cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22003049.v2
title: Long Read Samples readily usable in lasTEq

description: Long-read TE quantifications in 6 samples. Two HCT116 samples exist generated by our own lab and by SG-NEx study. <br> 1. long_read_TE_quantification_SG-NEx_K562: TE TPM counts in SG-NEx K562(sample id: ERR6053079) 2. long_read_TE_quantification_SG-NEx_HepG2: TE TPM counts in SG-NEx HepG2(sample id: ERR6053063) 3. long_read_TE_quantification_SG-NEx_A549: TE TPM counts in SG-NEx A549(sample id: ERR6053016) 4. long_read_TE_quantification_SG-NEx_MCF-7: TE TPM counts in SG-NEx MCF-7(sample id: ERR6053093) 5. long_read_TE_quantification_own_HCT116: TE TPM counts in own HCT116(GEO: ) 6. long_read_TE_quantification_SG-NEx_HCT116: TE TPM counts in SG-NEx HCT116(sample id: ERR6053040)
DOI: 10.6084/m9.figshare.21995072.v2
title: Files for Main Figure 3

description: Quantified TEs in TPM counts in simulated short-read measured by 7 approaches. File used for main figure 3. <br> Information about column names TE_name: Name of TE individuals TE_label: Positions of TE individuals length: TE lengths Long: Long-read TE output org_tel: Telescope TE output mod_tel: lasTEq TE output mod_tel_rescue: lasTEq TE output with --rescue_short option sets as 0 uniq: Unique counts from Telescope TE output best: Best counts from Telescope TE output rsem: RSEM TE output salmonTE: salmonTE TE output
DOI: 10.6084/m9.figshare.19524220
title: Questionnaire with consent form.docx

description: Sample questionnaire with prior consent form<br>
DOI: 10.6084/m9.figshare.19524220.v1
title: Questionnaire with consent form.docx

description: Sample questionnaire with prior consent form<br>
DOI: 10.5285/6fcc17ad-425b-4367-bd23-c4133a38e359
title: Shear wave splitting catalogue, Rutford Ice Stream (West Antarctica), November 2018 to February 2019

description: This dataset contains an ASCII file with shear wave splitting results for 202,652 station-event pairs from glacial micro-seismicity, recorded from a 35-station seismic network located ~40 km upstream of the grounding line of Rutford Ice Stream, West Antarctica. Microseismicity is located at the base of the ice stream at ~2.2 km depth (relative to the ice surface). Seismic waveform data, which was used to calculate shear wave splitting parameters is provided in miniseed format. Event hypocenter information, event times and coordinates of receiving stations are listed in the ASCII file. Shear wave splitting was calculated using the software MFAST. Shear wave splitting parameters can be used to determine seismic anisotropy along the ray path, which helps to characterise ice fabric. This work was funded within the BEAMISH project by NERC AFI award numbers NE/G014159/1 and NE/G013187/1. Seismic instruments were provided by NERC SEIS-UK (Loan 1017) and the Incorporated Research Institutions for Seismology (IRIS) through the PASSCAL Instrument Center at New Mexico Tech.
description: Icequake used for shear wave splitting analysis are chosen based on the event catalogue of Kufner et al. (2021). To calculate SWS parameters from the waveform data of these events, horizontal seismograms are filtered between 8 and 125 Hz, using a two-pole Butterworth filter, and downsampled from 1000 to 500 Hz. The MFAST (M. K. Savage et al., 2010) software is used for shear wave splitting analysis. MFAST implements a minimum eigenvalue analysis algorithm (Silver & Chan, 1991) to calculate shear wave splitting in multiple time windows around the S-onset. A cluster analysis method is then implemented on the splitting results from individual measurement windows to find the most stable set of splitting parameters (see Teanby et al. (2004) for more details). In MFAST, the start and end point of the measurement windows are variable, dependent on an event's dominant frequency. Detailed information on the methodology and interpretation of the results will be presented in Kufner et al. (in prep.).
description: Instrumentation: Each station of the seismic network consisted of a Reftek RT-130 data logger with a 4.5 Hz 3-component geophone (either GS11-3D or L28-3D), which was buried to ~1 m depth. The sampling frequency was set to 1000 Hz. Energy supply was ensured through a solar panel and batteries. Timing was obtained from an attached GPS antenna. Software: Shear wave splitting: MFAST (https://mfast-package.geo.vuw.ac.nz/); Version 2.2.
description: Errors on the splitting parameters are given in the ASCII data file.
DOI: 10.5281/zenodo.7729775
title: Pylake tutorial dataset: Piezo tracking

description: Force extension curve of Adenosine Kinase (AdK) with DNA handles tethered between polystyrene beads acquired with the LUMICKS C-Trap.
DOI: 10.5281/zenodo.7729774
title: Pylake tutorial dataset: Piezo tracking

description: Force extension curve of Adenosine Kinase (AdK) with DNA handles tethered between polystyrene beads acquired with the LUMICKS C-Trap.
DOI: 10.5281/zenodo.7729700
title: Pylake tutorial dataset: ImageStack

description: A set of files of protein binding acquired on a LUMICKS C-Trap. The system consists of lambda DNA tethered between two polystyrene beads protein labeled with an Atto565 fluorophore (green channel) TIF files are image stacks acquired from an sCMOS camera and the .h5 file is time-correlated force data. All data was acquired with LUMICKS Bluelake software.
DOI: 10.5281/zenodo.7729699
title: Pylake tutorial dataset: ImageStack

description: A set of files of protein binding acquired on a LUMICKS C-Trap. The system consists of lambda DNA tethered between two polystyrene beads protein labeled with an Atto565 fluorophore (green channel) TIF files are image stacks acquired from an sCMOS camera and the .h5 file is time-correlated force data. All data was acquired with LUMICKS Bluelake software.
DOI: 10.25909/64105b77730b3
title: AUS Tan Spot Phenotype/Genotype Data Sept 2022

description: AUS Tan Spot Phenotype Data Sept 2022.xslx Twelve tan spot severity phenotyping experiments conducted across Australia that incuded 192 internationally diverse wheat lines. Spreadsheet contains 12 data sheets that include: <br> Horsham, Victoria in 2015, 2016 Glasshouse Field South Perth, Western Australian in 2015, 2016 Controlled environment Field Toowoomba, Queensland in 2015, 2016 Controlled environment Field AUS Tan Spot Genotype Data Sept 2022.xslx Genotype data for 192 internationally diverse wheat lines. Spreadsheet contains three data sheets that include: 20519 markers with imputed numeric alleles 20519 markers with missing values (non-imputed) Physical map AUS ToxA ToxB Effector Screening Data Sept 2022.xlsx ToxA and ToxB effector screening data for the 192 internationally diverse wheat lines. Dataset contains two data sheets that include: ToxA screening ToxB screening <br>
DOI: 10.5281/zenodo.7729928
title: Pylake tutorial dataset: Force extension curves

description: Force extension curves of various constructs acquired on a LUMICKS C-Trap. The constructs are a DNA Hairpin Adenylate Kinase with DNA handles DNA in the presence and absence of RecA
DOI: 10.5281/zenodo.7729929
title: Pylake tutorial dataset: Force extension curves

description: Force extension curves of various constructs acquired on a LUMICKS C-Trap. The constructs are a DNA Hairpin Adenylate Kinase with DNA handles DNA in the presence and absence of RecA
DOI: 10.5281/zenodo.7729812
title: Pylake tutorial dataset: Population dynamics

description: A dataset of force data measured on a LUMICKS C-Trap. The system consists of a DNA hairpin construct tethered between two polystyrene beads held at a constant distance with the optical traps.
DOI: 10.5281/zenodo.7729811
title: Pylake tutorial dataset: Population dynamics

description: A dataset of force data measured on a LUMICKS C-Trap. The system consists of a DNA hairpin construct tethered between two polystyrene beads held at a constant distance with the optical traps.
DOI: 10.5281/zenodo.7729636
title: Pylake tutorial dataset: Scans

description: 2D confocal scans of protein binding acquired on a LUMICKS C-Trap. The system consists of lambda DNA with two Atto647N fluorophores attached at specific locations (red channel) protein labeled with an Atto565 fluorophore (green channel)
DOI: 10.5281/zenodo.7729635
title: Pylake tutorial dataset: Scans

description: 2D confocal scans of protein binding acquired on a LUMICKS C-Trap. The system consists of lambda DNA with two Atto647N fluorophores attached at specific locations (red channel) protein labeled with an Atto565 fluorophore (green channel)
DOI: 10.5281/zenodo.7729525
title: Pylake tutorial dataset: Kymograph

description: A kymograph of protein binding acquired on a LUMICKS C-Trap. The system consists of lambda DNA with two Atto647N fluorophores attached at specific locations (red channel) protein labeled with an Atto565 fluorophore (green channel)
DOI: 10.5281/zenodo.7729524
title: Pylake tutorial dataset: Kymograph

description: A kymograph of protein binding acquired on a LUMICKS C-Trap. The system consists of lambda DNA with two Atto647N fluorophores attached at specific locations (red channel) protein labeled with an Atto565 fluorophore (green channel)
DOI: 10.5281/zenodo.7732688
title: High spatial resolution satellite images for glacier outlines

description: Two RapidEye satellite images acquired on Sep 13, 2013 and Sep 17, 2018. The two satellite images have a high spatial resolution of 5 m × 5 m and were used to derive the outlines of the Parlung No. 94 Glacier in years 2013 and 2018, respectively. The GaoFen-7 (GF-7) satellite image with a high spatial resolution of 3 m × 3 m acquired on Feb 26, 2021 was used to derive the outlines of the Dongkemadi Glacier in 2021
DOI: 10.6084/m9.figshare.22269742.v1
title: Supplementary Material for: Immunomodulation Effect of Regional Citrate Anticoagulation in Acute Kidney Injury Requiring Renal Replacement Therapy

description: <b><i>Introduction:</i></b> Acute kidney injury (AKI) is a common syndrome in critically ill patients. Continuous renal replacement therapy (CRRT) is the standard treatment for patients with AKI. Research on the immunomodulating effects of regional citrate anticoagulation (RCA) remains limited in patients with AKI receiving CRRT. We aimed to evaluate the immunomodulating effects of RCA in patients with AKI receiving CRRT. <b><i>Methods:</i></b> A randomized controlled trial study on critically ill adult patients with AKI undergoing CRRT was undertaken. Participants were randomized into either a regional citrate group or control group (either heparin anticoagulant or normal saline). Measurements were taken at baseline, 6 and 24 h after commencing CRRT for CD11b expression, C3a, C5a, and plasminogen activator inhibitor-1 (PAI-1) levels. Clinical outcomes assessed were 28-day survival rate, length of ICU stay, renal support duration, and renal function at discharge. <b><i>Results:</i></b> Thirty patients were recruited and randomized into 2 groups of 15 subjects. Baseline demographic and clinical data were comparable between groups. In the citrate group, CD11b expression was significantly decreased at 24 h compared to the control group (1.84% [1.18–3.32] versus 4.92% [2.63–6.93], <i>p</i> &lt; 0.01). The complement level, including c3b and c5a, was stable during CRRT. Additionally, the PAI-1 levels were significantly decreased at 24 h compared to the control group (114 ng/mL [19–193] versus 359 ng/mL [264–491], <i>p</i> &lt; 0.01). No significant difference in survival rate was observed. <b><i>Conclusions:</i></b> RCA may have the potential to mitigate the inflammatory response by decreasing CD11b expression of neutrophil and improve fibrinolysis activity through a reduction of PAI-1 levels. Larger clinical trials are warranted to test this immunomodulation effect of RCA.
DOI: 10.5281/zenodo.7728895
title: Global Hydrogen Production during high-pressure Serpentinisation of Subducting Slabs—Dataset

description: Data-set and code for recreating results of: <strong>Global Hydrogen Production during high-pressure Serpentinisation of Subducting Slabs </strong> A manuscript submitted to G-cubed.
DOI: 10.6084/m9.figshare.22269751
title: Supplementary Material for: Patterns of Renal Dysfunction and Profile of Kidney Biopsies in Hematopoietic Stem Cell Transplant Recipients

description: Introduction: Post hematopoietic stem cell transplant (HSCT), kidney can be subjected to injury by various causes. Of these, Graft versus Host Disease (GvHD) affecting the kidney is an under-recognized entity with no clear guidelines on its diagnosis, clinicopathological manifestations and outcomes. Material and Methods: Out of 2930 patients who underwent HSCT at our centre between 2005 and 2020, kidney biopsy was performed in 19 allogenic and 5 autologous recipients. Results: The mean age of the cohort at transplant was 33.2 ± 7 years and 15 (62%) were males. Median time to kidney biopsy from HSCT was 14 (IQR, 9-30) months. Aplastic anemia was the most common underlying hematological disease (54.2%). All 19 allogenic recipients were classified based on clinicopathological manifestations into either thrombotic microangiopathy [TMA, 12/19 (63%)] or nephrotic syndrome [NS, 7/19 (37%)] pattern. Glomerular tuft ‘mesangiolysis’ was the dominant pattern of injury noted in 9/12 cases of TMA pattern. There was a predominance of acute microangiopathic changes restricted primarily to the glomerular compartment. Of the seven patients with NS pattern, membranous nephropathy (MN) was seen in 4 (57%) and minimal change disease (MCD) in 3 (43%) patients. Thirty nine percent (7/18) stained positive for C4d which was predominantly glomerular. Allogenic recipients who did not receive immunosuppression (IS) for renal disease had a lower eGFR at biopsy, a longer latency between withdrawal of GvHD prophylaxis and biopsy and were significantly at higher risk of kidney failure (IS: 2/11, 18.1% vs. No IS: 2/6, 33.3%, p=0.04). ‘Associated extra-renal GvHD’ occurred in 11/19 (57.9%) allogenic recipients. Patients with ‘associated extra-renal GvHD’ had significantly more death (6/11, 60% vs. 0, p=0.02) but comparable renal outcomes. Conclusion: Renal GvHD can present with or without ‘associated extra-renal GvHD’ after a prolonged period of withdrawal of GvHD prophylaxis, requiring careful diagnostic vigilance and consideration of immunosuppression.
DOI: 10.6084/m9.figshare.22269751.v1
title: Supplementary Material for: Patterns of Renal Dysfunction and Profile of Kidney Biopsies in Hematopoietic Stem Cell Transplant Recipients

description: Introduction: Post hematopoietic stem cell transplant (HSCT), kidney can be subjected to injury by various causes. Of these, Graft versus Host Disease (GvHD) affecting the kidney is an under-recognized entity with no clear guidelines on its diagnosis, clinicopathological manifestations and outcomes. Material and Methods: Out of 2930 patients who underwent HSCT at our centre between 2005 and 2020, kidney biopsy was performed in 19 allogenic and 5 autologous recipients. Results: The mean age of the cohort at transplant was 33.2 ± 7 years and 15 (62%) were males. Median time to kidney biopsy from HSCT was 14 (IQR, 9-30) months. Aplastic anemia was the most common underlying hematological disease (54.2%). All 19 allogenic recipients were classified based on clinicopathological manifestations into either thrombotic microangiopathy [TMA, 12/19 (63%)] or nephrotic syndrome [NS, 7/19 (37%)] pattern. Glomerular tuft ‘mesangiolysis’ was the dominant pattern of injury noted in 9/12 cases of TMA pattern. There was a predominance of acute microangiopathic changes restricted primarily to the glomerular compartment. Of the seven patients with NS pattern, membranous nephropathy (MN) was seen in 4 (57%) and minimal change disease (MCD) in 3 (43%) patients. Thirty nine percent (7/18) stained positive for C4d which was predominantly glomerular. Allogenic recipients who did not receive immunosuppression (IS) for renal disease had a lower eGFR at biopsy, a longer latency between withdrawal of GvHD prophylaxis and biopsy and were significantly at higher risk of kidney failure (IS: 2/11, 18.1% vs. No IS: 2/6, 33.3%, p=0.04). ‘Associated extra-renal GvHD’ occurred in 11/19 (57.9%) allogenic recipients. Patients with ‘associated extra-renal GvHD’ had significantly more death (6/11, 60% vs. 0, p=0.02) but comparable renal outcomes. Conclusion: Renal GvHD can present with or without ‘associated extra-renal GvHD’ after a prolonged period of withdrawal of GvHD prophylaxis, requiring careful diagnostic vigilance and consideration of immunosuppression.
DOI: 10.5281/zenodo.6472481
title: WES cropbioBonn WGGC CN 200M vcf results

description: Whole Exome Sequencing Data Analysis with https://github.com/tgstoecker/WES_WGGC_2021_AG_Schoof HG001/NA12878 Agilent v6 2x101bp PE, NovaSeq 6000, 200M reads
DOI: 10.5281/zenodo.6472480
title: WES cropbioBonn WGGC CN 200M vcf results

description: Whole Exome Sequencing Data Analysis with https://github.com/tgstoecker/WES_WGGC_2021_AG_Schoof HG001/NA12878 Agilent v6 2x101bp PE, NovaSeq 6000, 200M reads
DOI: 10.5281/zenodo.7712757
title: Fish size correlates to number and morphology of intermuscular bones in tambaqui Colossoma macropomum as shown by dissection and X-ray imaging methods

description: Dataset on intermuscular bones in Colossoma macropomum studied through dissection and X-ray analyses in one captive population in Brazil.
DOI: 10.5281/zenodo.7712756
title: Intermuscular bones in Colossoma macropomum studied through dissection and X-ray analyses

description: Dataset on intermuscular bones in Colossoma macropomum studied through dissection and X-ray analyses in one captive population in Brazil.
DOI: 10.5281/zenodo.7729724
title: Fish size correlates to number and morphology of intermuscular bones in tambaqui Colossoma macropomum as shown by dissection and X-ray imaging methods

description: Dataset on intermuscular bones in Colossoma macropomum studied through dissection and X-ray analyses in one captive population in Brazil.
DOI: 10.5281/zenodo.7729757
title: Intermuscular bones in Colossoma macropomum studied through dissection and X-ray analyses

description: Dataset on intermuscular bones in Colossoma macropomum studied through dissection and X-ray analyses in one captive population in Brazil.
DOI: 10.34740/kaggle/dsv/5164390
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.5281/zenodo.7731653
title: Effects of increasing phosphorus rate on microbial dynamics and soil available P under a Lixisol soil in Zimbabwe

description: Soil phosphorus (P) deficiency is a major challenge to the attainment of food security in most parts of sub-Saharan Africa, including Zimbabwe, where farmers largely depend on local organic nutrient resources in cropping. A greenhouse study was conducted to evaluate the influence of increasing inorganic P fertilizer rates (16, 26 and 36 kg P ha<sup>-1</sup>) on microbial dynamics, soil P pools and maize P uptake. using soils collected from a long-term (16 seasons) maize-monocropped field experiment where organic nutrient resources of different qualty namely <em>Crotalaria juncea</em> (high quality), <em>Calliandra Calothyrus</em> (medium quality), cattle manure ( variable quality), maize stover and <em>Pinus patula</em> sawdust ( both low quality) were applied at 4 t C ha<sup>-1</sup> with 16 kg P ha<sup>-1</sup> at the start of every season, a 3 x 6 factorial experiment was established by adding single super phosphate (8.5% P) as a basal fertilizer. Maize was used as the test crop and the experiment was conducted at Soil Productivity Research Laboratory in Zimbabwe. Using Pokovskays agar medium and serial dilution methods, phsophate-solubilizing microbes were monitored forthnightly from day 1 to 57 after maize planting. Ninetten (19) fungal and forty-two (42) bacterial colonies were identified over the study period, Fungi dominated bacteria on dayone, wth <em>Aspergillus niger</em> showing 20-98% abundance that depended on organic resources quality. Overall, a microbial explosion bulge characterized sucession on day 29 which coincided with a significant (P&lt; 0.05) increase in diversity (H') and soil available P. Increasing P rate to 26 kg ha<sup>-1 </sup>amplified the explosion bulge under medium-high quality resources while under the control the bulge emerged earlier on day 15. <em>Mucor</em> and <em>Bacillus</em> had peak abundance on day 43 and 57, respectively, across treatments regardless of P rates. Treatment and P rate had a significant (P&lt; 0.01) effect on microbial P. Bacteria were more rsponsive to added P than fungi. Increasing P to 36 kg P ha<sup>-1</sup> also stimulated an earlier bulge under maize stover on day 15. Addition of P alone, without supplying complementary nutrients such as nitrogen,did not have a positive effect on maize P uptake. Farmers need to co-apply medium-high quality organic resources with high fertilzier P rates to increase microbial diversity, soil available P and maize growth on sandy soils (Lixisols). Our results suggest the need to recondiser existing P fertilizer recommendations, currently pegged at between 26 and 30 kg P ha<sup>-1</sup>, for maize production on sandy soils as well develop new fertilizer formulations to intensify crop production in Zimbabwe.
DOI: 10.5281/zenodo.7731652
title: Effects of increasing phosphorus rate on microbial dynamics and soil available P under a Lixisol soil in Zimbabwe

description: Soil phosphorus (P) deficiency is a major challenge to the attainment of food security in most parts of sub-Saharan Africa, including Zimbabwe, where farmers largely depend on local organic nutrient resources in cropping. A greenhouse study was conducted to evaluate the influence of increasing inorganic P fertilizer rates (16, 26 and 36 kg P ha<sup>-1</sup>) on microbial dynamics, soil P pools and maize P uptake. using soils collected from a long-term (16 seasons) maize-monocropped field experiment where organic nutrient resources of different qualty namely <em>Crotalaria juncea</em> (high quality), <em>Calliandra Calothyrus</em> (medium quality), cattle manure ( variable quality), maize stover and <em>Pinus patula</em> sawdust ( both low quality) were applied at 4 t C ha<sup>-1</sup> with 16 kg P ha<sup>-1</sup> at the start of every season, a 3 x 6 factorial experiment was established by adding single super phosphate (8.5% P) as a basal fertilizer. Maize was used as the test crop and the experiment was conducted at Soil Productivity Research Laboratory in Zimbabwe. Using Pokovskays agar medium and serial dilution methods, phsophate-solubilizing microbes were monitored forthnightly from day 1 to 57 after maize planting. Ninetten (19) fungal and forty-two (42) bacterial colonies were identified over the study period, Fungi dominated bacteria on dayone, wth <em>Aspergillus niger</em> showing 20-98% abundance that depended on organic resources quality. Overall, a microbial explosion bulge characterized sucession on day 29 which coincided with a significant (P&lt; 0.05) increase in diversity (H') and soil available P. Increasing P rate to 26 kg ha<sup>-1 </sup>amplified the explosion bulge under medium-high quality resources while under the control the bulge emerged earlier on day 15. <em>Mucor</em> and <em>Bacillus</em> had peak abundance on day 43 and 57, respectively, across treatments regardless of P rates. Treatment and P rate had a significant (P&lt; 0.01) effect on microbial P. Bacteria were more rsponsive to added P than fungi. Increasing P to 36 kg P ha<sup>-1</sup> also stimulated an earlier bulge under maize stover on day 15. Addition of P alone, without supplying complementary nutrients such as nitrogen,did not have a positive effect on maize P uptake. Farmers need to co-apply medium-high quality organic resources with high fertilzier P rates to increase microbial diversity, soil available P and maize growth on sandy soils (Lixisols). Our results suggest the need to recondiser existing P fertilizer recommendations, currently pegged at between 26 and 30 kg P ha<sup>-1</sup>, for maize production on sandy soils as well develop new fertilizer formulations to intensify crop production in Zimbabwe.