation1_PathwayData.tar.gzDEAP Validation 1: Expression DataAll simulated expression data used for the section "DEAP Validation 1: Simulated Data on Simulated Pathways". Data is in the TSV format used for input into the DEAP algorithm. Simulated data was generated as described in "Methods: Simulated Data". File naming indicates the variables input into the simulation algorithm.Validation1_ExpressionData.tar.gzDEAP Validation 2: Pathway DataRepresentations of the simulated pathways from the section "DEAP Validation 2: Simulated Data on Biological Pathways" in the *.edg format utilized for input into the DEAP algorithm.Validation2_PathwayData.tar.gzDEAP Validation 2: Expression Data Part 1All simulated expression data used for the section "DEAP Validation 2: Simulated Data on Biological Pathways". Data is in the TSV format used for input into the DEAP algorithm. Simulated data was generated as described in "Methods: Simulated Data". File naming indicates the variables input into the simulation algorithm.Validation2_ExpressionData_Part1.tar.gzDEAP Validation 2: Expression Data Part 2All simulated expression data used for the section "DEAP Validation 2: Simulated Data on Biological Pathways". Data is in the TSV format used for input into the DEAP algorithm. Simulated data was generated as described in "Methods: Simulated Data". File naming indicates the variables input into the simulation algorithm.Validation2_ExpressionData_Part2.tar.gz
DOI: 10.5061/dryad.hv044
title: Data from: Monthly microclimate models in a managed boreal forest landscape

description: The majority of microclimate studies have been done in topographically
 complex landscapes to quantify and predict how near-ground temperatures
 vary as a function of terrain properties. However, in forests understory
 temperatures can be strongly influenced also by vegetation. We quantified
 the relative influence of vegetation features and physiography (topography
 and moisture-related variables) on understory temperatures in managed
 boreal forests in central Sweden. We used a multivariate regression
 approach to relate near-ground temperature of 203 loggers over the
 snow-free seasons in an area of ∼16,000 km2 to remotely sensed and on-site
 measured variables of forest structure and physiography. We produced
 climate grids of monthly minimum and maximum temperatures at 25 m
 resolution by using only remotely sensed and mapped predictors. The
 quality and predictions of the models containing only remotely sensed
 predictors (MAP models) were compared with the models containing also
 on-site measured predictors (OS models). Our data suggest that during the
 warm season, where landscape microclimate variability is largest, canopy
 cover and basal area were the most important microclimatic drivers for
 both minimum and maximum temperatures, while physiographic drivers (mainly
 elevation) dominated maximum temperatures during autumn and early winter.
 The MAP models were able to reproduce findings from the OS models but
 tended to underestimate high and overestimate low temperatures. Including
 important microclimatic drivers, particularly soil moisture, that are yet
 lacking in a mapped form should improve the microclimate maps. Because of
 the dynamic nature of managed forests, continuous updates of mapped forest
 structure parameters are needed to accurately predict temperatures. Our
 results suggest that forest management (e.g. stand size, structure and
 composition) and conservation may play a key role in amplifying or
 impeding the effects of climate-forcing factors on near-ground temperature
 and may locally modify the impact of global warming.
description: Maximum temperature maps
 2015zip.folder containing
 all maximum temperature maps for 2015Tmax2015.zipMaximum temperature maps 2016zip.folder containing all maximum temperature maps for 2016Tmax2016.zipMinimum temperature maps 2015zip.folder containing all minimum temperature maps for 2015Tmin2015.zipMinimum temperature maps 2016zip.folder containing all minimum temperature maps for 2016Tmin2016.zipREADMEmeta data for all temperature maps
DOI: 10.5061/dryad.5922k
title: Data from: Dissociable neural response signatures for slow amplitude and frequency modulation in human auditory cortex

description: Natural auditory stimuli are characterized by slow fluctuations in
 amplitude and frequency. However, the degree to which the neural responses
 to slow amplitude modulation (AM) and frequency modulation (FM) are
 capable of conveying independent time-varying information, particularly
 with respect to speech communication, is unclear. In the current
 electroencephalography (EEG) study, participants listened to amplitude-
 and frequency-modulated narrow-band noises with a 3-Hz modulation rate,
 and the resulting neural responses were compared. Spectral analyses
 revealed similar spectral amplitude peaks for AM and FM at the stimulation
 frequency (3 Hz), but amplitude at the second harmonic frequency (6 Hz)
 was much higher for FM than for AM. Moreover, the phase delay of neural
 responses with respect to the full-band stimulus envelope was shorter for
 FM than for AM. Finally, the critical analysis involved classification of
 single trials as being in response to either AM or FM based on either
 phase or amplitude information. Time-varying phase, but not amplitude, was
 sufficient to accurately classify AM and FM stimuli based on single-trial
 neural responses. Taken together, the current results support the
 dissociable nature of cortical signatures of slow AM and FM. These
 cortical signatures potentially provide an efficient means to dissect
 simultaneously communicated slow temporal and spectral information in
 acoustic communication signals.
description: HenryObleser_PLOSONE_rawdataThese four data files constitute a single large file that has been split to facilitate download and reuse. To recombine the files, please follow these instructions: On Unix, Linux, or Mac OSX, recombine files with the "cat" command, like this: cat xaa xab xac xad &gt; dataFile.zip On Windows, recombine files with the "copy" command, like this: copy /B xaa+xab+xac+xad dataFile.zipxaapart bxabpart cxacpart dxad
DOI: 10.5061/dryad.02f33n6
title: Data from: The Middle Triassic procolophonid Kapes bentoni: computed tomography of the skull and skeleton

description: Procolophonids were diverse small reptiles through the Late Permian and
 Triassic. Relatively complete specimens of various taxa are known from the
 Early and Late Triassic, but the ten or so Middle Triassic taxa, from
 South Africa, Russia, China and the UK, are mostly incomplete, being known
 only from skulls or partial and poorly preserved isolated elements.
 Because of their small size, it has often been difficult to establish
 details of anatomy using physical preparation methods, so application of
 scanning technology can massively improve knowledge. Here we describe the
 first substantial portion of a skull and anterior postcranial skeleton of
 the genus Kapes, known from Russia and the UK. CT scanning and 3D digital
 restoration of the new specimen from the Anisian Otter Sandstone of Devon,
 UK, reveal anatomical details previously unknown for this taxon, most
 notably the enlarged quadratojugal processes. This is also one of the few
 mature procolophonid specimens with a preserved postcranium, and it gives
 a valuable insight into ossification patterns. Fused sutures of the skull,
 fused scapulocoracoid, and heavily worn teeth show evidence of the common
 reptilian ossification pattern with a possible limitation in tooth
 replacement. There is sufficient anatomical information to include Kapes
 bentoni for the first time in a cladistic analysis, which shows that it is
 sister to the Russian Kapes majmesculae and part of a clade of Anisian
 taxa phylogenetically more basal than Procolophon. Inferences on the
 function of the quadratojugal spines and fossorial mode of life are also
 considered.
description: Appendix
 S1A
 collection of 3D models used in this study. It contains a 3D model of
 complete specimen BRSUG 29950-13 how it was positioned in the matrix, and
 individual elements. Individual elements are in some cases presented both
 in their original and retrodeformed state, where the description was based
 off retrodeformed versions. For methods used to create models see Zaher et
 al. (2018).BRSUG
 29950-13_3D_meshes.zipAppendix
 S2Image stack of the CT
 scan data with a text file that contains scan details and
 settings.TIFF_stack.zipAppendix S3NEXUS file of the data matrix used in a Phylogenetic analysis.Procolophonidae.nexAppendix S4Character list used in a Phylogenetic analysis.Character_list.pdf
DOI: 10.15468/dl.kx45h3
title: Occurrence Download

description: A dataset containing 12433778 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 12433778 records from 1505 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000397-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5066/p1v3xbta
title: Data Release: Long-term production trends in Taxodium distichum swamps at the northern range extreme in the Mississippi River Alluvial Valley, litter, 2002-2022

description: An ability to discern shifts in plant production may be vital to suggest management in support of vegetation stressed by climate or land-use change. This work asked if the production of mixed baldcypress swamps (Taxodium distichum (L.) Rich.) changed over decades of study with one study conducted during the 1990s and the other from 2002-2022. In the current study from 2002 to 2022, litter and root production levels were measured in seven swamps along the Cache River Illinois, which are at their northern extreme in the Mississippi River Alluvial Valley. The most important driver of production over the three decades of study was water regime. Swamps with wetter water regimes had higher leaf and reproductive tissue production. Over the last decade, root production increased by 2.5 times mostly in the upper soil layers (0-10 cm) but only in swamps in the drier and middle parts of the water gradient.
DOI: 10.5517/ccdc.csd.cc2mz0m8
title: CCDC 2441920: Experimental Crystal Structure Determination

description: Related Article: Ying yang, Yiming Ma, Guobin Ren, Ming-Hui Qi, Zhong Li, Xiaoyong Xu|2025|Cryst.Growth Des.|25|6050|doi:10.1021/acs.cgd.5c00507
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n0rk0
title: CCDC 2443592: Experimental Crystal Structure Determination

description: Related Article: G. Raghu Ramudu, Vaibhav B. Patil, Jagadeesh Babu Nanubolu, Rambabu Chegondi|2025|Chemical Science|16|14988|doi:10.1039/D5SC03007B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n0rl1
title: CCDC 2443593: Experimental Crystal Structure Determination

description: Related Article: G. Raghu Ramudu, Vaibhav B. Patil, Jagadeesh Babu Nanubolu, Rambabu Chegondi|2025|Chemical Science|16|14988|doi:10.1039/D5SC03007B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n6hn1
title: CCDC 2449113: Experimental Crystal Structure Determination

description: Related Article: Andrea O’Reilly, J. Robin Fulton, Martyn P. Coles|2025|Organometallics|44|1679|doi:10.1021/acs.organomet.5c00169
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n6hp2
title: CCDC 2449114: Experimental Crystal Structure Determination

description: Related Article: Andrea O’Reilly, J. Robin Fulton, Martyn P. Coles|2025|Organometallics|44|1679|doi:10.1021/acs.organomet.5c00169
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n6hq3
title: CCDC 2449115: Experimental Crystal Structure Determination

description: Related Article: Andrea O’Reilly, J. Robin Fulton, Martyn P. Coles|2025|Organometallics|44|1679|doi:10.1021/acs.organomet.5c00169
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n6hr4
title: CCDC 2449116: Experimental Crystal Structure Determination

description: Related Article: Andrea O’Reilly, J. Robin Fulton, Martyn P. Coles|2025|Organometallics|44|1679|doi:10.1021/acs.organomet.5c00169
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n6hs5
title: CCDC 2449117: Experimental Crystal Structure Determination

description: Related Article: Andrea O’Reilly, J. Robin Fulton, Martyn P. Coles|2025|Organometallics|44|1679|doi:10.1021/acs.organomet.5c00169
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2n6ht6
title: CCDC 2449118: Experimental Crystal Structure Determination

description: Related Article: Andrea O’Reilly, J. Robin Fulton, Martyn P. Coles|2025|Organometallics|44|1679|doi:10.1021/acs.organomet.5c00169
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2nq47s
title: CCDC 2464135: Experimental Crystal Structure Determination

description: Related Article: Jinxia Yang, Xiao-Qian Lin, Zi-Yi Miao, Jian-Shan Chen, Ming-Ling Sun, Xin Zhang, Ye-Yan Qin, Yuan-Gen Yao|2025|Cryst.Growth Des.|25|6468|doi:10.1021/acs.cgd.5c00897
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.