cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12038670
title: sgRNA library with comprehensive mismatch

description: The library of two sgRNAs with the comprehensive single or double mismatches. See Thesis chapter 5.
DOI: 10.6084/m9.figshare.12038670.v1
title: sgRNA library with comprehensive mismatch

description: The library of two sgRNAs with the comprehensive single or double mismatches. See Thesis chapter 5.
DOI: 10.6084/m9.figshare.12038829.v3
title: Figure data used in "Smart renewable electricity portfolios in West Africa"

description: This is the Source Data for the Figures 1-6 plotted in the main text of the publication "Smart renewable electricity portfolios in West Africa" by Sterl et al. (2020).
DOI: 10.6084/m9.figshare.12038829.v4
title: Figure data used in "Smart renewable electricity portfolios in West Africa"

description: This is the Source Data for the Figures 1-6 plotted in the main text of the publication "Smart renewable electricity portfolios in West Africa" by Sterl et al. (2020).
DOI: 10.6084/m9.figshare.12038652
title: Glycogen synthase kinase (GSK) 3 in pregnancy and parturition: a systematic review of literature

description: <b>Introduction:</b> Multiple factors and pathways have been reported as critical machineries for cell differentiation and survival during pregnancy; a number of them involve glycogen synthase kinase (GSK) 3a/β. Several reports on GSK3's functional role exist; however, the specific role of GSK3 in reproductive tissues and its contribution to normal or abnormal parturition are still unclear. To fill this knowledge gap, a systematic review of literature was conducted to better understand the functional role of GSK3 in various intrauterine tissues during implantation, pregnancy, and parturition. <b>Methods:</b> We conducted a systematic review of literature on GSK3's expression and function reported between 1980 and 2017 in reproductive tissues during pregnancy using three electronic databases (Web of Science, Medline, and ClinicalTrials.gov). Study selection, data extraction, quality assessment and analyses were performed in duplicate by two independent reviewers. <b>Results:</b> A total of 738 citations were identified; 80 were selected for full text evaluation and 25 were included for final review. GSK3's regulation and function were mostly studied in tissues and cells from placentas (12), fetuses (8), uteruses (6), and ovaries (2). GSK3 is primarily reported as a downstream responder of protein kinase B (AKT)-, Wnt-, and reactive oxygen species (ROS)-related pathways where it plays a critical role in cell survival and growth in reproductive tissues. <b>Conclusions:</b> Though GSK3 has been functionally linked to a number of biological processes in reproductive tissues, it has primarily been studied as a secondary signaler of various conserved cell signaling pathways. Lack of scientific rigor in studying GSK3's role in reproductive tissues makes this molecule's function still obscure. No studies have reported GSK3 in the cervix, and very few reports exist in myometrium and decidua. This systematic review suggests more functional and mechanistic studies focusing on GSK3 need to be conducted in reproductive biology.
DOI: 10.6084/m9.figshare.12038649
title: Highly active sgRNAs for E. coli

description: The best sgRNA for each gene, RBS and promoter in E. coli
DOI: 10.6084/m9.figshare.12038652.v1
title: Glycogen synthase kinase (GSK) 3 in pregnancy and parturition: a systematic review of literature

description: <b>Introduction:</b> Multiple factors and pathways have been reported as critical machineries for cell differentiation and survival during pregnancy; a number of them involve glycogen synthase kinase (GSK) 3a/β. Several reports on GSK3's functional role exist; however, the specific role of GSK3 in reproductive tissues and its contribution to normal or abnormal parturition are still unclear. To fill this knowledge gap, a systematic review of literature was conducted to better understand the functional role of GSK3 in various intrauterine tissues during implantation, pregnancy, and parturition. <b>Methods:</b> We conducted a systematic review of literature on GSK3's expression and function reported between 1980 and 2017 in reproductive tissues during pregnancy using three electronic databases (Web of Science, Medline, and ClinicalTrials.gov). Study selection, data extraction, quality assessment and analyses were performed in duplicate by two independent reviewers. <b>Results:</b> A total of 738 citations were identified; 80 were selected for full text evaluation and 25 were included for final review. GSK3's regulation and function were mostly studied in tissues and cells from placentas (12), fetuses (8), uteruses (6), and ovaries (2). GSK3 is primarily reported as a downstream responder of protein kinase B (AKT)-, Wnt-, and reactive oxygen species (ROS)-related pathways where it plays a critical role in cell survival and growth in reproductive tissues. <b>Conclusions:</b> Though GSK3 has been functionally linked to a number of biological processes in reproductive tissues, it has primarily been studied as a secondary signaler of various conserved cell signaling pathways. Lack of scientific rigor in studying GSK3's role in reproductive tissues makes this molecule's function still obscure. No studies have reported GSK3 in the cervix, and very few reports exist in myometrium and decidua. This systematic review suggests more functional and mechanistic studies focusing on GSK3 need to be conducted in reproductive biology.
DOI: 10.6084/m9.figshare.12038646
title: Raw sgRNA activity obtained from screen

description: Raw sgRNA activity for the genome-wide library, see Thesis chapter 3.
DOI: 10.6084/m9.figshare.12038634
title: sgRNA dataset used in machine learning

description: Two high-quality sgRNA activity datasets (Cas9 and eSpCas9,) used in the machine learning experiments (see Thesis chapter 4).
DOI: 10.6084/m9.figshare.12038646.v1
title: Raw sgRNA activity obtained from screen

description: Raw sgRNA activity for the genome-wide library, see Thesis chapter 3.
DOI: 10.6084/m9.figshare.12038598
title: Supplementary Material for: Persistence of Intraluminal Thrombus Makes Saccular Aneurysm More Biologically Active than Fusiform in an Experimental Rat Model

description: <b><i>Introduction:</i></b> Saccular aneurysms are thought to have a worse prognosis than fusiform aneurysms in humans, due to hemodynamic reasons. However, data comparing hemodynamic and biology in saccular and fusiform aneurysms are lacking. The main objective was to evaluate the impact of aneurysm morphology on intra-luminal thrombus (ILT) formation and activity. <b><i>Methods:</i></b> Forty Lewis rats were ran­domly divided into 2 groups of 20: “saccular” (Group A) and “fusiform” (Group B) aneurysms. Decellularized thoracic aortas from guinea pigs were xenografted to create saccular or fusiform aneurysms. Final imaging evaluation of the aneurysms was carried out during the third week, by quantitative Doppler ultrasound and magnetic resonance imaging. Assays of myeloperoxidase (MPO), platelet factor 4 (PF4), advanced oxidation protein products (AOPPs) iron and matrix metallopeptidase-9 (MMP-9) were performed as biological criteria. <b><i>Results:</i></b> Quantitatively, saccular aneurysms are characterized by a more thicker ILT, lower inflow velocities and more important relative backflow velocities as compared to fusiform aneurysms. Compared to fusiform, saccular aneurysms released significantly more MPO (<i>p</i> = 0.004), PF4 (<i>p</i> = 0.02), AOPPs (<i>p</i> &lt; 0.002), iron (<i>p</i> &lt; 0.0001) and MMP-9 (<i>p</i> &lt; 0.04). <b><i>Conclusion:</i></b> Experimental saccular and fusiform aneurysms show differential specific hemodynamics, which seem to impact the histology and the biology of the ILT in each type of aneurysm.
DOI: 10.6084/m9.figshare.12038565
title: Supplementary Material for: Evaluating a Clinical Pathway in Laparoscopic Cholecystectomy: Effective in Reducing Complications? A Propensity Score Matching Analysis

description: <b><i>Background:</i></b> Care pathways are primarily aimed at decreasing length of hospital stay (LOS) and preventing unnecessary costs while maintaining or improving the quality of care. In laparoscopic cholecystectomy, there is insufficient evidence for proving an impact upon postoperative complications. <b><i>Methods:</i></b> In this retrospective study, logistic regression was used to calculate a propensity score, and, after carrying out 1:1 nearest-neighbor matching, 296 patients were analyzed in both groups with regard to postoperative complications using the Clavien-Dindo classification system as a primary aim. In addition, secondary aims were LOS, compliance to care, and deviation from the care pathway with respect to patient discharge. Relative risk of the primary outcome was calculated and compared with the e-value as sensitivity testing approach. <b><i>Results:</i></b> Due to the mandatory part of the care pathway, patient record compliance was 100%. Deviation from the care pathway with respect to the planned patient discharge on postoperative day 2 was noted in 16% of the cases. After adjustment for potential factors, the relative risk when comparing Clavien-Dindo complication grades 0 versus 1–4 is 1.64 (95% CI 0.87–3.11), which did not reach significance (<i>p</i> = 0.127). After matching, LOS lasted 3.69 days without and 3.26 days with the care pathway, respectively. <b><i>Conclusions:</i></b> Against the background of already implemented structured standard operation procedures, a care pathway is not able to reduce postoperative complications. Nevertheless, we consider our clinical pathway a highly valuable tool for the interdisciplinary management of patient hospitalization under the supervision of experienced specialized surgeons.
DOI: 10.6084/m9.figshare.12038565.v1
title: Supplementary Material for: Evaluating a Clinical Pathway in Laparoscopic Cholecystectomy: Effective in Reducing Complications? A Propensity Score Matching Analysis

description: <b><i>Background:</i></b> Care pathways are primarily aimed at decreasing length of hospital stay (LOS) and preventing unnecessary costs while maintaining or improving the quality of care. In laparoscopic cholecystectomy, there is insufficient evidence for proving an impact upon postoperative complications. <b><i>Methods:</i></b> In this retrospective study, logistic regression was used to calculate a propensity score, and, after carrying out 1:1 nearest-neighbor matching, 296 patients were analyzed in both groups with regard to postoperative complications using the Clavien-Dindo classification system as a primary aim. In addition, secondary aims were LOS, compliance to care, and deviation from the care pathway with respect to patient discharge. Relative risk of the primary outcome was calculated and compared with the e-value as sensitivity testing approach. <b><i>Results:</i></b> Due to the mandatory part of the care pathway, patient record compliance was 100%. Deviation from the care pathway with respect to the planned patient discharge on postoperative day 2 was noted in 16% of the cases. After adjustment for potential factors, the relative risk when comparing Clavien-Dindo complication grades 0 versus 1–4 is 1.64 (95% CI 0.87–3.11), which did not reach significance (<i>p</i> = 0.127). After matching, LOS lasted 3.69 days without and 3.26 days with the care pathway, respectively. <b><i>Conclusions:</i></b> Against the background of already implemented structured standard operation procedures, a care pathway is not able to reduce postoperative complications. Nevertheless, we consider our clinical pathway a highly valuable tool for the interdisciplinary management of patient hospitalization under the supervision of experienced specialized surgeons.
DOI: 10.6084/m9.figshare.12038286
title: Additional file 5 of Quantitative proteomic, physiological and biochemical analysis of cotyledon, embryo, leaf and pod reveals the effects of high temperature and humidity stress on seed vigor formation in soybean

description: Additional file 5 : S1- S6. Differentially abundant proteins in cotyledons, embryos, and leaves between the stressed and control in soybean cvs. Ningzhen No. 1 and Xiangdou No. 3, respectively. S7- S9. Differentially abundant proteins in cotyledons, embryos, and leaves between the soybean cv. Ningzhen No. 1 and cv. Xiangdou No. 3 under HTH stress
DOI: 10.6084/m9.figshare.12038292
title: Additional file 6 of Quantitative proteomic, physiological and biochemical analysis of cotyledon, embryo, leaf and pod reveals the effects of high temperature and humidity stress on seed vigor formation in soybean

description: Additional file 6 : S1- S9. GO and KEGG analysis of the differentially abundant proteins in cotyledons, embryos, and leaves
DOI: 10.6084/m9.figshare.12038286.v1
title: Additional file 5 of Quantitative proteomic, physiological and biochemical analysis of cotyledon, embryo, leaf and pod reveals the effects of high temperature and humidity stress on seed vigor formation in soybean

description: Additional file 5 : S1- S6. Differentially abundant proteins in cotyledons, embryos, and leaves between the stressed and control in soybean cvs. Ningzhen No. 1 and Xiangdou No. 3, respectively. S7- S9. Differentially abundant proteins in cotyledons, embryos, and leaves between the soybean cv. Ningzhen No. 1 and cv. Xiangdou No. 3 under HTH stress
DOI: 10.6084/m9.figshare.12038280
title: Additional file 8 of Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp

description: Additional file 8. Gene annotations for cluster 75 of T. citrinoviride, manually curated and based on a Blastp v2.9.0+ (protein-protein BLAST) [25] search against a manually curated database, including protein accessions.
DOI: 10.6084/m9.figshare.12038292.v1
title: Additional file 6 of Quantitative proteomic, physiological and biochemical analysis of cotyledon, embryo, leaf and pod reveals the effects of high temperature and humidity stress on seed vigor formation in soybean

description: Additional file 6 : S1- S9. GO and KEGG analysis of the differentially abundant proteins in cotyledons, embryos, and leaves
DOI: 10.6084/m9.figshare.12038274
title: Additional file 7 of Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp

description: Additional file 7. Blastp v2.9.0+ output for cluster 75 of T. citrinoviride, containing the predicted RiPP precursor.
DOI: 10.6084/m9.figshare.12038274.v1
title: Additional file 7 of Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp

description: Additional file 7. Blastp v2.9.0+ output for cluster 75 of T. citrinoviride, containing the predicted RiPP precursor.
DOI: 10.6084/m9.figshare.12038262
title: Additional file 5 of Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp

description: Additional file 5. Blastp v2.9.0+ output for Cluster 55, containing the predicted RiPP precursors with similarities to amatoxins.
DOI: 10.6084/m9.figshare.12038256
title: Additional file 13 of Quantitative proteomic, physiological and biochemical analysis of cotyledon, embryo, leaf and pod reveals the effects of high temperature and humidity stress on seed vigor formation in soybean

description: Additional file 13 : Table S13. Sequences of primers used in this study
DOI: 10.6084/m9.figshare.12038262.v1
title: Additional file 5 of Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp

description: Additional file 5. Blastp v2.9.0+ output for Cluster 55, containing the predicted RiPP precursors with similarities to amatoxins.
DOI: 10.6084/m9.figshare.12038256.v1
title: Additional file 13 of Quantitative proteomic, physiological and biochemical analysis of cotyledon, embryo, leaf and pod reveals the effects of high temperature and humidity stress on seed vigor formation in soybean

description: Additional file 13 : Table S13. Sequences of primers used in this study
DOI: 10.6084/m9.figshare.12038241
title: Additional file 11 of Quantitative proteomic, physiological and biochemical analysis of cotyledon, embryo, leaf and pod reveals the effects of high temperature and humidity stress on seed vigor formation in soybean

description: Additional file 11 : Table S11. 7-plex iTRAQ experimental design
DOI: 10.6084/m9.figshare.12038244
title: Additional file 2 of Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp

description: Additional file 2. The output of the RiPPMiner prediction for the Ustiloxin B cluster extracted from the antiSMASH output.
DOI: 10.6084/m9.figshare.12038247
title: Additional file 12 of Quantitative proteomic, physiological and biochemical analysis of cotyledon, embryo, leaf and pod reveals the effects of high temperature and humidity stress on seed vigor formation in soybean

description: Additional file 12 : S1-S9. The list of all the identified proteins
DOI: 10.6084/m9.figshare.12038238
title: Additional file 1 of Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp

description: Additional file 1. The output of the RiPPMiner prediction for known precursor peptides of fungal RiPPs extracted from the UniProt database.
DOI: 10.6084/m9.figshare.12038241.v1
title: Additional file 11 of Quantitative proteomic, physiological and biochemical analysis of cotyledon, embryo, leaf and pod reveals the effects of high temperature and humidity stress on seed vigor formation in soybean

description: Additional file 11 : Table S11. 7-plex iTRAQ experimental design
DOI: 10.6084/m9.figshare.12038244.v1
title: Additional file 2 of Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp

description: Additional file 2. The output of the RiPPMiner prediction for the Ustiloxin B cluster extracted from the antiSMASH output.
DOI: 10.6084/m9.figshare.12038247.v1
title: Additional file 12 of Quantitative proteomic, physiological and biochemical analysis of cotyledon, embryo, leaf and pod reveals the effects of high temperature and humidity stress on seed vigor formation in soybean

description: Additional file 12 : S1-S9. The list of all the identified proteins
DOI: 10.6084/m9.figshare.12038232
title: Additional file 10 of Quantitative proteomic, physiological and biochemical analysis of cotyledon, embryo, leaf and pod reveals the effects of high temperature and humidity stress on seed vigor formation in soybean

description: Additional file 10 : Table S10. Key KEGG pathways for seed vigor formation in leaves, cotyledons, and embryos between the stressed and control in soybean cvs. Ningzhen No. 1 and Xiangdou No. 3, respectively, and between both the cultivars
DOI: 10.6084/m9.figshare.12038232.v1
title: Additional file 10 of Quantitative proteomic, physiological and biochemical analysis of cotyledon, embryo, leaf and pod reveals the effects of high temperature and humidity stress on seed vigor formation in soybean

description: Additional file 10 : Table S10. Key KEGG pathways for seed vigor formation in leaves, cotyledons, and embryos between the stressed and control in soybean cvs. Ningzhen No. 1 and Xiangdou No. 3, respectively, and between both the cultivars
DOI: 10.6084/m9.figshare.12038238.v1
title: Additional file 1 of Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp

description: Additional file 1. The output of the RiPPMiner prediction for known precursor peptides of fungal RiPPs extracted from the UniProt database.
DOI: 10.6084/m9.figshare.12038181
title: Additional file 4 of Probing the operability regime of an engineered ribocomputing unit in terms of dynamic range maintenance with extracellular changes and time

description: Additional file 4: Dataset S1. Experimental and theoretical data of the half adder behavior. The Excel file contains an implementation of the mathematical model.
DOI: 10.6084/m9.figshare.12038181.v1
title: Additional file 4 of Probing the operability regime of an engineered ribocomputing unit in terms of dynamic range maintenance with extracellular changes and time

description: Additional file 4: Dataset S1. Experimental and theoretical data of the half adder behavior. The Excel file contains an implementation of the mathematical model.
DOI: 10.6084/m9.figshare.12038091
title: Additional file 4 of TDP-43 promotes the formation of neuromuscular synapses through the regulation of Disc-large expression in Drosophila skeletal muscles

description: Additional file 4. Individual data values. Individual data values for: Fig. 3: pannel a; Fig. 4: pannels a,b,c; Fig. 5: pannels a,b,c; Additional file 1 Fig. S1.
DOI: 10.6084/m9.figshare.12038091.v1
title: Additional file 4 of TDP-43 promotes the formation of neuromuscular synapses through the regulation of Disc-large expression in Drosophila skeletal muscles

description: Additional file 4. Individual data values. Individual data values for: Fig. 3: pannel a; Fig. 4: pannels a,b,c; Fig. 5: pannels a,b,c; Additional file 1 Fig. S1.
DOI: 10.6084/m9.figshare.12038085
title: Additional file 2 of HeMoQuest: a webserver for qualitative prediction of transient heme binding to protein motifs

description: Additional file 2 Supplementary data Additionally, the datasets used to train and validate the application is also available for download from the “HeMoQuest Datasets” section of the webserver. A description of the files provided is given below. 1. Training data. 1a. Title: HeMoQuest KD prediction training data. 1b. Description: This comma separated values file contains 72 sequences along with their KD values used in the training of the ML algorithms of HeMoQuest. Column 1 (ID) contains a sequence identifier, column 2 (Seq) contains the sequence and column 3 (KD) contains the experimentally determined KD value of for the peptide sequence. 2. Test data. 2a. Title: HeMoQuest test data for heme binding residue and motif prediction. 2b. Description: This file contains 469 sequences in fasta format, obtained from the BioLip database, all of which are said to bind heme. This data was used to test HeMoQuest’s ability to detect heme binding residues in comparison to existing algorithms. 3. Test data. 3a. Title: HemoQuest test data with manually curated transient heme binding protein sequences. 3b. Description: This file contains 45 sequences in fasta format from 40 manually curated proteins (from Additional Table 1) that are known from literature to be transient heme binding proteins. Few of the proteins have their origins in more than one species and hence we end up with 45 sequences for 40 proteins. 4. Training features. 4a. Title: Features used in training the HeMoQuest KD prediction. 4b. Description: This comma separated values file contains 76 initial features that were generated for the KD prediction training from the R package Peptides. The final set of features used are from the columns ‘charge_vec’, ‘hydrof_vec_octanolScale_pH8’, ‘acidic’, ‘kideraFac3’, ‘vhseScale5_vec’, ‘vhseScale7_vec’, ‘protFP5_vec’ and ‘fasgaiVec4’.