cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12410729.v2
title: Confidence and Prediction in Linear Mixed Models: Do Not Concatenate the Random Effects. Application in an Assay Qualification Study

description: <b><i>Abstract–</i>In the pharmaceutical industry, all analytical methods must be shown to deliver unbiased and precise results. In an assay qualification or validation study, the trueness, accuracy, and intermediate precision are usually assessed by comparing the measured concentrations to their nominal levels. Trueness is assessed by using Confidence Intervals (CIs) of mean measured concentration, accuracy by Prediction Intervals (PIs) for a future measured concentration, and the intermediate precision by the total variance. ICH and USP guidelines alike request that all relevant sources of variability must be studied, for example, the effect of different technicians, the day-to-day variability or the use of multiple reagent lots. Those different random effects must be modeled as crossed, nested, or a combination of both; while concatenating them to simplify the model is often taken place. This article compares this simplified approach to a mixed model with the actual design. Our simulation study shows an under-estimation of the intermediate precision and, therefore, a substantial reduction of the CI and PI. The power for accuracy or trueness is consequently over-estimated when designing a new study. Two real datasets from assay validation study during vaccine development are used to illustrate the impact of such concatenation of random variables.</b>
DOI: 10.6084/m9.figshare.12410564.v1
title: Metadata record for: Chromosome-level genome assembly of Tarim red deer, Cervus elaphus yarkandensis

description: This dataset contains key characteristics about the data described in the Data Descriptor Chromosome-level genome assembly of Tarim red deer, Cervus elaphus yarkandensis. <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.12410498
title: Epilepsy data

description: (structure: data_filter{1,subj}(region_num,:) <br> All filtered data (BOLD after bandpass).
DOI: 10.6084/m9.figshare.12410729.v1
title: Confidence and Prediction in Linear Mixed Models: Don’t Concatenate the Random Effects. Application in an Assay Qualification Study

description: In the pharmaceutical industry, all analytical methods must be shown to deliver unbiased and precise results. In an assay qualification or validation study, the trueness, accuracy and intermediate precision are usually assessed by comparing the measured concentrations to their nominal levels. Trueness is assessed by using Confidence Intervals of mean measured concentration, accuracy by Prediction Intervals for a future measured concentration, and the intermediate precision by the Total Variance. ICH and USP guidelines alike request that all relevant sources of variability must be studied, e.g. the effect of different technicians, the day-to-day variability or the use of multiple reagent lots. Those different random effects must be modeled as crossed, nested or a combination of both; while concatenating them to simplify the model is often taken place. This paper compares this simplified approach to a mixed model with the actual design. Our simulation study shows an under-estimation of the intermediate precision and, therefore, a substantial reduction of the confidence and prediction intervals. The power for accuracy or trueness is consequently over-estimated when designing a new study. Two real datasets from assay validation study during vaccine development are used to illustrate the impact of such concatenation of random variables.
DOI: 10.6084/m9.figshare.12410498.v1
title: Epilepsy data

description: (structure: data_filter{1,subj}(region_num,:) <br> All filtered data (BOLD after bandpass).
DOI: 10.6084/m9.figshare.12410486
title: GI-00211-2020 Supplementary Information.docx

description: <b>Table S1.</b> The relative expression levels of proteins in UC versus healthy controls by SWATH<b>Table S2.</b> Statistically significant GO term related to differentially regulated proteins in UC versus healthy controls by SWATH<b>Table S3.</b> Statistically significant KEGG pathways related to differentially regulated proteins in UC versus healthy controls by SWATH<br>
DOI: 10.6084/m9.figshare.12410492
title: Distribution models of wintering raptor species in a semiarid Mediterranean region

description: We provided the presence data of the raptors that we compiled through of two sources (census itineraries and citizen science data) throughout the study period (2017-2018 and 2018-2019 winter periods) wich were used for the maximum entropy models (MaxEnt) to obtain potential distribution and habitat association of wintering raptor species in semiarid Mediterranean region. The dataset includes information about the specie, date and location (UTM 30S coordinates) of each raptor record obtained.
DOI: 10.6084/m9.figshare.12410441
title: Supplementary Material for: Functional Decoupling of Language and Self-Reference Networks in Patients with Persistent Auditory Verbal Hallucinations

description: <b><i>Background:</i></b> Accumulating neuroimaging evidence suggests that abnormal intrinsic neural activity could underlie auditory verbal hallucinations (AVH) in patients with schizophrenia. However, little is known about the functional interplay between distinct intrinsic neural networks and their association with AVH. <b><i>Methods:</i></b> We investigated functional network connectivity (FNC) of distinct resting-state networks as well as the relationship between FNC strength and AVH symptom severity. Resting-state functional MRI data at 3 T were obtained for 14 healthy controls and 10 patients with schizophrenia presenting with persistent AVH. The data were analyzed using a spatial group independent component analysis, followed by constrained maximal lag correlations to determine FNC within and between groups. <b><i>Results:</i></b> Four components of interest, comprising language, attention, executive control networks, as well as the default-mode network (DMN), were selected for subsequent FNC analyses. Patients with persistent AVH showed lower FNC between the language network and the DMN (<i>p</i> &lt; 0.05, corrected for false discovery rate). FNC strength, however, was not significantly related to symptom severity, as measured by the Psychotic Symptom Rating Scale. <b><i>Conclusion:</i></b> These findings suggest that disrupted FNC between a speech-related system and a network subserving self-referential processing is associated with AVH. The data are consistent with a model of disrupted self-attribution of speech generation and perception.
DOI: 10.6084/m9.figshare.12410486.v1
title: GI-00211-2020 Supplementary Information.docx

description: <b>Table S1.</b> The relative expression levels of proteins in UC versus healthy controls by SWATH<b>Table S2.</b> Statistically significant GO term related to differentially regulated proteins in UC versus healthy controls by SWATH<b>Table S3.</b> Statistically significant KEGG pathways related to differentially regulated proteins in UC versus healthy controls by SWATH<br>
DOI: 10.6084/m9.figshare.12410492.v1
title: Distribution models of wintering raptor species in a semiarid Mediterranean region

description: We provided the presence data of the raptors that we compiled through of two sources (census itineraries and citizen science data) throughout the study period (2017-2018 and 2018-2019 winter periods) wich were used for the maximum entropy models (MaxEnt) to obtain potential distribution and habitat association of wintering raptor species in semiarid Mediterranean region. The dataset includes information about the specie, date and location (UTM 30S coordinates) of each raptor record obtained.
DOI: 10.6084/m9.figshare.12410441.v1
title: Supplementary Material for: Functional Decoupling of Language and Self-Reference Networks in Patients with Persistent Auditory Verbal Hallucinations

description: <b><i>Background:</i></b> Accumulating neuroimaging evidence suggests that abnormal intrinsic neural activity could underlie auditory verbal hallucinations (AVH) in patients with schizophrenia. However, little is known about the functional interplay between distinct intrinsic neural networks and their association with AVH. <b><i>Methods:</i></b> We investigated functional network connectivity (FNC) of distinct resting-state networks as well as the relationship between FNC strength and AVH symptom severity. Resting-state functional MRI data at 3 T were obtained for 14 healthy controls and 10 patients with schizophrenia presenting with persistent AVH. The data were analyzed using a spatial group independent component analysis, followed by constrained maximal lag correlations to determine FNC within and between groups. <b><i>Results:</i></b> Four components of interest, comprising language, attention, executive control networks, as well as the default-mode network (DMN), were selected for subsequent FNC analyses. Patients with persistent AVH showed lower FNC between the language network and the DMN (<i>p</i> &lt; 0.05, corrected for false discovery rate). FNC strength, however, was not significantly related to symptom severity, as measured by the Psychotic Symptom Rating Scale. <b><i>Conclusion:</i></b> These findings suggest that disrupted FNC between a speech-related system and a network subserving self-referential processing is associated with AVH. The data are consistent with a model of disrupted self-attribution of speech generation and perception.
DOI: 10.6084/m9.figshare.12410348
title: Extended data

description: This contains the proteomic data tables obtained during analysis of the outcomes of the research titled "Towards understanding the cell surface phenotype, metabolic properties and immune functions of resident macrophages of the peritoneal cavity and splenic red pulp using high resolution quantitative proteomics"<br><br>
DOI: 10.6084/m9.figshare.12410372
title: 16S rRNA partial gene sequences of the bacterial strain LMJ (Bacterium strain clone LIB091_C05_1243 variant 16S ribosomal RNA; GenBank Accession # MN633292.1)

description: Dataset contains 2 abi extension files obtained from sequencing of the LMJ strain's 16S rRNA gene partially. There are 2 electropherogram files and corresponding text files of DNA sequences in the dataset. The 16S rRNA gene was partially amplified from LMJ and cloned in the TOPO-TA vector (Thermo Scientific Fisher) for DNA sequencing. Sanger dideoxy sequencing technology was used for DNA sequencing.<br>
DOI: 10.6084/m9.figshare.12410372.v1
title: 16S rRNA partial gene sequences of the bacterial strain LMJ (Bacterium strain clone LIB091_C05_1243 variant 16S ribosomal RNA; GenBank Accession # MN633292.1)

description: Dataset contains 2 abi extension files obtained from sequencing of the LMJ strain's 16S rRNA gene partially. There are 2 electropherogram files and corresponding text files of DNA sequences in the dataset. The 16S rRNA gene was partially amplified from LMJ and cloned in the TOPO-TA vector (Thermo Scientific Fisher) for DNA sequencing. Sanger dideoxy sequencing technology was used for DNA sequencing.<br>
DOI: 10.6084/m9.figshare.12410348.v2
title: Extended data

description: This contains the proteomic data tables obtained during analysis of the outcomes of the research titled "Towards understanding the cell surface phenotype, metabolic properties and immune functions of resident macrophages of the peritoneal cavity and splenic red pulp using high resolution quantitative proteomics"<br><br>
DOI: 10.6084/m9.figshare.12410348.v1
title: Tissue macrophages proteome

description: Tissue macrophages proteome<br>
DOI: 10.6084/m9.figshare.12409646
title: Data.sav

description: Data in IBM SPSS. The .sav archive includes all the analyzed data, related to sociodemographic variables and the PICCOLO.
DOI: 10.6084/m9.figshare.12409556
title: IEEE 33-bus system and practical-scale system in Shandong

description: 1.<b> IEEE 33-bus system and practical-scale system in Shandong.xlsx</b>：Base case three-phase load profiles and branch parameters for the IEEE 33-bus distribution system and practical-scale system in Shandong.<br>2. <b>Historical_data_in_simulation.xlsx</b>：Historical data in simulation of the IEEE 33-bus distribution system and the introduction of data file Shandong_power_15min.mat.<br>3.<b> Shandong_power_15min.mat</b>: Historical data in simulation of practical-scale system in Shandong.
DOI: 10.6084/m9.figshare.12409562
title: Supplemental table 3.docx

description: Systolic arterial pressure, DAP, MAP and HR declined (time, p&lt;0.01) similarly for older men and women and younger men and women (group × time, p&gt;0.05, supplemental <b>Table 3</b>) during the 3min recovery from the CPT. MSNA burst incidence trended towards recovering differently between groups (group × time, p=0.05, supplemental <b>Table 3</b>) because older men did not have the same increase during CPT and therefore had little changes throughout recovery, where older women and young men and women all declined similarly through the 3min recovery. MSNA frequency declined (time, p&lt;0.01) similar to that of MSNA incidence (group × time, p=0.06, supplemental <b>Table 3</b>). Recovery of total MSNA amplitude (%) was elevated at baseline at 30s of recovery for the younger men and women and then declined to baseline levels from 60s-180s, with no differences from baseline throughout recovery for the older men and women (group × time interaction, p=0.03, supplemental <b>Table 3).</b>
DOI: 10.6084/m9.figshare.12409562.v1
title: Supplemental table 3.docx

description: Systolic arterial pressure, DAP, MAP and HR declined (time, p&lt;0.01) similarly for older men and women and younger men and women (group × time, p&gt;0.05, supplemental <b>Table 3</b>) during the 3min recovery from the CPT. MSNA burst incidence trended towards recovering differently between groups (group × time, p=0.05, supplemental <b>Table 3</b>) because older men did not have the same increase during CPT and therefore had little changes throughout recovery, where older women and young men and women all declined similarly through the 3min recovery. MSNA frequency declined (time, p&lt;0.01) similar to that of MSNA incidence (group × time, p=0.06, supplemental <b>Table 3</b>). Recovery of total MSNA amplitude (%) was elevated at baseline at 30s of recovery for the younger men and women and then declined to baseline levels from 60s-180s, with no differences from baseline throughout recovery for the older men and women (group × time interaction, p=0.03, supplemental <b>Table 3).</b>
DOI: 10.6084/m9.figshare.12409556.v1
title: IEEE 33-bus system and 337-bus practical system

description: Base case three-phase load profiles and branch parameters for the IEEE 33-bus distribution system and 337-bus practical system.
DOI: 10.6084/m9.figshare.12409520
title: Data for Antimicrobial Susceptibility Prevalence in Cotonou-Benin

description: A retrospective analysis was carried out on results and antibiograms of cultures of urine and vaginal swabs from suspected cases of UTI and VI respectively, at the Medical Biology Laboratory of IRGIB-Africa University, Cotonou, Benin. The sex and age of patients as well as the species of isolated bacteria and their respective antibiotic susceptibility data were collected from the registration records. The data of patients with ages of less than a year were excluded.<br>
DOI: 10.6084/m9.figshare.12409433
title: BigWig files

description: ChIP-SEq data
DOI: 10.6084/m9.figshare.12409556.v2
title: IEEE 33-bus system and 337-bus practical system

description: Base case three-phase load profiles and branch parameters for the IEEE 33-bus distribution system and 337-bus practical system.
DOI: 10.6084/m9.figshare.12409433.v1
title: BigWig files

description: ChIP-SEq data
DOI: 10.17637/rh.12409394
title: Sulfide pore network model results

description: This dataset contains results of pore network modeling of microtomographic images of experimentally annealed olivine and Fe-FeS liquids.<br>
DOI: 10.6084/m9.figshare.12409556.v3
title: IEEE 33-bus system and practical-scale system in Shandong

description: Base case three-phase load profiles and branch parameters for the IEEE 33-bus distribution system and practical-scale system in Shandong.
DOI: 10.17637/rh.12409394.v1
title: Sulfide pore network model results

description: This dataset contains results of pore network modeling of microtomographic images of experimentally annealed olivine and Fe-FeS liquids.<br>
DOI: 10.6084/m9.figshare.12409379
title: Supplementary Material for: Factors Influencing Electrode Position and Bending of the Proximal Lead in Deep Brain Stimulation for Movement Disorders

description: <b><i>Background:</i></b> The introduction of intracranial air (ICA) during deep brain stimulation (DBS) surgery is thought to have a negative influence on targeting and clinical outcomes. <b><i>Objective:</i></b> To investigate ICA volumes following surgery and other patient-specific factors as potential variables influencing translocation of the DBS electrode and proximal lead bowing. <b><i>Methods:</i></b> High-resolution postoperative computed tomography scans (≤1.0 mm resolution in all directions) within 24 h following DBS surgery and 4–6 weeks of follow-up were acquired. A total of 50 DBS leads in 33 patients were available for analysis. DBS leads included Abbott/St. Jude Medical Infinity<sup>TM</sup>, Boston Scientific Vercise<sup>TM</sup>, and Medtronic 3389<sup>TM</sup>. <b><i>Results:</i></b> Both ICA volume and anatomical target were significantly associated with measures of DBS electrode translocation. ICA volume and DBS lead model were found to be significant predictors of proximal lead bowing. Measures of proximal lead bowing and translocation along the electrode trajectory for the Medtronic 3389<sup>TM</sup> DBS lead were significantly larger than measures for the Abbott/St. Jude Medical Infinity<sup>TM</sup> and Boston Scientific Vercise<sup>TM</sup> DBS leads. <b><i>Conclusion:</i></b> The association between ICA volume and translocation of the DBS electrode is small in magnitude and not clinically relevant for DBS cases within a normal range of postoperative subdural air volumes. Differences in proximal lead bowing observed between DBS leads may reflect hardware engineering subtleties in the construction of DBS lead models.
DOI: 10.6084/m9.figshare.12409181
title: Genome-Wide Association Study and Gene Specific Markers Identified a Large Number of Genes or QTL for Resistance to Stripe Rust in U.S. Winter Wheat Cultivars and Breeding Lines

description: To determine stripe rust resistance genes in U.S. winter wheat cultivars and breeding lines, we analyzed a winter wheat panel of 857 cultivars and breeding lines in a genome-wide association study (GWAS) using genotyping by multiplexed sequencing (GMS) and by genotyping with molecular markers of 18 important stripe rust resistance genes or quantitative trait loci (QTL).The 31 markers for the 18 previously reported <i>Yr</i> genes or QTL were successfully tested in the 857 winter wheat accessions and/or reference genotypes. The presence and absence of the markers are provided in Supplementary Table S3. The GMS-GWAS analysis identified 36 loci on 15 chromosomes (1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 5A, 5B, 5D, 6A, 6B, 7A, and 7B) significantly associated with stripe rust resistance in Supplementary Table S4.
DOI: 10.6084/m9.figshare.12409016
title: Three Sensitizing Dimensions of Quality, Epistemological Access and Student Satisfaction

description: This is a cross sectional survey from the university students.
DOI: 10.6084/m9.figshare.12408881
title: Supplementary Material for: An International Survey of Mediastinal Staging Practices amongst Interventional Bronchoscopists

description: <b><i>Introduction:</i></b> In potentially curable non-small-cell lung cancer, different practice guidelines recommend invasive me­diastinal staging in tumors larger than 3 cm, central, or hy­permetabolic N1 lymph nodes. There is no consensus concerning the use of an endosonographic procedure or a mediastinoscopy in the first line in patients with a radiologically normal mediastinum, while in case of a mediastinal involvement, the latest European guidelines recommend the combination of endobronchial ultrasound (EBUS) and endoscopic ultrasound/endoscopic ultrasound with EBUS endoscope (EUS/EUS-B), using a systematic endosonographic procedure. This international survey was conducted to describe current medical practices in endoscopic mediastinal staging amongst interventional bronchoscopists. <b><i>Methods:</i></b> A survey was developed and sent to all members of different interventional pulmonology societies, with the purpose to describe who, when and how an endoscopic mediastinal staging was performed. <b><i>Results:</i></b> One hundred and fifty-three bronchoscopists responded to the survey. Most of them practiced in Europe (<i>n</i> = 84, 55%) and North America (<i>n</i> = 52, 34%). In the first line, EBUS alone was the most widely used endoscopic procedure for mediastinal staging. Half of the responders performed a systematic endoscopic staging procedure, including a systematic examination of all accessible nodal stations and a sampling of all lymph nodes &gt;5 mm in the short axis at each station. A higher proportion of bronchoscopists who have completed a dedicated fellowship program performed systematic endoscopic mediastinal staging. Few endoscopists routinely perform combined EBUS/EUS(-B) for mediastinal staging and use the combination only in selected cases. <b><i>Conclusion:</i></b> There are several areas of divergence between published guidelines and current practices reported by interventional bronchoscopists. EBUS alone is the most widely used endoscopic procedure for mediastinal staging in lung cancer, and a combined endoscopic approach is frequently omitted by the responders. A fellowship program appears to be associated with a higher rate of systematic endoscopic staging procedures.
DOI: 10.6084/m9.figshare.12408860
title: Temperature data: summaries

description: Summaries of SST data
DOI: 10.6084/m9.figshare.12408857
title: Temperature data: max and min SST

description: .tif files of maximum and minimum sea surface temperatures between 2010 and 2018 as obtained from MODIS-Aqua
DOI: 10.6084/m9.figshare.12408860.v1
title: Temperature data: summaries

description: Summaries of SST data
DOI: 10.6084/m9.figshare.12408866
title: Raw Data and Code

description: Contains all raw data and code necessary to reproduce the results in Brandl et al.