cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7946594
title: Modified Sen1Floods11 Dataset for Change Detection

description: This is the dataset used for flood mapping as a change detection task in the IGARSS 22 conference paper "Attentive Dual Stream Siamese U-Net for Flood Detection on Multi-Temporal Sentinel-1 Data"


Paper Abstract:


Due to climate and land-use change, natural disasters such as flooding have been increasing in recent years. Timely and reliable flood detection and mapping can help emergency response and disaster management. In this work, we propose a flood detection network using bi-temporal SAR acquisitions. The proposed segmentation network has an encoder-decoder architecture with two Siamese encoders for pre and post-flood images. The network's feature maps are fused and enhanced using attention blocks to achieve more accurate detection of the flooded areas. Our proposed network is evaluated on publicly available Sen1Flood11 [1] benchmark dataset. The network outperformed the existing state-of-the-art (uni-temporal) flood detection method by 6% IOU. The experiments highlight that the combination of bi-temporal SAR data with an effective network architecture achieves more accurate flood detection than uni-temporal methods. 


Full Paper : https://ieeexplore.ieee.org/document/9883132
DOI: 10.34740/kaggle/dsv/7385770
title: Trending Youtube Video Statistics (113 Countries)
DOI: 10.6084/m9.figshare.24901878
title: <b>Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken caeca from Pakistan</b>

description: This article presents metagenomic-assembled genomes (MAGs) of prokaryotic organisms originating from chicken caeca. The samples originate from broiler chickens, one group was infected with Newcastle Disease Virus (NDV) and one uninfected control group. There were four birds per group. Both groups were raised on commercially available antibiotic free feed under a semi-controlled setup. The binning step of the samples identified 130 MAGs with50% completion, and10% contamination. The data presented includes sequences in FASTA format, tables of functional annotation of genes, and data from two different approaches for phylogenetic tree construction using these MAGs. Major geochemical cycles at community level including carbon, sulfur, and nitrogen cycles are also presented.
DOI: 10.6084/m9.figshare.24901878.v1
title: <b>Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken ceca from Pakistan</b>

description: This article presents metagenomic-assembled genomes (MAGs) of prokaryotic organisms originating from chicken caeca. The samples originate from broiler chickens, one group was infected with Newcastle Disease Virus (NDV) and one uninfected control group. There were four birds per group. Both groups were raised on commercially available antibiotic free feed under a semi-controlled setup. The binning step of the samples identified 130 MAGs with50% completion, and10% contamination. The data presented includes sequences in FASTA format, tables of functional annotation of genes, and data from two different approaches for phylogenetic tree construction using these MAGs. Major geochemical cycles at community level including carbon, sulfur, and nitrogen cycles are also presented.
DOI: 10.6084/m9.figshare.24901884.v1
title: <b>Dataset of 569 metagenome-assembled genomes from the ceca of multiple chicken breeds from commercial and backyard farming setups of Pakistan</b>

description: This article presents metagenomic-assembled genomes (MAGs) of prokaryotic organisms recovered from 9 different groups of chicken raised in different farm setups in Pakistan. The groups comprise three different breeds (Broilers, White Layers, Black Australorp) of chicken raised in different farming setups that include antibiotic-free control sheds, commercial, and backyard farms. The binning of the samples identified 569 MAGs with50% completion, and10% contamination. The data for each MAG includes sequences in FASTA format, tables of functional annotation of genes, along with two different strategies for recovery of phylogenetic tree for these MAGs. Major geochemical cycles at community level including carbon, sulfur, and nitrogen cycles are also recovered.
DOI: 10.34740/kaggle/dsv/7385786
title: Top Spotify Songs in 73 Countries (Daily Updated)
DOI: 10.34740/kaggle/dsv/7385787
title: Full TMDB Movies Dataset 2023 (930K Movies)
DOI: 10.25345/c5z02zk81
title: MassIVE MSV000093840 - Osteomacs promote maintenance of murine hematopoiesis through megakaryocyte-induced upregulation of Embigin and CD166
title: Maintenance of hematopoietic stem cell (HSC) function in the niche is an orchestrated event. Osteomacs (OM), are key cellular components of the niche. Previously, we documented that osteoblasts, OM, and megakaryocytes interact to promote hematopoiesis. Here, we further characterize OM and identify megakaryocyte-induced mediators that augment the role of OM in the niche. Single cell mRNAseq, mass spectrometry, and CyTOF examination of megakaryocyte-stimulated OM suggested that upregulation of CD166 and Embigin on OM augment their hematopoiesis maintenance function. CD166 knockout OM or shRNA-Embigin knockdown OM, confirmed that loss of these molecules significantly reduced OM ability to augment the osteoblast-mediated hematopoietic enhancing activity. Recombinant CD166 and Embigin partially substituted for OM function, characterizing both proteins as critical mediators of OM hematopoietic function. Our data identify Embigin and CD166 as OM-regulated critical components of HSC function in the niche and potential participants in various in vitro manipulations of stem cells.
DOI: 10.13026/9vd3-1y84
title: EHR-DS-QA: A Synthetic QA Dataset Derived from Medical Discharge Summaries for Enhanced Medical Information Retrieval Systems

description: This dataset was designed and created to enable advancements in healthcare-
focused large language models, particularly in the context of retrieval-
augmented clinical question-answering capabilities. Developed using a self-
constructed pipeline based on the 13-billion parameter Meta Llama 2 model,
this dataset encompasses 21466 medical discharge summaries extracted from the
MIMIC-IV-Note dataset, with 156599 synthetically generated question-and-answer
pairs, a subset of which was verified for accuracy by a physician. These pairs
were generated by providing the model with a discharge summary and instructing
it to generate question-and-answer pairs based on the contextual information
present in the summaries. This work aims to generate data in support of the
development of compact large language models capable of efficiently extracting
information from medical notes and discharge summaries, thus enabling
potential improvements for real-time decision-making processes in clinical
settings. Additionally, accompanying the dataset is code facilitating
question-and-answer pair generation from any medical and non-medical text.
Despite the robustness of the presented dataset, it has certain limitations.
The generation process was confined to a maximum context length of 6000 input
tokens, owing to hardware constraints. The large language model's nature in
generating these question-and-answer pairs may introduce an underlying bias or
a lack in diversity and complexity. Future iterations should focus on
rectifying these issues, possibly through diversified training and expanded
verification procedures as well as the employment of more powerful large
language models.
DOI: 10.6084/m9.figshare.23599695
title: <strong>A Flood Knowledge-Constrained Large Language Model Interactable with GIS: Enhancing Public Risk Perception of Floods</strong>

description: Partial experimental results data
DOI: 10.6084/m9.figshare.23599695.v1
title: <strong>A Flood Knowledge-Constrained Large Language Model Interactable with GIS: Enhancing Public Risk Perception of Floods</strong>

description: Partial experimental results data
DOI: 10.13026/f0hv-7037
title: ODD: A Benchmark Dataset for the NLP-based Opioid Related Aberrant Behavior Detection

description: Opioid related aberrant behaviors (ORAB) present novel risk factors for opioid
overdose. Previously, ORAB have been mainly assessed by survey results and by
monitoring drug administrations. Such methods however, cannot scale up and do
not cover the entire spectrum of aberrant behaviors. On the other hand, ORAB
are widely documented in electronic health record notes. This paper introduces
a novel biomedical natural language processing benchmark dataset named ODD,
for ORAB Detection Dataset. ODD is an expert-annotated dataset comprising of
more than 750 publicly available EHR notes. ODD has been designed to identify
ORAB from patients' EHR notes and classify them into nine categories; 1)
Confirmed Aberrant Behavior, 2) Suggested Aberrant Behavior, 3) Opioids, 4)
Indication, 5) Diagnosed opioid dependency, 6) Benzodiapines, 7) Medication
Changes, 8) Central Nervous System-related, and 9) Social Determinants of
Health.
DOI: 10.13026/qrje-z188
title: ODD: A Benchmark Dataset for the NLP-based Opioid Related Aberrant Behavior Detection

description: Opioid related aberrant behaviors (ORAB) present novel risk factors for opioid
overdose. Previously, ORAB have been mainly assessed by survey results and by
monitoring drug administrations. Such methods however, cannot scale up and do
not cover the entire spectrum of aberrant behaviors. On the other hand, ORAB
are widely documented in electronic health record notes. This paper introduces
a novel biomedical natural language processing benchmark dataset named ODD,
for ORAB Detection Dataset. ODD is an expert-annotated dataset comprising of
more than 750 publicly available EHR notes. ODD has been designed to identify
ORAB from patients' EHR notes and classify them into nine categories; 1)
Confirmed Aberrant Behavior, 2) Suggested Aberrant Behavior, 3) Opioids, 4)
Indication, 5) Diagnosed opioid dependency, 6) Benzodiapines, 7) Medication
Changes, 8) Central Nervous System-related, and 9) Social Determinants of
Health.
DOI: 10.5281/zenodo.10493314
title: Supplementary Simulation Data for "Concerted transformation of a hyper-paused transcription complex and its reinforcing protein"

description: Additional simulation data for "Concerted transformation of a hyper-paused transcription complex and its reinforcing protein", submitted as a preprint to BioRxiv (https://doi.org/10.1101/2023.06.26.546588), posted on June 28, 2023.

Content:

'smog2' folder: Contains Structure-Based Models (SBMs) for RfaH bound to the ops-paused elongation complex (opsPEC) in an encounter complex (opsPEC_Enc), complex 1 of RfaH bound to the opsPEC in a recruited complex (opsPEC_Rec), and a custom-built dual-basin SBM that combines topological information for both opsPEC_Enc and opsPEC_Rec. SBMs were generated using SMOG2 v2.4.5, whereas the dual-basin SBM was build using custom scripts.

'clusters' folder: Contains representative structures for intermediates I1, I2, I3 and I4 retrieved from 500 simulations of RfaH-opsPEC using a dual-basin SBM topology (top) file and the coordinates (gro file) for the opsPEC_Enc as the initial coordinates of the simulation. It also contains representative structures for intermediates I1, I2, I3 and I4 from control simulations for free RfaH (free_RfaH), starting from the coordinates for the opsPEC_Enc complex.

'traj' folder: Contains representative trajectories (xtc files, 2 out of 500) for the fold-switch of RfaH bound to opsPEC from the Enc to the Rec conformation.
DOI: 10.5281/zenodo.10493315
title: Supplementary Simulation Data for "Concerted transformation of a hyper-paused transcription complex and its reinforcing protein"

description: Additional simulation data for "Concerted transformation of a hyper-paused transcription complex and its reinforcing protein", submitted as a preprint to BioRxiv (https://doi.org/10.1101/2023.06.26.546588), posted on June 28, 2023.

Content:

'smog2' folder: Contains Structure-Based Models (SBMs) for RfaH bound to the ops-paused elongation complex (opsPEC) in an encounter complex (opsPEC_Enc), complex 1 of RfaH bound to the opsPEC in a recruited complex (opsPEC_Rec), and a custom-built dual-basin SBM that combines topological information for both opsPEC_Enc and opsPEC_Rec. SBMs were generated using SMOG2 v2.4.5, whereas the dual-basin SBM was build using custom scripts.

'clusters' folder: Contains representative structures for intermediates I1, I2, I3 and I4 retrieved from 500 simulations of RfaH-opsPEC using a dual-basin SBM topology (top) file and the coordinates (gro file) for the opsPEC_Enc as the initial coordinates of the simulation. It also contains representative structures for intermediates I1, I2, I3 and I4 from control simulations for free RfaH (free_RfaH), starting from the coordinates for the opsPEC_Enc complex.

'traj' folder: Contains representative trajectories (xtc files, 2 out of 500) for the fold-switch of RfaH bound to opsPEC from the Enc to the Rec conformation.
DOI: 10.25345/c5t727s48
title: MassIVE MSV000093841 - Filamin A is required for kindlin-3-driven activation of beta3 integrins in platelets
title: A critical aspect of hemostasis involves the regulation of beta3 integrins at the platelet surface. Integrins are transmembrane proteins whose activation by extracellular ligands (outside-in signaling) is intertwined with their activation by intracellular proteins (inside-out signaling). Inside-out signaling is orchestrated by proteins that interact with the cytoplasmic component of the beta3 integrin, including the actin cytoskeleton and actin-binding proteins. Here we evaluated the role of the actin-binding protein filamin A (FLNA) in modulating beta3 integrin function in platelets. FLNA-deficient platelets exhibit a defect in beta3 integrin function. Tandem mass spectrometry and co-immunoprecipitation revealed that the integrin-activating protein kindlin-3 preferentially associates with FLNA in activated platelets.
DOI: 10.25345/c5pg1j011
title: MassIVE MSV000093842 - IRF4 requires ARID1A to establish plasma cell identity in multiple myeloma
title: Multiple myeloma (MM) is an incurable malignancy of plasma cells that exploits transcriptional networks driven by IRF4. To discover unique molecular vulnerabilities in MM centered on IRF4, we employ a multi-omics approach integrating functional genomics screening, spatial proteomics, and global chromatin mapping. We find that ARID1A, a member of the SWI/SNF chromatin remodeling complex, is both required for IRF4 expression and functionally associated with IRF4 protein on chromatin. Deletion of Arid1a in activated murine B cells thwarts subsequent plasma cell differentiation by disrupting IRF4-dependent transcriptional networks, therefore defining ARID1A as a novel plasma cell vulnerability. Targeting ARID1A-dependent SWI/SNF activity via SMARCA2/4 inhibition induces a rapid loss of IRF4-target gene expression and quenches global amplification of oncogenic gene expression driven by MYC, resulting in profound toxicity to MM cells. Notably, MM patients with aggressive disease have markers of SWI/SNF activity, and SMARCA2/4 inhibitors retain their activity in immunomodulatory drug (IMiD)-resistant MM cells. To fully harness the potential of these drugs, we use combinatorial drug screens to uncover profound synergistic toxicity between SMARCA2/4 and MEK inhibitors. Thus, targeting SWI/SNF activity potently represses an IRF4-MYC feed forward loop and provides a feasible path to effectively treat this incurable disease.
DOI: 10.18739/a2xs5jj62
title: Gravity Recovery and Climate Experiment Non-Tidal Atmosphere Geopotential Coefficients Jet Propulsion Laboratory Release 6.0 - monthly mean non-tidal atmosphere (GAA), 2002-2017

description: FOR EXPERT USE ONLY. This dataset contains estimates of geopotential field derived from the Gravity Recovery and Climate Experiment (GRACE) mission measurements and a non-tidal atmospheric model produced by the National Aeronautics and Space Administration (NASA) Jet Propulsion Laboratory (JPL). The data are in spherical harmonics averaged over approximately a month. The primary objective of the GRACE mission is to obtain accurate estimates of the mean and time-variable components of the gravity field variations.
 This objective is achieved by making continuous measurements of the change in distance between twin spacecraft, co-orbiting in about 500 kilometers (km) altitude, near circular, polar orbit, spaced approximately 200 km apart, using a microwave ranging system. In addition to these range change, the non-gravitional forces are measured on each satellite using a high accuracy electrostatic, room-temperature accelerometer. The satellite orientation and position (and timing) are precisely measured using twin star cameras and a GPS receiver, respectively.
 Spatial and temporal variations in the gravity field affect the orbits (or trajectories) of the twin spacecraft differently. These differences are manifested as changes in the distance between the spacecraft, as they orbit the Earth. This change in distance is reflected in the time-of-flight of microwave signals transmitted and received nearly simultaneously between the two spacecraft. The change in this time of fight is continuously measured by tracking the phase of the microwave carrier signals. The so called dual-one-way range change measurements can be reconstructed from these phase measurements. This range change (or its numerically derived derivatives), along with other mission and ancillary data, is subsequently analyzed to extract the parameters of an Earth gravity field model.
 GRACE. 2018. GRACE_GAA_L2_GRAV_JPL_RL06. Ver. 6.0. PO.DAAC, CA, USA. Dataset accessed [2020-10-19] at https://doi.org/10.5067/GRGAA-20J06
DOI: 10.34740/kaggle/dsv/7385975
title: Daily Public Opinion on Israel-Palestine War
DOI: 10.34740/kaggle/dsv/7386002
title: Public Opinion on Climate Change (Updated Daily)
DOI: 10.6084/m9.figshare.24986235
title: Data files and code for "Bigger isn’t always better: challenging the associations between diapause, body weight, and overwintering survival "

description: These datasets correspond to the experiments described by Short, Walters, & Hahn (2024) in the manuscript submitted to Functional Ecology
DOI: 10.6084/m9.figshare.24986235.v2
title: Data files and code for "Bigger isn’t always better: challenging the associations between diapause, body weight, and overwintering survival "

description: These datasets correspond to the experiments described by Short, Walters, & Hahn (2024) in the manuscript submitted to Functional Ecology
DOI: 10.6084/m9.figshare.24986235.v1
title: Data files and code to analyze data files.

description: These datasets correspond to the experiments described by Short, Walters, & Hahn (2024) in the manuscript submitted to Functional Ecology
DOI: 10.6084/m9.figshare.21926127
title: EXCEL MODEL WITH WANING FOR POSTING REVISED v.2

description: This revised version of our earlier mixing model incorporates additional complexity including:<br>1. Waning immunity.2. Differential risk and infectivity by prior immune experience.3. Effects of hybrid immunity.4. Boosting.5. Diminished vaccine efficacy to reflect immune evasion with Omicron SARS-CoV-2 variants.
DOI: 10.6084/m9.figshare.21926127.v2
title: EXCEL MODEL WITH WANING FOR POSTING REVISED

description: This revised version of our earlier mixing model incorporates additional complexity including:
<br>
1. Waning immunity.
2. Differential risk and infectivity by prior immune experience.
3. Effects of hybrid immunity.
4. Boosting.
5. Diminished vaccine efficacy to reflect immune evasion with Omicron SARS-CoV-2 variants.
DOI: 10.6084/m9.figshare.24986211.v1
title: Table S3. <i>ARRDC3</i> and <i>NFIA</i> genotypes for 204 case-control animals corresponding to 12 SNPs listed in Table 2.

description: Bovine congestive heart failure (BCHF) has become increasingly prevalent among feedlot cattle in the Western Great Plains of North America with up to 7% mortality in affected herds. BCHF is an untreatable complex condition involving pulmonary hypertension that culminates in right ventricular failure and death. Genes associated with BCHF in feedlot cattle have not been previously identified. Our aim was to search for genomic regions associated with this disease. A retrospective, matched case-control design with 102 clinical BCHF cases and their unaffected penmates was used in a genome-wide association study. Paired nominal data from approximately 560k filtered single nucleotide polymorphisms (SNPs) were analyzed with McNemar’s test. The most significant genome-wide association was in the arrestin domain-containing 3 protein gene (ARRDC3), followed by the nuclear factor IA gene (NFIA, mid-p-values, 1x10E-8 and 2x10E-7, respectively). Animals with homozygous risk alleles at either gene were approximately 8-fold more likely to have BCHF than their matched penmates without those risk alleles (CI95 = 3-17). Animals with homozygous risk alleles at both genes were 28-fold more likely to have BCHF than all others (p-value = 1x10E-7, CI95 = 4-206). A linked missense variant in ARRDC3 (C182Y) represents a potential functional variant since C182 is conserved among all other jawed vertebrate species observed. A DNA test with two markers showed 29% of 273 BCHF cases had homozygous risk alleles in both genes, compared to 2.5% in 198 similar unaffected feedlot cattle. This DNA test may be useful for identifying feedlot animals with the highest risk for BCHF in the environments described here. Although pathogenic roles for ARRDC3 and NFIA variants associated with BCHF are unknown, their discovery facilitates classifying animals by genetic risk and allows cattle producers to make informed decisions for selective breeding and animal health management.
DOI: 10.6084/m9.figshare.24073800
title: Tarpon Gillnet Data Study

description: Data includes all TPWD gillnet data that pertains to tarpon in Texas.
DOI: 10.6084/m9.figshare.24073800.v1
title: Texas Parks and Wildlife Gillnet Tarpon Data

description: Data includes all TPWD gillnet data that pertains to tarpon in Texas.
DOI: 10.5281/zenodo.10484921
title: Model data and code in support of the main text of Azimrayat-Andrews et. al. Submitted to Environ. Res. Lett.

description: Model code and data in support of Azimrayat-Andrews et al. submitted to Environmental Research Letters
DOI: 10.5281/zenodo.10484922
title: Model data and code in support of the main text of Azimrayat-Andrews et. al. Submitted to Environ. Res. Lett.

description: Model code and data in support of Azimrayat-Andrews et al. submitted to Environmental Research Letters
DOI: 10.5281/zenodo.10484939
title: Model data and code in support of Appendix A of Azimrayat-Andrews et al. submitted to Environmental Research Letters

description: Model data and code in support of Appendix A of Azimrayat-Andrews et al. submitted to Environmental Research Letters
DOI: 10.5281/zenodo.10484940
title: Model data and code in support of Appendix A of Azimrayat-Andrews et al. submitted to Environmental Research Letters

description: Model data and code in support of Appendix A of Azimrayat-Andrews et al. submitted to Environmental Research Letters
DOI: 10.5281/zenodo.10070472
title: Reactivity of radiolytically- and photochemically-generated tertiary amine radicals towards a CO2 reduction catalyst

description: These data are related to a publication (https://doi.org/10.1063/5.0180065). The Igor Pro software is required to open the files (version 8 or higher). A free 30-day trial version of Igor Pro can be downloaded from the Wavemetrics website (https://www.wavemetrics.com/).
DOI: 10.5281/zenodo.10070473
title: Reactivity of radiolytically- and photochemically-generated tertiary amine radicals towards a CO2 reduction catalyst

description: These data are related to a publication (https://doi.org/10.1063/5.0180065). The Igor Pro software is required to open the files (version 8 or higher). A free 30-day trial version of Igor Pro can be downloaded from the Wavemetrics website (https://www.wavemetrics.com/).