cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11896317.v1
title: Additional file 12 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 12: Table S10. Consensus functional terms associated with GO enrichment and enriched TF binding sites for module target genes.
DOI: 10.6084/m9.figshare.11896338
title: Additional file 2 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 2: Table S2. Phenotype summary of 170 transcription factors as candidate regulators extracted from the originally reported by Son et al. 2011 in PLoS Pathogens.
DOI: 10.6084/m9.figshare.11896338.v1
title: Additional file 2 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 2: Table S2. Phenotype summary of 170 transcription factors as candidate regulators extracted from the originally reported by Son et al. 2011 in PLoS Pathogens.
DOI: 10.6084/m9.figshare.11896344
title: Additional file 3 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 3: Table S3. Weight of each regulator (R) in each module.
DOI: 10.6084/m9.figshare.13469131
title: Ropivacaine inhibits the proliferation and migration of colorectal cancer cells through ITGB1

description: To study whether ropivacaine inhibits the proliferation and migration of colon cancer cells through ITGB1 (Integrin beta-1). First, the effect of ropivacaine on cell proliferation and migration was detected by MTT and Transwell. DAPI staining, annexin V staining and Western blot were used to detect the expression of apoptosis-related proteins to investigate the effect of ropivacaine on cell apoptosis. Using bioinformatics software to predict the potential drug targets of ropivacaine. RT-PCR, Western blot and immunofluorescence verify the distribution and expression of the drug target ITGB1, and detect its downstream-related proteins to further prove that ropivacaine affects colon cancer cells by acting on ITGB1 protein. 1. Ropivacaine significantly inhibited the proliferation of colon cancer cells and promoted their apoptosis 2. Ropivacaine could interact with ITGB1 protein, and inhibited the expression of ITGB1 protein in colon cancer cells, thereby affecting its downstream signaling pathway. Ropivacaine regulates the function of colon cancer cells by targeting the expression of ITGB1 protein and affecting the activation of its downstream signaling pathways. <b>Abbreviation:</b> Integrin beta-1 (ITGB1); 3-(45)-dimethylthiahiazo (-z-y1)-35-di- phenytetrazoliumromide (MTT); 4. 6-diamimo-2-phenyl indole (DAPI); Reverse transcrption PCR (RT-PCR); Colorectal cancer (CRC); Local anesthetics (LA); voltage-gated sodium channel (VGSC); dulbecco s modifed eade medium (DMEM); propidium iodide (PI); dodecyl sulf ate, sodium salt-Polyacrylamide gel electrophoresis (SDS-PAGE); Polyvinylidene Fluoride (PVDF); BCL2 associated X (Bax); Focal Adhesion Kinase (FAK); extracellular signal-regulated kmase (ERK); alpha serme threcnime-proteim kinase (AKT); Glyceraldehyde-3-phosphate dehydrogenase (GAPDH); Tris-buffered salme with 0.1% Tween 20 (TBST); Similarty ensemble approach (SEA)
DOI: 10.6084/m9.figshare.24969456
title: Data and code for "superradiant and subradiant states in lifetime-limited organic molecules through laser-induced tuning"

description: Data and simulation code for figures 1-4 of "Superradiant and subradiant states in lifetime-limited organic molecules through laser-induced tuning." 

Data are stored as npz files with keys such as "frequency" and "counts," with the same units as the corresponding figures. 

Simulation code uses the QuTiP toolbox (version 4.7) as well as standard libraries such as NumPy, SciPy, and Matplotlib.
DOI: 10.6084/m9.figshare.24969456.v1
title: Data and code for "superradiant and subradiant states in lifetime-limited organic molecules through laser-induced tuning"

description: Data and simulation code for figures 1-4 of "Superradiant and subradiant states in lifetime-limited organic molecules through laser-induced tuning." 

Data are stored as npz files with keys such as "frequency" and "counts," with the same units as the corresponding figures. 

Simulation code uses the QuTiP toolbox (version 4.7) as well as standard libraries such as NumPy, SciPy, and Matplotlib.
DOI: 10.6084/m9.figshare.6653423.v2
title: The effect of shame on anger at others: awareness of the emotion-causing events matters

description: Numerous studies have found that shame increases individuals’ anger at others. However, according to recent theories about the social function of shame and anger at others, it is possible that shame controls individuals’ anger at others in specific conditions. We replicated previous findings that shame increased individuals’ anger at others’ unfairness, when others were not aware of the individual’s experience of shameful events. We also found for the first time that shame controlled or even decreased individuals’ anger at others’ unfairness, when others were aware of the individual’s experience of shameful events. The results were consistent when shame was induced by either a recall paradigm or an imagination paradigm, and in either the ultimatum game or the dictator game. This suggests that shame strategically controls individuals’ anger at others to demonstrate that they are willing to benefit others, when facing the risk of social exclusion. Our findings highlight the interpersonal function of shame and deepen the understanding of the relationship between shame and anger at others.
DOI: 10.6084/m9.figshare.7177682.v1
title: TGF-b1 or hypoxia enhance glucose metabolism and lactate production via HIF1A signaling in tendon cells

description: <b>Purpose/Aim of the study</b>: Healthy tendons are maintained in homeostasis through controlled usage of glucose for energy and redox equilibrium. Tendon cell stress imposed by overuse injury or vascular insufficiency is accompanied by activation of wound healing pathways which facilitate an adaptive response and the restoration of homeostasis. To understand this response at the gene expression level we have studied the in vivo effects of injected TGF-β1 in a murine model of tendinopathy, as well as treatment of murine tendon explants with either TGF-β1 or hypoxia in vitro. <b>Methods and Results</b>: We provide evidence (from expression patterns and immunohistochemistry) that both in vivo and in vitro, the stress response in tendon cells may be metabolically controlled in part by glycolytic reprogramming. A major feature of the response to TGF-β1 or hypoxia is activation of the Warburg pathway which generates lactate from glucose under normoxia and thereby inhibits mitochondrial energy production. <b>Conclusions</b>: We discuss the likely outcome of this major metabolic shift in terms of the potential benefits and damage to tendon and suggest how incorporation of this metabolic response into our understanding of initiation and progression of tendinopathies may offer new opportunities for diagnosis and the monitoring of therapies.
DOI: 10.6084/m9.figshare.11896353
title: Additional file 4 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 4: Table S4. Digital representation of various regulator phenotypes.
DOI: 10.6084/m9.figshare.11896353.v1
title: Additional file 4 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 4: Table S4. Digital representation of various regulator phenotypes.
DOI: 10.6084/m9.figshare.13469132
title: Downregulation of long non-coding RNA LINC00460 inhibits the proliferation, migration and invasion, and promotes apoptosis of pancreatic cancer cells via modulation of the miR-320b/ARF1 axis

description: Pancreatic adenocarcinoma (PAAD) ranks among the most lethal cancers worldwide with high mortality. A marked increase in the level of long non-coding RNA LINC00460 was reported in PAAD patients, in comparison with the healthy controls. However, the underlying mechanisms of the above phenomenon are not yet well understood. Hence, the present study was designed to investigate the molecular mechanism underlying the role of LINC00460 in proliferation, migration and invasion of pancreatic cancer (PC) cells. It was found in our study that LINC00460 knockdown inhibited SW1990 cell proliferation, migration and invasion and promoted its apoptosis. Moreover, miR-320b was targeted straight and its expression was downregulated by LINC00460, whose knockdown led to a reduction in ARF1 expression. Interestingly, miR-320b downregulation partly reversed the effect of LINC00460 knockdown on the proliferation, migration, invasion and apoptosis of SW1990 cells, as well as ARF1expression. In conclusion, LINC00460 knockdown inhibited the proliferation, migration and invasion, and promotes the apoptosis of SW1990 cells via modulation of the miR-320b/ARF1 axis. Thus, LINC00460 can be perceived as a promising target in the treatment of PAAD.
DOI: 10.6084/m9.figshare.25003345.v1
title: Using detrital zircon systematics to trace the sediment sources of Jurassic uranium-bearing sandstones in the western Ordos Basin, China: implications for uranium exploration in a sedimentary basin

description: The Jurassic Zhiluo Formation in the western Ordos Basin is known for hosting economically significant sandstone-type uranium deposits. However, the understanding of sediment sources for this formation, crucial for guiding uranium exploration, has been a subject of controversy. This study aims to address this issue by presenting a systematic dataset derived from detrital zircons found in the uranium-bearing sandstones of the Zhiluo Formation. The dataset includes U‒Pb dating, trace element analyses, and in-situ Hf isotope compositions. The detrital zircons analysed are predominantly of magmatic origin, as indicated by a Th/U ratio greater than 0.4. Their U‒Pb ages can be broadly categorized into a predominant population ranging from 170 to 500 Ma, with a peak ca. 300 Ma. Additionally, there are two minor age populations: 1600–2050 Ma (peaking at ca. 1850 Ma) and 2300–2650 Ma (peaking at ca. 2500 Ma). The εHf(t) values of these zircons exhibit a range from −27 to 7, concentrating mostly from −16 to 5. Importantly, none of them aligns above the deficit mantle evolutionary line in an εHf(t) vs. age covariant diagram. A comprehensive comparison of the analytical U‒Pb ages and Hf isotopic results with previously reported data from adjacent geological units surrounding the western Ordos Basin suggests that the primary provenance supply area for the sandstones is the Alxa Block, particularly the uranium-rich felsic rocks within it. Minor contributions are inferred from the Yinshan Block and the Qilian Orogenic Belt. The northwestern region of the study appears to be the primary prospect area for uranium exploration, and we have proposed effective measures to refine the exploration target area and enhance exploration efficiency. Overall, the study provided crucial insights into deducing provenance supply areas and transport paths, with implications for uranium exploration in sedimentary basins worldwide.
DOI: 10.6084/m9.figshare.11896344.v1
title: Additional file 3 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 3: Table S3. Weight of each regulator (R) in each module.
DOI: 10.6084/m9.figshare.11896371.v1
title: Additional file 6 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 6: Table S5. Lists of target genes in each module.
DOI: 10.6084/m9.figshare.22689790
title: RNA-seq of WT and ypg

description: RNA sequence results of wild type vs ygp mutant
DOI: 10.6084/m9.figshare.23909961.v1
title: A single cell atlas of frozen shoulder capsule identifies features associated with inflammatory fibrosis resolution

description: Supporting main figures and supplementary tables for manuscript describing human tissue samples used for the study, markers from major cell populations and gene expression comprising the shoulder joint capsule in human tissues and antibodies used for the study.
DOI: 10.6084/m9.figshare.13469132.v1
title: Downregulation of long non-coding RNA LINC00460 inhibits the proliferation, migration and invasion, and promotes apoptosis of pancreatic cancer cells via modulation of the miR-320b/ARF1 axis

description: Pancreatic adenocarcinoma (PAAD) ranks among the most lethal cancers worldwide with high mortality. A marked increase in the level of long non-coding RNA LINC00460 was reported in PAAD patients, in comparison with the healthy controls. However, the underlying mechanisms of the above phenomenon are not yet well understood. Hence, the present study was designed to investigate the molecular mechanism underlying the role of LINC00460 in proliferation, migration and invasion of pancreatic cancer (PC) cells. It was found in our study that LINC00460 knockdown inhibited SW1990 cell proliferation, migration and invasion and promoted its apoptosis. Moreover, miR-320b was targeted straight and its expression was downregulated by LINC00460, whose knockdown led to a reduction in ARF1 expression. Interestingly, miR-320b downregulation partly reversed the effect of LINC00460 knockdown on the proliferation, migration, invasion and apoptosis of SW1990 cells, as well as ARF1expression. In conclusion, LINC00460 knockdown inhibited the proliferation, migration and invasion, and promotes the apoptosis of SW1990 cells via modulation of the miR-320b/ARF1 axis. Thus, LINC00460 can be perceived as a promising target in the treatment of PAAD.
DOI: 10.6084/m9.figshare.23513412.v1
title: Datasets for: Opposing effects of human disturbances on wildlife behaviour and the consequences for predator-prey overlap

description: The captures datasets contain wildlife detections from camera trapping surveys conducted by Matthew Luskin and the Ecological Cascades Lab in 10 forested landscapes across Southeast Asia between 2013 to 2020. Furthermore, the metadata contains all camera-level covariates and trait information datasets contain information on species feeding guilds and their body mass (in kg).
DOI: 10.6084/m9.figshare.7177790
title: RBM-5 modulates U2AF large subunit-dependent alternative splicing in <i>C. elegans</i>

description: A key step in pre-mRNA splicing is the recognition of 3ʹ splicing sites by the U2AF large and small subunits, a process regulated by numerous <i>trans</i>-acting splicing factors. How these <i>trans</i>-acting factors interact with U2AF <i>in vivo</i> is unclear. From a screen for suppressors of the temperature-sensitive (ts) lethality of the <i>C. elegans</i> U2AF large subunit gene <i>uaf-1(n4588)</i> mutants, we identified mutations in the RNA binding motif gene <i>rbm-5</i>, a homolog of the tumor suppressor gene <i>RBM5. rbm-5</i> mutations can suppress <i>uaf-1(n4588)</i> ts-lethality by loss of function and neuronal expression of <i>rbm-5</i> was sufficient to rescue the suppression. Transcriptome analyses indicate that <i>uaf-1(n4588)</i> affected the expression of numerous genes and <i>rbm-5</i> mutations can partially reverse the abnormal gene expression to levels similar to that of wild type. Though <i>rbm-5</i> mutations did not obviously affect alternative splicing per se, they can suppress or enhance, in a gene-specific manner, the altered splicing of genes in <i>uaf-1(n4588)</i> mutants. Specifically, the recognition of a weak 3ʹ splice site was more susceptible to the effect of <i>rbm-5</i>. Our findings provide novel <i>in vivo</i> evidence that RBM-5 can modulate UAF-1-dependent RNA splicing and suggest that RBM5 might interact with U2AF large subunit to affect tumor formation.
DOI: 10.6084/m9.figshare.11896389
title: Additional file 9 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 9: Table S7. Summary of regulatory module validation results.
DOI: 10.6084/m9.figshare.11896389.v1
title: Additional file 9 of Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

description: Additional file 9: Table S7. Summary of regulatory module validation results.
DOI: 10.6084/m9.figshare.11896419
title: Additional file 1 of Integration, abundance, and transmission of mutations and transgenes in a series of CRISPR/Cas9 soybean lines

description: Additional file 1: Table S1. WPT construct metadata.
DOI: 10.6084/m9.figshare.11896419.v1
title: Additional file 1 of Integration, abundance, and transmission of mutations and transgenes in a series of CRISPR/Cas9 soybean lines

description: Additional file 1: Table S1. WPT construct metadata.
DOI: 10.6084/m9.figshare.19759307
title: Additional file 2 of Beyond the snapshot: identification of the timeless, enduring indicator microbiome informing soil fertility and crop production in alkaline soils

description: Additional file 2 Supplementary information including detailed experiment setup and indicator phylotypes: Table S1. Detailed fertilization regimes in this study; Table S2. Detailed information of indicator phylotypes (n = 604).
DOI: 10.6084/m9.figshare.19929908
title: NMR and GC data

description: NMR and HRMS characterization data on 13C labeled products.
DOI: 10.6084/m9.figshare.23909961
title: A single cell atlas of frozen shoulder capsule identifies features associated with inflammatory fibrosis resolution

description: Supporting main figures and supplementary tables for manuscript describing human tissue samples used for the study, markers from major cell populations and gene expression comprising the shoulder joint capsule in human tissues and antibodies used for the study.
DOI: 10.6084/m9.figshare.19759307.v1
title: Additional file 2 of Beyond the snapshot: identification of the timeless, enduring indicator microbiome informing soil fertility and crop production in alkaline soils

description: Additional file 2 Supplementary information including detailed experiment setup and indicator phylotypes: Table S1. Detailed fertilization regimes in this study; Table S2. Detailed information of indicator phylotypes (n = 604).
DOI: 10.6084/m9.figshare.23816796
title: Mild pH-decoupling Aqueous Flow Battery with Practical pH Recovery (data)

description: Data for Mild pH-decoupling Aqueous Flow Battery with Practical pH Recovery
DOI: 10.6084/m9.figshare.11896620
title: Additional file 1 of The behavioural and neuropathologic sexual dimorphism and absence of MIP-3α in tau P301S mouse model of Alzheimer’s disease

description: Additional file 1: Figure S1. Weight changes of mice. Figure S2. HE staining of lung. Figure S3. HE staining of spleen. Figure S4. HE staining of liver. Figure S5. HE staining of heart. Figure S6. HE staining of kidney. Figure S7. Composite phenotype scoring system test. Figure S8. Percent time in each quadrant in the MWM over 5 days. Figure S9. Latency and number of target platform crossings of four age groups of mice. Figure S10. Open field test. Figure S11. Nest building test. Figure S12. Concentrations of inflammatory cytokines and chemokines in RAB fraction of mouse brain homogenates. Figure S13. Concentration of inflammatory cytokines and chemokines in mouse plasma.
DOI: 10.6084/m9.figshare.14518028
title: Efficacy of statins on renal function in patients with chronic kidney disease: a systematic review and meta-analysis

description: Studies have shown that the use of statins could significantly improve lipid profiles; however, it remains controversial whether the use of statins could improve renal function in patients with chronic kidney disease (CKD). Therefore, we conducted a meta-analysis of randomized controlled trials (RCTs) to evaluate the effects of statins on renal function in patients with CKD. We systematically searched PubMed, EMBASE, and the Cochrane Library databases for eligible RCTs from inception to October 2020. Pooled effect estimates were assigned as weighted mean differences (WMDs) with 95% confidence intervals (CIs) using the random-effects model. We selected 33 RCTs that recruited 37,391 patients with CKD patients. The summary results suggested that statin use significantly reduced urinary albumin (WMD: −2.04; 95%CI: −3.53 to −0.56; <i>p</i> = .007) and protein (WMD: −0.58; 95%CI: −0.95 to −0.21; <i>p</i> = .002) excretions and increased creatinine clearance (WMD: 0.86; 95%CI: 0.32–1.41; <i>p</i> = .002). However, there were no significant differences between statin and control groups in terms of changes in estimated glomerular filtration rate (WMD: 0.38; 95%CI: −0.04 to 0.79; <i>p</i> = .075), and serum creatinine levels (WMD: −0.07; 95%CI: −0.25, 0.12; <i>p</i> = .475). We found that statin use in patients with CKD may slow CKD progression by lowering urinary albumin and protein excretions or increasing creatinine clearance. Further large-scale RCTs should be conducted to evaluate the long-term effects of statins on renal outcomes. <b>Abbreviations:</b> CKD: chronic kidney disease; RCT: randomized controlled trials; WMD: weighted mean differences; CI: confidence intervals; ACEI: angiotensin-converting enzyme inhibitors; eGFR: estimated glomerular filtration rate
DOI: 10.6084/m9.figshare.11896620.v1
title: Additional file 1 of The behavioural and neuropathologic sexual dimorphism and absence of MIP-3α in tau P301S mouse model of Alzheimer’s disease

description: Additional file 1: Figure S1. Weight changes of mice. Figure S2. HE staining of lung. Figure S3. HE staining of spleen. Figure S4. HE staining of liver. Figure S5. HE staining of heart. Figure S6. HE staining of kidney. Figure S7. Composite phenotype scoring system test. Figure S8. Percent time in each quadrant in the MWM over 5 days. Figure S9. Latency and number of target platform crossings of four age groups of mice. Figure S10. Open field test. Figure S11. Nest building test. Figure S12. Concentrations of inflammatory cytokines and chemokines in RAB fraction of mouse brain homogenates. Figure S13. Concentration of inflammatory cytokines and chemokines in mouse plasma.