cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21546141
title: Identification of potential key genes related to idiopathic male infertility using RNA-sequencing data: an <i>in-silico</i> approach

description: Among reproductive health problems, idiopathic infertility affects married couples. The current diagnosis of male infertility focuses on the concentration, motility, and morphology of sperm in the ejaculate. Since the molecular mechanism of idiopathic infertility is unknown, identification of Differentially Expressed Genes (DEGs) among the control and idiopathic infertile male can shed light on diagnosis and treatment. Here, we analyzed the dataset GSE65683 to identify DEGs in idiopathic human sperm in three groups of patients: (i) Timed Intercourse (TIC); (ii) Intrauterine Insemination (IUI); and (iii) Assisted Reproductive Technology (ART). The enrichment analysis was carried out using DAVID (Database for Annotation, Visualization and Integrated Discovery) and GeneCodis for the DEGs. Protein-Protein Interaction (PPI) network of these DEGs were constructed using the STRING database. The network parameters such as degree and betweenness were calculated to select the important hubs. In total, 118 DEGs in TIC, 446 in IUI, and 188 in ART were identified. PPI network was constructed and identified critical top hub genes such as <i>ACTB, BTBD6, EIF2S3, EIF3A, EIF4E, POLR2L, RPL4, RPL7, RPS11, RPL13, RPS15, RPL23, RPL27, RPL9, RPLP0 and UBA52</i> that may play an essential role in idiopathic male infertility. Thus, the identified hub genes may provide an insight into the molecular mechanism and contribute to discovering novel therapeutic targets and developing new strategies for idiopathic male infertility.
DOI: 10.6084/m9.figshare.21546141.v2
title: Identification of potential key genes related to idiopathic male infertility using RNA-sequencing data: an <i>in-silico</i> approach

description: Among reproductive health problems, idiopathic infertility affects married couples. The current diagnosis of male infertility focuses on the concentration, motility, and morphology of sperm in the ejaculate. Since the molecular mechanism of idiopathic infertility is unknown, identification of Differentially Expressed Genes (DEGs) among the control and idiopathic infertile male can shed light on diagnosis and treatment. Here, we analyzed the dataset GSE65683 to identify DEGs in idiopathic human sperm in three groups of patients: (i) Timed Intercourse (TIC); (ii) Intrauterine Insemination (IUI); and (iii) Assisted Reproductive Technology (ART). The enrichment analysis was carried out using DAVID (Database for Annotation, Visualization and Integrated Discovery) and GeneCodis for the DEGs. Protein-Protein Interaction (PPI) network of these DEGs were constructed using the STRING database. The network parameters such as degree and betweenness were calculated to select the important hubs. In total, 118 DEGs in TIC, 446 in IUI, and 188 in ART were identified. PPI network was constructed and identified critical top hub genes such as <i>ACTB, BTBD6, EIF2S3, EIF3A, EIF4E, POLR2L, RPL4, RPL7, RPS11, RPL13, RPS15, RPL23, RPL27, RPL9, RPLP0 and UBA52</i> that may play an essential role in idiopathic male infertility. Thus, the identified hub genes may provide an insight into the molecular mechanism and contribute to discovering novel therapeutic targets and developing new strategies for idiopathic male infertility.
DOI: 10.6084/m9.figshare.20473066
title: Clomiphene citrate priming increases sensitivity during ovarian stimulation in poor ovarian responders undergoing <i>in vitro</i> fertilization treatment: a retrospective cohort study

description: This single-centre retrospective cohort study aimed to investigate whether a clomiphene citrate (CC) priming protocol could increase ovarian sensitivity in poor ovarian responders. It included 294 patients (374 ovarian stimulation cycles). Of these, 193 cycles were treated by a CC priming antagonist protocol (study group) and 181 by the classical flexible gonadotropin-releasing hormone antagonist protocol (control group). Stimulation data and laboratory and clinical outcomes were compared between the groups. The results showed that in the study group, total gonadotropin dosage and dosage per follicle were considerably lower, the follicle-to-oocyte index was significantly higher, and the gonadotropin duration was shorter. After adjusting for potential confounders, multivariate regression analysis showed that cumulative ongoing pregnancy remained comparable between the groups (adjusted odds ratio: 0.761, 95% confidence interval: 0.300–1.933, <i>p</i> = 0.566). Age, body mass index, gonadotropin dosage per follicle, and the follicle-to-oocyte index were negatively associated with the reproductive outcomes. The result of the sensitivity analysis showed that patients in the study group were administered less gonadotropin at a lower gonadotropin dosage per follicle and for a shorter duration. In conclusion, the CC priming antagonist protocol offered a convenient and patient-friendly way to increase ovarian sensitivity during ovarian stimulation in poor ovarian responders.
DOI: 10.6084/m9.figshare.20473066.v1
title: Clomiphene citrate priming increases sensitivity during ovarian stimulation in poor ovarian responders undergoing <i>in vitro</i> fertilization treatment: a retrospective cohort study

description: This single-centre retrospective cohort study aimed to investigate whether a clomiphene citrate (CC) priming protocol could increase ovarian sensitivity in poor ovarian responders. It included 294 patients (374 ovarian stimulation cycles). Of these, 193 cycles were treated by a CC priming antagonist protocol (study group) and 181 by the classical flexible gonadotropin-releasing hormone antagonist protocol (control group). Stimulation data and laboratory and clinical outcomes were compared between the groups. The results showed that in the study group, total gonadotropin dosage and dosage per follicle were considerably lower, the follicle-to-oocyte index was significantly higher, and the gonadotropin duration was shorter. After adjusting for potential confounders, multivariate regression analysis showed that cumulative ongoing pregnancy remained comparable between the groups (adjusted odds ratio: 0.761, 95% confidence interval: 0.300–1.933, <i>p</i> = 0.566). Age, body mass index, gonadotropin dosage per follicle, and the follicle-to-oocyte index were negatively associated with the reproductive outcomes. The result of the sensitivity analysis showed that patients in the study group were administered less gonadotropin at a lower gonadotropin dosage per follicle and for a shorter duration. In conclusion, the CC priming antagonist protocol offered a convenient and patient-friendly way to increase ovarian sensitivity during ovarian stimulation in poor ovarian responders.
DOI: 10.21227/xngk-3p42
title: ISCX-URL-2016 

description: The Web has long become a major platform for online criminal activities. URLs are used as the main vehicle in this domain. To counter this issues security community focused its efforts on developing techniques for mostly blacklisting of malicious URLs.Benign URLs: Over 35,300 benign URLs were collected from Alexa top websites. The domains have been passed through a Heritrix web crawler to extract the URLs. Around half a million unique URLs are crawled initially and then passed to remove duplicate and domain only URLs. Later the extracted URLs have been checked through Virustotal to filter the benign URLs.Spam URLs: Around 12,000 spam URLs were collected from the publicly available WEBSPAM-UK2007 dataset.Phishing URLs: Around 10,000 phishing URLs were taken from OpenPhish which is a repository of active phishing sites.Malware URLs: More than 11,500 URLs related to malware websites were obtained from DNS-BH which is a project that maintain list of malware sites.Defacement URLs: More than 45,450 URLs belong to Defacement URL category. They are Alexa ranked trusted websites hosting fraudulent or hidden URL that contains both malicious web pages.
DOI: 10.6084/m9.figshare.24893001.v1
title: Procedure Operating Standard for Group Discussion Analysis

description: Standard Procedure
DOI: 10.6084/m9.figshare.24893001
title: Procedure Operating Standard for Group Discussion Analysis

description: Standard Procedure
DOI: 10.5281/zenodo.10091738
title: Supplementary data files for Sosa-Jiménez et. al. 2023 "A new guest to the blood feast: a novel symbiotic lineage associated with a haematophagous leech from the genus Haementeria"

description: The data set consists of four folders:

1) "COG_profile": COG assignment and count files from running similarity searches between selected genomes.

2) "genome_data": GenBank-formatted annotation file for newly sequenced Pluralibacter haementeriicola endosymbiont, 16S, and ANI identity/score calculation files.

3) "Haementeria_symbionts_orthoMCL": Flat-text output files from the OrthoMCL pipeline ran with Pr. siddallii srain officinalis-GTOCOR2 and Pluralibacter haementeriicola .

4) "phylongeny_data": MrBayes and IQ-TREE2 run/result files for cox1 mitochondrial gene from Hamenteria spp. and all single-copy shated genes among Pl. haementeriicola and an array of selected Enterobacteriaceae and Erwinaceae.

"compressed_dirs.md5sum": md5sums for compressed directory files.

After downloading, check with "$ md5sum -c compressed_dirs.md5sum"
DOI: 10.5281/zenodo.10091737
title: Supplementary data files for Sosa-Jiménez et. al. 2023 "A new guest to the blood feast: a novel symbiotic lineage associated with a haematophagous leech from the genus Haementeria"

description: The data set consists of four folders:

1) "COG_profile": COG assignment and count files from running similarity searches between selected genomes.

2) "genome_data": GenBank-formatted annotation file for newly sequenced Pluralibacter haementeriicola endosymbiont, 16S, and ANI identity/score calculation files.

3) "Haementeria_symbionts_orthoMCL": Flat-text output files from the OrthoMCL pipeline ran with Pr. siddallii srain officinalis-GTOCOR2 and Pluralibacter haementeriicola .

4) "phylongeny_data": MrBayes and IQ-TREE2 run/result files for cox1 mitochondrial gene from Hamenteria spp. and all single-copy shated genes among Pl. haementeriicola and an array of selected Enterobacteriaceae and Erwinaceae.

"compressed_dirs.md5sum": md5sums for compressed directory files.

After downloading, check with "$ md5sum -c compressed_dirs.md5sum"
DOI: 10.5517/ccdc.csd.cc2dj3qs
title: CCDC 2220025: Experimental Crystal Structure Determination

description: Related Article: Nikolay O. Grebennikov, Daniil A. Boiko, Darya O. Prima, Malena Madiyeva, Mikhail E. Minyaev, Valentine P. Ananikov|2023|J.Catalysis|429|115240|doi:10.1016/j.jcat.2023.115240
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc2ghm7v
title: CSD 2279127: Experimental Crystal Structure Determination

description: Related Article: R.J.C. Locke, T. Schleid|2023|IUCrData|8|x230654|doi:10.1107/S2414314623006545
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gpptp
title: CCDC 2284973: Experimental Crystal Structure Determination

description: Related Article: Muhammad Nadeem Akhtar, Murad A. AlDamen, Rahman Bikas, Zohreh Shaghaghi, Sahar Jafari, Aziz B. Ibragimov|2023|Int.J.Hydro.Eneg|51|383|doi:10.1016/j.ijhydene.2023.10.046
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gppvq
title: CCDC 2284974: Experimental Crystal Structure Determination

description: Related Article: Muhammad Nadeem Akhtar, Murad A. AlDamen, Rahman Bikas, Zohreh Shaghaghi, Sahar Jafari, Aziz B. Ibragimov|2023|Int.J.Hydro.Eneg|51|383|doi:10.1016/j.ijhydene.2023.10.046
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gppwr
title: CCDC 2284975: Experimental Crystal Structure Determination

description: Related Article: Muhammad Nadeem Akhtar, Murad A. AlDamen, Rahman Bikas, Zohreh Shaghaghi, Sahar Jafari, Aziz B. Ibragimov|2023|Int.J.Hydro.Eneg|51|383|doi:10.1016/j.ijhydene.2023.10.046
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.24893019.v1
title: Supplementary Material for: MASLD and MetALD increase the risk of developing hepatocellular carcinoma and incident or decompensated cirrhosis: a Korean nationwide study

description: Introduction: This study aimed to investigate the liver-related outcomes of newly suggested metabolic dysfunction-associated steatotic liver disease (MASLD) and MASLD with increased alcohol intake (MetALD), as well as alcohol-associated liver disease (ALD).
Methods: From a National Health Insurance Service Health Screening Cohort, we included 369,094 participants who underwent health check-ups between 2009 and 2010 in South Korea. SLD was defined as a fatty liver index ≥60. The risk of primary liver cancer (PLCa), hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (iCCA), incident cirrhosis, and decompensated cirrhosis was compared with no steatotic liver disease (SLD). The subdistribution hazard ratio (SHR) was calculated using the Fine–Gray model regarding competing risks.
Results: A total of 3,232 participants (0.9%) developed PLCa during the median follow-up of 3,227,176 person-years: 0.5% with no SLD, 1.1% with MASLD, 1.3% with MetALD, and 1.9% with ALD. Competing risk analysis revealed that compared with no SLD, MASLD (SHR, 1.65; 95% CI, 1.44−1.88), MetALD (SHR, 1.87; 95% CI, 1.52−2.29), and ALD (SHR, 1.86; 95% CI, 1.39−2.49) were associated with an increased risk of PLCa. MASLD (SHR, 1.96; 95% CI, 1.67−2.31), MetALD (SHR, 2.23; 95% CI, 1.75−2.84), and ALD (SHR, 2.34; 95% CI, 1.67−3.29) were associated with a higher risk of HCC. No significant difference was observed in the risk of iCCA. The risk of incident cirrhosis and decompensated cirrhosis increased in the order of no SLD, MASLD, MetALD, and ALD.
Conclusion: MASLD, MetALD, and ALD have an increased risk of PLCa, HCC, incident cirrhosis, and decompensated cirrhosis but not iCCA. These findings may serve as a robust ground for the prognostic value of the newly suggested MASLD and MetALD.
DOI: 10.5061/dryad.m37f684
title: Data from: Plastic senescence in the honey bee and the disposable soma theory
DOI: 10.5281/zenodo.10410494
title: A robust yeast chassis: comprehensive characterization of a fastgrowing Saccharomyces cerevisiae

description: Robust chassis are critical to facilitate advances in synthetic biology. This  study describes a comprehensive characterization of a new yeast isolate Saccharomyces cerevisiae XP that grows faster than commonly used research and industrial S. cerevisiae  strains. The genomic, transcriptomic, and metabolomic analyses suggest that the fast  growth rate is, in part, due to the efficient electron transport chain and key growth  factor synthesis. A toolbox for genetic manipulation of the yeast was developed; we  used it to construct L-lactic acid producers for high lactate production. The development  of genetically malleable yeast strains that grow faster than currently used strains may  significantly enhance the uses of S. cerevisiae in biotechnology.
DOI: 10.5281/zenodo.10410495
title: A robust yeast chassis: comprehensive characterization of a fastgrowing Saccharomyces cerevisiae

description: Robust chassis are critical to facilitate advances in synthetic biology. This  study describes a comprehensive characterization of a new yeast isolate Saccharomyces cerevisiae XP that grows faster than commonly used research and industrial S. cerevisiae  strains. The genomic, transcriptomic, and metabolomic analyses suggest that the fast  growth rate is, in part, due to the efficient electron transport chain and key growth  factor synthesis. A toolbox for genetic manipulation of the yeast was developed; we  used it to construct L-lactic acid producers for high lactate production. The development  of genetically malleable yeast strains that grow faster than currently used strains may  significantly enhance the uses of S. cerevisiae in biotechnology.
DOI: 10.6084/m9.figshare.24870378
title: MUG500+(B) Standardized Nifti Resampled Data

description: Following data is an extension of MUG500(B) DOI: 10.6084/m9.figshare.9616319If using this dataset, please cite 10.6084/m9.figshare.24870378The MUG500(B) set has a "nrrd" defective skull scan file, with its respective implants in "stl" format.Front these 29 pairs, 27 pairs had single defects and 2 pairs had double defects, hence, two implants for one particular file.This dataset includes the converted "Nifti" file(float32) formatted 29 pairs of craniotomy defective skulls, and its manually designed implants, with a pair of implants and skull being resampled to one common ROI. Each pair with double defects was simplified to different samples by combining the volumes of the defective skull with one implant at a time. Hence total available samples are 31.This standardized resampled nifti data is augmented with affine registration to obtain 930 pairs(31*30).<br>Following is the folder structure:-----MUG500+(B) Standardized Nifti Resampled Data - Part 1└──01└──01_32.nii└──1.nii└── B0001_implant_r_32.nii└── B0001_implant_r.nii└── B0001_implant.nii└──02└──02_32.nii└──2.nii└── B0002_implant_r_32.nii└── B0002_implant_r.nii└── B0002_implant.nii..............└──20└──20_32.nii└──20.nii└── B0020_implant_r_32.nii└── B0020_implant_r.nii└── B0020_implant.nii-----MUG500+(B) Standardized Nifti Resampled Data - Part 2└──21└──21_32.nii└──21.nii└── B0021_implant_r_32.nii└── B0021_implant_r.nii└── B0021_implant.nii└──22└──22_32.nii└──22.nii└── B0022_implant_r_32.nii└── B0022_implant_r.nii└── B0022_implant.nii..............└──31└──31_32.nii└──31.nii└── B0031_implant_r_32.nii└── B0031_implant_r.nii└── B0031_implant.nii
DOI: 10.6084/m9.figshare.24872079
title: MUG500+(B) Standardized Nifti Augmented Data

description: Following data is an extension of MUG500(B) DOI: 10.6084/m9.figshare.9616319If using this dataset, please cite 10.6084/m9.figshare.24872079The MUG500(B) set has a "nrrd" defective skull scan file, with its respective implants in "stl" format.Front these 29 pairs, 27 pairs had single defects and 2 pairs had double defects, hence, two implants for one particular file.This dataset includes the converted "Nifti" file(float32) formatted 29 pairs of craniotomy defective skulls, and its manually designed implants, with a pair of implants and skull being resampled to one common ROI. Each pair with double defects was simplified to different samples by combining the volumes of the defective skull with one implant at a time. hence total available samples are 31.This standardized resampled nifti data is augmented with affine registration to obtain 930 pairs(31*30).<br>Following is the folder structure of the augmented data:-----Augmented_data└── 03to01└── 4 files└── 03to02└── 4 files................
DOI: 10.6084/m9.figshare.24872079.v1
title: MUG500+(B) Standardized Nifti Augmented Data

description: Following data is an extension of MUG500(B) DOI: 10.6084/m9.figshare.9616319If using this dataset, please cite 10.6084/m9.figshare.24872079The MUG500(B) set has a "nrrd" defective skull scan file, with its respective implants in "stl" format.Front these 29 pairs, 27 pairs had single defects and 2 pairs had double defects, hence, two implants for one particular file.This dataset includes the converted "Nifti" file(float32) formatted 29 pairs of craniotomy defective skulls, and its manually designed implants, with a pair of implants and skull being resampled to one common ROI. Each pair with double defects was simplified to different samples by combining the volumes of the defective skull with one implant at a time. hence total available samples are 31.This standardized resampled nifti data is augmented with affine registration to obtain 930 pairs(31*30).<br>Following is the folder structure of the augmented data:-----Augmented_data└── 03to01└── 4 files└── 03to02└── 4 files................
DOI: 10.26007/8y5n-6d30
title: New Horizons Mission Documentation

description: This collection contains documents applicable to the entire New Horizons mission, 
 such as the Science Opertions Center (SOC) to Instrument Pipeline Interface Control
 Document (ICD), instrument descriptions, and trajectory information.
DOI: 10.26007/334w-8j61
title: New Horizons Documents for Ralph, Version 1.0

description: This collection contains documents applicable to the Ralph instrument package (housing 
 both the Multispectral Visible Imaging Camera Instrument (MVIC) and Linear Etalon Imaging 
 Spectral Array (LEISA) instruments) onboard the New Horizons spacecraft, such as
 documents describing the boresights, calibration techniques, and mission phase sequences 
 of these instruments. These documents were migrated from the Planetary Data System (PDS) 
 PDS3 format datasets, NH-A-MVIC-2-KEM1-V6.0 and NH-A-MVIC-3-KEM1-V6.0. Labels were 
 redesigned during migration.
DOI: 10.26007/d1av-c507
title: New Horizons Kuiper Belt Extended Mission 1 (KEM1) Multispectral Visible Imaging Camera (MVIC) Partially Processed Data, Version 1.0

description: This data set contains Partially Processed data taken by the New Horizons (NH)
 Multispectral Visible Imaging Camera (MVIC) instrument during the Kuiper Belt 
 Extended Mission 1 (KEM1) Encounter mission phase. This data was acquired by the 
 spacecraft between 14 August 2018 and 30 April 2022. It only includes data 
 downlinked before 01 May 2022. Future data releases may include more data acquired 
 by the spacecraft after 13 August 2018 but downlinked after 30 April 2022. The data 
 includes functional tests and images during the approach and departure of 
 486958 Arrokoth (2014 MU69). A look back at Pluto was also performed after the 
 Arrokoth flyby. A Color Scan of Neptune and Uranus was done along with a Solar Star 
 Calibration and Radiometric Calibration. These data were migrated from the Planetary 
 Data System (PDS) PDS3 format dataset: NH-A-MVIC-3-KEM1-V6.0. Labels were redesigned 
 during migration using the Flexible Image Transport (FIT) header and PDS3 label (LBL) 
 files, but the data files are unchanged from their PDS3 version.