cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1289320.v6
title: Phytosociological analysis of the <i>Genista</i> sp. pl. garrigues of the <i>Cisto-Lavanduletea</i> and <i>Rosmarinetea officinalis</i> classes in the South-Tyrrhenian area (Mediterranean Region)

description: The study reviews the <i>Genista</i> sp. pl. garrigues ascribable to the classes <i>Cisto-Lavanduletea</i> (acidophilous communities on volcanics and quartzarenites) and <i>Rosmarinetea officinalis</i> (basiphilous communities on calcareous and calcareous-dolomite substrates), in the southern territories of the Italo-Tyrrhenian Province. The floristic-synecological characterization of the identified coenoses led to the description and/or redefinition of various new syntaxa. They are distributed in the two new suballiances <i>Calicotomo villosae–Genistenion tyrrhenae</i> and <i>Genisto aristatae–Calicotomenion infestae</i> of the class <i>Cisto-Lavanduletea</i> (<i>Lavanduletalia stoechadis</i> and <i>Calicotomo villosae–Genistion tyrrhenae</i>), and in the alliance <i>Cisto eriocephali–Ericion multiflorae</i> of the class <i>Rosmarinetea officinalis</i> (<i>Rosmarinetalia officinalis</i>), with two new described associations.
DOI: 10.6084/m9.figshare.19967556.v1
title: Hazardous use of alcohol among undergraduate students at a public university

description: Background The potentially harmful consequences of alcohol use among undergraduates have become a growing concern in recent years. Objectives This study aimed to determine the prevalence of hazardous use of alcohol in this population and to identify demographic and psychosocial factors associated with this pattern of consumption. Methods This was a cross-sectional study using an anonymous and self-completed questionnaire in the classroom. The questionnaire was administered to 1,290 enrolled male and female students, which comprised a proportional sample of the main areas of knowledge at University of Campinas. The questionnaire produced sociodemographic and psychosocial profiles and the Alcohol Use Disorders Identification Test was used to detect hazardous use of alcohol. Results The prevalence of hazardous use of alcohol among the study participants was 24%. Male gender, subjective perceived social support in case of difficulties, being sexually active, not dating, having smoked tobacco cigarettes or marijuana, and having used other illicit psychoactive substances were associated with hazardous use of alcohol. Discussion Variables related to gender, sexuality, affective partnerships, and consumption of other psychoactive substances were associated with hazardous use of alcohol, which was identified in a quarter of the evaluated students, and indicate the need for strategies to prevent and to treat problems.
DOI: 10.6084/m9.figshare.25307374.v11
title: Compiler Design and Program Datasets - Course TC3002B

description: List of Source Codes used in Creating the example of Compiler Program and Exercises in Course - Development of Advanced Applications of Computer Science (TC3002B)
DOI: 10.6084/m9.figshare.28982846.v1
title: Soil physicochemical properties of China

description: This data contains six indicators of soil physicochemical properties at soil depths of topsoil (0-30 cm) and deep (30-100 cm). Among them, pH, BD (soil bulk density), CF (soil coarse content), SM (soil moisture content), Clay (soil clay content) and Sand (soil sand content).This data is from “National Earth System Science Data Center” and was completed by Liu et al. (2022).ReferenceLiu, F., Wu, H., Zhao, Y., Li, D., Yang, J. L., Song, X., Shi, Z., Zhu, A. X., & Zhang, G. L. (2022). Mapping high resolution National Soil Information Grids of China. Science Bulletin, 67(3), 328–340.https://doi.org/10.1016/j.scib.2021.10.013.
DOI: 10.17632/ft8gb8cn5b
title: Quantifying the unintended effects of research on farmers’ practices and social networks

description: Code used for the analyses in the paper titled "Quantifying the unintended effects of research on farmers’ practices and social networks". For a full description of the hypotheses, methods used and results, please refer to the paper. In short, we quantified the effects of an agroecological research project on farming practices and the social network in a village in Papua New Guinea. To track changes in farming practices and the community’s social network, we administered two waves of interviews, one at the beginning of the research project and one at the end. We show that the inferences that people draw from researchers' activities may be very different to those researchers are aiming to test. We also show that social networks may not always help spread information, and that research interventions can actively shape relationships between people, even if this is not the aim. Here we present the R scripts used to analyse (1) changes in farming behaviour using logistic regressions with household number as a random effect, (2) changes in farming behaviour using logistic regressions *without* household number as a random effect, (3) the joint evolution of farming behaviour and social networks using stochastic actor-oriented modelling, and (4) the evolution of social networks only using stochastic actor-oriented modelling.
DOI: 10.17632/m87ncfwccs
title: GROW Tile ms data

description: Eastern oyster recruitment and size on Oyster Castles (OC) and GROW Reef Tiles (GT) were assessed three times over 25 months in multiple locations with varying salinity. Four sites in the Chesapeake Bay region were examined: Cherrystone Inlet, Mockhorn Bay (eastern shore), Elizabeth River and, Lynnhaven Bay (western shore). Our hypothesis was that GROW Tiles would allow for higher oyster densities and larger oysters than the Oyster Castles due to habitat heterogeneity (varied orientation of the surfaces) and their special composition with concrete that is formulated to match oyster shell (GROW 2021). Additionally, we hypothesized that oyster densities would differ among sites due to abiotic stressors such as salinity, relative shoreline height, wave exposure. At each site, ten OC and ten GT were randomly placed parallel to shore in the intertidal zone in May 2019. Sites were sampled non-destructively in October 2019, July 2020, and June 2021. A quadrat (0.30 m x 0.30 m) was placed on top the structure, dividing the structure into four quadrants, and one random quadrant was chosen to count and measure oysters for shell height and mortality status. Data on oyster height and mortality status for each of the sites and years are shown in the dataset columns. Data from each year and combined data (2019-2021) were analyzed using the response variables oyster density and shell height along with combinations of the factors year, site, and substrate type. Both substrate types (OC and GT) had high oyster recruitment (&gt;400 oysters m-2). At 25 months post-deployment, mean oyster densities differed significantly by substrate, with 553.3 ± 59.8 (SE) oysters m-2 on OC and 423.0 ± 57.0 oysters m-2 on GT (24% higher on OC), associated with 27% higher surface area on OC. Oyster densities differed by site, with highest densities in Mockhorn Bay. Growth was ~60-70 mm over the 25 months, and oysters were smallest at the highest-salinity and highest-density site. Mean oyster shell height was greater on GT (61.7 ± 2.2 mm) compared to OC (57.3 ± 2.1) over the time frame.
DOI: 10.6084/m9.figshare.14442203.v1
title: Korso_cDNA.fa.gz

description: Korso cDNA sequences
DOI: 10.6084/m9.figshare.19345874.v1
title: Jia et al Nature materials_3D printed protein-based robotic structures actuated by molecular motor assemblies_Source Data_all.zip

description: Jia et al Nature materials_3D printed protein-based robotic structures actuated by molecular mo-tor assemblies_Source Datahttps://doi.org/10.21203/rs.3.rs-863696/v1<br><br><br>
DOI: 10.6084/m9.figshare.21708173.v1
title: Wealth Versus Poverty Mentality

description: This writing tries to describe why poor people are getting poorer and rich people are getting richer.
DOI: 10.6084/m9.figshare.25211777.v1
title: FVC2002_DB1.zip

description: Preprocessed fingerprint data
DOI: 10.6084/m9.figshare.27074832.v2
title: On Optimality of Mallows Model Averaging

description: In the past decades, model averaging (MA) has attracted much attention as it has emerged as an alternative tool to the model selection (MS) statistical approach. <i>Hansen</i> introduced a Mallows model averaging (MMA) method with model weights selected by minimizing a Mallows’ Cp criterion. The main theoretical justification for MMA is an asymptotic optimality (AOP), which states that the risk/loss of the resulting MA estimator is asymptotically equivalent to that of the best but infeasible averaged model. MMA’s AOP is proved in the literature by either constraining weights in a special discrete weight set or limiting the number of candidate models. In this work, it is first shown that under these restrictions, however, the optimal risk of MA becomes an unreachable target, and MMA may converge more slowly than MS. In this background, a foundational issue that has not been addressed is: When a suitably large set of candidate models is considered, and the model weights are not harmfully constrained, can the MMA estimator perform asymptotically as well as the optimal convex combination of the candidate models? We answer this question in both nested and non-nested settings. In the nested setting, we provide finite sample inequalities for the risk of MMA and show that without unnatural restrictions on the candidate models, MMA’s AOP holds in a general continuous weight set under certain mild conditions. In the non-nested setting, a sufficient condition and a negative result are established for the achievability of the optimal MA risk. Implications on minimax adaptivity are given as well. The results from simulations and real data analysis back up our theoretical findings. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
DOI: 10.6084/m9.figshare.28120991.v1
title: <b>Chromosome-Level Genome </b><b>Annotation </b><b>of</b><b> </b><b><i>Parafronurus youi</i></b>

description: <b>First Chromosome-Level Genome Assembly of </b><b>the</b><b> </b><b>H</b><b>eptageniid </b><b>Mayfly </b><b><i>Parafronurus youi</i></b><b> </b><b>(Ephemeroptera)</b><b>,</b><b> and Its Annotation</b>
DOI: 10.6084/m9.figshare.28879316.v1
title: <i>Saprolegnia ferax</i>, the second congener of <i>Saprolegnia</i><i> </i>reported for the Philippines

description: <i>Saprolegnia</i>, a notable genus within the <i>Saprolegniales</i>, is known for its pathogenic tendencies on a wide range of aquatic organisms, causing infections such as saprolegniasis and Epizootic Ulcerative Syndrome (EUS). From late 1985 to early 1986, accounts of local periodic EUS outbreaks were reported. However, the infection has primarily been associated with <i>Aphanomyces </i>sp., another genus within the same order, rather than <i>Saprolegnia </i>sp. The only species from this genus documented in the country thus far is <i>Saprolegnia diclina</i>, with the last recorded isolation occurring sixty years ago. No member of the genus has been isolated, much less rediscovered, since then. It is speculated that its rarity is due to elevated temperatures in the Philippines, which created unfavorable conditions for its growth. Considering this, the study deliberately targeted a remote highland area with low temperatures, specifically in Kibungan, Benguet, Philippines, in search of cold-dwelling <i>Saprolegnia </i>species in the tropics. Two isolates, collected from muddy water samples baited using sesame seeds, underwent morphological, physiological, and molecular analyses and were identified as <i>Saprolegnia ferax</i>. Further, the findings emphasize the importance of temperature as a key growth and dispersal factor as the isolates thrive within the range of 15 ºC to 30 ºC yet exhibit limited growth at temperatures equal to or beyond 35ºC. This paper describes the second Saprolegnia report for the Philippines.
DOI: 10.6084/m9.figshare.4028667.v3
title: Processed expression data of 40 tissues for RNAseq human PRJEB2445

description: A tab-separated values (TSV) file for RefEx_expression_RNAseq40_human_PRJEB2445<br>A value of "-1" means not applicable (N/A).<br>
DOI: 10.17632/jj35xcx98v
title: Peat water retention from different land-uses in Riau, Indonesia 

description: This dataset provides peat water retention, which was collected from Riau peatland, Indonesia. The data was collected from different land-uses situated in degraded peatland in 2019 and 2022. Information of water retention is of importance for eco-hydrological modeling of peat water. Water retention will determine the contribution of water table to rewetting the surface layer during dry season.
DOI: 10.5522/04/28519790.v1
title: numerical and experimental data on using coupled integral equation approach to model a cooling droplet

description: The physics and modelling of cooling and freezing of droplets in contact with a colder substrate are of interest in various engineering applications. This work provides experimental results of this process employing infrared thermography for temperature measurements at the droplet´s surface. From the experimental observation of a solidification front parallel to the substrate plane, a mixed lumped-differential model of the heat transfer process based on the Coupled Integral Equations Approach (CEIA) is proposed, reformulating the two-dimensional partial differential formulation in cylindrical coordinates into a one-dimensional transient energy equation for the droplet external surface temperature. Direct comparisons of the experimental and theoretical results for the supercooling period show excellent agreement for the droplet surface temperatures at different heights and for different values of the substrate-droplet contact angle.The reduced models, using the H<sub>1,1</sub>∣H<sub>0,0 </sub>and H<sub>0,0</sub>∣H<sub>0,0</sub> approximations, were symbolically derived and numerically solved with the NDSolve function in the Wolfram Mathematica® v.13.3 platform and compared with the experimental data collected in this study during the supercooling stage of the sessile droplets.The naming convention is used as follows. SHB, HYB, HYL refer to superhydrophobic hydrophobic and hydrophillic substrates, respectively. (a,b,c) refer to three different locations along the droplet's axis. Comparisons are made between existing and proposed models as well as with experiments while the droplet is cooling. For more details on conditions, see article.<br>
DOI: 10.6084/m9.figshare.10050419.v1
title: Calculation of Biodiversity Intactness Index (BII)

description: Excel files using output from the LandSHIFT model to calculate changes in BII in India for the four scenarios and the base year 2010.
DOI: 10.6084/m9.figshare.14153339.v3
title: Voltage imaging in zebrafish spinal cord with zArchon1

description: Glutamatergic neurons in the zebrafish ventral spinal cord expressing zArchon1 were imaged via light sheet fluorescence microscopy. The data has been used to test the <i>in vivo</i> voltage imaging signal extraction pipeline, Spike-Guided Penalized Matrix Decomposition-Nonnegative Matrix Factorization (SGPMD-NMF).<br>The experimental method is described in:<br>Xie et al., High-fidelity estimates of spikes and subthreshold waveforms from 1-photon voltage imaging <i>in vivo</i>, Cell Reports (2021), https://doi.org/10.1016/j.celrep.2021.108954.
DOI: 10.6084/m9.figshare.25027181.v1
title: <b>Integrated analysis of single-cell RNA-seq and bulk RNA-seq reveals immune suppression subtypes and establishes a novel signature for determining the prognosis in Lung Adenocarcinoma</b>

description: The single-cell RNA sequencing (scRNA-seq) of 6 paired primary and adjacent LUAD tissues
DOI: 10.17632/523gzcwhzb
title: Salmonella enterica Multi-Drug Resistance in Chicken Genomes: A Dataset for Machine Learning Applications

description: Data for this study were collected from the NCBI genome database (https://www.ncbi.nlm.nih.gov/genbank/), comprising a total of 496 genomes isolated from chickens. The collected data was preprocessed using a system biology approach where first the duplicated were removed and finally 299 samples were left. Following that the meta data were extracted from the samples and then the data was labeled
using the CARD-Resistance Gene Identifier where 11 drug classes were labeled.

Drug Classes: 

1. Amoxicillin-Clavulanic Acid
2. Ampicillin
3. Ceftriaxone
4. Chloramphenicol
5. Ciprofloxacin
6. Gentamicin
7. Nalidixic Acid
8. Streptomycin
9. Sulfamethoxazole-Sulfisoxazole
10. Tetracycline
11. Trimethoprim-Sulfamethoxazole
DOI: 10.4225/03/5a7a952836662
title: Generating static linguistic motion charts

description: The source (.Rmd) file for our R document (see "<b>References</b>" below) containing the R codes to generate the static motion charts in our 2014 paper (link: <br>https://doi.org/10.4225/03/564A9F35BEDB4). The present items also include the original .r file (2014 version), .bib, and csl files. The latter two files are required for one to render the .Rmd in RStudio without missing the references therein.<br><br>If you use these codes and find them useful, please cite our 2014 paper as well as the R codes by clicking on the "cite" (dark-pink button on the top-left) and select the citation style through the "datacite" option (right-hand side)<br><br>We are also happy to receive feedback and comments! Cheers!<br>
DOI: 10.6084/m9.figshare.1084449.v1
title: Sequence of the p007ampGFP plasmid

description: Sequence of a plasmid used in the teaching resoruces for synthetic biology developed in the UNIGEMS project. For more detailes please go to https://doi.org/10.1099/acmi.0.000596.v3.
DOI: 10.6084/m9.figshare.16574441
title: Featuring ACE2 binding SARS-CoV and SARS-CoV-2 through a conserved evolutionary pattern of amino acid residues

description: Spike (S) glycoproteins mediate the coronavirus entry into the host cell. The S1 subunit of S-proteins contains the receptor-binding domain (RBD) that is able to recognize different host receptors, highlighting its remarkable capacity to adapt to their hosts along the viral evolution. While RBD in spike proteins is determinant for the virus–receptor interaction, the active residues lie at the receptor-binding motif (RBM), a region located in RBD that plays a fundamental role binding the outer surface of their receptors. Here, we address the hypothesis that SARS-CoV and SARS-CoV-2 strains able to use angiotensin-converting enzyme 2 (ACE2) proteins have adapted their RBM along the viral evolution to explore specific conformational topology driven by the residues YGF to infect host cells. We also speculate that this YGF-based mechanism can act as a protein signature located at the RBM to distinguish coronaviruses able to use ACE2 as a cell entry receptor. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.28548242.v2
title: Dataset for "<b>A Broad Range of Aromatic Carboxylic Acids for Photocatalytic Methane Oxidation</b>"

description: Photocatalytic methane (CH₄) activation under mild conditions presents a sustainable strategy for converting methane into valuable chemicals. This study introduces a versatile class of conjugated aromatic carboxylic acids as efficient, metal-free photocatalysts for CH₄ oxidation in sodium chloride-trifluoroacetic acid (NaCl-TFA) media. Spectroscopic analysis and machine learning using spectroscopic features further elucidate key structural and electronic factors influencing catalytic activity, offering predictive insights for designing high-performance photocatalysts. The carboxyl group is important in generating electron-deficient carboxyl (RC(=O)O•) or carboperoxyl radicals (RC(=O)OO•), enabling selective hydrogen atom transfer (HAT) for CH₄ functionalization. Mechanistic investigations indicate the role of acyl chloride intermediates in enhancing reactivity. This work highlights the potential of aromatic carboxylic acids to address the challenges of methane functionalization, paving the way for greener chemical transformations and the utilization of inert feedstocks in sustainable chemistry.
DOI: 10.6084/m9.figshare.4543255.v3
title: Contributions of microbial activity and ash deposition to post-fire nitrogen availability in a pine savanna

description: This file contains data on inorganic nitrogen availability, soil moisture, soil organic matter, and soil pH across sites. It also contains data on soil d15N before and after prescribed burns. Data were collected in summer 2014.<br><br>
DOI: 10.6084/m9.figshare.707071.v1
title: Spatial GC content plot for Scaffolds in TGAC Chalara fraxinea assembly

description: Spatial GC content plot for scaffolds &gt; 250 kbp in https://github.com/ash-dieback-crowdsource/data/tree/master/ash_dieback/chalara_fraxinea/Kenninghall_wood_KW1/assemblies/gDNA/KW1_assembly_version1 calculated using IsoPlotter2.3 (Elhaik and Graur doi:10.1093/nar/gkq532) with domain size of 3008
DOI: 10.17632/7ffp22f78g
title: Isolated Bengali Vowel Character Dataset

description: This dataset contains TIF formatted images of handwritten 11 classes of Bengali vowels. Each class contains about 200 samples. About 200 students from the department of Electrical and Electronic Engineering, University of Dhaka participated in this data collection, ensuring large variability in the pattern. Each sample is scanned at 72 dpi. Please cite the dataset if you use it in all your academic or porefessional work.
DOI: 10.6084/m9.figshare.14709423.v1
title: Estimating rainfall intensity with a high spatiotemporal resolution using an image-based deep learning model

description: Six rainfall videos and the rainfall data measured by a rain gauge
DOI: 10.6084/m9.figshare.24998411.v4
title: Single-nucleus chromatin landscape dataset of mouse brain development and ageing

description: In this study, a single-cell assay for transposase-accessible chromatin with sequencing was employed to generate comprehensive chromatin accessibility maps, incorporating data from 69,178 cells obtained from four distinct brain regions – namely, the olfactory bulb (OB), cerebellum (CB), prefrontal cortex (PFC), and hippocampus (HP) – across key developmental time points at 7 weeks, 3 months, 12 months, and 18 months.
DOI: 10.6084/m9.figshare.6149207.v1
title: Labeled Dendritic Spines - Training Data

description: This is a collection of images of fluorescent spines, each labeled with bounding boxes indicating where the spines are. Each folder includes an image and its relative bounding boxes in a .csv file. Coordinates of spines centers are also redundantly shown included in the text file, along with the pixel per micron scale. Bounding Boxes are in the [x,y,width,length] format. This data is uses as training data in the linked 2018 Smirnov et al. paper.