cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/y27fngtkdw
title: DMFTwDFT: An open-source code combining Dynamical Mean Field Theory with various density functional theory packages

description: Dynamical Mean Field Theory (DMFT) is a successful method to compute the electronic structure of strongly correlated materials, especially when it is combined with density functional theory (DFT). Here, we present an open-source computational package (and a library) combining DMFT with various DFT codes interfaced through the Wannier90 package. The correlated subspace is expanded as a linear combination of Wannier functions introduced in the DMFT approach as local orbitals. In particular, we provide a library mode for computing the DMFT density matrix. This library can be linked and then internally called from any DFT package, assuming that a set of localized orbitals can be generated in the correlated subspace. The existence of this library allows developers of other DFT codes to interface with our package and achieve the charge-self-consistency within DFT+DMFT loops. To test and check our implementation, we computed the density of states and the band structure of well-known solid-state correlated materials, namely LaNiO_3, SrVO_3, and NiO. The obtained results are compared to those obtained from other DFT+DMFT implementations.
DOI: 10.6084/m9.figshare.25970938.v1
title: Verbatim & theme

description: Verbatim
DOI: 10.17632/2s9nt4fhy5
title: Data for: When information is not power: community-elected health facility committees and health facility performance indicators

description: Dataset for the paper, as well as do file for results (tables and figures)
DOI: 10.6084/m9.figshare.5249383.v1
title: Supplementary Material for: A Novel Evaluation for Predicting Aortic Complicated Lesions Using Calcification on Chest X-ray

description: <b><i>Background:</i></b> The aorta is a significant source of cerebral thromboembolisms. Aortic complicated lesions (ACLs) are key findings on transesophageal echocardiography (TEE) for assessing aortic sources of emboli to the brain. TEE is sometimes avoided due to its invasiveness. However, few reports have examined alternative methods for predicting ACLs. We investigated relationships between aortic arch calcification (AAC) on chest X-ray and ACLs. <b><i>Methods:</i></b> Participants comprised 300 patients with acute ischemic stroke or transient ischemic attack who underwent TEE for the evaluation of the aortic arch and heart. A postero-anterior plain chest X-ray in the recumbent position was evaluated on admission for each patient. AAC was evaluated using 4 grades (0-3) and “AAC thickness” defined as the distance from the inner margin of the most distant AAC to the outer margin of the aortic vessel wall. ACLs were defined by intima-media thickness (IMT) ≥4.0 mm or presence of ulcerated or mobile plaques. Carotid maximum IMT on ultrasonography was also evaluated. Comparison of the diagnostic ability to predict ACL was performed between AAC grades and AAC thickness or AAC thickness and carotid maximum IMT using the Delong method. <b><i>Results:</i></b> ACLs were identified in 71 patients (23.7%), including ACLs with ulcerated plaques in 24 (8.0%) and ACLs with mobile plaques in 9 (3.0%). Plaque thickness was greater in higher AAC grades or higher quartiles of AAC thickness (<i>p</i> for trend &lt;0.001 each). The Cochran-Armitage test showed that both higher AAC grade and higher quartile of AAC thickness were significantly associated with the presence of ACLs, as well as the presence of ulcerated or mobile plaques (<i>p</i> for trend &lt; 0.001 each). Receiver-operating characteristic (ROC) analysis showed optimal cut-off values for AAC thickness of 5.6 mm for ACLs and 6.0 mm for ulcerated or mobile plaques. Multivariate logistic regression revealed a higher grade of AAC (grades 2-3) and AAC thickness (≥6 mm) as significantly associated with ACLs and ulcerated or mobile plaques (<i>p</i> &lt; 0.001 each). ROC curve comparisons showed that AAC thickness offered a better marker of ACLs than AAC grade (<i>p</i> = 0.019), although no significant difference was evident between AAC thickness and carotid maximum IMT (<i>p</i> = 0.567). <b><i>Conclusions:</i></b> AAC on chest X-ray, evaluated by both AAC grade and AAC thickness to the outer aortic vessel wall, was significantly associated with ACLs on TEE. AAC thickness was suggested as more useful than AAC grade and equivalent to carotid IMT in predicting ACLs.
DOI: 10.17632/bxjknd7k38
title: Data for: Moisture and vegetation variations in the extremely cold-dry area of the Tibetan Plateau during past 5000 years

description: Pollen data of Buruo Co, including the pollen percentage, A/C ratio and the results of PCA analysis
DOI: 10.6084/m9.figshare.26370964.v1
title: Force Fields, Quantum-Mechanical- and Molecular-Dynamics-Based Descriptors of Radiometal–Chelator

description: Radiopharmaceuticals are currently a key tool in cancer diagnosis and therapy. Metal-based radiopharmaceuticals are characterized by a radiometal–chelator moiety linked to a bio-vector that binds the biological target (e.g., a protein overexpressed in a particular tumor). The right match between radiometal and chelator influences the stability of the complex and the drug’s efficacy. Therefore, the coupling of the radioactive element to the correct chelator requires consideration of several features of the radiometal, such as its oxidation state, ionic radius, and coordination geometry. In this work, we systematically investigated about 120 radiometal–chelator complexes taken from the Cambridge Structural Database. We considered 25 radiometals and about 30 chelators, featuring both cyclic and acyclic geometries. We used quantum mechanics methods at the density functional theoretical level to generate the general AMBER force field parameters and to perform 1 µs-long all-atom molecular dynamics simulations in an explicit water solution. From these calculations, we extracted several key molecular descriptors accounting for both electronic- and dynamical-based properties. The whole workflow was carefully validated, and selected test-cases were investigated in detail. Molecular descriptors and force field parameters for the complexes considered in this study are made freely available, thus enabling their use in predictive models, molecular modelling, and molecular dynamics investigations of the interaction of compounds with macromolecular targets. Our work provides new insights in understanding the properties of radiometal–chelator complexes, with a direct impact for rational drug design of this important class of drugs.
DOI: 10.6084/m9.figshare.19581718.v1
title: Original Data.xlsx

description: This is the original data of the article " A Life Extrapolation Model Using Accelerated Equivalent Luminance and Its Application".
DOI: 10.6084/m9.figshare.c.3643514_d2.v1
title: Additional file 3: of Development of a community health inclusion index: an evaluation tool for improving inclusion of people with disabilities in community health initiatives

description: Expert Panel Results.xlsx: A database of the items kept and removed by the Expert Panel as part of the development of the CHII. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.17040494.v1
title: Supplementary Material for: Communicating Bad News to Older Patients from the Physician’s Point of View: Focus on the Influence of Gender and Length of Work Experience

description: <b><i>Background:</i></b> Communicating bad news is of great interest in the geriatric field, but few works have considered the physician’s point of view in this regard. <b><i>Objectives:</i></b> The aim of this study was to explore possible differences related to physicians’ gender and work experience in how a terminal diagnosis is disclosed to older patients. <b><i>Methods:</i></b> Study participants were 420 Italian physicians (277 M, 143 F) working in clinical medicine (58.2%), surgery (33.3%), or other medical departments (8.5%). They completed an anonymous multiple-choice questionnaire that investigated various issues associated with communicating bad news to terminally ill older patients. <b><i>Results:</i></b> Men had more work experience than women (55.6% vs. 44.8% had worked for ≥23 years) and were more likely to work in surgery departments, while more women worked in clinical medicine. Most physicians declared that terminally ill older patients, if mentally competent, should always (14.4%) or generally (64.3%) be directly and openly informed of their condition. With no difference in gender, length of work experience, or specialty area, 36.9% of physicians thought that this was a human right and 18% that it would improve the patient’s quality of life. Where older patients were alone, male physicians were more likely than female (30.2% vs. 8.9%) to always communicate bad news directly to them. More than 70% of physicians, especially those with longer work experience, declared that they always or often took enough time to inform the patient. Female physicians and those working in clinical medicine were more likely to need psychological help when deciding to break bad news, but only a smaller proportion declared to have received it. <b><i>Conclusions:</i></b> Gender and work experience may influence how physicians communicate with patients and how often they seek psychological support.
DOI: 10.6084/m9.figshare.21965165.v1
title: Sources of funding for research articles in medical education journals from 1999-2019 - data.xlsx

description: Dataset of 1822 research articles published in Medical Education, Medical Teacher, Advances in Health Sciences Education and Academic Medicine in 1999, 2004, 2009, 2014 and 2019, analysed for declarations of funding sources and categorised by type of source.
DOI: 10.6084/m9.figshare.22670485.v1
title: Combining multi-typologies landslide susceptibility maps: a case study for the Visso area (central Italy)

description: The research proposes a simple but geomorphologically adequate method to produce a combined landslide susceptibility map. In fact, in a logic of real use, offering type-specific landslide susceptibility maps to land use planners and administration could be not a successful solution. On the other hand, the simple grouping of more types of landslides could be misleading for model calibration considering that the relationships between slope failures and geo-environmental predictors should be conveyed by the abundance of each type of landslide resulting not specific and diagnostic for each typology. In this test, after having produced independent models for flow, slide and complex landslide by exploiting MARS (Multivariate Adaptive Regression Splines) and a set of type-specific geo-environmental variables, a combined landslide susceptibility map was obtained by combining the scores of the three source maps. The combined map was finally validated with a new unknown archive, showing very good performances.
DOI: 10.6084/m9.figshare.25139015.v1
title: Parts of the Mizar Mathematical Library Knowledge Graph (MMLKG) dataset (YARS-PG version)

description: This dataset includes small parts of YARS-PG version of the Mizar Mathematical Library Knowledge Graph (MMLKG) dataset.MMLKG is a thesaurus for describing a comprehensive repository of mathematical papers written in the Mizar language and computer-verified by the Mizar proof-checker (Mizar Mathematical Library).Read more about the MMLKG project at the MMLKG website.Contents<code>README.md</code>: README file<code>LICENSE.txt</code>: A license for all files<code>10.yarspg</code>: First 10 MB of the YARS-PG version of the MMLKG (without line breaks)<code>20.yarspg</code>: First 20 MB of the YARS-PG version of the MMLKG (without line breaks)<code>30.yarspg</code>: First 30 MB of the YARS-PG version of the MMLKG (without line breaks)<code>40.yarspg</code>: First 40 MB of the YARS-PG version of the MMLKG (without line breaks)<code>50.yarspg</code>: First 50 MB of the YARS-PG version of the MMLKG (without line breaks)<code>60.yarspg</code>: First 60 MB of the YARS-PG version of the MMLKG (without line breaks)<code>70.yarspg</code>: First 70 MB of the YARS-PG version of the MMLKG (without line breaks)<code>80.yarspg</code>: First 80 MB of the YARS-PG version of the MMLKG (without line breaks)<code>90.yarspg</code>: First 90 MB of the YARS-PG version of the MMLKG (without line breaks)<code>100.yarspg</code>: First 100 MB of the YARS-PG version of the MMLKG (without line breaks)LicenseThe MMLKG dataset is licensed under the Creative Commons Attribution 4.0 International License.
DOI: 10.6084/m9.figshare.3553302.v1
title: Appendix D. Images of sublethal injuries caused by mosquitofish in the mesocosm experiment.

description: Images of sublethal injuries caused by mosquitofish in the mesocosm experiment.
DOI: 10.6084/m9.figshare.12581126.v1
title: Supplementary Material for: Clinical and Operative Determinants of Acute Kidney Injury after Cardiac Surgery

description: <b><i>Introduction:</i></b> Cardiac surgery-associated acute kidney injury (CSA-AKI) is associated with increased morbidity and mortality. <b><i>Objectives:</i></b> We aimed to identify potentially modifiable risk factors for CSA-AKI. <b><i>Methods:</i></b> This was a<b><i></i></b>single-center retrospective cohort study of 495 adult patients undergoing cardiac surgery. AKI was diagnosed and staged using full KDIGO criteria incorporating baseline serum creatinine (SC) levels and correction of postoperative SC levels for fluid balance. We examined the association of routinely available clinical and laboratory data with AKI using multivariate logistic regression modeling. <b><i>Results:</i></b> A total of 103 (20.8%) patients developed AKI: 16 (15.5%) patients were diagnosed with AKI upon hospital admission, and 87 (84.5%) patients were diagnosed with CSA-AKI. Correction of SC levels for fluid balance increased the number of AKI cases to 104 (21.0%), with 6 patients categorized to different AKI stages. Univariate logistic regression analysis identified five preoperative (age, sex, diabetes mellitus, preoperative systolic pulmonary arterial pressure [PSPAP], acute decompensated heart failure) and five intraoperative predictors of AKI (age, sex, red blood cell [RBC] volume transfused, use of minimally invasive surgery, duration of cardiopulmonary bypass). When all preoperative and intraoperative variables were incorporated into one model, six predictors remained significant (age, sex, use of minimally invasive surgery, RBC volume transfused, PSPAP, duration of cardiopulmonary bypass). Model discrimination performance showed an area under the curve of 0.69 for the model including only preoperative variables, 0.76 for the model including only intraoperative variables, and 0.77 for the model including all preoperative and intraoperative variables. <b><i>Conclusions:</i></b> Use of minimally invasive surgery and therapies mitigating PSPAP and intraoperative blood loss may offer protection against CSA-AKI.
DOI: 10.6084/m9.figshare.4994240.v1
title: Friedman test - XD

description: Friedman test - XD
DOI: 10.6084/m9.figshare.5907172.v13
title: GeoLink Dataset: Complex Ontology Alignment Benchmark

description: This is a real-world dataset from the GeoLink project as a potential complex alignment benchmark. The dataset consists of two ontologies, the GeoLink Base Ontology (GBO) and the GeoLink Modular Ontology (GMO), that were developed in consultation with numerous domain experts. The manually created alignment between these two ontologies includes 1:1, 1:n, and m:n equivalence and subsumption correspondences. The reference alignment for this benchmark is available in both EDOAL and rules syntax.<br><b>-ReadMe.txt:</b> ReadMe file that introduces the structure of the files<b>-gbo.owl:</b> GeoLink Base Ontology<b>-gmo.owl:</b> GeoLink Modular Ontology<b>-gboWithInstance.owl:</b> GeoLink Base Ontology with instance data populated<b>-gmoWithInstance.owl:</b> GeoLink Modular Ontology with instance data populated<b>-gbo-gmo.edoal:</b> the alignments in EDOAL format<b>-gbo-gmo-alignment.rdf:</b> the alignments in rule syntax <br><br>
DOI: 10.6084/m9.figshare.13148333.v1
title: Metadata record for: DISPERSE, a trait database to assess the dispersal potential of European aquatic macroinvertebrates

description: This dataset contains key characteristics about the data described in the Data Descriptor DISPERSE, a trait database to assess the dispersal potential of European aquatic macroinvertebrates. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> <br>
DOI: 10.6084/m9.figshare.26104861.v1
title: Supplementary Material for: Differences between chronically Hepatitis B Virus-infected pregnant women with and without intrafamilial infection: from viral gene sequences to clinical manifestations

description: Introduction: This study aimed to investigate the differences between pregnant women with chronic hepatitis B virus (HBV) infection and intrafamilial infection and those without intrafamilial infection.
Methods: HBV DNA was extracted from the sera of 16 pregnant women with chronic hepatitis B (CHB) and their family members for gene sequencing and phylogenetic analyses. A total of 74 pregnant women with CHB were followed up from the second trimester to three months postpartum. Viral markers and other laboratory indicators were compared between pregnant women with CHB with and without intrafamilial infection.
Results: The phylogenetic tree showed that HBV lines in the mother-spread pedigree shared a node, whereas there was an unrelated genetic background for HBV lines in individuals without intrafamilial infection. From delivery to three months postpartum, compared with those without intrafamilial infection, pregnant women with intrafamilial infection were related negatively to HBV DNA (β=-0.43, 95% Confidence Interval [CI]: -0.76 to -0.12, p=0.009), HBeAg (β=-195.15, 95% CI: -366.35 to -23.96, p=0.027), and hemoglobin changes (β=-8.09, 95%CI: -15.54 to -0.64, p=0.035) and positively to changes in the levels of alanine aminotransferase (β=73.9, 95%CI:38.92-108.95, p&lt;0.001) and albumin (β=2.73, 95% CI:0.23-5.23, p=0.033).
Conclusion: The mother-spread pedigree spread model differs from that of non-intrafamilial infections. Pregnant women with intra-familial HBV infection have less hepatitis flares and liver damage, but their HBV DNA and HBeAg levels rebound faster after delivery, than those without intra-familial infection by the virus.
DOI: 10.6084/m9.figshare.13041827.v1
title: Supplementary Material for: Digital Multiplexed Gene Expression Analysis of mRNA and miRNA from Routinely Processed and Stained Cytological Smears: A Proof-of-Principle Study

description: <b><i>Objective:</i></b> Although transcriptomic assessments of small samples using high-throughput techniques are usually performed on fresh or frozen tissues, there is a growing demand for those performed on stained cellular specimens already used for diagnostic purposes. <b><i>Study Design:</i></b> The possibility of detecting mRNAs and microRNAs (miRNAs) from routinely processed cytological samples using nCounter® technology was explored. Fresh samples from pleural and peritoneal effusions were analyzed using 2 parallel methods: samples were smeared and routinely stained using the May-Grünwald-Giemsa or Diff-Quik® method and mounted using conventional methods, and they were also studied following a snap freezing method, in which samples were maintained at −80°C until use. mRNAs and miRNAs were assessed and compared after total RNA extraction from both routinely processed samples and their matched frozen controls. <b><i>Results:</i></b> A good concordance was found between the gene expression measured in routinely processed samples and their matched frozen controls for the majority of mRNAs and miRNAs tested. However, the standard deviation of low-expressed miRNA was high. <b><i>Conclusions:</i></b> Although nCounter® technology is a robust method to measure and characterize both mRNAs and miRNAs from routinely processed cytological samples, caution is recommended for the interpretation of low-expressed miRNA.
DOI: 10.6084/m9.figshare.12797477.v1
title: Wind210

description: https://podaac-tools.jpl.nasa.gov/drive/files/allData/cygnss/L2/cdr_v1.0/2018/210
DOI: 10.17632/3f5p2p7hbs
title: Identification of phosphorylation site of Npas4 by LC-MS/MS

description: To identify the phosphorylation sites of Npas4, GST-Npas4-390-489 aa, GST-Npas4 490-597 aa or GST-Npas4 598-701 aa was expressed in COS7 cells with or without the coexpression of MAP2K1-CA. Cells were lysed in lysis buffer [20 mM Tris/HCl, 1 mM EDTA, 150 mM NaCl, 1% NP-40, protease inhibitor cocktail (Roche), and phosphatase inhibitor cocktail (PhosStop, Roche), pH 7.5], and sonicated 3 times for 5 sec. After centrifugation at 16,000×g at 4°C for 10 min, the soluble supernatant was incubated in 30 µl of glutathione-Sepharose 4B beads (GE Healthcare) for 1 hr at 4°C with rotation. The beads were then washed three times with lysis buffer and an additional three times with wash buffer (20 mM Tris/HCl, 1 mM EDTA, and 150 mM NaCl, pH 7.5). The bound proteins were extracted from the beads using urea solution, reduced via incubation in 5 mM dithiothreitol for 30 min, and alkylated using 10 mM iodoacetamide for 1 h in the dark. The proteins were digested with Trypsin/Lys-C (Promega) or Glu-C (Promega)/Asp-N (FUJIFILM Wako). Demineralization was performed using SPE c-tips according to the manufacturer’s instructions. The peptides were analyzed by LC−MS using an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific Inc). Dual-phosphorylated peptide DLVCTPPYTPHQPGGCAFLFSLHEPFQTHLPPPSSSLQE, containing T423 and T427 phosphorylation sites, was identified from digested fragments of GST-Npas4-390-489 aa; LPPSPSSPGNGDCTLLALAQLR, containing S577 and S580 phosphorylation sites, was identified from digested fragments of GST-Npas4 490-597 aa; and GLLTPEASPVKQSFFHYTEKE, containing T611 and S615 phosphorylation sites, was identified from digested fragments of GST-Npas4 598-701 aa. Selected ion monitoring (SIM) analysis revealed that the amount of these dual-phosphorylation was significantly increased by coexpression with MAP2K1-CA. These results suggest that Npas4 is phosphorylated by MAPK at T423, T427, S577, S580, T611 and S615 sites.
DOI: 10.17632/7ch6553xjp
title: The 22-bp Indel Variation in Chicken GLUT4: Transcriptional Regulation and Population Diversity
DOI: 10.17632/9g2w2fbjb9
title: Data_Kukofka et al. 2024

description: Kukofka, P., Young, R., Kunz, J.A., Nellissen, L., Alavi, S.E., Rahmaeti,
 T., Basalamah, F., Haun, D.B.M., Schuppli, C., The development of social attention in orangutans:
 comparing peering behavior in wild and zoo-housed individuals, ISCIENCE (2025), doi: https://
 doi.org/10.1016/j.isci.2024.111542.
DOI: 10.17632/nm33hszttd
title: LINF_140009300

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)