cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7029398
title: Supplementary Figures from Impact of the 2015–2016 El Nino on the terrestrial carbon cycle constrained by bottom-up and top-down approaches

description: Evaluating the response of the land carbon sink to the anomalies in temperature and drought imposed by El-Niño events provides insights into the present-day carbon cycle and its climate-driven variability. It is also a necessary step to build confidence in terrestrial ecosystems models' response to the warming and drying stresses expected in the future over many continents, and particularly in the tropics. Here we present an in-depth analysis of the response of the terrestrial carbon cycle to the 2015/2016 El-Niño that imposed extreme warming and dry conditions in the tropics and other sensitive regions. First, we provide a synthesis of the spatio-temporal evolution of anomalies in net land-atmosphere CO<sub>2</sub> fluxes estimated by two <i>in situ</i> measurements based on atmospheric inversions and 16 land-surface models (LSMs) from TRENDYv6. Simulated changes in ecosystem productivity, decomposition rates and fire emissions are also investigated. Inversions and LSMs generally agree on the decrease and subsequent recovery of the land sink in response to the onset, peak and demise of El-Niño conditions and point to the decreased strength of the land carbon sink: by 0.4–0.7 PgC yr<sup>−1</sup> (inversions) and by 1.0 PgC yr<sup>−1</sup> (LSMs) during 2015/2016. LSM simulations indicate that a decrease in productivity, rather than increase in respiration, dominated the net biome productivity anomalies in response to ENSO throughout the tropics, mainly associated with prolonged drought conditions.This article is part of a discussion meeting issue ‘The impact of the 2015/2016 El Nino on the terrestrial tropical carbon cycle: patterns, mechanisms and implications’.
DOI: 10.6084/m9.figshare.6505901
title: Melatonin promotes Cashmere goat (<i>Capra hircus</i>) secondary hair follicle growth: a view from integrated analysis of long non-coding and coding RNAs

description: The role of melatonin in promoting the yield of Cashmere goat wool has been demonstrated for decades though there remains a lack of knowledge regarding melatonin mediated hair follicle growth. Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are widely transcribed in the genome and play ubiquitous roles in regulating biological processes. However, the role of lncRNAs in regulating melatonin mediated hair follicle growth remains unclear. In this study, we established an <i>in vitro</i> Cashmere goat secondary hair follicle culture system, and demonstrated that 500 ng/L melatonin exposure promoted hair follicle fiber growth. Based on long intergenic RNA sequencing, we demonstrated that melatonin promoted hair follicle elongation via regulating genes involved in focal adhesion and extracellular matrix receptor pathways and further cis predicting of lncRNAs targeted genes indicated that melatonin mediated lncRNAs mainly targeted vascular smooth muscle contraction and signaling pathways regulating the pluripotency of stem cells. We proposed that melatonin exposure not only perturbed key signals secreted from hair follicle stem cells to regulate hair follicle development, but also mediated lncRNAs mainly targeted to pathways involved in the microvascular system and extracellular matrix, which constitute the highly orchestrated microenvironment for hair follicle stem cell. Taken together, our findings here provide a profound view of lncRNAs in regulating Cashmere goat hair follicle circadian rhythms and broaden our knowledge on melatonin mediated hair follicle morphological changes.
DOI: 10.6084/m9.figshare.6505910
title: Small RNA-induced INTS6 gene up-regulation suppresses castration-resistant prostate cancer cells by regulating β-catenin signaling

description: Small RNAs play an important role in gene regulatory networks. The gene suppressive effect of small RNAs was previously the dominant focus of studies, but during the recent decade, small RNA-induced gene activation has been reported and has become a notable gene manipulation technique. In this study, a putative tumor suppressor, <i>INTS6</i>, was activated by introducing a promoter-targeted small RNA (dsRNA-915) into castration-resistant prostate cancer (CRPC) cells. Unique dynamics associated with the gene upregulation phenomenon was observed. Following gene activation, cell proliferation and motility were suppressed in vitro. Downregulation of <i>Wnt</i>/β-catenin signaling was observed during the activation period, and the impairment of β-catenin degradation reversed the tumor suppressor effects of <i>INTS6</i>. These results suggest the potential application of small activating RNAs in targeted gene therapy for CRPC.
DOI: 10.6084/m9.figshare.22759029
title: Bidirectional fermentation of Monascus and Mulberry leaves enhances GABA and pigment contents: establishment of strategy, studies of bioactivity and mechanistic

description: Bidirectional fermentation is a technology that utilizes fungi to ferment medicinal edible substrates, with synergistic and complementary advantages. In this work, a fermentation strategy was established to produce a high yield of γ-aminobutyric acid (GABA) and <i>Monascus</i> pigments (MPs) using <i>Monascus</i> and mulberry leaves (MLs). Firstly, the basic fermentation parameters were determined using single-factor experiments, followed by Plackett-Burman (PB) experimental design to identify MLs, glucose, peptone, and temperature as significant influencing factors. The fermentation parameters were optimized using an artificial neural network (ANN). Finally, the effects of bidirectional fermentation of MLs and <i>Monascus</i> were investigated by bioactivity analysis, microstructure observation, and RT-qPCR. The outcomes showed that the bidirectional fermentation significantly increased the bioactive content and promoted the secondary metabolism of <i>Monascus</i>. The established fermentation conditions were 44.2 g/L of MLs, 57 g/L of glucose, 15 g/L of peptone, 1 g/L of MgSO<sub>4</sub>, 2 g/L of KH<sub>2</sub>PO<sub>4</sub>, 8% (v/v) of inoculum, 180 rpm, initial pH 6, 32 °C and 8 days. The content of GABA reached 13.95 g/L and the color value of MPs reached 408.07 U/mL. This study demonstrated the feasibility of bidirectional fermentation of MLs and <i>Monascus</i>, providing a new idea for the application of MLs and <i>Monascus</i>.
DOI: 10.6084/m9.figshare.7029398.v1
title: Supplementary Figures from Impact of the 2015–2016 El Nino on the terrestrial carbon cycle constrained by bottom-up and top-down approaches

description: Evaluating the response of the land carbon sink to the anomalies in temperature and drought imposed by El-Niño events provides insights into the present-day carbon cycle and its climate-driven variability. It is also a necessary step to build confidence in terrestrial ecosystems models' response to the warming and drying stresses expected in the future over many continents, and particularly in the tropics. Here we present an in-depth analysis of the response of the terrestrial carbon cycle to the 2015/2016 El-Niño that imposed extreme warming and dry conditions in the tropics and other sensitive regions. First, we provide a synthesis of the spatio-temporal evolution of anomalies in net land-atmosphere CO<sub>2</sub> fluxes estimated by two <i>in situ</i> measurements based on atmospheric inversions and 16 land-surface models (LSMs) from TRENDYv6. Simulated changes in ecosystem productivity, decomposition rates and fire emissions are also investigated. Inversions and LSMs generally agree on the decrease and subsequent recovery of the land sink in response to the onset, peak and demise of El-Niño conditions and point to the decreased strength of the land carbon sink: by 0.4–0.7 PgC yr<sup>−1</sup> (inversions) and by 1.0 PgC yr<sup>−1</sup> (LSMs) during 2015/2016. LSM simulations indicate that a decrease in productivity, rather than increase in respiration, dominated the net biome productivity anomalies in response to ENSO throughout the tropics, mainly associated with prolonged drought conditions.This article is part of a discussion meeting issue ‘The impact of the 2015/2016 El Nino on the terrestrial tropical carbon cycle: patterns, mechanisms and implications’.
DOI: 10.6084/m9.figshare.7029410.v1
title: Supplementary Datasets from Impact of the 2015–2016 El Nino on the terrestrial carbon cycle constrained by bottom-up and top-down approaches

description: Evaluating the response of the land carbon sink to the anomalies in temperature and drought imposed by El-Niño events provides insights into the present-day carbon cycle and its climate-driven variability. It is also a necessary step to build confidence in terrestrial ecosystems models' response to the warming and drying stresses expected in the future over many continents, and particularly in the tropics. Here we present an in-depth analysis of the response of the terrestrial carbon cycle to the 2015/2016 El-Niño that imposed extreme warming and dry conditions in the tropics and other sensitive regions. First, we provide a synthesis of the spatio-temporal evolution of anomalies in net land-atmosphere CO<sub>2</sub> fluxes estimated by two <i>in situ</i> measurements based on atmospheric inversions and 16 land-surface models (LSMs) from TRENDYv6. Simulated changes in ecosystem productivity, decomposition rates and fire emissions are also investigated. Inversions and LSMs generally agree on the decrease and subsequent recovery of the land sink in response to the onset, peak and demise of El-Niño conditions and point to the decreased strength of the land carbon sink: by 0.4–0.7 PgC yr<sup>−1</sup> (inversions) and by 1.0 PgC yr<sup>−1</sup> (LSMs) during 2015/2016. LSM simulations indicate that a decrease in productivity, rather than increase in respiration, dominated the net biome productivity anomalies in response to ENSO throughout the tropics, mainly associated with prolonged drought conditions.This article is part of a discussion meeting issue ‘The impact of the 2015/2016 El Nino on the terrestrial tropical carbon cycle: patterns, mechanisms and implications’.
DOI: 10.5281/zenodo.10652020
title: Leishmania mexicana whole cell electron tomography

description: High resolution three dimensional reconstructions of three Leishmania mexicana parasite cells, promastigote life cycle stage. These were captured as multiple fields of view across multiple serial thin sections, reconstructed into tomographic volumes, then montaged and stacked into a whole-cell three dimensional volume.

The three cells are named "c01", "c02" and "c03" and, for each, there are the following files:



"*_wholecell.zip", containing "*_wholecell.tif" 8-bit multi-slice TIFF file of the whole cell volume.

"*_cellmidline.mod" 3DMod/iMod model file of the coordinates of the cell midline.

"*_sp.mod" 3DMod/iMod model file of the sub-pellicular microtubules, prior to joining across serial section boundaries.

"*_sp.mod" 3DMod/iMod model file of the sub-pellicular microtubules, after joining across serial section boundaries.


The original raw tilt series are too large to fit in this deposition, and are listed under the following DOIs. In these, the data is raw .st files, generally named in the form "c<cell>s<section>l<location><tiltaxis>" or similar. Almost, but not all, are dual axis with a "<tiltaxis>" a and b image.

Raw data is available here:



c01 (20150114): 10.5281/zenodo.10652410

c02 (20150415): 10.5281/zenodo.10653751

c03 (20151016): 10.5281/zenodo.10653747
DOI: 10.5281/zenodo.10652021
title: Leishmania mexicana whole cell electron tomography

description: High resolution three dimensional reconstructions of three Leishmania mexicana parasite cells, promastigote life cycle stage. These were captured as multiple fields of view across multiple serial thin sections, reconstructed into tomographic volumes, then montaged and stacked into a whole-cell three dimensional volume.

The three cells are named "c01", "c02" and "c03" and, for each, there are the following files:



"*_wholecell.zip", containing "*_wholecell.tif" 8-bit multi-slice TIFF file of the whole cell volume.

"*_cellmidline.mod" 3DMod/iMod model file of the coordinates of the cell midline.

"*_sp.mod" 3DMod/iMod model file of the sub-pellicular microtubules, prior to joining across serial section boundaries.

"*_sp.mod" 3DMod/iMod model file of the sub-pellicular microtubules, after joining across serial section boundaries.


The original raw tilt series are too large to fit in this deposition, and are listed under the following DOIs. In these, the data is raw .st files, generally named in the form "c<cell>s<section>l<location><tiltaxis>" or similar. Almost, but not all, are dual axis with a "<tiltaxis>" a and b image.

Raw data is available here:



c01 (20150114): 10.5281/zenodo.10652410

c02 (20150415): 10.5281/zenodo.10653751

c03 (20151016): 10.5281/zenodo.10653747
DOI: 10.6084/m9.figshare.14368881
title: Additional file 1 of Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics

description: Additional file 1: Supplementary File 1. Parameters for Molecular Docking. The number of Points in Dimension, Spacing (Angstrom) and Center Grid Box values that were taken during the molecular docking of Wild type/ Mutant PLPros and GRL0617.
DOI: 10.6084/m9.figshare.14368883
title: Additional file 1 of Tropomyosin in mugwort cross-reacts to house dust mite, eliciting non-Th2 response in allergic rhinitis patients sensitized to house dust mite

description: Additional file 1: Table S1. Identified corresponding proteins in Artemisia sieversian.
DOI: 10.6084/m9.figshare.9128045.v2
title: Human chromatin remodeler cofactor, RNA interactor, eraser and writer sperm RNAs responding to obesity

description: In the United States almost 33% of adults are considered obese (BMI &gt; 30 kg/m<sup>2</sup>). Both animal models and to a lesser extent human studies, have associated BMI, a measure of obesity, with alterations in sperm DNA methylation and RNAs. Sperm RNAs from the Assessment of Multiple Gestations from Ovarian Stimulation trial, were isolated and sequenced. A Generalized Linear Model identified 487 BMI associated human sperm RNA elements (short exon-sized sequences). They partitioned into four patterns; a continual increase with BMI, increase once obese (BMI&gt;30 kg/m<sup>2</sup>); a steady decrease with BMI; and decrease once overweight (BMI 25 - 30 kg/m<sup>2</sup>). Gene Ontology revealed a unique relationship between BMI and transcripts associated with chromosome organization, adipogenesis, cellular stress and obesity-related inflammation. Coregulatory networks linked by Chromatin remodeler cofactors, RNA interactors, Erasers and Writers (CREWs) were uncovered to reveal a hierarchical epigenetic response pathway.
DOI: 10.6084/m9.figshare.14368881.v1
title: Additional file 1 of Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics

description: Additional file 1: Supplementary File 1. Parameters for Molecular Docking. The number of Points in Dimension, Spacing (Angstrom) and Center Grid Box values that were taken during the molecular docking of Wild type/ Mutant PLPros and GRL0617.
DOI: 10.6084/m9.figshare.6505601
title: The anaphase promoting complex promotes NHEJ repair through stabilizing Ku80 at DNA damage sites

description: Double-strand breaks (DSBs) are repaired through two major pathways, homology-directed recombination (HDR) and non-homologous end joining (NHEJ). The choice between these two pathways is largely influenced by cell cycle phases. HDR can occur only in S/G2 when sister chromatid can provide homologous templates, whereas NHEJ can take place in all phases of the cell cycle except mitosis. Central to NHEJ repair is the Ku70/80 heterodimer which forms a ring structure that binds DSB ends and serves as a platform to recruit factors involved in NHEJ. Upon completion of NHEJ repair, DNA double strand-encircling Ku dimers have to be removed. The removal depends on ubiquitylation and proteasomal degradation of Ku80 by the ubiquitin E3 ligases RNF8. Here we report that RNF8 is a substrate of APC<sup>Cdh1</sup> and the latter keeps RNF8 level in check at DSBs to prevent premature turnover of Ku80.
DOI: 10.6084/m9.figshare.24831567
title: M2CVD

description: Code and dataM2CVD:Multi-Model Collaboration for Code Vulnerability Detection
DOI: 10.6084/m9.figshare.16993174
title: Data for "Effect of elevated tropospheric ozone on soil carbon and nitrogen: A meta-analysis"

description: These data were extracted from 41 peer-reviewed studies to quantify the impact of O<sub>3</sub> on ten variables associated with soil C and N, i.e., total C (TC, including soil organic C), total N (TN), dissolved organic C (DOC), ammonia N (NH<sub>4</sub><sup>+</sup>), nitrate N (NO<sub>3</sub><sup>-</sup>), microbial biomass C (MBC) and N (MBN), rates of nitrification (NTF) and denitrification (DNF), as well as C/N ratio. The data were acquired from 17 experiments performed at 25°28' N to 60°49' N latitude and 88°14' W to 123°24' E longitude. The mean annual temperature (MAT) ranged from 1.1 °C to 26.6 °C, and the mean annual precipitation (MAP) ranged from 460 mm to 1280 mm. The average increment in [O<sub>3</sub>] across all studies was 27.6±18.7 nL/L.<br>
DOI: 10.6084/m9.figshare.19090340
title: sequencing data

description: Leaf is the main economic organ of tobacco. To explore the mechanism of chloride ion on its growth and development is of great significance for coordinating tobacco components and improving tobacco quality. In order to further explore the mechanism of tobacco plant response to chloride ion regulating leaf growth and development, and further explore and identify the key signal pathways and genes that chloride ion affects tobacco growth.In this study, 0kg/hm<sup>2</sup> was used(control group), 15kg/hm<sup>2</sup>, 30 kg/hm<sup>2</sup>And 45 kg/hm<sup>2</sup>.our mature tobacco leaves treated with chloride ion were used for transcriptome sequencing, and each treated sample contained 3 biological replicates with a total of 12 samples. WGCNA was used to construct a co-expression network for transcriptome data, and 30kg/hm<sup>2</sup> was screenedCompared with the control group, the co-expression modules were significantly different and analyzed. The results showed that green and lightgreen modules were significantly enriched in plant hormone signaling, starch and sucrose metabolism, and cell formation.Magenta and Turquoise genes were enriched in photosynthesis and amino acid metabolism. Through predicting protein interaction of the screened module genes, it was found that the genes in turquoise module had a strong interaction with the genes encoding PSⅠ structural protein PsaA, PsaB and PsaC in tobacco leaves. In addition, the interaction of key genes in the phosphoinositol pathway in lightGreen module was strong. Profile15 and Profile17 gene clusters were identified by core gene trend prediction analysis, and the experimental results were verified by qRT-PCR, which were highly consistent with transcriptomic results.In this study, WGCNA method was used to identify 4 related modules of leaf response to chloride ion regulation, and several related candidate genes were screened out, which laid a foundation for further analyzing the mechanism of chloride ion regulation on tobacco plant growth and improving tobacco quality.
DOI: 10.6084/m9.figshare.14369918.v1
title: Additional file 10 of Identification of the molecular regulation of differences in lipid deposition in dedifferentiated preadipocytes from different chicken tissues

description: Additional file 10: Table S6: Information on the specific primers used for qRT-PCR.
DOI: 10.6084/m9.figshare.14369921.v1
title: Additional file 1 of Identification of the molecular regulation of differences in lipid deposition in dedifferentiated preadipocytes from different chicken tissues

description: Additional file 1: Table S1: Expression of genes (DIMFPs vs DAFPs).
DOI: 10.6084/m9.figshare.14369927.v1
title: Additional file 3 of Identification of the molecular regulation of differences in lipid deposition in dedifferentiated preadipocytes from different chicken tissues

description: Additional file 3: Table S3: Enriched GO terms based on DEGs (DIMFPs vs DAFPs).
DOI: 10.6084/m9.figshare.6505601.v2
title: The anaphase promoting complex promotes NHEJ repair through stabilizing Ku80 at DNA damage sites

description: Double-strand breaks (DSBs) are repaired through two major pathways, homology-directed recombination (HDR) and non-homologous end joining (NHEJ). The choice between these two pathways is largely influenced by cell cycle phases. HDR can occur only in S/G2 when sister chromatid can provide homologous templates, whereas NHEJ can take place in all phases of the cell cycle except mitosis. Central to NHEJ repair is the Ku70/80 heterodimer which forms a ring structure that binds DSB ends and serves as a platform to recruit factors involved in NHEJ. Upon completion of NHEJ repair, DNA double strand-encircling Ku dimers have to be removed. The removal depends on ubiquitylation and proteasomal degradation of Ku80 by the ubiquitin E3 ligases RNF8. Here we report that RNF8 is a substrate of APC<sup>Cdh1</sup> and the latter keeps RNF8 level in check at DSBs to prevent premature turnover of Ku80.
DOI: 10.6084/m9.figshare.14369933.v1
title: Additional file 5 of Identification of the molecular regulation of differences in lipid deposition in dedifferentiated preadipocytes from different chicken tissues

description: Additional file 5: Table S5: Screened DEGs related to lipid metabolism (DIMFPs vs DAFPs).
DOI: 10.6084/m9.figshare.14369930
title: Additional file 4 of Identification of the molecular regulation of differences in lipid deposition in dedifferentiated preadipocytes from different chicken tissues

description: Additional file 4: Table S4: Enriched pathways based on DEGs (DIMFPs vs DAFPs).
DOI: 10.6084/m9.figshare.14369930.v1
title: Additional file 4 of Identification of the molecular regulation of differences in lipid deposition in dedifferentiated preadipocytes from different chicken tissues

description: Additional file 4: Table S4: Enriched pathways based on DEGs (DIMFPs vs DAFPs).
DOI: 10.6084/m9.figshare.14369924
title: Additional file 2 of Identification of the molecular regulation of differences in lipid deposition in dedifferentiated preadipocytes from different chicken tissues

description: Additional file 2: Table S2: Screened known DEGs (DIMFPs vs DAFPs).
DOI: 10.6084/m9.figshare.14369933
title: Additional file 5 of Identification of the molecular regulation of differences in lipid deposition in dedifferentiated preadipocytes from different chicken tissues

description: Additional file 5: Table S5: Screened DEGs related to lipid metabolism (DIMFPs vs DAFPs).
DOI: 10.6084/m9.figshare.14369924.v1
title: Additional file 2 of Identification of the molecular regulation of differences in lipid deposition in dedifferentiated preadipocytes from different chicken tissues

description: Additional file 2: Table S2: Screened known DEGs (DIMFPs vs DAFPs).
DOI: 10.6084/m9.figshare.14369927
title: Additional file 3 of Identification of the molecular regulation of differences in lipid deposition in dedifferentiated preadipocytes from different chicken tissues

description: Additional file 3: Table S3: Enriched GO terms based on DEGs (DIMFPs vs DAFPs).
DOI: 10.6084/m9.figshare.14369911
title: Additional file 1 of A novel method to establish the rabbit model of knee osteoarthritis: intra-articular injection of SDF-1 induces OA

description: Additional file 1.