cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6306077.v1
title: Novel model coupling approach for resilience analysis of coastal plant communities

description: Additional data for accepted publication (please cite):Schibalski, A., K. Körner, M. Maier, F. Jeltsch. <b>Novel model coupling approach for resilience analysis of<br>coastal plant communities</b>. <i>Ecological Applications</i>. <br><br>Contains: <br>- R-Markdown script (README.html) which explains content and format of provided data files which are:- time series data (2010-2100) for three example polygons at the German Baltic Sea coast, i.e. groundwater level and salinity, land use intensity, predicted species occurrence for <i>Lolium perenne</i> and <i>Scirpus maritimus</i>- lookup tables of return times following short-term disturbances from simulation experiments with individual-based model IBC-grass_coast- control-treatment differences of the same simulation experiments<br>This data allows reproducing central <b>Fig. 7</b> in Schibalski et al. (2018).<br>
DOI: 10.6084/m9.figshare.6304529
title: Data collected in this study and used for analysis (Figure 2A and inset) from A universal growth limit for circular lichens

description: Data for the 53 individuals included in Figure 2A and inset. Columns: original individual ID, individual #, surface area in the year 2005 to 2011 in square cm. Protocol described in the main text.
DOI: 10.6084/m9.figshare.6304529.v1
title: Data collected in this study and used for analysis (Figure 2A and inset) from A universal growth limit for circular lichens

description: Data for the 53 individuals included in Figure 2A and inset. Columns: original individual ID, individual #, surface area in the year 2005 to 2011 in square cm. Protocol described in the main text.
DOI: 10.6084/m9.figshare.6304427
title: Input file for R analysis (phenotypic data) from Macroevolutionary consequences of sexual conflict

description: File containing the phenotypic data used in the phylogenetic comparative analysis of intersexual trait integration. Convert to .xls before running script.
DOI: 10.6084/m9.figshare.6304427.v1
title: Input file for R analysis (phenotypic data) from Macroevolutionary consequences of sexual conflict

description: File containing the phenotypic data used in the phylogenetic comparative analysis of intersexual trait integration. Convert to .xls before running script.
DOI: 10.6084/m9.figshare.6304421
title: Input file for R analysis (phylogenetic tree, nexus format) from Macroevolutionary consequences of sexual conflict

description: File containing the phylogenetic tree (nexus format) used in the phylogenetic comparative analysis of intersexual trait integration.
DOI: 10.6084/m9.figshare.6304421.v1
title: Input file for R analysis (phylogenetic tree, nexus format) from Macroevolutionary consequences of sexual conflict

description: File containing the phylogenetic tree (nexus format) used in the phylogenetic comparative analysis of intersexual trait integration.
DOI: 10.6084/m9.figshare.6304418
title: R script from Macroevolutionary consequences of sexual conflict

description: R script for doing the phylogenetic comparative analysis of intersexual trait integration
DOI: 10.6084/m9.figshare.6304400
title: EtNAM data

description: This object includes original files and scripts for the EtNAM population paper by Kidane et al. published on the Plant Biotechnology Journal and available open acces at doi:10.1111/pbi.13062Included, you will find:-genotypic data developed on EtNAM RILs using the Illumina Infinium 15k wheat array at TraitGenetics GmbH (in hmp and vcf format). SNP positions are derived from the wild emmer wheat genome (see paper for details).-phenotypic data for phenology and plant height.-R scripts used to generate the analyses featured in the paper.<br><br>
DOI: 10.6084/m9.figshare.6304418.v1
title: R script from Macroevolutionary consequences of sexual conflict

description: R script for doing the phylogenetic comparative analysis of intersexual trait integration
DOI: 10.6084/m9.figshare.6304157
title: Example_Segmentation_BioconductorForum.R

description: Code (R, EBImage) for segmentation of Nucleus, cells and specks<br>
DOI: 10.6084/m9.figshare.6304157.v1
title: Example_Segmentation_BioconductorForum.R

description: Code (R, EBImage) for segmentation of Nucleus, cells and specks<br>
DOI: 10.6084/m9.figshare.6304148
title: Img405.tiff

description: Nuclei
DOI: 10.6084/m9.figshare.6304148.v1
title: Img405.tiff

description: Nuclei
DOI: 10.6084/m9.figshare.6303926
title: Supplementary Material for: Extracorporeal Photopheresis: An Efficacious and Well-Tolerated Treatment for Cutaneous and Oral Mucosal Chronic Graft-versus-Host Disease

description: <b><i>Background:</i></b> Extracorporeal photopheresis (ECP) is a second-line therapy for steroid-refractory chronic graft-versus-host disease (cGVHD). <b><i>Objective:</i></b> We describe the long-term efficacy and tolerability of ECP according to the cutaneous phenotype of cGVHD and report on the reduced need for immunosuppressant drugs in this setting. <b><i>Patients and Methods:</i></b> Fourteen patients (8 females) with cutaneous and/or mucosal cGVHD, treated with ECP between October 2010 and May 2016 within a single center, were included. Final analyses included patients who had received ECP for at least 12 months. We prospectively evaluated the efficacy of ECP using lesion-specific clinical scores and by recording changed doses of systemic immunosuppressants. <b><i>Results:</i></b> Of the 14 patients, sclerotic skin lesions were present in 10 (71%). The mRODNAN score decreased in all patients from month 9 onwards, with 40 and 77% reductions at 12 and 36 months, respectively. Six patients (43%) presented with cutaneous lichenoid lesions: this score was reduced in all patients by month 3, reaching a 93% reduction by month 12. Five patients (36%) experienced oral mucosal lichenoid lesions: these scores were decreased by 55% at month 12 and by 100% by month 33. The use of systemic immunosuppressants was reduced in all patients; 4 patients could stop all immunosuppressant drugs after 2 years. ECP was stopped in 3 patients after a complete response. No major ECP-associated adverse effects were observed. <b><i>Discussion and Conclusion:</i></b> ECP was an effective long-term therapy for oral and cutaneous cGVHD: consequently, dose levels of therapeutic immunosuppression could be reduced.
DOI: 10.6084/m9.figshare.6303926.v1
title: Supplementary Material for: Extracorporeal Photopheresis: An Efficacious and Well-Tolerated Treatment for Cutaneous and Oral Mucosal Chronic Graft-versus-Host Disease

description: <b><i>Background:</i></b> Extracorporeal photopheresis (ECP) is a second-line therapy for steroid-refractory chronic graft-versus-host disease (cGVHD). <b><i>Objective:</i></b> We describe the long-term efficacy and tolerability of ECP according to the cutaneous phenotype of cGVHD and report on the reduced need for immunosuppressant drugs in this setting. <b><i>Patients and Methods:</i></b> Fourteen patients (8 females) with cutaneous and/or mucosal cGVHD, treated with ECP between October 2010 and May 2016 within a single center, were included. Final analyses included patients who had received ECP for at least 12 months. We prospectively evaluated the efficacy of ECP using lesion-specific clinical scores and by recording changed doses of systemic immunosuppressants. <b><i>Results:</i></b> Of the 14 patients, sclerotic skin lesions were present in 10 (71%). The mRODNAN score decreased in all patients from month 9 onwards, with 40 and 77% reductions at 12 and 36 months, respectively. Six patients (43%) presented with cutaneous lichenoid lesions: this score was reduced in all patients by month 3, reaching a 93% reduction by month 12. Five patients (36%) experienced oral mucosal lichenoid lesions: these scores were decreased by 55% at month 12 and by 100% by month 33. The use of systemic immunosuppressants was reduced in all patients; 4 patients could stop all immunosuppressant drugs after 2 years. ECP was stopped in 3 patients after a complete response. No major ECP-associated adverse effects were observed. <b><i>Discussion and Conclusion:</i></b> ECP was an effective long-term therapy for oral and cutaneous cGVHD: consequently, dose levels of therapeutic immunosuppression could be reduced.
DOI: 10.6084/m9.figshare.6303908
title: Supplementary data to the article "Development of a marmalade for patients with type 2 diabetes: Sensory characteristics and acceptability"

description: This is a set of a raw data from sensory analysis of marmalades with modified carbohydrate profile. The data is prepared for further statistical analysis using R.
DOI: 10.6084/m9.figshare.6303812
title: Untitled ItemInvestigating arginine versus lysine relative contents as compared to GC-content in Prokaryotes

description: dataset of prokaryotic genomes, proteins and coding sequences for exercises in basic bioinformatics
DOI: 10.6084/m9.figshare.6303812.v1
title: Untitled ItemInvestigating arginine versus lysine relative contents as compared to GC-content in Prokaryotes

description: dataset of prokaryotic genomes, proteins and coding sequences for exercises in basic bioinformatics
DOI: 10.6084/m9.figshare.6303719
title: Multi-institutional study of the variability in target delineation for six targets commonly treated with radiosurgery

description: <b>Background:</b> Although accurate delineation of the target is a key factor of success in radiosurgery there are no consensus guidelines for target contouring. <b>Aim:</b> The aim of the present study was therefore to quantify the variability in target delineation and discuss the potential clinical implications, for six targets regarded as common in stereotactic radiosurgery. <b>Material and methods:</b> Twelve Gamma Knife centers participated in the study by contouring the targets and organs at risks and performing the treatment plans. Analysis of target delineation variability was based on metrics defined based on agreement volumes derived from overlapping structures following a previously developed method. The 50% agreement volume (AV<sub>50</sub>), the common and the encompassing volumes as well as the Agreement Volume Index (AVI) were determined. <b>Results:</b> Results showed that the lowest AVI (0.16) was found for one of the analyzed metastases (range of delineated volumes 1.27–3.33 cm<sup>3</sup>). AVI for the other two metastases was 0.62 and 0.37, respectively. Corresponding AVIs for the cavernous sinus meningioma, pituitary adenoma and vestibular schwannoma were 0.22, 0.37 and 0.50. <b>Conclusions:</b> This study showed that the variability in the contouring was much higher than expected and therefore further work in standardizing the contouring practice in radiosurgery is warranted.
DOI: 10.6084/m9.figshare.6303719.v1
title: Multi-institutional study of the variability in target delineation for six targets commonly treated with radiosurgery

description: <b>Background:</b> Although accurate delineation of the target is a key factor of success in radiosurgery there are no consensus guidelines for target contouring. <b>Aim:</b> The aim of the present study was therefore to quantify the variability in target delineation and discuss the potential clinical implications, for six targets regarded as common in stereotactic radiosurgery. <b>Material and methods:</b> Twelve Gamma Knife centers participated in the study by contouring the targets and organs at risks and performing the treatment plans. Analysis of target delineation variability was based on metrics defined based on agreement volumes derived from overlapping structures following a previously developed method. The 50% agreement volume (AV<sub>50</sub>), the common and the encompassing volumes as well as the Agreement Volume Index (AVI) were determined. <b>Results:</b> Results showed that the lowest AVI (0.16) was found for one of the analyzed metastases (range of delineated volumes 1.27–3.33 cm<sup>3</sup>). AVI for the other two metastases was 0.62 and 0.37, respectively. Corresponding AVIs for the cavernous sinus meningioma, pituitary adenoma and vestibular schwannoma were 0.22, 0.37 and 0.50. <b>Conclusions:</b> This study showed that the variability in the contouring was much higher than expected and therefore further work in standardizing the contouring practice in radiosurgery is warranted.
DOI: 10.6084/m9.figshare.6303713
title: bamboo-eating pandas gut metagenomes

description: The putative cyanide compounds degradation
DOI: 10.6084/m9.figshare.6303311
title: Supplementary Material for: The Neonatal Microbiome and Its Partial Role in Mediating the Association between Birth by Cesarean Section and Adverse Pediatric Outcomes

description: <b><i>Background:</i></b> Cesarean sections (CS) are among the most commonly performed surgical procedures in the world. Epidemiologic data has associated delivery by CS with an increased risk of certain adverse health outcomes in children, such as asthma and obesity. <b><i>Objective:</i></b> To explore what is known about the effect of mode of delivery on the development of the infant microbiome and discuss the potentially mediating role of CS-related microbial dysbiosis in the development of adverse pediatric health outcomes. Recommendations for future inquiry are also provided. <b><i>Methods:</i></b> This study provides a narrative overview of the literature synthesizing the findings of literature retrieved from searches of PubMed and other computerized databases and authoritative texts. <b><i>Results:</i></b> Emerging evidence suggests that mode of delivery is involved in the development of the neonatal microbiome and may partially explain pediatric health outcomes associated with birth by CS. Specifically, the gut microbiome of vaginally delivered infants more closely resembles their mothers’ vaginal microbiome and thus more commonly consists of potentially beneficial microbiota such as <i>Lactobacillus</i>,<i> Bifidobacterium</i>, and <i>Bacteroides</i>. Conversely, the microbiome of infants born via CS shows an increased prevalence of either skin flora or potentially pathogenic microbial communities such as <i>Klebsiella</i>, <i>Enterococcus</i>, and <i>Clostridium</i>. <b><i>Conclusions:</i></b> Mode of delivery plays an important role in the development of the postnatal microbiome but likely tells only part of the story. More comprehensive investigations into all the pre- and perinatal factors that have the potential to contribute to the neonatal microbiome are warranted.
DOI: 10.15131/shef.data.6302876
title: Adaptive designs CONSORT Extension: Delphi survey summaries

description: 1) Characteristics and demographics of registered participants and responders2) Summary of ratings in Delphi Round 1 and 2 surveys <br><br>
DOI: 10.15131/shef.data.6302876.v1
title: Adaptive designs CONSORT Extension: Delphi survey summaries

description: 1) Characteristics and demographics of registered participants and responders2) Summary of ratings in Delphi Round 1 and 2 surveys <br><br>
DOI: 10.6084/m9.figshare.6302042
title: Albacore only nanopore reads

description: These files contain the nanopore long reads produced by R9.4 MinION, basecalled and demultiplexed by Albacore v2.1.3. <br>Half of each strain's sample underwent FFPE repair, and half did not - these were sequenced under different barcodes. The samples here have had the reads from both barcodes pooled (see "Albacore + Porechop nanopore reads" for the individual readsets).<br><br>The "all" Porechopped reads will also be available from SRA (accessions SAMN09500966 to SAMN09500970).
DOI: 10.6084/m9.figshare.6301976
title: MM parameters for covalent adducts of Clavulanate degradation by beta-lactamases

description: This dataset contains parameters for the acyl-enzyme complexes simulated in the following work:<br>Multiscale simulations establish clavulanate inhibition efficiency and the responsible enzyme complex in class A β-lactamases. [1]Rubén A. Fritz, Jans H. Alzate-Morales, James Spencer, Adrian J. Mulholland and Marc W. Van der Kamp. <br>MM parameters for the following covalent complexes resulting from inhibition with clavulanate are present: <br>AEC - acyl-enzyme complex of clavulanate (incl. Ser70) Files: AEC.off, AEC.frcmod Residue name: AEC <br>TEDC - decarboxylated trans-enamine complex (incl. Ser70) that is the result of opening of the five-membered ring (leading to an imine intermediate) and subsequent rearrangement [2,3] <br>Files: TEDC.off, TEDC.frcmod Residue name: TDC<br>ADEC - aldehyde complex (incl. Ser70) that is the result of consecutive reactions of the cis-enamine [2,3] Files: ADEC.off, ADEC.frcmod Residue name: ADC <br>Parameterisation procedure: Initial Amber ff14SB force field parameters for the acylated residue in the models (adducts) were obtained from the RED Server (partial charges from HF/6-31G(d,p) RESP-fitting and atom types). For missing parameters, chemically equivalent parameters from the GAFF force field were used. <br>[1] Fritz RA, Alzate-Morales JH, Spencer J, Mulholland AJ and Van der Kamp MW. Biochemistry (2018). Under review.[2] Drawz, S. M., and Bonomo, R. a. (2010) Three decades of β-lactamase inhibitors. Clin. Microbiol. Rev. 23, 160–201. [3] Helfand, M. S., Totir, M. A., Carey, M. P., Hujer, A. M., Bonomo, R. A., and Carey, P. R. (2003) Following the Reactions of Mechanism-Based Inhibitors with β-Lactamase by Raman Crystallography. Biochemistry 42, 13386–13392.
DOI: 10.6084/m9.figshare.6301976.v1
title: MM parameters for covalent adducts of Clavulanate degradation by beta-lactamases

description: This dataset contains parameters for the acyl-enzyme complexes simulated in the following work:<br>Multiscale simulations establish clavulanate inhibition efficiency and the responsible enzyme complex in class A β-lactamases. [1]Rubén A. Fritz, Jans H. Alzate-Morales, James Spencer, Adrian J. Mulholland and Marc W. Van der Kamp. <br>MM parameters for the following covalent complexes resulting from inhibition with clavulanate are present: <br>AEC - acyl-enzyme complex of clavulanate (incl. Ser70) Files: AEC.off, AEC.frcmod Residue name: AEC <br>TEDC - decarboxylated trans-enamine complex (incl. Ser70) that is the result of opening of the five-membered ring (leading to an imine intermediate) and subsequent rearrangement [2,3] <br>Files: TEDC.off, TEDC.frcmod Residue name: TDC<br>ADEC - aldehyde complex (incl. Ser70) that is the result of consecutive reactions of the cis-enamine [2,3] Files: ADEC.off, ADEC.frcmod Residue name: ADC <br>Parameterisation procedure: Initial Amber ff14SB force field parameters for the acylated residue in the models (adducts) were obtained from the RED Server (partial charges from HF/6-31G(d,p) RESP-fitting and atom types). For missing parameters, chemically equivalent parameters from the GAFF force field were used. <br>[1] Fritz RA, Alzate-Morales JH, Spencer J, Mulholland AJ and Van der Kamp MW. Biochemistry (2018). Under review.[2] Drawz, S. M., and Bonomo, R. a. (2010) Three decades of β-lactamase inhibitors. Clin. Microbiol. Rev. 23, 160–201. [3] Helfand, M. S., Totir, M. A., Carey, M. P., Hujer, A. M., Bonomo, R. A., and Carey, P. R. (2003) Following the Reactions of Mechanism-Based Inhibitors with β-Lactamase by Raman Crystallography. Biochemistry 42, 13386–13392.
DOI: 10.21227/cjqz-hk03
title: Learning Behavior Analytics Dataset

description: This dataset represents the main different unique learning behaviors that may be found in any group of learners in e-learning/educational systems. It represents 20 learners through 17 OERs.
DOI: 10.6084/m9.figshare.6301070
title: Abundance percentages of variables and palynomorphs used for statistical analyses. Controls on sedimentation and vegetation in an Eocene pull-apart basin (Prinz von Hessen, Germany): evidence from palynology

description: Table 2: Abundance percentages of variables and palynomorphs used for statistical analyses.
DOI: 10.6084/m9.figshare.6301070.v1
title: Abundance percentages of variables and palynomorphs used for statistical analyses. Controls on sedimentation and vegetation in an Eocene pull-apart basin (Prinz von Hessen, Germany): evidence from palynology

description: Table 2: Abundance percentages of variables and palynomorphs used for statistical analyses.
DOI: 10.6084/m9.figshare.6300992
title: qPCR Senegalese sole juveniles Stress Coping Styles.xlsx

description: These data are related to behavioural traits in a population of early Senegalese sole juveniles and the linkage between these categories (personalities) and brain mRNAs abundance.
DOI: 10.6084/m9.figshare.6300992.v1
title: qPCR Senegalese sole juveniles Stress Coping Styles.xlsx

description: These data are related to behavioural traits in a population of early Senegalese sole juveniles and the linkage between these categories (personalities) and brain mRNAs abundance.
DOI: 10.6084/m9.figshare.6300260
title: Tabla 1.jpg

description: NÚMERO DE PARTICIPANTES EN TODA LA PROGRAMACIÓN DE MEDIALAB MADRID DURANTE EL PERÍODO 2002-2006.<br><br>NÚMERO DE VISITAS A LAS EXPOSICIONES. 2002-2006<br>Presencia en medios Medilab Madrid. 2002-2006<br><br>
DOI: 10.6084/m9.figshare.6300260.v1
title: Tabla 1.jpg

description: NÚMERO DE PARTICIPANTES EN TODA LA PROGRAMACIÓN DE MEDIALAB MADRID DURANTE EL PERÍODO 2002-2006.<br><br>NÚMERO DE VISITAS A LAS EXPOSICIONES. 2002-2006<br>Presencia en medios Medilab Madrid. 2002-2006<br><br>
DOI: 10.6084/m9.figshare.6300110
title: Dressed Primordial Black Holes Binaries - Simulations

description: Simulations results (in the form of Gadget-2 snapshots) for the paper "Black Holes' Dark Dress: On the merger rate of a subdominant population of primordial black holes".<br>The simulations follow the evolution of binary system of two primordial black holes, each dressed with a local Dark Matter halo.<br>Further details can be found at the associated GitHub repo - https://github.com/bradkav/BlackHolesDarkDress.
DOI: 10.6084/m9.figshare.12893441.v1
title: R0191_20171001a_videos

description: Rat 0191, skilled reaching data collected on 10/1/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.6300110.v1
title: Dressed Primordial Black Holes Binaries - Simulations

description: Simulations results (in the form of Gadget-2 snapshots) for the paper "Black Holes' Dark Dress: On the merger rate of a subdominant population of primordial black holes".<br>The simulations follow the evolution of binary system of two primordial black holes, each dressed with a local Dark Matter halo.<br>Further details can be found at...
DOI: 10.6084/m9.figshare.6300110.v2
title: Dressed Primordial Black Holes Binaries - Simulations

description: Simulations results (in the form of Gadget-2 snapshots) for the paper "Black Holes' Dark Dress: On the merger rate of a subdominant population of primordial black holes".<br>The simulations follow the evolution of binary system of two primordial black holes, each dressed with a local Dark Matter halo.<br>Further details can be found at...
DOI: 10.6084/m9.figshare.6300110.v3
title: Dressed Primordial Black Holes Binaries - Simulations

description: Simulations results (in the form of Gadget-2 snapshots) for the paper "Black Holes' Dark Dress: On the merger rate of a subdominant population of primordial black holes".<br>The simulations follow the evolution of binary system of two primordial black holes, each dressed with a local Dark Matter halo.<br>Further details can be found at...
DOI: 10.6084/m9.figshare.6300110.v4
title: Dressed Primordial Black Holes Binaries - Simulations

description: Simulations results (in the form of Gadget-2 snapshots) for the paper "Black Holes' Dark Dress: On the merger rate of a subdominant population of primordial black holes".<br>The simulations follow the evolution of binary system of two primordial black holes, each dressed with a local Dark Matter halo.<br>Further details can be found at...