cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19130002
title: Comprehensive analysis of peripheral blood non-coding RNAs identifies a diagnostic panel for fungal infection after transplantation

description: The occurrence of fungal infection seriously affects the survival and life quality of transplanted patients. The accurate diagnosis is of particular importance in the early stage of infection. To develop a novel diagnostic method for this kind of patient, we established a post-transplant immunosuppressed mice model with fungus inoculation and collected their peripheral blood at specific time points after infection. After screening by microarray, differentially expressed miRNAs and lncRNAs were selected and homologously analyzed with those of human beings from the gene database. These miRNAs and lncRNAs candidates were validated by qRT-PCR in peripheral blood samples from transplanted patients. We found that, compared with normal transplanted patients, the levels of miR-215 and miR-let-7 c were up-regulated in the plasma of patients with fungal infection (<i>P</i> &lt; 0.01), while levels of miR-154, miR-193a, NR_027669.1, and NR_036506.1 were down-regulated in their peripheral blood mononuclear cells (<i>P</i> &lt; 0.01). Principal component analysis shows that the expression pattern of the above RNAs was different between the two groups. A 6-noncoding-RNA detection panel was established by the support vector machine analysis, whose area under the ROC curve was 0.927. The accuracy, precision, sensitivity, and specificity of this model were 0.928, 0.919, 0.944, and 0.910, respectively. Though our detection panel has excellent diagnostic efficacy, its clinical application value still needs to be further confirmed by multi-center prospective clinical trials.
DOI: 10.6084/m9.figshare.19130002.v1
title: Comprehensive analysis of peripheral blood non-coding RNAs identifies a diagnostic panel for fungal infection after transplantation

description: The occurrence of fungal infection seriously affects the survival and life quality of transplanted patients. The accurate diagnosis is of particular importance in the early stage of infection. To develop a novel diagnostic method for this kind of patient, we established a post-transplant immunosuppressed mice model with fungus inoculation and collected their peripheral blood at specific time points after infection. After screening by microarray, differentially expressed miRNAs and lncRNAs were selected and homologously analyzed with those of human beings from the gene database. These miRNAs and lncRNAs candidates were validated by qRT-PCR in peripheral blood samples from transplanted patients. We found that, compared with normal transplanted patients, the levels of miR-215 and miR-let-7 c were up-regulated in the plasma of patients with fungal infection (<i>P</i> &lt; 0.01), while levels of miR-154, miR-193a, NR_027669.1, and NR_036506.1 were down-regulated in their peripheral blood mononuclear cells (<i>P</i> &lt; 0.01). Principal component analysis shows that the expression pattern of the above RNAs was different between the two groups. A 6-noncoding-RNA detection panel was established by the support vector machine analysis, whose area under the ROC curve was 0.927. The accuracy, precision, sensitivity, and specificity of this model were 0.928, 0.919, 0.944, and 0.910, respectively. Though our detection panel has excellent diagnostic efficacy, its clinical application value still needs to be further confirmed by multi-center prospective clinical trials.
DOI: 10.6084/m9.figshare.19114090
title: <i>In vivo</i> biocompatibility analysis of the recellularized canine tracheal scaffolds with canine epithelial and endothelial progenitor cells

description: Decellularized extracellular matrix (ECM) has frequently been applied as a biomaterial for tissue engineering purposes. When implanted, their role can be essential for partial trachea replacement in patients that require a viable transplant solution. Acellular canine tracheal scaffolds with preserved ECM structure, flexibility, and proteins were obtained by high pressure vacuum decellularization. Here, we aimed to evaluate the cell adhesion and proliferation of canine tracheal epithelial cells (EpC) and canine yolk sac endothelial progenitor cells (YS) cultivated on canine decellularized tracheal scaffolds and test the in vivo biocompatibility of these recellularized scaffolds implanted in BALB-c nude mice. In order to evaluate the recellularization efficiency, scaffolds were evaluated by scanning electron microscopy (SEM), immunofluorescence, DNA quantification, mycoplasma test, and in vivo biocompatibility. The scaffolds sterility was confirmed, and EpC and YS cells were cultured by 7 and 14 days. We demonstrated by SEM, immunofluorescence, and genomic DNA analyzes cell adhesion to tracheal ECM. Then, recellularized scaffolds were in vivo subcutaneously implanted in mice and after 45 days, the fragments were collected and analyzed by Hematoxylin-Eosin and Gömori Trichrome staining and PCNA, CD4, CD8, and CD68 immunohistochemistry. In vivo results confirmed that the implanted tissue remains preserved and proliferative, and no fibrotic tissue process was observed in animals. Finally, our results showed the recellularization success due the preserved ECM proteins, and that these may be suitable to future preclinical studies applications for partial trachea replacement in tissue engineering.
DOI: 10.6084/m9.figshare.19114090.v1
title: <i>In vivo</i> biocompatibility analysis of the recellularized canine tracheal scaffolds with canine epithelial and endothelial progenitor cells

description: Decellularized extracellular matrix (ECM) has frequently been applied as a biomaterial for tissue engineering purposes. When implanted, their role can be essential for partial trachea replacement in patients that require a viable transplant solution. Acellular canine tracheal scaffolds with preserved ECM structure, flexibility, and proteins were obtained by high pressure vacuum decellularization. Here, we aimed to evaluate the cell adhesion and proliferation of canine tracheal epithelial cells (EpC) and canine yolk sac endothelial progenitor cells (YS) cultivated on canine decellularized tracheal scaffolds and test the in vivo biocompatibility of these recellularized scaffolds implanted in BALB-c nude mice. In order to evaluate the recellularization efficiency, scaffolds were evaluated by scanning electron microscopy (SEM), immunofluorescence, DNA quantification, mycoplasma test, and in vivo biocompatibility. The scaffolds sterility was confirmed, and EpC and YS cells were cultured by 7 and 14 days. We demonstrated by SEM, immunofluorescence, and genomic DNA analyzes cell adhesion to tracheal ECM. Then, recellularized scaffolds were in vivo subcutaneously implanted in mice and after 45 days, the fragments were collected and analyzed by Hematoxylin-Eosin and Gömori Trichrome staining and PCNA, CD4, CD8, and CD68 immunohistochemistry. In vivo results confirmed that the implanted tissue remains preserved and proliferative, and no fibrotic tissue process was observed in animals. Finally, our results showed the recellularization success due the preserved ECM proteins, and that these may be suitable to future preclinical studies applications for partial trachea replacement in tissue engineering.
DOI: 10.6084/m9.figshare.25451692
title: Systematic map database for “What is the evidence that counter-wildlife crime interventions are effective for conserving African, Asian, and Latin American wildlife directly threatened by exploitation? A Systematic Map”

description: In this excel file we provide the coding (extracted data) for all articles/studies included in the map.Tab 1: Description of the coding form (i.e., layout of form with column headers and descriptions)Tab 2: Coding - provides the full coding for all articles/studies included in the mapTab 3: Codes sheet - provides a list of codes used and definitions Tab 4: Dropdown lists used to populate fields of the coding form
DOI: 10.48597/2fab-pjvf
title: Nitrogen_dioxide at Jungfraujoch

description: Measurement of Nitrogen_dioxide at Jungfraujoch
DOI: 10.48597/k2qj-abhe
title: Measurement of Nitrogen_dioxide at Jungfraujoch

description: Measurement of Nitrogen_dioxide at Jungfraujoch
DOI: 10.48597/zjjp-454e
title: Nitrogen_monoxide at Jungfraujoch

description: Measurement of Nitrogen_monoxide at Jungfraujoch
DOI: 10.48597/vc2z-re4p
title: Measurement of Nitrogen_monoxide at Jungfraujoch

description: Measurement of Nitrogen_monoxide at Jungfraujoch
DOI: 10.48597/rp9a-na67
title: Measurement of Nitrogen_monoxide at Jungfraujoch

description: Measurement of Nitrogen_monoxide at Jungfraujoch
DOI: 10.48597/vau9-ww7s
title: Measurement of Nitrogen_dioxide at Jungfraujoch

description: Measurement of Nitrogen_dioxide at Jungfraujoch
DOI: 10.5281/zenodo.10828341
title: Baseline model runs along with detailed result files presented in "pepMTL"

description: Within Article  "pepMTL: a synchronous multi-properties predictor for peptides enabled by multi-task framework and pre-trained protein language model", there exists a collection of executable files and detailed records of the operation results pertaining to the pepMTL model along with several benchmark models in the context of Retention Time (RT), Collision Cross Section (CCS), and Tandem Mass Spectrometry (MS/MS) methodologies. This compendium encompasses the source code for both the benchmark models and the pepMTL model itself—altered as necessary to accommodate the benchmark datasets—the specific datasets designed to execute these models effectively, the raw output files resulting from three parallel runs of each model, and corresponding log files meticulously documenting the execution history. Readers can garner extensive raw data concerning the direct comparisons between the pepMTL model and the array of benchmark models across the RT, CCS, and MS/MS domains as presented in the article. Furthermore, they have the ability to retrain these benchmark models on the designated datasets using the optimized code provided by the authors.这是文章 "pepMTL: a synchronous multi-properties predictor for peptides enabled by multi-task framework and pre-trained protein language model"中,pepMTL模型以及RT、CCS、MS/MS方面各个基准模型的运行文件以及详细运行结果的记录文件。该文件中包含了各个基准模型以及pepMTL模型运行的代码(有必要的话会经过作者的修改以适应基准数据集)、适应模型运行的基准数据集、模型平行运行三次后产生的原始结果文件以及运行日志记录文件。读者可以从这些数据中获取文章中关于pepMTL在RT、CCS、MS/MS方面与各个基准模型进行对比的详细原始信息,并可以通过运行作者优化后的代码将这些基准模型在基准数据集上进行模型训练。
DOI: 10.5281/zenodo.10828342
title: Baseline model runs along with detailed result files presented in "pepMTL"

description: Within Article  "pepMTL: a synchronous multi-properties predictor for peptides enabled by multi-task framework and pre-trained protein language model", there exists a collection of executable files and detailed records of the operation results pertaining to the pepMTL model along with several benchmark models in the context of Retention Time (RT), Collision Cross Section (CCS), and Tandem Mass Spectrometry (MS/MS) methodologies. This compendium encompasses the source code for both the benchmark models and the pepMTL model itself—altered as necessary to accommodate the benchmark datasets—the specific datasets designed to execute these models effectively, the raw output files resulting from three parallel runs of each model, and corresponding log files meticulously documenting the execution history. Readers can garner extensive raw data concerning the direct comparisons between the pepMTL model and the array of benchmark models across the RT, CCS, and MS/MS domains as presented in the article. Furthermore, they have the ability to retrain these benchmark models on the designated datasets using the optimized code provided by the authors.这是文章 "pepMTL: a synchronous multi-properties predictor for peptides enabled by multi-task framework and pre-trained protein language model"中,pepMTL模型以及RT、CCS、MS/MS方面各个基准模型的运行文件以及详细运行结果的记录文件。该文件中包含了各个基准模型以及pepMTL模型运行的代码(有必要的话会经过作者的修改以适应基准数据集)、适应模型运行的基准数据集、模型平行运行三次后产生的原始结果文件以及运行日志记录文件。读者可以从这些数据中获取文章中关于pepMTL在RT、CCS、MS/MS方面与各个基准模型进行对比的详细原始信息,并可以通过运行作者优化后的代码将这些基准模型在基准数据集上进行模型训练。
DOI: 10.57967/hf/1943
title: GPT4V-captions-from-LVIS-typography
DOI: 10.57967/hf/1945
title: GPT4V-captions-from-LVIS-typography
DOI: 10.5281/zenodo.10815184
title: docencia de percepcion artificial 2023/2024
DOI: 10.5281/zenodo.10849438
title: docencia de percepcion artificial 2023/2024
DOI: 10.5281/zenodo.10815183
title: docencia de percepcion artificial 2023/2024
DOI: 10.5281/zenodo.10849604
title: docencia de percepcion artificial 2023/2024
DOI: 10.5281/zenodo.10849586
title: Evaluation of JavaScript Instrumentation by OpenTelemetry visualized in ExplorViz

description: This dataset represents the results of a survey done with a small group, consisting mostly of experts in the research tool ExplorViz. The survey focused on evaluating whether the data that stem from automatic instrumentation by OpenTelemetry of JavaScript applications does benefit software comprehension.
DOI: 10.5281/zenodo.10849587
title: Evaluation of JavaScript Instrumentation by OpenTelemetry visualized in ExplorViz

description: This dataset represents the results of a survey done with a small group, consisting mostly of experts in the research tool ExplorViz. The survey focused on evaluating whether the data that stem from automatic instrumentation by OpenTelemetry of JavaScript applications does benefit software comprehension.
DOI: 10.6084/m9.figshare.25451689.v1
title: 1_perception&motor_EEGdata

description: EEG data for experiment 1 that contains both perception and motor rhythms in the TR-SRT task.Each folder contains the raw eeg files (named as X.cnt/evt),
DOI: 10.6084/m9.figshare.25451326
title: Table EV3: expression data of CBX3, STAT1, and CD274 according time/event overall survival of the patients from TCGA colorectal cancer cohort

description: expression data of CBX3, STAT1, and CD274 according time/event overall survival of the patients from TCGA colorectal cancer cohort
DOI: 10.6084/m9.figshare.25451326.v1
title: Table EV3: expression data of CBX3, STAT1, and CD274 according time/event overall survival of the patients from TCGA colorectal cancer cohort

description: expression data of CBX3, STAT1, and CD274 according time/event overall survival of the patients from TCGA colorectal cancer cohort
DOI: 10.5281/zenodo.10849600
title: Craters of Habit: Patterns of Deformation in the Western Galápagos

description: Datasets used in Reddin et al., Craters of Habit: Patterns of Deformation in the Western Galápagos.

LiCSBAS output files [in .h5 format] used in this study are provided, given by 128Dcum_filt.h5 for descending, and 106Acum_filt.h5 for ascending. These files contain displacement maps for both Isabela and Fernandina, and are used to produce time series, and conduct source modelling. 

.txt files contain time series information for their corresponding volcano, with track direction included [e.g. Darwin_Asc.txt].

Text files not beginning with Alcedo or Darwin contain time series of the 2020 eruption of Fernandina, with the location of the time series point, and corresponding track direction included in the title [e.g. NEFlank_ts_A.txt].
DOI: 10.5281/zenodo.10849601
title: Craters of Habit: Patterns of Deformation in the Western Galápagos

description: Datasets used in Reddin et al., Craters of Habit: Patterns of Deformation in the Western Galápagos.

LiCSBAS output files [in .h5 format] used in this study are provided, given by 128Dcum_filt.h5 for descending, and 106Acum_filt.h5 for ascending. These files contain displacement maps for both Isabela and Fernandina, and are used to produce time series, and conduct source modelling. 

.txt files contain time series information for their corresponding volcano, with track direction included [e.g. Darwin_Asc.txt].

Text files not beginning with Alcedo or Darwin contain time series of the 2020 eruption of Fernandina, with the location of the time series point, and corresponding track direction included in the title [e.g. NEFlank_ts_A.txt].
DOI: 10.15151/esrf-dc-1565254585
title: In situ serial crystallography (iSX) structure of Autotaxin at room temperature

description: Measurements from rat ATX microcrystals grown in CrystalDirect plates were carried at room temperature (293 K) with a 4 × 4 μm2 microfocus beam at 14.2 keV (wavelength at 0.8731 Å) on ID23-2. Approximately 5.7 million diffraction frames from 61 drops across 2 CrystalDirect plates were collected using MeshScan, a modular automated ESRF workflow system (EWOKS) routine available through MXCuBE-Web. Each drop was raster scanned with a 4 ✕ 4 µm2 X-ray beam at 14.2 keV photon energy, a flux of 7x1011 ph/sec (i.e., 10% of full flux) and 6 ms exposure per frame without any rotation. This in-situ serial data collection strategy yielded ~100,000 (average) still diffraction frames per drop in ~10 min, ensuring the diffraction weighted dose to be ~35 kGy/diffraction frame as calculated using RADDOSE-3D. The still diffraction frames, collected at room temperature, were processed using crystFEL v.0.10.1. TRUNCATE from ccp4i was used to convert Intensities (I) to Structure Factors (SF). The structure was determined by molecular replacement using PHASER from phenix with the PDB model as a reference model. Refinement was carried out using phenix.refine for the reciprocal space and for real space.
DOI: 10.18167/dvn1/twzlis
title: Essai intensification du maïs au Nord Cameroun (2013)

description: Essais mis en place chez des producteurs dans deux grappes de villages du Nord Cameroun en 2013 dans l'objectif d'étudier la faisabilité de l'intensification de la culture du maïs. Des résultats d'analyses de sols sur chaque essai sont parvenus après ces valorisations qui peuvent donner lieu à d'autres interprétations
DOI: 10.5285/142ca3c4-b400-2e79-e063-6c86abc09187
title: Measurements of the Secchi depth and Forel-Ule colour collected on the NERC PICCOLO cruise SD035 in January - March 2024.

description: This dataset contains measurements of the Secchi depth and the Forel-Ule colour collected on the NERC PICCOLO cruise SD035 in the Weddell Sea, including a total of 36 stations, collected between January and March 2024.
DOI: 10.5281/zenodo.10277302
title: Photoionization cross-sections from exited ionic levels: analytical fits

description: Analytical fits of photoionisation (bound-free) cross-sections from exited levels of ions with more than two electrons. The fits are based on the numerical tables computed by the Opacity Project (OP) and presented in the TOPBase database. The cross-section for each considered level was fitted using the following expression:

 \( \sigma(E) = \sigma_{\rm th} \left(A \bar E ^{p/2}+(1-A)\bar E^{1+p/2}\right) \)

where \(\bar E =E_{\rm th}/E \) and  \(E \) is the photon energy. Only a few energy levels were considered with the lowest excitation energies, typically not exceeding a quarter of the ionization energy. These fits were implemented in the code, that calculates hot LTE atmospheres of white dwarfs in the Super-Soft X-ray Sources, see the referenced paper for the details.The file 'bf_cross_hot.dat' contains, for each ion, the name of ion, the level's energy and statistical weight and the fitting parameters  \(E_{\rm th}, \sigma_{\rm th}, A, p \). The file 'bf_cross_hot.py' contains simple Python3 function for calculation the fitting cross-section for given ion and frequency or frequency array. In the latter case it also make a plot, if 'matplotlib' package is installed. The following ions were considered:

CII, CIII, CIV, NII, NIII, NIV, NV, OII, OIII, OIV, OV, OVI, NeIII, NeIV, NeV, NeVI, NeVII, NeVIII, NaIV, NaV, NaVI, NaVII, NaVIII, NaIX, MgVI, MgVII, MgVIII, MgIX, MgX, AlVI, AlVII, AlVIII, AlIX, AlX, AlXI, SiVII, SiVIII, SiIX, SiX, SiXI, SiXII, SIX, SX, SXI, SXII, SXIII, SXIV, ArV, ArVI, ArVII, ArVIII, ArXI, ArXII, ArXIII, ArXIV, ArXV, ArXVI, CaV, CaVI, CaVII, CaIX, CaXIII, CaXIV, CaXV, CaXVI, CaXVII, CaXVIII, FeVI, FeVII, FeXI, FeXII, FeXIII, FeXIV, FeXV, FeXVI, FeXVIII, FeXIX, FeXX, FeXXI, FeXXII, FeXXIII, FeXXIV, FeXXV.
DOI: 10.5281/zenodo.10277303
title: Photoionization cross-sections from exited ionic levels: analytical fits

description: Analytical fits of photoionisation (bound-free) cross-sections from exited levels of ions with more than two electrons. The fits are based on the numerical tables computed by the Opacity Project (OP) and presented in the TOPBase database. The cross-section for each considered level was fitted using the following expression:

 \( \sigma(E) = \sigma_{\rm th} \left(A \bar E ^{p/2}+(1-A)\bar E^{1+p/2}\right) \)

where \(\bar E =E_{\rm th}/E \) and  \(E \) is the photon energy. Only a few energy levels were considered with the lowest excitation energies, typically not exceeding a quarter of the ionization energy. These fits were implemented in the code, that calculates hot LTE atmospheres of white dwarfs in the Super-Soft X-ray Sources, see the referenced paper for the details.The file 'bf_cross_hot.dat' contains, for each ion, the name of ion, the level's energy and statistical weight and the fitting parameters  \(E_{\rm th}, \sigma_{\rm th}, A, p \). The file 'bf_cross_hot.py' contains simple Python3 function for calculation the fitting cross-section for given ion and frequency or frequency array. In the latter case it also make a plot, if 'matplotlib' package is installed. The following ions were considered:

CII, CIII, CIV, NII, NIII, NIV, NV, OII, OIII, OIV, OV, OVI, NeIII, NeIV, NeV, NeVI, NeVII, NeVIII, NaIV, NaV, NaVI, NaVII, NaVIII, NaIX, MgVI, MgVII, MgVIII, MgIX, MgX, AlVI, AlVII, AlVIII, AlIX, AlX, AlXI, SiVII, SiVIII, SiIX, SiX, SiXI, SiXII, SIX, SX, SXI, SXII, SXIII, SXIV, ArV, ArVI, ArVII, ArVIII, ArXI, ArXII, ArXIII, ArXIV, ArXV, ArXVI, CaV, CaVI, CaVII, CaIX, CaXIII, CaXIV, CaXV, CaXVI, CaXVII, CaXVIII, FeVI, FeVII, FeXI, FeXII, FeXIII, FeXIV, FeXV, FeXVI, FeXVIII, FeXIX, FeXX, FeXXI, FeXXII, FeXXIII, FeXXIV, FeXXV.
DOI: 10.6084/m9.figshare.25451689.v2
title: 1_perception&motor_EEGdata

description: EEG data for experiment 1 that contains both perception and motor rhythms in the TR-SRT task.Each folder contains the raw eeg files (named as X.cnt/evt),
DOI: 10.6084/m9.figshare.25450378.v2
title: SAMMY-seq 4f human tracks data

description: In this repository is stored the hub used to make the genomic track UCSC session to display and share all the tracks shown into "Biochemical properties of chromatin domains define genome compartmentalization" based on the human genome (fibroblasts).
DOI: 10.5281/zenodo.10849537
title: Magnetic field impact on ferronanofluid laminar flow