cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1509925.v1
title: Quantifying and mapping the supply of and demand for carbon storage and sequestration service from urban trees

description: This is a GIS dataset of the supply of and demand for carbon storage and sequestration service from urban trees in a portion of the Twin Cities Metropolitan Area (TCMA) of Minnesota, USA. It is a vector shapefile that contains data on the number of trees, supply of carbon storage (kgC), annual carbon sequestration (kgC), the net annual demand for carbon sequestration (kgC), the amount of carbon emitted due to mortality (kgC), the amount of carbon sequestrated due to replanting and tree growth (kgC), and the demand for carbon sequestration from seven sectors (kgCO2), including agricultural, commercial, electric utility, industrial, residential, transportation and waste, as well as the ratio of carbon sequestration supply and demand. All data are summaried by census tract.
DOI: 10.6084/m9.figshare.17040389.v1
title: Supplementary Material for: Impact of Diagnostic Delay on Disease Course in Pediatric Versus Adult-onset Patients with Ulcerative Colitis: Data from the Swiss IBD Cohort

description: Introduction: Given the lack of data we aimed to assess the impact of the length of diagnostic delay on natural history of ulcerative colitis in pediatric (diagnosed &lt;18 years) and adult patients (diagnosed ≥18 years). Methods: Data from the Swiss Inflammatory Bowel Disease cohort study were analyzed. Diagnostic delay was defined as interval between the first appearance of UC-related symptoms until diagnosis. Logistic regression modeling evaluated the appearance of the following complications in the long term according to the length of diagnostic delay: colonic dysplasia, colorectal cancer, UC-related hospitalization, colectomy, and extra-intestinal manifestations (EIM). Results: A total of 184 pediatric and 846 adult patients were included. Median diagnostic delay was 4 [IQR 2-7.5] months for the pediatric-onset group and 3 [IQR 2-10] months for the adult-onset group (P=0.873). In both, pediatric and adult-onset groups, length of diagnostic delay at UC diagnosis was not associated with colectomy, UC-related hospitalization, colon dysplasia, and colorectal cancer. EIM were significantly more prevalent at UC diagnosis in the adult-onset group with long diagnostic delay compared to the adult-onset group with short diagnostic delay (p = 0.022). In the long term, length of diagnostic delay was associated in the adult onset group with colorectal dysplasia (p=0.023), EIMs (p&lt;0.001) and more specifically arthritis/arthralgias (p&lt;0.001) and ankylosing spondylitis/sacroiliitis (p&lt;0.001). In the pediatric-onset UC group, length of diagnostic delay in the long term was associated with arthritis/arthralgias (p=0.017); however, it was not predictive for colectomy and UC-related hospitalization. Conclusions: As colorectal cancer and EIMs are associated with considerable morbidity and costs, every effort should be made to reduce diagnostic delay in UC patients.
DOI: 10.6084/m9.figshare.12941945.v4
title: Differential transcript usage in the Parkinson's disease brain

description: Raw data and findings of:<b>"Differential transcript usage in the Parkinson's disease brain".</b>Code to reproduce findings at: https://github.com/fifdick/DTUinPDbrain<br>- "DTU_events.txt" contains result statistics of both DRIMSeq and DEXSeq for all transcripts- "TPM_mat.txt" contains TPMs (after using tximport) for all transcripts. Additional column indicates whether the transcript was removed from further down-stream analysis or survived pre-filtering-"sample_info.txt" contains the meta-data file used to run the DTU analysis with the code provided. (Covariates and condition)<br>
DOI: 10.6084/m9.figshare.20761915.v4
title: Effects of climate and land-cover change on the conservation status of gibbons

description: <strong>Abstract</strong> Species shift their distribution in response to climate and land-cover change, which may result in a spatial mismatch between currently protected areas (PAs) and priority conservation areas (PCAs). We examined the effects of climate and land-cover change on potential range gibbons and sought to identify PCAs that would conserve them effectively. We collected global gibbon occurrence points and modeled (ecological niche model) their current and potential 2050s ranges under climate change and different landcover change scenarios. We examined change in range and PA coverage between the current and future ranges of each gibbon species. We applied spatial conservation prioritization to identify the top 30% PCAs for each species. We then determined how much of the PCAs are conserved in each country within the global range of gibbons. On average 31% (SD 22) of each species’ current range was covered in PAs. Protected-area coverage of the current range of 9 species was &lt;30%. Nine species lost on average 46% (SD 29) of their potential range due to climate change. Under climate change with an optimistic land-cover change scenario (B1), 12 species lost 39% (SD 28) of their range. In a pessimistic land-cover-change scenario (A2), 15 species lost 36% (SD 28) of their range. Five species lost significantly more range under the A2 scenario than the B1 scenario (<em>p</em> = 0.01, SD 0.01), suggesting that gibbons will benefit from effective land-cover management. Protected-area coverage of future range was &lt;30% for 11 species. On average 32% (SD 25) of PCAs was covered by PAs. Indonesia contained more species and PCAs and thus has the greatest responsibility for gibbon conservation. Indonesia, India, and Myanmar need to expand their PAs to fulfill their responsibility to gibbon conservation. Our results provide a baseline for global gibbon conservation, particularly for countries lacking gibbon research capacity. <br> Dataset here: 1 Environmental variables for modeling 2 Potential range for each gibbon (Present-absence Maps) 3 Priority conservation areas (PCAs) maps 4 Gibbon records (a map; All data were obtained from different dataset online) 5 ID from gbif Some of our data were assessed by GBIF using spocc package. We provides the all id in this table. Some of these data were the same but from different resources, like gbif and inatural. User can remove the duplicated records by spocc, sf or other package. <br> Please cites this data by our publication: Yang, Li., Chen, T., Shi, K.-C., Zhang, Lu., Lwin, N., & Fan, P.-F. (2022). Effects of climate and land-cover change on the conservation status of gibbons. <em>Conservation Biology</em>, 00, e14045. https://doi.org/10.1111/cobi.14045 <br> For gbif id table: Derived dataset GBIF.org (15 December 2022) Filtered export of GBIF occurrence data https://doi.org/10.15468/dd.zm2wbc <br> We also thank Daneil Noesgaard for making the derived data from GBIF. <br>
DOI: 10.6084/m9.figshare.24849774.v1
title: Ningdong (ND) coal base

description: The annual maximum NDVI dataset of Ningdong (ND) coal base in China (2013-2022).<br>
DOI: 10.6084/m9.figshare.1150286.v1
title: Monkey temporal preferences in a foraging task and an intertemporal choice task

description: The first letter in the file name indicates the subject. The numbers indicate the date, all files from the same date were collected in the same session. The file letter before the extension is the task type, C for the foraging task, F0 for the intertemporal choice task.
DOI: 10.6084/m9.figshare.23301731.v1
title: Supplementary Material for: The natural evolution of nevi with peripheral globules

description: Background: Peripheral globules (PG) in melanocytic lesions represent a concerning dermoscopic feature, since they might be present in growing nevi and melanomas. Their natural evolution has not been fully elucidated and an age-based management approach has been recommended. Objectives: To calculate the growth rate of lesions with PG and investigate possible association with age, sex, location and the global dermoscopic pattern. Methods: We retrospectively selected the lesions of interest from a cohort of Caucasian patients who underwent sequential digital dermoscopy monitoring. Lesions with PG distributed at 75% or more of their circumference with available follow up images or histopathologic report were included. The surface area was automatically calculated with the help of an incorporated tool used in the acquisition of the images. The images were also evaluated by independent investigators for the presence of pre-defined criteria. Growth-curve models were used to assess the growth rate. The outcome variable was the area of nevi in mm2 and scatterplots with Lowess curves were used to present the mean change of nevi during follow up. Results: A total of 208 lesions from 98 patients with a median age of 36 years (range 15-75) were included. The median follow-up time was 18 months (range 4-48). The mean growth rate for all nevi was 0.16 mm2/month (95% CI, 0.14 – 0.18, p&lt;0.001) ranging from -0.29 to 0.61 mm2/month. The growth rate was higher in nevi with a homogeneous dermoscopic pattern (p&lt;0.001). The number of peripheral globules during follow up varied from increasing to complete disappearance. None of the lesions developed any melanoma-specific structure at follow up. Conclusion: Nevi with PG grew at a mean rate of 0.16mm2/month and the growth rate was independent of age, gender or anatomic location. Nevi with homogeneous pattern demonstrated the highest growth rate in our cohort. None of the monitored nevi with PG developed melanoma-specific criteria at follow up.
DOI: 10.6084/m9.figshare.12781274.v1
title: Predicted secondary metabolite biosynthetic gene clusters (smBGCs) in H. alvei A23BA genome.

description: <b>Predicted secondary metabolite biosynthetic gene clusters (smBGCs) in <i>H. alvei</i> A23BA genome.</b>
DOI: 10.11583/dtu.9746324.v1
title: A room acoustics model and simulated impulse responses of a living room

description: A set of 21 room impulse responses simulated in ODEON (commercial and proprietary software, www.odeon.dk) and auralized for the audio-visual immersion lab (AVIL, 64 channels; Ahrens et al., 2019), using the LORA toolbox (Favrot et al., 2010).The dataset contains seven azimuth locations (-90:30:90 degrees) and three distances (1.4m, 2.4m, 3.4m).<br>Example:IR01 refers to -90degrees (left), 1.4m distance.IR07 refers to 90degrees (right), 1.4m distance.<br>IR08 refers to -90degrees (left), 2.4m distance.<br>IR21 refers to 90degrees (right), 3.4m distance.<br><br>This database contains the loudspeaker impulse responses, the ODEON room model as well as the raw ODEON output files.
DOI: 10.6084/m9.figshare.16545846.v1
title: Summary data of chamber-based oxygen and methane consumption and production in the streambed and outgassing of carbon dioxide and methane to the atmosphere collected seasonally for six tributaries of Hampshire River Avon (UK) during 2013-2014.

description: Data were collected in six headwater reaches of the lowland catchment of the Hampshire River Avon (UK), specifically on Chalk River Ebble and River Wylye, Greensand River Nadder and West Avon, and clay River Sem and Sem Tributary River Priors between April 23<sup>th</sup> 2013 and February 10<sup>th</sup> 2014. The setup consists of transparent and dark Perspex chambers (0.5 L enclosed volume, 73 cm<sup>2</sup> surface area) mounted on a steel-ring, which were used to quantify O<sub>2</sub> production and CH<sub>4</sub> release in the light and benthic O<sub>2</sub> consumption and CH<sub>4</sub> release in the dark, respectively. Concentrations of CH4 were obtained based on discrete samples (GC analysis); O<sub>2</sub> from Clark-type oxygen microelectrodes connected to an Unisense Under-Water Meter. The floating chambers consists of an inverted plastic bowl covered in reflective aluminum tape, fitted with a polyurethane tubing sample port to allow for gas-sampling (CH<sub>4</sub> measurements) and a SenseAir CO<sub>2</sub> sensor <br>A more comprehensive description of the datasets is available from the manuscript below.Rovelli L., L. A. Olde, C. M. Heppell, A. Binley, G. Yvon-Durocher, R. N. Glud, M. Trimmer. (2022) <sup></sup>Contrasting biophysical controls on carbon dioxide and methane outgassing from streams. <i>Journal of Geophysical Research: Biogeosciences </i>127(1): e2021JG006328, doi:10.1029/2021JG006328
DOI: 10.6084/m9.figshare.25878523.v1
title: Thresholded maps

description: <b>Model weight maps and model encoding maps for each SVM pattern</b>.
DOI: 10.6084/m9.figshare.17827307.v1
title: RNA sequencing of age-related fertility decrease

description: High-throughput transcriptome sequencing was used to identify differentially expressed genes in the ovarian granulosa cells of older women with infertility.
DOI: 10.6084/m9.figshare.1221856.v1
title: Evolutionary Insights into Cospeciation and Host Switching in Neotropical Streblidae (Diptera)

description: This work was an undergraduate project done by Gordon Bennett between 2003 and 2005. It was submitted for publication and reviewed but ultimately never published. We are providing the manuscript text and figures here for any interested parties. The sequences generated in this study have been submitted to Genbank. Voucher material is present in my lab. Please contact me if you are interested in any aspect of this work.
DOI: 10.6084/m9.figshare.20552223.v2
title: pretrained_models

description: Pretrained models that were used for OntoVAE manuscript. recount3_GTEx_GO: This model was trained with the ontobj GO_ensembl_ontobj.pickle recount3_GTEx_HPO: This model was trained with the ontobj HPO_ontobj.pickle Kang_PBMC_unstimulated_GO: This model was trained with the ontobj GO_symbol_ontobj.pickle
DOI: 10.6084/m9.figshare.21864507.v1
title: Incidence, risk factors, and prognosis of hypokalemia in patients with normokalemia at hospital admission.

description: <strong>Background</strong> Hypokalemia (K+&lt;3.5 mmol/L) is a common electrolyte abnormality observed in 20% of hospitalized patients. Previous studies have often dealt with the symptoms of hypokalemia, its prevalence, and risk factors in hospitalized patients. Very few studies have dealt with hospital-induced hypokalemia. The aim of this study was to find the incidence, predisposing risk factors, and prognosis of patients developing hypokalemia in patients with normokalemia at admission. <strong>Materials and methods</strong> A prospective observational study was performed over a period of two months. Patients with at least two potassium values after admission and normal K values at admission were considered for inclusion. Clinical features, diagnoses, laboratory reports, and treatment details, including antibiotics, were noted. Incidence of hypokalemia was determined. Patients with and without hypokalemia were compared. <strong>Results</strong> A total of 653 patients were studied; 138 (21.1%) developed hypokalemia. Diabetes, ischemic heart disease, heart failure, chronic kidney disease, hypertension, chronic liver disease, and COPD were the most associated comorbidities. Urea, creatinine, transaminases, and neutrophilia at admission differed significantly between those with and without hypokalemia groups. Most patients developed mild hypokalemia (78.2%); moderate and severe hypokalemia developed in 19.5% and 2% of patients, respectively. Hypokalemia developed mostly on the second(22.4%) and third (24.6%) day of hospitalization. Antibiotics were used in 60% of patients, with 23% and 24.5% receiving one and two antibiotics, respectively. Only linezolid and metronidazole use were significant with regard to the patient’s second potassium value. The potassium values returned to normal within 2.5±1.9 days. Three patients subsequently developed hyperkalemia. <strong>Conclusion</strong> Patients admitted under General Medicine mostly developed mild hypokalemia, even if they had multiple risk factors for developing hypokalemia. Inpatient hypokalemia had an incidence of 21%. An overwhelming majority (~88%) had at least one risk factor. Hypokalemia was not attributed to causing mortality in any patient.
DOI: 10.6084/m9.figshare.27050509.v8
title: Informational Processing and the Transparency-Trust Link: Political Affiliation, Values, and Information Search Behaviors

description: The literature has recognized that the relationship between transparency and trust in government depends on the characteristics of the messages, the informational environment, and the receivers. However, little research has examined how receivers’ political affiliation, values, and information search behaviors influence their information processing and thereby moderate the transparency-trust relationship. Using individual-level survey data combined with provincial-level data from China, the study finds that transparency on government websites is positively associated with trust in government. This positive effect is particularly pronounced among individuals who are Chinese Communist Party (CCP) members, more frequently use traditional media, or have stronger authoritarian values.
DOI: 10.6084/m9.figshare.28225520.v1
title: <b>Comparison of allele frequencies: Individuals versus Pooled datasets</b>

description: <i>Bromus auleticus</i>, a valuable forage grass native to the Pampa biome, is currently suffering genetic erosion. Therefore, it is central to assess the appropriate methodologies for developing population genomic studies and contributing to the conservation of this plant genetic resource. This study evaluated five accessions using two genotyping strategies: individual sequencing (ind-seq) and pooled sequencing (pool-seq). To compare their efficacy, was investigated the correlation between allele frequencies calculated using each approach. Geneticdiversity and population structure were also analyzed using both methods. These comparisons explicitly accounted for the potential effects of one or more of the following parameters: sample size, missing data, sequencing depth, and minor allele frequencies. Notably, the highest concordance and percentage of common SNPs between ind-seq and pool-seq was achieved using 30 to 60 plants per accession, with a maximum missing data threshold of 10% and a more tolerant minimum allele frequency threshold for pool-seq (0.01) compared to ind-seq (0.05). Reaching maximum similarity in allele frequencies also required a higher sequencing depth for pool-seq (4.8 million reads-Mr) than for ind-seq (0.9 Mr). Pools of 50 individuals yielded the highest number of polymorphic sites, averaging over 9,000 across all accessions at a sequencing depth of 4.8 Mr. Under these conditions, pool-seq consistently yielded a means across all accessions of 0.09 higher expected heterozygosity and 0.24 lower allelic richness compared to ind-seq across all accessions. The population structure detected with both methodologies showed agreement, aligning with the outcrossing nature of <i>B. auleticus</i> and the geographical origin of each accession. The average inbreeding coefficient of 0.2 indicates signs of inbreeding, highlighting the importance of conservation efforts of this valuable plant genetic resource. Based on these findings, two workflows were proposed to carry out population genomics studies of <i>Bromus auleticus</i>.
DOI: 10.6084/m9.figshare.3569637.v1
title: Supplementary Material for: Twelve-Month and Lifetime Prevalence of Mental Disorders in Cancer Patients

description: <strong><em>Background:</em></strong> Psychological problems are common in cancer patients. For the purpose of planning psycho-oncological interventions and services tailored to the specific needs of different cancer patient populations, it is necessary to know to what extent psychological problems meet the criteria of mental disorders. The purpose of this study was to estimate the 12-month and lifetime prevalence rates of mental disorders in cancer patients. <b><i>Methods:</i></b> A representative sample of patients with different tumour entities and tumour stages (n = 2,141) in outpatient, inpatient and rehabilitation settings underwent the standardized computer-assisted Composite International Diagnostic Interview for mental disorders adapted for cancer patients (CIDI-O). <b><i>Results:</i></b> The overall 12-month prevalence for any mental disorder was 39.4% (95% CI: 37.3-41.5), that for anxiety disorders was 15.8% (95% CI: 14.4-17.4), 12.5% (95% CI: 11.3-14.0) for mood disorders, 9.5% (95% CI: 8.3-10.9) for somatoform disorders, 7.3% (95% CI: 6.2-8.5) for nicotine dependence, 3.7% (95% CI: 3.0-4.6) for disorders due to general medical condition, and 1.1% (95% CI: 0.7-1.6) for alcohol abuse or dependence. Lifetime prevalence for any mental disorder was 56.3% (95% CI 54.1-58.6), that for anxiety disorders was 24.1% (95% CI: 22.3-25.9), 20.5% (95% CI: 18.9-22.3) for mood disorders, 19.9% (95% CI: 18.3-21.7) for somatoform disorders, 18.2% (95% CI: 16.6-20.0) for nicotine dependence, 6.4% (95% CI: 5.4-7.6) for alcohol abuse or dependence, 4.6% (95% CI: 3.8-5.6) for disorders due to general medical condition, and 0.2% (95% CI: 0.1-0.6) for eating disorders. <b><i>Conclusions:</i></b> Mental disorders are highly prevalent in cancer patients, indicating the need for provision of continuous psycho-oncological support from inpatient to outpatient care, leading to an appropriate allocation of direct personnel and other resources.
DOI: 10.6084/m9.figshare.14685903
title: Supplementary Material for: Supportive Hepatocyte Transplantation after Partial Hepatectomy Enhances Liver Regeneration in a Preclinical Pig Model

description: <b><i>Background:</i></b> Hepatocyte transplantation (HTx) is regarded as a potential treatment modality for various liver diseases including acute liver failure. We developed a preclinical pig model to evaluate if HTx could safely support recovery from liver function impairment after partial hepatectomy. <b><i>Methods:</i></b> Pigs underwent partial hepatectomy with reduction of the liver volume by 50% to induce a transient but significant impairment of liver function. Thereafter, 2 protocols for HTx were evaluated and compared to a control group receiving liver resection only (group 1, <i>n</i> = 5). Portal pressure-controlled HTx was performed either immediately after surgery (group 2, <i>n</i> = 6) or 3 days postoperatively (group 3, <i>n</i> = 5). In all cases, liver regeneration was monitored by conventional laboratory tests and the novel noninvasive maximum liver function capacity (LiMAx) test with a follow-up of 4 weeks. <b><i>Results:</i></b> Partial hepatectomy significantly impaired liver function according to conventional liver function tests as well as LiMAx in all groups. A mean of 4.10 ± 1.1 × 10<sup>8</sup> and 3.82 ± 0.7 × 10<sup>8</sup> hepatocytes were transplanted in groups 2 and 3, respectively. All animals remained stable with respect to vital parameters during and after HTx. The animals in group 2 showed enhanced liver regeneration as observed by mean postoperative LiMAx values (621.5 vs. 331.3 μg/kg/h on postoperative day 7; <i>p</i> &lt; 0.001) whereas HTx in group 3 led to a significant increase in mean liver-specific coagulation factor VII (112.2 vs. 54.0% on postoperative day 7; <i>p</i> = 0.003) compared to controls (group 1), respectively. In both experimental groups, thrombotic material was observed in the portal veins and pulmonary arteries on histology, despite the absence of clinical symptoms. <b><i>Conclusion:</i></b> HTx can be performed safely and effectively immediately after a partial (50%) hepatectomy as well as 3 days postoperatively, with comparable results regarding the enhancement of liver function and regeneration.