cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.657d4
title: Data from: Has Madagascar lost its exceptional leptospirosis free-like status?

description: Background: Leptospirosis is a widespread but underreported cause of
 morbidity and mortality. It has rarely been reported in either humans or
 animals in Madagascar. Methods: We conducted a cross-sectional survey of
 the inhabitants in Moramanga, Madagascar, in June 2011, to estimate the
 prevalence of human infection using the microscopic agglutination test
 (MAT). This activity was carried out as part of a workshop implemented by
 the Pasteur Institute of Madagascar, focusing on surveillance with a one
 week field study and targeting the health staff of the district level.
 Results: In total, we sampled 678 inhabitants from 263 households. The sex
 ratio (M/F) was 0.65 and the mean age 26.7 years. We obtained a value of
 2.9% for the first recorded seroprevalence of this disease in the human
 community of Moramanga. Questionnaire responses revealed frequent contacts
 between humans and rodents in Moramanga. However, activities involving
 cattle were identified as a risk factor significantly associated with
 seropositivity (OR=3). Conclusion: Leptospirosis remains a neglected
 disease in Madagascar. This study highlights the need to quantify the
 public health impact of this neglected disease in a more large scale, in
 all the country and to establish point-of-care laboratories in remote
 areas.
description: DataLeptoPublished
DOI: 10.5061/dryad.331sq
title: Data from: Patterns of intra- and inter-population genetic diversity in Alaskan coho salmon: implications for conservation

description: Little is known about the genetic diversity of coho salmon in Alaska,
 although this area represents half of the species’ North American range.
 In this study, nine microsatellite loci were used to genotype 32 putative
 coho salmon populations from seven regions of Alaska. The primary
 objectives were to estimate and evaluate the degree and spatial
 distribution of neutral genetic diversity within and among populations of
 Alaskan coho salmon. Genetic analysis yielded four results that provide
 insight into forces influencing genetic diversity in Alaskan coho salmon
 and have important conservation implications: 1) significant population
 differentiation was found within each region; 2) the degree of
 differentiation (FST = 0.099) among populations was as large or larger
 than that reported for other Pacific salmon species in Alaska; 3) phenetic
 clustering of populations showed weak geographic concordance; 4) strong
 genetic isolation by distance was only apparent at the finest geographic
 scale (within a drainage). These results suggest that coho salmon
 populations are small relative to populations of other Pacific salmon, and
 the genetic diversity within and among coho salmon populations is
 influenced primarily by genetic drift, and not gene flow. Resource
 management and conservation actions affecting coho salmon in Alaska must
 recognize that the populations are generally small, isolated, and probably
 exhibit local adaptation to different spawning and freshwater rearing
 habitats. These factors justify managing and conserving Alaskan coho
 salmon at a fine geographic scale.
description: Alaskan coho salmon
 genotypesGenotype data from nine
 microsatellite loci for 2584 coho salmon in 32 locations in Alaska. This
 data file is formatted for use in the computer program GenePop v4.0. The
 genotypes in this file have NOT been standardized with other laboratories
 -- see readme file for further information.c32p9lTable 1Location, site abbreviation (Abbr), sample year, sample size (n), and life stage (A = adult, J = juvenile) of fish sampled from 32 putative coho salmon populations in seven regions of Alaska.
DOI: 10.5517/ccdc.csd.cc2ql8sd
title: CCDC 2520014: Experimental Crystal Structure Determination

description: Related Article: Michael Bolte|2026|CSD Communication|||
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: 10.5061/dryad.1390
title: Data from: Differential introgression causes genealogical discordance in host races of Acrocercops transecta (Insecta: Lepidoptera)

description: Recently diverged populations often exhibit incomplete reproductive
 isolation, with a low level of gene flow continuing between populations.
 Previous studies have shown that, even under a low level of gene flow,
 genetic divergence between populations can proceed at the loci governing
 local adaptation and reproductive isolation but not at other neutral loci.
 A leaf-mining moth, Acrocercops transecta, consists of Juglans- and
 Lyonia-associated host races. The two host races differ in host
 preferences of ovipositing females and in larval adaptation to host plants
 but mate readily in the laboratory, producing fertile hybrids. The Juglans
 and Lyonia races are often sympatric in the wild, implying that gene
 introgression could occur in nature between the two host races. We tested
 this hypothesis by combining phylogenetic analyses with coalescent
 simulations, focusing on mitochondrial genes (COI and ND5) and the nuclear
 Tpi, Per and Ldh genes located on the Z-chromosome. The mitochondrial
 genes clearly distinguished the Lyonia race from the Juglnas race, whereas
 the Tpi, Per and Ldh genealogies did not reflect the two host races.
 Coalescent simulations indicated gene flow at the three Z-linked genes in
 both directions, whereas there was no introgression in the mitochondrial
 genes. The lack of introgression in mitochondrial genes suggests that
 female host preference is the primary force leading to the bifurcation of
 maternally inherited loci. Thus, the results show that a low level of gene
 flow coupled with the inflexible female host preference differentiates
 histories of divergence between maternally and biparentally inherited
 genes in this host race system.
description: Sendai_COI+ND5.nexPartial mitochondrial COI + ND5 sequences of moths collected in Sendai, Japan.Sendai_Tpi.nexPartial Tpi sequences of moths collected in Sendai, Japan.Sendai_Period.nexPartial Period sequences of moths collected in Sendai, Japan.Sendai_Ldh.nexPartial Ldh sequences of moths collected in Sendai, Japan.Niimi_COI+ND5.nexPartial mitochondrial COI + ND5 sequences of moths collected in Niimi, Okayama, Japan.Niimi_Tpi.nexPartial Tpi sequences of moths collected in Niimi, Okayama, Japan.Niimi_Period.nexPartial Period sequences of moths collected in Niimi, Okayama, Japan.Niimi_Ldh.nexPartial Ldh sequences of moths collected in Niimi, Okayama, Japan.
DOI: 10.5061/dryad.r51c7
title: Data from: A preliminary molecular phylogeny of shield-bearer moths (Lepidoptera: Adeloidea: Heliozelidae) highlights rich undescribed diversity

description: Heliozelidae are a widespread, evolutionarily early diverging family of
 small, day-flying monotrysian moths, for which a comprehensive phylogeny
 is lacking. We generated the first molecular phylogeny of the family using
 DNA sequences of two mitochondrial genes (COI and COII) and two nuclear
 genes (H3 and 28S) from 130 Heliozelidae specimens, including eight of the
 twelve known genera: Antispila, Antispilina, Coptodisca, Heliozela,
 Holocacista, Hoplophanes, Pseliastis, and Tyriozela. Our results provide
 strong support for five major Heliozelidae clades: (i) a large widespread
 clade containing the leaf-mining genera Antispilina, Coptodisca and
 Holocacista and some species of Antispila, (ii) a clade containing most of
 the described Antispila, (iii) a clade containing the leaf-mining genus
 Heliozela and the monotypic genus Tyriozela, (iv) an Australian clade
 containing Pseliastis and (v) an Australian clade containing Hoplophanes.
 Each clade includes several new species and potentially new genera.
 Collectively, our data uncover a rich and undescribed diversity that
 appears to be especially prevalent in Australia. Our work highlights the
 need for a major taxonomic revision of the family and for generating a
 robust molecular phylogeny using multi-gene approaches in order to resolve
 the relationships among clades.
description: 28S_COI_COII_H3_alignmentConcatenated four gene alignment (28S, COI, COII, H3) for 136 specimens used in phylogenetic analyses of Heliozelidae family.28S_COI_COII_H3_new_aligment.fasta
DOI: 10.5061/dryad.q2s7h
title: Data from: Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

description: Plastid DNA sequences have been widely used by systematists for
 reconstructing plant phylogenies. The utility of any DNA region for
 phylogenetic analysis is determined by ease of amplification and
 sequencing, confidence of assessment in phylogenetic character alignment,
 and by variability across broad taxon sampling. Often, a compromise must
 be made between using relatively highly conserved coding regions or highly
 variable introns and intergenic spacers. Analyses of a combination of
 these types of DNA regions yield phylogenetic structure at various levels
 of a tree (i.e., along the spine and at the tips of the branches). Here,
 we demonstrate the phylogenetic utility of a heretofore unused portion of
 a plastid protein-coding gene, hypothetical chloroplast open reading frame
 1 (ycf1), in orchids. All portions of ycf1 examined are highly variable,
 yet alignable across Orchidaceae, and are phylogenetically informative at
 the level of species. In Orchidaceae, ycf1 is more variable than matK both
 in total number of parsimony informative characters and in percent
 variability. The nrITS region is more variable than ycf1, but is more
 difficult to align. Although we only demonstrate the phylogenetic utility
 of ycf1 in orchids, it is likely to be similarly useful among other plant
 taxa.
description: Orchid
 3'ycf1Nexus matrix of 3'
 ycf1 sequences of various OrchidaceaeOrchid
 matKNexus matrix of matK
 sequences of various OrchidaceaeSobralieae
 ITSNexus matrix of nrITS
 sequences of various Sobralieae (Orchidaceae)Sobralieae
 matKNexus matrix of matK
 sequences of various Sobralieae (Orchidaceae)Sobralieae
 ycf1Nexus matrix of ycf1
 sequences of various Sobralieae (Orchidaceae)Vandeae
 ITSNexus matrix of nrITS
 sequences of various Vandeae (Orchidaceae)Vandeae
 matKNexus matrix of matK
 sequences of various Vandeae (Orchidaceae)Vandeae
 ycf1Nexus matrix of ycf1
 sequences of various Vandeae (Orchidaceae).
DOI: 10.5061/dryad.d0325
title: Data from: Root effect haemoglobins in fish may greatly enhance general oxygen delivery relative to other vertebrates

description: The teleost fishes represent over half of all extant vertebrates; they
 occupy nearly every body of water and in doing so, occupy a diverse array
 of environmental conditions. We propose that their success is related to a
 unique oxygen (O2) transport system involving their extremely pH-sensitive
 haemoglobin (Hb). A reduction in pH reduces both Hb-O2 affinity (Bohr
 effect) and carrying capacity (Root effect). This, combined with a large
 arterial-venous pH change (ΔpHa-v) relative to other vertebrates, may
 greatly enhance tissue oxygen delivery in teleosts (e.g., rainbow trout)
 during stress, beyond that in mammals (e.g., human). We generated oxygen
 equilibrium curves (OECs) at five different CO2 tensions for rainbow trout
 and determined that, when Hb-O2 saturation is 50% or greater, the change
 in oxygen partial pressure (ΔPO2) associated with ΔpHa-v can exceed that
 of the mammalian Bohr effect by at least 3-fold, but as much as 21-fold.
 Using known ΔpHa-v and assuming a constant arterial-venous PO2 difference
 (Pa-vO2), Root effect Hbs can enhance O2 release to the tissues by 73.5%
 in trout; whereas, the Bohr effect alone is responsible for enhancing O2
 release by only 1.3% in humans. Disequilibrium states are likely
 operational in teleosts in vivo, and therefore the ΔpHa-v, and thus
 enhancement of O2 delivery, could be even larger. Modeling with known
 Pa-vO2 in fish during exercise and hypoxia indicates that O2 release from
 the Hb and therefore potentially tissue O2 delivery may double during
 exercise and triple during some levels of hypoxia. These characteristics
 may be central to performance of athletic fish species such as salmonids,
 but may indicate that general tissue oxygen delivery may have been the
 incipient function of Root effect Hbs in fish, a trait strongly associated
 with the adaptive radiation of teleosts.
description: All trout OEC curve data
 and fitsThese are the values,
 standard errors, and curve fits for all oxygen equilibrium curves for
 trout determined from this study. All are plotted in Fig.
 1A.Human oxygen equilibrium
 curves from the literatureThis exercise took into
 consideration data from Itoh et al., 2001, Winslow et al., 1977, and
 Roughton and Severinghaus, 1973 to make human oxygen equilibrium curves
 that would eventually inspire the analyses for this
 paper.Human
 OECs from literature
 2Sept.2015.xlsxAll trout delta PO2
 valuesAll of these values were
 calculated directly from the oxygen equilibrium curves, i.e. by
 subtracting exact values from curve to curve. These values were then
 plotted for Fig. 1B.All human delta PO2
 valuesThese human delta PO2
 values were calculated by fitting data from Tyuma and Ueda, 1975 with the
 Equation 1 in the manuscript. These values are graphically displayed in
 Fig. 1B.
DOI: 10.5061/dryad.98m0m
title: Data from: Fusion transcript discovery in formalin-fixed paraffin-embedded human breast cancer tissues reveals a link to tumor progression

description: The identification of gene fusions promises to play an important role in
 personalized cancer treatment decisions. Many rare gene fusion events have
 been identified in fresh frozen solid tumors from common cancers employing
 next-generation sequencing technology. However the ability to detect
 transcripts from gene fusions in RNA isolated from formalin-fixed
 paraffin-embedded (FFPE) tumor tissues, which exist in very large sample
 repositories for which disease outcome is known, is still limited due to
 the low complexity of FFPE libraries and the lack of appropriate
 bioinformatics methods. We sought to develop a bioinformatics method,
 named gFuse, to detect fusion transcripts in FFPE tumor tissues. An
 integrated, cohort based strategy has been used in gFuse to examine
 single-end 50 base pair (bp) reads generated from FFPE RNA-Sequencing
 (RNA-Seq) datasets employing two breast cancer cohorts of 136 and 76
 patients. In total, 118 fusion events were detected transcriptome-wide at
 base-pair resolution across the 212 samples. We selected 77 candidate
 fusions based on their biological relevance to cancer and supported 61% of
 these using TaqMan assays. Direct sequencing of 19 of the fusion sequences
 identified by TaqMan confirmed them. Three unique fused gene pairs were
 recurrent across the 212 patients with 6, 3, 2 individuals harboring these
 fusions respectively. We show here that a high frequency of fusion
 transcripts detected at the whole transcriptome level correlates with poor
 outcome (P&lt;0.0005) in human breast cancer patients. This study
 demonstrates the ability to detect fusion transcripts as biomarkers from
 archival FFPE tissues, and the potential prognostic value of the fusion
 transcripts detected.
description: SAM files containing
 RNA-seq reads supporting fusion transcripts in Providence and Rush
 cohortsThese SAM files consist
 2 directories, one for Providence cohort, and another for Rush cohort.
 Each sample has one individual SAM file under each cohort directory. The
 data were generated by gFuse, a RNA-seq fusion detection bioinformatics
 method, from archived FFPE human breast cancer patients. As a part of
 gFuse pipeline, the SAM files were generated by GSNAP via mapping
 supporting RNA-seq reads against the fasta sequences of 5 template sets of
 100 unique fusion junctions in the length of 100bp, which are available
 here in the file “100fusiontemplates.fa”. The sequences and sample IDs are
 also described in Supplementary Table 1 of the manuscript titled “Fusion
 transcript discovery in formalin-fixed paraffin-embedded human breast
 cancer tissues reveals a link to tumor progression”.fusion_read_alignment.sam.tar.gz
DOI: 10.5061/dryad.b8h1n
title: Data from: Non-random patterns of genetic admixture expose the complex historical hybrid origin of unisexual leaf beetle species in the genus Calligrapha

description: Many unisexual animal lineages supposedly arose from hybridization.
 However, support for their putative hybrid origins mostly comes from
 indirect methodologies, which are rarely confirmatory. Here we provide
 compelling data indicating that tetraploid unisexual Calligrapha are true
 genetic mosaics obtained via analysis of mitochondrial DNA (mtDNA) and
 allelic variation and coalescence times for three single-copy nuclear
 genes (CPS, HARS, and Wg) in five of six unisexual Calligrapha and a
 representative sample of bisexual species. Nuclear allelic diversity in
 unisexuals consistently segregates in the gene pools of at least two but
 up to three divergent bisexual species, interpreted as putative parentals
 of interspecific hybridization crosses. Interestingly, their mtDNA
 diversity derives from an additional yet undiscovered older evolutionary
 lineage that is possibly the same for all independently originated
 unisexual species. One possibly extinct species transferred its mtDNA to
 several evolutionary lineages in a wave of hybridization events during the
 Pliocene, whereby descendant species retained a polymorphic mtDNA
 constitution. Recent hybridizations, in the Pleistocene and always
 involving females with the old introgressed mtDNA, seemingly occurred in
 the lineages leading to unisexual species, decoupling mtDNA introgression
 (and inferences derived from these data, such as timing and parentage)
 from subsequent acquisition of the new reproductive mode. These results
 illuminate an unexpected complexity in possible routes to animal
 unisexuality, with implications for the interpretation of ancient
 unisexuality. If the origin of unisexuality requires a mechanism where (1)
 hybridization is a necessary but insufficient condition and (2) multiple
 bouts of hybridization involving more than two divergent lineages are
 required, then the origins of several classical unisexual systems may have
 to be reassessed.
description: NEXUS alignment
 Calligrapha CPS dataCPS_alignment_Montelongo_Gomez-Zurita.nexNEXUS alignment Calligrapha HARS dataHARS_alignment_Montelongo_Gomez-Zurita.nexNEXUS alignment Calligrapha Wg dataWg_alignment_Montelongo_Gomez-Zurita.nexNEXUS alignment Calligrapha mtDNA datamtDNA_alignment_Montelongo_Gomez-Zurita.nex
DOI: 10.15482/usda.adc/27285159
title: Data from: Efficacy of long-lasting insecticide-incorporated netting in controlling preharvest and postharvest pest insects: a meta-analysis study

description: This dataset aims to provide a comprehensive analysis of existing literature on the utilization of LLINs in the management of pre- and postharvest pest insect species (excluding those in urban systems and vectors). By synthesizing findings from a broad spectrum of studies, we aim to discern patterns relative to system and experimental design and develop a new synthesized understanding of the effectiveness of LLINs in agriculture. Moreover, our dataset intends to identify and address gaps in current knowledge. Through a meta-analytical approach, this review aims to distill key insights that can inform future research directions, and practical applications in the integrated management programs of pre- and postharvest insect pests.<br>The goal of this dataset is to understand the efficacy of long-lasting insecticide netting in agriculture. We used databases such as Web of Science, Scopus, and Google Scholar to find studies related to LLIN. First, we carried out a literature search on the topic of insecticide netting. We used various Keyword combinations to identify a broad initial dataset, including various terms such as ‘netting’, ‘LLIN’ ‘insecticide netting’ in combination with either ‘insects’, ‘preharvest’, ‘postharvest’, and ‘agriculture’. Papers were individually checked to ensure they met criteria for inclusion in the meta-analysis, which included that 1) articles were published between 1990–2024, 2) the focus was on agricultural crops (not urban systems or vectored diseases), 3) netting was not solely used for exclusion (e.g., in the absence of an insecticidal ingredient), and 4) included a proper negative or stakeholder standard control. At the end, this left us with a total of 44 peer-reviewed publications (23 postharvest + 22 preharvest studies, one common study for pre and postharvest insects) with 285 data points on the efficacy of LLINs in agriculture. However, an additional required criterion was that all studies needed to present means, standard errors, and samples sizes for both controls and LLIN treatment. After this additional criterion, there was a final total of 31 peer-reviewed publications (19 postharvest + 12 preharvest studies). Additionally, potential publication bias was assessed by using funnel plots, and statistical tests were evaluated.
DOI: 10.15482/usda.adc/27285159.v1
title: Data from: Efficacy of long-lasting insecticide-incorporated netting in controlling preharvest and postharvest pest insects: a meta-analysis study

description: This dataset aims to provide a comprehensive analysis of existing literature on the utilization of LLINs in the management of pre- and postharvest pest insect species (excluding those in urban systems and vectors). By synthesizing findings from a broad spectrum of studies, we aim to discern patterns relative to system and experimental design and develop a new synthesized understanding of the effectiveness of LLINs in agriculture. Moreover, our dataset intends to identify and address gaps in current knowledge. Through a meta-analytical approach, this review aims to distill key insights that can inform future research directions, and practical applications in the integrated management programs of pre- and postharvest insect pests.<br>The goal of this dataset is to understand the efficacy of long-lasting insecticide netting in agriculture. We used databases such as Web of Science, Scopus, and Google Scholar to find studies related to LLIN. First, we carried out a literature search on the topic of insecticide netting. We used various Keyword combinations to identify a broad initial dataset, including various terms such as ‘netting’, ‘LLIN’ ‘insecticide netting’ in combination with either ‘insects’, ‘preharvest’, ‘postharvest’, and ‘agriculture’. Papers were individually checked to ensure they met criteria for inclusion in the meta-analysis, which included that 1) articles were published between 1990–2024, 2) the focus was on agricultural crops (not urban systems or vectored diseases), 3) netting was not solely used for exclusion (e.g., in the absence of an insecticidal ingredient), and 4) included a proper negative or stakeholder standard control. At the end, this left us with a total of 44 peer-reviewed publications (23 postharvest + 22 preharvest studies, one common study for pre and postharvest insects) with 285 data points on the efficacy of LLINs in agriculture. However, an additional required criterion was that all studies needed to present means, standard errors, and samples sizes for both controls and LLIN treatment. After this additional criterion, there was a final total of 31 peer-reviewed publications (19 postharvest + 12 preharvest studies). Additionally, potential publication bias was assessed by using funnel plots, and statistical tests were evaluated.