cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13720327.v1
title: Exploring the structural transition mechanisms of a pair of poly(<i>N</i>-isopropylacrylamide) chains in aqueous solution through coarse-grained molecular simulations coupled with metadynamics

description: Thermo-responsive polymers can experience the coil-to-globule transition with the temperature increases through the lower critical solution temperature (LCST). In this work, the coarse-grained molecular dynamics and Metadynamics (MetaD) are employed to investigate the dynamics and thermodynamics of structural change of a pair of poly(N-isopropylacrylamide) (PNIPAM) chains in aqueous solution. The results reveal that the PNIPAM molecules can move freely in aqueous solution below LCST, resulting in many extended conformations moving among several free energy basins on the free energy surface (FES); and these structures are dominated by the interaction force between PNIPAM and the water molecules. However, the PNIPAM molecules aggregate above LCST with collapsed conformations, leading to a deep basin on the FES; and these structures are dominated by the force between neighbouring PNIPAM chains. Each of the dominant mechanisms, namely, PNIPAM–water interaction force and intermolecular interaction force between PNIPAM chains, has an extreme tendency and corresponds to the extended and collapsed structures, respectively. However, the compromise in competition between these two mechanisms inevitably results in different characteristic structures including the extended and collapsed ones. In addition, the evolution of the trajectories at different temperatures are also analysed to examine the pathway of structural change.
DOI: 10.17028/rd.lboro.22633237.v1
title: Supplementary information files for: A light-management film layer induces dramatically enhanced acetate production in photo-assisted microbial electrosynthesis systems

description: Supplementary files for article A light-management film layer induces dramatically enhanced acetate production in photo-assisted microbial electrosynthesis systems.
 A light-management system consisting of a Al-doped ZnO (AZO) film layer was combined for the first time with different bio-photocathodes (<em>Serratia marcescens</em> Q1 electrotroph immobilized on g-C<sub>3</sub>N<sub>4</sub>, MnFe<sub>2</sub>O<sub>4</sub> or MnFe<sub>2</sub>O<sub>4</sub>/g-C<sub>3</sub>N<sub>4</sub>) to significantly enhance acetate production from bicarbonate in photo-assisted microbial electrosynthesis systems (MES). The AZO light-management system exhibiting optical properties independent of the light incident angle mitigated the shielding effect of light by electrotrophs, increasing light trapping and decreasing light reflection, ultimately allowing higher rates of photon absorption and redistributions of photons over the photo-active layers. As a result, more reducing equivalents as H<sub>2</sub> produced up to 242% (g-C<sub>3</sub>N<sub>4</sub>/AZO-filter) and 543% (g-C<sub>3</sub>N<sub>4</sub>/AZO) increase in acetate production at coulombic efficiencies of 70% (g-C<sub>3</sub>N<sub>4</sub>/AZO-filter) and 81% (g-C<sub>3</sub>N<sub>4</sub>/AZO). The record high solar-to-acetate efficiency obtained with the MnFe<sub>2</sub>O<sub>4</sub>/g-C<sub>3</sub>N<sub>4</sub>/AZO biocathode was 3.20%. The light-management system proposed in this study opens a new promising way to construct efficient bio-photocathodes for inorganic carbon reduction in photo-assisted MES.
DOI: 10.6084/m9.figshare.10057784
title: MOESM1 of Case report: whole genome sequencing based investigation of maternal-neonatal listeriosis in Sichuan, China

description: Additional file 1: Table S1. Location of the 57 SNPs between the patientâ s isolate and the RTE food isolate. The SNP differences and the location of the 57 SNPs between the RTE food isolate (LM8) and the patientâ s isolate (LM1) were listed using LM188 (GenBank accession No. CP015593.1) as the reference. The SNPs on the core genes of L. monocytogenes were also indicated. Table S2. The cgMLST types of the patients and food source L. monocytogenes strains isolated at different time point in this case investigation. The cgMLST types of the patients and food source L. monocytogenes were assigned by the cgMLST database ( https://bigsdb.pasteur.fr ), with allele profiles offered) Table S3. The annotation of plasmid pLM1686 and the distribution of the genes in the other three online plasmids (identity 70%). The circular sequence of the plasmid pLM1686 was assembled with SKESA v2.3 using the raw reads of Illumina sequencing. The plasmid sequence was annotated with Prokka v1.12. The annotation of the pLM1686 were compared with the online plasmids of L. monocytogenes using Roary v3.11.2 with the identity of 70% as the cut-off. Plasmid pLM1686 was found to be most similar to the previously reported Listeria plasmid pLMR479a sharing 79 genes. The remaining 12 unshared genes of pLM1686 with pLMR479a, were present in either plasmid pLM6179 or pLM5578.
DOI: 10.6084/m9.figshare.7429154.v1
title: Additional file 8: of Profiling the miRNA-mRNA-lncRNA interaction network in MSC osteoblast differentiation induced by (+)-cholesten-3-one

description: Primer sequences used for qRT-PCR. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.10057784.v1
title: MOESM1 of Case report: whole genome sequencing based investigation of maternal-neonatal listeriosis in Sichuan, China

description: Additional file 1: Table S1. Location of the 57 SNPs between the patientâ s isolate and the RTE food isolate. The SNP differences and the location of the 57 SNPs between the RTE food isolate (LM8) and the patientâ s isolate (LM1) were listed using LM188 (GenBank accession No. CP015593.1) as the reference. The SNPs on the core genes of L. monocytogenes were also indicated. Table S2. The cgMLST types of the patients and food source L. monocytogenes strains isolated at different time point in this case investigation. The cgMLST types of the patients and food source L. monocytogenes were assigned by the cgMLST database ( https://bigsdb.pasteur.fr ), with allele profiles offered) Table S3. The annotation of plasmid pLM1686 and the distribution of the genes in the other three online plasmids (identity 70%). The circular sequence of the plasmid pLM1686 was assembled with SKESA v2.3 using the raw reads of Illumina sequencing. The plasmid sequence was annotated with Prokka v1.12. The annotation of the pLM1686 were compared with the online plasmids of L. monocytogenes using Roary v3.11.2 with the identity of 70% as the cut-off. Plasmid pLM1686 was found to be most similar to the previously reported Listeria plasmid pLMR479a sharing 79 genes. The remaining 12 unshared genes of pLM1686 with pLMR479a, were present in either plasmid pLM6179 or pLM5578.
DOI: 10.6084/m9.figshare.10057808
title: MOESM1 of Neutral lipid storage disease with myopathy in China: a large multicentric cohort study

description: Additional file 1. Muscle fatty infiltration score on leg MRI of 21 NLSDM patients. Score of the fatty infiltration in individual muscles. (L): Left leg was more severe and selected for scoring; (R), Right leg was more severe and selected for scoring. Abbreviations: see Fig. 3.
DOI: 10.6084/m9.figshare.10057808.v1
title: MOESM1 of Neutral lipid storage disease with myopathy in China: a large multicentric cohort study

description: Additional file 1. Muscle fatty infiltration score on leg MRI of 21 NLSDM patients. Score of the fatty infiltration in individual muscles. (L): Left leg was more severe and selected for scoring; (R), Right leg was more severe and selected for scoring. Abbreviations: see Fig. 3.
DOI: 10.6084/m9.figshare.10057817
title: MOESM2 of Neutral lipid storage disease with myopathy in China: a large multicentric cohort study

description: Additional file 2. Muscle edema score on leg MRI of 21 NLSDM patients. Score of the muscle edema in individual muscles. Abbreviations: See Fig. 3.
DOI: 10.6084/m9.figshare.10057817.v1
title: MOESM2 of Neutral lipid storage disease with myopathy in China: a large multicentric cohort study

description: Additional file 2. Muscle edema score on leg MRI of 21 NLSDM patients. Score of the muscle edema in individual muscles. Abbreviations: See Fig. 3.
DOI: 10.6084/m9.figshare.5863527
title: Landfill leachate treatment by coagulation/flocculation combined with microelectrolysis-Fenton processes

description: Landfill leachate was pretreated by chemical flocculation with polyaluminum chloride (PAC) as a flocculant, and subsequently purified by the microelectrolysis-Fenton (MEF) process. Response surface methodology was employed to optimize the MEF process, and the optimal conditions were initial pH 3.20, H<sub>2</sub>O<sub>2</sub> concentration 3.57 g/L, and Fe-C dosage 104.52 g/L. The PAC coagulation combined with MEF processes obtained a superior decontamination performance, and the predicted chemical oxygen demand (COD) and humic acids (HA) removal were respectively 90.27% and 93.79%. The strong fluorescence peak at 425 nm and the trapping experiment showed that ⋅OH was generated during MEF, which had a strong oxidation ability to degrade organic recalcitrant pollutants. The ultraviolet–visible spectra and three-dimensional excitation–emission matrices spectra (3D-EEMs) indicated that PAC coagulation could preferentially remove protein-like substances, while the MEF process was effective in destructing organic recalcitrant pollutants, especially humic-like and fulvic-like substances.
DOI: 10.5281/zenodo.10634975
title: SWECO25: Remote Sensing (rs)

description: The remote-sensing indices category contains the "sdc" dataset. 

The sdc dataset (remote-sensing indices category) provides data on vegetation indices in Switzerland. After reprojecting and resampling data from the Swiss Data cube (Chatenoux et al., 2021) to the SWECO25 grid, we generated mean and standard deviation layers for five indices (NDVI, NDWI, LAI, GCI, and EVI) at a yearly time step for the 1996-2021 period, when available. This dataset includes a total of 243 layers. Final values were rounded and multiplied by 100. However, for layers that were initially multiplied by 1000 (LAI, GCI, EVI), they were divided by 10 instead. The detailed list of layers available is provided in SWECO25_datalayers_details_rs.csv and includes information on the category, dataset, variable name (long), variable name (short), period, sub-period, start year, end year, attribute, radii, unit, and path.

References:

Chatenoux, B. et al. The Swiss data cube, analysis ready data archive using earth observations of Switzerland. Scientific data 8, 295 (2021).

Külling, N., Adde, A., Fopp, F., Schweiger, A. K., Broennimann, O., Rey, P.-L., Giuliani, G., Goicolea, T., Petitpierre, B., Zimmermann, N. E., Pellissier, L., Altermatt, F., Lehmann, A., & Guisan, A. (2024). SWECO25: A cross-thematic raster database for ecological research in Switzerland. Scientific Data, 11(1), Article 1. https://doi.org/10.1038/s41597-023-02899-1

V2: metadata update
description: We gratefully acknowledge financial support through the Action Plan of the Swiss Biodiversity Strategy by the Federal Office for the Environment (FOEN) for financing the ValPar.CH and SwissCatchment projects. All the institutions and contributors who made the input data freely available are gratefully acknowledged.
DOI: 10.5281/zenodo.7994480
title: SWECO25: Remote Sensing (rs)

description: The remote-sensing indices category contains the "sdc" dataset. 

The sdc dataset (remote-sensing indices category) provides data on vegetation indices in Switzerland. After reprojecting and resampling data from the Swiss Data cube (Chatenoux et al., 2021) to the SWECO25 grid, we generated mean and standard deviation layers for five indices (NDVI, NDWI, LAI, GCI, and EVI) at a yearly time step for the 1996-2021 period, when available. This dataset includes a total of 243 layers. Final values were rounded and multiplied by 100. However, for layers that were initially multiplied by 1000 (LAI, GCI, EVI), they were divided by 10 instead. The detailed list of layers available is provided in SWECO25_datalayers_details_rs.csv and includes information on the category, dataset, variable name (long), variable name (short), period, sub-period, start year, end year, attribute, radii, unit, and path.

References:

Chatenoux, B. et al. The Swiss data cube, analysis ready data archive using earth observations of Switzerland. Scientific data 8, 295 (2021).

Külling, N., Adde, A., Fopp, F., Schweiger, A. K., Broennimann, O., Rey, P.-L., Giuliani, G., Goicolea, T., Petitpierre, B., Zimmermann, N. E., Pellissier, L., Altermatt, F., Lehmann, A., & Guisan, A. (2024). SWECO25: A cross-thematic raster database for ecological research in Switzerland. Scientific Data, 11(1), Article 1. https://doi.org/10.1038/s41597-023-02899-1

V2: metadata update
description: We gratefully acknowledge financial support through the Action Plan of the Swiss Biodiversity Strategy by the Federal Office for the Environment (FOEN) for financing the ValPar.CH and SwissCatchment projects. All the institutions and contributors who made the input data freely available are gratefully acknowledged.
DOI: 10.5281/zenodo.7994481
title: SWECO25: Remote Sensing (rs)

description: The remote-sensing indices category (SWECO25 v1.0.0) contains the "sdc" dataset. 

The sdc dataset (remote-sensing indices category) provides data on vegetation indices in Switzerland. After reprojecting and resampling data from the Swiss Data cube (Chatenoux et al., 2021) to the SWECO25 grid, we generated mean and standard deviation layers for five indices (NDVI, NDWI, LAI, GCI, and EVI) at a yearly time step for the 1996-2021 period, when available. This dataset includes a total of 243 layers. Final values were rounded and multiplied by 100. However, for layers that were initially multiplied by 1000 (LAI, GCI, EVI), they were divided by 10 instead. The detailed list of layers available is provided in SWECO25_datalayers_details_rs.csv and includes information on the category, dataset, variable name (long), variable name (short), period, sub-period, start year, end year, attribute, radii, unit, and path.

References:

Chatenoux, B. et al. The Swiss data cube, analysis ready data archive using earth observations of Switzerland. Scientific data 8, 295 (2021).
description: We gratefully acknowledge financial support through the Action Plan of the Swiss Biodiversity Strategy by the Federal Office for the Environment (FOEN) for financing the ValPar.CH and SwissCatchment projects. All the institutions and contributors who made the input data freely available are gratefully acknowledged.
DOI: 10.6084/m9.figshare.7436486
title: DEGs in transcriptome of virulent CN-Bx1 and avirulent US-Bx1. from Enhancement of oxidative stress contributes to increased pathogenicity of the invasive pine wood nematode

description: Reactive oxygen species (ROS) play important roles in defence response of host plants versus pathogens. While generation and detoxification of ROS is well understood, how varied ability of different isolates of pathogens to overcome host ROS, or ROS contribution to a particular isolate's pathogenicity, remains largely unexplored. Here, we report that transcriptional regulation of ROS pathway, in combination with the insulin pathway, increases the pathogenicity of invasive species <i>Bursaphelenchus xylophilus</i>. The results showed a positive correlation between fecundity and pathogenicity of different nematode isolates. The virulent isolates from introduced populations in Japan, China and Europe had significantly higher fecundity than native avirulent isolates from the USA. Increased expression of <i>Mn-SOD</i> and reduced expression of <i>catalase</i>/<i>GPX-5</i> and H<sub>2</sub>O<sub>2</sub> accumulation during invasion are associated with virulent strains. Additional H<sub>2</sub>O<sub>2</sub> could improve fecundity of <i>B. xylophilus</i>. Furthermore, depletion of <i>Mn-SOD</i> decreased fecundity and virulence of <i>B. xylophilus</i>, while insulin pathway is significantly affected. Thus, we propose that destructive pathogenicity of <i>B. xylophilus</i> to pines is partly due to upregulated fecundity modulated by insulin pathway in association with ROS pathway and further enhanced by H<sub>2</sub>O<sub>2</sub> oxidative stress. These findings provide a better understanding of pathogenic mechanisms in plant–pathogen interactions and adaptive evolution of invasive species.This article is part of the theme issue ‘Biotic signalling sheds light on smart pest management’.
DOI: 10.6084/m9.figshare.7436486.v1
title: DEGs in transcriptome of virulent CN-Bx1 and avirulent US-Bx1. from Enhancement of oxidative stress contributes to increased pathogenicity of the invasive pine wood nematode

description: Reactive oxygen species (ROS) play important roles in defence response of host plants versus pathogens. While generation and detoxification of ROS is well understood, how varied ability of different isolates of pathogens to overcome host ROS, or ROS contribution to a particular isolate's pathogenicity, remains largely unexplored. Here, we report that transcriptional regulation of ROS pathway, in combination with the insulin pathway, increases the pathogenicity of invasive species <i>Bursaphelenchus xylophilus</i>. The results showed a positive correlation between fecundity and pathogenicity of different nematode isolates. The virulent isolates from introduced populations in Japan, China and Europe had significantly higher fecundity than native avirulent isolates from the USA. Increased expression of <i>Mn-SOD</i> and reduced expression of <i>catalase</i>/<i>GPX-5</i> and H<sub>2</sub>O<sub>2</sub> accumulation during invasion are associated with virulent strains. Additional H<sub>2</sub>O<sub>2</sub> could improve fecundity of <i>B. xylophilus</i>. Furthermore, depletion of <i>Mn-SOD</i> decreased fecundity and virulence of <i>B. xylophilus</i>, while insulin pathway is significantly affected. Thus, we propose that destructive pathogenicity of <i>B. xylophilus</i> to pines is partly due to upregulated fecundity modulated by insulin pathway in association with ROS pathway and further enhanced by H<sub>2</sub>O<sub>2</sub> oxidative stress. These findings provide a better understanding of pathogenic mechanisms in plant–pathogen interactions and adaptive evolution of invasive species.This article is part of the theme issue ‘Biotic signalling sheds light on smart pest management’.
DOI: 10.6084/m9.figshare.7429151
title: Additional file 7: of Profiling the miRNA-mRNA-lncRNA interaction network in MSC osteoblast differentiation induced by (+)-cholesten-3-one

description: Core CNC network analyses based on the online databases. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.7429151.v1
title: Additional file 7: of Profiling the miRNA-mRNA-lncRNA interaction network in MSC osteoblast differentiation induced by (+)-cholesten-3-one

description: Core CNC network analyses based on the online databases. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.7429148
title: Additional file 6: of Profiling the miRNA-mRNA-lncRNA interaction network in MSC osteoblast differentiation induced by (+)-cholesten-3-one

description: The core CNC networks were analysed based on the 29 mRNAs obtained from GO and KEGG pathway analyses. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.23682168
title: Additional file 1 of Pulmonary interleukin 1 beta/serum amyloid A3 axis promotes lung metastasis of hepatocellular carcinoma by facilitating the pre-metastatic niche formation

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.14776692
title: Medical students’ quality of life and its association with harassment and social support

description: <b>Abstract</b>

<b><i>Objectives</i></b><b>: </b>To explore the associations between self-reported quality of life (QoL)
and harassment and the potential moderating effect of social support.<b> 
</b>

<b><i>Design</i></b><b>: </b>Senior medical students were invited to participate in a survey
consisting of a background section, the world health organisation QoL
questionnaire (New Zealand version), a version of the generalized workplace
harassment questionnaire, and the multidimensional scale of perceived social
support. A series of multivariate statistical analyses were conducted.

<b><i>Results</i></b><b>: </b>Two hundred and five students completed the online survey (response rate
= 25%). The findings indicated a high incidence of verbal (90%) and covert
harassment (87%), with relatively low levels of physical harassment (6%) and
manipulation (6%). The correlational analyses indicated that low levels of QoL
were associated with high levels of verbal and covert harassment and high
levels of social support were directly associated with high levels of QoL. The
moderation models indicated that social support conditionally influences the
impact of verbal and covert harassment on social and psychological QoL. 

<b><i>Conclusions</i></b><b>: </b>These findings imply that medical students experiencing harassment in
clinical learning environments likely experienced lowered levels of QoL. Social
support may moderate, in certain instances, the adverse impact of harassment on
QoL.<b> </b>
DOI: 10.6084/m9.figshare.20012265.v1
title: Additional file 1 of Analysis of influence of physical health factors on subjective wellbeing of middle-aged and elderly women in China

description: Additional file 1.
DOI: 10.6084/m9.figshare.22626341
title: Additional file 1 of Genetic diversity and signatures of selection in BoHuai goat revealed by whole-genome sequencing

description: Additional file 1: Figure S1. SNP intersection of BoHuai goat with Boer goat (male parent) and Huai goat (female parent).
DOI: 10.13012/b2idb-8783447_v1
title: Data for Taxonomic Identification and Phylogenetic Profiling

description: This dataset provides the data for Nguyen, Nam-phuong, et al. "TIPP: taxonomic identification and phylogenetic profiling." Bioinformatics 30.24 (2014): 3548-3555.
DOI: 10.25549/usctheses-ouc11290903
title: Microsoft Word - Thesis arum final final.doc
DOI: 10.6084/m9.figshare.23682273.v1
title: Additional file 1 of BMP4 upregulates glycogen synthesis through the SMAD/SLC2A1 (GLUT1) signaling axis in hepatocellular carcinoma (HCC) cells

description: Additional file 1: Table S1. BMP4 and SLC2A1 IHC score results. Table S2. List of TqPCR primers. Table S3. List of PCR primers for ChIP assay.
DOI: 10.6084/m9.figshare.23682286.v1
title: Additional file 1 of HER2-low breast cancer: evolution of HER2 expression from primary tumor to distant metastases

description: Additional file 1. Literature on HER2 (all scores) changes between primary tumors and metastases [39–47].
DOI: 10.5281/zenodo.10635516
title: Dimethylsulfoniopropionate-derived compound concentrations, volatile organic compound concentrations, and microorganism abundances over diel cycles in the tropical ocean and in a coral back reef lagoon of Moorea (French Polynesia)

description: These data belong in the paper: 

Marta Masdeu-Navarro, Jean-François Mangot, Lei Xue, Miguel Cabrera-Brufau, DavidJ. Kieber, Pablo Rodríguez-Ros, Stephanie G. Gardner, Kristin Bergauer, Gerhard J. Herndl, Cèlia Marrasé and Rafel Simó (2024). Diel variation of seawater volatile organic compounds, DMSP-related compounds, and microbial plankton inside and outside a tropical coral reef ecosystem. Frontiers in Marine Science.

Concentrations of DMSP, acrylate, DMSO, DMS, DMDS, COS, CS2, isoprene, CH3I, CH2ClI, CH2Br2 and CHBr3 in seawater samples at two sampling sites, one inside (named BR) and one outside (named OO), of the northern coral reef of Mo'orea, French Polynesia. Along with the afore mentioned compounds, the data set contains abundances of heterotrophic prokaryotes, Prochlorococcus, Synechococcus, picoeukaryotes and nanoeukaryotes as determined by flow cytometry, as well as concentrations of nutrients, chlorophyll a, DOC, DON, POC and FDOM. The data set is subdivided into two data sets, one per sampling site, each being composed of a time series of measurements done every 6h over a period of 36h. All samples were collected in April 2018.