cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24785745
title: PCGs annotation of <i>Diomorus aiolomorphi</i>

description: The .gff3 file contains the protein-coding genes (PCGs) annotation information of the <i>Diomorus aiolomorphi</i> genome.
DOI: 10.6084/m9.figshare.25422856
title: Supplementary Material for: Reference data for a quick speech-in-noise hearing test in the French language

description: Introduction: Difficulties in understanding speech in noise is the most common complaint of people with hearing impairment. Thus, there is a need for tests of speech-in-noise ability in clinical settings, which have to be evaluated for each language. Here, a reference dataset is presented for a quick speech-in-noise test in the French language (Vocale Rapide dans le Bruit, VRB; Leclercq, Renard & Vincent, 2018). 

Methods: A large cohort (N=641) was tested in a nationwide multicentric study. The cohort comprised normal-hearing individuals and individuals with a broad range of symmetrical hearing losses. Short everyday sentences embedded in babble noise were presented over a spatial array of loudspeakers. Speech level was kept constant while noise level was progressively increased over a range of signal-to-noise ratios. The signal-to-noise ratio for which 50% of keywords could be correctly reported (Speech Reception Threshold, SRT) was derived from psychometric functions. Other audiometric measures were collected for the cohort, such as audiograms and speech-in-quiet performance.

Results: The VRB test was both sensitive and reliable, as shown by the steep slope of the psychometric functions and by the high test-retest consistency across sentence lists. Correlation analyses showed that pure tone averages derived from the audiograms explained 74% of the SRT variance over the whole cohort, but only 29% for individuals with clinically normal audiograms. SRTs were then compared to recent guidelines from the French Society of Audiology (Joly et al., 2021). Among individuals who would not have qualified for hearing aid prescription based on their audiogram or speech intelligibility in quiet, 18.4% were now eligible as they displayed SRTs in noise impaired by 3 dB or more. For individuals with borderline audiograms, between 20 dB HL and 30 dB HL, the prevalence of impaired SRTs increased to 71.4%. Finally, even though five lists are recommended for clinical use, a minute-long screening using only one VRB list detected 98.6% of impaired SRTs. 

Conclusion: The reference data suggest that VRB testing can be used to identify individuals with speech-in-noise impairment.
DOI: 10.6084/m9.figshare.25780845
title: Supplementary Material for: Immunosuppressant Agents as Add-On Therapy Failed to Improve the Outcome of Immunoglobulin A Nephropathy with Crescent Score C1

description: Background The renoprotective benefits of adding immunosuppressant therapy to corticosteroid (CS) treatment for immunoglobulin A nephropathy (IgAN) patients with less than 25% crescent formation (C1) remains uncertain, warranting further research. 
Methods A retrospective study was conducted on IgAN patients with crescent C1 lesions confirmed by renal biopsy at Xinqiao Hospital between May 1, 2017, and May 1, 2020. Patients were stratified into either the CS treatment group or the CS combined with an additional immunosuppressant therapy group. Follow-up assessments were conducted within 24 months. Propensity score analysis was used to match patients receiving CS and CS+immunosuppressant drug treatment in a 1:1 ratio. Primary outcomes included changes in estimated glomerular filtration rate (eGFR) and urine albumin-to-creatinine ratio (UACR). Subgroup analyses were performed to evaluate the benefits of different populations. Composite endpoint outcomes comprised a 30% eGFR decrease, end-stage kidney disease (ESKD) necessitating dialysis or transplant, or kidney disease-related mortality. Adverse events were also compared between the two groups.
Results: 296 IgAN patients with C1 lesions were included in the analysis. Baseline characteristics indicated that IgAN patients in the CS+immunosuppressant group exhibited poorer renal function and higher UACR levels. Propensity score analysis effectively minimized the influence of baseline clinical characteristics, including age, serum creatinine, initial eGFR, UACR, and 24-hour proteinuria. Both treatment groups demonstrated continuous eGFR improvement and significant UACR reduction during follow-up, especially at 6 months. However, no significant differences in eGFR and UACR reduction rates were observed between the two groups throughout the entire follow-up period, both before and after matching. Subgroup analysis revealed improved eGFR in both treatment groups, notably among patients with an initial eGFR below 90 ml/min/1.73 m2. Conversely, IgAN patients with C1 lesions and a cellular crescent ratio exceeding 50% treated with CS and immunosuppressant therapy experienced a significant improvement in renal function and a decline in urinary protein creatinine ratio. Composite endpoint outcomes did not significantly differ between the two groups, while the incidence of adverse events was comparable.
Conclusion Our findings suggest that the addition of immunosuppressant therapy to corticosteroid monotherapy did not confer significant therapeutic advantages in patients with C1 lesions compared to CS monotherapy, although some specific patient populations appeared to derive modest benefits from this combined approach.
DOI: 10.48597/5kw6-hngt
title: Measurement of Ozone at Lough Navar

description: Measurement of Ozone at Lough Navar
DOI: 10.48597/9wuj-4kyv
title: Measurement of Ozone at Lough Navar

description: Measurement of Ozone at Lough Navar
DOI: 10.48597/e5s9-a4xg
title: Measurement of Ozone at Lough Navar

description: Measurement of Ozone at Lough Navar
DOI: 10.48597/t38f-cgss
title: Measurement of Ozone at Lough Navar

description: Measurement of Ozone at Lough Navar
DOI: 10.48597/uwgc-k73x
title: Measurement of Ozone at Lough Navar

description: Measurement of Ozone at Lough Navar
DOI: 10.48597/rg42-ychj
title: Measurement of Ozone at Lough Navar

description: Measurement of Ozone at Lough Navar
DOI: 10.22008/fk2/yeretl
title: Geological map of Greenland, 1:500 000, Sheet 4, Upernavik Isfjord

description: Geologisk kort over Grønland / Geological map of Greenland - 1:500 000, central and northern West Greenland,
DOI: 10.5281/zenodo.10715015
title: A spatial expression atlas of the adult human small intestine

description: We performed spatial transcriptomics (10x Visium) on adult humans small intestine samples alongside spatial proteomics (CODEX) to generate a spatial expression atlas of the adult human small intestine. we also preformed laser capture microdissection on epithelial segments from the villus bottom and top followed by RNAseq and MS-proteomics for validation.
DOI: 10.5281/zenodo.10797245
title: Validation of the IRI2016 Ionospheric Model Using SuperDARN Ground Backscatter Measurments. (Companion dataset for paper)

description: Companion data set for the paper titled 'On the use of SuperDARN Ground Backscatter Measurements for Ionospheric Propagation Model Validation'. Included within this repository is all data output from the validation study which was used to produce figures and perform analysis of the IRI2016 model. The corresponding interferometer calibration values are also included.

See repository the following repository for the Blackstone Radar TTFD antenna array gain patterns used to model this data:

Ruck, J. (2024). SuperDARN Blackstone Antenna Gain Patterns (Version 1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10797004
DOI: 10.5281/zenodo.11486911
title: Gamma rays from dark matter spikes in EAGLE simulations - IMBH mock catalogue

description: DArk Matter SPIkes (DAMSPI) is a fully Python-based software for the analysis of dark matter spikes around Intermediate Mass Black Holes (IMBHs) in the Milky Way. It allows to extract an IMBH catalogue and their corresponding dark matter spike parameters from the EAGLE simulations in order to probe a potential gamma-ray signal from dark matter self-annihilation. 

The dataset contains the IMBH catalogue including, among others, the coordinates, mass, formation redshift and spike parameters for each individual IMBH. Each column of the catalogue is described in detail in J. Aschersleben et al. (2024). We also provide separate files for which we calculated the gamma-ray fluxes for different dark matter masses and annihilation cross sections. Lastly, we provide a catalogue of our selection of Milky Way like galaxies within EAGLE. The columns of these files are also described in J. Aschersleben et al. (2024).

The source code to extract this dataset is publicy available here:





https://doi.org/10.5281/zenodo.11488472



Description of the data files

The imbh_catalogue/imbh/ directory contains the following files:



catalogue_nfw.h5

catalogue_cored_gamma_0p3.h5

catalogue_cored_gamma_0p9.h5

catalogue_cored_gamma_free.h5


They contain the IMBH catalogues, including the coordinates and dark matter spike parameters, calculated assuming the 1.) NFW profile, 2.) cored profile with a fixed core index of 0.0, 3.) cored profile with a fixed core index of 0.4 and 4.) cored profile with the core index as a free fitting parameter.

The imbh_catalogue/flux/<channel>/<energy_threshold>/ directory contains the gamma-ray fluxes of the IMBHs for a given annihilation channel, energy threshold, and dark matter mass. E.g. the imbh_catalogue/flux/b_channel/e_th_0.1GeV/m_dm_10.0GeV.h5 file contains the IMBH fluxes assuming the b-channel, an energy threshold of 0.1 GeV and a dark matter mass of 10 GeV. The IMBH fluxes are calculated for a variety of velocity weighted annihilation cross sections. 

The imbh_catalogue/galaxy/ directory contains the mw_galaxies_catalogue_nfw.h5 file which contains our selection of Milky Way-like galaxies within EAGLE.

The HDF files can be opened in Python with:

import pandas as pd

file_path = "<path_to_file>.h5"

df = pd.read_hdf(file_path, key="table")

# Printing the first few rows of the DataFrame
print(df.head())
DOI: 10.5281/zenodo.7401545
title: CheckM v1 reference data

description: <strong>Precalculated data files for CheckM v1.<br> <br> Manuscript:</strong><br> CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.<br> https://genome.cshlp.org/content/early/2015/05/14/gr.186072.114 <strong>Installation instructions:</strong><br> https://github.com/Ecogenomics/CheckM/wiki/Installation#how-to-install-checkm.
DOI: 10.6084/m9.figshare.21892986
title: Data_Carnicer-Lombarte-et-al-2023_2

description:  Analysed immunostain, electrophysiology, kinematic, and mechanical data for ultraflexible cuffs implanted into rat forearm nerves. Dataset contains:

 Mechanical Testing.xlsx : Mechanical characterisation of biocompatibility testing materials (tensile tests).
 Impedances new devices and chronic-use devices.xlsx : Impedances of microelectrodes in cuffs before, and after (various timepoints) implantation.
 Maps stim devices.xlsx : Coordinates of paw position during stimulation of nerves using microelectrodes in cuffs (kinematic analysis).
 FBR_Immunohist_analysis.xlsx : Immunostain aSMA intensity profile for nerves implanted with materials testing for biocompatibility and FBR.
 SNR chronic implants.xlsx : Analysed metrics from recordings in awake animals using cuffs at various timepoints (SNR, RMS noise, spike peak amplitude).
DOI: 10.6084/m9.figshare.25593717
title: Supplementary Material for: Non-O Blood Group is Associated with High Thrombus Burden and Poor short- and long-term Prognosis in STEMI Patients

description: Introduction: This study investigates how non-O blood groups relate to thrombus burden (TB) and prognosis in STEMI patients, aiming to shed light on their association with thrombotic complications in cardiovascular diseases. Methods: Retrospectively, 1180 STEMI patients undergoing primary percutaneous coronary intervention were included. The study population was divided into groups according to TB status and the groups were compared in terms of basic clinical characteristics, laboratory parameters and ABO blood group types. In addition, short- (30 days) and long-term (12 months) clinical outcomes were assessed to evaluate the prognostic implications. Results: The analysis revealed a significant association between non-O blood groups and increased thrombus burden in STEMI patients (p = 0.001). Non-O blood group was independently associated with high thrombus burden (OR: 1.726, 95% CI: 1.279-2.330, p &lt; 0.001). Additionally, patients with non-O blood groups had higher short and long-term mortality rates (HR: 2.480, 95% CI: 1.361-4.520, p = 0.003; HR: 2.347, 95% CI: 1.433-3.844, p = 0.001; respectively). Conclusions: This study emphasizes the significance of the ABO blood group system in STEMI outcomes, associating non-O blood groups with higher thrombus burden and poorer clinical outcomes. While proposing personalized treatment strategies based on blood group status to improve reperfusion interventions and outcomes, additional trials are needed to comprehensively evaluate their impact.
DOI: 10.6084/m9.figshare.26047837
title: Supplementary Material for: Weight-loss Endoscopy Trial (WET): a multi-center, randomized, controlled trial comparing weight loss in endoscopically implanted duodenal-jejunal bypass liners vs. intragastric balloons vs. a sham procedure

description: Introduction: Obesity is associated with reduced life expectancy and various comorbidities. Surgical interventions are effective but accompanied by risk of serious complications. Less invasive endoscopic procedures mainly comprise the intragastric balloon (IB) and the duodenal-jejunal bypass liner (DJBL). A randomized, sham-controlled study comparing both procedures has not been undertaken so far. 
Methods: We performed a randomized, patient- and assessor-blinded, controlled trial comparing weight loss in IB vs. DJBL vs. a sham procedure (2:2:1 ratio). Patients with a BMI &gt; 35 kg/m2 or &gt; 30 with obesity-related comorbidities were included. The IB was removed after 6 months and the DJBL after 12 months. Main objective was successful weight loss (&gt;10% from baseline) 12 months after explantation of the devices. Secondary outcomes were changes in comorbidities, quality of life and complications.
Results: 33 patients were randomized. Recruitment has to be stopped suddenly in after the DJBL device lost its CE mark in Europe. 11 patients received DJBL, 15 IB and 7 were allocated to sham group. Blinding was feasible in all patients. Weight decreased from baseline until explantation (DJBL: 129.4±28.3kg to 107.4±16.7kg; IB: 118.3±22.8kg to 107.4±25.7kg; sham: 134.6±18.0kg to 131.2±14.3kg) but patients regained weight almost to baseline level 12 months after explantation. Only one patient in IB group reached the primary endpoint. Severe device-related complications were very rare.
Conclusion: Endoscopic bariatric procedures failed to achieve effective weight loss 12 months after explantation of the devices. The results of this trial need to be interpreted with caution due to its early termination.
DOI: 10.6084/m9.figshare.26063614
title: Supplementary Material for: Pharmacist-led medication management in acute geriatric medicine and its associations with rehospitalizations: A cohort study

description: Introduction: Hospitalization and discharge in older patients are critical and clinical pharmacists have shown to ameliorate risks. Our objective was to assess their benefit as part of the geriatric team regarding rehospitalizations and related outcomes after discharge focusing on general practitioners’ decision to continue or change discharge medication (GPD).

Methods: Prospective implementation study with six months follow-up in an acute geriatric clinic. Patients ≥ 70 years with comorbidities, impairments and a current drug therapy were consecutively assigned to three groups: control group (CG), implementation group (IG) and wash-out group (WG). CG only received medication reconciliation (MR) at admission; IG and their hospital physicians received a pharmaceutical counseling and medication management; during WG, pharmaceutical counseling except for MR was discontinued. We used a negative-binomial models to calculate rehospitalizations and days spent at home as well as a recurrent events survival model to investigate recurrent rehospitalizations.

Results: 132 patients (mean age 82 years, 76 women [57,6 %]) finished the project. In most of the models for rehospitalizations, a positive GPD led to fewer events. We also found an effect of pharmaceutical counseling on rehospitalizations and recurrent rehospitalizations in the CG vs. WG group but not in the CG vs IG models. 95.3% of medication recommendations by the pharmacist in the clinic setting were accepted. While the number of positive GPDs in CG was low (38%), pharmaceutical counseling directly to the GP in IG led to a higher number of positive GPDs (60 %).

Discussion: Although rehospitalizations were not directly reduced by our intervention in the CG vs. IG groups, the pharmacist’s acceptance rate in the hospital was very high and a positive GPD led to fewer rehospitalization in most models.
ClinicalTrials Identifier NCT03412903
DOI: 10.6084/m9.figshare.26105731
title: Supplementary Material for: Reducing distress from auditory verbal hallucinations: A multicentre, parallel, single-blind, randomised controlled feasibility trial of Relating Therapy

description: Introduction
There is significant demand for interventions that reduce distress related to auditory verbal hallucinations (AVH). AVH-distress is associated with the way voice hearers relate with AVH. We aimed to establish the feasibility of a randomised controlled trial to demonstrate that adding ‘Relating Therapy” (RT) to Treatment as Usual (TAU) is superior to TAU in reducing AVH distress. 
Methods
We conducted a multicentre, parallel, single-blind, randomised controlled feasibility trial in five mental health centres in Germany. Participants were ≥16 years of age, had persistent and distressing AVH, and a diagnosis of a schizophrenia-spectrum disorder. RT was delivered over a maximum of 16 sessions within 5 months. Blind assessments were conducted at baseline, at 5 and 9 months. Feasibility outcomes were the numbers of patients recruited and retained, safety and therapist adherence. The primary endpoint was the distress factor score of the AVH-subscale of the Psychotic Symptoms Rating Scales at 9 months. 
Results
Eighty-five of 177 enrolled participants were randomised into RT+TAU (n=43) or TAU (n=42). Feasibility was excellent with 87% retention at 9 months, 86% reaching ‘treatment uptake’, 98% therapist adherence and no unexpected serious adverse reactions. Compared to TAU, RT+TAU showed non-significant trends towards less AVH-distress (b=-2.40, SE=1.52, p = 0.121, 90% CI (-4.94 to 0.15) and stronger improvement on all but one secondary outcomes. 
Conclusion
A randomised controlled trial of RT is feasible, safe, and well accepted. Our results provide an encouraging basis to further test the efficacy of RT in a definitive multicentre trial.
DOI: 10.18141/2007303
title: Energy Assets Transformation Web Mapping Application

description: This submission contains the link and geospatial materials used in the Energy Assets Transformation Web Mapping Application. The zip file contains 19 geospatial layers in a file geodatabase called EAT.gdb to be grouped in the following categories. 1. Industrial Assets: Coal Generation Units Retirements 2012-2040 (EIA); Examples of Repurposing Projects (32 projects in total); Abandoned Coal Mines (CORD, SkyTruth); Abandoned or Orphaned Wells (for ten states only). 2. Energy Transition Communities: 48C (e) Tax Credits - Designated Energy Communities (IRA); Index of Deep Disadvantage; Local Energy Action Program (LEAP); EJ Index for Proximity to Hazardous Waste (EPA). 3. Regional Landscape: State-Level Funding Programs (relevant to repurposing projects, for 2022 and 2023 only); Coal Flows from Mine to Plant 2021 (EIA), Variable Renewable Energy Shares (Wind and Solar, 2021, EIA). 4. Supporting Infrastructure: Railroads (HIFLD), Electric Power Transmission Lines (HIFLD), Major Highways (NHPN, DOT), Major Ports (National Atlas of the U.S.); Independent System Operators (HIFLD), NERC Regions and Subregions (HIFLD).
DOI: 10.18150/lslm10
title: Turbulence properties for June-September period at rural and urban environment

description: The dataset contains the set of turbulent properties obtained using the measurements from Streamline XR (Halo Photonics ) Doppler lidar. The datasets cover a period of June-September 2018 and 2023 respectively for the rural environment in Rzecin, Poland (52◦45’N, 16◦18’E) and urban in Warsaw, Poland (52◦12’N, 20◦58’E).The files are in .mat format and contain, in a form of structure, sequentially (content, [unit]):date, [YYYYMMDD]slopes of wind velocity spectra, [au]slopes of structure functions, [au]mean horizontal wind, [m/s]integral length scale, [m]turbulence velocity scale, [m/s]]sunrise time, [UTC]sunset time, [UTC]time vector, [UTC]altitude vector, [m]For each of the dates (1) the full set of turbulent properties (2-6), sunrise and sunset times (7-8), and time and altitude vectors (9-10) are included. The spatial and temporal resolution for the turbulence properties (2-6) are respectively 30 m and 30 min.The dataset comprises 8 files which consist of turbulent properties for each location and each month of the measurements(filename, number of full days of measurements which file contains):1. Dataset for rural environment (Rzecin)RZECIN_turbulent_properties_201806.mat, (12 days)RZECIN_turbulent_properties_201807.mat, (28 days)RZECIN_turbulent_properties_201808.mat, (30 days)RZECIN_turbulent_properties_201809.mat, (15 days)2. Dataset for urban environment (Warsaw) WARSAW_turbulent_properties_202306.mat, (18 days)WARSAW_turbulent_properties_202307.mat, (26 days)WARSAW_turbulent_properties_202308.mat, (30 days)WARSAW_turbulent_properties_202309.mat, (23 days)ATTENTION:We offer a free access to this dataset. The user is however encouraged to share the information on the data use with the Remote Sensing Laboratory by sending an e-mail to rslab@fuw.edu.pl.In the case this dataset is used for a scientific communication (publication, conference contribution, thesis) we would like to kindly ask for considering to acknowledge data provision by adding the following statement in Acknowledgments: "We acknowledge the data originators M. Karasewicz, M. Wacławczyk, P. Ortiz-Amezcua and I.S. Stachlewska for the quality-assurance, evaluation, and provision of data sets of the Remote Sensing Laboratory at the Faculty of Physics of the University of Warsaw, Poland."