cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22644550.v1
title: Supplementary Material for: Diagnostic and Prognostic Performance of Serum Albumin and Cholinesterase in Patients with Sepsis and Septic Shock

description: Background: Despite improved risk stratification tools and identification of novel biomarkers, sepsis-related mortality has not significantly improved during the past years. Objective: This study investigates the diagnostic and prognostic role of the serum albumin and cholinesterase (ChE) in patients with sepsis and septic shock. Methods: Consecutive patients with sepsis and septic shock from 2019 to 2021 were included. Blood samples were retrieved from day of disease onset (day 1), day 2,3,5 and 7. Firstly, the diagnostic value of the serum albumin for the diagnosis of a septic shock was compared to the ChE. Secondly, the prognostic value of the serum albumin and the ChE for 30-day all-cause mortality was tested. Results: A total of 239 patients were included. With an area under the curve (AUC) of 0.641 to 0.762 on day 3 and 5, the ChE revealed a moderate but better diagnostic discrimination between sepsis and septic shock than the serum albumin. Furthermore, the ChE was able to discriminate between non-survivors and survivors of the 30-day time inter-val (range of AUC 0.612 to 0.686). Patients with a ChE below the median had higher rates of 30-days all-cause mortality in comparison to patients with a ChE above the median (65% vs. 42%, log rank p = 0.001; HR = 1.820; 95% CI 1.273 – 2.601; p = 0.001). Conclusion: The ChE reflects a reliable diagnostic and prognostic tool in patients with sepsis and septic shock.
DOI: 10.6084/m9.figshare.12448997.v1
title: JARVIS-DFT Finite Difference Elastic Constants (JVASP-12330 to JVASP-14180)

description: Contains input/output files for finite difference method based elastic calculations in the JARVIS-DFT.
DOI: 10.6084/m9.figshare.21804048.v7
title: Supplementary materials: Feeding spent hemp biomass to lactating dairy cows: effects on performance, nitrogen metabolism, milk components and quality, methane emission, and blood parameters

description: Spent hemp biomass (SHB) is a hemp byproduct after the extraction of cannabinoids and, although it is still illegal in the US to do so, it could be used as a feed ingredient for livestock in the future. For legalization to happen, it is essential to assess the effects of SHB on health and performance of animals. In our study, feeding SHB to lactating dairy cows revealed a relative low palatability of SHB but no effect on performance, activity, immune system, or methane production but improved nitrogen use efficiency. Data suggested a possible low-grade inflammation and a decrease in liver clearance. Overall, our data suggest SHB to be a safe feedstuff for dairy cows.
DOI: 10.1184/r1/14773335.v1
title: COVID air quality RAMP datasets

description: There are two data files uploaded into this project a description of each is shown here:<br><br><b>Rebecca_Spring2020_all_1hr</b>: (Spring 2020 pre- and post- covid closure data) first column has the date and time, on an hourly basis from March 1st 2020 through May 14th 2020, each column after that has a different RAMP location, data that was available is filled in in the appropriate location and time.<br><b>Mar2019_all_1hr</b>: (pre covid data) under the tab labelled Mar2019_all_1hr, first column has the date and time, on an hourly basis from March 1th 2019 through March 31st 2019, each column after that has a different RAMP location, data that was available is filled in in the appropriate location and time.<br>
DOI: 10.6084/m9.figshare.19361213.v1
title: Supplementary Material for: Effects of Exergaming on Physical and Cognitive Outcomes of Older Adults Living in Long-Term Care Homes: A Systematic Review

description: <b><i>Background:</i></b> Aging is often associated with increasing functional decline as measured by deterioration in mobility and activities of daily living. Older adults (OAs) living in residential long-term care (LTC) homes in particular may not engage in regular physical exercise, significantly increasing their risk of further cognitive and functional decline. Exergaming may hold promise for OAs by combining exercise and technology-based gaming systems, but evidence for its use in LTC is unknown. <b><i>Methods:</i></b> A systematic review was conducted to summarize the effects of exergaming interventions on physical, cognitive, and quality of life (QoL) outcomes for OAs (&gt;65 years of age) living in LTC. <b><i>Results:</i></b> Twenty-one studies involving 657 OAs living in LTC met the inclusion criteria. Most studies were associated with a high risk of bias and many used uncontrolled designs and small samples. Across studies, exergame interventions were associated with preliminary benefits relative to control conditions on standardized measures of physical outcomes (e.g., Timed Up & Go, 5-meter gait speed). No consistent effects were found for cognitive and QoL outcomes. <b><i>Conclusions:</i></b> Exergames might be a promising intervention to benefit the physical health of OAs (&gt;65 years) living in LTC, but more research is required to determine the effects of exergaming on physical health, as well as cognitive and QoL outcomes. More specifically, larger and more methodologically robust evaluations are needed.
DOI: 10.6084/m9.figshare.23259086.v2
title: Chatwoot - code revew analysis

description: Chatwoot data set for analysing code review tools: ESLint & SonarQube
DOI: 10.6084/m9.figshare.24579109.v3
title: Blastocystis genomes

description: Blastocystis tortoise isolate Rus-B (Blastoise) genome, Blastocystis ST1 JDR genome, Blastocystis ST1 NandII genome, Blastocystis ST3 DL genome, Blastocystis ST3 NMH genome, Blastocystis ST4 BT1 genome, Blastocystis Hermann's tortoise isolate, Blastocystis Rus-S (Steve) genome
DOI: 10.6084/m9.figshare.28805657.v1
title: <b>Developing heterospecific Sterile Insect Technique for pest control: insights from the spotted wing fly </b><b><i>Drosophila suzukii</i></b>

description: <b>Background</b><b>:</b> Reproductive interference (i.e., sexual interaction between males of one species and females of another species that reduce the fitness of one or both the interacting individuals) is an important species interaction significantly affecting population dynamics and persistence. However, its exploitation in pest control remains overlooked. Here, we investigated the possible integration of reproductive interference into the Sterile Insect Technique (SIT) to develop a heterospecific SIT (h-SIT). Under this approach, contrary to the classic SIT, sterile heterospecific males from closely related, non-pest species are released to compete with the pest population for mates. At this aim, we focused on the invasive pest species <i>Drosophila suzukii</i> and used <i>D. melanogaster</i> as the control species. First, we investigated we investigated the effect of irradiation on D. melanogaster sterility and longevity. Then, we tested the mating performance of irradiated males and their ability to reduce the D. suzukii fitness.<b>Results:</b> We found by microcosm experiments that: i) irradiation induced high levels of <i>D. melanogaster</i> male sterility without reducing longevity; ii) irradiated <i>D. melanogaster</i> males court <i>D. suzukii</i> females as much as <i>D. suzukii</i> males and they couple, mate and fecund heterospecific females; iii) irradiated <i>D. melanogaster</i> males significantly reduce the offspring of <i>D. suzukii</i> females under two different species ratios.<b>Conclusion:</b> Our results provide the first foundation to develop a heterospecific Sterile Insect Technique against <i>D. suzukii</i> and fuel to test this approach against other groups of pest species.
DOI: 10.6084/m9.figshare.19669047.v1
title: Data File 3.csv

description: Data file for Power spectral analysis at the corresponding axial depths plot in Fig.5J
DOI: 10.6084/m9.figshare.11881332.v9
title: Development and Evaluation of a Low-Cost Data Acquisition System using Heterogeneous Sensors

description: Acquiring the human’s musculoskeletal movements is pivotal in conducting physiotherapeutic studies, rehabilitation exercises and, designing assistive devices to cater mobility impairments. Existing studies are generally more focused on measuring a specific phenomenon and/or lack the diversity needed to cover a range of human activities. In this context, the research presented herein is aimed to develop a low-cost wearable sensory system, having a diverse set of sensors, which can acquire data of healthy and rehabilitated subjects alike during diverse locomotor activities in both indoor and outdoor environments. The system consists of twenty wearable sensors, and two off-the-shelf NI’s myRIO microcontroller boards. The statistical analysis showed no significant difference between and among the subjects for various locomotor activities (P-values &lt; 0.05), hence, showing the system’s reliability and reproducibility. Gait-event identification (i.e., heel contact/toe off) has also been evaluated and showed promising results (overall time difference= ±50ms during level ground and ramp activities).
DOI: 10.6084/m9.figshare.19866634.v1
title: levine-CyTOF-AML-Healthy-AML-annData

description: Subset of Data from Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis (10.1016/j.cell.2015.05.047).
DOI: 10.6084/m9.figshare.28691480.v1
title: Parameter Definitions and Proofs

description: Parameter Definitions and Proofs
DOI: 10.6084/m9.figshare.3439049.v1
title: Supplementary Material for: The Relative Functionality of Freshly Isolated and Cryopreserved Human Adipose-Derived Stromal/Stem Cells

description: The capability of multipotent mesenchymal stem cells to maintain cell viability, phenotype and differentiation ability upon thawing is critical if they are to be banked and used for future therapeutic purposes. In the present study, we examined the effect of 9-10 months of cryostorage on the morphology, immunophenotype, colony-forming unit (CFU) and differentiation capacity of fresh and cryopreserved human adipose-derived stromal/stem cells (ASCs) from the same donors. Cryopreservation did not reduce the CFU frequency and the expression levels of CD29, CD73, CD90 and CD105 remained unchanged with the exception of CD34 and CD45; however, the differentiation capacity of cryopreserved ASCs relative to fresh cells was significantly reduced. While our findings suggest that future studies are warranted to improve cryopreservation methods and agents, cryopreserved ASCs retain sufficient features to ensure their practical utility for both research and clinical applications.
DOI: 10.6084/m9.figshare.19752820.v2
title: repo2dep.json

description: Towards Understanding Third-party Library Dependency in C/C++ Ecosystem
DOI: 10.6084/m9.figshare.26308642.v1
title: Source Data

description: Durable factor VIII expression that normalizes hemostasis is an unrealized goal of hemophilia A adeno-associated virus-mediated gene therapy. Trials with initially normal factor VIII activity observed unexplained year-over-year declines in expression while others reported low-level, stable expression inadequate to restore normal hemostasis. Here we demonstrate that male mice recapitulate expression-level-dependent loss of factor VIII levels due to declines in vector copy number. We show that an enhanced function factor VIII variant (factor VIII-R336Q/R562Q), resistant to activated protein C-mediated inactivation, normalizes hemostasis at below-normal expression without evidence of prothrombotic risk in male hemophilia A mice. These data support that factor VIII-R336Q/R562Q may restore normal factor VIII function at low-levels of expression to permit durability using low vector doses to minimize dose-dependent adeno-associated virus toxicities. This work informs the mechanism of factor VIII durability after gene transfer and supports that factor VIII-R336Q/R562Q may safely overcome current hemophilia A gene therapy limitations.
DOI: 10.6084/m9.figshare.28601372.v2
title: Figure S2

description: Raw dataset
DOI: 10.6084/m9.figshare.14711232.v1
title: Risk Factors Of Postpartum Depression: A Study At 4-Weeks Postnatal

description: The study aims to identify possible risk factors of developing postpartum depression of mothers 4 weeks postpartum, this study is a descriptive self-administered study conducted on mothers at 4 week postnatal visits to OB-GYN clinic. Patients were excluded if they were currently using anti-depressants and/or were not at their 4-week post-natal visit. The 10-question Edinburgh Postnatal Depression Scale (EPDS) was used as a screening tool for PPD. Analyses were performed to determine whether smoking, breastfeeding status, marital status, mode of delivery, number of births, income, working status, having chronic diseases, history of psychiatric diseases, previous diagnosis of postpartum depression, gestational age, other variables which identified risk cases.this data set includes the spreadsheet including all the data collected from participants and the analysis obtained from those data
DOI: 10.6084/m9.figshare.20174072.v1
title: The Harvard Medical School Pathways curriculum: A comprehensive curricular evaluation

description: The Harvard Medical School Pathways curriculum represents a major reform effort. Our goals were to enhance reasoning and clinical skills and improve the learning environment and students’ approach to learning via use of collaborative, case-based pedagogy; early clinical exposure; and enhanced approaches to teaching and evaluating clinical skills. We evaluated the impact of Pathways on key outcomes related to these goals. In this prospective, mixed-methods study, we compared the last prior-curriculum cohort (2014 matriculation, <i>n</i> = 135) and first new-curriculum cohort (2015 matriculation, <i>n</i> = 135). Measures included Likert-type surveys, focus groups, and test scores to assess outcomes. Compared with prior-curriculum students, new-curriculum students reported higher mean preclerkship learning environment ratings (Educational Climate Inventory, 62.4 versus 51.9, <i>p</i> &lt; 0.0001) and greater satisfaction with the quality of their preclerkship education (88% versus 73%, <i>p</i> = 0.0007). Mean USMLE Step-1 and Step-2 scores did not differ between groups. At graduation, new-curriculum students rated their medical school experience higher in 6 of 7 domains, including ‘fostering a culture of curiosity and inquiry’ (4.3 versus 3.9, <i>p</i> = 0.006) and focus on ‘student-centered learning’ (3.9 versus 3.4, <i>p</i> = 0.002). The new curriculum outperformed or was equal to the prior one on most measures of learning environment and perceived quality of education, without a decline in medical knowledge or clinical skills. Robust longitudinal evaluation provided important feedback for ongoing curriculum improvement.
DOI: 10.6084/m9.figshare.21967388.v1
title: Raw data for microbial processes rates

description: This is the raw data for bacterial growth, fungal growth and respiration rates.
DOI: 10.6084/m9.figshare.12462410.v1
title: JARVIS-DFT Finite Difference Elastic Constants (JVASP-66035 to JVASP-68256)

description: Contains input/output files for finite difference method based elastic calculations in the JARVIS-DFT.
DOI: 10.6084/m9.figshare.8059784.v1
title: Dataset: Patterns of illicit drug use in PLHIV Spain.xls

description: This dataset is part of a study that assessed the prevalence and patterns of drug use among people living with HIV (PLHIV) in Spain. We conducted an observational cross-section study in which 1401 PLHIV participated. Data were collected through 33 sites across Spain using an online computer-assisted self-administered interview. The survey measured use of illicit drugs and other substances, treatment adherence and other health-related variables. This dataset contains 188 of these variables that were used for the analysis. It is on Excel format. The file contains three sheets:<br>Sheet . It contains the dataset. The first row of the table corresponds to variable names.<br>Sheet . It contains a description of each variable. Some of the variables correspond to items from the questionnaire. In those cases, the descriptions corresponds to the translation of the question asked to the participants. <br>Sheet . It contains the labels of the values in the dataset, for each categorical codified variable. Variables not listed in this sheet are numeric, meaning that the numbers on those variables are the real values of the variables, and not a code. <br><br><br>
DOI: 10.6084/m9.figshare.21679874.v1
title: Supplementary Material for: Interference with Lipoprotein Maturation Sensitizes Methicillin-Resistant <b><i>Staphylococcus aureus</i></b> to Human Group IIA-Secreted Phospholipase A<sub>2</sub> and Daptomycin

description: Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) has been classified as a high priority pathogen by the World Health Organization underlining the high demand for new therapeutics to treat infections. Human group IIA-secreted phospholipase A<sub>2</sub> (hGIIA) is among the most potent bactericidal proteins against Gram-positive bacteria, including <i>S. aureus</i>. To determine hGIIA-resistance mechanisms of MRSA, we screened the Nebraska Transposon Mutant Library using a sublethal concentration of recombinant hGIIA. We identified and confirmed the role of <i>lspA</i>, encoding the lipoprotein signal peptidase LspA, as a new hGIIA resistance gene in both in vitro assays and an infection model in hGIIA-transgenic mice. Increased susceptibility of the <i>lspA</i> mutant was associated with enhanced activity of hGIIA on the cell membrane. Moreover, <i>lspA</i> deletion increased susceptibility to daptomycin, a last-resort antibiotic to treat MRSA infections. MRSA wild type could be sensitized to hGIIA and daptomycin killing through exposure to LspA-specific inhibitors globomycin and myxovirescin A1. Analysis of &gt;26,000 <i>S. aureus</i> genomes showed that LspA is highly sequence-conserved, suggesting universal application of LspA inhibition. The role of LspA in hGIIA resistance was not restricted to MRSA since <i>Streptococcus mutans</i> and <i>Enterococcus faecalis</i> were also more hGIIA-susceptible after <i>lspA</i> deletion or LspA inhibition, respectively. Overall, our data suggest that pharmacological interference with LspA may disarm Gram-positive pathogens, including MRSA, to enhance clearance by innate host defense molecules and clinically applied antibiotics.
DOI: 10.6084/m9.figshare.24131562.v1
title: Supplementary Material for: Effectiveness treatment of a BRAF-ZKSCAN5 fusion gene melanoma case with dabrafenib/trametinib

description: The most important driver gene in malignant melanoma is the BRAF mutation, and molecularly targeted therapies targeting mutations, mainly V600E and V600K, are used in clinical practice. In this report, we treated a patient with malignant melanoma expressing a rare BRAF-ZKSCAN5 fusion gene with dabrafenib/trametinib. The patient was a 71-year-old female. She was diagnosed with malignant melanoma (pT4aN3M0, STAGE IIIC) of the abdomen with axillary lymph node metastasis. She underwent extended resection and axillary lymph node dissection and was treated with adjuvant therapy, but lung and mediastinal lymph node metastases developed. The patient was treated with immune checkpoint inhibitors for metastatic lesions and achieved complete remission, but relapsed and metastatic lesions appeared in the cervical lymph nodes. Next-generation sequencing revealed the BRAF-ZKSCAN5 fusion gene, and treatment with dabrafenib/trametinib was initiated. After one month of treatment, tumor growth stopped and the length of the tumor shrank by 22.2%, but she developed Grade 3 adverse events of nausea, fatigue, and diarrhea and had difficulty exercising, forcing her to discontinue treatment after six weeks. The tumor continued to shrink during drug administration. This case report may provide insight into treatment options for cases that BRAF fusion gene was observed, which are expected to be detected in large numbers by next-generation sequencing in the future.
DOI: 10.6084/m9.figshare.25470028.v1
title: Supplementary Material for: A Klotho-based Machine Learning Model for Prediction of both Kidney and Cardiovascular Outcomes in Chronic Kidney Disease

description: Background: This study aimed to develop and validate a machine learning (ML) model based on serum Klotho for predicting end-stage kidney disease (ESKD) and cardiovascular disease (CVD) in patients with chronic kidney disease (CKD).
Methods: Five different ML models were trained to predict the risk of ESKD and CVD at three different time points (3, 5, and 8-year) using a cohort of 400 non-dialysis CKD patients. The dataset was divided into a training set (70%) and an internal validation set (30%). These models were informed by data comprising 47 clinical features, including serum Klotho. The best-performing model was selected and used to identify risk factors for each outcome. Model performance was assessed using various metrics.
Results: The findings showed that the Lasso regression model had the highest accuracy (C-index=0.71) in predicting ESKD. The features mainly included in this model were estimated glomerular filtration rate (eGFR), 24-hour urinary microalbumin, serum albumin, phosphate, parathyroid hormone, and serum Klotho, which achieved the highest area under the curve (AUC) of 0.930 (95% CI: 0.897-0.962). In addition, for the CVD risk prediction, the Random Survival Forest (RSF) model with the highest accuracy (C-index=0.66) was selected and achieved the highest AUC of 0.782 (95% CI: 0.633-0.930). The features mainly included in this model were age, history of primary hypertension, calcium, tumor necrosis factor-alpha, and serum Klotho.
Conclusion: We successfully developed and validated Klotho-based ML risk prediction models for CVD and ESKD in CKD patients with good performance, indicating their high clinical utility.
DOI: 10.6084/m9.figshare.5121544.v1
title: Supplementary Material for: Laboratory Review: The Role of Gait Analysis in Seniors’ Mobility and Fall Prevention

description: Walking is a complex motor task generally performed automatically by healthy adults. Yet, by the elderly, walking is often no longer performed automatically. Older adults require more attention for motor control while walking than younger adults. Falls, often with serious consequences, can be the result. Gait impairments are one of the biggest risk factors for falls. Several studies have identified changes in certain gait parameters as independent predictors of fall risk. Such gait changes are often too discrete to be detected by clinical observation alone. At the Basel Mobility Center, we employ the GAITRite electronic walkway system for spatial-temporal gait analysis. Although we have a large range of indications for gait analyses and several areas of clinical research, our focus is on the association between gait and cognition. Gait analysis with walking as a single-task condition alone is often insufficient to reveal underlying gait disorders present during normal, everyday activities. We use a dual-task paradigm, walking while simultaneously performing a second cognitive task, to assess the effects of divided attention on motor performance and gait control. Objective quantification of such clinically relevant gait changes is necessary to determine fall risk. Early detection of gait disorders and fall risk permits early intervention and, in the best-case scenario, fall prevention. We and others have shown that rhythmic movement training such as Jaques-Dalcroze eurhythmics, tai chi and social dancing can improve gait regularity and automaticity, thus increasing gait safety and reducing fall risk.
DOI: 10.6084/m9.figshare.c.3615806_d2.v1
title: Additional file 14: Table S7. of Single-cell analysis of long non-coding RNAs in the developing human neocortex

description: Related to Fig.Â 4. Table of 105 cell type-specific mRNAs (1st tab) and lncRNAs (2nd tab) and their expression enrichment scores, which are log2 transformed, for each of the seven cell type clusters. (XLS 42 kb)