cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4877375.v1
title: alex_martie_2016.rar

description: Data represent a compressed version of the whole dataset used in the simulation of microwave effect in a modified microwave oven used for in vivo hyperthermia. Do open documents one neeed to run CST 2014
DOI: 10.6084/m9.figshare.4877348.v1
title: Identifying viable theoretical frameworks with essential parameters for real-time and real world alcohol craving research: a systematic review of craving models

description: <b>Background:</b> Substance use is known to be episodic, dynamic, complex, and highly influenced by the environment, therefore a situational and momentary focus to alcohol craving research is appropriate. Current advances in mobile and wearable technology provide novel opportunities for craving research. However, the lack of consensus within craving theory impedes the identification and prioritization of parameters to be monitored. The aim of this study is to critically review current craving models in order to determine viable theoretical frameworks of alcohol craving and its essential parameters. <b>Methods:</b> Eighteen models of craving were reviewed by applying a literature search with a five-step strategy that accounted for the momentary nature of craving and included a snowballing search and a key term extraction algorithm. Based on this review, multiple decision criteria were defined upon which to evaluate the models. <b>Results:</b> Six models for alcohol craving were supported by sufficient empirical research to be eligible. The inferences drawn on these six models resulted in three decision criteria: the model should (1) incorporate negative affect as a predictor of relapse; (2) explain that dependent drinkers have a higher attentional bias towards alcohol cues than nondependent drinkers; (3) incorporate increased risk of relapse with heightened stress levels. <b>Conclusions:</b> The affective processing model of negative reinforcement, the cognitive processing model, the incentive sensitization theory of addiction and the theory of neural opponent motivation are classified as viable theoretical frameworks, resulting in negative affect and stress as relevant parameters to include in real-time craving monitoring research.
DOI: 10.6084/m9.figshare.4877360
title: F-exsecta_TA_New.fasta

description: This file(fasta format) is obtained by using raw sequencing data from <i>F. exsecta</i>. This Transcriptome Shotgun Assembly project has been deposited at GenBank under the accession GFLV00000000.
DOI: 10.6084/m9.figshare.4876832
title: Raw dataset for the upcoming article of Boudjabi et al. 2017

description: The title of the article is: "Sewage sludge fertilization alleviates drought stress and improves physiological adaptation and yield performances in Durum Wheat (<i>Triticum durum</i>): a double edged sword"
DOI: 10.6084/m9.figshare.4876847
title: Found_magpie X elk mutualism data

description: Data from personality observations and experiments, for magpies and elk, and results for cleaner-bird interactions.<br>
DOI: 10.6084/m9.figshare.4876811.v2
title: Data Science for Basic Scientists

description: My slides from the OHSU educational symposium 2017.
DOI: 10.6084/m9.figshare.4876799.v1
title: A probabilistic record linkage model for survival data

description: In absence of an unique identifier, combining information from multiple files relies on partially identifying variables (e.g. gender, initials). With a record linkage procedure, these variables are used to distinguish record pairs that belong together (matches) from record pairs that do not belong together (non-matches). Generally, the combined strength of the partially identifying variables is too low causing imperfect linkage; some true non-matches are identified as match and, on the other hand, some true matches as non-match. To avoid bias in further analyses, it is necessary to correct for imperfect linkage. In this paper, pregnancy data from the Perinatal Registry of the Netherlands was used to estimate the associations between the (baseline) characteristics from the first delivery and the time to a second delivery. Because of privacy regulations, no unique identifier was available to determine which pregnancies belonged to the same woman. To deal with imperfect linkage in a time-to-event setting, where we have a file with baseline characteristics and a file with event times, we developed a joint model in which the record linkage procedure and the time-to-event analysis are performed simultaneously. R code and example data are available as online supplemental material.
DOI: 10.6084/m9.figshare.4876766
title: New experimental model for single liver lobe hyperthermia in small animals using non-directional microwaves

description: Single liver lobe hyperthermia using non-directional microwave. Prototype demonstration
DOI: 10.6084/m9.figshare.4876766.v1
title: New experimental model for single liver lobe hyperthermia in small animals using non-directional microwaves

description: Single liver lobe hyperthermia using non-directional microwave. Prototype demonstration
DOI: 10.6084/m9.figshare.4876679
title: Development of quantitative monoclonal antibody-specific immobilization of platelet antigens assay for antibodies against human platelet antigen-1a, 3a, and 5b

description: Human platelet antigens (HPAs) are platelet-specific alloantigens that cause alloimmunization. Alloantibodies induced <i>via</i> pregnancy and transfusion may result in various clinical syndromes. The monoclonal antibody-specific immobilization of platelet antigens (MAIPA) assay is the gold standard for the detection and identification of HPA antibodies. The present study aimed to develop standardized quantitative MAIPA assays for antibodies against HPA-1a, 3a, and 5b. MAIPA protocol was applied on serial dilutions of standard or reference reagents containing antibodies against HPA-1a, 3a, and 5b. Optimal experimental parameters were determined, and standard curves were constructed with a linear regression. The sensitivity, specificity, and reproducibility of the assays were also evaluated. The optimum reagents and conditions for the MAIPA assays were decided through repeated testing and comparison. The intra-assay coefficients of variation (CVs) are 1.3~3.6%, 2.7~5.2%, and 4.7~5.3%; the inter-assay CVs are 4.0~5.6%, 4.4~5.9%, and 3.2~6.3%, respectively, for HPA-1a, HPA-3a, and HPA-5b antibodies. In specificity tests, some monoclonal antibodies and sera with other antibodies were tested and no obvious positive result was observed. The standardized quantitative MAIPA assays for antibodies against HPA-1a, 3a, and 5b have good sensitivity, reproducibility, and specificity. They have important application value in clinical diagnosis of alloimmunization disease caused by HPA antibodies and safe transfusion of platelets.
DOI: 10.6084/m9.figshare.4876679.v1
title: Development of quantitative monoclonal antibody-specific immobilization of platelet antigens assay for antibodies against human platelet antigen-1a, 3a, and 5b

description: Human platelet antigens (HPAs) are platelet-specific alloantigens that cause alloimmunization. Alloantibodies induced <i>via</i> pregnancy and transfusion may result in various clinical syndromes. The monoclonal antibody-specific immobilization of platelet antigens (MAIPA) assay is the gold standard for the detection and identification of HPA antibodies. The present study aimed to develop standardized quantitative MAIPA assays for antibodies against HPA-1a, 3a, and 5b. MAIPA protocol was applied on serial dilutions of standard or reference reagents containing antibodies against HPA-1a, 3a, and 5b. Optimal experimental parameters were determined, and standard curves were constructed with a linear regression. The sensitivity, specificity, and reproducibility of the assays were also evaluated. The optimum reagents and conditions for the MAIPA assays were decided through repeated testing and comparison. The intra-assay coefficients of variation (CVs) are 1.3~3.6%, 2.7~5.2%, and 4.7~5.3%; the inter-assay CVs are 4.0~5.6%, 4.4~5.9%, and 3.2~6.3%, respectively, for HPA-1a, HPA-3a, and HPA-5b antibodies. In specificity tests, some monoclonal antibodies and sera with other antibodies were tested and no obvious positive result was observed. The standardized quantitative MAIPA assays for antibodies against HPA-1a, 3a, and 5b have good sensitivity, reproducibility, and specificity. They have important application value in clinical diagnosis of alloimmunization disease caused by HPA antibodies and safe transfusion of platelets.
DOI: 10.6084/m9.figshare.4874870
title: Data from Gopko M, Mikheev VN, Taskinen J (2017) Positive density-dependent growth supports cost sharing hypothesis and population density sensing in manipulative parasite.

description: Supplementary dataset for<br>Gopko M, Mikheev VN, Taskinen J (2017) Positive density-dependent growth supports cost sharing hypothesis and population density sensing in manipulative parasite.<i>Submitted to Parasitology</i><b></b>Dataset_Gopko_Mikheev_Taskinen.xlsx - contained all data used in the statistical analysis. The legend can be found within the Excel file.GLMM_long_data.csv - data prepared for the mixed modelling, if needed. The lgend for these data is dowloaded as a separate file.
DOI: 10.6084/m9.figshare.4876574
title: BMT decreases HFD-induced weight gain associated with decreased preadipocyte number and insulin secretion

description: This data set describes the metabolic effects of BMT on WT mice
DOI: 10.6084/m9.figshare.4874870.v1
title: Data from Gopko M, Mikheev VN, Taskinen J (2017) Positive density-dependent growth supports cost sharing hypothesis and population density sensing in manipulative parasite.

description: Supplementary dataset for<br>Gopko M, Mikheev VN, Taskinen J (2017) Positive density-dependent growth supports cost sharing hypothesis and population density sensing in manipulative parasite.<i>Submitted to Parasitology</i><b></b>Dataset_Gopko_Mikheev_Taskinen.xlsx - contained all data used in the statistical analysis. The legend can be found within the Excel file.GLMM_long_data.csv - data prepared for the mixed modelling, if needed. The lgend for these data is dowloaded as a separate file.
DOI: 10.6084/m9.figshare.4876574.v1
title: BMT decreases HFD-induced weight gain associated with decreased preadipocyte number and insulin secretion

description: This data set describes the metabolic effects of BMT on WT mice
DOI: 10.6084/m9.figshare.4873544
title: VectorNet gap analysis: Tick vector distribution models utilised to identify areas of potential species distribution in areas lacking records.

description: The data package described here includes Tick species modelled as part of the VectorNet project. It comprises four species <i>Dermercentor reticulatus</i>, <i>Hyaloma marginatum, Ixodes ricinus </i>and<i> Rhipicephalus sanguinius.<br><br></i><i>This data is planned to be presented in the Open Health Data Journal.</i>
DOI: 10.6084/m9.figshare.4873544.v1
title: VectorNet gap analysis: Tick vector distribution models utilised to identify areas of potential species distribution in areas lacking records.

description: The data package described here includes Tick species modelled as part of the VectorNet project. It comprises four species <i>Dermercentor reticulatus</i>, <i>Hyaloma marginatum, Ixodes ricinus </i>and<i> Rhipicephalus sanguinius.<br><br></i><i>This data is planned to be presented in the Open Health Data Journal.</i>
DOI: 10.6084/m9.figshare.4873427
title: Data depository of the manuscript untitled "Reconstructing grassland fire history using sedimentary charcoal: considering count, size and shape", PlosONE 2017

description: The dataset is organized by csv files of raw data for the Flint Hills (FH) and the Great Plains (GP) samples. All the samples have metadata, pollen, vegetation derived from satelite imagery, area burned, and charcoal data.<br>
DOI: 10.6084/m9.figshare.4873415
title: Formal Proofs for the paper: How to Simulate It in Isabelle: Towards Formal Proof for Secure Multi-Party Computation

description: The formal proofs in Isabelle for the work shown in the paper as in the title.
DOI: 10.6084/m9.figshare.4873415.v2
title: Formal Proofs for the paper: How to Simulate It in Isabelle: Towards Formal Proof for Secure Multi-Party Computation

description: The formal proofs in Isabelle for the work shown in the paper as in the title.
DOI: 10.6073/pasta/dffec7707936c2e5b902bf29cc543f6e
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 10 meteorological station: Daily average soil volumetric water content data: 2013 - ongoing

description: Daily Average of 30-minute Soil Volumetric Water Content data at 10 cm at CSIS Block-10. Collection of soil water content data at Jornada LTER Cross-scale Interactions Study (CSIS) blocks, New Mexico, supports the environmental monitoring objectives of the Jornada LTER monitoring program that look at plant-soil water dynamics. Soil volumetric water content is measured every 30 minutes at 10 cm depth at 3 locations at each of the 4 plots per block and averaged for the daily value. The locations in each plot are under bare soil, under perennial grass, and under shrub. Volumetric water content, bulk electrical conductivity, soil temperature, and bulk dielectric permittivity are recorded at an automated meteorological station installed at Jornada LTER CSIS Block-10 site. This is an ONGOING dataset.
DOI: 10.6084/m9.figshare.4873415.v1
title: How to Simulate It in Isabelle: Towards Formal Proof for Secure Multi-Party Computation

description: The formal proofs in Isabelle for the work shown in the paper as in the title.
DOI: 10.6084/m9.figshare.4873163
title: Supplementary data from Olson's Extinction and the latitudinal biodiversity gradient of tetrapods in the Permian

description: Specimen counts and localities of all for included formations, and diversity estimates.
DOI: 10.6084/m9.figshare.4873163.v1
title: Supplementary data from Olson's Extinction and the latitudinal biodiversity gradient of tetrapods in the Permian

description: Specimen counts and localities of all for included formations, and diversity estimates.
DOI: 10.6084/m9.figshare.4873022
title: Pan genome reference fasta

description: This is a file generated by Roary pan genome pipeline of the E. coli pan genome for the reference publication. It can be used to decode the gene names in the core genome files to the corresponding sequences.<br>
DOI: 10.6084/m9.figshare.4873055
title: Data for: What makes a reach movement effortful? – Physical effort discounting supports common minimization principles in decision making and motor control

description: Data for all figures and supporting information.
DOI: 10.6084/m9.figshare.4873022.v1
title: Pan genome reference fasta

description: This is a file generated by Roary pan genome pipeline of the E. coli pan genome for the reference publication. It can be used to decode the gene names in the core genome files to the corresponding sequences.<br>
DOI: 10.6084/m9.figshare.4873010
title: Neoproterozoic basement history of Wrangel Island and Arctic Chukotka: integrated insights from zircon U–Pb, O and Hf isotopic studies

description: SIMS zircon <sup>18</sup>O/<sup>16</sup>O isotopic data.
DOI: 10.6084/m9.figshare.4873013
title: Neoproterozoic basement history of Wrangel Island and Arctic Chukotka: integrated insights from zircon U–Pb, O and Hf isotopic studies

description: Secondary ion mass spectrometry (SIMS) U–Pb zircon geochronology data.
DOI: 10.6084/m9.figshare.4873007
title: Neoproterozoic basement history of Wrangel Island and Arctic Chukotka: integrated insights from zircon U–Pb, O and Hf isotopic studies

description: Laser ablation inductively coupled mass spectrometry zircon Lu–Hf isotopic data.
DOI: 10.6084/m9.figshare.4873013.v1
title: Neoproterozoic basement history of Wrangel Island and Arctic Chukotka: integrated insights from zircon U–Pb, O and Hf isotopic studies

description: Secondary ion mass spectrometry (SIMS) U–Pb zircon geochronology data.
DOI: 10.6084/m9.figshare.4872908
title: Accretion rates and hole size table for Fig.6 from The dispersal of planet-forming discs: theory confronts observations

description: This file contains that data on Accretion rates and Transition Disc hole sizes used to generate Figure 6.
DOI: 10.6084/m9.figshare.4872872
title: Strain improvement of <i>Lentzea</i> sp. 7887 for higher yield per unit volume on hydroxylation of cyclosporine derivative FR901459

description: A Gram-positive bacterium <i>Lentzea</i> sp. 7887 hydroxylates a cyclosporine derivative FR901459 into AS1837812 (9-hydroxide), which is an important intermediate of candidate drugs that target the hepatitis C virus. We screened a UV-induced mutant, named M-1, which showed about 1.2-fold higher conversion yields, 2-fold higher substrate concentrations (3.69 mM), and 2.5-fold higher yield per unit volume than the wild-type strain.
DOI: 10.6084/m9.figshare.4872875
title: Supplementary Material for: Combining Cystatin C and Creatinine Yields a Reliable Glomerular Filtration Rate Estimation in Older Adults in Contrast to β-Trace Protein and β2-Microglobulin

description: <b><i>Background:</i></b> The glomerular filtration rate (GFR) is the most important measure of kidney function and chronic kidney disease (CKD). This study aims to validate commonly used equations for estimated GFR (eGFR) based on creatinine (cr), cystatin C (cys), β-trace protein (BTP), and β2-microglobulin (B2M) in older adults. <b><i>Method:</i></b> We conducted a validation study with 126 participants aged between 72 and 98 with a mean measured GFR (mGFR) by iohexol clearance of 54 mL/min/1.73 m<sup>2</sup>. The eGFR equations (CKD-Epidemiology collaboration [CKD-EPI], Berlin Initiative Study [BIS], Full Age Spectrum [FAS], Modification of Diet in Renal Disease [MDRD]<sub>cr</sub>, Caucasian-Asian-Pediatric-Adult [CAPA]<sub>cys</sub>, Lund-Malmö Revised [LM-REV]<sub>cr</sub>, and MEAN-LM-CAPA<sub>cr-cys</sub>), were assessed in terms of bias (median difference: eGFR-mGFR), precision (interquartile range of the differences), and accuracy (P30: percentage of estimates ±30% of mGFR). The equations were compared to a benchmark equation: CKD-EPI<sub>cr-cys</sub>. <b><i>Results:</i></b> All cystatin C-based equations underestimated the GFR compared to mGFR, whereas bias was mixed for the equations based only on creatinine. Accuracy was the highest for CKD-EPI<sub>cr-cys</sub> (98%) and lowest for MDRD (82%). Below mGFR 45 mL/min/1.73 m<sup>2</sup> only equations incorporating cystatin C reached P30 accuracy &gt;90%. CKD-EPI<sub>cr-cys</sub> was not significantly more accurate than the other cystatin C-based equations. In contrast, CKD-EPI<sub>cr-cys</sub> was significantly more accurate than all creatinine-based equations except LM-REV<sub>cr</sub>. <b><i>Conclusion:</i></b> This study confirms that it is reasonable to use equations incorporating cystatin C and creatinine in older patients across a wide spectrum of GFR. However, the results call into question the use of creatinine alone below mGFR 45 mL/min/1.73 m<sup>2</sup>. B2M and BTP do not demonstrate additional value in eGFR determination in older adults.
DOI: 10.6084/m9.figshare.4872881
title: Supplementary Material for: Pulmonary Carcinoids and Low-Grade Gastrointestinal Neuroendocrine Tumors Show Common MicroRNA Expression Profiles, Different from Adenocarcinomas and Small Cell Carcinomas

description: <b><i>Background:</i></b> It is still uncertain whether small cell lung carcinomas (SCLCs), pulmonary carcinoids, and the gastrointestinal neuroendocrine tumors (GI-NETs) have a common origin. MicroRNA (miRNA) expression may clarify their genetic relationships and origin. <b><i>Methods:</i></b> First, we compared the miRNA expression signature of formalin-fixed paraffin-embedded (FFPE) samples with frozen samples to verify the applicability of microarray analysis. Second, we compared the comprehensive miRNA expression patterns of pulmonary carcinoids and GI-NETs as well as other types of tumors and normal tissues from each organ using FFPE samples. These data were analyzed by hierarchical clustering and consensus clustering with nonnegative matrix factorization. <b><i>Results:</i></b> We confirmed that FFPE samples retained the miRNA signatures. In the first hierarchical clustering comparing carcinoids/NETs with adenocarcinomas and normal tissues, most of the carcinoids (48/50) formed 1 major cluster with loose subpartitioning into each organ type, while all the adenocarcinomas (9/9) and normal tissues (15/15) formed another major cluster. The nonnegative matrix factorization approach largely matched the classification of the hierarchical clustering. In the additional cluster analysis comparing carcinoids/NETs with SCLCs, most carcinoids/NETs (17/22) formed a major cluster, while SCLCs (9/9) grouped together with pulmonary adenocarcinomas (3/3) and normal tissues (6/6) in another major cluster. Furthermore, a subset of miRNAs was successfully identified that exhibited significant expression in carcinoids/NETs. <b><i>Conclusion:</i></b> Carcinoids/NETs had a characteristic pattern of miRNA expression, suggesting a common origin for pulmonary carcinoids and GI-NETs. The expression profiles of pulmonary carcinoids and SCLCs were quite different, indicating the distinct histogenesis of these neuroendocrine neoplasms.
DOI: 10.6084/m9.figshare.4872908.v1
title: Accretion rates and hole size table for Fig.6 from The dispersal of planet-forming discs: theory confronts observations

description: This file contains that data on Accretion rates and Transition Disc hole sizes used to generate Figure 6.
DOI: 10.6084/m9.figshare.4872872.v1
title: Strain improvement of <i>Lentzea</i> sp. 7887 for higher yield per unit volume on hydroxylation of cyclosporine derivative FR901459

description: A Gram-positive bacterium <i>Lentzea</i> sp. 7887 hydroxylates a cyclosporine derivative FR901459 into AS1837812 (9-hydroxide), which is an important intermediate of candidate drugs that target the hepatitis C virus. We screened a UV-induced mutant, named M-1, which showed about 1.2-fold higher conversion yields, 2-fold higher substrate concentrations (3.69 mM), and 2.5-fold higher yield per unit volume than the wild-type strain.