cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6302817
title: A massive proteogenomic screen identifies thousands of novel human protein coding sequences

description: Accurate annotation of genes in the human genome is fundamental for biomedical research and genomic data interpretation. The Ensembl, RefSeq, and GENCODE consortiums continuously update the human genome annotations based on new computational and experimental evidence, and new proteins were identified constantly. The Genotype-Tissue Expression (GTEx) project has generated more than 15,000 RNA sequencing dataset from multiple-tissues of more than 800 donors which allows to model almost all transcripts and proteins in the human genome. Using proteins translated from the GTEx transcript model, more than 21 million in-silico trypsin-digested peptides were generated. To identify high-confidence novel proteins with proteomic support, we screened more than 2,000 proteomic projects in the PRIDE database and selected more than 50,000 mass spectrometry (MS) runs from 923 projects. These MS data were used to validate the predicted novel peptides. With a stringent standard, we identified almost 20,000 novel peptides. 


This dataset include files used in the the above analysis. More details can be found in the GitHub page (https://github.com/ATPs/human_novo_protein_2022).
DOI: 10.5281/zenodo.6302818
title: A massive proteogenomic screen identifies thousands of novel human protein coding sequences

description: Accurate annotation of genes in the human genome is fundamental for biomedical research and genomic data interpretation. The Ensembl, RefSeq, and GENCODE consortiums continuously update the human genome annotations based on new computational and experimental evidence, and new proteins were identified constantly. The Genotype-Tissue Expression (GTEx) project has generated more than 15,000 RNA sequencing dataset from multiple-tissues of more than 800 donors which allows to model almost all transcripts and proteins in the human genome. Using proteins translated from the GTEx transcript model, more than 21 million in-silico trypsin-digested peptides were generated. To identify high-confidence novel proteins with proteomic support, we screened more than 2,000 proteomic projects in the PRIDE database and selected more than 50,000 mass spectrometry (MS) runs from 923 projects. These MS data were used to validate the predicted novel peptides. With a stringent standard, we identified almost 20,000 novel peptides. This dataset include files used in the the above analysis. More details can be found in the GitHub page (https://github.com/ATPs/human_novo_protein_2021).
DOI: 10.5281/zenodo.7509106
title: A massive proteogenomic screen identifies thousands of novel human protein coding sequences

description: Accurate annotation of genes in the human genome is fundamental for biomedical research and genomic data interpretation. The Ensembl, RefSeq, and GENCODE consortiums continuously update the human genome annotations based on new computational and experimental evidence, and new proteins were identified constantly. The Genotype-Tissue Expression (GTEx) project has generated more than 15,000 RNA sequencing dataset from multiple-tissues of more than 800 donors which allows to model almost all transcripts and proteins in the human genome. Using proteins translated from the GTEx transcript model, more than 21 million in-silico trypsin-digested peptides were generated. To identify high-confidence novel proteins with proteomic support, we screened more than 2,000 proteomic projects in the PRIDE database and selected more than 50,000 mass spectrometry (MS) runs from 923 projects. These MS data were used to validate the predicted novel peptides. With a stringent standard, we identified almost 20,000 novel peptides. This dataset include files used in the the above analysis. More details can be found in the GitHub page (https://github.com/ATPs/human_novo_protein_2022).
DOI: 10.5281/zenodo.8296655
title: A massive proteogenomic screen identifies thousands of novel human protein coding sequences

description: Accurate annotation of genes in the human genome is fundamental for biomedical research and genomic data interpretation. The Ensembl, RefSeq, and GENCODE consortiums continuously update the human genome annotations based on new computational and experimental evidence, and new proteins were identified constantly. The Genotype-Tissue Expression (GTEx) project has generated more than 15,000 RNA sequencing dataset from multiple-tissues of more than 800 donors which allows to model almost all transcripts and proteins in the human genome. Using proteins translated from the GTEx transcript model, more than 21 million in-silico trypsin-digested peptides were generated. To identify high-confidence novel proteins with proteomic support, we screened more than 2,000 proteomic projects in the PRIDE database and selected more than 50,000 mass spectrometry (MS) runs from 923 projects. These MS data were used to validate the predicted novel peptides. With a stringent standard, we identified almost 20,000 novel peptides. This dataset include files used in the the above analysis. More details can be found in the GitHub page (https://github.com/ATPs/human_novo_protein_2022).
DOI: 10.6084/m9.figshare.24874557
title: Consensus HBV sequences from HCC/non-HCC patients

description: These are full-length consensus HBV sequences from adults in South Africa, representing individuals with and without hepatocellular carcinoma (HCC). Sequences were derived through a whole genome sequencing Illumina protocol. Ethical approval was granted from the health research ethics committee at the University of Stellenbosch (S13/04/072 and N11/09/284).
DOI: 10.6084/m9.figshare.24874557.v1
title: HCC-1.fasta.gz

description: Consensus sequences for HBV HCC study.
DOI: 10.5281/zenodo.7808510
title: SoccerNet_v3_H250/

description: This is our proposed dataset for evaluating long-shot Football (Soccer) player and ball detection models. It is a subset of SoccerNet-v3. It consists of the frames in which the length (height) of the bounding box that locates a person does not exceed 250 pixels. The SoccerNet v3 compressed .png images have been extracted to the proper directory structure and converted to .jpg. Additionally, the corresponding annotations of the bounding boxes have been filtered and converted into a format compatible with YOLO annotation. Two classes are present:



	
“0” for ball, and
	
“1” for person bounding boxes. As "person" we have included all 7 classes of human annotations.



The division into training, validation and testing parts has been preserved, and the corresponding number of images is now: 14,368/2,726/2,692. Relevant code is available at [https://github.com/kmouts/FootAndBall]


More info regarding the dataset is available here: [https://github.com/kmouts/SoccerNet_v3_H250]
description: Setting a Baseline in long-shot real-time Soccer Player and Ball detection
DOI: 10.5281/zenodo.7808511
title: SoccerNet_v3_H250/

description: This is our proposed dataset for evaluating long-shot Football (Soccer) player and ball detection models. It is a subset of SoccerNet-v3. It consists of the frames in which the length (height) of the bounding box that locates a person does not exceed 250 pixels. The SoccerNet v3 compressed .png images have been extracted to the proper directory structure and converted to .jpg. Additionally, the corresponding annotations of the bounding boxes have been filtered and converted into a format compatible with YOLO annotation. Two classes are present:



	
“0” for ball, and
	
“1” for person bounding boxes. As "person" we have included all 7 classes of human annotations.



The division into training, validation and testing parts has been preserved, and the corresponding number of images is now: 14,368/2,726/2,692. Relevant code is available at [https://github.com/kmouts/FootAndBall]


More info regarding the dataset is available here: [https://github.com/kmouts/SoccerNet_v3_H250]
description: Setting a Baseline in long-shot real-time Soccer Player and Ball detection
DOI: 10.5281/zenodo.10400091
title: Optical Coherence Tomography Angiography-OCTA Dataset for Detection of Diabetic Retinopathy

description: This dataset consists of 268 OCTA images acquired on Optovue Avanti Edition for 179 patients. Out of 262, 133 are left-eye images and 135 are right-eye images. The acquisition is done at Natasha Eye Care and Research Institute, Pimple Saudager Pune. This dataset is curated for early detection of Diabetic Retinopathy and contains three categories of data viz NO_DR, Mild_DR, and Moderate_DR.
DOI: 10.5281/zenodo.10400092
title: Optical Coherence Tomography Angiography-OCTA Dataset for Detection of Diabetic Retinopathy

description: This dataset consists of 268 OCTA images acquired on Optovue Avanti Edition for 179 patients. Out of 262, 133 are left-eye images and 135 are right-eye images. The acquisition is done at Natasha Eye Care and Research Institute, Pimple Saudager Pune. This dataset is curated for early detection of Diabetic Retinopathy and contains three categories of data viz NO_DR, Mild_DR, and Moderate_DR.
DOI: 10.5067/vwth7s6218sg
title: GLDAS VIC Land Surface Model L4 monthly 1.0 x 1.0 degree V2.1
DOI: 10.6073/pasta/312e8060350f443b5e885ff33a2ddee8
title: Parameters from discrete bottle samples on a hydrographic CTD (Conductivity Temperature Depth) cast during CCE LTER process cruises in the CCE region, 2006 - 2019 (ongoing).

description: Hydrographic CTD (Conductivity Temperature Depth) measurements from discrete water samples are taken on individual CTD rosette casts, deployed on CCE Process cruises (since 2006, ongoing) in the Southern California region. Seawater is collected in up to 24 Niskin bottles at specific depths (up to 1000m), determined by the chlorophyll maximum and mixed layer depth as the instrument is lowered through the water column. The samples are filtered and analyzed at sea and used to assess the CTD sensor data quality. Measurements include depth, temperature, salinity, density (sigma theta), oxygen, O2 saturation, PAR (radiation, surface radiation and irradiance), fluorescence and transmission. Salinity checks are performed with a salinometer back at the lab.
DOI: 10.6073/pasta/50a0a46193bc6cbe7eaa1ba7510278e3
title: Measurements, from CCE LTER process cruises in the California Current region, of dissolved inorganic concentrations of nutrient iron and of iron limitation at selected stations and depths, 2006 - 2019 (ongoing).

description: Measurements are made of dissolved iron, total iron and the potential for phytoplankton iron limitation on CCE LTER Process cruises (since 2006, ongoing) in coastal transition zones of the southern California Current System. This is a weak upwelling regime that is relatively low in nutrients and chlorophyll. Changes in phytoplankton (Chla response to Fe+) and nutrient parameters upon iron addition are also investigated.
DOI: 10.6073/pasta/831e099fb086954d3d73638d33d3dd05
title: High Performance Liquid Chromatography (HPLC) pigment analysis from rosette bottle samples at various depths from CCE LTER process cruises in the California Current System, 2006 to 2017.

description: High Performance Liquid Chromatography (HPLC) samples are collected from rosette bottles (from three to eight different depths in the photic zone) at stations located within the CCE region on Process cruises (since 2006, ongoing). The HPLC method is used to measure concentrations of chlorophylls and carotenoids in samples of particulate matter, which includes filtering and freezing the filter while at sea. The taxon-specific phyto-pigments are extracted back onshore. Concentrations of chlorophyll a are used as a proxy for phytoplankton biomass and concentrations of other taxon-specific pigments are used to determine contributions of phytoplankton taxa to total phytoplankton biomass.
DOI: 10.6073/pasta/c1a975ce7bec5ee2b5bf7e10f9b9a8ac
title: Particulate organic carbon and nitrogen measurements at selected depths in the water column in the CCE region since 2006 - 2019 (ongoing).

description: Water column bottle samples at multiple depths are taken during CCE Process cruises (since 2006, ongoing) at various CTD stations, filtered, and stored at -20°C. Measurements of particulate organic carbon (POC) and nitrogen (PON) are performed onshore in the lab where samples are acidified, dried and analyzed by high-temperature combustion. The sample and tin capsule react with oxygen and combust at 1000°C, and the sample is broken down, thus converting organic carbon to CO2 and reducing nitrogen oxides to N2 gas. Both gases are measured by thermal conductivity. Samples analyzed within the CCE constrain the mean C:N ratio of small particulates and by difference relative to measured living biomass, the biomass of suspended detritus.
DOI: 10.6084/m9.figshare.23567034.v2
title: Dataset of dissolved inorganic nitrogen data and dissolved inorganic carbon data in stations in the Canada Basin and the Chukchi shelf during 2010-2014 Chinese Arctic Scientific Expedition (CHINARE).xlsx

description: The file contaions stations, longitude, latitude, depth, dissolved inorganic nitrogen, dissolved inorganic carbon in stations in the Chukchi shelf and the Canada Basin stations from 2010-2014 Chinese Arctic Scientific Expedition (CHINARE) . This is the dataset used in the paper by Zhang et al. (2023) submitted to JGR-Oceans.
DOI: 10.6084/m9.figshare.24573007
title: Supplementary Material for: Response of brain and meningeal metastases to trastuzumab-deruxtecan in a patient with HER2-low breast cancer

description: Introduction: nervous system metastases (CNSm) are late events associated with poor outcomes in endocrine-sensitive HER2-negative breast cancer (BC) patients, especially in the presence of leptomeningeal disease (LMD). Effective treatments are extremely limited in this setting. The antibody-drug conjugate, trastuzumab-deruxtecan (T-DXd), which combines the anti-HER2 antibody trastuzumab with a topoisomerase type 1 inhibitor, showed high efficacy not only against HER2-positive, but also HER2-low metastatic breast cancers (BC), expressing HER2 at a lower level. Case presentation: To the best of our knowledge, this is the first report of a patient with metastatic endocrine-sensitive HER2-low BC suffering from BMs associated with LMD and sustained disease control when treated with T-DXd. Conclusion: Several recent case series have reported the activity of T-DXd in patients with HER2-positive disease and brain metastases (BMs) or leptomeningeal disease (LMD), but none in HER2-low patients. This case is particularly relevant since more than 50% of BCs are HER2-low.
DOI: 10.6084/m9.figshare.24573043
title: Supplementary Material for: Esophageal Infiltration by High-grade Serous Ovarian Carcinoma: A very Rare Case Report.

description: Introduction Esophageal involvement in high-grade serous ovarian carcinoma is a rare phenomenon when advanced systemic disease is detected. Dysphagia is the most common guide symptom. However, diagnosis is often delayed due to its submucosal process that is not early seen in endoscopic initial evaluation, while computerized tomography (CT) scan usually shows concentric thickening of the esophageal layers and gives the suspected diagnosis. Case presentation We present the case of a patient who died of mediastinitis caused by an esophageal perforated ulceration due to infiltration of high-grade serous ovarian carcinoma. In addition, this is the first case report of severe esophageal candidiasis associated that delayed diagnosis and subsequent oncological treatment. Conclusion Esophageal secondary infiltration must be suspected when a patient has a history of malignancy combined with consistent CT findings.
DOI: 10.5281/zenodo.8321186
title: Field Line Resonances estimated using Machine Learning methods

description: This data set contains the machine learning input matrix (composed by 1D Fourier cross-spectra) + additional information, for the Classification algorithm implemented in Foldes et al. (Automatic Detection of Field Line Resonance Frequencies in the Earth’s Plasmasphere, 2023) for the pair of station Tartu-Birzai (TAR-BRZ). Each file contains the following header at line 1. Columns are: - P(f0)-P(f211): Cross-phase value per frequency bin - YEAR - DOY (Day Of Year) - HOUR - ToD_flag: "Umbra", "Penumbra", 'Light' - L: McIllwain parameter - stat_tag: "tarbrz" - Kp - Kp_w_05d: Kp index weighted on a 12hrs time window - Kp_w_10d: Kp index weighted on a 24hrs time window - Kp_w_15d: Kp index weighted on a 36hrs time window - Kp_w_20d: Kp index weighted on a 2-day time window - Kp_w_25d: Kp index weighted on a 2.5-day time window - Kp_w_30d: Kp index weighted on a 3-day time window - Kp_m_05d: Kp index max on a 12hrs time window - Kp_m_10d: Kp index max on a 24hrs time window - Kp_m_15d: Kp index max on a 36hrs time window - Kp_m_20d: Kp index max on a 2-day time window - Kp_m_25d: Kp index max on a 2.5-day time window - Kp_m_30d: Kp index max on a 3-day time window - DST - DST_m_05d: DST index min on a 12hrs time window - DST_m_10d: DST index min on a 24hrs time window - DST_m_15d: DST index min on a 36hrs time window - DST_m_20d: DST index min on a 2-day time window - DST_m_25d: DST index min on a 2.5-day time window - DST_m_30d: DST index min on a 3-day time window - F107: F10.7 solar activity proxy - EField: Earth Electric co-rotation field - f(mHz): FLR frequency in mHz - df(mHz): Uncertainty on the validated frequency - class: 0 for "NoFreq", 1 for "Freq" and 2 for "PBL"
DOI: 10.6084/m9.figshare.22141247
title: Supplementary Material for: Impaired Decision-Making and Skin Conductance Responses Are Associated with Reward and Punishment Sensitivity in Individuals with Severe Alcohol Use Disorder

description: <b><i>Introduction:</i></b> Individuals with alcohol use disorder (AUD) have difficulties regulating alcohol consumption, despite adverse drinking-related consequences. This may be due to incapacity incorporating previous negative feedback from drinking, resulting in impaired decision-making. <b><i>Methods:</i></b> We assessed whether decision-making is impaired in participants with AUD related to severity of AUD, indexed by severe negative drinking consequences using the Drinkers Inventory of Consequences (DrInC) and reward and punishment sensitivity with the Behavioural Inhibition System Behavioural Activation System (BIS BAS) scales. 36 treatment-seeking alcohol-dependent participants completed the Iowa gambling task (IGT) with skin conductance responses (SCRs) measured continuously as an index of somatic autonomic arousal to evaluate impaired expectancy of negative outcomes. <b><i>Results:</i></b> Two-thirds of the sample showed behavioural impairment during the IGT, with greater AUD severity related to worse performance. BIS moderated IGT performance according to severity of AUD, with increased anticipatory SCRs for those with fewer reported DrInC severe consequences. Participants with more DrInC severe consequences showed IGT deficits and reduced SCRs regardless of BIS scores. BAS-Reward was associated with increased anticipatory SCRs to disadvantageous deck choices among those with lower AUD severity, while SCRs did not differ related to AUD severity for reward outcomes. <b><i>Discussion:</i></b> Effective decision-making in the IGT and adaptive somatic responses were moderated by punishment sensitivity contingent on severity of AUD in these drinkers, with impairments in expectancy to negative outcomes from risky choices, including reduced somatic responses, resulting in poor decision-making processes that may help explain impaired drinking and worse drinking-related consequences.
DOI: 10.6084/m9.figshare.22616599
title: Supplementary Material for: Low-Molecular-Weight Hyaluronic Acid Contributes to Noise-Induced Cochlear Inflammation

description: Introduction: Our previous work indicated that the activation of the Toll-like receptor (TLR) 4 signaling pathway contributed to noise-induced cochlear inflammation. Previous studies have reported that low-molecular-weight hyaluronic acid (LMW-HA) accumulates during aseptic trauma and promotes inflammation by activating the Toll-like receptor (TLR) 4 signaling pathway. We hypothesized that LMW-HA or enzymes synthesizing or degrading HA might be involved in noise-induced cochlear inflammation. Methods: The present study included two arms. The first arm was the noise exposure study, in which TLR4, proinflammatory cytokines, HA, hyaluronic acid synthases (HASs) and hyaluronidases (HYALs) in the cochlea as well as auditory brainstem response (ABR) thresholds were measured before and after noise exposure. The second arm was analysis of HA delivery-induced reactions, in which control solution, high-molecular-weight hyaluronic acid (HMW-HA) or LMW-HA was delivered into the cochlea by cochleostomy or intratympanic injection. Then, the ABR threshold and cochlear inflammation were measured. Results: After noise exposure, the expression of TLR4, proinflammatory cytokines, HAS1 and HAS3 in the cochlea significantly increased over the 3rd to 7th day post-noise exposure (PE3, PE7). The expression of HYAL2 and HYAL3 dramatically decreased immediately after noise exposure, gradually increased thereafter to levels significantly greater than the preexposure level on PE3, and then rapidly returned to the preexposure level on PE7. The expression of HA, HAS2 and HYAL1 in the cochlea remained unchanged after exposure. After cochleostomy or intratympanic injection, both the hearing threshold shifts and the expression of TLR4, TNF-α and IL-1β in the cochleae of the LMW-HA group were obviously greater than those of the control group and HMW-HA group. The expression of proinflammatory cytokines in the LMW-HA and control groups on the 7th day (D7) after cochleostomy tended to increase compared to that on the 3rd day (D3), whereas levels in the HMW-HA group tended to decrease on D7 compared to D3. Conclusion: HAS1, HAS3, HYAL2 and HYAL3 in the cochlea are involved in acoustic trauma-induced cochlear inflammation through the potential proinflammatory function of LMW-HA.
DOI: 10.6084/m9.figshare.22664002
title: Supplementary Material for: Post-Traumatic Stress Disorder in Patients with Alopecia Areata: A Survey Study in the US

description: Alopecia areata (AA) is comorbid with mental health disorders. This study aimed to evaluate the presence of post-traumatic stress disorder (PTSD) in AA patients. Participants completed a survey containing the PTSD Checklist for the DSM-5 (PCL-5) in the context of their AA. Of the 1,449 completed surveys (completion rate 79.6%), most were female (83.8%) and white (76.6%) with an average age of 50.6±15.6 years. Respondents had AA for an average of 17.7±15.8 years, with 91.4% experiencing active hair loss. 33.9% of respondents screened positively for PTSD. Participants with alopecia totalis (AT) has the highest average PCL-5 score of 30.1±19.2, followed by alopecia universalis (AU) with 26.0±19.9, and lastly patchy AA with 24.5±18.3 (p=0.003). Intrusion and avoidance were the predominant symptoms. Total PTSD scores were significantly higher in respondents who were younger, Black, and Hispanic when compared to older, white, and non-Hispanic respondents respectively. One in three patients with AA in this cohort meet the screening criteria for PTSD. These results further highlight the mental health comorbidities with AA and that these symptoms may persist even after hair regrowth. Limitations include the nonrandomized NAAF population with most participants being white females. Finally, respondent’s baseline mental health was not assessed, therefore a causal relationship between AA and PTSD cannot be deduced.