cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17299263
title: PD-L1 and Notch as novel biomarkers in pancreatic sarcomatoid carcinoma: a pilot study

description: The improved immunological understanding revealed the tumor microenvironment as an appealing driver to restore the immune response against cancer cells resulting in a paradigm shift in the oncology field. However, the complexity of the tumor milieu suggests the role of several pathways linking in immunomodulation mechanisms. Pancreatic cancer represents a model of the intricate relationship between malignant cells and their surrounding neighborhood. In this study, we analyzed, retrospectively, six cases of rare pancreatic sarcomatoid carcinoma (PSC) and evaluated the expression of PD-L1 and Notch, aiming to explore new attributes in immunophenotype. PD-L1 CPS ≥ 1was common in PSCs (83%) with half samples expressing PD-L1 CPS ≥ 50. Notch1 and Notch3 demonstrated a high range of expression. A direct significant correlation between PD-L1 and Notch3 overexpression (r = 0.7; p = 0.036) has been observed. Immunofluorescence studies revealed a co-localization of Notch3 and PD-L1 when both proteins were over-expressed within cytoplasmic or membranous compartments of the same cells. Our data identify a unique biological characterization of this rare pancreatic histotype. These findings provide a rationale for future studies evaluating the potential crosstalk between PD-L1/PD-1 axis and Notch pathways and prompting the development of novel therapeutics strategy.
DOI: 10.6084/m9.figshare.17299263.v1
title: PD-L1 and Notch as novel biomarkers in pancreatic sarcomatoid carcinoma: a pilot study

description: The improved immunological understanding revealed the tumor microenvironment as an appealing driver to restore the immune response against cancer cells resulting in a paradigm shift in the oncology field. However, the complexity of the tumor milieu suggests the role of several pathways linking in immunomodulation mechanisms. Pancreatic cancer represents a model of the intricate relationship between malignant cells and their surrounding neighborhood. In this study, we analyzed, retrospectively, six cases of rare pancreatic sarcomatoid carcinoma (PSC) and evaluated the expression of PD-L1 and Notch, aiming to explore new attributes in immunophenotype. PD-L1 CPS ≥ 1was common in PSCs (83%) with half samples expressing PD-L1 CPS ≥ 50. Notch1 and Notch3 demonstrated a high range of expression. A direct significant correlation between PD-L1 and Notch3 overexpression (r = 0.7; p = 0.036) has been observed. Immunofluorescence studies revealed a co-localization of Notch3 and PD-L1 when both proteins were over-expressed within cytoplasmic or membranous compartments of the same cells. Our data identify a unique biological characterization of this rare pancreatic histotype. These findings provide a rationale for future studies evaluating the potential crosstalk between PD-L1/PD-1 axis and Notch pathways and prompting the development of novel therapeutics strategy.
DOI: 10.17632/w7cmfcgyb2.1
title: Serum IgG1 and IgG4 could contribute to partial control of viral rebound in chronically HIV-1 infected patients

description: DOI for this work is: 10.1097/QAD.0000000000002944
Published in 2021 by Lucia Lopalco et al.
All the enrolled patients studied in this work were previously described in the APACHE study. The study was conducted on HIV chronically infected patients,  with HIV-RNA <50 cps/mL for ≥10 years, CD4+ cell count >500 cells/μL and HIV-DNA <100 copies/106 PBMC. The ART regimen in use at the time of ATI was resumed at confirmed viral rebound (CVR, defined as two consecutive HIV-RNA >50 copies/mL). Raw data of clinical data of all described patients are reported in table I of the manuscript. Collection of sera and analysis of both binding antibodies (BAbs) and neutralizing antibodies (NAbs) was performed at three different time points: ATI, CVR and time of viral re-suppression after antiretroviral treatment (ART) resumption. IgG subclasses (IgG1, IgG2, IgG3 and IgG4) from the 4 patients with highest levels of neutralization were found to block viral infection (raw data are reported here in fig 2 Fig3 IgG HIV). All subjects had CVR after ATI at a median time of 21 days (14-56). After ART resumption, all the enrolled subjects achieved HIV-RNA<50 copies/mL in 42 days (21-98) (as shown in fig 1 of the manuscript). We observed a strong increase of either BAbs and NAbs titers from ATI to viral re-suppression in one patient, who showed the longest period of virus undetectability during ATI. In this patient, BAbs and NAbs specifically belonged to both IgG1 and IgG4 subclasses, directed to env antigen. Raw data  (fig4 HIV) here reported reports the characterization of antibodies in this patients. Further details are shown in fig 4 of the manuscript.
DOI: 10.5286/isis.e.rb2210015
title: Drainage studies of highly dynamic interfaces as viewed by SANS

description: Many polymer/surfactant formulations involve a trapped kinetic state that provides some beneficial character to the formulation. However, the vast majority of studies on formulations focus on equilibrium states. Here, nanoscale structures present at dynamic interfaces in the form of air-in-water foams will be investigated, stabilised by mixtures of commonly used small molecule ionic surfactants. Transient foams formed from binary mixtures of these surfactants and polymers shows considerable changes in stability which correlate with the strength of the solution interaction which delineate the interfacial structures. This experiment wil focus on explrojgn correaltions between the foam drainage rates and the nature of the solution interactions.
DOI: 10.5286/isis.e.rb2210015-1
title: Drainage studies of highly dynamic interfaces as viewed by SANS

description: Many polymer/surfactant formulations involve a trapped kinetic state that provides some beneficial character to the formulation. However, the vast majority of studies on formulations focus on equilibrium states. Here, nanoscale structures present at dynamic interfaces in the form of air-in-water foams will be investigated, stabilised by mixtures of commonly used small molecule ionic surfactants. Transient foams formed from binary mixtures of these surfactants and polymers shows considerable changes in stability which correlate with the strength of the solution interaction which delineate the interfacial structures. This experiment wil focus on explrojgn correaltions between the foam drainage rates and the nature of the solution interactions.
DOI: 10.5286/isis.e.rb2210218
title: How does in-membrane structuring affect antimicrobial efficiency of AMPs?

description: A short designed antimicrobial peptide (AMP) G(IIKK)3I (GIK) kills pathogenic microbes by disrupting their membranes. Our recent study has revealed that substitution of Ile (I) by Trp (W) or Phe (F), or substitution of Lys (K) by Arg (R) in GIK leads to GWK, GFK and GIR and improves AMP’s antimicrobial performance in terms of antimicrobial efficiency measured by minimum inhibition concentration and dynamic killing measured by minimum contact time to achieve 99.9% killing at a fixed AMP concentration. We hypothesize the efficiency improvement is related to membrane leakage underpinned by AMP binding. We request 3 days of SANS2D time to examine how the 4 AMPs bind small unilamellar vesicles mimicking outer/inner bacterial membranes of E. coli. This experiment is crucial to provide vital data about different in-membrane nanostructures to guide MD simulations and future SANS data analysis.
DOI: 10.5286/isis.e.rb2210218-1
title: How does in-membrane structuring affect antimicrobial efficiency of AMPs?

description: A short designed antimicrobial peptide (AMP) G(IIKK)3I (GIK) kills pathogenic microbes by disrupting their membranes. Our recent study has revealed that substitution of Ile (I) by Trp (W) or Phe (F), or substitution of Lys (K) by Arg (R) in GIK leads to GWK, GFK and GIR and improves AMP’s antimicrobial performance in terms of antimicrobial efficiency measured by minimum inhibition concentration and dynamic killing measured by minimum contact time to achieve 99.9% killing at a fixed AMP concentration. We hypothesize the efficiency improvement is related to membrane leakage underpinned by AMP binding. We request 3 days of SANS2D time to examine how the 4 AMPs bind small unilamellar vesicles mimicking outer/inner bacterial membranes of E. coli. This experiment is crucial to provide vital data about different in-membrane nanostructures to guide MD simulations and future SANS data analysis.
DOI: 10.5281/zenodo.5960686
title: LTEP-Biochar

description: The dataset inventories and compares experiments regarding on field application of biochar for agronomic purposes and its environmental effects (<em>e.g.</em> carbon sequestration) over a significative timeframe. Remediation of polluted soils is not in scope. The field experiments shall take place under dynamically, meteorologically and biologically complex conditions. We are mapping activities across Europe, North Africa and the Middle East (see the Highlights box here below). The LTEP project is an ICHAR initiative implemented and managed by the EMRG group of the University of Bologna.
DOI: 10.5281/zenodo.5960685
title: LTEP-Biochar

description: The dataset inventories and compares experiments regarding on field application of biochar for agronomic purposes and its environmental effects (<em>e.g.</em> carbon sequestration) over a significative timeframe. Remediation of polluted soils is not in scope. The field experiments shall take place under dynamically, meteorologically and biologically complex conditions. We are mapping activities across Europe, North Africa and the Middle East (see the Highlights box here below). The LTEP project is an ICHAR initiative implemented and managed by the EMRG group of the University of Bologna.
DOI: 10.6084/m9.figshare.19114976
title: Microbiological_qac_MRSA.xlsx

description: Microbiological data of Staphylococcus aureus bloodstream isolates
DOI: 10.6084/m9.figshare.19114976.v2
title: Microbiological_qac_MRSA.xlsx

description: Microbiological data of Staphylococcus aureus bloodstream isolates
DOI: 10.6084/m9.figshare.19114976.v1
title: Microbiological_qac_MRSA.xlsx

description: microbiological data of Staphylococcus aureus bloodstream isolates
DOI: 10.5517/ccdc.csd.cc22bb81
title: CCDC 1916552: Experimental Crystal Structure Determination

description: Related Article: W. Selmi, N. Hosni, M. Marchivie, J. Ben Naceur, H. Maghraoui-Meherzi, M.F. Zid|2022|J.Mol.Struct.|1254|132320|doi:10.1016/j.molstruc.2021.132320
DOI: 10.5517/ccdc.csd.cc27mxg8
title: CCDC 2074720: Experimental Crystal Structure Determination

description: Related Article: Haotian Sun, Baojian Xiong, Yuan Yang, Jiangjun Liu, Xuemei Zhang, Zhong Lian|2022|Org.Chem.Front.|9|305|doi:10.1039/D1QO01406D
DOI: 10.6084/m9.figshare.19115741
title: meta-data climate changes.xlsx

description: The dataset for this analysis of WTP for climate change policies and online appendix
DOI: 10.6084/m9.figshare.18390740.v1
title: Microseismic Imaging with Geometric-mean Reverse Time Migration Using Vertical and Horizontal Borehole Optical Fibers

description: We provide three example waveforms in binary format (.rsf@). They're bandpass-filtered, FK filtered and processed data. All data are bandpass to 15-38 Hz. We provided the well log (C) data in .las and .mat formats. A Matlab script for plotting is also provided. The elliptical VTI velocity model is also provided in the excel file. You can read the data using the open-source package Madagascar (https://www.reproducibility.org/wiki/Main_Page) or Matlab. A Matlab script to read and display the waveform data is included. An example display figure is also included. You can find the geometry information from the .rsf file or the Matlab script file. Let me know if you need more information: Zhendong Zhang (zdzhang@mit.edu).
DOI: 10.6084/m9.figshare.16794742.v1
title: Data and script "Asynchronous recovery of predator ..."

description: Dataset related to "Asynchronous recovery of predator...."
DOI: 10.6084/m9.figshare.16794742
title: Data and script "Asynchronous recovery of predator ..."

description: Dataset related to "Asynchronous recovery of predator...."
DOI: 10.6084/m9.figshare.16794742.v3
title: Data and script "Asynchronous recovery of predator ..."

description: Dataset related to "Asynchronous recovery of predator...."
DOI: 10.6084/m9.figshare.16794742.v2
title: Data and script "Asynchronous recovery of predator ..."

description: Dataset related to "Asynchronous recovery of predator...."
DOI: 10.17903/fk2/t1bt5o
title: Ελληνική Εκδοχή Του 7ου Γύρου Της Παγκόσμιας Έρευνας Αξιών (World Values Survey-7)

description: Η World Values Survey (WVS) είναι μια παγκόσμια έρευνα αξιών που διεξάγεται από το 1981 σε δεκάδες χώρες του κόσμου, με σκοπό να παρακολουθεί τη διαχρονική εξέλιξη των αξιών και των πεποιθήσεων των πολιτών στις σύγχρονες κοινωνίες καθώς και τον αντίκτυπο που έχουν οι αξίες αυτές στην κοινωνική και πολιτική ζωή της κάθε χώρας. Η έρευνα περιλαμβάνει ένα εκτεταμένο ερωτηματολόγιο σχεδόν 300 ερωτήσεων, κοινό σε όλες τις χώρες, που διεξάγεται με αυστηρές, κοινές προδιαγραφές σε "κύματα", περίπου κάθε πέντε χρόνια. Μέχρι το 2017 είχαν διεξαχθεί έξι "κύματα" της έρευνας χωρίς τη συμμετοχή της Ελλάδας. Η διαΝΕΟσις σε συνεργασία με το Εθνικό Κέντρο Κοινωνικών Ερευνών (ΕΚΚΕ) ανέλαβε να υποστηρίξει την υλοποίηση της έρευνας και τη συμμετοχή της Ελλάδας στο έβδομο "κύμα", με σκοπό να χαρτογραφήσει το αξιακό προφίλ της ελληνικής κοινωνίας.
DOI: 10.34740/kaggle/dsv/3134596
title: Mahanagar Yatayat Dataset
DOI: 10.6084/m9.figshare.14892087
title: Data from: Biodiversity effects of food system sustainability actions from farm to fork

description: The data archived here are the raw data required to reproduce all analysis presented in a manuscript published in <i>PNAS</i>.<br><br>Read, Q. D., Hondula, K. L., & Muth, M. K. Biodiversity effects of food system sustainability actions from farm to fork. <i>PNAS</i>.<br><br>This dataset is intended for use with the code archived in the git repository at https://doi.org/10.5281/zenodo.5949590. Please refer to the <b>README.md</b> file in that repository for instructions on how to download the data and reproduce the analysis.<br><br>Note that the dataset is archived as a set of eight .zip archives. The archives all contain one or more directories. You will need to unzip all the archives into the same root directory to reproduce the directory structure described in the included documentation file.<br><br>The data archived here are from a variety of different sources. As much as is practicable, they are presented here in their raw form as they were downloaded, without any processing. All processing steps can be replicated using the code archived in the accompanying code repository.<br><b><br>Manuscript abstract</b><br><br>Diet shifts and food waste reduction have the potential to reduce the land and biodiversity footprint of the food system. In this study, we estimated the amount of land used to produce food consumed in the United States, and the number of species threatened with extinction as a result of that land use. We predicted potential changes to biodiversity threat under scenarios of food waste reduction and shifts to recommended healthy and sustainable diets. Domestically produced beef and dairy, which require vast land areas, and imported fruit, which has an intense impact on biodiversity per unit land, have especially high biodiversity footprints. Adopting the Planetary Health diet or the USDA-recommended vegetarian diet nationwide would reduce the biodiversity footprint of food consumption. However, increases in consumption of foods grown in global biodiversity hotspots both inside and outside the United States, especially fruits and vegetables, would partially offset the reduction. In contrast, the USDA-recommended US-style and Mediterranean-style diets would increase the biodiversity threat due to increased consumption of dairy and farmed fish. Simply halving food waste would benefit global biodiversity over half as much as all Americans simultaneously shifting to a sustainable diet. Combining food waste reduction with adoption of a sustainable diet could reduce the biodiversity footprint of United States food consumption by roughly half. Species facing extinction because of unsustainable food consumption practices could be rescued by reducing agriculture's footprint; diet shifts and food waste reduction can help us get there.<br><br>
DOI: 10.6084/m9.figshare.19115681
title: Lactobacillus acidophilus and L. reuteri on bone , serum inflammatory factors and gut microbiota in OVX mice

description: After probiotic feeding, the bone volume fraction (BV/TV), the trabecular number (Tb.N), and the trabecular thickness (Tb.Th) increased, and the trabecular spacing (Tb.Sp) decreased in OVX mice. The inflammatory factors IL-1, IL-6, and TNF-α in the blood significantly decreased. The composition and proportion of gut microbiota changed.
DOI: 10.6084/m9.figshare.19115681.v1
title: Lactobacillus acidophilus and L. reuteri on bone , serum inflammatory factors and gut microbiota in OVX mice

description: After probiotic feeding, the bone volume fraction (BV/TV), the trabecular number (Tb.N), and the trabecular thickness (Tb.Th) increased, and the trabecular spacing (Tb.Sp) decreased in OVX mice. The inflammatory factors IL-1, IL-6, and TNF-α in the blood significantly decreased. The composition and proportion of gut microbiota changed.
DOI: 10.15129/262f2646-d082-4396-954a-e0ebaeddbbad
title: Demo of Enhanced Sliding DFT (eSDFT) Algorithm

description: eSDFT is an algorithm that computes the sliding DFT based on the momentary matrix transformation. The algorithm offers both speed and accuracy when using in real time, especially a long run that may suffer from the error accumulation caused by recursive formula. The eSDFT can minimize the error with an update from the direct FFT, which can be run concurrently on another core. This program uses FFTW for computing the direct FFT on multithreading architecture.
DOI: 10.5281/zenodo.5896796
title: Untargeted metabolomics peak intensity on CIA mouse plasma

description: Untargeted metabolomics with ultrahigh performance liquid chromatography-tandem mass spectroscopy (UPLC-MS/MS) was done on plasma of collagen-induced arthritis (CIA) mouse model. Data keys and explanations are below. mouseID: Mouse ID for the current study Treatment: CIA or control Time: Time of sacrifice and sample collection Intensity: Metabolite peak intensity measured by UPLC-MS/MS CHEM_ID: Internal ID for metabolite SUPER_PATHWAY: The general biochemical class assigned to the identified biochemical (e.g. lipid, amino acid, carbohydrate, etc.) intended for sorting compounds by broad biochemical classes SUB_PATHWAY: A more specific biochemical class assigned to the identified biochemical (e.g. TCA cycle, monoacylglycerols, etc.) intended for grouping/sorting compounds by biochemical pathway/class The rest of the data keys includes metabolite identifiers in multiple public databases and analysis platform.
DOI: 10.5281/zenodo.5896795
title: Untargeted metabolomics peak intensity on CIA mouse plasma

description: Untargeted metabolomics with ultrahigh performance liquid chromatography-tandem mass spectroscopy (UPLC-MS/MS) was done on plasma of collagen-induced arthritis (CIA) mouse model. Data keys and explanations are below. mouseID: Mouse ID for the current study Treatment: CIA or control Time: Time of sacrifice and sample collection Intensity: Metabolite peak intensity measured by UPLC-MS/MS CHEM_ID: Internal ID for metabolite SUPER_PATHWAY: The general biochemical class assigned to the identified biochemical (e.g. lipid, amino acid, carbohydrate, etc.) intended for sorting compounds by broad biochemical classes SUB_PATHWAY: A more specific biochemical class assigned to the identified biochemical (e.g. TCA cycle, monoacylglycerols, etc.) intended for grouping/sorting compounds by biochemical pathway/class The rest of the data keys includes metabolite identifiers in multiple public databases and analysis platform.
DOI: 10.5281/zenodo.5961277
title: Mechanical_Test_Mode I

description: SmartFan Project public data
DOI: 10.5281/zenodo.5961276
title: Mechanical_Test_Mode I

description: SmartFan Project public data
DOI: 10.5287/bodleian:xqe449dex
title: Examples of automated workflows for processing UAV-derived multispectral data in the Yukon-Kuskokwim Delta
DOI: 10.6084/m9.figshare.19115909
title: data.traits.GCB.csv

description: mean trait values for trait and species used at "Wood density and hydraulic traits influence species' growth response to drought across biomes"
DOI: 10.6084/m9.figshare.19115909.v2
title: data.traits.GCB.csv

description: mean trait values for trait and species used at "Wood density and hydraulic traits influence species' growth response to drought across biomes"
DOI: 10.6084/m9.figshare.19115909.v1
title: data.traits.GCB.csv

description: mean trait values for trait and species used at "Wood density and hydraulic traits influence species' growth response to drought across biomes"
DOI: 10.24376/rd.sgul.19070372
title: Cochrane Airways Specialised Register of Trials: database search strategies

description: This dataset contains details of the search strategies used to identify relevant records of trial reports for the Cochrane Airways Specialised Register of trials. The database name and platform are contained in the individual file names:<br>AMED_EBSCOhost_Airways scope search_24-01-2022.txtAPA PsycInfo_Ovid_Airways scope search_24-01-2022.txtCENTRAL_Cochrane Register of Studies_Airways scope search_24-01-2022.txtCINAHL_EBSCOhost_Airways scope search_24-01-2022.txtEmbase_Ovid_Airways scope search_24-01-2022.txtGlobal Health_Ovid_Airways scope search_24-01-2022.txtMEDLINE_ALL_Ovid_Airways scope search_24-01-2022.txtPubMed_NLM_Airways abbreviated scope search_24-01-2022.txt<br>The Cochrane Airways Specialised Register of Trials is a unique database containing references to reports of definite, probable and possible randomised controlled trials (RCTs) and quasi-randomised trials (CCTs) relevant to the Group's scope and topics. The Register includes references to reports on asthma, chronic obstructive pulmonary disease (COPD), sleep apnoea, bronchiectasis, interstitial lung diseases, and pulmonary hypertension.<br>The Register was developed, maintained and administered by the Information Specialist at the Cochrane Airways editorial base. References to trial reports were identified through systematic searches of bibliographic databases, and handsearching of respiratory conference abstracts.<br><br>The Register was used for the following purposes: To support the production of Cochrane Airways reviews.To inform prioritisation of Cochrane Airways Reviews. Review authors working with Cochrane Airways had access to the Trials Register via the Group’s Information Specialist. The Trials Register was made available to a wider audience through the CENTRAL database on the Cochrane Library (https://www.cochranelibrary.com/).<br>To identify this subset of CENTRAL, search all fields on the Cochrane Library using the code SR-AIRWAYS.<br>The Register was updated until August/September 2021.