cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6879710
title: Structure in talker variability: How much is there and how much can it help?

description: One of the persistent puzzles in understanding human speech perception is how listeners cope with talker variability. One thing that might help listeners is structure in talker variability: rather than varying randomly, talkers of the same gender, dialect, age, etc. tend to produce language in similar ways. Listeners are sensitive to this covariation between linguistic variation and socio-indexical variables. In this paper I present new techniques based on ideal observer models to quantify (1) the amount and type of structure in talker variation (<i>informativity</i> of a grouping variable), and (2) how useful such structure can be for robust speech recognition in the face of talker variability (the <i>utility</i> of a grouping variable). I demonstrate these techniques in two phonetic domains—word-initial stop voicing and vowel identity—and show that these domains have different amounts and types of talker variability, consistent with previous, impressionistic findings. An R package (phondisttools) accompanies this paper, and the source and data are available from osf.io/zv6e3.
DOI: 10.7910/dvn/npjsho/eselgw
title: 2V-1

description: sigma=2Volts
DOI: 10.6084/m9.figshare.6879704
title: The CRISPR/Cas system in <i>Neisseria meningitidis</i> affects bacterial adhesion to human nasopharyngeal epithelial cells

description: <i>Neisseria meningitidis</i>, a commensal β-proteobacterium of the human nasopharynx, constitutes a worldwide leading cause of sepsis and epidemic meningitis. A recent genome-wide association study suggested an association of its type II-C CRISPR/Cas system with carriage and thus less invasive lineages. Here, we show that knock-out strains lacking the Cas9 protein are impaired in the adhesion to human nasopharyngeal cells which constitutes a central step in the pathogenesis of invasive meningococcal disease. Transcriptome sequencing data further suggest that meningococcal Cas9 does not affect the expression of surface adhesins but rather exerts its effect on cell adhesion in an indirect manner. Consequently, we speculate that the meningococcal CRISPR/Cas system exerts novel functions beyond its established role in defence against foreign DNA.
DOI: 10.7910/dvn/npjsho/paxgbx
title: 2V-56

description: sigma=2Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6879710.v1
title: Structure in talker variability: How much is there and how much can it help?

description: One of the persistent puzzles in understanding human speech perception is how listeners cope with talker variability. One thing that might help listeners is structure in talker variability: rather than varying randomly, talkers of the same gender, dialect, age, etc. tend to produce language in similar ways. Listeners are sensitive to this covariation between linguistic variation and socio-indexical variables. In this paper I present new techniques based on ideal observer models to quantify (1) the amount and type of structure in talker variation (<i>informativity</i> of a grouping variable), and (2) how useful such structure can be for robust speech recognition in the face of talker variability (the <i>utility</i> of a grouping variable). I demonstrate these techniques in two phonetic domains—word-initial stop voicing and vowel identity—and show that these domains have different amounts and types of talker variability, consistent with previous, impressionistic findings. An R package (phondisttools) accompanies this paper, and the source and data are available from osf.io/zv6e3.
DOI: 10.6084/m9.figshare.6879704.v1
title: The CRISPR/Cas system in <i>Neisseria meningitidis</i> affects bacterial adhesion to human nasopharyngeal epithelial cells

description: <i>Neisseria meningitidis</i>, a commensal β-proteobacterium of the human nasopharynx, constitutes a worldwide leading cause of sepsis and epidemic meningitis. A recent genome-wide association study suggested an association of its type II-C CRISPR/Cas system with carriage and thus less invasive lineages. Here, we show that knock-out strains lacking the Cas9 protein are impaired in the adhesion to human nasopharyngeal cells which constitutes a central step in the pathogenesis of invasive meningococcal disease. Transcriptome sequencing data further suggest that meningococcal Cas9 does not affect the expression of surface adhesins but rather exerts its effect on cell adhesion in an indirect manner. Consequently, we speculate that the meningococcal CRISPR/Cas system exerts novel functions beyond its established role in defence against foreign DNA.
DOI: 10.7910/dvn/npjsho/zrvqfn
title: 2V-25

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/agq22j
title: 2V-44

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/psyske
title: 2V-38

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/x7zzz3
title: 2V-26

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/mcju7r
title: 2V-37

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/1pjra2
title: 2V-13

description: sigma=2Volts
DOI: 10.6084/m9.figshare.6878552
title: 火星救援

description: 火星救援豆瓣评论数据
DOI: 10.7910/dvn/npjsho/axppo4
title: 2V-31

description: sigma=2Volts
DOI: 10.6084/m9.figshare.6877619
title: Soil B-glucosidase activity, rate of decomposition, and mass loss data sets

description: These data sets contain the soil B-glucosidase potential enzyme activity, precipitation data, and rate of residue decomposition data for the 2016 decomposition period.
DOI: 10.7910/dvn/npjsho/6eqult
title: 2V-51

description: sigma=2Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6878552.v1
title: 火星救援

description: 火星救援豆瓣评论数据
DOI: 10.7910/dvn/npjsho/edql1i
title: 2V-22

description: sigma=2Volts
DOI: 10.6084/m9.figshare.6877607
title: LEfSe analyses data

description: Each of the files can be used in collaboration with the LEfSe algorithm (scripts available on GitHub) to create LEfSe figures.
DOI: 10.6084/m9.figshare.6877604
title: Genus level community data and environmental data for CCA model

description: Genus level community data and environmental data used to complete a canonical correspondence analysis
DOI: 10.7910/dvn/npjsho/zd2jso
title: 2V-39

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/ekhqsv
title: 2V-18

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/tbik1v
title: 2V-32

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/tgwpcp
title: 2V-35

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/ox1brx
title: 2V-19

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/gkr0w3
title: 2V-52

description: sigma=2Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/npjsho/hegan8
title: 2V-42

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/wglz3k
title: 2V-55

description: sigma=2Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6877556
title: Supplementary Tables from Balancing selection and introgression of newt immune-response genes

description: The importance of interspecific introgression as a source of adaptive variation is increasingly recognized. Theory predicts that beneficial genetic variants cross species boundaries easily even when interspecific hybridization is rare and gene flow is strongly constrained throughout the genome. However, it remains unclear whether certain classes of genes are particularly prone to adaptive introgression. Genes affected by balancing selection (BS) may constitute such a class, because forms of BS that favour novel, initially rare alleles, should facilitate introgression. We tested this hypothesis in hybridizing newts by comparing 13 genes with signatures of BS, in particular an excess of common non-synonymous polymorphisms, to the genomic background (154 genes). Parapatric hybridizing taxa were less differentiated in BS candidate genes than more closely related allopatric lineages, while the opposite was observed in the control genes. Coalescent and forward simulations that explored neutral and BS scenarios under isolation and migration showed that processes other than differential gene flow are unlikely to account for this pattern. We conclude that BS, probably involving a form of novel allele advantage, promotes introgression. This mechanism may be a source of adaptively relevant variation in hybridizing species over prolonged periods.
DOI: 10.7910/dvn/npjsho/gco4lw
title: 2V-54

description: sigma=2Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6877556.v1
title: Supplementary Tables from Balancing selection and introgression of newt immune-response genes

description: The importance of interspecific introgression as a source of adaptive variation is increasingly recognized. Theory predicts that beneficial genetic variants cross species boundaries easily even when interspecific hybridization is rare and gene flow is strongly constrained throughout the genome. However, it remains unclear whether certain classes of genes are particularly prone to adaptive introgression. Genes affected by balancing selection (BS) may constitute such a class, because forms of BS that favour novel, initially rare alleles, should facilitate introgression. We tested this hypothesis in hybridizing newts by comparing 13 genes with signatures of BS, in particular an excess of common non-synonymous polymorphisms, to the genomic background (154 genes). Parapatric hybridizing taxa were less differentiated in BS candidate genes than more closely related allopatric lineages, while the opposite was observed in the control genes. Coalescent and forward simulations that explored neutral and BS scenarios under isolation and migration showed that processes other than differential gene flow are unlikely to account for this pattern. We conclude that BS, probably involving a form of novel allele advantage, promotes introgression. This mechanism may be a source of adaptively relevant variation in hybridizing species over prolonged periods.
DOI: 10.7910/dvn/npjsho/lfu8s7
title: 2V-29

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/pkekmn
title: 2v

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/uubg7l
title: 2V-24

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/4sr4wc
title: 2V-34

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/pf0efz
title: 2v-1

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/yhbjcc
title: 2V-16

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/lprhfj
title: 2V-2

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/ktqw2u
title: 2V-50

description: sigma=2Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/npjsho/y0akxo
title: 2V-28

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/gjwx5z
title: 2V-10

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/hrc1xw
title: 2V-11

description: sigma=2Volts
DOI: 10.5281/zenodo.3902586
title: Natural-Color-Cloud-and-Contrail-Image-Dataset

description: The natural color cloud and contrail image (NCCI) dataset is a dataset for satellite cloud image super resolution. The NCCI dataset is generated based on Himawari-8 satellite data. The NCCI dataset contains 1100 satellite images, including 1000 natural color images and 100 contrail images. It is worth noting that contrails have consideration in our dataset.
DOI: 10.7910/dvn/npjsho/tdu8fj
title: 2V-21

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/o9mcad
title: 2V-40

description: sigma=2Volts
DOI: 10.5281/zenodo.3902585
title: Natural-Color-Cloud-and-Contrail-Image-Dataset

description: The natural color cloud and contrail image (NCCI) dataset is a dataset for satellite cloud image super resolution. The NCCI dataset is generated based on Himawari-8 satellite data. The NCCI dataset contains 1100 satellite images, including 1000 natural color images and 100 contrail images. It is worth noting that contrails have consideration in our dataset.
DOI: 10.7910/dvn/npjsho/r6unog
title: 2V-45

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/mh6rty
title: 2V-30

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/ecpsiw
title: 2V-15

description: sigma=2Volts
DOI: 10.7910/dvn/npjsho/fwlupr
title: Nano.pdf

description: Manuscript
DOI: 10.6084/m9.figshare.6877388
title: The Virtuous Cycle of News Sharing on Facebook: Effects of Platform Affordances and Journalistic Routines on News Sharing

description: Replication data for the paper "The Virtuous Cycle of News Sharing on Facebook: Effects of Platform Affordances and Journalistic Routines on News Sharing"<br>
DOI: 10.6084/m9.figshare.6877400
title: R code for Davis-Stober, Dana and Rouder (2018). Estimation accuracy in the psychological sciences.

description: This zip file contains the raw R code used to make all of the figures in the paper.<br>Davis-Stober, C. P., Dana, J., & Rouder, J.N. (2018). Estimation accuracy in the psychological sciences.
DOI: 10.7910/dvn/npjsho
title: Amplification of DNA Brownian Motion Using Electrokinetic Noise

description: This dataset was collected to study the effects of applied white Gaussian electrokinetic noise on the diffusivity of single DNA molecules inside a nanofluidic slit. Our raw data consists of image sequences in FITS format (Flexible Image Transport System). Each image shows a fluorescent Lambda DNA molecule stained by YOYO-1 dye at a 10:1 base-pair to dye ratio diffusing inside a 110 nm deep nanoslit under specified amounts of applied noise. An imaging system comprising an inverted Nikon TE2000U microscope, an ANDOR iXon 897 EMCCD camera, an X-Cite UV illumination system, and a 60X, 0.7 NA, water-immersion objective lens with an extra 1.5X magnification factor was used to acquire the images. We applied 8 different noise intensities and recorded about 50-70 molecules per noise intensity. These data can be used to find trajectories of the centers of mass of the molecules and to analyze the radii of gyration and DNA shapes. Sigma represents the standard deviation of the applied Gaussian noise.
DOI: 10.6084/m9.figshare.6877400.v2
title: R code for Davis-Stober, Dana and Rouder (2018). Estimation accuracy in the psychological sciences.

description: This zip file contains the raw R code used to make all of the figures in the paper.<br>Davis-Stober, C. P., Dana, J., & Rouder, J.N. (2018). Estimation accuracy in the psychological sciences.
DOI: 10.6084/m9.figshare.6877307
title: ATSeqMAF05.hmp.txt

description: Filtered and imputed reads from the F2 population of B73 x 707G. This population was developed for the purpose of discovering the position of the reduced acylation trait in the genome.
DOI: 10.6084/m9.figshare.6877304
title: ATSeqMAF05REF.txt

description: Genotype dataset from the F2 population of B73 x 707G coded as 1 = major allele, 0.5 = heterozygote, and 0 = minor allele.
DOI: 10.6084/m9.figshare.6877307.v1
title: ATSeqMAF05.hmp.txt

description: Filtered and imputed reads from the F2 population of B73 x 707G. This population was developed for the purpose of discovering the position of the reduced acylation trait in the genome.
DOI: 10.6084/m9.figshare.6877304.v1
title: ATSeqMAF05REF.txt

description: Genotype dataset from the F2 population of B73 x 707G coded as 1 = major allele, 0.5 = heterozygote, and 0 = minor allele.
DOI: 10.6084/m9.figshare.6877271
title: Mechanisms by which senescent cells promote ageing and age-related disease

description: Mechanisms by which senescent cells promote ageing and age-related disease
DOI: 10.6084/m9.figshare.6877271.v1
title: Mechanisms by which senescent cells promote ageing and age-related disease

description: Mechanisms by which senescent cells promote ageing and age-related disease
DOI: 10.6084/m9.figshare.6877220
title: Two different <i>Xylella fastidiosa</i> strains circulating in Italy: phylogenetic and evolutionary analyses

description: <i>Xylella fastidiosa</i>, a bacterial species infecting a broad range plants, includes five subspecies, <i>fastidiosa, multiplex, pauca, mulberry and sandyi.</i> In Europe, <i>Xylella</i> was isolated in olive trees in southern Italy (Apulia region) during the year 2013. The aim of the present study was to apply phylogenetic and evolutionary analysis to trace the possible origin and way of the entrance of <i>Xylella fastidiosa</i> in Italy. All the genomes available for <i>Xylella fastidiosa</i> spp were downloaded from NCBI. A phylogeographic analysis was performed using BEAST. <i>X. fastidiosa</i> strains belonging to <i>X. fastidiosa</i> subsp. <i>pauca</i> and subsp. <i>sandyi</i> have been reported to infect olive trees and coffee plants, respectively. The phylogeographic analysis also revealed and confirmed these two different ways of provenience <i>X. fastidiosa</i> subsp. <i>pauca</i> from Costa Rica and <i>X. fastidiosa</i> subsp <i>sandyi</i> from California Phylogeny have been an important tool to validate and support the recent hypothesis for <i>X. fastidiosa pauca</i> provenience.
DOI: 10.6084/m9.figshare.6877220.v1
title: Two different <i>Xylella fastidiosa</i> strains circulating in Italy: phylogenetic and evolutionary analyses

description: <i>Xylella fastidiosa</i>, a bacterial species infecting a broad range plants, includes five subspecies, <i>fastidiosa, multiplex, pauca, mulberry and sandyi.</i> In Europe, <i>Xylella</i> was isolated in olive trees in southern Italy (Apulia region) during the year 2013. The aim of the present study was to apply phylogenetic and evolutionary analysis to trace the possible origin and way of the entrance of <i>Xylella fastidiosa</i> in Italy. All the genomes available for <i>Xylella fastidiosa</i> spp were downloaded from NCBI. A phylogeographic analysis was performed using BEAST. <i>X. fastidiosa</i> strains belonging to <i>X. fastidiosa</i> subsp. <i>pauca</i> and subsp. <i>sandyi</i> have been reported to infect olive trees and coffee plants, respectively. The phylogeographic analysis also revealed and confirmed these two different ways of provenience <i>X. fastidiosa</i> subsp. <i>pauca</i> from Costa Rica and <i>X. fastidiosa</i> subsp <i>sandyi</i> from California Phylogeny have been an important tool to validate and support the recent hypothesis for <i>X. fastidiosa pauca</i> provenience.
DOI: 10.6084/m9.figshare.6877085
title: There are Other Fish in the Sea: How Do Community Smells Influence the Intensity of Code Smells?

description: Code smells are poor design or implementation choices applied by developers during software evolution that often lead to critical flaws or failure. Much in the same way, community smells reflect the presence of organizational and socio-technical issues within a software community that may lead to additional project costs. Recent empirical studies provide evidence that community smells are often---if not always---connected to circumstances such as code smells. In this paper we look deeper into this connection by conducting a mixed-methods empirical study of 117 releases from 9 open-source systems. The qualitative and quantitative sides of our mixed-methods study were run in parallel and assume a mutually-confirmative connotation. On the one hand, we survey 162 developers of the 9 considered systems to investigate whether developers perceive relationship between community smells and the code smells found in those projects. On the other hand, we perform a fine-grained analysis into the 117 releases of our dataset to measure the extent to which community smells impact code smell intensity (i.e., criticality). We then propose a code smell intensity prediction model that relies on both technical and community-related aspects. The results of both sides of our mixed-methods study lead to one conclusion: community-related factors contribute to the intensity of code smells. This conclusion supports the joint use of community and code smells detection as a mechanism for the joint management of technical and social problems around software development communities.
DOI: 10.6084/m9.figshare.6876998
title: Table S1. Specimen and transcriptome details from Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics

description: Details on all individuals and their transcriptomes incorporated in this study. The IZ numbers correspond to the respective registration number in the Invertebrate Zoology collection of the Museum of Comparative Zoology (MCZ; Harvard University). Transcriptomes newly sequenced for this study are marked in bold GenBank accession numbers. The adaptors refer to the PrepX library preparation kit indexing adaptors used to multiplex samples during Illumina sequencing. The number of transcripts for OMA provides the number of contigs after CD-HIT, translation with and selection of longest isoform that were used for orthology prediction with OMA
DOI: 10.6084/m9.figshare.6876998.v1
title: Table S1. Specimen and transcriptome details from Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics

description: Details on all individuals and their transcriptomes incorporated in this study. The IZ numbers correspond to the respective registration number in the Invertebrate Zoology collection of the Museum of Comparative Zoology (MCZ; Harvard University). Transcriptomes newly sequenced for this study are marked in bold GenBank accession numbers. The adaptors refer to the PrepX library preparation kit indexing adaptors used to multiplex samples during Illumina sequencing. The number of transcripts for OMA provides the number of contigs after CD-HIT, translation with and selection of longest isoform that were used for orthology prediction with OMA
DOI: 10.6084/m9.figshare.6876995
title: Table S3. Occupancy per species from Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics

description: Occupancy per species. For each species the mean frequency with which it occurs in the respective matrices' orthogroups is presented. E.g., a value of 0.5 means that the species was present in 50% of the orthogroups of the respective matrix.
DOI: 10.6084/m9.figshare.6876995.v1
title: Table S3. Occupancy per species from Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics

description: Occupancy per species. For each species the mean frequency with which it occurs in the respective matrices' orthogroups is presented. E.g., a value of 0.5 means that the species was present in 50% of the orthogroups of the respective matrix.
DOI: 10.6084/m9.figshare.6876989
title: Table S2. Orthogoup details from Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics

description: Usage and identity of orthogroups (OG). For each orthogroup its usage in all seven matrices as well as the respecteive best BLAST hit in the NCBI nr database arte reported. Because Eoleptestheria cf. ticinensis has been added to the OMA run for Matrix 7, the naming of the orthogroups differes between Matrix 7 and all others. A) Matrices 1-6; B) Matrix 7.
DOI: 10.6084/m9.figshare.6876746
title: Data Bachelorproject Dagmar Verel 2018

description: Data collected during the bachelorproject (may-june 2018) at the Bacterial Cell Biology group of SILS. <br>Data consists of images of cells taken during growth experiments, optical density values measured during growth experiments, measurements of cell length and diameter and raw data of the FRET experiment.