cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14134745.v1
title: Supplementary Table S1: LA–ICP–MS zircon U–Pb data for the Ordovician–Silurian granitoids in southern Yunnan. Tracking Prototethyan assembly felsic magmatic suites in southern Yunnan (SW China): Evidence for an Early Ordovician–Early Silurian arc-back arc system

description: <b>Supplementary Table S1:</b> LA–ICP–MS zircon U–Pb data for the Ordovician–Silurian granitoids in southern Yunnan.
DOI: 10.6084/m9.figshare.14134751
title: Supplementary Table S2: Zircon in-situ Hf isotopic compositions for the Ordovician–Silurian granitoids in southern Yunnan. Tracking Prototethyan assembly felsic magmatic suites in southern Yunnan (SW China): Evidence for an Early Ordovician–Early Silurian arc-back arc system

description: <b>Supplementary Table S2:</b> Zircon in-situ Hf isotopic compositions for the Ordovician–Silurian granitoids in southern Yunnan.
DOI: 10.6084/m9.figshare.14134748
title: Supplementary Table S3: Major oxides, trace elemental and Sr–Nd isotopic data for the Ordovician–Silurian granitoids in southern Yunnan. Tracking Prototethyan assembly felsic magmatic suites in southern Yunnan (SW China): Evidence for an Early Ordovician–Early Silurian arc-back arc system

description: <b>Supplementary Table S3:</b> Major oxides, trace elemental and Sr–Nd isotopic data for the Ordovician–Silurian granitoids in southern Yunnan.
DOI: 10.5281/zenodo.4569532
title: Data and scripts for the analysis of fruit flies' species distributions in Reunion island (v2)

description: Supplementary informations
DOI: 10.5281/zenodo.4569531
title: Data and scripts for the analysis of fruit flies' species distributions in Reunion island (v2)

description: Supplementary informations
DOI: 10.6084/m9.figshare.13560548
title: Data from: Method of place cell classification determines the population of cells identified

description: Data from manuscript "Method of place cell classification determines the population of cells identified".<br>Each zip file is one session, with the filename indicating the mouse name and the date of recording (i.e. mouse_date.zip). Each zip file contains a mat-file called 'Fall.mat'. This was generated by using Suite2P<sup>1</sup> on the recordings, which were recorded at 7.51 fps. Within this, F represents the fluorescence traces (ROIs by timepoints), and Fneu represents the neuropil fluorescence traces (ROIs by timepoints). We calculated the fluorescence using: F-0.7*Fneu. For more information on the Suite2P outputs see: https://suite2p.readthedocs.io/en/latest/outputs.html<br>The zip files also contain a mat-file called 'locomotion.mat'. This contains the location trace for each session, scaled between 0-1. The length of the track was 200 cm, so in order to get the location in cm, one can simply do: loco * 200. <br><br>1. Pachitariu, Marius, et al. "Suite2p: beyond 10,000 neurons with standard two-photon microscopy." <i>Biorxiv</i> (2017).
DOI: 10.6084/m9.figshare.13793744
title: Data for Cardoni et al. (2021): High-Throughput Sequencing of 5S-IGS rDNA in Fagus L.

description: Data dump of and supplement to <b>Cardoni et al. (2021)</b> High-Throughput Sequencing of 5S-IGS rDNA in Fagus L. (Fagaceae) reveals complex evolutionary patterns and hybrid origin of modern species. <i>bioRxiv</i>. https://doi.org/10.1101/2021.02.26.433057<br> <br>This fileset reports intra-/inter-genomic variation of the nuclear-encoded ribosomal 5S region in <i>Fagus</i> (beech). We used a multi-copy, potentially multi-locus marker, the non-transcribed intergenic spacer (IGS) of the 5S nuclear ribosomal DNA, and high-throughput target sequencing to address taxonomy, diversity, and evolution of the <i>F. crenata – F. sylvatica</i> s.str. lineage, and including <i>F. japonica</i> as outgroup. The collected data detail the distribution of divergent main 5S sequence types in the studied species pointing to deep polymorphism (allopolyploid origins), incomplete lineage sorting and repeated phases of reticulation. <br><br>The fileset includes:<br><b>Graphical abstract</b>: <br><i>5S_IGS...png</i>—Doodle summarising results of the study and distribution of sampled 5S-IGS variants.<i>GC_length...png</i>—Violin and scatterplots of the GC content and length of 5S-IGS amplicons, sorted by samples and sequence major types.<br><b>Data dump</b><i><br></i><i>ODA.zip</i>—Zipped online data archive prodiving used phylogenetic data and analysis files. See archive’s ReadMe.txt for content and archive structure.<br><b>Supplementary information</b><br>Also included are Cardoni et al. (2021) supplementary files S1–S4, which provide extended materials, results and discussion (<b>File S1; PDF</b>); basic information about samples, obtained HTS reads, an annotated lists for the 4,693 variants with an abundance of ≥ 4 summarised also as Pivot tables (<b>File S2, spread-sheet XLSX</b>; optimised for and using Excel autoformatting); graphical representation of the EPA analysis of 4007 5S-IGS variants with a total abundance &lt; 25 (<b>File S3, PDF</b>); and a fully annotated alignment of select-sequence subset in tabulated, graphically enhanced form (<b>File S4, spread-sheet XLSX</b>, includes colouration).<br>
DOI: 10.21421/d2/rio2qm/jsx3eb
title: SorghumPangenome.fa.gz

description: Sorghum pangenome sequence assembly
DOI: 10.21421/d2/rio2qm/7krocj
title: SorghumPangenomeGenesAnnotations.gff.gz

description: Gene models and annotations
DOI: 10.21421/d2/rio2qm
title: Sorghum pan-genome explores the functional utility for genomic-assisted breeding to accelerate the genetic gain

description: The sorghum pangenome consists of 210,805 sequences including the 10 chromosomes and 860 scaffolds sequences from the sorghum reference genome assembly v3.1.0. Additionally, 209935 assembled contig sequence from 176 sorghum accessions were the genetic gain from the pangenome assembly. The reference gene models and gene prediction on the assembled contigs together report a total of overall 35719 genes, of which 34211 genes are from reference and remaining gene models were predicted with ab initio and homology-based gene prediction. Furthermore, the gene models were annotated with UniRef90 protein database.
DOI: 10.5281/zenodo.4529647
title: All-atom Molecular Dynamics Simulations of Meiosis 1-associated protein (M1AP) to Investagate the Impact of Known Missense Mutations Associated with Male Infertility through Non-obstructive Azoospermia

description: Protein structure of meiosis 1-associated protein (M1AP) was modelled by using two of the best tools in CASP13, namely Robetta (from Baker Lab) and GalaxyWeb (from Seok Lab). Even though some other available best CASP tools were also utilized for modeling, they were not included this dataset because of low quality (The related results are included the paper that will be published soon). After these two best models were compared by analyzing the stability via molecular dynamics (MD) simulations, GalaxyWeb model were used to investigate the impact of mutations (i.e., S50P, R266Q, P389L, G317R, and L430P) in M1AP which were recently associated with non-obstructive azoospermia (NOA). NOA is a male infertility-related condition causing absence of sperm in the seminal fluid due to meiosis failure. We aimed to elucidate the pathogenicity mechanisms of these five missense NOA-related mutations on M1AP by performing molecular modeling and MD simulations. This dataset includes the results of 500 ns MD simulations (two repeats, each 250 ns) for each of the mutant and wild-type systems. Systems were prepared in Visual Molecular Dynamics (VMD 1.9.3) by placing them in a TIP3P water box with approximately 20 Å thickness from the protein surface and neutralizing the system charge with 0.15 M KCl. Of note, only protein parts were kept for the submission to reduce the size of files. Nanoscale Molecular Dynamics (NAMD 2.13-CUDA) was used to perform MD simulations with CHARMM36m force field. For pressure and temperature controls, Nosé-Hoover Langevin barostat and Langevin thermostat were used. ShakeH algorithm of NAMD was applied for water molecule constraints. 12 Å cut-off distance was used for van der Waals interactions. Switching function starts at 10 Å and reaches zero at 14 Å. Integration time-step was 2 fs. To compute the long-range Coulomb interactions, the particle-mash Ewald method was used. NPT ensemble was applied for whole simulations. Two step minimization & equilibration procedure was performed: (1) 5,000-step minimization and 1 ns equilibrium with constraints on the protein; (2) 5,000-step minimization and 1 ns equilibrium without the constraints on the protein. All related configuration files for wild-type system were also included to the dataset. Production simulations were run twice along 250 ns by using different random seeds to assign the velocities from Boltzmann distribution (total simulation time for each system was 500 ns, which are given as 250 ns repeat 1, and 250 ns repeat 2). Only the production simulations were supplied in the dataset whereas the minimization and equilibration trajectories are available upon a reasonable request.
DOI: 10.5281/zenodo.4549679
title: Dataset related to article "Validation of the Red Flags Index for Early Diagnosis of Crohn's Disease: A Prospective Observational IG-IBD Study Among General Practitioners"

description: This record contains raw data related to article "Validation of the Red Flags Index for Early Diagnosis of Crohn's Disease: A Prospective Observational IG-IBD Study Among General Practitioners" Diagnostic delay &gt;12 months is frequent in Crohn's disease [CD]. Recently, the International Organization for Inflammatory Bowel Disease [IO-IBD] developed a tool to identify early CD and reduce diagnostic delay. Subjects with an index ≥8 are more likely to have suspected CD (odds ratio [OR] 205, p &lt;0.0001). We aimed to validate this questionnaire at the community level in patients seen by the general practitioners [GPs] in two large areas of Lombardy, Italy. <strong>Methods: </strong> Consecutive adult patients referring to the GP were screened. The GPs administered the Red Flags [RF] questionnaire to the eligible patients. All patients were referred to the nearest participating centre to confirm or exclude the diagnosis of CD. Sensitivity, specificity, and positive and negative predictive values [PPV, NPV] of the RF index [RFI] were calculated. Patients lost to follow-up after the first gastroenterological visit were analysed using a non-responder imputation, assuming they were negative for CD diagnosis. <strong>Results: </strong> From November 2016 to November 2019, 112 patients were included. A total of 66 subjects [59%] completed the study after the first gastroenterological visit. The prevalence of CD was 3.6% in the study population [4/112]. The RF index had 50% sensitivity, 58% specificity, 4% PPV, and 97% NPV. A combined diagnostic strategy with faecal calprotectin [FC] [RFI ≥8 and/or FC &gt;250 ng/g] resulted in significantly improved accuracy: sensitivity 100% [29-100%], specificity 72% [55-85%], PPV = 21% [5-51%], NPV = 100% [88-100%]. <strong>Conclusions: </strong> The RF Index combined with FC is a valid tool to identify patients with high probability of having CD at early stage.
DOI: 10.5281/zenodo.4549678
title: Dataset related to article "Validation of the Red Flags Index for Early Diagnosis of Crohn's Disease: A Prospective Observational IG-IBD Study Among General Practitioners"

description: This record contains raw data related to article "Validation of the Red Flags Index for Early Diagnosis of Crohn's Disease: A Prospective Observational IG-IBD Study Among General Practitioners" Diagnostic delay &gt;12 months is frequent in Crohn's disease [CD]. Recently, the International Organization for Inflammatory Bowel Disease [IO-IBD] developed a tool to identify early CD and reduce diagnostic delay. Subjects with an index ≥8 are more likely to have suspected CD (odds ratio [OR] 205, p &lt;0.0001). We aimed to validate this questionnaire at the community level in patients seen by the general practitioners [GPs] in two large areas of Lombardy, Italy. <strong>Methods: </strong> Consecutive adult patients referring to the GP were screened. The GPs administered the Red Flags [RF] questionnaire to the eligible patients. All patients were referred to the nearest participating centre to confirm or exclude the diagnosis of CD. Sensitivity, specificity, and positive and negative predictive values [PPV, NPV] of the RF index [RFI] were calculated. Patients lost to follow-up after the first gastroenterological visit were analysed using a non-responder imputation, assuming they were negative for CD diagnosis. <strong>Results: </strong> From November 2016 to November 2019, 112 patients were included. A total of 66 subjects [59%] completed the study after the first gastroenterological visit. The prevalence of CD was 3.6% in the study population [4/112]. The RF index had 50% sensitivity, 58% specificity, 4% PPV, and 97% NPV. A combined diagnostic strategy with faecal calprotectin [FC] [RFI ≥8 and/or FC &gt;250 ng/g] resulted in significantly improved accuracy: sensitivity 100% [29-100%], specificity 72% [55-85%], PPV = 21% [5-51%], NPV = 100% [88-100%]. <strong>Conclusions: </strong> The RF Index combined with FC is a valid tool to identify patients with high probability of having CD at early stage.
DOI: 10.5281/zenodo.4569577
title: Azotea Dataset

description: Latest monthly AZOTEA reduced CSV files
DOI: 10.6084/m9.figshare.14036786
title: textures

description: sample description to publish
DOI: 10.6084/m9.figshare.14036786.v1
title: textures

description: sample description to publish
DOI: 10.25345/c5x80n
title: MassIVE MSV000086967 - GNPS - Peptidoglycan Cell Wall Digest (Cellosyl) - E.coli
title: Archived PG digest analyses collected on LTQ-FT using a shallow RP-HPLC Gradient (triplicates).
DOI: 10.5281/zenodo.4569578
title: Practitioner Views on the Interrelation of Microservice APIs and Domain-Driven Design -- A Grey Literature Study Based on Grounded Theory: Dataset and Code

description: This is the dataset and related code artifact for the article "Practitioner Views on the Interrelation of Microservice APIs and Domain-Driven Design: A Grey Literature Study Based on Grounded Theory". <strong>Abstract of the article:</strong> Microservice API design is a critical aspect in crafting a microservice architecture. While API design in general has been studied, the specific relation of API design to design practices and models commonly used in microservice architectures is yet understudied. In particular, practitioners frequently use Domain-Driven Design (DDD) in their microservice architecture and API designs. We thus decided to study existing Architectural Design Decisions (ADDs), their solutions options, their relations, and the decision drivers in these decisions. Using the Grounded Theory research method we studied grey literature sources. In this study, we identified 6 ADDs with 27 decision options, numerous relations between them, and 27 decision drivers. The decisions cover mapping domain models to APIs, defining API contracts in relation to domain models, designing API resources based on domain model elements, segregation of API resources, mapping domain model links to the API, and designing the operations of an API resource.
DOI: 10.5281/zenodo.4486013
title: Practitioner Views on the Interrelation of Microservice APIs and Domain-Driven Design -- A Grey Literature Study Based on Grounded Theory: Dataset and Code

description: This is the dataset and related code artifact for the article "Practitioner Views on the Interrelation of Microservice APIs and Domain-Driven Design: A Grey Literature Study Based on Grounded Theory". <strong>Abstract of the article:</strong> Microservice API design is a critical aspect in crafting a microservice architecture. While API design in general has been studied, the specific relation of API design to design practices and models commonly used in microservice architectures is yet understudied. In particular, practitioners frequently use Domain-Driven Design (DDD) in their microservice architecture and API designs. We thus decided to study existing Architectural Design Decisions (ADDs), their solutions options, their relations, and the decision drivers in these decisions. Using the Grounded Theory research method we studied grey literature sources. In this study, we identified 6 ADDs with 27 decision options, numerous relations between them, and 27 decision drivers. The decisions cover mapping domain models to APIs, defining API contracts in relation to domain models, designing API resources based on domain model elements, segregation of API resources, mapping domain model links to the API, and designing the operations of an API resource.
DOI: 10.25345/c5sj7t
title: MassIVE MSV000086968 - GNPS - Peptidoglycan Cell Wall Digest (Cellosyl) - H.pylori
title: Helicobacter pylori muropeptide profiles from cellosyl digestion, Shallow gradient RP-HPLC / LTQ-FT analysis (in triplicate).
DOI: 10.1285/i25327518v4i2
title: JDReAM. Journal of InterDisciplinary Research Applied to Medicine - Vol. 4, issue 2
DOI: 10.1285/i25327518v4i2p1
title: Title page
DOI: 10.1285/i25327518v4i2p3
title: Index
DOI: 10.1285/i25327518v4i2p5
title: Introduction
DOI: 10.1285/i25327518v4i2p7
title: The mechanobiology of the nucleus

description: In addition to biochemical and molecular signals coming from the microenvironment, cells are able to sense and integrate mechanical stresses, additional fundamental regulators of cell behaviour. Emerging demonstrations indicate that mechanical cues go far beyond the plasma membrane and the cytoskeleton, since, exerting tension on the outside local microenvironment via adhesions, cells develop an equal cytoskeletal stress on the nucleus inside, leading to 3D nuclear modifications. In this context, dynamic changes in nuclear lamina and the surrounding cytoskeleton modify mechanical properties of the nucleus affecting its structural arrangement, chromatin anchoring, 3D chromosome conformation and gene expression. Here we discuss findings supporting the role of the nucleus in cellular mechanosensing, ranging from how mechanical cues are transduced to the nucleus to how genome organization is influenced by cell mechanics.
DOI: 10.1285/i25327518v4i2p15
title: The impact of COVID-19 in women with intimate partner violence (IPV): a psychological and psychophysiological study

description: Domestic violence is characterized by coercive actions of various kinds (psychological, physical, sexual and economic) that persist over time; the chronicity of these same actions implies the development of short, medium and long term consequences that compromise the daily functioning of the woman. The aim of this study was to investigate, through a web Survey based on psychophysiological assessments, the relationship between the stress perceived with intimate partner violence and the dysfunctional coping strategies used during the pandemic phase 1 of the health emergency in Italy. The results highlighted a greater sensitivity to perceived stress, resulting in the use of dysfunctional strategies in the management of emergency situations. The levels of perceived anxiety are decreased. High levels of perceived stress produced effects in the management of the health emergency situation, consequences of behavioral, emotional, perceptual and psychophysiological nature (i.e, pain perception, sensory perception, sleep habits).
DOI: 10.1285/i25327518v4i2p21
title: Automatic detection of Voice Disorders: recent literature advancements

description: A short review of some recent findings in the field of automatic voice disorders detection and classification is provided in this article. The matter is getting more and more interest due to appealing non-invasiveness of the methods as well as the good achievable performances. An increasing role is played by Artificial Neural Networks (ANN), especially Deep ones, despite the need for large amounts of data for such networks, that are not always available for the task in question. The research in this field is directed in other directions too, including the investigation of new features and the capability to process running speech other than sustained sounds.
DOI: 10.1285/i25327518v4i2p31
title: Prevention Strategy of Intrauterine Adhesions: update and future perspective

description: Intrauterine adhesions (IUAs) caused by endometrial injury have a serious impact on women's fertility and morbility and involves a wide range of patients. Although the first case of IUAs was published in 1984 by Heinrich Fritsch, a full description of Asherman syndrome was done by Joseph Asherman. IUAs lead to a lot of complications in women, as the partial or complete closure of the uterine cavity, which may result in symptoms including abnormal menstruation, pelvic pain, recurrent pregnancy loss, secondary infertility, and pregnancy complications. Hysteroscopy, which has relegated blind curettage, is currently considered the gold standard diagnostic and therapeutic approach also as for outpatients. However, an integrated approach, including preoperative, intraoperative and postoperative procedures is needed to improve the reproductive outcome of the complex syndrome. In the post-operative care, the patient can benefit from some therapeutic and prophylactic methods used alone or in combination with each other. In this review, authors discuss on the efficacy of traditional methods for the prevention of complications of IUAs after surgery, such as hormonal therapy, physical barriers, vasodilators and antibiotics, as well as novel strategies such as stem cell therapy and novel therapeutic agents.
DOI: 10.6084/m9.figshare.14134943
title: Air_por_Entireflat_21-03.csv

description: dataset airbnb
DOI: 10.6084/m9.figshare.14134943.v1
title: Air_por_Entireflat_21-03.csv

description: dataset airbnb
DOI: 10.1285/i25327518v4i2p41
title: Tracheobronchial Amyloidosis

description: Amyloidosis is a form of plasma cell dyscrasia of unknown etiology, pathologically characterized by the extracellular deposit of fibrils derived from the light chain of monoclonal immunoglobulin. The involvement of the airways is more common in primary amyloidosis and is classified into: tracheobronchial amyloidosis, nodular parenchymal, diffuse parenchymal. The tracheobronchial form is usually the most frequent and is characterized by the presence of multiple submucosal plaques or, more rarely, by pseudotumoral endobronchial masses. Symptoms in the initial phase may be silent, subsequently manifesting themselves with cough, dyspnea, hemoptysis.
DOI: 10.1285/i25327518v4i2p45
title: A Case of Retroperitoneal Fibroid and Literature Review

description: Uterine fibroids or leiomyomas are the most common benign female genital tumors, although this pathology can also manifest itself outside the uterus, as in the case we present, with a retroperitoneal development. In this article, authors showed a rare case of 81-year-old women, with a right pelvic mass and lower abdominal discomfort. Basing on a preoperative radiological imaging, clinicians oriented to a provisional diagnosis of mesenchymal neoplasm of an uncertain origin. During surgery in the retroperitoneal space, it was detected a huge mass close to the uterus, beneath the right broad ligament. After the opening of the retroperitoneal spaces, surgeons enucleated a well-demarcated tumor, measuring 12 x 7 cm in diameter and histopathological findings demonstrated a rare retroperitoneal uterine leiomyoma.