cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.st56h
title: Data from: Niche divergence promotes rapid diversification of East African sky island white-eyes (Aves: Zosteropidae)

description: The Eastern Afromontane biodiversity hotspot composed of highly fragmented
 forested highlands (sky islands) harbours exceptional diversity and
 endemicity, particularly within birds. To explain their elevated diversity
 within this region, models founded on niche conservatism have been
 offered, although detailed phylogeographic studies are limited to a few
 avian lineages. Here we focus on the recent songbird genus Zosterops,
 represented by montane and lowland members, to test the roles of niche
 conservatism versus niche divergence in the diversification and
 colonization of East Africa’s sky islands. The species-rich white-eyes are
 a typically homogeneous family with an exceptional colonizing ability, but
 in contrast to their diversity on oceanic islands, continental diversity
 is considered depauperate and has been largely neglected. Molecular
 phylogenetic analysis reveals extensive polyphyly among different montane
 populations of Z. poliogastrus with these larger and heavier endemic
 populations more closely related to taxa with divergent habitat types,
 altitudinal distributions and dispersal abilities than they are to
 populations of restricted endemics that occur in neighbouring montane
 forest fragments. This repeated transition between lowland and highland
 habitats over time demonstrate that diversification of the focal group is
 explained by niche divergence. The results also highlight an
 underestimation of diversity compared to morphological studies that has
 implications for their taxonomy and conservation. Molecular dating
 suggests that the spatially extensive African radiation arose
 exceptionally rapidly (1-2.5 Ma) during the fluctuating Plio-Pleistocene
 climate, which may have provided the primary driver for lineage
 diversification.
description: Zosterops_matrixConcatenated mtDNA matrixAFLP_matrixAFLP Zosterops matrixZosterops_Kenyan_Photos
DOI: 10.5281/zenodo.18381130
title: IDENTIFICATION OF THE CAUSES OF MENINGOCOCCAL INFECTION IN CHILDREN AND IMPROVEMENT OF PREVENTIVE MEASURES

description: Meningococcal infection is one of the most severe, rapidly progressing, and life-threatening diseases in children. This study focuses on the clinical manifestations of meningococcal infection, its early diagnosis, modern treatment methods, and preventive measures. In addition, the main principles of care for children affected by meningococcal infection, immunization approaches, and epidemiological control methods are discussed. Early diagnosis and effective prevention significantly reduce mortality and complication rates among children.
DOI: 10.34740/kaggle/dsv/14631101
title: Dataset jadwal event lariku.info
DOI: 10.5281/zenodo.18381129
title: IDENTIFICATION OF THE CAUSES OF MENINGOCOCCAL INFECTION IN CHILDREN AND IMPROVEMENT OF PREVENTIVE MEASURES

description: Meningococcal infection is one of the most severe, rapidly progressing, and life-threatening diseases in children. This study focuses on the clinical manifestations of meningococcal infection, its early diagnosis, modern treatment methods, and preventive measures. In addition, the main principles of care for children affected by meningococcal infection, immunization approaches, and epidemiological control methods are discussed. Early diagnosis and effective prevention significantly reduce mortality and complication rates among children.
DOI: 10.5061/dryad.kq201
title: Data from: "Transcriptome resources for the oriental rat flea and primary plague vector, Xenopsylla cheopis" in Genomic Resources Notes Accepted 1 August 2015 to 31 September 2015

description: This article documents the public availability of raw transcriptome
 sequence data, 45,254 assembled unigenes as well as their functional
 annotations of a plague vector Xenopsylla cheopis.
description: unigeneUnigenes of Xenopsylla cheopis transcriptome, assembled busing Trinity programannotationThe functional annotations by NR, SWISS-PROT, COG, KEGG, and GO databases.
DOI: 10.5061/dryad.t013r0s
title: Data from: WisecondorX: improved copy number detection for routine shallow whole-genome sequencing

description: Shallow whole-genome sequencing to infer copy number alterations (CNAs) in
 the human genome is rapidly becoming the method par excellence for routine
 diagnostic use. Numerous tools exist to deduce aberrations from massive
 parallel sequencing data, yet most are optimized for research and often
 fail to redeem paramount needs in a clinical setting. Optimally, a read
 depth-based analytical software should be able to deal with single-end and
 low-coverage data—this to make sequencing costs feasible. Other important
 factors include runtime, applicability to a variety of analyses and
 overall performance. We compared the most important aspect, being
 normalization, across six different CNA tools, selected for their assumed
 ability to satisfy the latter needs. In conclusion, WISECONDOR, which uses
 a within-sample normalization technique, undoubtedly produced the best
 results concerning variance, distributional assumptions and basic ability
 to detect true variations. Nonetheless, as is the case with every tool,
 WISECONDOR has limitations, which arise through its exclusiveness for
 non-invasive prenatal testing. Therefore, this work presents WisecondorX
 in addition, an improved WISECONDOR that enables its use for varying types
 of applications. WisecondorX is freely available at
 https://github.com/CenterForMedicalGeneticsGhent/WisecondorX.
description: WisecondorX output
 tablesProcessed copy number
 alteration files. Includes 20 healthy NIPT and gDNA samples; and another
 15 NIPT and 5 gDNA cases with validated aberrations. The loci of the
 rearrangements can be found in Supplementary material of the
 paper.samples.zip
DOI: 10.5061/dryad.2h7d2
title: Data from: Optical data compression in time stretch imaging

description: Time stretch imaging offers real-time image acquisition at millions of
 frames per second and subnanosecond shutter speed, and has enabled
 detection of rare cancer cells in blood with record throughput and
 specificity. An unintended consequence of high throughput image
 acquisition is the massive amount of digital data generated by the
 instrument. Here we report the first experimental demonstration of
 real-time optical image compression applied to time stretch imaging. By
 exploiting the sparsity of the image, we reduce the number of samples and
 the amount of data generated by the time stretch camera in our
 proof-of-concept experiments by about three times. Optical data
 compression addresses the big data predicament in such systems.
description: 0420_AST_115_1p05_p201_20Gs_Ave8_10mV2us_step250umDigitized signal by oscilloscope for non-linear dispersion, measured on April 20, 2014. Experiment parameters: sampling rate = 20 Gs/s. Mechanical scan = 0.25 mm/step.0420_DCF3200_115_4p05_p201_20Gs_Ave8_5mV2us_step250um_filtered865MHzDigitized signal by oscilloscope for linear dispersion, measured on April 20, 2014. Experiment parameters: sampling rate = 20 Gs/s. Mechanical scan = 0.25 mm/step.Data FBG group delayDesigned and measured group delay profile of the fiber Bragg grating used in experiment
DOI: 10.5061/dryad.k77nh
title: Data from: Population genomic variation reveals roles of history, adaptation, and ploidy in switchgrass

description: Geographic patterns of genetic variation are shaped by multiple
 evolutionary processes, including genetic drift, migration, and natural
 selection. Switchgrass (Panicum virgatum L.) has strong genetic and
 adaptive differentiation despite life history characteristics that promote
 high levels of gene flow and can homogenize intraspecific differences,
 such as wind-pollination and self-incompatibility. To better understand
 how historical and contemporary factors shape variation in switchgrass, we
 use genotyping-by-sequencing to characterize switchgrass from across its
 range at 98,042 SNPs. Population structuring reflects biogeographic and
 ploidy differences within and between switchgrass ecotypes and indicates
 that biogeographic history, ploidy incompatibilities, and differential
 adaptation each have important roles in shaping ecotypic differentiation
 in switchgrass. At one extreme, we determine that two Panicum taxa are not
 separate species but are actually conspecific, ecologically divergent
 types of switchgrass adapted to the extreme conditions of coastal sand
 dune habitats. Conversely, we identify natural hybrids among lowland and
 upland ecotypes and visualize their genome-wide patterns of admixture.
 Furthermore, we determine that genetic differentiation between primarily
 tetraploid and octoploid lineages is not caused solely by ploidy
 differences. Rather, genetic diversity in primarily octoploid lineages is
 consistent with a history of admixture. This suggests that polyploidy in
 switchgrass is promoted by admixture of diverged lineages, which may be
 important for maintaining genetic differentiation between switchgrass
 ecotypes where they are sympatric. These results provide new insights into
 the mechanisms shaping variation in widespread species and provide a
 foundation for dissecting the genetic basis of adaptation in switchgrass.
description: De-multiplexing
 FunctionsFunctions in R for
 de-multiplexing (assigning sample identify for each read using the
 sequence barcode at the beginning of the read) the raw sequencing data.
 The raw data itself is stored on the NCBI SRAdemultiplexing_functions.rDiploid GenotypesTab-delimited file for the diploid genotypes.diploid_genotypes.tabPseudo-haploid genotypesTab-delimited file with the pseudo-haploid genotypes used for analysis.haploid_genotypes_1.tabBarcode Information for Sequencing LibrariesExample of a tab-delimited table containing the information to connect barcodes to samples in different sequencing libraries. This can be used in conjunction with the R functions to de-multiplex the raw data.library_barcodes.tabSample MetadataMetadata for the samples. Includes sample name, population, ploidy, phenotype, sequencing read count, and inferred gene pool.sample_metadata.tab
DOI: 10.5061/dryad.hk860
title: Data from: Cryptic ecology among host generalist Campylobacter jejuni in domestic animals

description: Homologous recombination between bacterial strains is theoretically
 capable of preventing the separation of daughter clusters, and producing
 cohesive clouds of genotypes in sequence space. However, numerous barriers
 to recombination are known. Barriers may be essential such as adaptive
 incompatibility, or ecological, which is associated with the opportunities
 for recombination in the natural habitat. Campylobacter jejuni is a gut
 colonizer of numerous animal species and a major human enteric pathogen.
 We demonstrate that the two major generalist lineages of C. jejuni do not
 show evidence of recombination with each other in nature, despite having a
 high degree of host niche overlap and recombining extensively with
 specialist lineages. However, transformation experiments show that the
 generalist lineages readily recombine with one another in vitro. This
 suggests ecological rather than essential barriers to recombination,
 caused by a cryptic niche structure within the hosts.
description: Assembled 128
 Campylobacter whole genome sequences128 Campylobacter whole
 genomes sequenced using a Illumina HiSeq 2000 and assembled using Velvet.
 Filenames refer to IDs in Table S1 in the associated
 publication.MolEcol2014.zipComplete set of available STs for C. jejuni (sequences)Sequences of every alleles for MLST profiles of 3,834 STs present in the pubMLST Campylobacter database as of the 26th of May 2011 and used in the associated publication.Complete_set_of_available_STs_for_Cjejuni_(sequences).xlsComplete host associations with C. jejuni ST clonal complexesComplete host associations with C. jejuni ST clonal complexes, using data extracted from pubMLST as of 26th May 2011, used in the associated publication to produce Fig. 1B.Complete_host_associations_with_ST_clonal_complexes_(pubMLST).xlsx
DOI: 10.5061/dryad.7d467b6
title: Data from: A high density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour

description: High density SNP microarrays (‘SNP chips’) are a rapid, accurate and
 efficient method for genotyping several hundred thousand polymorphisms in
 large numbers of individuals. While SNP chips are routinely used in human
 genetics and in animal and plant breeding, they are less widely used in
 evolutionary and ecological research. In this paper we describe the
 development and application of a high density Affymetrix Axiom chip with
 around 500 000 SNPs, designed to perform genomics studies of great tit
 (Parus major) populations. We demonstrate that the per-SNP genotype error
 rate is well below 1% and that the chip can also be used to identify
 structural or copy number variation (CNVs). The chip is used to explore
 the genetic architecture of exploration behaviour (EB), a personality
 trait that has been widely studied in great tits and other species. No
 SNPs reached genome-wide significance, including at DRD4, a candidate
 gene. However, EB is heritable and appears to have a polygenic
 architecture. Researchers developing similar SNP chips may note: (i) SNPs
 previously typed on alternative platforms are more likely to be converted
 to working assays, (ii) detecting SNPs by more than one pipeline, and in
 independent datasets, ensures a high proportion of working assays, (iii)
 allele frequency ascertainment bias is minimised by performing SNP
 discovery in individuals from multiple populations and (iv) samples with
 the lowest call rates tend to also have the greatest genotyping error
 rates.
description: PRJEB24964A description and genome assembly locations of the SNPs used on the HD chipWythamCNV_cleanA list of CNVs in the filtered Wytham Woods datasetWythamCNV_Plink_clean.cnvWythamCNVA list of CNVs in the unfiltered Wytham Woods datasetPlink .bed file used for Exploratory Behaviour analysisContains data on 415 birds typed at 459,502 autosomal SNPspersonality2_noZ.bedPlink .fam file used for Exploratory Behaviour analysisContains ID information for 415 birdspersonality2_noZ.famPlink .bim file used for Exploratory Behaviour analysisContains marker information for 459,502 autosomal SNPspersonality2_noZ.bimSequence read archive link to 30 resequenced birdsThe 30 birds used for the SNP discovery have resequenced genomes available on the NCBI Sequence Read Archive, under project ID SRP066678
DOI: 10.5061/dryad.60916
title: Data from: Odontochilus napoensis sp. nov. (Orchidoideae: Orchidaceae) from southwestern Guangxi, China

description: Odontochilus napoensis, a new species from southwestern Guangxi, China, is
 described and illustrated. It is close to Odontochilus inabae (Hayata) T.
 P. Lin, but can be distinguished by its glabrous ovary, solitary flower,
 and 2.0–3.5 mm long filaments of flanges. It is also similar to O.
 nanlingensis (L. P. Siu & K. Y. Lang) Ormerod, but differs by the
 solitary, not resupinate flower, and light greenish–brown lateral sepals.
description: The ink line figure of
 Odontochilus napoensis sp. nov.The ink line figure of
 Odontochilus napoensis sp. nov.The ink line figure — Figure 2.
 Odontochilus napoensis sp.
 nov..jpgThe habitat figure of
 Odontochilus napoensis sp. nov.The habitat figure of
 Odontochilus napoensis sp. nov.The habitat figure — Figure 1.
 Odontochilus napoensis sp.
 nov..jpgThe longitude and
 latitude figure of Odontochilus napoensis sp. nov.Odontochilus napoensis,
 the new species from southwestern Guangxi, China, was found in 23°06´28.37
 N, 105°43´25.84E, alt. 1450 m a.s.l. 16 June 2013.The longitude and latitude
 figure — Odontochilus napoensis sp.
 nov.JPGThe size and anatomical
 structure figures — Odontochilus napoensis sp. nov.The size and anatomical
 structure figures of Odontochilus napoensis sp. nov.The habitat figures of
 Odontochilus napoensis sp. nov.The habitat figures of
 Odontochilus napoensis sp. nov.The habitat figures —
 Odontochilus napoensis sp. nov..jpg.zip
DOI: 10.5061/dryad.r5b51
title: Data from: Spectral diversity area relationships for assessing biodiversity in a wildland-agriculture matrix

description: Species-area relationships have long been used to assess patterns of
 species diversity across scales. Here this concept is extended to spectral
 diversity using hyperspectral data collected by NASA's Airborne
 Visible/Infrared Imaging Spectrometer (AVIRIS) over western Michigan. This
 mixture of mesic forest and agricultural lands offers two end-points on
 the local-scale diversity continuum – one set of well mixed forest patches
 and one set of highly homogeneous agricultural patches. Using the sum of
 the first three principal component values and the principal components’
 convex hull volume, spectral diversity was compared within and among these
 plots and to null expectations for perfectly random and perfectly patchy
 landscapes. Overall the spectral diversity area relationship confirms the
 patterns that would be expected for this landscape, but this application
 suggests that this approach could be extended to less well understood
 landscapes and could reveal key insights about the relative importance of
 different drivers of community assembly, even in the absence of additional
 data about plant functional traits or species’ identities.
description: kbs_aviris2009_CRspectra_FINALTab delimited .txt file of continuum removed spectral data for the 300 50x50 m plots used in this study, with header row of column names. First column is plot id, second is whether the plot is in forest or agriculture (0 = forest, 1 = agriculture), followed by the continuum removed spectral data. More info and R code to process can be found in the associated manuscript. Original data is from AVIRIS flightline f090720t01p00r05 which was supported by funding from the NASA Terrestrial Ecology program (Grant # NNX11AB88G; PI S. Ollinger); contact S. Ollinger for total flightline reflectance data.
DOI: 10.5061/dryad.41ng6
title: Data from: Genomic islands of differentiation in two songbird species reveal candidate genes for hybrid female sterility

description: Hybrid sterility is a common first step in the evolution of postzygotic
 reproductive isolation. According to Haldane’s Rule it affects
 predominantly the heterogametic sex. While the genetic basis of hybrid
 male sterility in organisms with heterogametic males has been studied for
 decades, the genetic basis of hybrid female sterility in organisms with
 heterogametic females has received much less attention. We investigated
 the genetic basis of reproductive isolation in two closely related avian
 species, the Common Nightingale (Luscinia megarhynchos) and the Thrush
 Nightingale (L. luscinia), that hybridize in a secondary contact zone and
 produce viable hybrid progeny. In accordance with Haldane’s Rule, hybrid
 females are sterile, while hybrid males are fertile, allowing gene flow to
 occur between the species. Using transcriptomic data from multiple
 individuals of both nightingale species we identified genomic islands of
 high differentiation (FST) and of high divergence (Dxy), and we analyzed
 gene content and patterns of molecular evolution within these islands.
 Interestingly, we found that these islands were enriched for genes related
 to female meiosis and metabolism. The islands of high differentiation and
 divergence were also characterized by higher levels of linkage
 disequilibrium than the rest of the genome in both species indicating that
 they might be situated in genomic regions of low recombination. This study
 provides one of the first insights into genetic basis of hybrid female
 sterility in organisms with heterogametic females.
description: Luscinia svecica mRNA
 454 readsA file with 454 FLX
 reads, demultiplexed and converted to FASTQ with Roche sfffile
 tool.luscinia-svecica-mrna-454.tar.bz2doi:10.5061/dryad.2p4t3Remaining Luscinia samples used in "Genomic islands of differentiation in two songbird species reveal candidate genes for hybrid female sterility" are archived in a previous Dryad submission. Mořkovský L, Pačes J, Rídl J, Reifová R (2015) Data from: Scrimer: designing primers from transcriptome data. Dryad Digital Repository. https://doi.org/10.5061/dryad.2p4t3
DOI: 10.5061/dryad.53629
title: Data from: De novo active sites for resurrected Precambrian enzymes

description: Protein engineering studies often suggest the emergence of completely new
 enzyme functionalities to be highly improbable. However, enzymes likely
 catalysed many different reactions already in the last universal common
 ancestor. Mechanisms for the emergence of completely new active sites must
 therefore either plausibly exist or at least have existed at the
 primordial protein stage. Here, we use resurrected Precambrian proteins as
 scaffolds for protein engineering and demonstrate that a new active site
 can be generated through a single hydrophobic-to-ionizable amino acid
 replacement that generates a partially buried group with perturbed
 physico-chemical properties. We provide experimental and computational
 evidence that conformational flexibility can assist the emergence and
 subsequent evolution of new active sites by improving substrate and
 transition-state binding, through the sampling of many potentially
 productive conformations. Our results suggest a mechanism for the
 emergence of primordial enzymes and highlight the potential of ancestral
 reconstruction as a tool for protein engineering.
description: Molecular Dynamics
 Simulations of Ancestral and Modern β-LactamasesThe data package
 contains topology and coordinate files, the neutralized system in a water
 box, the first and last frames of three independent 100ns molecular
 dynamics simulations per system, structures of representative
 conformational clusters, cluster summary files, and TSA parameter
 files.OPEN_ACESS.zip