cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.13410/2
title: Common garden dispersal data

description: Data collected from a common garden experiment following experimental laboratory invasions of the bean beetle Callosobruchus maculatus. Data show the dispersal distance of beetles from each replicate population of the invasion experiment. Columns (in order) are date, start time, end time, population ID, common garden generation (1-2), treatment (0 = spatially sorted, 1 = shuffled), replicate (1-3; within-population replicate dispersal trials), sex (0 = female, 1 = male), distance (number of patches dispersed), and notes.
DOI: 10.5061/dryad.13410/3
title: Common garden fecundity data

description: Data collected from a common garden experiment following experimental laboratory invasions of the bean beetle Callosobruchus maculatus. Data show the lifetime reproductive success of females from each replicate population of the invasion experiment. Columns (in order) are date that offspring were counted, population ID, common garden generation (1-2), female ID (1-11 for each population), treatment (0 = spatially sorted, 1 = shuffled), and number of offspring produced by each female.
DOI: 10.5061/dryad.13410/4
title: Dispersal heritability data

description: Data collected from half-sib breeding design to investigate the additive genetic variance of dispersal distance in the bean beetle Callosobruchus maculatus. Data show the dispersal distance of beetles from each full-sib family. Columns (in order) are date, experiment start time, sire ID, dam ID, offspring ID, replicate (varies for each dam-sire combination depending on the number of offspring the pair produced), sex (0 = female, 1 = male), and distance (number of patches dispersed).
DOI: 10.5061/dryad.1h272/1
title: Amazonian cichlid genomes contigs

description: We are submitting 24 contigs from three whole genomes assemblies that are unpublished. Three Amazonian cichlid species were sampled in the Amazon basin, processed with Illumina next generation sequencing, and assembled with Velvet. These contigs in particular, contain different opsin genes :SWS1, SWS2B, SWS2A, RH2Aa, RH2Ab, RH2B, LWS and RH1. The full genome assemblies will be submitted in the near future. We have already annotated a handful of genes out of these contigs which are in GenBank (KX382917-57). Reviewers have asked us to submit these contigs as part of the raw data for the article. Because we have improved on these contig sequences in producing the gene annotations, we prefer not to annotate in these contigs as the improved sequences are already in GenBank. The gaps (NNNs) are of estimated size based on the paired reads spacing of the library that was sequenced by Illumina next generation sequencing.
DOI: 10.5061/dryad.2358m/1
title: DATA FOR Increased breakdown of kynurenine towards its neurotoxic branch in bipolar disorder PLOS ONE

description: The study was conducted at the Medical University of Graz, Department of Psychiatry. All patients took part in the ongoing single centre BIPFAT study, that assesses demographic parameters, complete actual and lifetime psychiatric history using the Structured Clinical Interview according to DSM-IV (SCID I),, history of medication, anthropometric measure, blood pressure, fasting blood, cognitive testing, EEG, stool sample, different lifestyle questionnaires and magnetic resonance imaging (MRI) of the brain. All patients included were former in- or outpatients of the Medical University of Graz and had a diagnosis of BD I or BD II according to the DSM-IV criteria. Patients needed to be in the state of euthymia or mild depression (HAM-D score &lt;14 and YMRS &lt;9) and had given written informed consent prior to participating in the study. 
The study has been approved by the local ethics committee (Medical University of Graz, Austria) in compliance with the current revision of the Declaration of Helsinki, ICH guideline for Good Clinical Practice and current regulations (EK-number: 24-123 ex 11/12).
Exclusion criteria were the presence of chronic obstructive pulmonary disease, rheumatoid arthritis, systemic lupus erythematosus, inflammatory bowel disease, neurodegenerative and neuroinflammatory disorders (i.e. Alzheimer's, Huntington's and Parkinson's disorder, multiple sclerosis), hemodialysis and interferon-α-based immunotherapy. Further exclusion criteria for controls were the presence of lifetime psychiatric diagnoses (verified by SCID I) and first and second grade relationship to relatives with psychiatric disorders.  

We took peripheral TRYCAT blood levels of 143 euthymic and mild depressive BD patients and 101 healthy controls. Targeted parameters were the levels of KYN, KYNA, 3-HK and AA, the ratio between end-products and substrates as proxies for the specific enzymatic activity (3-HK/KYN, KYNA/KYN, AA/KYN) as well as 3-HK/KYNA as a proxy for neurotoxic vs. neuroprotective end-product relation. Because of technical issues AA could only be evaluated in 113 BD and 88 HC.
The analyzation took place at the Institute of Laboratory Medicine, Medical Center of Ludwig Maximilian University, Munich, Germany.
DOI: 10.5061/dryad.24767/3
title: Eurypterid Morphospace

description: Files, results and workspaces from the morphospace analyses in R. All taxa, including inferred ancestors.
DOI: 10.5061/dryad.24767/4
title: Originator only Morphospace analyses

description: Files, results and workspaces from the morphospace analyses in R. Originating taxa, including inferred ancestors.
DOI: 10.5061/dryad.24767/5
title: Survivor Only Morphospace

description: Files, results and workspaces from the morphospace analyses in R. Surviving taxa, including inferred ancestors.
DOI: 10.48420/14398790.v1
title: A computational approach to quantifying miscounting of radiation-induced double-strand break immunofluorescent foci

description: Data set for the following work: <br> A computational approach to quantifying miscounting of radiation-induced double-strand break immunofluorescent foci. Ingram et al., <em>Commun Biology (2022)</em>. <br> Please see Readme.txt for details on the file formats.
DOI: 10.25345/c5736m58j
title: MassIVE MSV000089431 - Salivary proteomic profile in Periodontitis
title: Scientific rationale for the study: The familial aggregation of periodontitis can help finding individuals with higher susceptible for periodontitis and open-ended approaches, such as proteomics, allow the identification of biomarker candidates. Principal findings: PerioC patients and their descendants presented lower expression of AnnexinA1 in saliva, what was confirmed in a cell culture assay with inflammatory stimulation and gingival fibroblast from unrelated periodontitis patients. AnnexinA1 was selected as a potential biomarker for periodontitis.
DOI: 10.17632/pj5jk82w55.4
title: Dataset of Coal Bio-gasification and Coalbed Methane Stimulation by Single Well Nutrition Injection in Qinshui Anthracite Coalbed Methane Wells

description: In-situ coal bio-gasification is a coal microbial mining technology that utilizes the anearobic digestion of organic components in coal by methanogenic bacteria. In experiments, one vertical well and one horizontal well were used as experiment wells and two vertical wells were used as control wells, the pilot test was carried out with single well nutrition injection method. The concentration of Cl- ion and number changes of Methanogen spp. were used to trace nutrition diffusion. CH4 production changes and coalbed biome evolution were used to analyze technical implementation results. Gas production rates in each well were monitored using FLLQ gas roots flow mete. The concentration of CH4 and CO2 were analyzed using Agilent 7890A gas chromatograph. Concentrations of Cl- were identified using an ICS-1100 ion chromatography system. The F420 fluorescence method was used to test for the presence of methanogenic bacteria. At the end of experiment, the bacterial diversity was analyzed by high-pass sequencing of underground water of Z-7H well. The experiment lasted a total of 814 days. Gas production data showed that the gasification of coal lasted 635 and 799 days, and yielded 74817 m3 and 251754 m3 coalbed methane in Z-159 and Z-7H wells, respectively. One nutrition injection in coalbed achieved an average of 717 days of continuous gas production in experimental wells. This experiment was the first one to successfully use the native bacterial fermentation of anthracite to achieve coal bio-gasification and coalbed methane production stimulation in-situ.
DOI: 10.17632/zvktdj6xyd.1
title: LINF_270011200

description: radial spoke protein 3 | RSP3
Leishmania infantum (strain JPCM5)
DOI: 10.17632/6ww83kt8k3.1
title: De novo transcriptome assembly in yerba mate cultivar 16318 INASE-Argentina

description: We present here two de novo transcriptome assemblies from leaves of I. paraguariensis cultivar 16318 INASE-Argentina, NCBI PRJNA251985-SRR1411087. Trinity-assembled sequences account 243,006 -[Busco embryophyta_odb10; C:87.7%(S:28.1%,D:59.6%),F:5.3%,M:7.0%]- and those assembled via rnaSPAdes account 258,352 -[Busco embryophyta_odb10; C:85.0%(S:58.3%,D:26.7%),F:7.4%,M:7.6%]-.
DOI: 10.17632/mkmb8v9cs6.1
title: Actual household tapwater consumption by hot and cold channel, respective temperatures, and artificial total flowrate with use of an innovative pulse model

description: The data shared are linked to the published article "A methodology for synthetic household water consumption data generation", by D. Kofinas, A. Spyropouloy, and C. Laspidou, in Environmental Modelling and Software, 2018. The attached sheets include data sets linked to 19 household pilots, 10 in Skiathos and 9 in Socnowiec. The sheets contain actual flowrates through the hot and cold channels, respective temperatures, and the synthetic flows that are generated by the algorithm described in the paper. The data sets refer to water flowrate values that are recorded every 30 sec of water consumption. Once there is flow in the monitored faucet/appliance, the sensor generates a record with the corresponding timestamp; at the end of the 30-sec period, it records the water consumption (in liters/min) during the 30-sec period. If the faucet/appliance is still on, the next timestamp is recorded and then the corresponding consumption, and so on. Every 30 sec, the sensor checks for flow and when the faucet/ appliance is off, no record is produced, thus finalizing the creation of a water consumption incident record. When the next water consumption incident starts, the procedure repeats itself. For the period in-between the two incidents, no record is produced. All incidents themselves have a 30-sec time step, but the starting time of an incident might be for example 45 s after the previous one. This means that sensor-produced data are not in the form of a single time series with a 30-sec time step, but are recorded in the form of numerous clusters each one representing a small time series of the equivalent incident. In reality, in order to distinguish between incidents, one detects when the time distance between two consecutive records is greater than 30 s. The number of records per incident is used to calculate its duration.
This work was supported by the project ISS EWATUSdIntegrated Support System for Efficient Water Usage and Resources Managementdwhich is implemented in the framework of the EU 7th Framework Programme, Specific programme Cooperation Information and Communication Technologies; Grant Agreement Number 619228.
DOI: 10.17632/f52vm8g8t5.1
title: LINF_270011100

description: calpain-like cysteine peptidase
Leishmania infantum (strain JPCM5)
DOI: 10.17632/d37ww32fmp.1
title: LINF_270010300

description: calpain-like cysteine peptidase
Leishmania infantum (strain JPCM5)
DOI: 10.17632/399zsh64gr.1
title: LINF_270010200

description: calpain-like cysteine peptidase
Leishmania infantum (strain JPCM5)
DOI: 10.17632/96xhwsngg6.1
title: LINF_270010100

description: calpain-like cysteine peptidase
Leishmania infantum (strain JPCM5)
DOI: 10.17632/tb72f9nypw.1
title: Bio-augmentation with dissimilatory nitrate reduction to ammonium (DNRA) driven sulfide-oxidizing bacteria enhances the durability of nitrate-mediated souring control

description: In Qi et al. 2022, comparative and functional genomics analyses were used to deduce the potential functions (denitrification, sulfide oxidation, and dissimilatory nitrate-reduction to ammonium) of the dominant genus of NR-SOB (Thioclava) and SRB (including Desulfomicrobium, Desulfobulbus, and Desulfovibrio).  This dataset is the genome annotation results of NR-SOB (Thioclava) and SRB (including Desulfomicrobium, Desulfobulbus, and Desulfovibrio).
DOI: 10.17632/95b49jjd25.1
title: Chondroitin sulfate

description: The use of non-drug intervention for calcium deficiency has attracted attention in recent years. Although calcium carbonate is the preferred raw material for calcium supplementation, the mechanism of chondroitin sulfate, a drug for the treatment of osteoarthritis, in alleviating osteoporosis from the perspective of intestinal flora and metabolomics, has been rarely reported. In this study, intestinal microflora abundance and fecal and plasma metabolite expression levels were compared in control rats fed a basal diet, rats fed a low-calcium diet, rats fed a low-calcium diet plus calcium carbonate, and rats fed a low-calcium diet plus chondroitin sulfate. The results showed that calcium content and bone mineral density in the midpoint and distal femur in the calcium carbonate and chondroitin sulfate groups were significantly increased compared with the low-calcium group. 16s rRNA sequencing and metabolomics analysis showed that chondroitin sulfate intervention changed the intestinal microflora composition and fecal and plasma metabolic profiles of low-calcium fed rats, and promoted calcium absorption and alleviated osteoporosis through anti-inflammatory and antioxidant mechanisms. Correlation analysis showed that the selected intestinal flora was significantly correlated with metabolites enriched in feces and plasma. In conclusion, chondroitin sulfate intervention may promote calcium absorption, alleviate the symptoms of osteoporosis in low-calcium rats, and affect intestinal microflora composition and metabolic characteristics. This study provides scientific evidence of the potential impact of chondroitin sulfate as a palliative agent or dietary supplement for patients with osteoporosis.
DOI: 10.6084/m9.figshare.19633668
title: Chromosomal-level reference genome of moth Heortia vitessoides (Lepidoptera: Crambidae), a pest of agarwood-producing trees

description: Moth <em>Heortia vitessoides</em> Moore (Lepidoptera: Crambidae) is a major pest of ecological, commercial and cultural important agarwood-producing trees <em>Aquilaria sinensis</em>. Nevertheless, genomic resource of <em>H. vitessoides</em> is lacking. Here, we present a chromosomal-level assembly for <em>H. vitessoides</em>. A 517 megabase (Mb) genome assembly was obtained with high physical contiguity (scaffold N50 of 18.2 Mb) and high completeness (97.9% complete BUSCO score). 8 transcriptomes from different developmental stages were included, and a total of 16,421 gene models were predicted. Phylogenetic analysis revealed <em>H. vitessoides </em>was diverged from the non- Pyraustinae-Spilomelinae clade that emerged ~58 million years ago. Expansion of gene families that are involved in xenobiotic metabolisms and development were also detected, from which we highlighted the gene duplication of cytosolic sulfotransferase across lepidopterans for the first time. Moreover, small RNA sequencing on 5 developmental stages facilitated the identification of 85 conserved and 94 novel microRNAs in <em>H. vitessoides</em>. Together with annotations on essential hormonal pathways, neuropeptides and microRNAs, the high-quality moth <em>H. vitessoides</em> genome data will provide valuable resources to address a variety of fundamental genomic and evolutionary questions in the lepidopterans, as well as contribute to the development of technology for pest management.
DOI: 10.6084/m9.figshare.19633668.v2
title: Chromosomal-level reference genome of moth Heortia vitessoides (Lepidoptera: Crambidae), a pest of agarwood-producing trees

description: Moth <em>Heortia vitessoides</em> Moore (Lepidoptera: Crambidae) is a major pest of ecological, commercial and cultural important agarwood-producing trees <em>Aquilaria sinensis</em>. Nevertheless, genomic resource of <em>H. vitessoides</em> is lacking. Here, we present a chromosomal-level assembly for <em>H. vitessoides</em>. A 517 megabase (Mb) genome assembly was obtained with high physical contiguity (scaffold N50 of 18.2 Mb) and high completeness (97.9% complete BUSCO score). 8 transcriptomes from different developmental stages were included, and a total of 16,421 gene models were predicted. Phylogenetic analysis revealed <em>H. vitessoides </em>was diverged from the non- Pyraustinae-Spilomelinae clade that emerged ~58 million years ago. Expansion of gene families that are involved in xenobiotic metabolisms and development were also detected, from which we highlighted the gene duplication of cytosolic sulfotransferase across lepidopterans for the first time. Moreover, small RNA sequencing on 5 developmental stages facilitated the identification of 85 conserved and 94 novel microRNAs in <em>H. vitessoides</em>. Together with annotations on essential hormonal pathways, neuropeptides and microRNAs, the high-quality moth <em>H. vitessoides</em> genome data will provide valuable resources to address a variety of fundamental genomic and evolutionary questions in the lepidopterans, as well as contribute to the development of technology for pest management.
DOI: 10.5517/ccdc.csd.cc296bsn
title: CCDC 2121261: Experimental Crystal Structure Determination

description: Related Article: Aditya Chakrabarty and Santanu Mukherjee|2022|Angew.Chem.,Int.Ed.|61|e202115821|doi:10.1002/anie.202115821
DOI: 10.5066/p9u5xsry
title: Data release for Hydroclimate response of spring ecosystems to a two-stage Younger Dryas event in western North America

description: The Younger Dryas (YD) climate event is the preeminent example of abrupt climate change in the recent geologic past. Climate conditions during the YD were spatially complex, and high-resolution sediment cores in the North Atlantic, western Europe, and East Asia have revealed it unfolded in two distinct stages, including an initial stable climatic period between ~12.9 and 12.2 ka associated with a weakened Atlantic Meridional Overturning Circulation (AMOC) and a second phase characterized by variable conditions until 11.7 ka as the AMOC recovered. Decades of investigations into the climate of western North America during the YD have failed to identify this stepped phenomenon. Here we present hydroclimate data from paleospring deposits [...]
DOI: 10.5281/zenodo.6524847
title: Training data for 'Preparing genomic data for phylogeny reconstruction' (Galaxy Training Material)

description: This data is used for Galaxy Training Network training 'Preparing genomic data for phylogeny reconstruction'. There are four nucleotide sequences from chromosome 5 of four strains of S. cerevisiae. The protein sequences were obtained using 'funannotate predict annotation' (Galaxy Version 1.8.9+galaxy2) on the nucleotide sequences sequences. References: DOI: 10.1126/science.274.5287.546; DOI: 10.1126/science.1189015; DOI: 10.1016/j.cell.2016.08.020
DOI: 10.6084/m9.figshare.18865214
title: VDK_recruit density

description: Density of coral recruits (&lt;10 cm diameter) at coral sites in the Velondriake Locally Managed Marine Area for two years before and two years after Cyclone Haruna (22nd February 2013).<br>Coral recruits and juvenile corals ≤ 10 cm diameter were surveyed using 20 randomly placed 0.1 m2 quadrats at each site. Quadrat surveys were undertaken by two observers per quadrat. <br>Density column is recruits per meter squared.
DOI: 10.6084/m9.figshare.18865193.v1
title: VDK_hard coral cover

description: Hard coral cover at reef sites in the Velondriake LMMA two years before and two years after the occurrence of Cyclone Haruna.<br>Point Intersect Transects (PITs) were used to survey hard coral cover (HCC) and the morphology of adult corals (&gt;10cm in diameter). Transects were placed randomly at each site running east to west for all patch reefs and west-facing sites and, north to south for south facing sites. The number of transects undertaken ranged between 6 and 30 and was determined by the size of the site. One observer per transect made fifty observations at 20 cm intervals along each 9.8 m transect: the first being at 0.0 m and the fiftieth at 9.8 m. <br><br><br><br>
DOI: 10.6084/m9.figshare.18865217
title: VDK_adult coral morphology

description: Coral morphology at reef sites in the Velondriake Locally Managed Marine Area 2 years before and 2 years after Cyclone Haruna.<br>Point Intersect Transects (PITs) were used to survey hard coral cover (HCC) and the morphology of adult corals (&gt;10cm in diameter). Transects were placed randomly at each site running east to west for all patch reefs and west-facing sites and, north to south for south facing sites. The number of transects undertaken ranged between 6 and 30 and was determined by the size of the site. One observer per transect made fifty observations at 20 cm intervals along each 9.8 m transect: the first being at 0.0 m and the fiftieth at 9.8 m. The type of benthic organism or substrate at each point was identified. <br>N is number of times morphology was recorded at each site in that year.
DOI: 10.6084/m9.figshare.18865217.v1
title: VDK_adult coral morphology

description: Coral morphology at reef sites in the Velondriake Locally Managed Marine Area 2 years before and 2 years after Cyclone Haruna.<br>Point Intersect Transects (PITs) were used to survey hard coral cover (HCC) and the morphology of adult corals (&gt;10cm in diameter). Transects were placed randomly at each site running east to west for all patch reefs and west-facing sites and, north to south for south facing sites. The number of transects undertaken ranged between 6 and 30 and was determined by the size of the site. One observer per transect made fifty observations at 20 cm intervals along each 9.8 m transect: the first being at 0.0 m and the fiftieth at 9.8 m. The type of benthic organism or substrate at each point was identified. <br>N is number of times morphology was recorded at each site in that year.
DOI: 10.6084/m9.figshare.18865190
title: VDK_coral_genera

description: Number of occurrences of different coral genera recorded at sites in Velondriake Locally Managed Marine Area in surveys one year before and one year after Cyclone Haruna (22nd February 2013). Survey method: Seven randomly positioned 4 m2 quadrats were completed at each site. Quadrats were haphazardly placed by the observer who randomly selected a direction of travel and a random amount of fin kicks (between 5 and 20) to determine the quadrat location. All colonies with diameter &gt;10 cm were counted in each quadrat.
DOI: 10.6084/m9.figshare.18865235.v2
title: VDK_recruit coral genera

description: Count of the occurence of different genera of coral recruits (&lt;10 cm diameter) at coral sites in the Velondriake Locally Managed Marine Area one year before and one year after Cyclone Haruna (February 22nd 2013).<br>Coral recruits and juvenile corals ≤ 10 cm diameter were surveyed using 20 randomly placed 0.1 m2 quadrats. Quadrat surveys were undertaken by two observers per quadrat. The size of each colony was measured to the nearest 0.5 cm and recorded to genus level. <br>N is total count of genera at each site.
DOI: 10.6084/m9.figshare.17290148
title: PIT_Transects

description: Coral data<br>