cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7665281
title: Source Data: No evidence for a common blood microbiome based on a population study of 9,770 healthy humans

description: Source data for manuscript titled: 'No evidence for a common blood microbiome based on a population study of 9,770 healthy humans' (https://www.biorxiv.org/content/10.1101/2022.07.29.502098v1)
DOI: 10.5281/zenodo.7665001
title: Data on youth understandings of and attitudes towards carbon-smart urban green infrastructure in Kumpula, Helsinki

description: A workshop survey -dataset detailing youth understandings of and attitudes towards carbon-smart urban green infrastructure in Kumpula, Helsinki, Finland.
description: This dataset was funded by the Strategic Research Council, Academy of Finland through the CO-CARBON project (project number: 335203).
DOI: 10.5281/zenodo.7665002
title: Data on youth understandings of and attitudes towards carbon-smart urban green infrastructure in Kumpula, Helsinki

description: A workshop survey -dataset detailing youth understandings of and attitudes towards carbon-smart urban green infrastructure in Kumpula, Helsinki, Finland.
description: This dataset was funded by the Strategic Research Council, Academy of Finland through the CO-CARBON project (project number: 335203).
DOI: 10.5281/zenodo.7561771
title: Quantum state resolved molecular dipolar collisions over four decades of energy - online data

description: Data for submission of "Quantum state resolved molecular dipolar collisions over four decades of energy" Authors: Guoqiang Tang<sup>1</sup>, Matthieu Besemer<sup>1</sup>, Stach Kuijpers<sup>1</sup>, Gerrit C. Groenenboom<sup>1</sup>,<br> Ad van der Avoird<sup>1</sup>, Tijs Karman<sup>1</sup>**, Sebastiaan Y.T. van de Meerakker<sup>1</sup>** <sup>1</sup>Radboud University, Institute for Molecules and Materials<br> Heijendaalseweg 135, 6525 AJ Nijmegen, the Netherlands **To whom correspondence should be addressed;<br> E-mail: basvdm@science.ru.nl, t.karman@science.ru.nl
DOI: 10.5281/zenodo.7561770
title: Quantum state resolved molecular dipolar collisions over four decades of energy - online data

description: Data for submission of "Quantum state resolved molecular dipolar collisions over four decades of energy" Authors: Guoqiang Tang<sup>1</sup>, Matthieu Besemer<sup>1</sup>, Stach Kuijpers<sup>1</sup>, Gerrit C. Groenenboom<sup>1</sup>,<br> Ad van der Avoird<sup>1</sup>, Tijs Karman<sup>1</sup>**, Sebastiaan Y.T. van de Meerakker<sup>1</sup>** <sup>1</sup>Radboud University, Institute for Molecules and Materials<br> Heijendaalseweg 135, 6525 AJ Nijmegen, the Netherlands **To whom correspondence should be addressed;<br> E-mail: basvdm@science.ru.nl, t.karman@science.ru.nl
DOI: 10.5281/zenodo.7665315
title: Input data for Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations

description: As described in the main text, here is the input data used for simulation, as well as analysis directories. The archive was generated in my project folder with "tar --exclude=*trr --exclude=pbctools --exclude=qtwrap --exclude=old* --exclude=*npz --exclude=*pdf --exclude=*png --exclude=*ppm --exclude=*dcd* --exclude=*xtc --exclude=*slurm* --exclude=core* --exclude=*sh --exclude=*xvg --exclude=*out --exclude=*git* --exclude=*edr --exclude=*log --dereference -zcvf kulke-$(date +"%F").tar.gz data figures scripts Simulations". Big data and trajectory files were excluded to keep the archive size small. The archive includes all necessary files to reproduce the simulations, analysis and figures for the publication.
DOI: 10.5281/zenodo.7665314
title: Input data for Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations

description: As described in the main text, here is the input data used for simulation, as well as analysis directories. The archive was generated in my project folder with "tar --exclude=*trr --exclude=pbctools --exclude=qtwrap --exclude=old* --exclude=*npz --exclude=*pdf --exclude=*png --exclude=*ppm --exclude=*dcd* --exclude=*xtc --exclude=*slurm* --exclude=core* --exclude=*sh --exclude=*xvg --exclude=*out --exclude=*git* --exclude=*edr --exclude=*log --dereference -zcvf kulke-$(date +"%F").tar.gz data figures scripts Simulations". Big data and trajectory files were excluded to keep the archive size small. The archive includes all necessary files to reproduce the simulations, analysis and figures for the publication.
DOI: 10.6084/m9.figshare.22141094
title: Lithic Analytical Framework for GHN.docx

description: This document provides the lithic traits and definitions recorded during the analysis of Ga-Mohana North Rockshelter (GHN). The analytical framework was adopted from Wilkins <em>et al</em>. (2017) and it was modified in order to record traits that were suitable to answer the research questions at GHN.
DOI: 10.6084/m9.figshare.22141094.v1
title: Lithic Analytical Framework for GHN.docx

description: This document provides the lithic traits and definitions recorded during the analysis of Ga-Mohana North Rockshelter (GHN). The analytical framework was adopted from Wilkins <em>et al</em>. (2017) and it was modified in order to record traits that were suitable to answer the research questions at GHN.
DOI: 10.6084/m9.figshare.22086533.v1
title: Supplementary Material for: Characteristics and graft outcomes of kidney transplant candidates with enteric risk factors and elevated plasma oxalate levels

description: Introduction: This study describes patient characteristics and examines graft function of kidney transplant recipients (without primary hyperoxaluria) with elevated plasma oxalate (POx) and enteric risk factors prior to transplant at our institution. Methods: Kidney transplant recipients between 2012 to 2020 with elevated POx at the time of kidney transplant evaluation were included. A matched control cohort was gathered using patient/donor age, living/deceased donor type, panel reactive antibody (PRA), kidney donor profile index (KDPI), and human leukocyte antigen (HLA) mismatch as matching variables. Graft function at 1 year and at last follow-up was reported. Results: A total of 106 patients with elevated POx were identified. A third of the patients had Roux-en-Y gastric bypass, a third had other enteric risks, and a third did not have an identifiable enteric risk. Median eGFR (estimated glomerular filtration rate) at 1-year and at last follow-up were similar between cases and controls except for subgroup of patients with pre-transplant POx &gt;30mcmol/L where 1-year eGFR was lower compared to controls. Across eGFR categories, more cases were in eGFR category &lt;30ml/min/1.73m2 compared to controls. Discussion/Conclusion: Roux-en-Y gastric bypass is the most common identifiable risk for elevated POx in kidney transplant candidates. 1-year graft function was not inferior in cases compared to matched controls except for subgroup with POx&gt;30mcmol/L pre-transplant.
DOI: 10.6084/m9.figshare.22093760.v1
title: Supplementary Material for: Twenty years of quiescence after non-stop Remicade® (infliximab) infusions in a child with ocular Behçet disease presenting as hypopyon-anterior uveitis refractory to immunosuppressants

description: I report a case with ocular Behçet disease presenting as hypopyon-anterior uveitis refractory to conventional immunosuppressive drugs who was safely and effectively managed for 20 years by non-stop infusions of a modern anti-TNF-agent, infliximab. 14-year-old girl who had a history of recurrent oro-genital ulcers, arthralgia and pathergy test positivity presented with the symptoms of bilateral blurred vision, ocular pain, photophobia and lacrimation. Initial visual acuities were 20/25 bilaterally and biomicroscopy revealed bilateral iridocyclitis with left shifting cold hypopyon formation in the anterior chamber of the eye. The diagnosis of ocular Behçet disease was made and topical anti-inflammatory drops were initiated with a cycloplegic agent. In due course, the child complained of chronic floaters and decreased vision from 20/25 to 20/200 bilaterally. Vitreitis, retinitis, perivasculitis and cystoid macular edema (CME) were encountered and the combination of corticoid, azathioprine and cyclosporine-A was immediately started. However, the child did not respond to this conventional management for 3 months. A prompt and dramatic response was obtained with repeated Remicade® (infliximab) infusions (weeks 0, 2, 6 and 10), which led to fast improvement in her systemic and ocular symptoms. Long-term remission of 20 years was obtained by regular infliximab infusions at each 6-9 week interval with stabilized vision (20/20) and resolution of CME. The present case shows the significant role of biologicals in pediatric severe panuveitis and that non-stop infliximab infusions initiated early led to rapid and long-term control of intraocular inflammation and recurrent sight-threatening uveitis attacks for protecting the vision in children with severe OBD.
DOI: 10.5281/zenodo.7665340
title: Multi-objective near-optimal necessary conditions for multi-sectoral planning - Dataset

description: Dataset (input and output) of the paper 'Multi-objective near-optimal necessary conditions for multi-sectoral planning'
DOI: 10.5281/zenodo.7665339
title: Multi-objective near-optimal necessary conditions for multi-sectoral planning - Dataset

description: Dataset (input and output) of the paper 'Multi-objective near-optimal necessary conditions for multi-sectoral planning'
DOI: 10.3886/e185341
title: A Fully Bayesian Approach to Model Process Data in a Newly Developed Computer-based Assessment

description: Writing requires substantial conscious effort compared to other literacy skills (e.g., reading). Cognitive models of writing have been proposed to reflect the underlying mechanisms of the writing process. In a computer-based writing assessment, keystroke log data can capture a student’s writing process (e.g., their typing behavior) as the student responds to a writing assignment prompt. Quantification of the writing process may contribute to establishing a writing profile for each student and influence the ongoing writing instruction. Extracting meaningful features from writing process data remains challenging. In this research, for interpretability purposes, we endorse the idea that cognitive models should be the foundation to extract process features. Specifically, we have (1) designed a computer-based assessment to capture students’ writing process; (2) administered the assessment to students to collect response process data; (3) parsed the raw data into pause data; and (4) modeled the pause data with a hierarchical mixture model using a fully Bayesian approach. Under the Bayesian model’s assumption of exchangeability, essays (students) are treated as similar data units, meaning that the model borrows strength from longer essays to enhance the efficiency of estimation for shorter essays. In addition, we provided the source code for designing the keystroke logging system. Therefore, if future researchers intend to develop their own keystroke logging system, they can modify our callback functions, instead of creating the code from scratch.
DOI: 10.25345/c5w08ws15
title: MassIVE MSV000091344 - Effects of high-resistance wheel running on hallmarks of endurance and resistance training adaptations in mice
title: Exercise effectively promotes and preserves cardiorespiratory, neuromuscular, metabolic and cognitive function throughout life. The molecular mechanisms underlying the beneficial adaptations to exercise training are, however, still poorly understood. To improve the mechanistic study of specific exercise training adaptations, standardized, physiological and well-characterized training interventions are required. Therefore, we performed a comprehensive interrogation of systemic changes and muscle-specific cellular and molecular adaptations to voluntary low-resistance wheel running (Run) and progressive high-resistance wheel running (RR) in young mice. Following 10 weeks of training, both groups showed similar improvements in body composition and peak oxygen uptake (VO2peak), as well as elevated mitochondrial proteins and capillarization markers in the M. plantaris. Run mice clearly outperformed RR mice in a forced treadmill running capacity test, while RR mice displayed increased grip strength as well as superior mass gains in the M. soleus concomitant with an elevation in cytoskeletal and extracellular matrix proteins involved in structural organization. Thus, even though both training modalities induce overlapping adaptations, Run interventions preferably improve submaximal running performance, while progressive RR is a valid model to study training-induced gains in grip strength and plantar flexor hypertrophy concomitant with associated extra- and intracellular structural remodeling.
DOI: 10.6084/m9.figshare.20055611.v2
title: Data and R codes for Fan et al. Reconciling Darwin’s naturalization conundrum at the global scale

description: Data and R codes for Fan et al. Reconciling Darwin’s naturalization conundrum at the global scale
DOI: 10.5281/zenodo.4674889
title: Dataset on: First genetic identification of Sundevall's jird Meriones crassus (Rodentia, Muridae) in Morocco and the hypothesis of range extension

description: Rodents from the subfamily Gerbillinae Gray, 1825, are an important component of small fauna in arid and desertic regions in Africa and Asia. Among this group of rodents, Sundevall's jird, <em>Meriones crassus,</em> is one of the most widespread desert species, found in countries ranging from Morocco to Pakistan. In this study, we sequenced the cytochrome b gene of the mitochondrial DNA in two specimens captured in Morocco, constituting the first genetic identification for this species in the African continent. Molecular identification was complemented and supported with morphological evidence. Additionally, we propose the hypothesis of a northward extension of 250 km of the geographic distribution of Sundevall's jird in Morocco, perhaps indicating the increasing desertification affecting North Africa. Further evidence will be required to test the latter hypothesis.
DOI: 10.5281/zenodo.4674888
title: Dataset on: First genetic identification of Sundevall's jird Meriones crassus (Rodentia, Muridae) in Morocco and the hypothesis of range extension

description: Rodents from the subfamily Gerbillinae Gray, 1825, are an important component of small fauna in arid and desertic regions in Africa and Asia. Among this group of rodents, Sundevall's jird, <em>Meriones crassus,</em> is one of the most widespread desert species, found in countries ranging from Morocco to Pakistan. In this study, we sequenced the cytochrome b gene of the mitochondrial DNA in two specimens captured in Morocco, constituting the first genetic identification for this species in the African continent. Molecular identification was complemented and supported with morphological evidence. Additionally, we propose the hypothesis of a northward extension of 250 km of the geographic distribution of Sundevall's jird in Morocco, perhaps indicating the increasing desertification affecting North Africa. Further evidence will be required to test the latter hypothesis.
DOI: 10.6084/m9.figshare.22141154
title: WingShapeBSA

description: Data and code for Pelletier et al 2023 (Genetics) <br> This is the static copy (with DOI) of the data and scripts associated with Pelletier. et al. (2023) Genetics (In Press). Complexities of recapitulating polygenic effects in natural populations: replication of genetic effects on wing shape in artificially selected and wild caught populations of <em>Drosophila melanogaster.</em> <br> <em>scripts and data are also available https://github.com/DworkinLab/WingShapeBSA</em> <br> <em>Sequence data has all been added to NCBI as part of </em> <em>https://www.ncbi.nlm.nih.gov/bioproject/PRJNA936488/</em> <br> <em>pre-print is currently available at</em> <br> <em>https://www.biorxiv.org/content/10.1101/2022.05.12.491649v2</em>
DOI: 10.5281/zenodo.7664617
title: Tampere - Surface runoff in relation to precipitation

description: Results of the computed runoff coefficients from two methods in Vuores neighbourhood of Tampere: 1. direct runoff measurement from a stream; 2. process-based hydraulic modelling for storms with 1-, 10- and 100-year return period with and without the NBS interventions.
DOI: 10.5281/zenodo.7664618
title: Tampere - Surface runoff in relation to precipitation

description: Results of the computed runoff coefficients from two methods in Vuores neighbourhood of Tampere: 1. direct runoff measurement from a stream; 2. process-based hydraulic modelling for storms with 1-, 10- and 100-year return period with and without the NBS interventions.
DOI: 10.5281/zenodo.6557376
title: Dataset on: New finds of naked amoebae in the Black Sea (Ukraine).

description: Our research identified 12 species of naked amoebae of eight morphotypes in the Black Sea (coastal zone of Zatoka village, Odessa region). In more than half of the samples, Vannella devonica, Vannella aberdonica and Thecamoeba orbis were present. The species Saccamoeba marina, Vexillifera armata, Vannella plurinucleolus, Cochliopodium gulosum, and Stenamoeba sp. were rare and infrequent in our samples. The upper layers of the bottom sediment were inhabited by all 12 species of amoebae; two layers were inhabited by S. marina, V. armata, V. devonica, V. aberdonica, Mayorella gemmifera, T. orbis, Stenamoeba sp., Acanthamoeba griffin; three layers were colonized by V. armata, V. devonica, V. aberdonica, T. orbis, Stenamoeba sp., and A. griffini. All amoebae species and their morphotypes occurred at Black Sea water temperatures of +22 ºС to +26 ºС and salinity of 15.5 ‰ to 17.6 ‰. The species V. simplex and A. griffini, which belong to the fan–shaped and acanthopodial morphotypes, respectively, were collected in samples from the Mediterranean Sea at water temperatures of +29 ºС and salinity of 37.8 ‰. The amoebas identified belong to two classes, seven orders, eight families and eight genera.
DOI: 10.5281/zenodo.6557375
title: Dataset on: New finds of naked amoebae in the Black Sea (Ukraine).

description: Our research identified 12 species of naked amoebae of eight morphotypes in the Black Sea (coastal zone of Zatoka village, Odessa region). In more than half of the samples, Vannella devonica, Vannella aberdonica and Thecamoeba orbis were present. The species Saccamoeba marina, Vexillifera armata, Vannella plurinucleolus, Cochliopodium gulosum, and Stenamoeba sp. were rare and infrequent in our samples. The upper layers of the bottom sediment were inhabited by all 12 species of amoebae; two layers were inhabited by S. marina, V. armata, V. devonica, V. aberdonica, Mayorella gemmifera, T. orbis, Stenamoeba sp., Acanthamoeba griffin; three layers were colonized by V. armata, V. devonica, V. aberdonica, T. orbis, Stenamoeba sp., and A. griffini. All amoebae species and their morphotypes occurred at Black Sea water temperatures of +22 ºС to +26 ºС and salinity of 15.5 ‰ to 17.6 ‰. The species V. simplex and A. griffini, which belong to the fan–shaped and acanthopodial morphotypes, respectively, were collected in samples from the Mediterranean Sea at water temperatures of +29 ºС and salinity of 37.8 ‰. The amoebas identified belong to two classes, seven orders, eight families and eight genera.
DOI: 10.5281/zenodo.7035551
title: Dataset on: First record of Brongersma's toad Barbarophryne brongersmai (Anura, Bufonidae) in the central High Atlas Mountains, Morocco.

description: Brongersma’s toad Barbarophryne brongersmai is known in the southern Moroccan Atlantic coast, in the Anti–Atlas, in the arid plain of Marrakech, and in several localities in North–western Algeria. However, its distribution in Morocco is far from clear and its range is not well known. We report a new record of B. brongersmai in Morocco, in the region of the central High Atlas. The habitat type in this region is different from areas where the species has been observed previously. It consists of temporary ponds, located between rock outcrops and filled by stormy rains or snow during the winter. We recommend conducting surveys to collect additional information about this toad in other Moroccan regions, such as in the Middle Atlas where suitable conditions for this species may exist.
DOI: 10.5281/zenodo.7035550
title: Dataset on: First record of Brongersma's toad Barbarophryne brongersmai (Anura, Bufonidae) in the central High Atlas Mountains, Morocco.

description: Brongersma’s toad Barbarophryne brongersmai is known in the southern Moroccan Atlantic coast, in the Anti–Atlas, in the arid plain of Marrakech, and in several localities in North–western Algeria. However, its distribution in Morocco is far from clear and its range is not well known. We report a new record of B. brongersmai in Morocco, in the region of the central High Atlas. The habitat type in this region is different from areas where the species has been observed previously. It consists of temporary ponds, located between rock outcrops and filled by stormy rains or snow during the winter. We recommend conducting surveys to collect additional information about this toad in other Moroccan regions, such as in the Middle Atlas where suitable conditions for this species may exist.
DOI: 10.5281/zenodo.7589891
title: Mercury particle precipitation using full-PIC global simulations

description: Datasets and scripts concerning particle precipitation on the surface of Mercury derived from two implicit full-PIC simulations. We use the code iPIC3D to simulate the interaction between the solar-wind and the planet's magnetic environment. In this file we include (i) the 3D magnetic field data at steadystate, (ii) the particle precipitating on the planets at different times and (iii) the cross-sections of electron induced X-ray fluorescence emission between precipitating electrons and surface ions. Further details on the simulations can be found in: arXiv:2209.08517 To clarify the usage of such different datasets, we include two modules to process the data in python (directory <em>src</em>) and few tests showing the capabilities of these modules (directory <em>test</em>). Images created from such tests can be found in the directory <em>images</em>.
DOI: 10.5281/zenodo.7589890
title: Mercury particle precipitation using full-PIC global simulations

description: Datasets and scripts concerning particle precipitation on the surface of Mercury derived from two implicit full-PIC simulations. We use the code iPIC3D to simulate the interaction between the solar-wind and the planet's magnetic environment. In this file we include (i) the 3D magnetic field data at steadystate, (ii) the particle precipitating on the planets at different times and (iii) the cross-sections of electron induced X-ray fluorescence emission between precipitating electrons and surface ions. Further details on the simulations can be found in: arXiv:2209.08517 To clarify the usage of such different datasets, we include two modules to process the data in python (directory <em>src</em>) and few tests showing the capabilities of these modules (directory <em>test</em>). Images created from such tests can be found in the directory <em>images</em>.