cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26819086
title: Supplementary Material for: Pathologic Outcomes and Survival in Patients with Rectal Cancer and Increased Body Mass Index

description: Introduction: We assessed any association between increased body mass index (BMI) and rectal cancer outcomes.
Methods: We included patients who underwent surgery for stage I-III rectal adenocarcinoma who were divided according to BMI at diagnosis: ideal BMI (18.5-24.9 kg/m2) and increased BMI (≥25 kg/m2). Groups were compared using univariate association analyses relative to baseline characteristics, pathologic outcomes, overall survival (OS) and disease-free survival (DFS). Main outcome measures involved circumferential resection margin (CRM), pathologic TNM stage, total mesorectal incision (TME) grade, OS, and DFS.
Results: 243 patients (64.6% male; median age 59 years) with median BMI of 26.3 kg/m2 were included. 62.1% had BMI ≥25 kg/m2. Increased BMI patients had similar proportions of males (66.9% vs 60.9%;p=0.407) and comorbidities (ASA III: 47% vs 37.4%;p=0.24) to ideal BMI patients. There were no significant differences in cN1-2 stage (p=0.279) or positive CRM (p=0.062) rates. The groups had similar complete/near-complete TME, pathologic TN stage, and survival rates. Pathologic and survival outcomes were also similar with a BMI cutoff of 30. 
Conclusions: There was a trend toward more nodal involvement in preoperative assessment and less CRM involvement in the final pathology of increased BMI patients. Complete/near-complete TME and survival rates were comparable between the groups.
DOI: 10.6084/m9.figshare.26935750
title: Supplementary Material for: Comparison of Machine Learning Algorithms and Nomogram Construction for Diabetic Retinopathy Prediction in Type-2 Diabetes Mellitus Patients

description: Introduction: To compare various machine learning algorithms for constructing a diabetic retinopathy (DR) prediction model among type 2 diabetes mellitus (DM) patients and to develop a nomogram based on the best model.
Methods: This cross-sectional study included DM patients receiving routine DR screening. Patients were randomly divided into training (244) and validation (105) sets. Least absolute shrinkage and selection operator regression was used for the selection of clinical characteristics. Six machine learning algorithms were compared: decision tree (DT), k-nearest neighbours (KNN), logistic regression model (LM), random forest (RF), support vector machine (SVM), and XGBoost (XGB). Model performance was assessed via receiver operating characteristic (ROC), calibration, and decision curve analyses (DCAs). A nomogram was then developed on the basis of the best model.
Results: Compared with the five other machine learning algorithms (DT, KNN, RF, SVM, and XGB), the LM demonstrated the highest area under the ROC curve (AUC, 0.894) and recall (0.92) in the validation set. Additionally, the calibration curves and DCA results were relatively favourable. Disease duration, DPN, insulin dosage, urinary protein, and ALB were included in the LM. The nomogram exhibited robust discrimination (AUC: 0.856 in the training set and 0.868 in the validation set), calibration, and clinical applicability across the two datasets after 1,000 bootstraps.
Conclusions: Among the six different machine learning algorithms, the LM algorithm demonstrated the best performance. A logistic regression-based nomogram for predicting DR in type-2 DM patients was established. This nomogram may serve as a valuable tool for DR detection, facilitating timely treatment.
DOI: 10.6084/m9.figshare.27003355
title: Metagenome sequencing and 982 microbial genomes from Kermadec and Diamantina Trenches sediments

description: phylogenomic analysis of bacteria and archaeal MAGs from trenches(gtdbtk based)
DOI: 10.6084/m9.figshare.27141390
title: Supplementary Material for: Comparative Assessment of Mitochondria Isolation Buffers for Optimizing Tissue-Specific Yields in Buffalo

description: Introduction: Mitochondrial studies are crucial for assessing livestock health and performance. While extensive research has been done on cattle and pigs, the influence of mitochondria in Indian buffalo remains unexplored. Therefore, in order to understand functions of mitochondria, their energy-related processes, or any additional mitochondrial traits in buffaloes’; it is imperative to isolate high-yield mitochondria with purity and functionality. Mitochondria are extracted by few conventional buffers. These buffers were previously characterized for their effectiveness in isolating mitochondria from rodent and human tissues. Therefore, the present study is to assess the performance of mitochondria isolation buffers specifically in buffalo tissues. 
Methods: The study involved isolation of mitochondria from four different tissues i.e. liver, brain, heart and muscles of slaughtered buffalo (n= 3), using: (i) Tris-Mannitol buffer (ii) Tris-Sucrose buffer and (iii) MOPS-Sucrose buffer. Buffer efficiency in preserving high fidelity during mitochondria isolation was assessed by comparison with Cayman's MitoCheck® Mitochondrial Isolation Kit (control). Further mitochondrial purity and functionality was assessed through comparative estimation of protein concentration and marker enzyme assays respectively. 
Results: Our results revealed insights into the suitability of specific buffer for functional mitochondria isolation from specific type of buffalo tissue. Notably for obtaining high quality functional mitochondria from buffalo, MOPS-Sucrose buffer appeared optimal for soft tissues (liver and brain), while Tris-Mannitol buffer was efficient for hard tissues (muscles and heart). 
Conclusions: Thus, Our research highlights the influence of buffer composition and tissue-specific variations in buffer effectiveness on mitochondrial activity in different tissues, leading to improved mitochondrial isolation in buffalo.
DOI: 10.6084/m9.figshare.5639197.v2
title: Wellcome Open Research - publication data year 1 (Nov 2016-Nov 2017)

description: On November 15<sup>th</sup> 2017 we celebrated Wellcome Open Research first year of publishing (see more in the blog here: https://blog.wellcomeopenresearch.org/2017/11/16/wellcome-open-research-first-year-in-numbers/).<br> As part of this annual milestone we created an infographic that highlighted some of the key numbers that represent our achievements to-date with regards to our authors, articles, publishing process and peer review.<br> This first dataset <i>only</i> includes information around the publishing process. It does not include the individual article data for authors or for the software and data repositories. This will be added in due course
DOI: 10.6084/m9.figshare.9929054
title: Agricultural intensification drives the evolution of host specialism in the ecological generalist bacterium Campylobacter jejuni

description: Modern agriculture has dramatically changed the distribution of animal species on earth. Changes to host ecology have a major impact on the microbiota, potentially increasing the risk of zoonotic pathogens being transmitted to humans, but the impact of intensive livestock production on host-associated bacteria has rarely been studied. Here we use large isolate collections and comparative genomics techniques, linked to phenotype studies, to understand the time-scale and genomic adaptations that promote proliferation of the most common food-born bacterial pathogen (<i>C. jejuni</i>) in the most extensively farmed agricultural mammal (cattle). Our findings reveal the emergence of cattle specialist <i>C. jejuni </i>lineages from a background of host generalist strains that coincided with the dramatic rise in cattle numbers in the 20<sup>th</sup> century. Cattle adaptation was facilitated by horizontal gene transfer and significant gene gain and loss, related to differences in host diet, anatomy and histology, leading to the proliferation of globally disseminated cattle specialists of major public health importance. This work highlights how genomic plasticity can allow important zoonotic pathogens to exploit altered niches in the face of anthropogenic change and provides information for mitigating some of the risks posed by modern agricultural systems.
DOI: 10.17632/3hr8f5nkhb.1
title: Analysis of counting data: Development of the SATLAS Python package

description: For the analysis of low-statistics counting experiments, a traditional nonlinear least squares minimization routine may not always provide correct parameter and uncertainty estimates due to the assumptions inherent in the algorithm(s). In response to this, a user-friendly Python package (SATLAS) was written to provide an easy interface between the data and a variety of minimization algorithms which are suited for analysing low, as well as high, statistics data. The advantage of this package is that it allows the user to define their own model function and then compare different minimization routines to determine the optimal parameter values and their respective (correlated) errors. Experimental validation of the different approaches in the package is done through analysis of hyperfine structure data of 203Fr gathered by the CRIS experiment at ISOLDE, CERN.
DOI: 10.17909/q524-zn59
title: GTO Program 1414 (PI: Perrin; HD 19467 B)

description: Dataset includes reference star HD 18511. Unfortunately, the observations in program 1414 partially failed due to a guide star acquisition error. A repeat of the full sequence including the failed ones was approved, and is expected in January 2024
DOI: 10.24432/c5r02g
title: Cirrhosis Patient Survival Prediction
DOI: 10.34943/1a3ad186-0a5e-44fb-9210-aa58cb64668c
title: Patricia Bay Echosounder, Bioacoustic Deployed 2020-03-03

description: The ASL AZFP Echosounder 55167 was deployed on 2020-03-03 at Patricia Bay. Patricia Bay is located in the Saanich Inlet, on the southern tip of Vancouver Island. This device is a Echosounder, Bioacoustic. Echosounders are used to measure acoustic backscatter as a proxy for detecting zooplankton, fish, bubbles or other particles in the water-column. An echosounder has one or more transducers which emit acoustic pulses at a particular frequency. When the pulses strike animals or other objects in the water, echoes are produced, which can be detected and converted by the transducers back into electrical signals. Software is then used to determine distances, sizes, concentrations and movements of organisms and other objects in the water. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.5281/zenodo.12769923
title: Coral Geochemical Proxy Thermometer via Machine Learning

description: Table S1. Model input data of different corals. Monthly satellite SST records with a spatial resolution of 0.25° × 0.25° for each coral reef region are obtained from the NOAA OISSTv2 AVHRR SST dataset (https://www.psl.noaa.gov/data/gridded/data.noaa.oisst.v2.highres.html) and used as SST data. The coral proxy dataset was collected from the following 4 studies(see References)

Table S2. Performance  metric of models trained with different sub-dataset and proxy combinations
DOI: 10.5281/zenodo.12776692
title: Response of convectively coupled Kelvin waves to surface temperature forcing in aquaplanet simulations: data and code

description: This is the data and code used for a journal paper entitled "Response of convectively coupled Kelvin waves to surface temperature forcing in aquaplanet simulations", written by Mu-Ting Chien and Daehyun Kim in 2024. This paper is in minor revision in the Journal of Advances in Modeling Earth System. The submitted paper is here: (https://essopenarchive.org/doi/full/10.22541/essoar.171322728.86206700/v1).
DOI: 10.5281/zenodo.12780137
title: Multicontextual Phenotype Models: Biomedical Database and Literature Phenotype and Social Media Phenotype
DOI: 10.5281/zenodo.13325111
title: Velocity and strain rate fields of the Southern Tibetan Plateau

description: This data set contains velocity and strain rate fields over the southern Tibetan Plateau, which are derived from Sentinel-1A and -1B synthetic aperture radar satellite data (SAR) and NETCDF (.grd) formats.

This repository contains:

(1) asc.grd : the InSAR LOS velocity field in the ascending tracks in a resolution of ~1000 m.

(2) desc.grd : the InSAR LOS velocity field in the descending tracks in a resolution of ~1000 m.

(3) dilatation_strain_rate.grd : the dilatational strain rate calculated from the interpolated GNSS Vn and InSAR-derived Ve.

(4) second_invariant_horizontal_strain_rate.grd:  the second invariant horizontal strain rate calculated from the interpolated GNSS Vn and InSAR-derived Ve.
DOI: 10.6084/m9.figshare.23954781
title: Alignment of all Onchocerca volvulus RNA Virus 1 and Onchocerca ochengi RNA Virus 1 sequences

description: This file contains five sequences in fasta format. The five sequences are viral genomes for different strains of Onchocerca volvulus RNA Virus 1, and Onchocerca ochengi RNA Virus 1, described in the project-associated manuscript. Sequences were aligned using the online implementation of MAFFT, with alignment algorithm FFT-NS-2.
DOI: 10.6084/m9.figshare.24899388
title: Supplementary Material for: DHX37 and the implications in Disorders of Sex Development: an update review

description: Background: DHX37 is an autosomal gene responsible for encoding a helicase from the DExD/H-box family that plays an essential role in ribosome biogenesis. Variants in this gene were previously reported in two different phenotypes: neurodevelopmental disorders and disorders/differences of sex development (DSD). Particularly for the DSD group, variants were mainly reported associated with gonadal dysgenesis and testicular regression syndrome. Summary: Focusing specific in the DSD group, we revised the 21 DHX37 variants described across a total of 55 cases published in the literature so far. We summarized the most important clinical and molecular features of all cases, trying to have a better comprehensiveness about this gene in the sexual development. Key Messages: The trick question regarding DHX37 is how a helicase involved in basic cell function could have a specific role in testis development. Little is known about the impact of DHX37 variants in DSD individuals. Nevertheless, current research strongly suggests that DHX37 is involved in the male sex development pathway, particularly in testis determination and maintenance. This is evidenced by the predominant assignment of affected individuals as males and the presence of Wolffian structures in most of the cases. Advancements in molecular techniques, such as the generation of induced pluripotent stem cells, and the digenic inheritance for DHX37 cases, are also addressed in this paper. This represents the first comprehensive review of all DHX37 variants published in the literature to date.
DOI: 10.6084/m9.figshare.25013312
title: Supplementary Material for: Magnetic resonance imaging-based Classifications for Symptom of Adenomyosis

description: Objectives: To identify an optimal magnetic resonance imaging (MRI)-based classification for the severity of adenomyosis and explore the factors associated with disease severity (dysmenorrhea or menorrhagia).
Design and Participants: Several classifications based on MRI have been proposed, and their phenotypes are reported to be associated with the severity of adenomyosis. However, a consensus classification based on MRI findings has not yet been reached. Our study was designed to retrospectively analyze data from a cohort of patients in the Affiliated Nanchong Central Hospital of North Sichuan Medical College from June 2017 to December 2021 before focused ultrasound ablation surgery (FUAS), to identify the optimal classification of adenomyosis severity from different classification criteria and explore factors associated with the presence of symptoms.
Methods: The proportions of disease severity among different classification groups were compared to obtain the one generating the most considerable chi-square value, which was identified as the optimal classification for informing disease severity. A logistic regression model was constructed to explore factors associated with disease severity.
Results: Classification of Kobayashi H (classification 4) concerning the affected areas and size (volumes of lesions) was recognized as the optimal one, which identified dysmenorrhea (χ2=18.550, p-value=0.002) and menorrhagia (χ2=15.060, p-value=0.010) secondary to adenomyosis. For volumes of uterine wall &lt;2/3, the dysmenorrhea rate in subtype-4 was higher than that in subtype-1 (χ2=4.114, p-value=0.043), and the dysmenorrhea rate in subtype-5 was higher than that in subtype-2 (χ2=4.357, p-value=0.037). Age (OR=0.899, 95%CI=0.810～0.997, p-value=0.044) and external phenotype (OR=3.588, 95%CI=CI 1.018～12.643, p-value=0.047) were associated with dysmenorrhea. Concerning volumes of uterine wall ≥2/3, the menorrhagia rate in subtype-3 remarkably increased compared with that in subtype-6 (χ2=9.776, p-value=0.002), and internal phenotype was identified as an independent factor associated with menorrhagia (OR=1.706, 95%CI=1.131～2.573, p-value=0.011).
Limitations: Patients in our study were all included before FUAS, which limited our result interpretation for the general patient population.
Conclusions: MRI-based classification 4 is identified as an optimal classification for informing the severity of adenomyosis. The phenotype of classification is the main characteristic associated with disease severity.
DOI: 10.6084/m9.figshare.25867090
title: Supplementary Material for: ORCA-EFCD consensus report on clinical recommendations for caries diagnosis. Paper III: caries diagnosis at the individual level.

description: The aim of the present consensus paper was to provide recommendations for clinical practice on the individual etiological and modifying factors to be assessed in the individual diagnosis of caries, and the methods for their assessment, supporting personalized treatment decisions.
The executive councils of the European Organisation for Caries Research (ORCA) and the European Federation of Conservative Dentistry (EFCD) nominated ten experts each to join the expert panel. The steering committee formed three work groups which were asked to provide recommendations on 1) caries detection and diagnostic methods, 2) caries activity assessment and 3) forming individualised caries diagnoses. The experts responsible for “individualised caries diagnosis” searched and evaluated the relevant literature, drafted this manuscript and made provisional consensus recommendations. These recommendations were discussed and refined during the structured process in the whole work group. Finally, the agreement for each recommendation was determined using an anonymous eDelphi survey. The threshold for approval of recommendations was determined at 70% agreement.
Ten recommendations were approved and agreed by the whole expert panel, covering medical history, caries experience, plaque, diet, fluoride and saliva. While the level of evidence was low, the level of agreement was typically very high, except for one recommendation on salivary flow measurement, where 70% agreed. 
It is recommended that all aspects of caries lesion progression and activity, recent caries experience, medical conditions and medications, plaque, diet, fluoride and saliva should be synthesized to arrive at an individual diagnosis.
The expert panel merged evidence from existing guidelines and scientific literature with practical considerations and provided recommendations for their use in daily dental practice.
DOI: 10.6084/m9.figshare.26002789
title: Supplementary Material for: Future directions for respiratory muscle training in neuromuscular disorders: a scoping review

description: Background: Respiratory muscle training (RMT) aims to improve inspiratory and/or expiratory muscle function in neuromuscular disorders (NMDs). A comprehensive overview of the available literature is lacking. This scoping review explores methodological characteristics, (adverse) effects, and adherence of RMT studies in NMDs. Moreover, it identifies limitations and research gaps in the literature, and provides future research directions. 
Summary: Eligible studies were identified using MEDLINE, Embase, Cochrane Database of Systematic Reviews, and Cochrane Central Register of Controlled Trials databases
Three reviewers independently selected articles. Inclusion criteria were English language, original research articles on RMT using a device, patients with an NMD, and pulmonary function tests or respiratory muscle strength as outcome measures. We included NMDs with slow, intermediate and fast progression. Exclusion criteria were critically ill patients, weaning from mechanical ventilation, other neurological disorders, and RMT combined with non-respiratory interventions. One reviewer extracted the data on patients characteristics, methodological characteristics, results of outcome measures, adverse events, and patient adherence. Forty-five studies were identified. We found a large diversity in study designs and training protocols. The effects of RMT on respiratory muscle strength and/or endurance are variable. Patient adherence was high and no serious adverse events were reported.
Key Messages: The diversity in studies across the available literature precludes definitive conclusions regarding effects of RMT on respiratory muscle function and clinically relevant outcomes in NMDs. Therefore, well-powered and -designed studies that focus on clinically relevant outcomes and assess whether RMT can improve or offset deterioration of respiratory muscle weakness in NMDs are needed.
DOI: 10.5281/zenodo.10570139
title: E2P4 COVID19 Trial Cytokine profile data

description: E2P4 treated COVID-19 donor serum samples, cytokine protein expression data set. 

Proteins were measured using the Olink® Target 48 Cytokine panel* (Olink Proteomics AB, Uppsala, Sweden) according to the manufacturer's instructions. The Proximity Extension Assay (PEA) technology used for the Olink protocol has been well described,49 and enables 45 analytes to be analyzed simultaneously, using 1 µL of each sample. In brief, pairs of oligonucleotide-labeled antibody probes bind to their targeted protein, and if the two probes are brought in close proximity the oligonucleotides will hybridize in a pair-wise manner. The addition of a DNA polymerase leads to a proximity-dependent DNA polymerization event, generating a unique PCR target sequence. The resulting DNA sequence is subsequently detected and quantified using a microfluidic real-time PCR instrument (Biomark HD, Fluidigm). Data is then quality controlled and normalized using an internal extension control and calibrators, to adjust for intra- and inter-run variation. The final assay read-out is presented in pg/ml using a 4-Pl fit for absolute quantification. All assay validation data (detection limits, intra- and inter-assay precision data, etc.) are available on manufacturer's website (www.olink.com).