cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16729009.v1
title: Supplementary Material for: Which Is the Best Biologic for Nasal Polyps: Dupilumab, Omalizumab, or Mepolizumab? A Network Meta-Analysis

description: <b><i>Introduction:</i></b> Compared with the placebo, biologics are beneficial in reducing nasal polyp mass and safe in patients with chronic rhinosinusitis with nasal polyps (CRSwNP). However, there lacks a head-to-head randomized trial comparing biologics. We aimed to determine the best biologic for CRSwNP. <b><i>Methods:</i></b> We performed a systematic review and network meta-analysis (NMA), which was registered with PROSPERO (No. CRD42021226766). A comprehensive search was performed in PubMed, Embase, Web of Science, and the Cochrane Library on December 29, 2020. Only randomized controlled trials (RCTs) assessing biologics in adult patients for CRSwNP were included. <b><i>Results:</i></b> Nine RCTs with 1,190 patients comparing 3 different biologics (dupilumab, omalizumab, and mepolizumab) and the placebo were included. Dupilumab had the best efficacy in terms of nasal polyp score (NPS), Sino-Nasal Outcome Test-22 (SNOT-22) score, University of Pennsylvania Smell Identification Test (UPSIT) score, and nasal congestion score (NCS) for surface under the cumulative ranking curve (SUCRA) values of 0.900, 0.916, 1.000, and 0.807, respectively. Omalizumab ranked second in efficacy in terms of SNOT-22, UPSIT, and NCS for SUCRA values of 0.606, 0.500, and 0.693, respectively. Mepolizumab ranked second in efficacy in terms of NPS for SUCRA values of 0.563 and had the highest risk of adverse events (AEs) for SUCRA values of 0.746. <b><i>Conclusion:</i></b> This is the first NMA that compared different biologics in patients with CRSwNP. Based on the efficacy (NPS) and safety (AEs), dupilumab is the best choice and omalizumab is the second best option for CRSwNP. Although mepolizumab ranked second in efficacy, it had the highest risk of AEs.
DOI: 10.6084/m9.figshare.26789641.v1
title: Data_for_IRRMIP_first_results

description: This is the dataset for the article: "Impacts of irrigation expansion on moist-heat stress: first results from IRRMIP"Energy_and_Water: energy and water fluxesExposure_Hours: Annual hours of exposure to extreme eventsIrrigation_Water_Withdrawal: Irrigated area and irrigation water withdrawalPercentile_Value: Absolute values of events and impacts of different forcingsProbability_Ratio: Probability ratio of different forcingsTemperature_Humidity: Extreme values of temperature and humididty
DOI: 10.6084/m9.figshare.28774508.v1
title: APP FINAL DATASET.xlsx

description: This study examines disparities in treatment initiation and engagement among individuals with opioid use disorder (OUD) receiving care at Capital Area Human Services District, a publicly funded behavioral health agency in Louisiana. Using a cross-sectional design and electronic health record data from 252 adult treatment episodes (2022–2023), the study analyzes patterns by race and birth sex. Initiation occurred in 52.4% of cases, but only 38.5% achieved engagement. Race was not significantly associated with either outcome, suggesting that low-barrier, publicly funded care may help reduce racial disparities in treatment access. However, females were significantly more likely than males to engage in treatment, highlighting a gender gap in retention. Guided by the Behavioral Model for Vulnerable Populations and Social Determinants of Health, findings underscore the value of agency-level data in identifying local disparities. Results support the need for gender-responsive interventions and further research into structural barriers influencing long-term engagement in OUD care.
DOI: 10.6084/m9.figshare.5128345.v1
title: Supplementary Material for: A Revised Genome Assembly of the Region 5′ to Canine <b><i>SOX9</i></b> Includes the <b><i>RevSex</i></b> Orthologous Region

description: The <i>SOX</i> gene family includes many genes that play a determinant role in several developmental pathways. The <i>SOX9</i> gene has been identified as a major factor in testis development in mammals after it is activated by the <i>SRY</i> gene. However, duplication of the gene itself in some mammalian species, or of a well-delimited upstream ‘<i>RevSex'</i> region in humans, has been shown to result in testis development in the absence of the <i>SRY</i> gene. In the current study, we present an accurate analysis of the genomic organization of the <i>SOX9</i> locus in dogs by both in silico and FISH approaches. Contrary to what is observed in the current dog genome assembly, we found that the genomic organization is quite similar to that reported in humans and other mammalian species, including the position of the <i>RevSex</i> region in respect to <i>SOX9</i>. The analysis of the conserved sequences within this region in 7 mammalian species facilitated the highlighting of a consensus sequence for SRY binding. This new information could help in the identification of evolutionarily conserved elements relevant for <i>SOX9</i> gene regulation, and could provide valid targets for mutation analysis in XY DSD patients.
DOI: 10.6084/m9.figshare.19800025.v1
title: NorESM-L modeling data for the study of tropical seaways

description: This data archive is shared for our prepared manuscript entitled "Recognizing the Role of Tropical Seaways in Modulating the Pacific Circulation", which will be submitted to the journal "Geophysical Research Letters ". A description of the data can be found in the "README" file.
DOI: 10.6084/m9.figshare.21857997.v1
title: Supplementary Material for: Subtotal parathyroidectomy successfully controls calcium levels of patients with neonatal severe hyperparathyroidism carrying a novel CASR mutation

description: Introduction: Inactivating mutations of the calcium-sensing receptor (CASR) gene result in neonatal severe hyperparathyroidism (NSHPT). Total parathyroidectomy is an effective way to control life-threatening hypercalcemia in NSHPT but leads to permanent hypoparathyroidism. An alternative surgical option is subtotal parathyroidectomy. However, few cases were reported in the literature. Here, we report two unrelated NSHPT patients with p.Leu606Pro novel CASR mutation. The outcomes of subtotal parathyroidectomy in these patients are also described. Case presentation: Two infants presented with an alteration of consciousness, respiratory distress, and bradycardia. Severe hypercalcemia, hypophosphatemia, and markedly elevated parathyroid hormone (PTH) levels were identified, suggesting NSHPT. Cinacalcet was unable to control calcium (Ca) levels of both patients. A novel heterozygous and homozygous missense mutation c.1817T&gt;C; p.Leu606Pro were identified in patients 1 and 2, respectively. Based on the model prediction, proline substitution at Leu606 is likely to disrupt conversion between the active and inactive conformations at the extracellular to transmembrane domain interface of CASR. In addition, two extremely rare intronic variants in CASR (chr3:g.122180314A&gt;G and chr3:g.122251601G&gt;A, based on GRCh38), were identified in patient 1 and his mother. These variants might have contributed to the clinical manifestations of patient 1 who was heterozygous for the c.1817T&gt;C; p.Leu606Pro variant. Subtotal parathyroidectomy was performed by removing three and a half parathyroid glands. So far, patient 1 has been in normocalcemia for five years. Patient 2 was in normocalcemia for sixteen months after surgery and subsequently developed mild hypoparathyroidism which required only low-dose calcitriol treatment. Discussion/Conclusion: We report a novel heterozygous and homozygous missense variant (c.1817T&gt;C; p.Leu606Pro) in CASR in two NSHPT patients. The mutation likely disrupts conformational changes of CASR and results in cinacalcet unresponsiveness. Intronic variants in CASR identified in the patient with heterozygous variant might have contributed to the clinical manifestations of the patient. Although total parathyroidectomy is wildly accepted as a standard treatment for NSHPT, we demonstrate that subtotal parathyroidectomy is also an effective procedure to normalize Ca levels and allow these patients to be in normocalcemia or mild hypoparathyroidism, which is simply controlled by low-dose calcitriol treatment. Subtotal parathyroidectomy appeared to be an effective treatment for NSHPT regardless of the molecular etiologies.
DOI: 10.6084/m9.figshare.23926251.v4
title: RedCandy_assembly_dataset

description: Contains seven items:<i>V. vitis-idaea</i> ssp. <i>vitis-idaea</i><i> </i>var. 'Red Candy' <i>de novo</i> assembly in fasta format.<i>V. vitis-idaea</i> ssp. <i>vitis-idaea</i><i> </i>var. 'Red Candy' scaffolded assembly by mapping to the bilberry genome in agp format based on contig names in the <i>de novo</i> assembled genome (<i>V. myrtillus</i>; Wu et al. 2021).<i>V. vitis-idaea</i> ssp. <i>vitis-idaea</i><i> </i>var. 'Red Candy' scaffolded assembly by mapping to the bilberry genome in fasta format (<i>V. myrtillus</i>; Wu et al. 2021).Annotation of genes/mRNAs associated with the scaffolded genome in gff3 format.Protein sequences from gene annotation in amino acid fasta or faa format.Coding sequences in nucleotide fasta format.Annotation of transposable elements associated with the scaffolded genome in gff3 format.Raw sequences generated in this study are found in NCBI under PRJNA998787: Oxford Nanopore (SRR25468442-SRR25468450), Illumina NovaSeq (SRR25477290)The contig-level assembly fasta can also be found in NCBI: JAUYVE000000000Reference: Wu,C., Deng,C., Hilario,E., Albert,N., Lafferty,D., Plunkett,B., Elborough,C., Saei,A., Jaakola,L., Karppinen,K., Grande,A., Kylli,R., Allan,A., Espley,R. and Chagne,D. 2021. A chromosome-scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition. Molecular Ecology Resources, DOI 10.1111/1755-0998.13467
DOI: 10.6084/m9.figshare.25592919.v1
title: Replication data for the manuscript "Beyond Division: Loss-Aversion and Security as Dominant Values of Polarized Societies"

description: This is the replication package of the manuscript "Beyond Division: Loss-Aversion and Security as Dominant Values of Polarized Societies" see abstract below.<br>Researchers mainly associate political polarization with profound ideological differences, values, and ideals. Strongly polarized societies, however, are similar to each other and differ from less polarized societies in terms of the values their citizens prioritize. This paper aims to introduce an important empirical finding on the cultural and value background of political polarization, opening up a novel perspective in the research of polarization, which, until now, has remained understudied in the literature. It demonstrates that people in more polarized societies are more firmly attached to anxiety-based values, have more conservative value profiles, and are especially concerned about security. The analysis relies on data from the European Social Survey (ESS) collected between 2002 and 2022, resulting in a maximum of 232 observations from 32 countries. As values and cultural dimensions change slowly over time, the hypothesis emerges that they are drivers of – or at least risk factors for - polarization. The results enhance our knowledge of the context and background of polarization, suggesting that polarization may be deeply embedded in cultural, ideological, and value factors.
DOI: 10.6084/m9.figshare.26964901.v1
title: Genome assembly and annotation of <i>Salix cheilophila</i> in Xizang (QT) and Inner Mongolia (IM).

description: Genome assembly and annotation of <i>Salix cheilophila</i> in Xizang (QT) and Inner Mongolia (IM).
DOI: 10.17632/by37d26hr5
title: Supplementary appendix: Alpha-1 Antitrypsin Deficiency-Associated Panniculitis.

description: Supplementary appendix to "Alpha-1 Antitrypsin Deficiency-Associated Panniculitis".
DOI: 10.17632/xgtjgzf28r
title: The Least Cost Directed Perfect Awareness Problem - Benchmark Instances and Solutions

description: This dataset contains complementary data to the paper "The Least Cost Directed Perfect Awareness Problem: Complexity, Algorithms and Computations" [1]. Here, we make available two sets of instances of the combinatorial optimization problem studied in that paper, which deals with the spread of information on social networks. We also provide the best known solutions and bounds obtained through computational experiments for each instance.

The first input set includes 300 synthetic instances composed of graphs that resemble real-world social networks. These graphs were produced with a generator proposed in [2]. The second set consists of 14 instances built from graphs obtained by crawling Twitter [3].

The directories "synthetic_instances" and "twitter_instances" contain files that describe both sets of instances, all of which follow the format: the first two lines correspond to:




where and are the number of vertices and edges in the graph. Each of the next lines contains:

 

where identifies a vertex while and are the cost and threshold associated to that vertex. Each of the remaining lines contains:

 

where and identify an ordered pair of vertices that determines a directed edge with weight .

The directories "solutions_for_synthetic_instances" and "solutions_for_twitter_instances" contain files that describe the best known solutions for both sets of instances, all of which follow the format: the first line corresponds to:



where is the number of vertices in the solution. Each of the next lines contains:



where identifies a seed vertex. The last line contains:



where is the solution cost.

Lastly, two files, namely, "bounds_for_synthetic_instances.csv" and "bounds_for_twitter_instances.csv", enumerate the values of the best known lower and upper bounds for both sets of instances.

This work was supported by grants from Santander Bank, Brazil, Brazilian National Council for Scientific and Technological Development (CNPq), Brazil, São Paulo Research Foundation (FAPESP), Brazil.

Caveat: the opinions, hypotheses and conclusions or recommendations expressed in this material are the responsibility of the authors and do not necessarily reflect the views of Santander, CNPq, or FAPESP.


References

[1] F. C. Pereira, P. J. de Rezende. The Least Cost Directed Perfect Awareness Problem: Complexity, Algorithms and Computations. Submitted. 2023.

[2] B. Bollobás, C. Borgs, J. Chayes, and O. Riordan. Directed scale-free graphs. In Proceedings of the Fourteenth Annual ACM-SIAM Symposium on Discrete Algorithms, SODA ’03, pages 132–139, 2003.

[3] C. Schweimer, C. Gfrerer, F. Lugstein, D. Pape, J. A. Velimsky, R. Elsässer, and B. C. Geiger. Generating simple directed social network graphs for information spreading. In Proceedings of the ACM Web Conference 2022, WWW ’22, pages 1475–1485, 2022.
DOI: 10.6084/m9.figshare.24101742.v1
title: Prediction of bacterial amino acid auxotrophy

description: Project to predict amino acid biosynthesis capabilities across the bacterial tree of life and to investigate associated life history strategies. This repository contains the data and code required to annotate genomes into amino acid biosynthesis pathways using the annotation tool GapMind (https://doi.org/10.1128/msystems.00291-20) and to replicate the figures in the original publication. For the full list of amino acid biosynthesis predictions across the &gt;26,000 genomes included in the study please see file 2022-10-09_bacteria_auxotrophies_subset_all.txt.
DOI: 10.6084/m9.figshare.29025686.v1
title: S5-IQTREE-PhA-PhN

description: Complete results folder of IQ-TREE phylogenetic analyses, for the inference of a phylogeny covering the flora of the biodiversity hotspot of the European Alps, along with related lineages occurring in other mountain ranges and the arctic region.
DOI: 10.6084/m9.figshare.12310052.v1
title: Supplementary Material for: In vitro and in vivo Antiallergic Effects of Taurine on Allergic Rhinitis

description: <b><i>Background:</i></b> The current treatment for allergic rhinitis (AR) is inadequate. <b><i>Objective:</i></b> The present study aimed to investigate the therapeutic effect of taurine on AR and to identify the underlying molecular mechanisms. <b><i>Methods:</i></b> The serum level of the antioxidant enzyme extracellular superoxide dismutase (SOD3) was determined in AR patients and in healthy controls. The antiallergic inflammatory effects of taurine were evaluated in a dinitrophenyl-human serum albumin (DNP-HSA)-stimulated human mast cell line (HMC-1) and in an ovalbumin (OVA)-induced AR mouse model. <b><i>Results:</i></b> Clinically, a reduction in serum level of SOD3 was observed in AR patients. Taurine treatment led to dose-dependent increases in SOD3 at both protein and mRNA levels in HMC-1 cells. SOD3 production was regulated by peroxisome proliferator-activated receptor-γ (PPAR-γ) in response to taurine. SOD3 overexpression inhibited the release of proinflammatory cytokines including tumor necrosis factor-α (, interleukin (IL)-4, and IL-6. Its overexpression also ameliorated the loss of interferon-γ. SOD3 and PPAR-γ influenced inflammatory cytokine production via regulation of the phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2). An OVA-induced AR animal model study showed that taurine was efficacious in alleviating allergic inflammatory reactions by relieving behavior symptoms of AR mice and reducing eosinophilic and mast cell infiltration into the nasal cavity. In addition, taurine treatment increased the production of SOD3 and PPAR-γ, which, in turn, suppressed expression of proinflammatory cytokines through phosphorylation of ERK1/2. <b><i>Conclusion:</i></b> Taurine could potentially serve as a therapeutic treatment for allergic disorders.
DOI: 10.6084/m9.figshare.14552145.v3
title: Domestic Violence NC

description: The NC Domestic Violence dataset is from https://ncadmin.nc.gov/about-doa/divisions/council-for-women/women-statistics.<br>Here we focus on the datasets corresponding to 2004-2019.<br><br>The curated datasets are included here along with a research question and guiding questions.<br>See the codebook for full details.
DOI: 10.6084/m9.figshare.22655089.v1
title: Propulsive cell entry diverts pathogens from immune degradation by remodeling phagocytic synapse

description: Phagocytosis is a critical immune function for infection control and tissue homeostasis. This process is typically described as pathogens being internalized passively and degraded in phagolysosomes. For pathogens that evade immune degradation, the prevailing view is that virulence factors that biochemically disrupt the biogenesis of phagoslysosomes are required. In contrast, here we report that physical forces exerted by pathogens during cell entry divert them away from the canonical phagolysosomal degradation pathway, and this altered intracellular fate was determined at the time of phagocytic synapse formation. To differentiate the effect of physical forces from the that of virulence factors in phagocytosis, we developed a strategy that used magnetic forces to induce propulsive entry of inactivated parasite <em>Toxoplasma gondii </em>into macrophage cells. Experiments and computer simulations collectively reveal that large propulsive forces suppress productive activation of receptors by hindering their spatial segregation from phosphatases at the phagocytic synapse. Consequently, the inactivated parasites, instead of being degraded in phagoslysosomes, are engulfed into vacuoles that fail to mature into degradative units, following an intracellular pathway strikingly similar to that of the live motile parasite. These results reveal previously unknown aspects of immune evasion by demonstrating how physical forces, independent of virulence factors, can help pathogens circumvent phagolysosomal degradation.
DOI: 10.6084/m9.figshare.23607642.v1
title: patient10.rar

description: A Patient with fundus images that taken by Ret-cam.
DOI: 10.6084/m9.figshare.24213231.v1
title: S039.zip

description: Data for S039
DOI: 10.6084/m9.figshare.24804948.v1
title: <b>Rat superior colliculus encodes the transition between static and dynamic vision modes</b>

description: The project comprises fMRI, electrophysiology and behavioural data from Long-Evans rats. The animals were binocularly visually stimulated at different frequencies and the modulations in responses in the superior colliculus were investigated.<br>
DOI: 10.17632/36tpcd3ykb
title: ipRGC_Integrated_Tran_scRNASeq

description: Reanalysis of Tran et al., 2019 ipRGC and ipRGC-proximal clusters (original annotations C33_M1, C40_M1dup, C31_M2, C43_M4, C22_M5, C7, and C8) used in Dyer et al., 2014. Dataset includes integrated Seurat object of aforementioned clusters and csv files with all differentially expressed genes / top 10 differentially expressed genes.
DOI: 10.17632/9tp9y6nvmx
title: Plasmonics simulations with the MNPBEM toolbox: Consideration of substrates and layer structures

description: Abstract Within the MNPBEM toolbox, developed for the simulation of plasmonic nanoparticles using a boundary element method approach, we show how to include substrate and layer structure effects. We develop the methodology for solving Maxwell’s equations using scalar and vector potentials within the inhomogeneous dielectric environment of a layer structure. We show that the implementation of our approach allows for fast and efficient simulations of plasmonic nanoparticles situated on top of substrates... Title of program: MNPBEM toolbox Catalogue Id: AEKJ_v3_0 Nature of problem Simulation of plasmonic nanoparticles placed on substrates or within layer structures. Versions of this program held in the CPC repository in Mendeley Data AEKJ_v1_0; MNPBEM; 10.1016/j.cpc.2011.09.009 AEKJ_v2_0; MNPBEM toolbox; 10.1016/j.cpc.2013.12.010 AEKJ_v3_0; MNPBEM toolbox; 10.1016/j.cpc.2015.03.023 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/n2zgptvtn2
title: Dataset

description: The data provide insight into the current knowledge on the influence on the effect of heat treatments processes on the microstructures and mechanical properties of metals and metal alloys.
DOI: 10.6084/m9.figshare.19375103.v1
title: Global Multiscale Road Network Patterns

description: This is the outcome data of the paper "Global Urban Road Network Patterns". It contains the spatial data of grid cells of our cities of interests, with multiscale road network patterns. The grid cells are 1km-resolution (mid scale in this study) WorldPop grids. <br>To briefly describe the properties, <i>small_cls</i>, <i>mid_cls</i> and <i>large_cls </i>denote the pattern at each scale of the grid. <i>small_cls </i>consists of four patterns delimited by commas, indicating the pattern of the top left, top right, bottom left and bottom right small grids. <i>largeGroup </i>is the large grid this mid grid belongs to, and <i>position</i> is its position on the large grid.