cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20733091.v2
title: Example Timeseries -- Drosophila midgut, minimal data

description: Minimal ingredients for running example TubULAR pipeline for timeseries data, from surface extraction to kinematic analysis. See also Example Timeseries -- Drosophila midgut, analyzed data for an expanded package with example analysis. <br> This dataset is a downsampled and clipped version of data investigated in: N. P. Mitchell, D. J. Cislo, S. Shankar, Y. Lin, B. I. Shraiman, S. J. Streichan, “Visceral organ morphogenesis via calcium-patterned muscle contractions.” eLife 11:e77355 (2022). <br> <br> Support for the development of the TubULAR analysis codebase was provided by NSF Grant No. PHY-2047140.
DOI: 10.6084/m9.figshare.29161949.v1
title: pelvic organ prolapse through transcriptomic analyses in uterosacral ligament tissues of postmenopausal women

description: We enrolled five pelvic organ prolapse patients and three normal controls. Uterosacral ligament tissue samples were collected and analyzed using high-throughput transcriptome sequencing. Differential expression was determined using the criteria of |log2 (fold change)|&gt;1 and an adjusted p-value (padj) &lt; 0.05. The mentioned five POP groups include SSK,WCX,WGX,SYZ,JSL and other three Control groups include TWF,YXF,WX.
DOI: 10.6084/m9.figshare.4762495.v4
title: Reducing workplace burnout through exercise

description: Objectives. The global burden of burnout cost is in excess of $300 billion annually. Locally, just under half of working Australians experience high levels of occupational burnout. Consequently, burnout interventions are paramount to organisational productivity. Exercise has the potential to provide a multilevel and cost effective burnout intervention. The current study aims to extend the literature by comparing cardiovascular with resistance exercise to assess their relative effectiveness against well-being, perceived stress, and burnout. Design. Participants were 49 (36 females and 13 males) previously inactive volunteers ranging in age from 19 to 68 that completed a four week exercise program of either cardiovascular, resistance, or no exercise (control). Randomised control trial design was employed. Method. Participants were measured against the Subjective Exercise Experience Scale, the Perceived Stress Scale, and the Maslach Burnout Inventory. Results. After four weeks of exercise participants had greater positive well-being and personal accomplishment, and concomitantly less psychological distress, perceived stress, and emotional exhaustion. Cardiovascular exercise was found to increase well-being and decrease psychological distress, perceived stress, and emotional exhaustion. Resistance training was noticeably effective in increasing well-being and personal accomplishment and to reduce perceived stress. The present findings revealed large effect sizes suggesting that exercise may be an effective treatment for burnout. However, given a small sample size further research needs to be conducted. Conclusion. Exercise has potential to be an effective burnout intervention. Different types of exercise may assist employees in different ways. Organisations wishing to proactively reduce burnout can do so by encouraging their employees to access regular exercise programs.
DOI: 10.6084/m9.figshare.706369.v1
title: PhyloSift: Phylogenetic analysis of genomes and metagenomes

description: Poster presented at the 2013 Annual Meeting of the American Society for Microbiology (May 18-21, Denver, Colorado). For software download and documentation please visit http://phylosift.wordpress.com
DOI: 10.6084/m9.figshare.16802080.v1
title: Supplementary Material for: Physical and Chemical Compatibility of Etomidate and Propofol Injectable Emulsions

description: <b><i>Introduction:</i></b> The mixture of etomidate and propofol is widely used in clinical practice to improve efficacy of general anesthesia and to minimize side effects. As a thermodynamically unstable system, emulsion is prone to destabilization through mechanisms including coalescence, flocculation, and creaming. Such unwanted phenomenon can induce fat embolism after intravenous administration. This study was aimed to investigate the physical and chemical stability of the mixture of etomidate and propofol in the dosage form of emulsion. <b><i>Methods:</i></b> This compatibility study focused on the critical quality attributes (CQAs) of drug-containing emulsions, such as appearance, pH, particle size and distribution, <i>zeta</i> potential, the observation under centrifugation, and drug content and impurity. <b><i>Results:</i></b> As the results, there were no significant changes in the CQAs of the mixed emulsions up to 24 h after mixing at refrigeration temperature (4°C), room temperature (25°C), and body temperature (37°C). <b><i>Conclusions:</i></b> These results demonstrate that etomidate emulsion is physically and chemically compatible with propofol emulsions up to 24 h at 4°C, 25°C, and 37°C, suggesting that etomidate and propofol can be administrated in mixture without adversely affecting product characteristics, at least in vitro.
DOI: 10.6084/m9.figshare.24977925.v1
title: Data and code archive for baleen whale behavioral ecology study

description: This archive contains all data and code required to reproduce a study of baleen whale behavioral ecology. The archive includes
DOI: 10.6084/m9.figshare.5124913.v1
title: Supplementary Material for: Noonan Syndrome: Comparing Mutation-Positive with Mutation-Negative Dutch Patients

description: Noonan syndrome (NS) is an autosomal dominant disorder characterized by facial dysmorphisms, short stature and congenital heart defects. The disorder is genetically heterogeneous and shows clinical overlap with other RASopathies. These syndromes are caused by mutations in a variety of genes leading to dysregulation of the RAS-MAPK pathway: <i>PTPN11, KRAS, SOS1, RAF1, CBL, SHOC2, NRAS, BRAF, MAP2K1, MAP2K2, HRAS, NF1 and SPRED1.</i> In this study, we conduct a genotype-phenotype analysis of 33 patients with a clinical diagnosis of NS without a <i>PTPN11</i> mutation. Mutation analysis of the genes involved in RASopathies was performed, except for <i>NF1 and SPRED1.</i> In 14 (42%) NS patients, a mutation was found, 7 (21%) had a mutation in <i>SOS1</i>, 3 (9%) in <i>RAF1</i> and 1 (3%) in <i>KRAS</i>, <i>MAP2K2</i>, <i>BRAF</i> and <i>SHOC2</i> each. The phenotype of these mutation-positive cases corresponded to that described in the literature. In the cases with a <i>BRAF</i> and <i>MAP2K2</i> mutation, the diagnosis cardio-facio-cutaneous syndrome was made. The patient with the <i>SHOC2</i> mutation had features compatible with ‘Noonan-like syndrome with loose anagen hair'. Three major clinical features of NS - a typical face, short stature and a pulmonary valve stenosis - were less frequently present in the group without a mutation. Missense mutations in genes encoding proteins of the RAS-MAPK pathway cause NS. The 3 major clinical features of NS were less frequently present in the mutation-negative patients, which stresses the importance of the syndrome-specific symptoms of the face, heart and short stature in NS. However, all mutation-negative cases met the NS criteria, indicating that the involvement of novel genes is to be expected.
DOI: 10.17632/bk2bt9cxwc
title: A low-cost quantitative continuous measurement of movements in the extremities of healthy men with typical development

description: Detection of movements in the extremities of people with Parkinson disease was developed to enhance the gold-standard structured assessment of people with Parkinson’s disease assessed by the visual observation by the examiner of the person with Parkinson’s disease (Goetz, et al., 2008). This data represents the administration of a low-cost quantitative continuous measurement of movements in the extremities of people with Parkinson's disease by examiners certified in the Movement Disorders Society-sponsored revision of the Unified Parkinson’s Disease Rating Scale (MDS-UPDRS) (Goetz, et al., 2008) to healthy men with typical development in person. The examiner instructed the participant how to perform each task. The examiner demonstrated the movements. The examiner did not continue to perform the task while the participant was performing the tasks. The examiner instructed the participant to perform each movement as quickly and fully as possible. The examiner encouraged the participant to execute each motion with the maximal speed and range of motion. The examiner sought to capture at least 60 optimal repetitions for each motion. A technologist recorded the output of the instrumentation of each assessment (Harrigan, et al., 2020) and operated a video camera to record the movements of the participants during the testing session. A second (retest) assessment of the protocol was performed after a month for each participant. Two experts certified in the MDS-UPDRS (Goetz, et al., 2008) then edited the original videotapes to extract only the administration of each task. One expert had participated as examiner and participant in the videotaped segments. The videotape segments correspond to the tasks of the protocol (3.17RTU: 3.17 Rest tremor amplitude upper limbs, 3.17RTUC: 3.17 Rest tremor amplitude upper limbs counting, 3.15PT: 3.15 Postural tremor of the hands, 3.4FT: 3.4 Finger tapping, 3.5HM: 3.5 Hand movements, 3.6PS: 3.6 Pronation-supination movements of the hands, 3.9ACU: 3.9 Arising from chair upper limbs, 3.9ACL: 3.9 Arising from chair upper limbs, 3.17RTL: 3.17 Rest tremor amplitude lower limbs, 3.17RTLC: 3.17 Rest tremor amplitude lower limbs counting, 3.7TT: 3.7 Toe tapping, 3.8LA: 3.8 Leg agility) (McKay, et al., 2019). The participants are identified by their original identification number (Harrigan, et al., 2020). The first (test) session was designated with "F." The second (retest) session was designated with "S."
DOI: 10.6084/m9.figshare.25136942.v1
title: Multimodal-fusion-severe-hypo-data

description: Datasets (raw and preprocessed) for reproducibility results of the paper "Interpretable and multimodal fusion methods to identify severe hypoglycemia in adults with T1D".This study aims to identify severe hypoglycemia (SH) in Type 1 diabetes patients, leveraging machine learning and explainable artificial intelligence (XAI) techniques. Using clinical data from the Jaeb Center for Health Research, including tabular, text, and time series data, multimodal fusion models outperform single-modality models by 5.8%, achieving an AUCROC of 0.779. XAI reveals a higher incidence of cardiovascular diseases and associated drugs in individuals with SH, along with a correlation between consistently low blood glucose levels and SH risk. These findings hold promise for early detection and intervention, benefiting both clinicians and patients.<br>
DOI: 10.6084/m9.figshare.28920119.v1
title: The link between range size, niche specialization, and diversification in one of the most successful avian radiations, the New World flycatchers (Tyrannoidea)

description: Dataset including the following information for each species:Diversification rate (DR)Number of occupied ecoregions following criterion I (Index)Number of occupied ecoregions following criterion II (Index2)Min. elevation (MinElev)Max. elevation (MaxElev)Mean elevation (MeanElev)Elevational range (RangeElev)Geographic range size (RangeSize)Hand-wing index (HWI)Body size (mass)<br><br>
DOI: 10.6084/m9.figshare.5270926.v4
title: Transcriptomic characterization of MRI contrast with focus on the T1-w/T2-w ratio in the cerebral cortex

description: Magnetic resonance (MR) images of the brain are of immense clinical and research utility. At the atomic and subatomic levels, the sources of MR signals are well understood. However, we lack a comprehensive understanding of the macromolecular correlates of MR signal contrast. To address this gap, we used genome-wide measurements to correlate gene expression with MR signal intensity across the cerebral cortex in the Allen Human Brain Atlas (AHBA). We focused on the ratio of T1-weighted and T2-weighted intensities (T1-w/T2-w ratio image) which is considered to be a useful proxy for myelin content. As expected, we found enrichment of positive correlations between myelin-associated genes and the ratio image, supporting its use as a myelin marker. Genome-wide, there was an association with protein mass, with genes coding for heavier proteins expressed in regions with high T1-w/T2-w values. Oligodendrocyte gene markers were strongly correlated with the T1-w/T2-w ratio, but this was not driven by myelin-associated genes. Mitochondrial genes have the strongest relationship, showing higher expression in regions with low T1-w/T2-w ratio. This may be due to the pH gradient in mitochondria as genes up-regulated by pH in the brain were also highly correlated with the ratio. While we corroborate associations with myelin and synaptic plasticity, differences in the T1-w/T2-w ratio across the cortex are more strongly linked to molecule size, oligodendrocyte markers, mitochondria, and pH. We evaluate correlations between AHBA transcriptomic measurements and a group averaged T1-w/T2-w ratio image, showing agreement with in-sample results. Expanding our analysis to the whole brain results in strong positive T1-w/T2-w correlations for immune system, inflammatory disease, and microglia marker genes. Genes with negative correlations were enriched for neuron markers and synaptic plasticity genes. Lastly, our findings are similar when performed on T1-w or inverted T2-w intensities alone. These results provide a molecular characterization of MR contrast that will aid interpretation of future MR studies of the brain.<br>
DOI: 10.6084/m9.figshare.6182180.v3
title: Database_Physiological responses to acute cold exposure in young lean men.xlsx

description: Here we provide the database of the paper titled: Physiological responses to acute cold exposure in young lean men. Pay attention only to the Database version 3
DOI: 10.6084/m9.figshare.790764.v2
title: Science Gateways and the Importance of Sustainability

description: This is a position paper for a workshop on software sustainability (http://wssspe.researchcomputing.org.uk). The paper specifically focuses on the issue of science gateway or web portal sustainability in research communities.
DOI: 10.6084/m9.figshare.25467676.v2
title: <b>Fat body lipogenic capacity in honey bee workers is affected by age, social role, and dietary protein</b>

description: <b>Abstract</b>All organisms need to balance processes that consume energy against those that produce energy. With an increase in biological complexity over evolutionary time, regulation of this balance has become much more complex, resulting in specialization of metabolic tasks between organelles, cells, organs, and in the case of eusocial organisms, between the individuals who comprise the ‘superorganism.’ Exemplifying this, nurse honey bees maintain high abdominal lipids, while foragers have very low lipid stores, likely contributing to efficient performance of their social role, and thus to colony fitness. The proximate mechanisms responsible for these metabolic differences remain poorly understood. Here, we investigated the effects of age, worker class, and dietary macronutrients on the abdominal activity of fatty acid synthase (FAS), the enzyme responsible for <i>de novo</i> synthesis of fatty acids as well as age on lipase activity, enzymes responsible for breakdown of stored lipids. We found that FAS but not lipase activity declines as bees age past peak nursing age. Feeding both nurses and foragers carbohydrates increased FAS activity compared with starved bee, but, whether fed or starved, nurses had much higher FAS activity than similarly treated foragers, implicating reduced lipid synthesis as one component of foragers’ low lipid stores. Finally, we used artificial diets with different amounts of protein and fat to precociously induce low, forager-like FAS activity levels in nurse-age bees deprived of protein. We speculate that reduced protein appetite and consumption during the nurse-forager transition is responsible for suppressed lipid synthesis in foragers.
DOI: 10.6084/m9.figshare.28999208.v1
title: Assessment of mechanical bond and surface chemistry of commercial and alternatives steel fibers embedded in concretes with varying water-to-cement ratios via pullout testing

description: This research investigates the influence of steel fiber reinforced concrete (SFRC) mechanical properties when residual domestic water is incorporated, as well as the physical and chemical effects of the steel fibers (SF). The study involves chemical and mechanical concrete characterization, including pullout tests. The experimental analysis utilized alternatives steel fibers (annealed and galvanized) and industrial steel fibers (3D). Specimens were prepared by varying the proportion of treated water mixed with regular water at 0%, 25%, 50%, 75%, and 100%, resulting in 75 samples. The results revealed that none of the fibers outperformed the control samples; an increased concentration of treated water corresponded to a decline in mechanical performance. The steel fiber (SF) that exhibited the most significant reduction in mechanical properties was the annealed steel fiber exposed to 100% treated water. This decline was linked to the concentrations of hardness, phosphates, nitrates, nitrites, sulfates, and chlorides found in the surface sediments of the fibers, analyzed using a YSI 9000 probe. The results indicate that the reduction in mechanical performance is multifactorial, influenced by various chemical species. However, mechanical performance decreases as the treated water increases.
DOI: 10.6084/m9.figshare.7040315.v1
title: File S1. E. coli strains and plasmids, plasmid construction details, nucleotide sequences of select genetic parts, and primers.

description: File S1. <i>E. coli</i> strains and plasmids, plasmid construction details, nucleotide sequences of select genetic parts, and primers.
DOI: 10.6084/m9.figshare.22126610.v2
title: ITPROJ REVIEW DATA

description: Systematic Review data-IT Project Management
DOI: 10.17632/5ft3m5t4f5
title: Data for: Flipping the switch versus switching the bulb: Investigating why people prefer turning off the lights over using more efficient bulbs

description: Data for paper: Flipping the switch versus switching the bulb: Investigating why people prefer turning off the lights over using more efficient bulbs
DOI: 10.6084/m9.figshare.22802816.v2
title: Supplemental materials for "Diploid and triploid chinook salmon (<em>Oncorhynchus tshawytscha</em>) have altered microRNA responses in immune tissues after infection with <em>Vibrio</em> <em>anguillarum</em> "

description: Supplemental files for study investigating the impact of <em>Vibrio</em> <em>anguillarum</em> infection on diploid and triploid Chinook salmon (<em>Oncorhynchus tshawytscha</em>) was investigated to identify if there was any significant immune regulation by microRNAs (miRNA). Small RNAs from hindgut (hg), head kidney (hk), and spleen (sp) were sequenced to determine if miRNA transcript abundance was altered due to ploidy and infection in nine-month old full-sibling diploids and triploids. MiARma-seq and bowtie1 were utilized to align reads to the Chinook salmon genome, and then read abundance associated with miRNA genes quantified using FeatureCounts. Read counts were then analyzed using DESeq2 to identify differentially expressed miRNA between ploidies as well as after infection in all three tissues. Finally, targets of differentially expressed miRNA were predicted using miRanda and pathway impacts predicted using KEGG analysis. <br> Files included: <strong>run_log.log</strong> - miARma-seq logfiles for hindgut (hg), head kidney (hk), and spleen (sp) <strong>stats.log</strong> - miARma-seq stats information for hindgut (hg), head kidney (hk), and spleen (sp) <strong>miarma.cadonic.known.tshawyt.sample.ini</strong> - initiation file for miARma-seq which includes all parameters that were utilized to analyze raw reads <strong>deseq2_cadonic_sample.R</strong> - sample of R code for DEseq2 used to identify differentially expressed miRNA genes <strong>Sasa_Ensembl_3UTR_clean.fasta </strong>- File of 3' untranslated region (UTR) for annotated genes in Ensembl biomart (Ensembl release 105) that was analyzed with miRanda (version v3.3a) to predict miRNA-mRNA relationships. Sequences with unavailable UTRs were cleaned by replacing empty spaces with N using "sed -e '/^[^&gt;]/s/[^ATGC]/N/g' Sasa_Ensembl_3UTR.txt &gt; Sasa_Ensembl_3UTR_clean.fasta". <strong>cadonic_2023_Bioinformatics_protocol_extended.docx - </strong>Extended explanation for the bioinformatic steps and justification for the workflow used in the study.
DOI: 10.6084/m9.figshare.3452993.v1
title: New single crystal <sup>40</sup>Ar/<sup>39</sup>Ar ages improve time scale for deposition of the Omo Group, Omo–Turkana Basin, East Africa

description: Six tuffaceous beds within the Omo Group of the Omo–Turkana Basin have been dated using the <sup>40</sup>Ar/<sup>39</sup>Ar single crystal total fusion method on anorthoclase, yielding eruption ages. The Omo Group constitutes up to 800 m of subaerially exposed sediments surrounding Lake Turkana within the East African Rift system in northern Kenya and southern Ethiopia. Rhyolitic explosive eruptions produced tuffs and pumice clasts that are considered to have been deposited shortly after eruption. The new age data on feldspars from the pumice clasts range from 4.02 ± 0.04 Ma for the Naibar Tuff of the Koobi Fora Formation to 1.53 ± 0.02 Ma for Tuff K of the Shungura Formation. The Orange Tuff in the KBS Member of the Koobi Fora Formation was dated at 1.76 ± 0.03 Ma, providing good control in this part of the sequence where formerly there was a &gt;200 ka gap. Data are consistent with earlier measurements and significantly improve age resolution within the Omo Group, which has yielded many vertebrate fossils, including hominin fossils comprising a number of species. We suggest new age estimates for a limited number of hominin specimens.
DOI: 10.17632/cx268tmrwn
title: YembaTones: An Annotated Dataset for Tonal and Syllabic Analysis of the Yemba Language

description: YembaTones is a meticulously annotated dataset that focuses on tonal and syllabic variations in the Yemba language. It was created to facilitate automatic tone detection and enhance resources available for speech recognition and synthesis in this tonal language. This dataset is derived from a dictionary containing 344 Yemba/French words, carefully selected from commonly used phrases in the language. The words are grouped based on their spelling differences in terms of tones. Audio recordings of the pronunciation of these words were made by 11 native Yemba speakers, primarily linguistics specialists with a strong command of the language's sounds. The recordings were captured in various locations such as speakers' homes, university campuses, and workplaces. Subsequently, the recordings were cleaned and segmented into individual audio files corresponding to isolated word pronunciations using Audacity software. The YembaTones dataset consists of 3420 high-quality audio files that have been meticulously annotated at the syllabic and tonal levels using Praat software. It serves as a valuable resource not only for training and evaluating automatic tone detection models, but also for automatic speech recognition, speech synthesis in tonal and low-resource languages, as well as research in prosody, Yemba phonetics, speech acoustics, and phonetic linguistics. YembaTones provides a comprehensive foundation for further advancements in tonal analysis, speech technology, and linguistic research for the Yemba language. By addressing the scarcity of resources in this domain, this dataset paves the way for the development of more accurate and effective speech processing applications for tonal languages.
DOI: 10.17632/jp26ftpn7t
title: Data for: Long-term predictors of dengue outbreaks in Bangladesh: a data mining approach

description: Raw dengue and climate variables, Bangladesh