cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7303/syn47164761
title: SMILE-UHURA: Small Vessel Segmentation at Mesoscopic Scale from Ultra-High Resolution 7T Magnetic Resonance Angiograms
DOI: 10.17632/2nt447bcbw.1
title: Universidad de Santander - Colombia. Balance de los resultados de Investigación 2017-2022

description: Objetivo del informe:
Analizar la evolución de los resultados de investigación, en especial los que se derivan de la producción de artículos científicos y esfuerzo de innovación, y su impacto científico, innovación, visibilidad y societal.
Fuente de datos:
Los datos han sido generados a partir de Scopus y la Oficina Europea de Patentes, y analizados con herramientas de SCImago y SciVal. Se usaron indicadores comúnmente aceptados, los que dan un panorama comprensivo de los resultados en diferentes niveles de significancia. La ventana de observación utilizada es 2017-2022.  Los datos 2022 son provisionales.
DOI: 10.17632/d88fk28jbz.1
title: TRP14 is the rate limiting enzyme for intracellular cystine reduction and regulates proteome cysteinylation. Figure 2C

description: Identification of cysteinylated proteins in parental HEK cells and TRP14 knockdown HEK cells.
For the obtention of cysteinylated cell lysates, both control and TRP14 KD cell cultures were incubated with 250 µM biotinylated cysteine (Cys-BIO) for 1 h, the incubation medium was discarded, cells were washed with ice-cold PBS and collected in 300 µL of lysis buffer containing 50 mM Tris-HCl (pH 7.5), 2 mM EDTA, 150 mM NaCl, 1% Triton, 10 mM N-ethylmaleimide (NEM), and a protease inhibitor cocktail (Sigma-Aldrich, Missouri, USA). Cells were lysed by three freezing-thawing cycles, and cell lysates were centrifuged at 3500 rpm for 10 min to collect supernatants for analysis. Pierce™ Monomeric Avidin Agarose Kit (Thermo Scientific, Massachusetts, USA) was used to purify cysteinylated proteins tagged with biotin according to the manufacturer’s instructions. 
14 µg were loaded in a 1D PAGE gel , which were later in-gel reduced with dithiothreitol (DTT) and S-alkylated with iodoacetamide as previously described50. 
Samples were digested with 100 ng sequencing-grade trypsin (Promega, Madison, USA). The digestion mixture was dried and re-suspended in 20 µL of 2% acetonitrile, and 0.1% trifluoroacetic acid (TFA). 5 µL of sample were loaded onto a trap column (NanoLC Column, 3µ C18-CL, 350 µm x 0.5 mm; Eksigent) and desalted with 0.1% TFA at 2 µL/min during 10 min. Desalted samples were then loaded into an analytical column (LC Column, 3C18-CL-120, 3 µ, 120 Å 75 µm x 15 cm, Eksigent) equilibrated with 5% acetonitrile 0.1% formic acid. Elution was carried out with a linear gradient of 5 to 35% B in A for 60 min (A: 0.1% formic acid; B: acetonitrile, 0.1% formic acid) at a flow rate of 300 nL/min. Eluted samples were analyzed in a mass spectrometer (5600 TripleTOF, ABSCIEX, Massachusetts, USA). Samples were ionized applying 2.8 kV to the spray emitter. Analysis was carried out in a data-dependent mode. Survey MS1 scans were acquired from 350-1250 m/z for 250 ms. The quadrupole resolution was set to ‘UNIT’ for MS2 experiments, which were acquired at 100-1500 m/z for 50 ms in the high sensitivity mode.  Up to 25 ions were selected for fragmentation after each survey scan. Dynamic exclusion was set to 15 s.
ProteinPilot default parameters were used to generate a peak list from 5600 TripleTof wiff files. The Paragon algorithm was used to search the SwisProt database with the parameters: trypsin specificity and cys-alkylation with taxonomy restricted to human, and false discovery rate (FDR) correction for proteins. All eluted samples from all experiments were combined to create a spectra library for differential expression analysis.  Peak View 1.1. software (Sciex, Massachusetts, USA) was used to quantify the areas for all the peptides assigned in the library and the computed areas for proteins.
DOI: 10.17632/xh2g877zy5.1
title: A Roadmap to Integrating Cascading Risk into Local Resilience Strategies in Central Asia

description: This research developed a roadmap to integrate cascading risk into local resilience strategies in Nur-Sultan, Bishkek, and Dushanbe, the respective capitals of Kazakhstan, Kyrgyzstan, and Tajikistan. To do so, it met three core objectives: 
1) To examine stakeholder awareness and perceptions of cascading risk and interconnected failures.
2) To evaluate the extent to which cascading risk and interconnected failures are considered in existing strategies for resilience.  
3) To understand local capacities and priorities for actions to integrate cascading risk into local resilience strategies.  

It was hypothesised that if the integration of cascading risk and interconnected failures in existing resilience strategies was insufficient, then the results could outline: 
1) Inadequate awareness (consciousness) and understanding (knowledge) of cascading risk amongst key stakeholders.  
2) Acknowledgement of the relevance of cascading risk to resilience but limited local capacities to develop and implement strategies.  

Research followed a mixed methods approach comprising a questionnaire and semi-structured interviews. This dataset includes only the questionnaire data, to preserve anonymity. Data collection was carried out in July 2021 and targeted mixed stakeholders working in fields relating to disaster risk reduction, resilience, infrastructure, urban development, and urban policy in Central Asia. 

The questionnaire was designed in SurveyMonkey, comprising 20 questions across six pages including an introduction which stated the target audience and completion time (5–10 minutes). Judgment and snowball sampling identified participants. The questionnaire was made available in English and Russian and completed online on a self-administered basis, accessible via two web-links distributed via email and LinkedIn. Question 1 asked what location participants answers best related to, with an option for general/regional if participant knowledge was not specific to one locality.

The questionnaire received 115 responses, of which 55 were considered valid based on a completion rate of at least 50 percent. The high number of responses with low completion was considered a result of the questionnaire design and sampling method. Almost half of participants only answered Q1 (location). Subsequent questions were not visible until ‘next’ was clicked, and whilst the introduction stated the target audience, participants contacted through snowball sampling may have deemed their experience not relevant after reviewing questions in the following sections.  

Sheet 1 'Raw' is the raw data for the 115 responses collected. Sheet 2 'Accepted' includes the 55 responses that were accepted for this research, based on a completion rate of at least 50 percent. Sheet 3 'Accepted & Translated' includes the accepted responses, with the 15 Russian responses translated to English. Sheet 4 'Numerical' details the accepted responses, converted to numerical data where possible.
DOI: 10.17632/xh2g877zy5.2
title: A Way Forward to Integrating Cascading Risk into Local Resilience Strategies in Central Asia

description: This research developed a way forward to integrate cascading risk into local resilience strategies in Nur-Sultan, Bishkek, and Dushanbe, the respective capitals of Kazakhstan, Kyrgyzstan, and Tajikistan. To do so, it met three core objectives: 
1) To examine stakeholder awareness and perceptions of cascading risk and interconnected failures.
2) To evaluate the extent to which cascading risk and interconnected failures are considered in existing strategies for resilience.  
3) To understand local capacities and priorities for actions to integrate cascading risk into local resilience strategies.  

It was hypothesised that if the integration of cascading risk and interconnected failures in existing resilience strategies was insufficient, then the results could outline: 
1) Inadequate awareness (consciousness) and understanding (knowledge) of cascading risk amongst key stakeholders.  
2) Acknowledgement of the relevance of cascading risk to resilience but limited local capacities to develop and implement strategies.  

Research followed a mixed methods approach comprising a questionnaire and semi-structured interviews. This dataset includes only the questionnaire data, to preserve anonymity. Data collection was carried out in July 2021 and targeted mixed stakeholders working in fields relating to disaster risk reduction, resilience, infrastructure, urban development, and urban policy in Central Asia. 

The questionnaire was designed in SurveyMonkey, comprising 20 questions across six pages including an introduction which stated the target audience and completion time (5–10 minutes). Judgment and snowball sampling identified participants. The questionnaire was made available in English and Russian and completed online on a self-administered basis, accessible via two web-links distributed via email and LinkedIn. Question 1 asked what location participants answers best related to, with an option for general/regional if participant knowledge was not specific to one locality.

The questionnaire received 115 responses, of which 55 were considered valid based on a completion rate of at least 50 percent. The high number of responses with low completion was considered a result of the questionnaire design and sampling method. Almost half of participants only answered Q1 (location). Subsequent questions were not visible until ‘next’ was clicked, and whilst the introduction stated the target audience, participants contacted through snowball sampling may have deemed their experience not relevant after reviewing questions in the following sections.  

Sheet 1 'Raw' is the raw data for the 115 responses collected. Sheet 2 'Accepted' includes the 55 responses that were accepted for this research, based on a completion rate of at least 50 percent. Sheet 3 'Accepted & Translated' includes the accepted responses, with the 15 Russian responses translated to English. Sheet 4 'Numerical' details the accepted responses, converted to numerical data where possible.
DOI: 10.17632/g7n58mjkdh.1
title: Data generated

description: Complexes generated by molecular docking and molecular dynamics simulation from where the interaction analyzes were performed.
DOI: 10.17632/fg5y858j44.1
title: Cysteinylation of peroxiredoxin 2 upon incubation with BODIPY® FL L-Cystine

description: It has remained unknown how cells reduce cystine taken up from the extracellular space, which is a required step for further utilization of cysteine in key processes such as protein or glutathione synthesis. Here we show that the thioredoxin-related protein of 14 kDa (TRP14, encoded by TXNDC17) is the rate limiting enzyme for intracellular cystine reduction. When TRP14 is genetically knocked out, cysteine synthesis through the transsulfuration pathway becomes the major source of cysteine in human cells, and knockout of both pathways becomes lethal in C. elegans subjected to proteostatic stress. TRP14 can also reduce cysteinyl moieties on proteins, rescuing their activities as here shown with cysteinylated peroxiredoxin 2. Txndc17 knock-out mice were, surprisingly, protected in an acute pancreatitis model, concomitant with activation of Nrf2-driven antioxidant pathways and upregulation of transsulfuration. We conclude that TRP14 is the evolutionary conserved enzyme principally responsible for intracellular cystine reduction in C. elegans, mice and humans.			
Cysteinylation of recombinant human Prx2 (hPrx2)
Protein cysteinylation was achieved in vitro upon incubation of purified hPrx2 with BODIPY™ FL L-Cystine (Thermo Fisher, Massachusetts, USA). hPrx2 samples were pre-reduced with 1 mM DTT for 30 min at room temperature (RT), and then desalted using a Zeba™ Spin Desalting Column, 40 K MWKO, 0.5 mL (Thermo Fisher, Massachusetts, USA) and incubated with 100 µM BODIPY™ FL L-Cystine overnight at 4°C protected from light. After incubation, the remaining non-bound BODIPY™ FL L-Cystine was removed by desalting. Protein samples were loaded into a gel (Novex™ 4-20% Tris-Glycine, Invitrogen, California, USA) using non-reducing loading buffer (NuPAGE™LDS Sample Buffer, Invitrogen, California, USA) to conserve the mixed disulfide formed in the previous step. Electrophoretic separation was performed at a constant voltage of 200 V for 20-25 min while the gel was protected from light. Once resolved, the gel was developed in a UV transilluminator (ChemiDoc™ XRS+ Imaging System, Bio-Rad, California, USA) and Coomassie staining was later performed as loading control.
DOI: 10.17632/4zntcrby5d.1
title: Gut-mediated macrophage pyroptosis increases vulnerability to sepsis  during pregnancy. Chen et al.

description: (1A–1D) The cytokine and chemokine mRNAs in BALF (A), liver (B), kidney (C) and lung (D) from CLP mice. n=5-12. 

(2A, 2B) Bacterial load in cecal content and HE staining of liver, kidney and lung from ABX treated-mice. (2C-2F) The cytokine and chemokine mRNAs in PLF (C), liver (D), kidney (E), and lung (F) from ABX-pretreated pregnant and nonpregnant CLP mice. n=3-7. 

(3A-3D) Venn diagram comparing the shared genera in gut microbiome of donors and recipient mice. (3E, 3F) Plasma ALT, AST and Cr in microbiota-recipient mice. (3G, 3H) HE staining of liver, kidney, and lung from microbiota-recipient mice. (3I, 3J) HE staining of liver, kidney, and lung from septic recipient mice. (3K, 3L) The percentage of CD11b+ cells in the lung from septic recipient mice. (3M) The cytokine and chemokine mRNAs in PLF from septic recipient mice. n=4-18.

(4A–4E) The cytokine and chemokine mRNAs in PLF (A), BALF (B), liver (C), kidney (D), and lung (E) from septic recipient mice. n=6-9.

(5A-5D) Alpha diversity and abundance of gut microbiota in pregnant and nonpregnant individuals. (5E) Heatmap for cecal metabolites from pregnant and nonpregnant mice. (5F) Genome map circular view of P. merdae. n=8-42.

(6A-6J) The percentages of macrophages and neutrophils in PLF from nonpregnant and pregnant septic mice, ABX-pretreated septic mice and septic recipient mice. n=6-9. 

(7A-7C) The percentages of lymphocytes in PLF of nonpregnant and pregnant septic mice, ABX-pretreated septic mice and septic recipient mice. (7D-7G) The percentages of monocytes and neutrophils in blood of pregnant and nonpregnant mice, FMT-recipient mice with P. aeruginosa (PAE) infection. n=6-8.

(8A-8J) The percentages of monocytes and neutrophils in blood of nonpregnant and pregnant septic mice, ABX-pretreated septic mice and septic recipient mice. (8K, 8L) The percentages of monocytes and neutrophils in blood of septic recipient mice. FMT was performed in germ-free mice. n=4-8. 

(9A-9C) Flow-cytometric enumeration of macrophages in PLF from nonpregnant and pregnant septic mice, ABX-pretreated mice and septic recipient mice. (9D) The percentages of macrophages in PLF of CLP mice treated with ferrostatin-1 (10 mg/kg), necrostatin-1 (1.65 mg/kg), or Z-DEVD-FMK (8 mg/kg). (9E, 9F) Transcriptomic analysis of LPS plus ATP treated-BMDMs with or without FMN treatment. (9G–9I) The expression of p20 of caspase1 and N-terminus of GSDMD. After priming with LPS for 2 h, BMDMs were treated with FMN for an additional 2 h, in the presence or absence of VX765 (50 μM), which was followed by triggering with 5 mM ATP for 30 min. n=3-6. 

(10A) Proteomic analysis of LPS plus ATP-treated BMDMs with or without FMN treatment. (10B, 10C) The expression of hnRNPUL2 in BMDMs transfected with siRNA targeting hnRNPUL2. (10D) A docking model showing the interactions between FMN and hnRNPUL2. (10E) The mRNA of hnRNPUL2 in mice subjected to injection of AAV9-hnRNPUL2. n=3-8. *p<0.05 by two-tailed unpaired t-test.
DOI: 10.17632/5f3mszkykh.1
title: Double launch

description: Double launch of radiosoundes for detecting of oscillations in atmosphere
DOI: 10.5285/efcc09dc-ed05-775c-e053-6c86abc0bb49
title: Seaglider data from the Indian Ocean as part of the Equatorial Line Observations (ELO), January-April 2019.

description: The data included in this publication are from conductivity, temperature, and pressure sensors attached to two Seagliders deployed near Christmas Island in the Indian Ocean (10.47 °S, 105.73 °E) on the 23rd of January 2019. They travelled to two waypoints in the direction of the coast of Java; Seaglider SG641 arrived at waypoint ELOX1 (10.166 °S 105.9 °E) on the 25th January 2019 and SG537 at waypoint ELOX2 (9.25 °S 106.533 °E) on 30th of January 2019. They then stayed at their waypoints until their final dives on the 4th of April 2019 and 13th of April 2019, respectively. Each glider dataset was processed using the UEA Seaglider toolbox. The corrections did not remove all uncertainty from the salinity data in the thermocline region, therefore, salinity and other derived variables were set to null if still not considered trustworthy. The sampling interval varied throughout the deployment for the SG537 with a minimum sampling rate of 4-5 seconds. The measurements were carried out in succession and the time stamp corresponds to the first measurement of each cycle. The data from the SG641, a scicon glider, was interpolated to 1 second intervals. Depth estimates for each different sensor are also provided. Both Seagliders are from the University of East Anglia (UEA), UK glider facility, and were deployed and piloted by UEA and associated personnel. These gliders were deployed as part of the Equatorial Line Observations (ELO) project, whose primary objective was to understand ocean-atmosphere interactions associated with atmospheric convectively coupled equatorial waves (CCEWs) and the Madden-Julian Oscillation (MJO). The ELO project is funded jointly by the Natural Environmental Research Council, UK (grant reference NE/R012431/1), and the National Science Foundation, USA (grant reference 1724741).
DOI: 10.5281/zenodo.7463835
title: Data for: The structure of evolutionary model space for proteins across the tree of life

description: Supporting data for "The structure of evolutionary model space for proteins across the tree of life," submitted by GE Scolaro and EL Braun. The data files correspond to three gzipped tarballs including protein multiple sequence alignments, PAML format models of protein evolution, and model fit data; see included README for details.
DOI: 10.5281/zenodo.7463834
title: Data for: The structure of evolutionary model space for proteins across the tree of life

description: Supporting data for "The structure of evolutionary model space for proteins across the tree of life," submitted by GE Scolaro and EL Braun. The data files correspond to three gzipped tarballs including protein multiple sequence alignments, PAML format models of protein evolution, and model fit data; see included README for details.
DOI: 10.6084/m9.figshare.21758534
title: Supplementary docs.xlsx

description: Gut microbiota data
DOI: 10.6084/m9.figshare.21758534.v1
title: Supplementary docs.xlsx

description: Gut microbiota data
DOI: 10.5281/zenodo.7133462
title: Supplementary Data for "Earth's Volatile Depletion Trend Consistent with a High-Energy Moon-Forming Impact"

description: Vaporization statistics for pyrolite melts containing In, Cd, S, Zn and Hg. Please refer to "Computational Methods" of the main text for details of the simulations and Supplementary Table 2 for the stoichiometry of the melts.
DOI: 10.5281/zenodo.7133461
title: Supplementary Data for "Earth's Volatile Depletion Trend Consistent with a High-Energy Moon-Forming Impact"

description: Vaporization statistics for pyrolite melts containing In, Cd, S, Zn and Hg. Please refer to "Computational Methods" of the main text for details of the simulations and Supplementary Table 2 for the stoichiometry of the melts.
DOI: 10.23708/aexqld
title: Microplastic concentrations in urban lake environments of Hanoi and rivers in Bac Ninh, Northern Vietnam, under COMPOSE (2019-2021) and CounterMEASUREII (2021-2022) projects

description: Microplastic (300-5000µm) concentrations were measured in Ho Tay lake, Yen So lake, Bay Mau lake and Hoan Kiem lake of Hanoi, and Cam river and Thai Binh river of Bac Ninh province, Northern Vietnam, under the COMPOSE project (2019-2021). Microplastic were sampled using a 80µm mesh size net from a local boat. The samples were extracted in the laboratory using enzymatic digestion, NaCl density separation and were filtrated on GF-A filter. Then microplastic were observed on stereomicroscope and length, area, color were measured for fragments, line and circle. Concentrations are given in total microplastic per m3, fragment per m3 and fibers per m3. The sampling dates are October 2019, February 2020, July 2020, October 2020, January 2021, October 2021 and January 2022
DOI: 10.23708/d6skqe
title: Microplastic concentrations in riverine and lake environments of Da Nang province and Quang Nam provinces, Central Vietnam, under COMPOSE (2019-2021) and CounterMEASUREII (2021-2022) projects

description: Microplastic (300-5000µm) concentrations were measured in the Central Park Lake, Hoa Phu Lake and Han River environments of Da Nang city, and in the Thu Bon River and Cu De River of Quang Nam province Central Vietnam, under the COMPOSE project (2019-2021)and the CounterMEASUREII project (2021-2022). Microplastic were sampled using a 80µm mesh size net from a local boat. The samples were extracted in the laboratory using enzymatic digestion, NaCl density separation and were filtrated on GF-A filter. Then microplastic were observed on stereomicroscope and length, area, color were measured for fragments, line and circle. Concentrations are given in total microplastic per m3, fragment per m3 and fibers per m3. The sampling dates are October 2019, January 2020, May 2020, July 2020, October 2020, January 2021 and March 2021 under COMPOSE Project and October 2021 and January 2022 under the CounterMEASUREII project.
DOI: 10.5517/ccdc.csd.cc285kjk
title: CCDC 2090718: Experimental Crystal Structure Determination

description: Related Article: Xing Peng, Meng-Meng Zheng, Pei Qin, Xiao-Song Xue, Fa-Guang Zhang, Jun-An Ma|2022|Org.Chem.Front.|10|74|doi:10.1039/D2QO01585D
description: Related Article: Xing Peng|2021|CSD Communication|||
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.cc285kkl
title: CCDC 2090719: Experimental Crystal Structure Determination

description: Related Article: Xing Peng, Meng-Meng Zheng, Pei Qin, Xiao-Song Xue, Fa-Guang Zhang, Jun-An Ma|2022|Org.Chem.Front.|10|74|doi:10.1039/D2QO01585D
description: Related Article: Xing Peng|2021|CSD Communication|||
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.cc285klm
title: CCDC 2090720: Experimental Crystal Structure Determination

description: Related Article: Xing Peng, Meng-Meng Zheng, Pei Qin, Xiao-Song Xue, Fa-Guang Zhang, Jun-An Ma|2022|Org.Chem.Front.|10|74|doi:10.1039/D2QO01585D
description: Related Article: Xing Peng|2021|CSD Communication|||
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.