cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14252966.v1
title: WSSV-IN-NS.fasta

description: The genome sequences of two White Spot Syndrome Virus (WSSV) strains from India (WSSV-IN-LS and WSSV-IN-NS) that were previously studied by Sivakumar et al 2018 could not be found in public databases. The raw Illumina read sequences corresponding to these WSSV strains were downloaded from the NCBI Short Read Archive (SRR3233836 - WSSV-IN-LS and SRR3233837 - WSSV-IN-NS) and adapter sequences and low-quality bases (including poly-G and low complexity sequences) were removed using fastp v0.20.0 (Chen et al 2018). For each sample, sequences were normalised using BBNorm, part of BBTools v38.03 (Bushnell) (parameters used: ecc=t, bits=16, prefilter) prior to de novo assembly with SPAdes v3.13.1 (Bankevich et al 2012) using the only-assembler flag and k-mers of 21, 33, 55, 77, 99 and 127. Assembled contigs were blasted against a reference WSSV genome sequence (WSSV-CN, GenBank Accession AF332093.3) using Blastn v2.9.0+ (Camacho et al 2009) to identify contigs representing WSSV.<br><br>This file contains the contigs that represent the WSSV-IN-NS genome sequences.<br><b>References</b>Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477.<br>Bushnell B. https://sourceforge.net/projects/bbmap/.Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10:421.<br>Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890.<br>Sivakumar, S., Vimal, S., Abdul Majeed, S., Santhosh Kumar, S., Taju, G., Madan, N., Rajkumar, T., Thamizhvanan, S., Shamsudheen, K.V., Scaria, V., Sivasubbu, S., and Sahul Hameed, A.S. 2018. A new strain of white spot syndrome virus affecting <i>Litopenaeus vannamei</i> in Indian shrimp farms. J Fish Dis. 41:1129–1146.
DOI: 10.6084/m9.figshare.21220283.v2
title: First Round Expert Feedback, Ratings and Question Feedback

description: This dataset contains the ratings given by 9 experts for every questionnaire item as well as feedback on how each questionnaire item can be improved.
DOI: 10.6084/m9.figshare.24099477.v2
title: The annotation file of the chromosome-level genome of <i>Chaetoderma</i> sp.

description: The chromosome-level and high-quality genome annotation file of <i>Chaetoderma</i> sp.
DOI: 10.6084/m9.figshare.7306364.v3
title: CHOICE NSCLC RNAseq Data

description: To better prioritize treatment options and develop a more comprehensive picture of the tumor microenvironment, We sequenced 245 treatment naive Chinese NSCLC patients using Exome-seq and RNA-seq. The mutation profile (n=241) was compared with TCGA results. The relationship between the immune cell composition in TME and tumor genomic alteration was investigated using the immune cell signatures.
DOI: 10.6084/m9.figshare.16439073.v2
title: Source Data

description: Source data
DOI: 10.6084/m9.figshare.25807498.v2
title: <b>Inappropriate application of mapping algorithms results in length-dependent gene abundances in metagenomic analysis</b>

description: Multiple biases still exist in metagenomic analysis workflows compromising a precise quantification of microbial species and function. In this study, we demonstrated that inappropriate reads mapping could result in length-dependent gene abundances and in turn influence downstream analyses. Specifically, mapping reads directly to predicted genes using Bowtie 2 with the default global-alignment mode resulted in a gradual decrease of abundance values with the diminution of gene length. A local-alignment mode could reduce a large part, but not all, of such technical variability. Particularly, the alignment-free Salmon, which was originally designed and tested for the mapping of RNA-seq reads, were not suitable for metagenomes due to a rapid increase of the TPM (transcripts per million) measure with the diminution of gene length. Different mapping methodologies identified different sets of KEGG Orthologs with significant differences in abundance. For short-read sequencing datasets, we proposed the 'contig mapping' method, i.e., calculating gene abundances using coverage depths of contigs and gene coordinates, which minimized the technical variability.
DOI: 10.17632/fxdphtkwt2
title: Commercially Important Coral Reef Fishes of Tawi-Tawi

description: From Muallil et al., 2020: "Species inventory was conducted by opportunistically visiting the public market (“tabuh”) and ﬁsh warehouses (“bodega”) in Bongao, Tawi-Tawi at least twice a month from October 2015 to December 2018 (Fig. 2). The public market is the only wet market in Bongao where common foodﬁsh are sold. High value and live reef ﬁshes are usually brought by ﬁshers to ﬁsh warehouses or “bodega”. According to the warehouse owners/operators, ﬁshes sold here come from nearby municipalities such as Simunul, Panglima Sugala, Sapa-Sapa, Tandubas, South Ubian and Languyan. Fishes from the farther Sibutu and Sitangkai municipalities are also reportedly brought to ﬁsh warehouses in Bongao. Fish at the warehouses are mostly shipped out of Tawi-Tawi by boat to Zamboanga City. Local buyers can also buy ﬁsh from the ﬁsh warehouses but at higher price than those at the public market. There are also anecdotal accounts of traders from Malaysia coming to TawiTawi or traders from Tawi-Tawi going to Malaysia to buy or sell ﬁsh, respectively. Bongao, Tawi-Tawi is less than ﬁve hours away by boat from the coast of Sabah, Malaysia. According to ﬁsh vendors and traders, all their ﬁsh were caught exclusively from the waters of TawiTawi as it would be impractical for ﬁshers/traders from Malaysia and other provinces to bring their ﬁsh to Tawi-Tawi considering the distance and the relatively low market value of ﬁsh in Tawi-Tawi.

All the surveys were conducted during daytime, mostly during the peak hours of the market from 7:00 to 11:00 in the morning. Sometimes, we proceeded to the warehouses to continue the surveys. However, ﬁshes in the warehouses were not openly accessible for researchers as the ﬁsh are kept inside storage boxes. We could only do the surveys while the ﬁsh were still outside the boxes usually when ﬁshers from nearby islands delivered their ﬁsh or when the traders sorted the ﬁsh in preparation for shipping. With the permission of the vendors, each ﬁsh was put on its lateral side and photographed from the top just high enough to capture the entire length of the specimen.

Species identiﬁcation was done using the following references, namely, Allen et al. (2003), Allen and Erdmann (2012), Gonzales (2013) and White et al. (2013). The names of the species were validated from Eschmeyer’s Catalog of Fishes online (http://researcharchive.calacademy.org/research/ichthyology/catalog/ﬁshcatmain.asp) and their conservation status was determined from the IUCN Redlist of Threatened Species website (https://www.iucnredlist.org/)."
DOI: 10.6084/m9.figshare.11794503.v4
title: Flower visitor records in Monte desert sites of Villavicencio Nature Reserve, Mendoza, Argentina in 2006-2011

description: Flower visitor records in Monte desert sites of Villavicencio Nature Reserve, Mendoza, Argentina during Austral springs for six flowering seasons (2007-2011). Data used in Chacoff NP, Resasco J, Vázquez DP. 2018. Interaction frequency, network position, and the temporal persistence of interactions in a plant-pollinator network. Ecology 99: 21-28, https://doi.org/10.1002/ecy.2063
DOI: 10.6084/m9.figshare.12360902.v5
title: InSAR Postseismic deformation of 2015 Gorkha Mw7.8 earthquake

description: The InSAR time serials resloved by Hong & Liu (2020) in the manuscript of "Postseismic deformation and afterslip evolution of the 2015 Gorkha earthquake constrained by InSAR and GPS observations"<br>The manuscript is submitted to JGR:SOLID EARTH for review.<br>The deformation time sequences are resloved based on the Sentinel-1 SLC data provided by the European Space Agency (ESA).<br>################################################<br>Please download, unzip and read the readme.txt under the folders of RemoveSeason, Fitting_Fun and Fitting_Fun_ReftoGPSandQuadtree, firstly.<br>Note:Fitting_Fun, including the InSAR time serials fitted by Logarithm/Linear functionFitting_Fun_ReftoGPSandQuadtree, Fitting_Fun is referred to GPS sites and downsampled with quadtree method.RemoveSeason, including the InSAR time serials with seasonal signals removed<br>&gt;slc-19.list, for the observation time of T19&gt;slc-85.list, for the observation time of T85<br>
DOI: 10.6084/m9.figshare.25000307.v1
title: SuppData10.xlsx

description: Supplementary Data
DOI: 10.6084/m9.figshare.25201322.v2
title: Game-Based STEM Education Trends: 2013-2023 Dataset Analysis

description: This dataset was used to encompass a comprehensive quantitative textual analysis of scholarly publications from 2013 to 2022, focusing on the application of gamified approaches to STEM education in secondary schools. The study scrutinizes the evolution of game-based educational methodologies, pinpointing main research trends, shifts in educational priorities, and technological advancements in the teaching and learning of STEM subjects. Initiated with a systematic collection from Web of Science and Scopus databases in March 2023, the dataset includes titles and abstracts of peer-reviewed research articles (n=116), conference papers (n=160), book chapters (n=7) and reviews (n=3), filtered through meticulously designed selection criteria to highlight relevant research in game-based learning, serious gaming, and edutainment within STEM disciplines. The final compilation, after rigorous screening for duplicates and relevance, presents 286 eligible abstracts, offering invaluable insights into the evolving landscape of gamified STEM education research over the past decade.
DOI: 10.6084/m9.figshare.28399805.v1
title: R Code for analysis of our article 'Clinical Trials for Hepatitis Delta Virus in WHO African region: A neglected virus among neglected viruses'

description: This is the R code used to analyse the clinical trial registries with instruction for adequate reproducibility
DOI: 10.6084/m9.figshare.5554558.v1
title: Experiment HaLT-SubjectB-160225-6States

description: Experiment in which subject performed 6 imageries of left and right hand motion, left and right leg motion, tongue motion, and a passive state.
DOI: 10.6084/m9.figshare.16763764.v3
title: Momentum Portfolios applied to Statistical Arbitrage

description: These datasets are constructed based on momentum strategies for testing the efficiency of the Tehran Stock Exchange using Statistical Arbitrage Model. The name of each dataset X_Y denotes that the portfolios are constructed by X months formation period and Y months holding periods which is the fundamental of creating momentum portfolios.
DOI: 10.6084/m9.figshare.19253594.v1
title: Data.xls

description: Near-surface (10 m) wind speed (NWS) plays a crucial role in many areas, including the hydrological cycle, wind energy production, and the dispersion of air pollution. Based on wind speed data from Tazhong and the northern margins of the Taklimakan Desert in Xiaotang in spring, summer, autumn, and winter of 2014 and 2015, statistical methods were applied to determine the characteristics of the diurnal changes in wind speed near the ground and the differences in the wind speed profiles between the two sites. The average wind speed on a sunny day increased slowly with height during the day and rapidly at night. At heights below 4 m the wind speed during the day was higher than at night, whereas at 10 m the wind speed was lower during the day than at night. The semi-empirical theory and Monin-Obukhov (M-O) similarity theory were used to fit the NWS profile in the hinterland of the Tazhong Desert. A logarithmic law was applied to the neutral stratification wind speed profile, and an exponential fitting correlation was used for non-neutral stratification. The more unstable the stratification, the smaller the n. Using M-O similarity theory, the “linear to tens of” law was applied to the near-neutral stratification. According to the measured data, the distribution of with stability was obtained. The was obtained when the near-surface stratum was stable in the hinterland of Tazhong Desert and the was obtained when it was unstable. In summer, and were 5.84 and 15.1, respectively, while in winter, and were 1.9 and 27.1, respectively.
DOI: 10.6084/m9.figshare.22643299.v1
title: Supplementary File 1 from Seed size variation impacts local adaptation and life-history strategies in a perennial grass

description: Genotype information, collection site, bioclim variables and mean phenotypes collected from the greenhouse experiment
DOI: 10.6084/m9.figshare.29066894.v1
title: <b>Experimental drought suppresses amphibian pathogen yet intensifies transmission and disrupts protective skin microbiome</b>

description: Shifting precipitation regimes driven by global climate change can alter vertebrate behavior and host-symbiont relationships, potentially compromising host resistance to pathogen invasion. In Brazil's Atlantic Forest, a biodiversity hotspot, prior research identified drought as a key factor disrupting the skin microbiome, contributing to a die-off of pumpkin toadlets due to the invasive waterborne fungal pathogen <i>Batrachochytrium dendrobatidis</i> (Bd). However, observational studies cannot distinguish the direct effect of moisture on Bd growth from increased amphibian activity during wet breeding seasons. Using field enclosures, we experimentally tested the influence of drought conditions on host microhabitat use, Bd disease dynamics, and the composition and predicted Bd-inhibitory function of cutaneous bacterial communities. Each tent housed ecologically realistic densities of <i>Brachycephalus pitanga</i>, a micro-endemic pumpkin toadlet. We simulated a short-term drought in half of the enclosures using translucent tarp coverings. To track individual toadlets, we identified their unique markings and collected skin swabs biweekly over three months. We then implemented molecular techniques to quantify Bd loads and characterize skin bacterial diversity and composition over time. Our findings indicate that while drought may reduce overall Bd loads on hosts, this effect is partially offset by an increase in the use of water-filled areas of the enclosures and by a disruption of the protective host skin microbiome. This study provides valuable insights into the cascading impacts of climate change on animal behavior, host-symbiont interactions, and disease dynamics.
DOI: 10.6084/m9.figshare.22587262.v1
title: Dataset for: RPLC chemical space prediction

description: Datasets used for development of the retention index random forest regression models and RPLC chemical space classification model. The files contain atom pair count and PubChem fingerprints for the chemicals.
DOI: 10.6084/m9.figshare.24559903.v1
title: Supplementary Material for: Green nail syndrome treated with ozenoxacin: two case reports

description: Green nail syndrome (GNS) is a persistent greenish pigmentation of the nail plate, originally described in 1944 by Goldman and Fox, due to Pseudomonas aeruginosa infection. Recently, pulmonary co-infection of P. aeruginosa and Achromobacter spp. have been described in patients with cystic fibrosis. Achromobacter xylosoxidans is a multidrug-resistant (MDR) pathogen involved in lung and soft tissue skin infections. Both Achromobacter xylosoxidans and P. aeruginosa are mainly found in humid environments or in water. There are no recognized co-infections due to P. aeruginosa and A. xylosoxidans in the skin and appendages. We describe two cases of GNS, the first due to P. aeruginosa associated with Achromobacter xylosoxidans; the other due to MDR P. aeruginosa, both successfully treated with topical ozenoxacin 1% cream daily for 12 weeks. The clinical management of GNS can be confusing, especially when the bacterial culture result is inconsistent or when non-Pseudomonas bacteria are isolated. In our case, due to the co-infection of P. aeruginosa and Achromobacter spp., local treatment with ozenoxacin - the first nonfluorinated quinolone - could be a safe and effective treatment in case of MDR nail infections. Further studies are required to evaluate clinical isolation from nail infections and the co-presence of P. aeruginosa and A. xylosoxidans.
DOI: 10.6084/m9.figshare.25669998.v1
title: <b>Genomes of two </b><b>indigenous clams </b><b><i>Anomalocardia flexuosa</i></b><b> (Linnaeus, 1767) and </b><b><i>Meretrix petechialis </i></b><b>(Lamarck, 1818)</b>

description: Clam digging has a long history in Hong Kong, but unregulated clam digging activities depletes clam populations and threatens the ecosystem. Population genomics is useful to unravel the connectivity of clams at different geographical locations and to provide necessary conservation measures; and yet, only limited number of clams in Hong Kong have genomic resources. Here, we present chromosomal-level genome assemblies for two clams commonly found in Hong Kong, <i>Anomalocardia flexuosa</i> and <i>Meretrix petechialis</i>, using a combination of PacBio HiFi and Omni-C reads. For <i>A. flexuosa</i>, we assembled the genome into 19 pseudochromosomes with a genome size of 1.09 Gb (scaffold N50 = 58.5 Mb), and BUSCO scores of 94.4%. A total of 20,881 gene models were also predicted using the transcriptomes generated in this study. For <i>M. petechialis</i>, the genome was mainly assembled into 19 pseudochromosomes with a genome size of 1.04 Gb (scaffold N50 = 53.5 Mb), and BUSCO scores of 95.7%. A total of 20,084 gene models were also predicted using the transcriptomes generated in this study. The two new genomic resources established in this study will be useful for further study of biology, ecology, and evolution of clams, as well as setting up a foundation for evidence-informed decision making in conservation measures and implementation.
DOI: 10.6084/m9.figshare.4560790.v1
title: Supplementary Material for: Hepatitis C Virus of Subtype 2l in Marseille, Southeastern France

description: The rate of eradication of chronic hepatitis C considerably increases with direct-acting antiviral agents, particularly hepatitis C virus (HCV) polymerase inhibitors. While implementing full-length HCV NS5B polymerase sequencing in our clinical microbiology laboratory, we identified atypical HCV sequences, classified as subtype 2l, from 2 patients. HCV-2l NS5B polymerase sequences were detected from 5 and 14 additional patients by screening our laboratory hepatitis virus sequence database and the NCBI GenBank sequence database. Phylogenetic analyses show unambiguously that all HCV-2l sequences are clustered apart from HCV 2 non-l sequences, which compose a second cluster. Mean (±SD) nucleotide identity between near full-length NS5B fragments of subtype 2l was 93.4 ± 0.8% (range: 92.4-95.1). Of note, all HCV-2l sequences obtained in our laboratory and in other centers were from serum samples collected in France. Analysis of the HCV-2l NS5B polymerase amino acid sequences at 30 positions critical for interaction with or resistance to HCV polymerase inhibitors showed specific patterns.
DOI: 10.17632/bn6n2639xh
title: RT-based dataset (V2.0) for 3D radio map under dynamic built-up scenario (1.25kmX1.25km)

description: The radio map, spectrum environment map (SEM), or RSSI map, can visualize the information of invisible electromagnetic spectrum, and is vital for monitoring, management, and security of spectrum
resources in cognitive radio (CR) networks. It is useful for the abnormal spectral activity detection,
radiation source localization, spectrum resource management, etc.

The performance of different 3D SEM construction methods should be compared based on the data under realistic scenarios. However, 3D RSSI data collecting by a spectrum sensing system is quite different and high costing. Moreover, it's unrepeatable and uncontrolable. So we obtained the RSSI by the RT-based calculation method under urban scenario . It includes two datasets as
1) dynamic scenario (radiation sources are moving for 600 seconds): Collecting data at the height of 2m, 25m, 50m and 80m.
2) static scenario (radiation sources are fixed) : Collecting data at the height of 2m, 10m, 20m, 30m, 40m, 50m, 80m.

The dataset has been applied and validated in the following references.
[1]. J. Wang, Q. Zhu, Z. Lin, Q. Wu, Y. Huang, X. Cai, et al., “Sparse Bayesian Learning-Based 3D Radio Environment Map Construction—Sampling Optimization, Scenario-Dependent Dictionary Construction and Sparse Recovery,” IEEE Transactions on Cognitive Communications and Networking, vol.10, pp.80-93, Feb. 2024. 
[2]. J. Wang, Q. Zhu, Z. Lin, J. Chen, G. Ding, Q. Wu, G. Gu, Q. Gao, "Sparse Bayesian Learning-Based Hierarchical Construction for 3D Radio Environment Maps Incorporating Channel Shadowing," IEEE Transactions on Wireless Communications, vol.23, no.10, pp.14560-14574, Oct. 2024. 
[3]. Q. Gao, Q. Zhu, Z. Lin et al., "Time-variant radio map reconstruction with optimized distributed sensors in dynamic spectrum environments,", IEEE Internet of Things Journal, early access, Feb. 2025, doi: 10.1109/JIOT.2025.3545542.
[4]. Y. Zhao, Q. Zhu, Z. Lin, L. Guo, Q. Wu, J. Wang, W. Zhong. “Temporal prediction for spectrum environment maps with moving radiation sources,” IET Communications, vol. 17, no. 5, pp. 538–548, 2023.

More details and instrucitons can be found in the guidemanual.pdf.
DOI: 10.17632/c8ny9zsf97
title: Alpha-naphthoflavone Attenuates Non-Alcoholic Fatty Liver Disease in Oleic Acid-Treated HepG2 Hepatocytes and in High Fat Diet-Fed Mice

description: 1A1 cell : CYP1A1 protein of cell A cell : β-actin of cell T cell : TNF-α protein of cell AHR cell : AHR protein of cell T tissue ：TNF-α protein of liver A tissue ： β-actin of liver 1A1 tissue : CYP1A1 protein of liver AHR tissue : AHR protein of liver
DOI: 10.17632/wh9xk5mp9m
title: The COVID-19 risk perception: A survey on socioeconomics and media attention

description: From a sample of 391 Vietnamese respondents aged from 15 to 47 years, the present study found that geographical regions and behaviors in using social media have a positive impact on the risk perception of COVID-19 epidemic in Vietnam.
DOI: 10.6084/m9.figshare.21946883.v1
title: Governanace Materiality Map: MSCI

description: The dataset was collected from MSCI Industry Materiality Map: "MSCI ESG Ratings assess the resilience of companies to long-term, financially relevant environmental, social, and governance (ESG) risks. Our ESG Industry Materiality Map is a representation of the current ESG Key Issues and their contribution to companies' ESG Ratings. This map is part of our ESG Ratings transparency initiatives, through which we have made ESG Ratings of companies and funds accessible to the public." - MSCI We collected MSCI Materiality Map and structured. Further information regarding the data collection process and codebook will be published in the future.