cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21346041
title: Brazil Data S1 from Genomic evidence for ancient human migration routes along South America's Atlantic coast

description: An increasing body of archaeological and genomic evidence has hinted to a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level.
DOI: 10.6084/m9.figshare.20071745
title: Supplementary Material for: Identification of hub gene and transcription factor related to chronic allograft nephropathy based on WGCNA analysis

description: Abstract Introduction Kidney transplantation has surpassed dialysis as the optimal therapy for end-stage kidney disease (ESKD). Yet, most patients could suffer from a slow but continuous deterioration of kidney function leading to graft loss mostly due to chronic allograft nephropathy (CAN) after KT. The dysregulated gene expression for CAN is still poorly understood. Methods To explore the pathogenesis of genomics in CAN, we analyzed the differentially expressed genes (DEGs) of kidney transcriptome between CAN and non-rejecting patients by downloading gene expression microarrays from the Gene Expression Omnibus (GEO) database. Then, we used weighted gene co-expression network analysis (WGCNA) to analyze the co-expression of DEGs to explore key modules, hub genes, and transcription factors in CAN. Functional enrichment analysis of key modules was performed to explore pathogenesis. ROC curve analysis was used to validate hub genes. Results As a result, 3 key modules and 15 hub genes were identified by WGCNA analysis. 3 key modules had 21 mutual Gene Ontology (GO) term enrichment functions. Extracellular structure organization, extracellular matrix organization, and extracellular region were identified as significant functions in CAN. Furthermore, transcription factor 12 was identified as the key transcription factor regulating key modules. All 15 hub genes: Yip1 interacting factor homolog B, membrane trafficking protein(YIF1B), toll like receptor 8 (TLR8), neutrophil cytosolic factor 4 (NCF4), glutathione peroxidase 8 (GPX8), mesenteric estrogen dependent adipogenesis (MEDAG), decorin(DCN), serpin family F member 1 (SERPINF1), integrin subunit beta like 1 (ITGBL1), SRY-box transcription factor 15 (SOX15), trophinin associated protein (TROAP), SRY-box transcription factor 1 (SOX1), metallothionein 3 (MT3), lysosomal protein transmembrane (5LAPTM5), FERM domain containing kindlin 3 (FERMT3), cathepsin S (CTSS) had a great diagnostic performance (AUC&gt;0.7). Conclusion This study updates information and provides a new perspective for understanding the pathogenesis of CAN by bioinformatics means. More research is needed to validate and explore the results we have found to reveal the mechanisms underlying CAN.
DOI: 10.6084/m9.figshare.20071745.v1
title: Supplementary Material for: Identification of hub gene and transcription factor related to chronic allograft nephropathy based on WGCNA analysis

description: Abstract Introduction Kidney transplantation has surpassed dialysis as the optimal therapy for end-stage kidney disease (ESKD). Yet, most patients could suffer from a slow but continuous deterioration of kidney function leading to graft loss mostly due to chronic allograft nephropathy (CAN) after KT. The dysregulated gene expression for CAN is still poorly understood. Methods To explore the pathogenesis of genomics in CAN, we analyzed the differentially expressed genes (DEGs) of kidney transcriptome between CAN and non-rejecting patients by downloading gene expression microarrays from the Gene Expression Omnibus (GEO) database. Then, we used weighted gene co-expression network analysis (WGCNA) to analyze the co-expression of DEGs to explore key modules, hub genes, and transcription factors in CAN. Functional enrichment analysis of key modules was performed to explore pathogenesis. ROC curve analysis was used to validate hub genes. Results As a result, 3 key modules and 15 hub genes were identified by WGCNA analysis. 3 key modules had 21 mutual Gene Ontology (GO) term enrichment functions. Extracellular structure organization, extracellular matrix organization, and extracellular region were identified as significant functions in CAN. Furthermore, transcription factor 12 was identified as the key transcription factor regulating key modules. All 15 hub genes: Yip1 interacting factor homolog B, membrane trafficking protein(YIF1B), toll like receptor 8 (TLR8), neutrophil cytosolic factor 4 (NCF4), glutathione peroxidase 8 (GPX8), mesenteric estrogen dependent adipogenesis (MEDAG), decorin(DCN), serpin family F member 1 (SERPINF1), integrin subunit beta like 1 (ITGBL1), SRY-box transcription factor 15 (SOX15), trophinin associated protein (TROAP), SRY-box transcription factor 1 (SOX1), metallothionein 3 (MT3), lysosomal protein transmembrane (5LAPTM5), FERM domain containing kindlin 3 (FERMT3), cathepsin S (CTSS) had a great diagnostic performance (AUC&gt;0.7). Conclusion This study updates information and provides a new perspective for understanding the pathogenesis of CAN by bioinformatics means. More research is needed to validate and explore the results we have found to reveal the mechanisms underlying CAN.
DOI: 10.6084/m9.figshare.21345879
title: Responses of Bacterial Community Structure, Diversity, and Chemical Properties in the Rhizosphere Soil on Fruiting-Body Formation of Suillus luteus

description: Data of the article "Responses of Bacterial Community Structure, Diversity, and Chemical Properties in the Rhizosphere Soil on Fruiting-Body Formation of <em>Suillus luteus"</em>
DOI: 10.6084/m9.figshare.21345879.v1
title: Responses of Bacterial Community Structure, Diversity, and Chemical Properties in the Rhizosphere Soil on Fruiting-Body Formation of Suillus luteus

description: Data of the article "Responses of Bacterial Community Structure, Diversity, and Chemical Properties in the Rhizosphere Soil on Fruiting-Body Formation of <em>Suillus luteus"</em>
DOI: 10.6084/m9.figshare.21087025
title: Supplementary Material for: Influences of the interactions of genetic variations of seven core circadian clock genes with lifestyle factors on metabolic parameters

description: Introduction: In mammals, circadian rhythms regulate many behavioral and physiological processes. Genetic and epidemiological studies have shown that dysregulation of the circadian rhythm induces chronic metabolic diseases, such as obesity, diabetes, and dyslipidemia. We aimed to know the interactions of genetic variations of seven core circadian clock genes with lifestyle factors on the determination of metabolic parameters. Methods: We have analyzed the impacts of genotype of seven core circadian clock genes (i.e., CLOCK, BMAL1, PER1, PER2, PER3, CRY1 and CRY2) and lifestyle factors (i.e., physical activity and sleep duration) in 575 Japanese males on the determination of metabolic parameters (i.e., BMI, glucose, HbA1c, LDL-C and HDL-C). Results: We have detected the associations between genotypes of PER3 and serum HbA1c level, and genotypes of CRY1 and serum LDL-C level. Additionally, the interactions of the genotypes of PER1 and PER3 with physical activity for determining BMI, the genotypes of CLOCK with physical activity for determining serum HbA1c levels, was observed. Furthermore, for determining of serum HDL-C levels, the interactions of the genotypes of CRY2 with physical activity or sleep duration was observed. Discussion/Conclusion: Our findings indicate that the interactions of genotypes for core circadian clock genes and lifestyle factors (i.e., physical activity and sleep duration) are important for determining of metabolic parameters.
DOI: 10.6084/m9.figshare.21346002.v1
title: Supplementary Material for: Alcohol Consumption Post-Liver Transplantation: A Cross-Sectional Study

description: <b><i>Background:</i></b> Listing patients with alcohol-associated liver disease (ALD) for liver transplant (LT) remains challenging especially due to the risk of alcohol resumption post-LT. We aimed to evaluate post-LT alcohol consumption at a Portuguese transplant center. <b><i>Methods:</i></b> We conducted a cross-sectional study including LT recipients from 2019 at Curry Cabral Hospital, Lisbon, Portugal. A pretested survey and a validated Portuguese translation of the Alcohol Use Disorder Identification Test (AUDIT) were applied via a telephone call. Alcohol consumption was defined by patients’ self-reports or a positive AUDIT. <b><i>Results:</i></b> In 2019, 122 patients underwent LT, and 99 patients answered the survey (June 2021). The mean (SD) age was 57 (10) years, 70 patients (70.7%) were males, and 49 (49.5%) underwent ALD-related LT. During a median (IQR) follow-up of 24 (20–26) months post-index LT, 22 (22.2%) recipients consumed any amount of alcohol: 14 had a drink monthly or less and 8 drank 2–4 times/month. On drinking days, 18 patients usually consumed 1–2 drinks and the remainder no more than 3–4 drinks. One patient reported having drunk ≥6 drinks on one occasion. All post-LT drinking recipients were considered low risk (score &lt;8) as per the AUDIT score (median [IQR] of 1 [1–2]). No patient reported alcohol-related problems, whether self-inflicted or toward others. Drinking recipients were younger (53 vs. 59 years, <i>p</i> = 0.020), had more non-ALD-related LT (72.7 vs. 44.2%, <i>p</i> = 0.018) and active smoking (31.8 vs. 10.4%, <i>p</i> = 0.037) than abstinent ones. <b><i>Conclusion:</i></b> In our cohort, about a quarter of LT recipients consumed alcohol early posttransplant, all with a low-risk pattern according to the AUDIT score.
DOI: 10.5281/zenodo.7215210
title: PRJNA311274 gVCFs part 1

description: Sequencing reads were aligned to the Amel_HAv3.1 reference genome using BWA-MEM v0.7.17. Reads were sorted with SAMtools v1.9 and duplicates marked (MarkDuplicates) with GATK v4.0.11.0. Variants for each sample were called using GATK’s HaplotypeCaller with the following non-default parameters --ERC GVCF, --sample-ploidy 1 and -A AlleleFraction. This dataset comprises the gVCF files for a subset of samples belonging to project accession: PRJNA311274.
description: Two missing files (SRR6236970.g.vcf.gz and SRR6236970.g.vcf.gz.csi) were added 17/10/2022.
DOI: 10.5281/zenodo.6685083
title: PRJNA311274 gVCFs part 1

description: Sequencing reads were aligned to the Amel_HAv3.1 reference genome using BWA-MEM v0.7.17. Reads were sorted with SAMtools v1.9 and duplicates marked (MarkDuplicates) with GATK v4.0.11.0. Variants for each sample were called using GATK’s HaplotypeCaller with the following non-default parameters --ERC GVCF, --sample-ploidy 1 and -A AlleleFraction. This dataset comprises the gVCF files for a subset of samples belonging to project accession: PRJNA311274.
description: Two missing files (SRR6236970.g.vcf.gz and SRR6236970.g.vcf.gz.csi) were added 17/10/2022.
DOI: 10.5281/zenodo.7199207
title: [IO Islamic 475] قصّۀ چهار درويش

description: <strong>Ḳiṣṣa-i-ćahâr darwîsh.</strong> <strong>This manuscript is now IO Islamic 742 in the India Office collections.</strong> <strong>[metadata:</strong> <strong>Hermann Ethé</strong><strong><em>, </em></strong><strong><em>Catalogue of Persian Manuscripts in the Library of the India Office,</em></strong> <strong>2 vols. (Oxford: India Office, 1903): volume 1,</strong> <strong>number 475 here with notations and hyperlinks].</strong> 742 The same. Beginning: راويان اخبار و ناقلان آثار الخ No date. No. 475, ff. 104, ll. 17-21 written very unequally, partly in Nasta’lîḳ, partly in Shikasta; a little worm-eaten here and there; size, 8¾ in. by 4¾ in.
DOI: 10.5281/zenodo.7199206
title: [IO Islamic 475] قصّۀ چهار درويش

description: <strong>Ḳiṣṣa-i-ćahâr darwîsh.</strong> <strong>This manuscript is now IO Islamic 742 in the India Office collections.</strong> <strong>[metadata:</strong> <strong>Hermann Ethé</strong><strong><em>, </em></strong><strong><em>Catalogue of Persian Manuscripts in the Library of the India Office,</em></strong> <strong>2 vols. (Oxford: India Office, 1903): volume 1,</strong> <strong>number 475 here with notations and hyperlinks].</strong> 742 The same. Beginning: راويان اخبار و ناقلان آثار الخ No date. No. 475, ff. 104, ll. 17-21 written very unequally, partly in Nasta’lîḳ, partly in Shikasta; a little worm-eaten here and there; size, 8¾ in. by 4¾ in.
DOI: 10.6084/m9.figshare.21345939
title: supp-table4-new.xlsx

description: Supplementary table 4
DOI: 10.6084/m9.figshare.21346110.v1
title: Supplementary tables

description: Associated supplementary tables
DOI: 10.5281/zenodo.7199702
title: Simulation input files and analysis scripts for "Optimal bond-constraint topology for molecular dynamics simulations of cholesterol"

description: Simulation input files and analysis scripts for "Optimal bond-constraint topology for molecular dynamics simulations of cholesterol". See ... for details.
DOI: 10.5281/zenodo.7199701
title: Simulation input files and analysis scripts for "Optimal bond-constraint topology for molecular dynamics simulations of cholesterol"

description: Simulation input files and analysis scripts for "Optimal bond-constraint topology for molecular dynamics simulations of cholesterol". See ... for details.
DOI: 10.5281/zenodo.2531989
title: Frøya wind data

description: Herewith we present the dataset of wind measurements from a Skipheia meteorological station on the island of Frøya on the western coast of Norway, Trondelag.

The site represents an exposed coastal wind climate with open sea, land and mixed fetch from various directions. UTM-coordinates of the Met-mast: 8.34251 E and 63.66638 N.

Presented data were gathered between years 2009-2015;

Hardware summary: 6 pairs of 2D sonic anemometers at 10, 16, 25, 40, 70, 100 m above the ground, independent temperature measurements at the same heights and near the ground; pressure and relative humidity from local meteostation (Sula, 20 km away).

Database summary: approx. 180 000 of 10 min data samples of full data recovery. Wind speed and direction, temperature, pressure & relative hummidity (from a nearby meteostation).

Data description: Two data files of different formats are available: a *.txt comma-separated values file and a native MATLAB *.mat file. Both contain the same data, starting with the first column: timestamp, wind speed (columns WS1-WS12) for 6 anemometers pairs, wind direction (columns WD1-WD12) for 6 anemometers pairs, temprature at 0.2 m (AT0), temeratures at levels of wind measurement (AT1-AT6), SUla. Columns have headers describing the data (first row).

Detailed site description with wind climate description can be found in attached asnalisys: Site analisys.pdf.

Additional information and analisys can be found in listed below works, using data from Frøya site, or nearby sites:

IEA Wind TCP Task 27 Compendium of IEA Wind TCP Task 27 Case Studies, Technical Report, Prepared by Ignacio Cruz Cruz, CIEMAT, Spain Trudy Forsyth, WAT, United States, October 2018; Chapter 1.8 

Domagalski, P., Bardal, L. M., & Satran, L. Vertical Wind Profiles in Non-neutral Conditions-Comparison of Models and Measurements from Froya. <em>Journal of Offshore Mechanics and Arctic Engineering</em>.

Mathias Møller , Piotr Domagalski and Lars Roar Sætran, Characteristics of abnormal vertical wind profiles at a coastal site, <em>Journal of Physics: Conference Series</em>, IOPscience, in rewiev (Feb 2019).

Bardal, L. M., Onstad, A. E., Sætran, L. R., & Lund, J. A. (2018). Evaluation of methods for estimating atmospheric stability at two coastal sites. <em>Wind Engineering</em>, 0309524X18780378. 

Bardal, L. M., & Sætran, L. R. (2016, September). Spatial correlation of atmospheric wind at scales relevant for large scale wind turbines. In <em>Journal of Physics: Conference Series</em> (Vol. 753, No. 3, p. 032033). IOP Publishing.

Bardal, L. M., & Sætran, L. R. (2016). Wind gust factors in a coastal wind climate. <em>Energy Procedia,</em> 94, 417-424.
DOI: 10.5281/zenodo.2541205
title: Frøya wind data

description: Herewith we present the dataset of wind measurements from a Skipheia meteorological station on the island of Frøya on the western coast of Norway, Trondelag.

The site represents an exposed coastal wind climate with open sea, land and mixed fetch from various directions. UTM-coordinates of the Met-mast: 8.34251 E and 63.66638 N.

Presented data were gathered between years 2009-2015;

Hardware summary: 6 pairs of 2D sonic anemometers at 10, 16, 25, 40, 70, 100 m above the ground, independent temperature measurements at the same heights and near the ground; pressure and relative humidity from local meteostation (Sula, 20 km away).

Database summary: approx. 180 000 of 10 min data samples of full data recovery. Wind speed and direction, temperature, pressure & relative hummidity (from a nearby meteostation).

Data description: Two data files of different formats are available: a *.txt comma-separated values file and a native MATLAB *.mat file. Both contain the same data, starting with the first column: timestamp, wind speed (columns WS1-WS12) for 6 anemometers pairs, wind direction (columns WD1-WD12) for 6 anemometers pairs, temprature at 0.2 m (AT0), temeratures at levels of wind measurement (AT1-AT6), SUla. Columns have headers describing the data (first row).

Detailed site description with wind climate description can be found in attached asnalisys: Site analisys.pdf.

Additional information and analisys can be found in listed below works, using data from Frøya site, or nearby sites:

IEA Wind TCP Task 27 Compendium of IEA Wind TCP Task 27 Case Studies, Technical Report, Prepared by Ignacio Cruz Cruz, CIEMAT, Spain Trudy Forsyth, WAT, United States, October 2018; Chapter 1.8 

Domagalski, P., Bardal, L. M., & Satran, L. Vertical Wind Profiles in Non-neutral Conditions-Comparison of Models and Measurements from Froya. <em>Journal of Offshore Mechanics and Arctic Engineering</em>.

Mathias Møller , Piotr Domagalski and Lars Roar Sætran, Characteristics of abnormal vertical wind profiles at a coastal site, <em>Journal of Physics: Conference Series</em>, IOPscience, in rewiev (Feb 2019).

Bardal, L. M., Onstad, A. E., Sætran, L. R., & Lund, J. A. (2018). Evaluation of methods for estimating atmospheric stability at two coastal sites. <em>Wind Engineering</em>, 0309524X18780378. 

Bardal, L. M., & Sætran, L. R. (2016, September). Spatial correlation of atmospheric wind at scales relevant for large scale wind turbines. In <em>Journal of Physics: Conference Series</em> (Vol. 753, No. 3, p. 032033). IOP Publishing.

Bardal, L. M., & Sætran, L. R. (2016). Wind gust factors in a coastal wind climate. <em>Energy Procedia,</em> 94, 417-424.
DOI: 10.6084/m9.figshare.21346110.v2
title: Supplementary tables

description: Associated supplementary tables and data
DOI: 10.5281/zenodo.7199182
title: [IO Islamic 2480] قصّۀ چهار درويش

description: <strong>Ḳiṣṣa-i-ćahâr darwîsh.</strong> <strong>This manuscript is now IO Islamic 739 in the India Office collections.</strong> <strong>[metadata:</strong> <strong>Hermann Ethé</strong><strong><em>, </em></strong><strong><em>Catalogue of Persian Manuscripts in the Library of the India Office,</em></strong> <strong>2 vols. (Oxford: India Office, 1903): volume 1,</strong> <strong>number 2480 here with notations and hyperlinks].</strong> 739 Ḳiṣṣa-i-ćahâr darwîsh (قصّۀ چهار درويش). The Persian version of the story of the Sulṭân of Rûm, Âzâdbakhsh, his son Bakhtyâr, and the four dervishes, popularly ascribed to the greatest Persian Poet of India, Amîr Khusrau of Dihlî , who died A.H. 725 (A.D. 1325), comp. Bodleian Cat., No. 443; Rieu ii. p. 762; A. F. Mehren, p. 32; [Edward B.] Eastwick, translation of the Bâgh-o-Bahâr, Hertford, 1852, p. vii. Beginning: امّا بعد راويان اخبار و ناقلان آثار و طوطيان شكر شكن الخ. <em>Dâstân I</em>, story of the first Dervish, on fol. 6<sup>a</sup>. <em>Dâstân II</em>, story of the second Dervish, on fol. 32<sup>b</sup>. <em>Dâstân III</em>, story of the Sulṭân, on fol. 56<sup>b</sup>. <em>Dâstân IV</em>, story of the third Dervish (here called درويش چهارم by mistake), on fol. 100<sup>b</sup>. Dâstân V, story of the fourth Dervish, on fol. 120<sup>b</sup>. <em>Epilogue</em> or final story (داستان اخير), on fol. 135<sup>b</sup>. The book ends on fol. 141<sup>a</sup>; the remaining two pages and a half are filled with a detailed colophon, in which the transcriber, who does not mention his name, gives a short historical account of the circumstances under which he made this copy, in A.H. 1188, the sixteenth year of Shâh ‘Âlam’s reign (A.D. 1774, 1775). Bibliotheca Leydeniana No. 2480, ff. 142, ll. 18-19, but the greater number of pages are written in diagonal lines; Shikasta; size, 8<sup>3/8</sup> in. by 3<sup>1/2</sup> in. [<strong>ed note</strong>: Quick link to other manuscript copies of this work.]
DOI: 10.5281/zenodo.7199181
title: [IO Islamic 2480] قصّۀ چهار درويش

description: <strong>Ḳiṣṣa-i-ćahâr darwîsh.</strong> <strong>This manuscript is now IO Islamic 739 in the India Office collections.</strong> <strong>[metadata:</strong> <strong>Hermann Ethé</strong><strong><em>, </em></strong><strong><em>Catalogue of Persian Manuscripts in the Library of the India Office,</em></strong> <strong>2 vols. (Oxford: India Office, 1903): volume 1,</strong> <strong>number 2480 here with notations and hyperlinks].</strong> 739 Ḳiṣṣa-i-ćahâr darwîsh (قصّۀ چهار درويش). The Persian version of the story of the Sulṭân of Rûm, Âzâdbakhsh, his son Bakhtyâr, and the four dervishes, popularly ascribed to the greatest Persian Poet of India, Amîr Khusrau of Dihlî , who died A.H. 725 (A.D. 1325), comp. Bodleian Cat., No. 443; Rieu ii. p. 762; A. F. Mehren, p. 32; [Edward B.] Eastwick, translation of the Bâgh-o-Bahâr, Hertford, 1852, p. vii. Beginning: امّا بعد راويان اخبار و ناقلان آثار و طوطيان شكر شكن الخ. <em>Dâstân I</em>, story of the first Dervish, on fol. 6<sup>a</sup>. <em>Dâstân II</em>, story of the second Dervish, on fol. 32<sup>b</sup>. <em>Dâstân III</em>, story of the Sulṭân, on fol. 56<sup>b</sup>. <em>Dâstân IV</em>, story of the third Dervish (here called درويش چهارم by mistake), on fol. 100<sup>b</sup>. Dâstân V, story of the fourth Dervish, on fol. 120<sup>b</sup>. <em>Epilogue</em> or final story (داستان اخير), on fol. 135<sup>b</sup>. The book ends on fol. 141<sup>a</sup>; the remaining two pages and a half are filled with a detailed colophon, in which the transcriber, who does not mention his name, gives a short historical account of the circumstances under which he made this copy, in A.H. 1188, the sixteenth year of Shâh ‘Âlam’s reign (A.D. 1774, 1775). Bibliotheca Leydeniana No. 2480, ff. 142, ll. 18-19, but the greater number of pages are written in diagonal lines; Shikasta; size, 8<sup>3/8</sup> in. by 3<sup>1/2</sup> in. [<strong>ed note</strong>: Quick link to other manuscript copies of this work.]
DOI: 10.6084/m9.figshare.20119952.v2
title: Codes and raw data of identifications, experiments and bioassays

description: Codes and raw data of the article "On the functional role of chemically insignificant cues in multitrophic caterpillar-ant-plant interactions".
DOI: 10.6084/m9.figshare.21346110
title: Supplementary data

description: Associated supplementary tables and data
DOI: 10.6084/m9.figshare.21346110.v3
title: Supplementary data

description: Associated supplementary tables and data