cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/8r5ww3w7mn
title: Phylogenetic data of the publication: “Worldwide forest surveys reveal forty-three new species in Phytophthora Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity”

description: This repository provides additional data to accompany the paper:
“Worldwide forest surveys reveal forty-three new species in Phytophthora Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity”.
T. Jung, I. Milenković, Y. Balci, J. Janoušek, T. Kudláček, Z.Á. Nagy, B. Baharuddin, J. Bakonyi, K.D. Broders, S.O. Cacciola, T.-T. Chang, N.M. Chi, T. Corcobado, A. Cravador, B. Đorđević, A. Durán, M. Ferreira, C.-H. Fu, L. Garcia, A. Hieno, H.-H. Ho, C. Hong, M. Junaid, K. Kageyama, T. Kuswinanti, C. Maia, T. Májek, H. Masuya, G. Magnano di San Lio, B. Mendieta-Araica, N. Nasri, L. Oliveira, A. Pane, A. Pérez-Sierra, A. Rosmana, E. Sanfuentes von Stowasser, B. Scanu, R. Singh, Z. Stanivuković, M. Tarigan, P.Q. Thu, Z. Tomić, M. Tomšovský, S. Uematsu, J.F. Webber, H.-C. Zeng, F.-C. Zheng, C.M. Brasier, M. Horta Jung.

This article reports the finding and official description of 43 new Phytophthora species belonging to the Clade 02.
For phylogenetic analyses, the DNA sequences obtained in this study were complemented with publicly available sequences of isolates sourced from the GenBank Nucleotide Collection and GenBank Whole-Genome Shotgun contigs.
The phylogenetic structure of Clade 2 was studied using a 13-partition (LSU, ITS, βtub, hsp90, tigA, rpl10, tef-1α, enl, ras-ypt1, cox1, cox2, nadh1, rps10) dataset of 91 type and other key isolates from the 43 new and 36 previously described species and two informally designated taxa within Clade 2 with P. infestans from Clade 1c and P. pseudosyringae from Clade 3 as outgroup taxa. The relative phylogenetic positions of the 43 new species within their respective subclades were studied using six separate 13-partition (LSU, ITS, βtub, hsp90, tigA, rpl10, tef-1α, enl, ras-ypt1, cox1, cox2, nadh1, rps10) datasets for subclades 2a (120 isolates from 6 new and 11 known species and 5 informally designated taxa); 2b (104 isolates from 9 new and 9 known species and 3 informally designated taxa); 2c (106 isolates from 15 new and 9 known species); 2d (39 isolates from 6 new and 5 known species and 1 informally designated taxon); 2e (26 isolates from 3 new and 1 known species and 1 informally designated taxon); and 2f (13 isolates from 4 new species). In all analyses P. infestans from Clade 1c and P. pseudosyringae from Clade 3 were used as outgroup taxa.
Briefly, the sequences of all loci used in the analyses were aligned using the MAFFT v. 7. Bayesian Inference (BI) analyses were performed using BEAST 2 and Maximum-Likelihood (ML) analyses were carried out using RAxML-NG.

This repository makes available the input files for the phylogenetic analysis (sequence alignments) and the output results (trees obtained from BI and ML analyses). For details of how these data were generated, users are referred to the published article and supplementary information.
DOI: 10.6084/m9.figshare.14417654.v1
title: Legumes' meta-network

description: Binary matrix on the interactions reported between Fabaceae of economic importance (rows) and floral visitors (columns), resulted from a systematic review without year restriction (last search was conducted in September 2019) in the scholarly data bases Web of Science<sub>TM</sub> (https://www.webofknowledge.com), Google Scholar<sub>®</sub> (www.scholar.google.com) and SciELO (http://www.scielo.br).
DOI: 10.6084/m9.figshare.24461302.v1
title: Supplementary Material for: Chemoradiotherapy combined with immunotherapy in stage III non-small cell lung cancer: a systematic review and meta-analysis of efficacy and safety outcomes

description: Background Since the success of the PACIFIC trial, durvalumab has become the clear standard of care for many patients with stage III non-small cell lung cancer (NSCLC) after concurrent chemoradiotherapy (CRT). However, the duration of immune consolidation and the efficacy and safety of different immune agents remain unclear. We conducted a systematic review of relevant studies. Methods We searched all the relevant studies in PubMed, Embase and Cochrane Library databases. We also reviewed abstracts of relevant conferences, to prevent omissions. The meta-analysis was performed using Stata version 16.0. Results Chemoradiotherapy combined with immunotherapy can improve PFS (HR: 0.60, 95%CI :0.55-0.60) and OS (HR: 0.59, 95%CI :0.53-0.66) compared with no immunotherapy. The pooled 24-month PFS and 24-month OS rates were 48.1% (95% CI, 43.5%-52.7%) and 71.3% (95% CI, 67.3%-75.2%), respectively. Subgroup analysis showed that 24-month OS rates were 60.7% (95%CI, 51.0%-70.3%) and 77.4% (95%CI, 73.2%-81.7%) at 1 year and 2 years of immune consolidation, respectively. The pooled 1-year completion rate for immune consolidation was 35.6% (95%CI, 31.3%-39.8%). The pooled rate of pneumonitis for all grades was 41.7% (95%CI, 31.9%-51.9%). The pooled rate of pneumonitis ≥ grade 3 was 6.7% (95%CI, 5.0%-8.5%). The incidence of pneumonitis ≥ grade 3 after 1 year of immunotherapy is 4.8% (95%CI, 3.1%-6.5%). The incidence of pneumonitis ≥ grade 3 after 2 years of immunotherapy is 5.1% (95%CI, 2.9%-7.3%). Conclusions Prolonging the duration of immunotherapy consolidation increases survival benefits in patients with stage III NSCLC without causing higher side effects. Older patients, due to high incidence of pneumonia and low immunotherapy completion rate, have less survival benefit.
DOI: 10.17632/8s5bdz6rx4
title: Gestational Diabetes Mellitus - Neonatal and Maternal Outcomes in Patients Treated with Insulin or Diet: A Propensity Matched Analysis

description: Pregnant women worldwide face the risk of developing gestational diabetes mellitus (GDM), if left untreated, can cause complications. The study explores factors influencing the choice between diet control and insulin therapy for pregnant women with GDM. It aims to understand how these choices impact maternal and neonatal outcomes. In this quasi-experimental study, clinicians determined treatment (diet control or insulin) for 1030 patients with GDM at a private practice from 2010 to 2020 based on baseline characteristics. Propensity scores (PS), reflecting the probability of treatment allocation, were derived through multiple logistic regression.
DOI: 10.17632/jm62fx668j
title: Evaluation of a community education tool for detection of nail melanoma by nail salon technicians_JAAD

description: Supplementary materials for "Evaluation of a community education tool for detection of nail melanoma by nail salon technicians"
DOI: 10.17632/hm6m233ws5
title: Thesis data

description: Data colllection of my thesis
DOI: 10.17632/yxnw67z24b
title: Range of motion change in the straight leg raise test following lumbar mobilization, proprioceptive neuromuscular facilitation and control

description: We aimed to verify and compare the immediate effect of unilateral lumbar mobilization grade III to the L4/L5 joints, hold-relax proprioceptive neuromuscular facilitation and control on hamstring flexibility. This data shows hip range of motion in degrees, which was measured using photogrammetry before and immediately after intervention through the Straight Leg Raise Test.
DOI: 10.6084/m9.figshare.28625198.v1
title: Sex drives intraspecific scaling of home range size in mammals

description: Animal home range sizes (HR) are fundamental ecological measures, encompassing the area necessary for an organism to obtain food and nonfood resources needed for survival and reproduction. Understanding variation in HR provides important insights into underlying ecological processes driving space use, contributing to species management and conservation. HR is widely known to increase allometrically at an interspecific level. However, it remains unclear whether the interspecific allometric scaling of mammals’ HR can also be consistently observed within species. Additionally, the influence of sex-specific metabolic and behavioral patterns on intraspecific variation in both HR and HR scaling is not well understood. To address this knowledge gap, we GPS-tracked 475 individuals across Brazil, encompassing 18 mammal species. We estimated individuals’ HR and modeled intraspecific variation in HR against body mass and sex, while controlling for habitat quality and phylogenetic relationships. Males used larger areas and displayed steeper HR scaling than females. While males showed a positive allometric scaling similar to interspecific findings reported in the literature (exponent = 1.23), females’ body mass had no statistically discernible effect on HR. Our findings suggest that sex-related metabolic and behavioral traits influence space use across mammals. In general, males have greater energetic and evolutionary incentives to expand their HR with increasing BM, as well as more physical capacity to do so, compared to females. We highlight that traditional studies on HR and, especially, HR scaling that disregard individual sex may, in reality, reflect an average of two distinct patterns, while failing to accurately represent either one.
DOI: 10.17632/d79vb52nwd
title: Barrier database (AMBER-GB) for: A comprehensive assessment of stream fragmentation in Great Britain

description: Artificial barriers are one of the main threats to river ecosystems, resulting in habitat fragmentation and loss of connectivity. Yet, the abundance and distribution of most artificial barriers, excluding high head dams, is poorly documented. We provide a global assessment of the distribution and typology of artificial barriers in Great Britain, and estimate for the first time the extent of river fragmentation. To this end, barrier data were compiled from existing databases and were ground truthed by field surveys in England, Scotland and Wales to derive a correction factor for barrier density across Great Britain. Field surveys indicate that existing barrier databases underestimate barrier density by 68%, particularly in the case of low-head structures (&lt;1 m) which are often missing from current records. Field-corrected barrier density estimates ranged from 0.48 barriers/km in Scotland to 0.63 barriers/km in Wales, and 0.75 barriers/km in England. Corresponding estimates of stream fragmentation, measured as mean barrier-free length, were 12.30 km in Scotland, 6.68 km in Wales and 5.29 km in England, reflecting different anthropogenic pressures. Our study indicates that 97% of the river network in Great Britain is fragmented and none of the rivers are free of artificial barriers. Update. Version 3. Data added from OSM Dams and GOOD2 following the same method. GOOD2: 65 dams OSM: 47 dams, 1 weir New total 23731 barriers.
DOI: 10.17632/sp3tg2bs55
title: CoaddNet

description: Dataset of paper: CoaddNet: Enhancing Signal-to-Noise Ratio in Single-shot Images using Convolutional Neural Networks with Coadded Image Effect
DOI: 10.6084/m9.figshare.6858056.v1
title: Impact of Alloy Composition and Thermal Stabilization on Martensitic Phase Transformation Structures in CuAlMn Shape Memory Alloys

description: Alloys of CuAlMn are known as cheap, high strength shape memory alloys with an excellent damping capacity within their austenitic-martensitic phase transformation, compared to alloy systems like NiTi, CuZnAl or MnCu. But CuAlMn alloys have disadvantage due to generation of voids by a high shrinkage which further increases the existing proneness to stress cracks during rapid cooling. Alloying grain refining elements improves the stress crack resistance and enables a wide range of rapid quenching parameters which are needed to control the temperature of martensitic phase transformation. Additionally, the elements itself influence the in- or decreasing of the phase transformation temperature and the SMA effects. Furthermore, some of these elements can reduce the internal friction indirectly by decomposing areas of metastable martensite into its stabilized forms, where no transformation occurs. This thermic stability can be calculated by the concentration of valence electrons in a unit cell. The proneness to ageing is controlled by multistep heat treatments. Annealing and rapid quenching into the area of martensitic phase transformation maximize the generation of point defects. A high amount of point defects contradicts the negative effect of pinning. It also preserves the material from extreme brittleness. The influences of these effects are shown at single cantilever bending beams by elastic strain amplitude (ε = 12E-4) depending measurements of internal friction at natural frequency along the ageing at room temperature (293 K) up to 2500 h. The samples are annealed at 1123 K for 15 min (CuAl14Mn2) and 1100K for 30min (CuAl11Mn5) afterwards rapid quenched to 370 K with no further thermic stabilisation. The base alloy of CuAl14.1Mn2.0Ni1.9Fe0.4 had an internal friction measured as logarithmic Decrement (δ) of 0.155 and 0.11 after 2500 h of ageing at RT. The phase transformation is located between 284 K and 352 K, measured by DSC. The alloy of CuAl11.1Mn5.5Zn2.9Ni2.1 had a logarithmic decrement of 0.31 and diminish continuously to 0.12 after 2500 h of ageing at RT. The phase transformation is located between 287 K and 318 K.
DOI: 10.6084/m9.figshare.13643066.v1
title: Supplementary Material for: Dynamic Changes of Lymphocyte Subsets in the Course of COVID-19

description: <b><i>Background:</i></b> Although the pathophysiology of coronavirus disease 2019 (COVID-19) is not clearly defined, among the proposed mechanisms, immune system dysfunction is more likely than others. The aim of this study was to clarify the characteristics and clinical significance of dynamic changes of lymphocyte subsets in the course of COVID-19. <b><i>Methods:</i></b> In this prospective study, the levels of peripheral lymphocyte subsets including CD4<sup>+</sup>, CD8<sup>+</sup>, CD4<sup>+</sup>CD25<sup>+</sup>FOXP3<sup>+</sup>, CD38<sup>+</sup>, CD3<sup>+</sup>HLA-DR<sup>+</sup>, CD19<sup>+</sup>, CD20<sup>+</sup>, and CD16<sup>+</sup>CD56<sup>+</sup> cells were measured by flow cytometry in 52 confirmed hospitalized patients with COVID-19 at the day of admission and after 7 days of care. Clinical response was defined as improvement in symptoms (fever, dyspnea, and cough as well as blood oxygen saturation), and patients who met these criteria after 1 week of admission were classified as early responders; others who survived and finally discharged from the hospital were classified as late responders and patients who died were categorized as nonresponders. Immunophenotyping of studied cell changes on the first day of admission and 7 days after treatment were compared. Besides, the correlation between cellular subset variation and clinical response and outcome were analyzed. <b><i>Results:</i></b> Total counts of white blood cell, T cells, CD4<sup>+</sup> T cells, CD8<sup>+</sup> T cells, CD38<sup>+</sup> lymphocytes, and CD3<sup>+</sup>HLA-DR<sup>+</sup> lymphocytes were significantly increased in both early and late responders. No statistically significant difference was observed in CD4<sup>+</sup>/CD8<sup>+</sup> ratio, B cells, FOXP3<sup>+</sup><i>T</i><sub>reg</sub> lymphocytes, and FOXP3 median fluorescence intensity among studied groups. According to the multivariate analysis, an increase in CD4<sup>+</sup> T cells (<i>p</i> = 0.019), CD8<sup>+</sup> T cells (<i>p</i> = 0.001), and administration of interferon (<i>p</i> &lt; 0.001) were independent predictors of clinical response. <b><i>Conclusion:</i></b> We found an increasing trend in total T cells, T helpers, cytotoxic T cells, activated lymphocytes, and natural killer cells among responders. This trend was not statistically significant among nonresponders. The findings of this study may enhance our knowledge about the pathogenesis of COVID-19.
DOI: 10.6084/m9.figshare.24080478.v1
title: Supplementary Material for: Automatic deep learning-based pipeline for automatic delineation and measurement of fetal brain structures in routine mid-trimester ultrasound images

description: Introduction: The aim of this study was to develop a pipeline using state-of-the-art deep learning methods to automatically delineate and measure several of the most important brain structures in fetal brain ultrasound images. Methods: The dataset was composed of 5,331 images of fetal brain acquired during the routine mid-trimester ultrasound scan. Our proposed pipeline automatically performs the following three steps: brain plane classification (transventricular, transthalamic or transcerebellar plane); brain structures delineation (9 different structures); and automatic measurement (from the structure delineations). The methods were trained on a subset of 4,331 images and each step was evaluated on the remaining 1,000 images. Results: Plane classification reached 98.6% average class accuracy. Brain structure delineation obtained an average pixel accuracy higher than 96% and a Jaccard index higher than 70%. Automatic measurements get an absolute error below 3.5% for the four standard head biometries (head circumference, biparietal diameter, occipitofrontal diameter and cephalic index), 9% for transcerebellar diameter, 12% for cavum septi pellucidi ratio and 26% for Sylvian fissure operculization degree. Conclusions: The proposed pipeline shows the potential of deep learning methods to delineate fetal head and brain structures and obtain automatic measures of each anatomical standard plane acquired during routine fetal ultrasound examination.
DOI: 10.6084/m9.figshare.12471749.v1
title: FAL18505_fccbc80b8b81a4540fc5188e93969fe2aa7fee18_10.fast5

description: Sample data for testing Deeplexicon direct RNA demultiplexing software
DOI: 10.6084/m9.figshare.5121640.v1
title: Supplementary Material for: Antiviral Resistance Mutations and Genotype-Associated Amino Acid Substitutions in Treatment-Naïve Hepatitis B Virus-Infected Individuals from the Indian Subcontinent

description: <i>Background/Aims:</i> Antiviral resistance is a major challenge to the treatment currently available for hepatitis B virus (HBV). In this study, mutations that may affect the antiviral efficacy in treatment-naïve HBV-infected individuals were analyzed. <i>Methods:</i> Ninety-seven treatment-naïve HBV-infected individuals were included in this study. HBV reverse transcriptase (rt) domains were sequenced and nucleotide differences were compared to GenBank wild-type sequences. Furthermore, HBV genotypes, subgenotypes and subtypes were determined by analyzing surface gene sequences. <i>Results:</i> An adefovir-related rtI233V mutation was identified in 4 subjects. The rtS213T lamivudine and entecavir refractory mutant was presented in 3 individuals. Altogether, drug-related, atypical and novel HBVrt amino acid substitutions were seen in 73 positions. The HBV genotypes A, C, D and G were depicted in 15, 21, 60 and 1 individuals, respectively. There were 17 HBVrt amino acid substitutions that are associated with certain genotypes of HBV. Mutations in HBVrt corresponded to established surface gene mutations in 9 patients. <i>Conclusion:</i> This data shows that antiviral-resistant HBV strains do exist in treatment-naïve individuals in this region. Further studies are essential to characterize the role of HBVrt amino acid substitutions in response to anti-HBV therapy.
DOI: 10.17632/7gmxvbk96p
title: Understanding Quiet Quitting Through a Dataset on Organizational Support and Role Conflict

description: This study explores the phenomenon of quiet quitting by analyzing a dataset focused on organizational support and role conflict among school teachers in Uttar Pradesh. It investigates how perceived support and conflicting job roles influence employees' decisions to disengage from extra-role behaviors without formally resigning.
DOI: 10.17632/gz73jn4fsv
title: Carbon sequestration induced by enhanced silicate rock weathering in a temperate larch plantation in Northeastern China

description: Carbon sequestration induced by enhanced silicate rock weathering in a temperate larch plantation in Northeastern China
DOI: 10.17632/4d6stj3w34
title: Research 674

description: Research
DOI: 10.17632/3c3gpfhxpg
title: QA Durga (Membaca Durga)

description: This corpus was built and compiled based on a book entitled "Reading Durga" which was then made into question-answer pairings using Indonesian. The corpus contains more than 30,000 words in question and answer pairs. The data was collected as text in .xlsx format.
DOI: 10.17632/vvtkwx59b7
title: Data for: Heat Transfer Characteristic Analysis of a Novel Annular Nuclear Heat Exchanger for Propulsion System

description: The model in this paper is an engine model with MA&lt;1. In order to study the air heating and flow process in the combustion chamber, the model is simplified. A one-dimensional adiabatic flow model is used to simplify the engine intake and exhaust processes. A steady one-dimensional heating model is used to simplify the combustion and heating process of the combustion chamber. At present, these simplifications accord with the general rule of flow heat transfer in engine and have been widely used in numerical simulation.
DOI: 10.25403/upresearchdata.22193347.v1
title: Assessing the impact of fire on tree density and plant diversity in Loskop, Irene, and Roodeplaat farms

description: The dataset displays random GPS coordinates as sampling points where data on tree density and plant diversity was collected. The in-situ data (tree density and plant diversity) was collected by the Agricultural Research Council (ARC) – Range and Forage Sciences research team. The sampling points were selected based on normalized difference vegetation index (NDVI) values determined before data collection, and areas that had statistically similar NDVI values were excluded when placing the transect lines for data collection. Data for both tree density and plant diversity was obtained using the same transect line for each sample point. This data was gathered during the wet season of October 2018 and March 2019 and the dry season is from April to September 2019. The sampling points were different in quantity among the three farms studied, Loskop had 41, Irene had 26 and Roodeplaat had 22 due to logistical challenges and the farm sizes. These were the same sampling points used to collect satellite data. Both active fire data and burned data were sampled within a threshold of these sampling points.By excluding the areas of similar NDVI values, the data collected was more representative of the range of vegetation conditions within the study area, rather than being dominated by a single condition. The datasets also contains vegetation indices(NDVI, Soil -adjusted vegetation index (SAVI), Atmospherically resistant vegetation index (ARVI), Enhanced vegetation index (EVI),Green chlorophyll index (GCI), and Structure-independent pigment index (SIPI) calculated from Landsat 8 OLI including spectral bands(NIR, BLUE, RED, GREEN and SWIR1) used for the calculation of impirical models.
DOI: 10.17632/x9cxhshb3v
title: Data for: Defining a termite sampling protocol for ecological studies: an effective method to increase statistical power

description: The table contains summary data used to the analysis comparing the Jones and Eggleton Sampling protocol (JE) and long 250m belt transects in Amazonia. Termites were separated in trophic groups (TG)