cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14158559.v1
title: Frailty_Nepal

description: The data was collected in both the old age homes and communities of Kathmandu Valley in Nepal, and STATA version 15.1 was used to create the data file.
DOI: 10.6084/m9.figshare.20381448.v1
title: Supplementary Material for: Agreement of Cardiac Output Estimates between Electrical Cardiometry and Transthoracic Echocardiography in Very Preterm Infants

description: <b><i>Introduction:</i></b> The aim was to evaluate the agreement between cardiac output estimates obtained by electrical cardiometry (EC) and transthoracic echocardiography (TTE) in very preterm infants. <b><i>Methods:</i></b> This is a single-center prospective observational study in infants born&lt;32 weeks gestational age within 48 h of birth. Continuous EC was recorded and simultaneous TTE obtained on day 1 and day 2 of life. Blinded TTE measurements were performed within a 10 s timeframe using beat-to-beat EC data. The primary outcome was %error of left ventricular (LV) output in milliliters per kilogram per minute (cardiac index (CI)) obtained by TTE compared to LV-CI from EC. Secondary outcome parameters were bias, %bias, limits of agreement and include measures of right ventricular (RV) output and LV systolic time intervals. <b><i>Results:</i></b> Analysis was performed for 34 infants (median (IQR) gestational age 29 + 0 (24 + 5 to 30 + 6) weeks + days, birthweight 960 (748 to 1,490) grams) including 44 pairwise LV output measurements on 24 participants (22 on day 1 and day 2). The %error was 54% for LV-CI (EC: 214 (38) mL/kg/min vs. TTE: 163 (47) mL/kg/min). The %error was 78% for RV-CI (EC: 213 (37) mL/kg/min vs. TTE: 241 (77) mL/kg/min). While only LV-CI values affected LV-CI bias, signal quality, heart rate, and RV-CI values affected RV-CI bias. <b><i>Conclusion:</i></b> EC is not interchangeable with TTE to estimate indices of LV or RV output in very preterm infants within the first 48 h postnatally. EC may not measure LV output distinctly in very preterm infants with intra- and extracardiac shunts.
DOI: 10.6084/m9.figshare.5868192.v1
title: Protein trajectories

description: Protein trajectories analyzed in the paper "Computer simulations reveal changes in the conformational space of the transcriptional regulator MosR upon the formation of a disulphide bond an in the collective motions that regulate its DNA-binding affinity."
DOI: 10.6084/m9.figshare.19134608.v1
title: Achieving minimum standards for Infection Prevention and Control in Sierra Leone

description: This MS Excel files contains datasets and codebooks for Fofanah BD et al's Operational Research paper on AMR in Sierra Leone, Year 2022.
DOI: 10.6084/m9.figshare.7568699.v2
title: Fasting Values of Glucose, NEFA, Insulin, C-Peptide, and Glucagon During Sleep Restriction

description: Fasting Values of Glucose, Insulin, C-Peptide, NEFA, and Glucagon by Condition. Values are reported as mean (SD) for fasting time points (minutes -15 through 0). Fasting c-peptide was significantly suppressed in the recovery condition compared to baseline (p = 0.02).
DOI: 10.6084/m9.figshare.8325389.v1
title: Supplementary Material for: The Specific Organism: Not Bacterial Gram Type: Drives the Inflammatory Response in Septic Shock

description: <b><i>Background and Hypothesis:</i></b> The inflammatory response was targeted by unsuccessful therapies but ignored pathogen. We hypothesized that the inflammatory response differs according to organism in human septic shock. <b><i>Materials and Methods:</i></b> We measured 39 cytokines at baseline and 24 h in patients (<i>n</i> = 363) in the Vasopressin and Septic Shock Trial (VASST). We compared cytokine profiles (cytokine functional class) at baseline and at 24 h by organism and used hierarchical clustering to classify cytokines according to 28-day outcomes. <b><i>Results:</i></b> In 363 patients, 88 and 176 patients had at least 1 species isolated from blood and other sites, respectively. Cytokine levels differed significantly according to organism: <i>Neisseria meningitidis</i> and <i>Streptococcus pneumoniae</i> had the highest (baseline and at 24 h), while <i>Enterococcus faecalis</i> (blood) had the lowest mean cytokine levels. <i>N. meningitidis</i> and <i>Klebsiella pneumoniae</i> had significantly higher cytokine levels at baseline versus 24 h (<i>p</i> = 0.01 and 0.02, respectively); <i>E. faecalis</i> had significantly higher cytokine levels at 24 h versus baseline. Hierarchical clustering heat maps showed that pathogens elicited similar cytokine responses not related to the functional cytokine class. <b><i>Conclusion:</i></b> The organism type induces different cytokine profiles in septic shock. Specific gram-positive and gram-negative pathogens stimulated similar plasma cytokine-level patterns.
DOI: 10.6084/m9.figshare.14327586.v1
title: Uncommon bilateral maxillary exostosis: case report

description: ABSTRACT Exostoses or hyperostoses are benign bony outgrowths originating from the cortical bone and depend on their location for a more precise designation. The most common types found in the oral cavity are the torus palatinus and the torus mandibularis. Buccal and palatal exostoses are located along the buccal aspect of the maxilla and/or the mandible (commonly in the premolar and molar areas) and on the palatal aspect of the maxilla (usually in the tuberosity area), respectively. The etiology of exostoses still hasn’t been enlightened but an interaction between environmental and genetic factors is accredited. They are usually asymptomatic, unless the mucosa becomes ulcerated. The frequency of exostoses increases with age, having their biggest prevalence from 60 years old, being more common in men and suffering ethnic influences. A thorough evaluation is important for the correct diagnosis since other lesions have similar clinical characteristics to the exostoses such as osteomas. The majority of exostoses are diagnosed clinically along with radiographic interpretations, making the biopsy dispensable and the treatment is usually unnecessary. The aim of this article was to describe a case report of bilateral maxillary exostosis, unusual, in a female patient. If an excessive amount of bone is present the exostoses may exhibit a relative radiopacity on dental radiographs. Initially, periapical and panoramic radiographs were performed to evaluate the alterations. Due to the size of the exostoses a concomitant Cone Beam Computed Tomography was performed to confirm the diagnosis. The patient is in follow-up.
DOI: 10.6084/m9.figshare.27159180.v1
title: Genome annotations of critically endangered tree <i>Pellacalyx yunnanensis</i>

description: The genome assembly sequences and raw Illumina reads have been deposited in the NCBI with BioProject number PRJNA1043905.
DOI: 10.6084/m9.figshare.9728021.v1
title: Contained herein is the raw data underlying the findings described in the manuscript entitled, "Environmental impact on the temporal production of chasmogamous and cleistogamous flowers in the mixed breeding system of Viola pubescens".

description: The datasets include those used for modeling of the zero-inflated negative binomial and logistic regressions (Modeling_Data.xlsx) as well as canopy cover (Canopy_Cover.xlsx) and soil pH (soilpH.xlsx) data that were excluded from the modeling but still discussed within the manuscript.
DOI: 10.6084/m9.figshare.7907963.v1
title: GO and KEGG analysis of differential coding genes in hypothalamus, pituitary and folllicles

description: differential coding genes in hypothalamus, pituitary and folllicles
DOI: 10.6084/m9.figshare.28746902.v1
title: The raw transcriptome data during the study"SEC24D depletion induces osteogenic differentiation deficiency by inactivating the ATF6/TGF-β/Runx2 regulatory loop"

description: To determine the molecular mechanisms and signaling pathways of Sec24D in the osteogenic differentiation of human mesenchymal stem cells, transcriptome sequencing was conducted. The raw transcriptome data during the study"SEC24D depletion induces osteogenic differentiation deficiency by inactivating the ATF6/TGF-β/Runx2 regulatory loop" were provided.
DOI: 10.6084/m9.figshare.3187147.v1
title: Thirteen-week study of toxicity of fiber-like multi-walled carbon nanotubes with whole-body inhalation exposure in rats

description: Cancer development due to fiber-like straight type of multi-walled carbon nanotubes (MWCNTs) has raised concerns for human safety because of its shape similar to asbestos. To set concentrations of MWCNT for a rat carcinogenicity study, we conducted a 13-week whole body inhalation study. F344 male and female rats, 6-week-old at the commencement of the study, were exposed by whole-body inhalation to MWCNT at concentrations of 0, 0.2, 1 and 5 mg/m<sup>3</sup> with a generation and exposure system utilizing the cyclone sieve method. Measured concentrations in the exposure chambers were 0.20 ± 0.02, 1.01 ± 0.11 and 5.02 ± 0.25 mg/m<sup>3</sup> for 13 weeks. The MMAD (GSD) of MWCNT were 1.4–1.6 μm (2.3–3.0), and mean width and length were 94.1–98.0 nm and 5.53–6.19 μm, respectively, for each target concentration. Lung weights were increased 1.2-fold with 1 mg/m<sup>3</sup> and 1.3-fold with 5 mg/m<sup>3</sup> in both sexes compared to the controls. In the bronchoalveolar lavage fluid (BALF) analyses, inflammatory parameters were increased concentration-dependently in both sexes from 0.2 mg/m<sup>3</sup>. Granulomatous changes in the lung were induced at 1 and 5 mg/m<sup>3</sup> in females and even at 0.2 mg/m<sup>3</sup> in males. Focal fibrosis of the alveolar wall was observed in both sexes at 1 mg/m<sup>3</sup> or higher. Inflammatory infiltration in the visceral pleural and subpleural areas was induced only at 5 mg/m<sup>3</sup>. In conclusion, we determined 0.2 mg/m<sup>3</sup> as the low-observed-adverse-effect level (LOAEL) for respiratory tract toxicity in the present inhalation exposure study of rats.
DOI: 10.6084/m9.figshare.26539993.v1
title: Arabidopsis Araport11 genome annotation

description: This is a stable link for the Araport11 genome annotation that my scripts will pull from.
DOI: 10.4121/22004108.v1
title: Data underlying the research of: The mRNA expression of CACYBP in bladder and kidney cancer.

description: <strong>qRT-PCR </strong> Cellular RNA was extracted using Trizol, and total RNA (500 ng) was transcribed into cDNA using the PrimeScript kit. Actin primers were used as an internal control. Real-time fluorescence quantitative RT-PCR assays were performed using Lightcycler 480ii. The qRT-PCR primer sequences used in this study are shown below: Cacybp: forward primer: 5-CTCCCATTACAACGGGCTATAC-3, reverse primer: 5-GAACTGCCTTCCACAGAGATG-3; hactin: forward primer: 5-GGCATCGTCACCAACTGGGAC-3; reverse primer: 5-CGATTTCCCGCTCGGCCGTGG-3. Obtain the Cq datas of the actin and CACYBP gene of HK-2, O-786, SV-HUC-1, T24 cells for analysis.
DOI: 10.6084/m9.figshare.22707415.v1
title: CON_tag.ucsc.bedGraph.gz

description: CON_tag.ucsc.bedGraph.gz
DOI: 10.6084/m9.figshare.27249207.v1
title: RawData_Shapeshifter W-tau peptide inhibits tau aggregation and disintegrate paired helical filaments

description: Tauopathies comprise a range of neurodegenerative conditions characterized by an aberrant accumulation of tau protein clumps in the brain. These aggregates are formed by different tau splicing isoforms. Here, we analyzed the role of the specific intron-derived peptide called W-Tau peptide on the polymerization-depolymerization of tau filaments. This peptide originates from a new isoform of the tau protein, named W-Tau, which is formed due to the retention of intron 12. AlphaFold3 (AF3)-based <i>in silico</i> investigations suggested that W-Tau peptide interacts with tau monomers. Our <i>in vitro</i> experiments confirmed these predictions and showed that W-Tau peptide inhibited tau aggregation. In addition, W-Tau peptide successfully disrupted pre-existing paired helical filaments (PHFs) isolated from postmortem brain samples of patients with Alzheimer’s disease, thereby supporting its potential therapeutic value. The effectiveness of the W-Tau peptide was demonstrated in cell cultures by a noteworthy decrease in tau aggregation observed after co-transfection, of W-Tau peptide and PHFs’ seeds, as demonstrated by analysis involving a fluorescence resonance energy transfer (FRET) cell biosensor. The W-Tau peptide breaks PHFs by selectively attaching to their ends, causing the structures to unwind and convert into circle-like formations. Considering the potential neuroprotective effects against tauopathies, the W-Tau isoform and its peptide are interesting candidates for future therapeutic interventions
DOI: 10.6084/m9.figshare.9944414.v1
title: Supplementary Material for: Excess Significance Bias in Repetitive Transcranial Magnetic Stimulation Literature for Neuropsychiatric Disorders

description: <b><i>Introduction:</i></b> Repetitive transcranial magnetic stimulation (rTMS) has been widely tested and promoted for use in multiple neuropsychiatric conditions, but as for many other medical devices, some gaps may exist in the literature and the evidence base for the clinical efficacy of rTMS remains under debate. <b><i>Objective:</i></b> We aimed to test for an excess number of statistically significant results in the literature on the therapeutic efficacy of rTMS across a wide range of meta-analyses and to characterize the power of studies included in these meta-analyses. <b><i>Methods:</i></b> Based on power calculations, we computed the expected number of “positive” datasets for a medium effect size (standardized mean difference, SMD = 0.30) and compared it with the number of observed “positive” datasets. Sensitivity analyses considered small (SMD = 0.20), modest (SMD = 0.50), and large (SMD = 0.80) effect sizes. <b><i>Results:</i></b> A total of 14 meta-analyses with 228 datasets (110 for neurological disorders and 118 for psychiatric disorders) were assessed. For SMD = 0.3, the number of observed “positive” studies (<i>n</i> = 94) was larger than expected (<i>n</i> = 35). We found evidence for an excess of significant findings overall (<i>p</i> &lt; 0.0001) and in 8/14 meta-analyses. Evidence for an excess of significant findings was also observed for SMD = 0.5 for neurological disorders. Of the 228 datasets, 0 (0%), 0 (0%), 3 (1%), and 53 (23%) had a power &gt;0.80, respectively, for SMDs of 0.30, 0.20, 0.50, and 0.80. <b><i>Conclusion:</i></b> Most studies in the rTMS literature are underpowered. This results in fragmentation and waste of research efforts. The somewhat high frequency of “positive” results seems spurious and may reflect bias. Caution is warranted in accepting rTMS as an established treatment for neuropsychiatric conditions.
DOI: 10.6084/m9.figshare.27083158.v1
title: <b>A review of the genus </b><b><i>Sciomesa </i></b><b>(Lepidoptera: Noctuidae: Apameini: Sesamiina) with the description of 12 new species, and new insights from morphological, ecological and molecular data</b>

description: In this study, the genus <i>Sciomesa</i> Tams & Bowden, 1953 (Lepidoptera: Noctuidae: Noctuinae: Apameini: Sesamiina) is reviewed. Based on the examination, 12 new species are hereby described: <i>S. lalokeli</i> <b>n. sp.</b> and <i>S. metiminko</i> <b>n. sp.</b> from Ethiopia; <i>S. elgonensis</i> <b>n. sp.</b>, <i>S. nigra</i> <b>n. sp.</b> and <i>S. simillima</i> <b>n. sp.</b> from Kenya; <i>S. umvoti </i><b>n. sp.</b> from the Republic of South Africa; <i>S. iboya</i> <b>n. sp.</b>, <i>S. lilomwi</i> <b>n. sp.</b>, <i>S. makete</i> <b>n. sp.</b>, <i>S. njombe</i> <b>n. sp.</b> and <i>S. tanganyika </i><b>n. sp.</b> from Tanzania; <i>S. kalinzu</i> <b>n. sp.</b> from Uganda. We propose to re-establish as valid species <i>S. constantini</i>, <i>S. etchecopari</i> and <i>S. mirifica</i>, which were synonymized with <i>S. mesophaea</i> by Moyal et al. (2010) <i>. </i>Similarly,<i> </i>we propose to re-establish <i>S. minuscula</i> which was synonymized with <i>S. boulardi </i>by Moyal et al. (2010) as a good species and we synonymize <i>S. congitae</i>,<i> </i>which was synonymized with <i>S. boulardi </i>by Moyal et al. (2010), as a synonym of <i>S. minuscula</i>. <i>Sciomesa franciscae</i> is synonymized with <i>S. mesophaea </i>and<i> Sesamia punctipennis </i>transferred to the <i>Sciomesa</i> genus by<i> </i>Moyal et al. (2010) is temporarily removed from the genus <i>Sciomesa</i> pending a new combination. We also provide a supplemental description of the previously described species: <i>S. boulardi </i>(Laporte, 1984), <i>S. bua</i> Moyal et al., 2010, <i>S. constantini</i> Laporte, 1984, <i>S. etchecopari</i> Laporte, 1975, <i>S. excelsa</i> (Laporte, 1976), <i>S. gnosia </i>Moyal et al., 2010, <i>S. mesophaea</i> (Hampson, 1910), <i>S. minuscula</i> (Laporte, 1991), <i>S. mirifica</i> Laporte, 1984, <i>S. renibifida </i>Berio, 1973<i>, S. scotochroa</i> (Hampson, 1914) and <i>S. venata</i> Fletcher, 1961. Host plant records are provided for eight species.
DOI: 10.6084/m9.figshare.11314526.v1
title: The place of particles among words, morphemes, and phrases in Kubeo

description: Abstract This article describes the definition of words, morphemes, and phrases in Kubeo, with a critical assessment of particle status. After initially pointing out the methodological difficulties of defining boundaries between words and phrases in this language (as well as the different criteria for differentiating word and morpheme types from structural, functional, and phonological points of view), we approach particles as a class of words which mainly act as pragmatic markers. This understanding is not assumed a priori, but rather is the result of a methodological trajectory which questions the necessity of this descriptive category, carefully demarcating it and differentiating it from other classes of morphemes.
DOI: 10.6084/m9.figshare.19974116.v1
title: Hoiho - Paterson Inlet

description: Maxent models for hoiho/Yellow-eyed penguins breeding in Paterson Inlet, Rakiura/Stewart Island. Tracking data used for model were recorded between 2019 and 2020 using GPS dive loggers.
DOI: 10.6084/m9.figshare.25701069.v1
title: HIT-ISOseq paper

description: HIT-ISOseq paper Supplementary Data and relevant file
DOI: 10.6084/m9.figshare.7825403.v1
title: genome_annotation.zip

description: genome annotation of the black-necked crane genome
DOI: 10.26180/5c047596095a1
title: participant 12 EEG.zip

description: participant 12, day 1 and 2 EEG<br>
DOI: 10.6084/m9.figshare.1015787.v1
title: Animal and Plant Phylogenies

description: Phylogenies associated with a paper in review in Plant Ecology. There is a zip file of animal trees and one for plant trees. All are in newick format. Description of tree creation: <strong>* Plants</strong> Plant phylogenies were built using Phylomatic (see http://phylodiversity.net/phylomatic; Webb & Donoghue 2004). Phylomatic is an online interface to retrieve a phylogeny based on a user-defined set of plant species taxonomic names. Branch lengths were estimated for the master plant phylogeny using the branch length adjustment algorithm (BLADJ) in the software Phylocom (Webb, Ackerly & Kembel 2008), which fixes a set of nodes in the tree to specified ages and evenly distributes the ages of the remaining nodes. We used node age estimates from Wikström et al. (2001) as incorporated in the “ages” file in the Phylocom installation. The tree file we used to run the bladj command in Phylocom is provided in multiple formats in Appendix B. See the master plant phylogeny in Appendix B and on Figshare.org. We pruned the master phylogeny for each network. <strong>* Pollinators</strong> For pollinator phylogenies for the unpublished Canadian networks we built a master phylogeny of all animal pollinators across all networks in the study in Mesquite v.2.75 (Maddison & Maddison 2011), based on a variety of published phylogenies. We then pruned the master phylogeny for each network. Pollinator phylogenies from Rezende et al. (2007) were built using a variety of sources (see Rezende et al. 2007 for details). No information on branch lengths was available for pollinator phylogenies, so we assumed all branch lengths equaled one time unit. See the master plant phylogeny in Appendix B and on Figshare.org.
DOI: 10.6084/m9.figshare.7523429.v2
title: Synchronization of two modes

description: Synchronization of two modes<br>
DOI: 10.6084/m9.figshare.28742549.v1
title: Earth_future_paper_data

description: All the files belong to Earth Future paper
DOI: 10.6084/m9.figshare.28659218.v1
title: design program

description: Metasurface-Based Polarization Aberrations Compensation Method for Optical Systems.
DOI: 10.6084/m9.figshare.22256578.v3
title: events

description: wyscout
DOI: 10.6084/m9.figshare.c.3651749_d5.v1
title: Additional file 5: of SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides

description: Showing interactions between 5,022 putative BY-kinases and 586 approved drugs (from the DrugBank database). Open in Excel. (XLSX 1778 kb)
DOI: 10.6084/m9.figshare.13049617.v2
title: New Specimens of <i>Scutellosaurus Lawleri</i> Colbert, 1981, from the Lower Jurassic Kayenta Formation in Arizona Elucidate the Early Evolution of Thyreophoran Dinosaurs

description: We describe new specimens of the ornithischian dinosaur <i>Scutellosaurus lawleri</i> Colbert, 1981, from the Lower Jurassic Kayenta Formation of Arizona and discuss their systematic importance. The new specimens represent at least 46 individuals and include two associated skeletons that preserve regions that were poorly known until now, including the skull and pelvis. Computed tomography (CT) assisted our interpretation of these specimens. Using an ornithischian data matrix, we first tested whether the two associated skeletons were justifiably assigned to <i>Scutellosaurus lawleri</i> and found that they group unequivocally with the holotype and paratype specimens. This enabled scoring of 35 character states that were previously unknown, raising the scoring completeness of <i>Scutellosaurus lawleri</i> from 52% to 67%. The results recovered <i>Lesothosaurus diagnosticus</i> as the basal-most member of Neornithischia, while corroborating the monophyly of Thyreophora and <i>Scutellosaurus lawleri</i> as its most basally branching member. In terms of numbers of specimens, <i>Scutellosaurus lawleri</i> is now the most abundant dinosaur known in any Early Jurassic vertebrate fauna. The presence of a second thyreophoran in the Kayenta Formation, along with the presence of Early Jurassic thyreophorans in Europe and Asia, suggests that Thyreophora may have originated in the northern hemisphere. The ornithischians from the Kayenta Formation support a pattern of dinosaurian diversification after the end-Triassic extinction in North America, if not a broader area, that was fueled by independent northward dispersals from the southern hemisphere, supporting dispersal as an early driver of dinosaurian evolution.