cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26340565.v1
title: high-quality_bacterial_bins

description: The temporal dynamics of phage-host interactions in full-scale wastewater treatment plants (WWTP) remain poorly understood. Here, we investigated viral and bacterial dynamics over a nine-year period in an activated sludge WWTP employing bleach addition for sludge foaming control. Metagenomic analysis of 98 time-series samples yielded 3,486 high-quality bacterial bins and 2,435 complete or near-complete viral genomes, grouped into 361 bacterial and 889 viral clusters, respectively. Through CRISPR analysis, we identified 45 virus-host pairs (VHPs) at the bacterial species level. Our findings revealed that the primary bleaching event significantly altered both host and viral dynamics, as well as virus-host relationships as evidenced by changes in virus-to-host ratios. The viral community exhibited similar shifts to the bacterial community following bleaching, suggesting a strong coupling of phage-host interactions. Linear regression analyses of viral and bacterial abundances unveiled complex phage-host dynamics, with many VHPs exhibiting positive slopes significantly &lt; 1, especially for viruses harboring integrase genes, suggesting the prevalence of Piggyback-the-Winner (PtW)-like temperate dynamics. Notably, we found that bleaching treatment appeared to trigger a shift from lysogeny to lysis for the viruses associated with certain foaming-related bacterial species. Such intrinsic biological interactions may contribute to the sustained control of sludge foaming issues.
DOI: 10.6084/m9.figshare.20939335.v1
title: UMAP visualization of WBC and RBC morphotypes

description: JSON files containing UMAP coordinates for WBC and RBC morphometry and their morphotype classification.
DOI: 10.6084/m9.figshare.27936345.v1
title: Data for <b>Decelerating Runoff Response to Declining Snowpacks in the Warming Western U.S.</b>

description: This dataset contains the needed data for manuscript Decelerating Runoff Response to Declining Snowpacks in the Warming Western U.S.Data includes sub-basin delineated shapefiles for the three major river basins (PNW, UCRB, and CA), parameters for VIC historical simulation, long-term average outputs of VIC control-warming experiments and sub-basin averaged GCM-VIC outputs.
DOI: 10.6084/m9.figshare.28633340.v1
title: Joint Angle Data for "Quantifying the Effect of Anthropometric Assumptions on Upper Limb Joint Angles Derived from Inverse Kinematics".

description: Data supporting the publication of the study entitled Quantifying the Effect of Anthropometric Assumptions on Upper Limb Joint Angles Derived from Inverse Kinematics. The data includes joint angles calulated using inverse dynamic simulations with two methods of segment length definitions.Files named idSubject_#_Euler_Averaged and idSubject_#_Euler_Individual contain joint angle trajectories during single reaches toward targets in different spatial locations. The angles were calulated using either averaged or individual segment length definition respectively. metaSignal.csv contains meta information on the degrees of freedom that define each angle.metaTrialType.csv contains meta information about the target location relative to the central target in angular notation within each plane. All targets were equidistal from the central target. Reaching was done from the central target to one of the outward targets and return.metaTrial.csv contains meta information that relates the idTrials in raw data files to the corresponding target and subject IDs.StatsTable.csv contains meta information from ANOVA.<br><br>
DOI: 10.6084/m9.figshare.24873438.v1
title: skills addressed.docx

description: The table shows 21st-century skills addressed in each of the studies regarding rural STEM educational tool.
DOI: 10.6084/m9.figshare.5126995.v1
title: Supplementary Material for: Assessment of the Pharmacogenomics Educational Environment in Southeast Europe

description: <b><i>Background/Aims:</i></b> Pharmacogenomics aims to use the information derived from an individual's genomic profile in the context of individualizing medical treatment modalities. However, currently, pharmacogenomics education is not uniformly provided to health care professionals. This study investigates the status of pharmacogenomics education in Southeast Europe. <b><i>Methods:</i></b> University websites served as information sources in order to investigate the discrepancies in pharmacogenomics education in Southeast Europe. In parallel, a survey was conducted at the University of Cagliari (Italy) to test pharmacogenomics knowledge and understanding among specialists, residents and undergraduate students. <b><i>Results:</i></b> Our study shows that pharmacogenomics knowledge is not uniformly spread in universities in Southeast Europe and provides the basis for the harmonization of pharmacogenomics education that would directly impact on a smoother integration of pharmacogenomics into mainstream medical practice. Also, a considerable gap in pharmacogenomics education was obvious between the group of specialists and the groups of residents and undergraduate students. <b><i>Conclusions:</i></b> Pharmacogenomics education as well as the continuous enrichment of pharmacogenomics knowledge for health care professionals are fundamental approaches toward personalized medicine. Ideally, pharmacogenomics should be taught as a stand-alone course or at least in the context of genetics courses that already exist in universities in Southeast Europe.
DOI: 10.6084/m9.figshare.14152679.v1
title: Supplementary Material for: Incidence of Cognitive Impairment during Aging in Rural South Africa: Evidence from HAALSI, 2014 to 2019

description: <b><i>Introduction:</i></b> Despite rapid population aging, there are currently limited data on the incidence of aging-related cognitive impairment in sub-Saharan Africa. We aimed to determine the incidence of cognitive impairment and its distribution across key demographic, social, and health-related factors among older adults in rural South Africa. <b><i>Methods:</i></b> Data were from in-person interviews with 3,856 adults aged ≥40 who were free from cognitive impairment at baseline in the population-representative cohort, “Health and Aging in Africa: a Longitudinal Study of an INDEPTH Community in South Africa” (HAALSI), in Agincourt sub-district, Mpumalanga province, South Africa (2014–19). Cognitive impairment was defined as scoring &lt;1.5 standard deviations below the mean of the baseline distribution of orientation and episodic memory scores. Incidence rates and rate ratios for cognitive impairment were estimated according to key demographic, social, and health-related factors, adjusted for age, sex/gender, and country of birth. <b><i>Results:</i></b> The incidence of cognitive impairment was 25.7/1,000 person-years (PY; 95% confidence interval [CI]: 23.0–28.8), weighted for mortality (12%) and attrition (6%) over the 3.5-year mean follow-up (range: 1.5–4.8 years). Incidence increased with age, from 8.9/1,000 PY (95% CI: 5.2–16.8) among those aged 40–44 to 93.5/1,000 PY (95% CI: 75.9–116.3) among those aged 80+, and age-specific risks were similar by sex/gender. Incidence was strongly associated with formal education and literacy, as well as marital status, household assets, employment, and alcohol consumption but not with history of smoking, hypertension, stroke, angina, heart attack, diabetes, or prevalent HIV. <b><i>Conclusions:</i></b> This study presents some of the first incidence rate estimates for aging-related cognitive impairment in rural South Africa. Social disparities in incident cognitive impairment rates were apparent in patterns similar to those observed in many high-income countries.
DOI: 10.6084/m9.figshare.24646248.v1
title: Potential Distribution of Global Wetlands_PDGW.rar

description: Dataset for "Global wetlands: Potential distribution, wetland loss, and status."
DOI: 10.6084/m9.figshare.12357593.v1
title: Perceived stress and well-being of Polish migrants in the UK after Brexit vote

description: <b><i>Objective:</i></b> This study aimed to investigate factors affecting personal well-being of Polish immigrants living in the UK in the face of a significant political change - the Brexit vote. Possible perceived changes in attitude or behaviour of supervisors and co-workers of Polish migrants, their perceived stress, and its consequences on their psychological well-being and intention to leave the UK after the Brexit vote were subject to statistical analysis. <b><i>Method:</i></b> 551 Polish migrants residing in various regions of the UK took part in the study in the form of Qualtrics online survey. We used self-report measures: Perceived Stress Scale, The Satisfaction with Life Scale, Scale of Psychological Well-being. <b><i>Results:</i></b> Negative change in attitude or behaviour of supervisors or co-workers are associated with perceived stress, and later is linked with intention to leave the UK and decrease in positive outcomes: psychological well-being and life satisfaction. <b><i>Conclusion:</i></b> Further study should consider personal psychological resources, for instance, in the form of coping strategies that might influence the well-being of immigrants due to external political conditions.
DOI: 10.6084/m9.figshare.13049690.v1
title: In Vitro and In Situ Induction of Myogenic Stem Cells for Muscle Regeneration

description: Raw data for the article published in Nature Biomedical Engineering. Title: In Vitro and In Situ Induction of Myogenic Stem Cells for Muscle Regeneration
DOI: 10.6084/m9.figshare.28244198.v2
title: Datasets for Ma and Hull - Impact of wavelength, exposure sequence, and organic matter on UVdisinfection and DNA repair

description: UV disinfection testing was performed on E. coli and MS2 under various experimental conditions to evaluate the impact of natural organic matter (NOM), sequence of UV-C wavelength (222 vs 265 nm), and pre-irradiation by UV-A 365 nm. Culture and molecular enumeration techniques were used to quantify bacteria counts and DNA damage in E. coli. UV inactivation effectiveness was measured by quantifying the log inactivation before and after UV exposure. Regrowth of bacteria was measured by culturing bacteria for 24 hours after UV exposure in light or dark conditions. Photorepair fluence was calculated to quantify the exposure to photorepair light over the 24 hours. DNA damage and repair was quantified using CPD ELISA (Cell Biolabs STA-322) to measure the presence of CPDs in non-irradiated, irradiated, light, and dark repair samples. Electrical energy per order (EEO) disinfection (kWh/m3) was calculated for treatment conditions to evaluate the energy cost to achieve comparable levels of treatment.
DOI: 10.6084/m9.figshare.13182947.v3
title: Efficacy of quetiapine for delirium prevention in hospitalized older medical patients: A randomized double-blind controlled trial

description: Data and information of all participants in research "Efficacy of quetiapine for delirium prevention in hospitalized older medical patients: A randomized double-blind controlled trial"
DOI: 10.6084/m9.figshare.23803653.v1
title: Supplementary Material for: Circadian clock genes are regulated by rhythmic corticosterone at physiological levels in the rat hippocampus

description: Introduction: In the hippocampus, clock gene expression is important for memory and mood; however, the signaling mechanism controlling clock gene expression in the hippocampus is unknown. Recent findings suggest that circadian glucocorticoid rhythms driven by the suprachiasmatic nucleus (SCN) control rhythmic clock gene expression in neurons; in addition, dexamethasone modulates hippocampal clock gene expression. We therefore hypothesized that oscillations of clock genes in the hippocampus could be driven by SCN-controlled circadian rhythms in glucocorticoids. Methods: Temporal profiles of hippocampal clock gene expression were established by qRT-PCR on rat hippocampi, while cellular distribution was established by in situ hybridization. To determine the effect of rhythmic glucocorticoids on hippocampal clock gene expression, the SCN was lesioned, adrenal glands removed and a 24h exogenous corticosterone rhythm at physiological levels was reestablished by use of a programmable infusion pump. Results: Daily rhythms were detected for Per1, Per2, Bmal1, Nr1d1, and Dbp, while clock gene products were confirmed in both the hippocampus proper and the dentate gyrus. In sham controls, differential hippocampal expression of Per1 and Dbp between ZT3 and ZT15 was detectable. This rhythm was abolished by SCN-lesion; however, reestablishing the natural rhythm in corticosterone restored differential rhythmic expression of both Per1 and Dbp. Further, a 6h phase-delay in the corticosterone profile caused a predictable shift in expression of Nr1d1. Conclusion: Our data show that rhythmic corticosterone can drive hippocampal clock gene rhythms suggesting that the SCN regulates the circadian oscillator of the hippocampus by controlling the circadian rhythm in circulating glucocorticoids.
DOI: 10.6084/m9.figshare.22579267.v2
title: BSC Data

description: Data is that used for this project to map BSCs and characterize their spatial patterns
DOI: 10.6084/m9.figshare.3824451.v3
title: Simulation data

description: Simulation data for a calcium adatom on doped graphene.<br>
DOI: 10.6084/m9.figshare.14540394.v1
title: Supplementary Material for: Safety and Suitability of the SmartPill® after Abdominal Surgery: Results of the Prospective, Two-Armed, Open-Label PIDuSA Trial

description: <b><i>Introduction:</i></b> Postoperative ileus (POI) is a common complication after abdominal surgery. Until today, an evidence-based treatment of prolonged POI is still lacking, which can be attributed to the poor quality of clinical trials. Various different surrogate markers used to define POI severity are considered to be the cause of low-quality trials making it impossible to derive treatment recommendation. The SmartPill®, which is able to record pH values, temperature and pressure after ingestion, could be an ideal tool to measure transit times and peristalsis and therefore analyze POI severity. Unfortunately, the device has no approval for postoperative use due to safety concerns. The primary objective of the study is to determine safety of the SmartPill® in patients undergoing surgery. Secondary objectives were the quality of the recorded data and the suitability of the SmartPill® for analyzing intestinal motility after different surgical procedures. <b><i>Methods:</i></b> The PIDuSA Study is a prospective, 2-arm, open-label trial. At the end of surgery, the SmartPill® was applied to 49 patients undergoing abdominal surgery having a high risk for impaired intestinal motility and 15 patients undergoing extra-abdominal surgery. Patients were visited daily to access safety data of the SmartPill® on the basis of adverse and serious adverse events (AEs/SAEs). Suitability and data quality were investigated by analyzing data completeness and feasibility to determine transit times and peristalsis for all sections of the gastrointestinal tract. <b><i>Results:</i></b> In total, 179 AEs and 8 SAEs were recorded throughout the study affecting 42 patients in the abdominal (158 AEs) and 9 patients in the extra-abdominal surgery group (21 AEs, <i>p</i> = 0.061); none of them were device related. Primary capsule failure was observed in 5 patients, ultimately resulting in an impossibility of data analysis in only 3 patients (4.4%). 9% of the recorded data were incomplete due to the patient’s incompliance in keeping the receiver close to the body. In 3 patients (4.4%), isolated small bowel transit could not be determined due to pH alterations as a result of prolonged POI. <b><i>Discussion:</i></b> Our study demonstrates that the use of the SmartPill® is safe after surgery but requires a reasonable patient compliance to deliver meaningful data. An objective analysis of transit times and peristalsis was possible irrespective of type and site of surgery in over 95% indicating that the SmartPill® has the potential to deliver objective parameters for POI severity in future clinical trials. However, in some patients with prolonged POI, analysis of small bowel transit could be challenging.
DOI: 10.6084/m9.figshare.1575662.v1
title: Genome-wide analysis of microsatellite markers based on sequenced database in Chinese SpringWheat ( Tr.aestivum. L )

description: SSR characters from chinese spring wheat
DOI: 10.6084/m9.figshare.17230490.v1
title: Temperature data

description: Temperature records of experimental and control plots.
DOI: 10.6084/m9.figshare.6736997.v2
title: The mitotic spindle is chiral due to torques within microtubule bundles

description: Scientific data from paper: The mitotic spindle is chiral due to torques within microtubule bundles<br>Bundles in 3D images of metaphase spindles of human cells were tracked manually using Multi-point tool in Fiji (ImageJ).<br>Attached tables contain the coordinates (x, y, z) of all bundles and spindle poles. Coordinates of bundles and poles from images of spindles were transformed so that both poles are on the z-axis. First and last row of each table contain coordinates of spindle poles.<br><br><br>
DOI: 10.6084/m9.figshare.16563888.v1
title: Vegetation Succession in Elk Exclosures of Olympic National Park

description: Data describe changes in abundance of herbs, ferns, shrubs and trees inside and outside of elk exclosures over 36 years in Olympic National Park. Data were collected annually early in the time series and subsequently less frequently. Two exclosures sited on different alluvial terraces were sampled within old-growth Sitka spruce-Douglas fir forests on the western side of the Olympic Peninsula in Olympic National Park. Roosevelt elk were the primary herbivore with much lesser effects from Columbia black-tailed deer. Changes in elk density outside of the exclosure varied over time and was quantified for some of the time period.
DOI: 10.6084/m9.figshare.28621220.v1
title: Head-on bites (Siganus magnificus)

description: Head-on bites from Siganus magnificus. ID= identification of the specific bite. landmark= name of the landmark. x_mm and y_mm = standardised landmarks for each timestep. Time= standardised timesteps.
DOI: 10.6084/m9.figshare.21695837.v1
title: E8.5_Embryo1.h5ad

description: 3D registered data of E8.5 embryo_1 for <em>sc3D-visualizer</em>
DOI: 10.6084/m9.figshare.2875591.v1
title: Data of a science knowledge test: Simulation of item preknowledge

description: Context If test items are known in advance (item preknowledge) the validity of a test is in jeopardy. How can we know if this has happened? Methods In order to simulate how data would look like if some test takers possessed item preknowledge we compromised two original datasets: Responses to a predetermined set of items were set to correct for 10% of test takers, randomly selected. In reruns, the proportion was varied to be 5%, 2.5%, and 1%. Item difficulty, item discrimination, item fit, and local dependence were computed using an IRT 2PL model. Then changes in these item properties from the non-compromised to the compromised dataset were scrutinized for their sensitivity to item preknowledge. Data In each file the responses to a test with 80 items are given (0 = not correct / 1= correct). The compromised datasets (that contain simulated test takers with item preknowledge) are flagged with the suffix _pX, where X desribes the prevalence of item preknowledge.
DOI: 10.6084/m9.figshare.15656697.v1
title: covid_first_wave.xlsx

description: Daily case of the first wave of covid-19 in Madagascar
DOI: 10.6084/m9.figshare.28816295.v1
title: <b>Supplementary Table S1: </b>Phytochemicals data extracted from IMPPAT

description: This study focuses on identifying potential antibacterial phytochemicals in medicinal plants using an in silico approach. We performed molecular docking, ADMET analysis, and 3D interaction visualization to evaluate the binding affinities of selected compounds against MexAB-OprM efflux pump proteins of <i>Pseudomonas aeruginosa</i>. Notably, Beta-Eudesmol, Aromadendrene, and Spathulenol showed strong binding to MexB and OprM subunits, indicating potential as efflux pump inhibitors. Our findings provide valuable insights into plant-based alternatives for combating multidrug resistance.
DOI: 10.6084/m9.figshare.6837956.v2
title: inDelphi-LibA+LibB-processed-indel-data

description: This folder contains processed data of indels from our experiments in two libraries of 2000 designed sequences for the inDelphi work, using code from https://github.com/maxwshen/indelphi-dataprocessinganalysis.<br><br>Note: mES-Cas9-Tol2-BioRep1-r1.csv is misnamed, it should be mES-Lib1-Cas9-Tol2-BioRep1-r1.csv.
DOI: 10.6084/m9.figshare.4040124.v3
title: loghub

description: This is a sample log of HDFS dataset. Please visit our project page for the full set of system logs: https://github.com/logpai/loghub
DOI: 10.6084/m9.figshare.5171752
title: Postoperative neoadjuvant temozolomide before radiotherapy versus standard radiotherapy in patients 60 years or younger with anaplastic astrocytoma or glioblastoma: a randomized trial

description: <b>Introduction:</b> A pilot study of temozolomide (TMZ) given before radiotherapy (RT) for anaplastic astrocytoma (AA) and glioblastoma (GBM) resulted in prolonged survival compared to historical controls receiving RT alone. We therefore investigated neoadjuvant TMZ (NeoTMZ) in a randomized trial. During enrollment, concomitant and adjuvant radio-chemotherapy with TMZ became standard treatment. The trial was amended to include concurrent TMZ. <b>Patients and methods:</b> Patients, after surgery for GBM or AA, age ≤60 years and performance status (PS) 0–2, were randomized to either 2–3 cycles of TMZ, 200 mg/m<sup>2</sup> days 1–5 every 28 days, followed by RT 60 Gy in 30 fractions or RT only. Patients without progressive disease after two TMZ cycles, received the third cycle. From March 2005, TMZ 75 mg/m<sup>2</sup> was administered daily concomitant with RT. TMZ was recommended first-line treatment at progression. Primary endpoint was overall survival and secondary safety. <b>Results:</b> The study closed prematurely after enrolling 144 patients, 103 with GBM and 41 with AA. Median age was 53 years (range 24–60) and 89 (62%) were male. PS was 0–1 for 133 (92%) patients, 53 (37%) had complete surgical resection and 18 (12%) biopsy. Ninety-two (64%) received TMZ concomitant with RT. Seventy-two (50%) were randomized to neoadjuvant treatment. For the overall study population survival was 20.3 months for RT and 17.7 months for NeoTMZ (<i>p</i> = .76), this not reaching the primary objective. For the preplanned subgroup analysis, we found that NeoTMZ AA patients had a median survival of 95.1 months compared to 35.2 months for RT (<i>p</i> = .022). For patients with GBM, no difference in survival was observed (<i>p</i> = .10). MGMT and IDH status affected outcome. <b>Conclusions:</b> No advantage of NeoTMZ was noted for the overall study population or subgroup of GBM, while NeoTMZ resulted in 5 years longer median survival for patients diagnosed as AA.
DOI: 10.6084/m9.figshare.11342630.v1
title: THE DATA COLLECTION OF Saccharomyces cerevisiae TURBIDITY MODELING IN LIQUID MEDIA

description: Numeric processing on analysis and diagnostic dataset of relationship between light spectrum and cell particles of <i>S cerevisiae</i> was performed to result models. The one model should be chosen and the relationship of that consists of the model for standard curve on turbidimetry and the cell that were growing in liquid nutrients medium. The numeric processing used the statistical application from International Business Machine (IBM) v.16.0, Excel under Windows 10 OS, R v3.6.1, and the statistic principles were used for Biology system. This document consists of Tables, sketch (electronic) and image (camera) figures.