cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13615017
title: A new flexible generalized family for constructing many families of distributions

description: We propose a <i>new flexible generalized family</i> (NFGF) for constructing many families of distributions. The importance of the NFGF is that any baseline distribution can be chosen and it does not involve any additional parameters. Some useful statistical properties of the NFGF are determined such as a linear representation for the family density, analytical shapes of the density and hazard rate, random variable generation, moments and generating function. Further, the structural properties of a special model named the <i>new flexible Kumaraswamy</i> (NFKw) distribution, are investigated, and the model parameters are estimated by maximum-likelihood method. A simulation study is carried out to assess the performance of the estimates. The usefulness of the NFKw model is proved empirically by means of three real-life data sets. In fact, the two-parameter NFKw model performs better than three-parameter transmuted-Kumaraswamy, three-parameter exponentiated-Kumaraswamy and the well-known two-parameter Kumaraswamy models.
DOI: 10.6084/m9.figshare.13615017.v1
title: A new flexible generalized family for constructing many families of distributions

description: We propose a <i>new flexible generalized family</i> (NFGF) for constructing many families of distributions. The importance of the NFGF is that any baseline distribution can be chosen and it does not involve any additional parameters. Some useful statistical properties of the NFGF are determined such as a linear representation for the family density, analytical shapes of the density and hazard rate, random variable generation, moments and generating function. Further, the structural properties of a special model named the <i>new flexible Kumaraswamy</i> (NFKw) distribution, are investigated, and the model parameters are estimated by maximum-likelihood method. A simulation study is carried out to assess the performance of the estimates. The usefulness of the NFKw model is proved empirically by means of three real-life data sets. In fact, the two-parameter NFKw model performs better than three-parameter transmuted-Kumaraswamy, three-parameter exponentiated-Kumaraswamy and the well-known two-parameter Kumaraswamy models.
DOI: 10.6084/m9.figshare.13668561.v1
title: Testing differentially methylated regions through functional principal component analysis

description: DNA methylation is an epigenetic modification that plays an important role in many biological processes and diseases. Several statistical methods have been proposed to test for DNA methylation differences between conditions at individual cytosine sites, followed by a post hoc aggregation procedure to explore regional differences. While there are benefits to analyzing CpGs individually, there are both biological and statistical reasons to test entire genomic regions for differential methylation. Variability in methylation levels measured by Next-Generation Sequencing (NGS) is often observed across CpG sites in a genomic region. Evaluating meaningful changes in regional level methylation profiles between conditions over noisy site-level measurements is often difficult to implement with parametric models. To overcome these limitations, this study develops a nonparametric approach to detect predefined differentially methylated regions (DMR) based on functional principal component analysis (FPCA). The performance of this approach is compared with two alternative methods (GIFT and M3D), using real and simulated data.
DOI: 10.6084/m9.figshare.13668561
title: Testing differentially methylated regions through functional principal component analysis

description: DNA methylation is an epigenetic modification that plays an important role in many biological processes and diseases. Several statistical methods have been proposed to test for DNA methylation differences between conditions at individual cytosine sites, followed by a post hoc aggregation procedure to explore regional differences. While there are benefits to analyzing CpGs individually, there are both biological and statistical reasons to test entire genomic regions for differential methylation. Variability in methylation levels measured by Next-Generation Sequencing (NGS) is often observed across CpG sites in a genomic region. Evaluating meaningful changes in regional level methylation profiles between conditions over noisy site-level measurements is often difficult to implement with parametric models. To overcome these limitations, this study develops a nonparametric approach to detect predefined differentially methylated regions (DMR) based on functional principal component analysis (FPCA). The performance of this approach is compared with two alternative methods (GIFT and M3D), using real and simulated data.
DOI: 10.6084/m9.figshare.19697365
title: SIFT4G (SARS-CoV-2)

description: GTF file containing the SARS-CoV-2 genome sequences, and VCF file comprising all the SNP of SARS-CoV-2 were obtained from the Ensembl genome database.
DOI: 10.6084/m9.figshare.19697365.v2
title: SIFT4G (SARS-CoV-2)

description: GTF file containing the SARS-CoV-2 genome sequences, and VCF file comprising all the SNP of SARS-CoV-2 were obtained from the Ensembl genome database.
DOI: 10.6084/m9.figshare.19697365.v1
title: SIFT4G (SARS-CoV-2)

description: GTF file containing the SARS-CoV-2 genome sequences, and VCF file comprising all the SNP of SARS-CoV-2 were obtained from the Ensembl genome database.
DOI: 10.34740/kaggle/ds/2080545
title: ATM Image (ATM-I)
DOI: 10.34740/kaggle/dsv/3455016
title: ATM Anomaly Video Dataset (ATMA-V)
DOI: 10.6073/pasta/6a335878e07521f4543f4857a60cce1e
title: SBC LTER: Reef: Bottom Temperature: Continuous water temperature, ongoing since 2000

description: Giant kelp forests and the organisms living within them are exposed to a variable environment where biotic and abiotic drivers may affect populations and biological processes on the scale of hours to decades. To examine temporal and spatial patterns of temperature in giant kelp forests, SBC has measured ambient water temperature at nine reef sites located along the mainland coast of the Santa Barbara Channel and at two sites on the north side Santa Cruz Island beginning in 2000. Two submersible temperature loggers, sampling every 30 minutes and offset from each other by 15 minutes, are deployed so that data is recorded every 15 minutes at each site. Temperature loggers were retrieved and replaced bi-annually with a new logger, typically in the early summer (June-July) and in early winter (January-March). These temperature loggers measure temperature in water within a range of -20°C to 30°C, and accuracy of ± 0.20°C at 25°C.
DOI: 10.5281/zenodo.6517583
title: ProteinKG65

description: A Large-scale Knowledge Graph for Protein Science.
DOI: 10.5281/zenodo.6517582
title: ProteinKG65

description: A Large-scale Knowledge Graph for Protein Science.
DOI: 10.6084/m9.figshare.19721506
title: Supplementary Material for: Vitamin D Receptor/Vitamin D Response Element Directly Modulate <b><i>Nestin</i></b> Transcription to Ameliorate PAN-Induced Podocyte Morphological Changes

description: <b><i>Background:</i></b> The change of podocyte morphology is a pathologic feature of chronic kidney disease. Several studies have suggested that vitamin D plays a role in the protection of podocytes, but the underlying mechanism remains unclear. <b><i>Methods:</i></b> The effects of paricalcitol on podocyte injury were tested in a puromycin aminonucleoside (PAN)-induced rat model and cultured mouse podocytes. Proteinuria, podocyte foot process (FP) effacement, and the expression of nestin and vitamin D receptor (VDR) were evaluated. VDR-siRNA or plasmids containing VDR-shRNA were transfected into podocytes to silence <i>VDR</i> expression. Chromatin immunoprecipitation (ChIP) and luciferase reporter assays were performed to verify the connection between <i>VDR</i> and <i>nestin</i> gene expression. <b><i>Results:</i></b> Paricalcitol significantly alleviated proteinuria and podocyte FP effacement in PAN-induced nephrosis, which was accompanied by increased VDR expression in the glomeruli. Paricalcitol also inhibited PAN-induced nestin overexpression in the glomeruli. In an in vivo study, PAN significantly inhibited VDR protein expression, stimulated nestin protein expression, and resulted in nestin filament derangement in mouse podocytes, while paricalcitol treatment abolished these effects. In contrast, downregulation of VDR resulted in derangement and overexpression of nestin. ChIP assays demonstrated the presence of a vitamin D response element (VDRE) in the <i>nestin</i> promoter, and paricalcitol enhanced the binding of VDR to VDRE. Furthermore, luciferase reporter assays of the <i>nestin</i> promoter fragment showed that paricalcitol effectively repressed nestin reporter gene expression after PAN treatment, and mutation of VDRE abolished this effect. <b><i>Conclusions:</i></b> Paricalcitol directly regulates nestin transcription through the interaction of VDR/VDRE, thereby preventing morphological changes of podocytes in PAN nephropathy.
DOI: 10.7910/dvn/wmohlc
title: Replication Data for: Data dictionary of Programmatic mapping and estimating the size of Female sex workers, Men who have sex with men and People who inject drugs, in Kenya

description: Data dictionary of KPSE data
DOI: 10.6084/m9.figshare.19721539
title: Figures_CenturyLongColumnOzoneRecords

description: Data plotted as figures in the paper: "<strong>Century-long column ozone records" </strong>
DOI: 10.3886/e169821
title: Data and Code for: How common is the common-ratio effect?

description: The common-ratio effect and the Allais Paradox (common-consequence effect) are the two best‐known violations of Expected Utility Theory. We reexamine data from 39 articles reporting experiments (143 designs/ parameterizations, 14,909 observations) and find that the common-ratio effect is systematically affected by experimental design and implementation choices. The common-ratio effect is more likely to be observed in experiments with a low common-ratio factor, a high ratio of middle to highest outcome, when lotteries are presented as simple probability distributions (not in a compound/frequency form), and with high hypothetical incentives.
DOI: 10.3886/e169821v1
title: Data and Code for: How common is the common-ratio effect?

description: The common-ratio effect and the Allais Paradox (common-consequence effect) are the two best‐known violations of Expected Utility Theory. We reexamine data from 39 articles reporting experiments (143 designs/ parameterizations, 14,909 observations) and find that the common-ratio effect is systematically affected by experimental design and implementation choices. The common-ratio effect is more likely to be observed in experiments with a low common-ratio factor, a high ratio of middle to highest outcome, when lotteries are presented as simple probability distributions (not in a compound/frequency form), and with high hypothetical incentives.
DOI: 10.5281/zenodo.6523208
title: Research Artifact: Dockerfile Meta-Maintenance for Updating Multiple Version-Pinned Packages

description: This is a research artifact for the paper "Dockerfile Meta-Maintenance for Updating Multiple Version-Pinned Packages". This artifact is a data repository including a list of studied 7,914 repositories on GitHub, 17,139 dockerfiles, 363 repositories containing comparable package sets, and 335 repositories that provide the packages included in the identified 385 package sets.
DOI: 10.5281/zenodo.6523207
title: Research Artifact: Dockerfile Meta-Maintenance for Updating Multiple Version-Pinned Packages

description: This is a research artifact for the paper "Dockerfile Meta-Maintenance for Updating Multiple Version-Pinned Packages". This artifact is a data repository including a list of studied 7,914 repositories on GitHub, 17,139 dockerfiles, 363 repositories containing comparable package sets, and 335 repositories that provide the packages included in the identified 385 package sets.
DOI: 10.6084/m9.figshare.19721560
title: PF-circRNA-Supplementary Tables.pdf

description: PF-circRNA-Supplementary Table 1 and 2
DOI: 10.6084/m9.figshare.19721560.v1
title: PF-circRNA-Supplementary Tables.pdf

description: PF-circRNA-Supplementary Table 1 and 2
DOI: 10.6084/m9.figshare.19572040
title: Supplementary Material for: Poor Treatment Outcomes with Second-Line Chemotherapy in Advanced Synovial Sarcoma

description: Introduction: Synovial sarcoma predominantly affects adolescents and young adults. Doxorubicin with or without ifosfamide therapy is the standard first-line treatment for unresectable or metastatic synovial sarcoma. However, there is no standard second-line chemotherapy regimen. The purpose of the current study was to evaluate the outcomes of second-line chemotherapy for patients with synovial sarcoma. Methods: We retrospectively evaluated the outcomes of 61 patients with unresectable or metastatic synovial sarcoma who had received first-line chemotherapy at our institution between 1997 and 2017. Patients who received second-line chemotherapy were included in the analysis. Outcomes of the chemotherapy were evaluated. Results: Among the 61 patients treated with first-line chemotherapy, we identified 32 patients who received second-line chemotherapy. Most patients (62.5%) were under 40 years of age. Regarding second-line chemotherapy regimens, 6 (18.8%) patients were treated with doxorubicin with/without ifosfamide, 6 (18.8%) with ifosfamide and etoposide, 4 (12.5%) with docetaxel and gemcitabine, 5 (15.6%) with pazopanib, 2 (6.2%) with trabectedin, and 1 (3.1%) with eribulin. The overall response rate according to the Response Evaluation Criteria in Solid Tumors for all patients was 9.4%. Eleven patients (34.3%) achieved disease-control for &gt; 6 months. The median follow-up duration was 15.2 months. The 1-year progression-free and overall survival rates were 33.1% and 67.1%, respectively. Conclusion: Our exploratory study revealed that the response rate of second-line chemotherapy regimens for patients with synovial sarcoma was 9.4%. Therefore, there is an urgent need to develop more active therapeutic regimens for synovial sarcomas.
DOI: 10.15151/esrf-es-686567275
title: ITABAG: 3D structures of macromolecules related to human health

description: The ITABAG includes structural biologists from Universities, National Research Council and Hospital research centres in Italy. The laboratories apply various diffraction methods to study the structure-function relationships in various macromolecules. A unifying factor for the vast majority of the macromolecules under study is that they are related to human health, either directly, being human proteins involved in some disease, or indirectly, as proteins expressed by human pathogens and validated as potential pharmacological targets. Other projects investigate basic chemical processes, such as crystal growth and polymer association and formation of nanostructures.
DOI: 10.15151/esrf-es-701730194
title: Macromolecular Crystallography in Bordeaux/Lyon/Toulouse IECB IBGC CBMN / IBCP-MMSB ICBMS / IPBS

description: The different research teams who are part of this BAG are located in Bordeaux, Lyon and Toulouse. They are mainly working on worldwide health concerns or biotechnological relevant projects. In more details, infectiology, molecular assemblies, biosynthetic pathways or glycobiology are their main research axises. Important results have been obtained so far regarding the development of new therapeutic strategies against several infectious diseases or regarding plastic bioremediation. In order to go further into details of all these studies, access to ESRF facilities is a requirement.
DOI: 10.15151/esrf-es-705660632
title: Molecular machines in energy transduction, cellular signaling and defense processes

description: Since this BAG is composed of 7 different working groups from 3 different locations (universities of Cologne, Bochum and Düsseldorf), the projects within this proposal are of rather heterogeneous nature. Nonetheless, we are focusing on five main topics: 1.) proteins involved in transport processes, transporters or channels, either embedded in the membrane or acting in the cytosol (e. g. ABC transporters, resistance proteins) 2.) proteins involved in the immune system or resistance processes of prokaryotic bacteria and plants (dehydratases, cyclases, binding proteins) 3.) proteins involved or associated with diseases like cancer or developmental disorders (e. g. metallopeptidase, protein kinase, chaperones) 4.) enzymes of putative industrial use in order to encounter increasing environmental pollution (e. g. transaminases, estereases) 5.) proteins involved in synthesis of light harvesting pigments and chromophore binding proteins (e. g. reductases, photosensor domains)
DOI: 10.15151/esrf-es-618967117
title: Multi-scale Multi-techniques investigations of Li-ion batteries: towards a European Battery Hub

description: In this science-driven Long-Term proposal, we propose a 3-years multi-beamline program tackling grand challenges for actual, emerging and future battery technologies. We will deploy advanced methodologies for accelerating research by setting new cooperation modes for multi-techniques multi-scale studies. Three chemistry-neutral scientific cases have been identified to fulfil this LTP: bulk-to-surface mechanisms, high energy system and smart sensing. Multiple, time-coordinated, interoperable spectroscopic, imaging & scattering techniques will be implemented. This proposal is the Pilot Phase towards a European Battery Hub aiming at accelerating workflows in battery research by optimizing the exceptional diversity of means available at ESRF. We expect to demonstrate the added value of a new “proposal” mechanism, e.g. science-driven beamtime allocation group, serving the fast growing, highly competitive and rapidly evolving European battery community.
DOI: 10.15151/esrf-es-753373989
title: Calibration of the diamond anvil Raman pressure gauge to above 500 GPa in a toroidal-DAC.

description: The diamond anvil Raman phonon frequency shift at the interface with the sample is now currently used as a pressure measurement above 100 GPa for laboratory experiments. However, this spectroscopic pressure measurement could largely overestimate pressure above 400 GPa. The aim of this proposal is to accurately calibrate the Raman diamond pressure gauge up to 500 GPa. Three calibrants will be selected: Au, Pt and diamond, all embedded in Ne, by relating their XRD volumes to pressure through their EOS. The Raman shift of diamond under hydrostatic pressure, hence the diamond Gruneisen parameter, will also be measured up to 500 GPa. Toroidal-DACs will be used to reach the 500 GPa range.
DOI: 10.15151/esrf-es-753380011
title: Fast in situ nanothermographies of 3D printed structures during a heat treament up to 1000°C for investigating their sintering

description: The CEA and the IRCER are interested in the 3D printing of ceramic structures in order to look for innovative heat exchangers applied to the energy transition. The chosen technique is stereolithography, which uses a polymer resin loaded with silica microparticles. To obtain ceramics, a heat treatment is applied to eliminate the organic part and to promote the formation of bridges between microparticles by sintering. In order to ensure the mechanical properties, it is important to control the heat treatment parameters (temperature, speed and heating time) as they influence the final microstructure of the ceramic object. The objective of high resolution tomographic measurements on beamline ID16B is to access the evolution of the microstructure (neck growth at the early stages of sintering) in situ at different times during the application of the heating profile up to 1000°C. This data will help to validate a model of sintering behavior using the discrete element method.
DOI: 10.15151/esrf-es-754325334
title: Nano-scale morphological and chemical characterization of cardiac, coronary and carotid macro-/micro-thrombi in COVID-19 positive and negati

description: This project aims at gaining novel insight in two pathological mechanisms observed in the vascular system supplying the heart and brain of COVID-19 patients as an adverse consequence of a SARS-CoV-2 infection, i.e. the development of 1) macroscopic thrombi (MTs) in epicardial coronary and carotid arteries and 2) peripheral microscopic thrombi (µTs) in myocardial and brain microvasculature. Few pathology studies have been conducted thus far and a precise mechanistic understanding is still needed. We propose the use of a combination of different synchrotron analysis techniques (X-ray micro- & nano-CT, fluorescence & SAXS/WAXS) for the characterization of the morphology, composition and structure of the MTs and µTs. In this specific experiment, we will apply X-ray nano-holotomography and fluorescence microscopy to obtain an unprecedented morphological and chemical characterization of the MTs and µTs at the level of individual thrombi, endothelial cells and possibly SARS-CoV-2 virions.
DOI: 10.15151/esrf-es-764146616
title: Following dissolved nickel from advanced Pt-alloyed ORR catalysts in a real fuel cell

description: The main bottleneck in proton exchange membrane fuel cell (PEMFC) is the inefficient catalyst for cathodic oxygen reduction reaction (ORR) limiting both maximum current density and efficiency. Shape-controlled octahedra oh-PtNiIr nanoparticles (NPs) exhibit a 3-fold increment in activity when compared to commercial Pt catalysts. However, in the membrane electrode assembly (MEA) of a fuel cell, these catalysts suffer from dissolution. Compared to protons, nickel cations have a higher affinity for sulfonic acid groups in the PEM and when dissolved out of the nanoparticle, they might migrate into the membrane, reducing the overall performance of the FC. We designed an innovative cell that will enable us to perform operando XAS depth profiling of the MEA and thus follow nickel cations in the membrane. This information is important for our industrial partner Johnson Matthey as it must be addressed to improve performance thus helping with decarbonization goals of the EU.
DOI: 10.6084/m9.figshare.17067647
title: Analysis of inferior nasal turbinate volume in subjects with nasal septum deviation: a retrospective cone beam tomography study

description: Analysis of inferior nasal turbinate volume in subjects with nasal septum deviation: a cone beam tomography study"
DOI: 10.6084/m9.figshare.17067647.v10
title: Analysis of inferior nasal turbinate volume in subjects with nasal septum deviation: a retrospective cone beam tomography study

description: Analysis of inferior nasal turbinate volume in subjects with nasal septum deviation: a cone beam tomography study"
DOI: 10.6084/m9.figshare.17067647.v9
title: Analysis of inferior nasal turbinate volume in subjects with nasal septum deviation: a cone beam tomography study

description: Analysis of inferior nasal turbinate volume in subjects with nasal septum deviation: a cone beam tomography study"
DOI: 10.48370/ofd/8bkhzk/qhnxfm
title: IBL_coll_537_SorexAraneus_1947_scan.jpg

description: :unav
DOI: 10.48370/ofd/8bkhzk/bbnhrc
title: IBL_coll_537_SorexAraneus_1947_ct.swf

description: :unav
DOI: 10.48370/ofd/8bkhzk
title: Sorex araneus - IBL_537, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute PAS. Collected 1947-04-05, in: Białowieża National Park, Poland. Material type: head
DOI: 10.48370/ofd/gp2ujj/xzrcbc
title: IBL_coll_725_SorexAraneus_1947_scan.jpg

description: :unav
DOI: 10.48370/ofd/gp2ujj/toizxp
title: IBL_coll_725_SorexAraneus_1947_ct.swf

description: :unav
DOI: 10.48370/ofd/gp2ujj
title: Sorex araneus - IBL_725, Zoological collection of the Mammal Research Institute, PAS

description: Sorex araneus (Common shrew) from Zoological collection of the Mammal Research Institute PAS. Collected 1947-06-05, in: Białowieża National Park, Poland. Material type: head