cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/9sxs2gg2jh.1
title: Systematic Fluoroscopic-Echocardiographic Fusion Imaging Protocol for Transcatheter Edge-to-Edge Mitral Valve Repair Intraprocedural Monitoring.

description: DOI: 10.1016/j.echo.2021.01.010
Fluoroscopic-echocardiographic fusion imaging (FI) is able to acquire imaging data from both fluoroscopy and transesophageal images and co-register and align them in the 3D space and time by putting onto the same coordinate system. The aim of this single-center study was to test and validate a FI protocol for intraprocedural monitoring of transcatheter edge-to-edge mitral valve repair and assess its clinical usefulness. Eighty patients underwent MitraClip implantation using FI guidance (FI+) were compared with the last 80 patients before FI introduction. 
The study firstly describes the systematic use of an FI protocol for intraprocedural guidance during transcatheter edge-to-edge mitral valve repair, demonstrating a reduction in fluoroscopy time and an improvement in procedural success in a population with a high prevalence of challenging mitral anatomy for percutaneous repair.
DOI: 10.5286/isis.e.rb2210128-1
title: Elucidating the structure of DNA linkers tethered to electrode surfaces

description: Recent results have pointed to an unexpected role of DNA as a possible agent for electron transfer. This could be crucial in understanding the purpose of DNA in bacterial biofilms, in which electron transfer from the cells to external acceptors (such as an electrode surface) is essential for the wellbeing and survival of the biofilm. However, the ability of DNA to conduct is thought to be strongly linked to its structure, and it is unclear how this may be affected by external conditions such as applied potential, or the presence and binding of small redox molecules. This proposal aims to study tethered DNA layers at electrode surfaces to model these more complex systems. Neutron reflectometry will allow us an unprecedented opportunity to monitor the structure and how it changes in situ during the electron-transfer processes of interest.
DOI: 10.6084/m9.figshare.19152908
title: Data collection sheets

description: Data collection sheets
DOI: 10.5286/isis.e.rb2210309
title: Determination of the magnetic structure in piezomagnetic Mn3SnN thin films using neutron diffraction

description: The family of manganese antiperovskites with the formula Mn3AN (A = Sn, Ni, Ga…) have recently attracted much attention due to the range of interesting properties they display due to geometric magnetic frustration, such as barocaloric and Invar effects, baromagnetism and temperature independent resistivity. We have recently experimentally determined a giant piezomagnetic effect (PME) in Mn3NiN thin films, which provides a novel method for control of magnetism via electric field in spintronics applications, with several advantages over current magnetostriction-based devices as complete reversal of the magnetisation can be achieved. A 4-fold larger PME is expected in Mn3SnN and here we propose to use WISH to determine the magnetic structure in Mn3SnN thin films. The results will guide the engineering of Mn3SnN thin films to optimise the PME for spintronics applications.
DOI: 10.5286/isis.e.rb2210309-1
title: Determination of the magnetic structure in piezomagnetic Mn3SnN thin films using neutron diffraction

description: The family of manganese antiperovskites with the formula Mn3AN (A = Sn, Ni, Ga…) have recently attracted much attention due to the range of interesting properties they display due to geometric magnetic frustration, such as barocaloric and Invar effects, baromagnetism and temperature independent resistivity. We have recently experimentally determined a giant piezomagnetic effect (PME) in Mn3NiN thin films, which provides a novel method for control of magnetism via electric field in spintronics applications, with several advantages over current magnetostriction-based devices as complete reversal of the magnetisation can be achieved. A 4-fold larger PME is expected in Mn3SnN and here we propose to use WISH to determine the magnetic structure in Mn3SnN thin films. The results will guide the engineering of Mn3SnN thin films to optimise the PME for spintronics applications.
DOI: 10.25345/c59w08
title: MassIVE MSV000088811 - Cysteine residues are responsible for the sulfurous off-flavor formed in heated whey protein solutions
title: Odor-active volatile sulfur compounds are formed in heated food protein systems. In the present study, hydrogen sulfide (H2S) was found to be the most abundant sulfur volatile in whey protein systems (whey protein isolate (WPI), a whey model system and single whey proteins) by Gas Chromatography-Flame Photometric Detector (GC-FPD) analysis after different heat treatments (60-90 C for 10 min, 90 C for 120 min and a UHT-like condition). Site-specific LC-MS/MS-based proteomic analysis was conducted to monitor desulfurization reactions in these protein systems to investigate the mechanism of H2S formation in heated WPI. H2S was detected in WPI after heating at 90 C for 10 min, and significantly increased at higher heat load (90 C for 120 min and the UHT treatment), which revealed the temperature- and time-dependence of heat-induced H2S generation in WPI. Cysteine (Cys) residues from beta-lactoglobulin were found to be responsible for the formation of H2S in heated WPI, presumably via beta-elimination.
DOI: 10.5281/zenodo.5940218
title: JACUSA2 - use cases: 1 - 3

description: <strong>Supplementary data</strong> for use cases presented in: RNA modification mapping with JACUSA2<br> Michael Piechotta, Qi Wang, Janine Altmüller, Christoph Dieterich<br> doi: https://doi.org/10.1101/2021.07.02.450888 <strong>Use case 1: m6A mapping by MazF</strong> MazF_vs_cond2_FTO_rtarrest_plain_result.out.gz (JACUSA2 output) Cutoff01_MazF_vs_cond2_FTO_rtarrest_plain_result.out.gz (filtered by pvalue &lt;=0.1) MazF (BAM files): SRR8450805_STARmapping_uniq_rmdup.bam SRR8450807_STARmapping_uniq_rmdup.bam SRR8450809_STARmapping_uniq_rmdup.bam FTO: (BAM files): SRR8450806_STARmapping_uniq_rmdup.bam SRR8450808_STARmapping_uniq_rmdup.bam SRR8450810_STARmapping_uniq_rmdup.bam <strong>Use case 2: </strong><strong>DART-seq</strong> APOBEC1YTH_APOBEC1YTHmut_call2_result.out.gz (JACUSA2 output) APOBEC1YTH (BAM files): SRR9940470_STARmapping_uniq_rmdup.bam SRR9940471_STARmapping_uniq_rmdup.bam SRR9940472_STARmapping_uniq_rmdup.bam APOBEC1YTHmut (BAM files): SRR9940474_STARmapping_uniq_rmdup.bam SRR9940475_STARmapping_uniq_rmdup.bam SRR9940476_STARmapping_uniq_rmdup.bam <strong>Use case 3: Nanopore</strong> WT_vs_KO_call2_result.out.gz & WT100_vs_WT0_call2_result.out.gz (JACUSA2 output) WT (BAM files): HEK293T-WT-rep2.bam HEK293T-WT-rep3.bam HEK293T-WT-100-rep1.bam HEK293T-WT-100-rep2.bam HEK293T-WT-100-rep3.bam KO (BAM files): HEK293T-KO-rep2.bam HEK293T-KO-rep3.bam HEK293T-WT-0-rep1.bam HEK293T-WT-0-rep2.bam [1] Zhang, Z., Chen, L.-Q., Zhao, Y.-L., Yang, C.-G., Roundtree, I.A., Zhang, Z., Ren, J., Xie, W., He, C., Luo, G.-Z.: Single-base mapping of m6a by an antibody-independent method. Science advances 5, 0250 (2019). doi:10.1126/sciadv.aax0250 [2] Garcia-Campos, M.A., Edelheit, S., Toth, U., Safra, M., Shachar, R., Viukov, S., Winkler, R., Nir, R., Lasman, L., Brandis, A., Hanna, J.H., Rossmanith, W., Schwartz, S.: Deciphering the ”m6a code” via antibody-independent quantitative profiling. Cell 178, 731–74716 (2019). doi:10.1016/j.cell.2019.06.013 [3] Meyer, K.D.: Dart-seq: an antibody-free method for global m6a detection. Nature methods 16, 1275–1280 (2019). doi:10.1038/s41592-019- 0570-0 [4] Pratanwanich, P.N., Yao, F., Chen, Y., Koh, C.W.Q., Hendra, C., Poon, P., Goh, Y.T., Yap, P.M.L., Yuan, C.J., Chng, 6 made available under aCC-BY-NC-ND 4.0 International license. (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is bioRxiv preprint doi: https://doi.org/10.1101/2021.07.02.450888; this version posted July 4, 2021. The copyright holder for this preprint W.J., Ng, S., Thiery, A., Goh, W.S.S., G¨oke, J.: Detection of differential rna modifications from direct rna sequencing of human cell lines. bioRxiv (2020). doi:10.1101/2020.06.18.160010. https://www.biorxiv.org/content/early/2020/06/20/2020.06.18.160010.full.pdf
DOI: 10.5281/zenodo.5930728
title: JACUSA2 - use cases: 1 - 3

description: <strong>Supplementary data</strong> for use cases presented in: RNA modification mapping with JACUSA2<br> Michael Piechotta, Qi Wang, Janine Altmüller, Christoph Dieterich<br> doi: https://doi.org/10.1101/2021.07.02.450888 <strong>Use case 1: m6A mapping by MazF</strong> MazF_vs_cond2_FTO_rtarrest_plain_result.out.gz (JACUSA2 output) Cutoff01_MazF_vs_cond2_FTO_rtarrest_plain_result.out.gz (filtered by pvalue &lt;=0.1) MazF (BAM files): SRR8450805_STARmapping_uniq_rmdup.bam SRR8450807_STARmapping_uniq_rmdup.bam SRR8450809_STARmapping_uniq_rmdup.bam FTO: (BAM files): SRR8450806_STARmapping_uniq_rmdup.bam SRR8450808_STARmapping_uniq_rmdup.bam SRR8450810_STARmapping_uniq_rmdup.bam <strong>Use case 2: </strong><strong>DART-seq</strong> APOBEC1YTH_APOBEC1YTHmut_call2_result.out.gz (JACUSA2 output) APOBEC1YTH (BAM files): SRR9940470_STARmapping_uniq_rmdup.bam SRR9940471_STARmapping_uniq_rmdup.bam SRR9940472_STARmapping_uniq_rmdup.bam APOBEC1YTHmut (BAM files): SRR9940474_STARmapping_uniq_rmdup.bam SRR9940475_STARmapping_uniq_rmdup.bam SRR9940476_STARmapping_uniq_rmdup.bam <strong>Use case 3: Nanopore</strong> WT_vs_KO_call2_result.out.gz & WT100_vs_WT0_call2_result.out.gz (JACUSA2 output) WT (BAM files): HEK293T-WT-rep2.bam HEK293T-WT-rep3.bam HEK293T-WT-100-rep1.bam HEK293T-WT-100-rep2.bam HEK293T-WT-100-rep3.bam KO (BAM files): HEK293T-KO-rep2.bam HEK293T-KO-rep3.bam HEK293T-WT-0-rep1.bam HEK293T-WT-0-rep2.bam [1] Zhang, Z., Chen, L.-Q., Zhao, Y.-L., Yang, C.-G., Roundtree, I.A., Zhang, Z., Ren, J., Xie, W., He, C., Luo, G.-Z.: Single-base mapping of m6a by an antibody-independent method. Science advances 5, 0250 (2019). doi:10.1126/sciadv.aax0250 [2] Garcia-Campos, M.A., Edelheit, S., Toth, U., Safra, M., Shachar, R., Viukov, S., Winkler, R., Nir, R., Lasman, L., Brandis, A., Hanna, J.H., Rossmanith, W., Schwartz, S.: Deciphering the ”m6a code” via antibody-independent quantitative profiling. Cell 178, 731–74716 (2019). doi:10.1016/j.cell.2019.06.013 [3] Meyer, K.D.: Dart-seq: an antibody-free method for global m6a detection. Nature methods 16, 1275–1280 (2019). doi:10.1038/s41592-019- 0570-0 [4] Pratanwanich, P.N., Yao, F., Chen, Y., Koh, C.W.Q., Hendra, C., Poon, P., Goh, Y.T., Yap, P.M.L., Yuan, C.J., Chng, 6 made available under aCC-BY-NC-ND 4.0 International license. (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is bioRxiv preprint doi: https://doi.org/10.1101/2021.07.02.450888; this version posted July 4, 2021. The copyright holder for this preprint W.J., Ng, S., Thiery, A., Goh, W.S.S., G¨oke, J.: Detection of differential rna modifications from direct rna sequencing of human cell lines. bioRxiv (2020). doi:10.1101/2020.06.18.160010. https://www.biorxiv.org/content/early/2020/06/20/2020.06.18.160010.full.pdf
DOI: 10.5281/zenodo.6003687
title: uprolls2022-206

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.6003686
title: uprolls2022-206

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5975509
title: uprolls2022-180

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5975508
title: uprolls2022-180

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.6084/m9.figshare.807681.v9
title: Supervision and guidance during the process of essay writing in the life sciences

description: Many years of supervision in essay writing have led to a strategy that has worked for many students and is based on a clearly structured schedule of events. It is highly effective, saves the student's and supervisor's time, and it provides opportunities to give high quality feedback and detailed guidance at appropriate stages of the writing process. Any feedback given during this process is cost neutral for the student, i.e. will not be considered when deciding the final mark, since the student performs the final write-up phase independently and has therefore sufficient opportunity to show his/her abilities and understanding. Notably, the structured approach applied here presents a transferable skill that will improve the student's performance also during exam essay writing.
DOI: 10.5281/zenodo.5966325
title: uprolls2022-78

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5966324
title: uprolls2022-78

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5955824
title: uprolls2022-43

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5955823
title: uprolls2022-43

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5954232
title: uprolls2022-199

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5954231
title: uprolls2022-199

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5953019
title: uprolls2022-245

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5953018
title: uprolls2022-245

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.6084/m9.figshare.807681
title: Supervision and guidance during the process of essay writing in the life sciences

description: Many years of supervision in essay writing have led to a strategy that has worked for many students and is based on a clearly structured schedule of events. It is highly effective, saves the student's and supervisor's time, and it provides opportunities to give high quality feedback and detailed guidance at appropriate stages of the writing process. Any feedback given during this process is cost neutral for the student, i.e. will not be considered when deciding the final mark, since the student performs the final write-up phase independently and has therefore sufficient opportunity to show his/her abilities and understanding. Notably, the structured approach applied here presents a transferable skill that will improve the student's performance also during exam essay writing.
DOI: 10.25678/0005w3
title: Data for SNSF Spark grant CRSK-3_190920: CRISPR-Cas9 gene editing to dissect the molecular mechanisms of rainbow trout antimicrobial peptides (AMPs)

description: Antimicrobial peptides (AMPs) are small amphipathic molecules (10-50 amino acids) that are produced by all life forms, from prokaryotes to humans, and are involved in the protection of the host against infections. Fish AMPs have rapidly captured the attention as novel drug candidates in aquaculture thanks to their broad antimicrobial activity against both Gram-positive and Gram-negative bacteria, as well as fungi, parasites and viruses. In addition, their low propensity for the development of bacterial resistance makes AMPs a promising therapeutic alternative to the excessive and indiscriminate use of antibiotics in veterinary health.The molecular mechanism how AMPs exert their antimicrobial activity in fish cells is not fully understood. To overcome this lack of knowledge, we seek to identify the functional domains of AMPs in a rainbow trout (Oncorhynchus mykiss) gut cell line (RTgutGC). To achieve this aim, we propose to utilize an episomal CRISPR-Cas9 system to genetically screen for such functional AMP domains. The resulting gene-edited cell lines will be challenged with bacterial pathogens, such as Streptococcusdysgalactiae and Yersinia ruckeri and the ability of these gene-edited cell lines to overcome the bacterial burden will be assessed. Moreover, a time-course transcriptome (RNA-seq) and proteome (mass spectrometry) analysis of RTgutGC cells that express AMPs upon exposure to synthetic bacterial molecules will be conducted.Taking together, these findings will give us the opportunity to shed light on the molecular mechanisms that drive the therapeutic effect of AMPs in fish cells and to gain a global view on the molecular pathways that are affected when AMPs are expressed.
DOI: 10.5281/zenodo.5951399
title: uprolls2022-28

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5951398
title: uprolls2022-28

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5950708
title: uprolls2022-131

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5950707
title: uprolls2022-131

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5949571
title: uprolls2022-141

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5949570
title: uprolls2022-141

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5949242
title: uprolls2022-164

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5949241
title: uprolls2022-164

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5948766
title: uprolls2022-84

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5948765
title: uprolls2022-84

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5948522
title: uprolls2022-51

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5948521
title: uprolls2022-51

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5948965
title: uprolls2022-88

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5948964
title: uprolls2022-88

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5946617
title: uprolls2022-107

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022
DOI: 10.5281/zenodo.5946616
title: uprolls2022-107

description: This deposit serves as a long-term archive for the unprocessed raw data behind the uprolls2022 table in my comprehensive dataset on religion and politics in India, which is available at https://github.com/raphael-susewind/india-religion-politics/tree/master/uprolls2022