cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/ksxv9hxdwb
title: Microcirculation Endotoxemia in horses

description: Microcirculation is the essential link between macrocirculation and cellular metabolism. We hypothesized that acute endotoxemia affects microcirculatory variables in anaesthetized horses.
This was a prospective, experimental trial. Six healthy adult horses were anesthetized with dexmedetomidine, ketamine, and midazolam and were mechanically ventilated under isoflurane anaesthesia. Endotoxemia was induced with 30 ng kg-1 E. coli lipopolysaccharide intravenously. A fluid bolus and noradrenaline (NA) infusion were administered to produce normotension. Microcirculation variables were obtained by a side-stream darkfield camera (de Backer density (DBD), perfused de Backer density (PDBD), proportion of perfused vessels (PPV), microvascular flow index (MFI), heterogeneity index (HI)), laser-doppler flowmetry (blood flow), and white light spectrometry (tissue oxygen saturation (tSO2)) in sublingual, jejunal, and genital area. Measurements were obtained at baseline, after endotoxin, at 60 and 120 minutes and during the normotensive phase. Data were analyzed by one-way ANOVA and Tukey-Kramer adjustment (p ≤ 0.05). 
The PPV decreased significantly over time by 30% (p &lt; 0.001) at the jejunum. MFI decreased from baseline to ET60 and from baseline to ET120 in sublingual and genital mucosa (2.9 vs. 1.4, p = 0.0004 and 2.8 vs. 1.9, p &lt; 0.01), respectively. The sublingual HI increased from baseline to ET60, ET120 and NA (0.1 vs. 0.9, p = 0.02; 0.1 vs. 0.6, p = 0.01; 0.1 vs. 0.3, p = 0.01), respectively. The genital HI increased from baseline to ET120 (0.2 vs 1.1 p ≤ 0.01) and NA (0.16 vs. 0.53, p &lt; 0.05, respectively). Moderate agreement between observers for MFI assessment was present with total kappa = 0.4. The other assessed parameters were not statistically significantly different.
Overall, short-term experimental endotoxemia did not alter tSO2, blood flow, DBD, PDBD or PPV, however, it did negatively alter MFI and HI. Fluids and NA were unable to restore MFI and HI to baseline values.
DOI: 10.6084/m9.figshare.24451714.v1
title: Fluoxetine mesocosm experiment

description: Fluoxetine mesocosm experiment
DOI: 10.6084/m9.figshare.24961617.v1
title: <b>Association between </b><b><i>ACE</i></b><b> (I/D) polymorphism and playing position in Brazilian junior handball players</b>

description: Handball is team sport a characterized by fast-paced, dynamic play, involving a combination of physical strength, agility, and tactical skills. Sports performance can be influenced by various factors that can have effects on athletes and the influence of genetic polymorphisms on athletic performance has been widely explored. This study investigated the interactions between the polymorphisms ACE (I/D) and their association with endurance and strength phenotypes in Brazilian handball junior players considering their playing position. 90 junior handball players and 72 age-matched controls were evaluated. DNA was extracted using a QIAamp DNA Blood Mini kit and ACE I/D polymorphism was genotyped by conventional PCR followed by electrophorese in agarose gel. All participants were anthropometrically evaluated and performed the standing long jump (SLJ) and medicine ball throw (MBT) tests. Handball players presented superior performance in the SLJ and MBT tests compared to the control group in all playing positions (p &lt; 0.01). No significant differences observed in ACE genotype or allele frequencies when comparing handball athletes and controls or among playing positions. However, a significant difference was observed when comparing all athletes to controls using the over-dominant model (p = 0.035). Additionally, athletes with II + ID and II + DD genotypes exhibited superior performance in the standing long jump test (p = 0.04) and ID athletes demonstrated increased height compared to II + DD counterparts (p = 0.04). In conclusion, our data showed a potential association between ACE (I/D) polymorphism and the overall athletic predisposition in handball players, with no association with playing position.
DOI: 10.6084/m9.figshare.25127297.v1
title: Irrigation area data

description: Netcdf used to generate Figure 1d in <b><i>The importance of irrigation for the accurate simulation of fog over northern India. </i></b>Values of 1 indicates irrigated and 0 indicates not irrigated in the netcdf. This is used to decide the area to increase soil moisture to saturation. The irrigated area is derived using the CCI land use data and a global irrigation water use dataset. A 1 is assigned to a grid point if it is identified as irrigated cropland in the CCI dataset and the irrigated water use for January is above 5 mm.
DOI: 10.6084/m9.figshare.8323334.v1
title: SPATIAL ANALYSIS OF THICKNESS CHANGES IN TEN RETINAL LAYERS OF ALZHEIMER’S DISEASE PATIENTS BASED ON OPTICAL COHERENCE TOMOGRAPHY. Data Files

description: Thickness of ten retinal layers in Alzheimer disease patients (19) and control (24) groups.<br>
DOI: 10.17632/v7nmy2296k
title: Proteins with amino acid repeats constitute a rapidly evolvable and human-specific essentialome. Anjali K Singh et al.

description: Essential genes, and their protein products, are necessary for organismal survival. These proteins, owing to their functional indispensability, are conserved and perform fundamental biological processes. Contrarily, proteins which contain stretches of identical amino acids (referred as homorepeats) tend to evolve rapidly, as repetitive sequences are hypermutable. Strikingly, eukaryotic essentialomes are enriched for proteins with amino acid homorepeats. This presents a function versus evolution paradox, as to why are the hypermutable homorepeats prevalent in essential proteins with conserved functionalities. In this study, we resolve this paradox by undertaking systems-level analyses in humans by assembling and integrating 60 publicly-available large-scale datasets spanning sequence, structure, molecular networks, regulation, spatio-temporal expression, phenotype and evolution. We found that essential proteins with homorepeats
(i) Show molecular pleiotropy, i.e., they are multifunctional and bring about cross-talk between processes,
(ii) Participate in regulatory processes and bring about expansive regulation at the genomic and transcriptomic levels, while essential proteins without repeats, are preponderantly involved in housekeeping functions
(iii) Rapidly evolve, with amino acid substitutions often affecting functionally important sites such as Post translational modification sites aiding rapid network rewiring and
(iv) Are involved in dynamic and human-specific temporal regulation of human embryonic and brain development, facilitating the emergence and evolution of human-specific processes.
The presence of repeats in essentialomes brings about a trade-off between robustness and evolvability facilitating rapid adaptability.

Here, we have uploaded all molecular interaction networks that were compiled and investigated in this study. We have also added the source code to facilitate repetition of this work and address other fundamental systems- and molecular-level questions. The instructions regarding usage of the codes are provided in individual scripts.
DOI: 10.6084/m9.figshare.12475718.v1
title: A list of eeb conferences in 2020

description: A non-exhaustive list of conferences in ecology, evolutionary biology, and to a lesser extent ecology. Items populated from rapid online searches and several key aggregation sites such as Nature Ecology and Evolution website and The World Academy of of Science, Engineering, and Technology list filtered using the key term 'ecology'.<br>There are potential duplicate listings to some extent because of differences in conference title listings between resource listing sites.
DOI: 10.6084/m9.figshare.1533296.v1
title: Coding of Interlink-analysis

description: Coding of Interlink-analysis
DOI: 10.6084/m9.figshare.21551280.v2
title: Fitting results of viscosity-temperature models

description: Fitting results of the Arrhenius, Reynolds and Doolittle equations to the viscosity-temperature data of fluids in the paper "Modeling of the Temperature Effects on Magnetorheological Fluids over a Wide Temperature Range based on Free Volume Theory".
DOI: 10.6084/m9.figshare.25934302.v4
title: Living in the Afterlife

description: Raw materials used in the study "Living in the Afterlife: clues from direct experiencers".Preprint available open-access at: https://osf.io/preprints/psyarxiv/7n9gr
DOI: 10.6084/m9.figshare.28742313.v1
title: Data for figures from Learning from nature: photosynthetic traits conferring superior salt tolerance in wild rice Oryza coarctata

description: raw data for revised figs.xlsx
DOI: 10.6084/m9.figshare.5127103.v1
title: Supplementary Material for: Patients' Perceptions of Research Biopsies in Phase I Oncology Trials

description: <b><i>Objective:</i></b> Research biopsies are increasingly incorporated into phase I oncology trials resulting in ethical and logistical challenges for patients and clinicians. Patients' understanding and willingness to undergo these biopsies are crucial. <b><i>Methods:</i></b> Over 12 months, we administered a questionnaire comprising three sections: demographics and previous cancer therapy, understanding of phase I trials and personalized medicine, and understanding of biopsies and associated risks. <b><i>Results:</i></b> Out of 56 patients approached, 47 patients completed the questionnaire. Overall, the patients were well informed about the concepts of personalized medicine and 89% (n = 42) were aware that early phase clinical trials aim to define a dose and explore side effects of new drugs. Interestingly, 76% (n = 36) expected early phase trials to improve symptoms, quality of life and survival. Offering hope and feeling in control of their treatment were important components for 80% (n = 38) and 57% (n = 27), respectively. The majority of this highly selective patient cohort understood the concept of research biopsies, with 59% (n = 28) willing to have a fresh research biopsy for trial participation. Although 72% (n = 34) felt that research biopsies should be optional, only 19% (n = 9) would not participate in a clinical trial with mandatory biopsies. Compared to diagnostic biopsies, the patients were less likely to accept associated risks with research biopsies. <b><i>Conclusion:</i></b> As research biopsies are crucial to many components of the drug development process, our study provides evidence for patients' overall willingness to undergo research biopsies for trial purposes. A consent process tailored to the biopsy site may help patients weigh up the associated risks versus benefits. © 2014 S. Karger AG, Basel
DOI: 10.6084/m9.figshare.6736169.v1
title: Configure iTerm to open chromosome positions in the UCSC Genome Browser

description: How to configure the iTerm2 terminal emulator to open a chromosome position in the UCSC Genome Browser
DOI: 10.17632/b2y882mzg3
title: PREVELANCE OF FOREARM AND WRIST PAIN DUE TO PROLONGED BIKE RIDING

description: Forearm and wrist pain due to prolonged bike riding is a common issue among motorcyclists. The prevalence of this condition varies across studies, but it is clear that it is a significant problem that can lead to discomfort and injury. The position of the handlebars, the type of handlebars, and the size and shape of the handlebars are all factors that can contribute to forearm and wrist pain in Bikers.
DOI: 10.17632/hxrtddggsx
title: Urban tree canopy has greater cooling effects in socially vulnerable communities in the US

description: This data is a geodatabase, which includes data of the socioeconomic indicators and land surface temperature we used at the blockgroup level for 38 US cities in 2010
DOI: 10.6084/m9.figshare.11497032.v3
title: Global Annual Urban Dynamics (1985-2015)

description: High spatiotemporal resolution mapping of global urban change from 1985 to 2015<br>
DOI: 10.6084/m9.figshare.14673399.v1
title: Supplemental Table 1

description: <b>Supplemental Table 1.</b> Animal weights at time of SU5416 (or vehicle control) injection, 5 and 10 weeks post-injection.
DOI: 10.6084/m9.figshare.24129012.v2
title: Supplementary figures, tables, and code used to train models and produce input files for "<b>Predicting fungal secondary metabolite activity from biosynthetic gene cluster data using machine learning</b>" (Riedling et al. 2023).

description: All biosynthetic gene cluster and secondary metabolite bioactivities used to train the models can be found in supplemental tables 1 and 2. The Jupyter notebooks fungal_only_trained_model and NP_prediction_bacterial_and_fungal contain the code necessary to train the models. The Jupyter notebooks titled Running_predictions contain the code to make predictions on SM bioactivity from antiSMASH and RGI input. The Jupyter notebooks require the additional Python scripts so keep all scripts in the same directory as the notebooks. The scripts to extract the features from the antiSMASH and RGI files are included in the notebooks.
DOI: 10.6084/m9.figshare.25011752.v1
title: Raw data from [Ocampo J, Chereji RV, Eriksson PR, Clark DJ. Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination. Genome research. 2019;29(3):407–417, and Ocampo J, Chereji RV, Eriksson PR, Clark DJ. The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo. Nucleic acids research. 2016;44(10):4625–4635] processed as indicated in material and methods .

description: Living organisms, including baker yeast, tightly package and separate genetic information from the rest of the cell. The DNA is wrapped around nucleosomes to achieve folding at its lowest level. The arrangement of nucleosomes along the genome modulates the access and use of genetic information, which ultimately affects the cell's functioning. Despite efforts to study nucleosome profiles, the mechanism of their collective arrangement along the genome is poorly understood. We addressed this issue by directly comparing and classifying nucleosome profiles along the genes, which are known to support necessary information for cell functioning. Our findings show that the spatial organization of nucleosomes in genes is different from other genomic regions, and this difference is actively maintained by energy-consuming factors. The regulation and compartmentalization of nucleosomal organization require the simultaneous action of local and global processes.
DOI: 10.6084/m9.figshare.27221061.v2
title: Single-nucleus chromatin landscape dataset of mouse PDX models of medulloblastoma

description: In this study, a single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) was employed to generate comprehensive chromatin accessibility maps. The data were obtained from 80,273 cells derived from four distinct medulloblastoma xenografts: subcutaneous (SUB) and orthotopic (ORTH) xenograft models of the G3 and SHH subtypes of medulloblastoma.<br>
DOI: 10.6084/m9.figshare.7513478.v1
title: ANTIBACTERIAL POTENTIAL OF NATIVE PLANTS FROM THE CAATINGA BIOME AGAINST Staphylococcus spp. ISOLATES FROM SMALL RUMINANTS WITH MASTITIS

description: ABSTRACT The aim of the present study is to assess the antibacterial potential of plants from the Caatinga biome of the semi-arid region of Pernambuco, against Staphylococcus spp. isolates from cases of subclinical mastitis in small ruminants, such as goats and ewes. Ethanolic extracts of the following plants from the Caatinga biome were used: Encholirium spectabile Mart., Bromelia laciniosa Mart., Neoglaziovia variegata Mez., Amburana cearensis (Fr. Allem.) A. C. Smith, Hymenaea martiana Hayne, and Selaginella convoluta Spring. The presence of phenolic components, flavonoids, steroids, and terpenoids was verified for all the tested extracts. The mean minimal bactericide concentrations of the extracts of E. spectabile, B. laciniosa, and N. variegate were 11,379, 11,405, and 11,995 µg/mL, respectively. The highest inhibitory activities were observed for A. cearensis and H. martiana, which inhibited 88.1 and 99.4% of the isolates, respectively. Other studies focusing on in vitro and in vivo activities should be undertaken.
DOI: 10.17632/pj9hzmp7ym
title: Screen use, sleep duration, daytime somnolence, and academic failure in school-aged adolescents

description: We surveyed 1,257 12- to 18-year-old adolescents attending 52 schools in urban or suburban areas of Argentina. We recorded the daily exposure to various screen-based activities, including video- and online-gaming, social media, TV or streaming. Screen time and device type in the hour before bedtime, sleep patterns during weekdays and weekends, somnolence (Pediatric Daytime Sleepiness Scale score), and grades in language and mathematics were also assessed.
DOI: 10.17632/rsd9bcjb2f
title: Political Crowdsourcing on Social Media - Survey Data

description: This dataset collected from a survey carried out in the United Kingdom, Malaysia, and Pakistan, with the goal of understanding various variables impacting political trust. The data was collected from September to November 2021 via an online survey on Google Forms, obtaining 472 valid responses. Based on relevant literature, the survey instrument was designed to cover respondents' opinions on partisanship, social media utilization, online social capital, voluntary online and offline political participation, and political trust. The dataset provides useful insights for institutional practitioners and policymakers in democracy and political communication, facilitating the policy formulation to bolster political trust through collaborative crowdsourcing.

dataset/
 PC-SM.csv: CSV file containing coded item survey data.
 item-description.xls: Description of coded survey items.
DOI: 10.17632/t9ndx37v5h
title: Digital Knee X-ray Images

description: The dataset consists of 1650 digital X-ray images of knee joint which are collected from well reputed hospitals and diagnostic centres. The X-ray images are acquired using PROTEC PRS 500E X-ray machine. Original images are 8-bit grayscale image. Each radiographic knee X-ray image is manually annotated /labelled as per Kellgren and Lawrence grades by 2 medical experts. A novel approach has been developed to automatically extract the Cartilage region (region of interest) based on density of pixels.
DOI: 10.17632/tbdw7pxd5r
title: AI-driven mechanistic analysis of conformational dynamics in CNNM/CorC Mg2+ transporters

description: Data 1. PDB files of AlphaFold structures
Data 2. Numerical data for MD simulations and Mg2+ export assay
Data 3. Raw image files for immunoblotting and biochemical cross-linking assays
DOI: 10.6084/m9.figshare.11856039.v4
title: Dataset for manuscript: Effects of polyisoprenoids from Avicennia lanata and Avicennia alba leaves on the gene expression of P13K, Akt1, mTOR, P53, and EGFR in human colorectal adenocarcinoma WiDr cells

description: This dataset contains raw material for Figure 2 and Figure 3
DOI: 10.6084/m9.figshare.12853107.v1
title: Sounds produced by bottlenose dolphins (<i>Tursiops</i>): a review of the defining characteristics and acoustic criteria of the dolphin vocal repertoire

description: Bottlenose dolphins make many different sounds that have been recorded and described by researchers for over 60 years. This species, <i>Tursiops truncatus</i>, is arguably the most studied marine mammal. They have the ability to hear and produce sounds over a range of at least 150 kilohertz (kHz). Although the human hearing is limited in bandwidth to less than 20 kHz, dolphin sounds have historically been described as humans perceive them (e.g. whistles, squeals, buzzes, barks, quacks, pops, etc.). Often the same names have been used for different sounds and different names have been used for sounds that are apparently the same. In this review, we try and summarize the dolphin sound literature and provide standardized spectrograms where possible. Our goal is to provide a foundation for future research to build upon by providing a tool for identifying whether a sound has been described before. Novel sound types can then be recognized. Also, we encourage future studies that show when dolphins perceive two sound types as different. Detailed reports linking sound and behaviour are also essential. Only then can we have a complete idea of the dolphin repertoire and begin to understand how they use sound for communication.
DOI: 10.6084/m9.figshare.19548547.v1
title: Supplementary Material for: Dynamic observation: Immune-privileged microenvironment limited the effectiveness of immunotherapy in an intraocular metastasis mouse model

description: Introduction: Intraocular metastasis (IM) occurred in approximately 8-10% of patients with metastatic malignancy, for whom oncological immunotherapies showed poor visual potential. However, the mechanism for that inefficiency remains unclear and requires further exploration. Methods: we established a novel mouse model of intraocular metastasis by intracarotid injection of cutaneous melanoma cells. We investigated disease progression using ophthalmic and histological examinations. We used combined anti-PD-1 and anti-CTLA4 antibodies for immunotherapy and evaluate the therapeutic effects in mice model. In addition, we characterized the immune microenvironment of tumor infiltrating CD8+ T by fluorescence staining and assessed their cytotoxicity by flow cytometry. Results: All mice presented IM in the left eye, while the right eye was healthy. Uveal tissues with rich vascularity (e.g., the iris, ciliary body, and choroid) initiated intraocular metastasis at an early stage, and intraocular metastasis development resulted in several secondary changes, including corneal swelling, retinal detachment, and intratumoral haemorrhage. Immunotherapy could inhibit intraocular metastasis, prolong the time to eye rupture but did not prevent rupture ending. This inefficiency might be attributed to ocular tissues specificities that inhibited CD8+ T cells infiltration via PD-L1 expression. PD-L1low corneal tissue resisted tumor invasion with high levels of CD8+ T cells infiltration, whereas CD8+ T cells were deficient in PD-L1high uveal metastasis. Furthermore, we found a significantly increased PD-1+/- CD4+ and PD-1+/- CD8+ T cells infiltrating the intratumoral haemorrhage area. Although these CD8+ T cells in the IM were not exhausted and had a higher capacity of cytotoxicity (higher Interferon-γ ratio) than CD8+ T cells in the blood, FasL+ PD-L1+ ocular tissue can strongly inhibit these IM infiltrating T cells. Conclusions: Immunotherapy can inhibit the disease progression of intraocular metastasis. Enhancing the effects of tumor-infiltrating CD8+ T cells should be one of the highest potentials to improve the visual potential.