cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/w6esrt
title: Prieskum svištov, Chopok juh, lyžiarske stredisko

description: Monitoring svištích kolónií v záujmovom území Chopku bol vykonaný podľa rovnakej metodiky, aká bola stanovená na počiatku výskumu v roku 2004. Založený je na zisťovaní zemepisných súradníc všetkých nájdených nôr pomocou GPS prístroja. (bližšie viď BALLO, SÝKORA, 2005; BALLO, SÝKORA, 2006; BALLO, SÝKORA, 2007). 
Ide hlavne o techniku spracovania koordinátov GPS, ktorá bola stanovená a vyskúšaná v priebehu deviatich rokov výskumu (2004 – 2012) v Tatranskom národnom parku. 
Z dôvodu vytvorenia obrazu komplexnosti kolónie, boli zaznamenávané zemepisné súradnice všetkých nájdených nôr. Od polovice júna boli vyhľadávané dominantné materské nory, ktoré boli evidentne osídlené potomstvom (svištia matka a mláďatá). Preskúmaná bola každá svištia rodina objavená a zameraná v južných a neskôr aj severných svahoch Chopka. Pozornosť bola venovaná tiež ekológii, etológii, trofickej základni a antropickým vplyvom.
DOI: 10.6084/m9.figshare.25382440
title: <b>Does university</b><b>-</b><b>industry collaboration improve </b><b>firm</b><b> productivity? </b><b>：</b><b>Evidence from</b><b> Chin</b><b>a</b>

description: University has been an indispensable force in China's innovation and economic growth, and China's government intensively promotes university-firm collaboration to stimulate knowledge and technology transfer between firms and universities. Thus, analyzing the impact of university-industry collaboration on the performance of firms will help us understand the significance of universities to China's economic development. As existing research lacks attention to the impact of UIC on the productivity of China's firms, this study examines the impact of university-industry collaboration on firm productivity using natural language processing and by matching China's intellectual property and listed firms' operation databases. The empirical results show that university-industry collaboration can promote firm productivity by improving the quality of firms' innovation, strengthening internalization efficiency, and broadening firms' research horizons. Moreover, the university-industry collaboration process has a pronounced effect on promoting firm productivity in technology-intensive and intellectual property-intensive industries. From the university-industry collaboration perspective, this study interprets China's economic development and provides new insights for developing countries regarding using universities to alleviate the insufficiency of private R&D investment.
DOI: 10.6084/m9.figshare.25382440.v1
title: <b>Does university</b><b>-</b><b>industry collaboration improve </b><b>firm</b><b> productivity? </b><b>：</b><b>Evidence from</b><b> Chin</b><b>a</b>

description: University has been an indispensable force in China's innovation and economic growth, and China's government intensively promotes university-firm collaboration to stimulate knowledge and technology transfer between firms and universities. Thus, analyzing the impact of university-industry collaboration on the performance of firms will help us understand the significance of universities to China's economic development. As existing research lacks attention to the impact of UIC on the productivity of China's firms, this study examines the impact of university-industry collaboration on firm productivity using natural language processing and by matching China's intellectual property and listed firms' operation databases. The empirical results show that university-industry collaboration can promote firm productivity by improving the quality of firms' innovation, strengthening internalization efficiency, and broadening firms' research horizons. Moreover, the university-industry collaboration process has a pronounced effect on promoting firm productivity in technology-intensive and intellectual property-intensive industries. From the university-industry collaboration perspective, this study interprets China's economic development and provides new insights for developing countries regarding using universities to alleviate the insufficiency of private R&D investment.
DOI: 10.17037/data.00001311
title: TUMIKIA Project Household Questionnaire & Stool Sample Collection Form

description: This form was used by TUMIKIA field officers during cross-sectional parasitological surveys and includes a census, sociodemographic questions, and reported and observed measures of water & sanitation access. A randomisation function selects a household member to answer individual-level behaviour questions and provide a stool sample. The form includes scanning of QR codes on sample pots, efficiently linking household and individual data with laboratory results.
DOI: 10.5519/qd.ygprb97h
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (10 records)
DOI: 10.14473/csda/qjphkn/mp2toy
title: D_CSDA00239-CSDA00241.pdf

description: Dotazník
DOI: 10.14473/csda/qjphkn/dhpfau
title: 3_Czech_Expert_Survey_2013_CZ.tab

description: Data
DOI: 10.14473/csda/qjphkn/rywn6x
title: TI_CSDA00239-CSDA00241.pdf

description: Technická informace
DOI: 10.14473/csda/qjphkn
title: Výzkum českých politických stran - 2013 - Šetření mezi odborníky

description: Výzkumný tým se rozhodl pro použití 38 škál, přičemž většina z nich replikovala Laverovy a Benoitovy (2006)* položky. Díky tomu, že dotazník byl implementován v rozhraní LimeSurvey, měl výzkumný tým možnost měřit také časové délky jednotlivých odpovědí, které mohou být užitečné pro zhodnocení kvality dat bez toho, aby tento krok představoval nějaké dodatečné zatížení respondentů. Politické strany zahrnuté ve výzkumném šetření: 1. Česká strana sociálně demokratická (ČSSD): středo-levá, proevropská 2. Komunistická strana Čech a Moravy (KSČM): levicová, protievropská 3. Tradice, odpovědnost, prosperita (TOP 09): středo-pravá, fiskálně konzervativní, proevropská 4. Občanská demokratická strana (ODS): pravicová, liberální, euroskeptická 5. ANO 2011: pravicová, liberální, populistická, protievropská 6. Úsvit přímé demokracie Tomia Okamury (Úsvit): pravicová, populistická, protievropská 7. Křesťanská a demokratická unie – Československá strana lidová (KDU-ČSL): pravicová, sociálně konzervativní, proevropská 8. Strana zelených (SZ): ekologie, sociálně liberální, proevropská Hlavním účelem tohoto neformálního výzkumu bylo zjistit, zda se skóry odborníků významně liší od „dobře informovaných“ občanů z neakademické sféry.
DOI: 10.25824/redu/7phbhy
title: DP6 46B (Imagem 7_2).jpg

description: SEM image of thin-section DP6/46B. Possible filament preserved, EDS analysis shows composition of silica cementation (Point 5), quartz grain (Point 6) and alkali feldspar (Point 7).
DOI: 10.25824/redu/hh2rm7
title: CP6_356.jpg

description: Sample CP6 356, Contraction crack with possible mats chips (Botucatu Formation, Jacarezinho-PR).
DOI: 10.25824/redu/po2xkz
title: CP6_292.jpg

description: Sample CP6 292, ichnogenus Brasilichnium, (Botucatu Formation, Araraquara-SP).
DOI: 10.25824/redu/rt09zq
title: CP6_329.jpg

description: Sample CP6 329, circular and concentric structures (Botucatu Formation, Jacarezinho-PR).
DOI: 10.25824/redu/wo0y7d
title: DP6 46B (Imagem 6).jpg

description: SEM image of thin-section DP6/46B. EDS analysis of a possible biotite (Point 1 and 2) and the matrix with presence of iron oxides ( Point 3 and 4).
DOI: 10.25824/redu/xbyu0d
title: CP6_293.jpg

description: Sample CP6 293, Theropoda footprint (Botucatu Formation, Araraquara-SP).
DOI: 10.25824/redu/fok5ju
title: DP6 46B (Imagem 4).jpg

description: SEM image of thin-section DP6/46B. Composition of a detrital grain of muscovite (point 1 to 3).
DOI: 10.25824/redu/grlymw
title: DP6 46A (Imagem 7).jpg

description: SEM image of thin-section DP6/46A. EDS analysis of different points of filament (Points 1 to 5).
DOI: 10.25824/redu/sckhyt
title: CP6_333.jpg

description: Sample CP6 333, Theropoda footprint (Botucatu Formation, Jacarezinho-PR).
DOI: 10.25824/redu/sjszll
title: CP6 313 (Imagem 2).jpg

description: SEM image of thin-section CP6/313. EDS results showing the composition of the matrix and titanium oxide cementation (points 2 to 4) and quartz grain (point 1).
DOI: 10.25824/redu/v35guy
title: DP6 46B (Imagem 7).jpg

description: SEM image of thin-section DP6/46B. Possible filament preserved, EDS analysis shows composition of iron oxides (Point 1 and 2) and aluminosilicates (Point 3 to 4).
DOI: 10.25824/redu/10ocws
title: DP6 46B (Imagem 3).jpg

description: SEM image of thin-section DP6/46B. Composition of coatings on the grain surface (Point 1 to 3).
DOI: 10.25824/redu/783qg3
title: CP6_332.jpg

description: Sample CP6 332, Contraction crack (Botucatu Formation, Jacarezinho-PR).
DOI: 10.25824/redu/bffvo5
title: CP6_291.jpg

description: Sample CP6 291, Theropoda footprint (Botucatu Formation, Araraquara-SP).
DOI: 10.25824/redu/lvqcn1
title: CP6_288.jpg

description: Sample CP6 288, ichnogenus Paleohelcura (Botucatu Formation, Araraquara-SP).
DOI: 10.25824/redu/tpzdkb
title: DP6 46B (Imagem 6_2).jpg

description: SEM image of thin-section DP6/46B. Presence of possible biotite and EDS analysis of silica cementation (Point 5 and 6) and quartz grain (point 7).
DOI: 10.25824/redu/yr1wd2
title: DP6 46B (Imagem 5).jpg

description: SEM image of thin-section DP6/46B. Presence of possible filament, EDS analysis in three differents points (1 to 3).
DOI: 10.25824/redu/cdyhag
title: CP6_330.jpg

description: Sample CP6 330, circular and concentric structures (Botucatu Formation, Jacarezinho-PR
DOI: 10.25824/redu/fwi9ux
title: CP6 313 (Imagem 3).jpg

description: SEM image of thin-section CP6/313. EDS analysis in a moldic pore, presence of titanium oxide (point 2 and 3). Composition of matrix (point 4) and quartz (point 1).
DOI: 10.25824/redu/izttzf
title: DP6 46A (Imagem 1_1).jpg

description: SEM image of thin-section DP6/46A, composition of filaments (point 1 and 2), and silica cementation (point 3) and quartz (point 4).
DOI: 10.25824/redu/jmxfo4
title: DP6 46B (Imagem 9_2).jpg

description: SEM image of thin-section DP6/46B. Different grains of the framework, such altered ilmenite (Point 5) and alkali feldspar (Point 6 and 7).
DOI: 10.25824/redu/oot5uv
title: CP6 313 (Imagem 4).jpg

description: SEM image of thin section CP6/313, detail of the region analyzed in image 3. EDS results showing the composition of mica grain (point 1 and 2).
DOI: 10.25824/redu/xf6wyw
title: DP6 46A (Imagem 5).jpg

description: SEM image of thin-section DP6/46A. EDS analysis showing composition of possible filament (Point 1 and 2), cementation (Point 3), quartz grain (Point 4) and alkali feldspar (Point 5).
DOI: 10.25824/redu/7s9fkz
title: CP6_331.jpg

description: Sample CP6 331, Contraction crack (Botucatu Formation, Jacarezinho-PR).
DOI: 10.25824/redu/jlqtbf
title: DP6 46A (Imagem 9_2).jpg

description: SEM image of thin-section DP6/46A. EDS analysis of muscovite grains (Point 5 to 7).
DOI: 10.25824/redu/jq6wg2
title: CP6_308.jpg

description: Sample CP6 308, possible wrinkle marks (Botucatu Formation, Jacarezinho-PR).
DOI: 10.25824/redu/jzzqzk
title: DP6_46.jpg

description: Sample DP6 46, Theropoda footprint (Botucatu Formation, Araraquara-SP).
DOI: 10.25824/redu/nfxwf4
title: DP6 46A (Imagem 7_2).jpg

description: SEM image of thin-section DP6/46A. EDS analysis of different points of filament (Points 6 to 9).
DOI: 10.25824/redu/l0vwxx
title: DP6 46A (Imagem 9).jpg

description: SEM image of thin-section DP6/46A. EDS analysis of altered detrital minerals (Point 1 to 4).
DOI: 10.25824/redu/pymlto
title: CP6_290.jpg

description: Sample CP6 290, Theropoda footprint preserved in undertrack (Botucatu Formation, Araraquara-SP).
DOI: 10.25824/redu/qbxso6
title: CP6_305.jpg

description: Sample CP6 305, ichnogenus Taenidium, (Botucatu Formation, Jacarezinho-PR).
DOI: 10.25824/redu/v63tmd
title: CP6 313 (Imagem 1).jpg

description: SEM image of thin-section CP6/313. EDS results showing the composition of point 1, which corresponds to an intensely altered ilmenite. Point 2 shows the composition of silica cementation. Point 3 corresponds to a matrix.
DOI: 10.25824/redu/z6ocsr
title: DP6 46B (Imagem 9).jpg

description: SEM image of thin-section DP6/46B. Different grains of the framework, such as ilmenite in different stages of alteration (Point 1, 4 and 5), silica cementation (Point 3) and quartz (Point 2).
DOI: 10.25824/redu/cus7cj
title: Ichnofossiliferous assemblage, sedimentary structures and their analysis in SEM/EDS (Botucatu Formation, Cretaceous, Paraná Basin)

description: This dataset contains results of the scanning electron microscopy and energy dispersive spectroscopy (SEM/EDS) analyses of 3 thin sections (DP6/46A, CP6/46B, CP6/313),which corresponds to a Theropoda footprint (DP6/46) and a contraction crack (CP6/313), obtained with the JEOL electron microscope (JSM IT500HR) coupled energy dispersive spectrometer (EDS JEOL EX-74600U4L2Q), carried out at the Scanning Electron Microscopy Laboratory, at the Geoscience Institute (Unicamp). There are also pictures of trace fossil and sedimentary structures present in the study areas of Botucatu Formation, São Bento quarry (Araraquara - SP) and Jacarezinho (PR).
DOI: 10.25824/redu/hpspfp
title: CP6_312.jpg

description: Sample CP6 312, Contraction crack (Botucatu Formation, Jacarezinho-PR).
DOI: 10.25824/redu/kuddte
title: CP6_318.jpg

description: Sample CP6 318, possible footprint preserved in undertrack (Botucatu Formation, Jacarezinho-PR).
DOI: 10.25824/redu/lrzzzd
title: DP6 46B (Imagem 2).jpg

description: SEM image of thin-section DP6/46B. EDS analysis of matrix and iron oxides (Point 3 to 5), silica cementation (Point 2) and quartz (point 1).
DOI: 10.5281/zenodo.8029100
title: DNA methylation in the chromatin landscape of healthy and injured cell types in the human kidney

description: *** To access this data, please go to Kidney Precision Medicine Project (KPMP) 

Whole Genome Bisulfite Sequence WGBS in human kidney tissue. There are 13 nephrectomies, two biopsies each split into two kidney compartments glomerulus (GLOM) and tubule interstitium (TI). One of the nephrectomies was sequenced in the first and second batches to evaluate the sequence quality. Then we had 30 kidney samples plus three blood samples added like controls with 2 negative and 1 positive.Genomic DNA is isolated using the PureLink Pro 96 Genomic DNA Kit (Cat# K182104A). DNA quantity and quality are assessed using the Qubit Fluorometer 4.1 (Invitrogen). Bisulfite conversion was performed using the EpiTect Fast DNA Bisulfite Kit (Qiagen Cat# 59824). An input of 10 ng was used for library prep. Library prep with QIAseq Methyl DNA Library Kit (Cat# 180502) was used to amplify and laminate Illumina adaptors. Library purification was performed using QIAseq Beads. The library quality was assessed using the Agilent Bioanalyzer 2100 and Qubit Fluorometer 4.1. Multiple libraries were pooled in equal molarity. A final concentration of 300 pM was loaded onto the NovaSeq 6000 sequencer (Illumina) for 150 bp paired-end sequencing. Approximately 200 million read pairs (400 million reads total) were generated per library. An EpiTect Unmethylated DNA control (Qiagen Cat# 59568) was used for the first and second batches. The EpiTect Methylated DNA control (Qiagen Cat# 59655) was sequencing run the second batch. Sequencing quality control, mapping, and methylation analysis were performed using the pipeline with FastC 0.11.5, MultiQC v1.8 TrimGalore 0.6.7 to remove Illumina adapter sequences and 10 bp 5' prime and 5bp 3' prime. Bismark 0.23.1 DNA Mapping: Non-directional mapping to the hg38/GRCh38. The data in Zenodo are the bigwig for each experiment  33 (15 GLOM and 15 TI and blood 2 Negative 1 Positive), There are two merged bigwigs for GLOM and TI samples and a metadata file.

Published in: DOI:  10.1038/s41467-023-44467-6
DOI: 10.5281/zenodo.8029101
title: DNA methylation in the chromatin landscape of healthy and injured cell types in the human kidney

description: *** To access this data, please go to Kidney Precision Medicine Project (KPMP) 

Whole Genome Bisulfite Sequence WGBS in human kidney tissue. There are 13 nephrectomies, two biopsies each split into two kidney compartments glomerulus (GLOM) and tubule interstitium (TI). One of the nephrectomies was sequenced in the first and second batches to evaluate the sequence quality. Then we had 30 kidney samples plus three blood samples added like controls with 2 negative and 1 positive.Genomic DNA is isolated using the PureLink Pro 96 Genomic DNA Kit (Cat# K182104A). DNA quantity and quality are assessed using the Qubit Fluorometer 4.1 (Invitrogen). Bisulfite conversion was performed using the EpiTect Fast DNA Bisulfite Kit (Qiagen Cat# 59824). An input of 10 ng was used for library prep. Library prep with QIAseq Methyl DNA Library Kit (Cat# 180502) was used to amplify and laminate Illumina adaptors. Library purification was performed using QIAseq Beads. The library quality was assessed using the Agilent Bioanalyzer 2100 and Qubit Fluorometer 4.1. Multiple libraries were pooled in equal molarity. A final concentration of 300 pM was loaded onto the NovaSeq 6000 sequencer (Illumina) for 150 bp paired-end sequencing. Approximately 200 million read pairs (400 million reads total) were generated per library. An EpiTect Unmethylated DNA control (Qiagen Cat# 59568) was used for the first and second batches. The EpiTect Methylated DNA control (Qiagen Cat# 59655) was sequencing run the second batch. Sequencing quality control, mapping, and methylation analysis were performed using the pipeline with FastC 0.11.5, MultiQC v1.8 TrimGalore 0.6.7 to remove Illumina adapter sequences and 10 bp 5' prime and 5bp 3' prime. Bismark 0.23.1 DNA Mapping: Non-directional mapping to the hg38/GRCh38. The data in Zenodo are the bigwig for each experiment  33 (15 GLOM and 15 TI and blood 2 Negative 1 Positive), There are two merged bigwigs for GLOM and TI samples and a metadata file.

Published in: DOI:  10.1038/s41467-023-44467-6
DOI: 10.5281/zenodo.8029795
title: CUT&RUN in the chromatin landscape of healthy and injured cell types in the human kidney

description: *** To access this data, please go to Kidney Precision Medicine Project (KPMP) 

CUT&RUN of human kidney nephrectomy tissue using 66,000-200,000 cells/reaction. H3K4me3 (1 biological replicate, with 3 technical replicates). H3K27ac (4 biological replicates, one with 3 technical replicates).  H3K4me1 (1 biological replicate, with 3 technical replicates). H3K27me3 (6 biological replicates, one with 3 technical replicates, and two with isogenic replicates). Liquid nitrogen or OCT-embedded frozen kidney tissue from 6 donors was processed according to the protocol from Epicypher (https://www.epicypher.com/content/documents/protocols/cutana-cut&run-protocol.pdf) with modification. The full modified protocol is published on protocols.io and available here: https://www.protocols.io/view/cut-amp-run-chromatin-profiling-of-human-kidney-ti-bp2l615o1vqe/v1. Antibodies used in this study for CUT&RUN reactions: H3K27ac (Cell Signaling, 8173), H3K27me3 (Cell Signaling, 9733), H3K4me1 (Cell Signaling, 5326), H3K4me3 (Cell Signaling, 9751), and IgG (Cell Signaling, 2729). Up to 3ng of DNA from KPMP donor samples (21-020, 20-687, 20-688) was used to prepare sequencing libraries using the Ion Plus Fragment Library Kit (Thermo Fisher Scientific, 4471252), following manufacturer’s instructions, using 17 cycles to amplify the library. Up to 0.5ng of DNA from KTRC donor samples (3399, 3409, 3447) was used to prepare sequencing libraries using NEBNext Ultra II Library Kit (NEB, E7645), following manufacturer’s instructions, using 18 cycles to amplify the library. Sequencing: 100pM KPMP donor libraries were sequenced on the Ion Torrent Proton to a sequencing depth of 30 million reads (2-3X genome coverage). 0.8 pm KTRC donor libraries were sequenced on the NovaSeq 6000 (Illumina) targeting 100 million paired-end reads. Detailed bioinformatic analysis with command line examples for Illumina sequences can be found here: https://www.protocols.io/view/cut-amp-run-chromatin-profiling-of-human-kidney-ti-bp2l615o1vqe/v1?step=36. Briefly, trimmed fastq files were aligned to the hg38 reference genome using Bowtie2 (for Illumina sequenced) or TMAP (for Ion Torrent sequenced). Aligned reads were extracted and converted to a sorted bam file using SAMtools. Scaled bigWig files were generated using Deeptools, and peaks were called using Macs2.

Published in: DOI:  10.1038/s41467-023-44467-6
DOI: 10.5281/zenodo.8029796
title: CUT&RUN in the chromatin landscape of healthy and injured cell types in the human kidney

description: *** To access this data, please go to Kidney Precision Medicine Project (KPMP) 

CUT&RUN of human kidney nephrectomy tissue using 66,000-200,000 cells/reaction. H3K4me3 (1 biological replicate, with 3 technical replicates). H3K27ac (4 biological replicates, one with 3 technical replicates).  H3K4me1 (1 biological replicate, with 3 technical replicates). H3K27me3 (6 biological replicates, one with 3 technical replicates, and two with isogenic replicates). Liquid nitrogen or OCT-embedded frozen kidney tissue from 6 donors was processed according to the protocol from Epicypher (https://www.epicypher.com/content/documents/protocols/cutana-cut&run-protocol.pdf) with modification. The full modified protocol is published on protocols.io and available here: https://www.protocols.io/view/cut-amp-run-chromatin-profiling-of-human-kidney-ti-bp2l615o1vqe/v1. Antibodies used in this study for CUT&RUN reactions: H3K27ac (Cell Signaling, 8173), H3K27me3 (Cell Signaling, 9733), H3K4me1 (Cell Signaling, 5326), H3K4me3 (Cell Signaling, 9751), and IgG (Cell Signaling, 2729). Up to 3ng of DNA from KPMP donor samples (21-020, 20-687, 20-688) was used to prepare sequencing libraries using the Ion Plus Fragment Library Kit (Thermo Fisher Scientific, 4471252), following manufacturer’s instructions, using 17 cycles to amplify the library. Up to 0.5ng of DNA from KTRC donor samples (3399, 3409, 3447) was used to prepare sequencing libraries using NEBNext Ultra II Library Kit (NEB, E7645), following manufacturer’s instructions, using 18 cycles to amplify the library. Sequencing: 100pM KPMP donor libraries were sequenced on the Ion Torrent Proton to a sequencing depth of 30 million reads (2-3X genome coverage). 0.8 pm KTRC donor libraries were sequenced on the NovaSeq 6000 (Illumina) targeting 100 million paired-end reads. Detailed bioinformatic analysis with command line examples for Illumina sequences can be found here: https://www.protocols.io/view/cut-amp-run-chromatin-profiling-of-human-kidney-ti-bp2l615o1vqe/v1?step=36. Briefly, trimmed fastq files were aligned to the hg38 reference genome using Bowtie2 (for Illumina sequenced) or TMAP (for Ion Torrent sequenced). Aligned reads were extracted and converted to a sorted bam file using SAMtools. Scaled bigWig files were generated using Deeptools, and peaks were called using Macs2.

Published in: DOI:  10.1038/s41467-023-44467-6