cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23383865
title: Circulation of Lassa virus across the endemic Edo-Ondo axis, Nigeria, with cross-species transmission between multimammate mice

description: We phylogenetically compared sequences of the zoonotic Lassa virus (LASV) obtained from <i>Mastomys</i> rodents in seven localities across the highly endemic Edo and Ondo States within Nigeria. Sequencing 1641 nt from the S segment of the virus genome, we resolved clades within lineage II that were either limited to Ebudin and Okhuesan in Edo state (2g-beta) or along Owo-Okeluse-Ifon in Ondo state (2g-gamma). We also found clades within Ekpoma, a relatively large cosmopolitan town in Edo state, that extended into other localities within Edo (2g-alpha) and Ondo (2g-delta). LASV variants from <i>M. natalensis</i> within Ebudin and Ekpoma in Edo State (dated approximately 1961) were more ancient compared to those from Ondo state (approximately 1977), suggesting a broadly east-west virus migration across south-western Nigeria; a pattern not always consistent with LASV sequences derived from humans in the same localities. Additionally, in Ebudin and Ekpoma, LASV sequences between <i>M. natalensis</i> and <i>M. erythroleucus</i> were interspersed on the phylogenetic tree, but those from <i>M. erythroleucus</i> were estimated to emerge more recently (approximately 2005). Overall, our results show that LASV amplification in certain localities (reaching a prevalence as high as 76% in Okeluse), anthropogenically-aided spread of rodent-borne variants amidst the larger towns (involving communal accommodation such as student hostels), and virus-exchange between syntopic <i>M. natalensis</i> and <i>M. erythroleucus</i> rodents (as the latter, a savanna species, encroaches southward into the degraded forest) pose perpetual zoonotic hazard across the Edo-Ondo Lassa fever belt, threatening to accelerate the dissemination of the virus into non endemic areas.
DOI: 10.6084/m9.figshare.23300528
title: Perioperative mortality for radical cystectomy in the modern Era: experience from a tertiary referral center

description: ABSTRACT Purpose To evaluate the perioperative mortality and contributing variables among patients who underwent radical cystectomy (RC) for bladder cancer in recent decades, with comparison between modern (after 2010) and premodern (before 2010) eras. Materials and Methods Using our institutional review board-approved database, we reviewed the records of patients who underwent RC for primary urothelial bladder carcinoma with curative intent from January 2003 to December 2019. The primary and secondary outcomes were 90- and 30-day mortality. Univariate and multivariable logistic regression models were applied to assess the impact of perioperative variables on 90-day mortality. Results A total of 2047 patients with a mean±SD age of 69.6±10.6 years were included. The 30- and 90-day mortality rates were 1.3% and 4.9%, respectively, and consistent during the past two decades. Among 100 deaths within 90 days, 18 occurred during index hospitalization. Infectious, pulmonary, and cardiac complications were the leading mortality causes. Multivariable analysis showed that age (Odds Ratio: OR 1.05), Charlson comorbidity index ≥ 2 (OR 1.82), blood transfusion (OR 1.95), and pathological node disease (OR 2.85) were independently associated with 90-day mortality. Nevertheless, the surgical approach and enhanced recovery protocols had no significant effect on 90-day mortality. Conclusion The 90-day mortality for RC is approaching five percent, with infectious, pulmonary, and cardiac complications as the leading mortality causes. Older age, higher comorbidity, blood transfusion, and pathological lymph node involvement are independently associated with 90-day mortality.
DOI: 10.25402/fon.17092121
title: Supplementary Table – Plasma SNORD83A as a potential biomarker for early diagnosis of non-small cell lung cancer

description: <b>Supplementary
 Figure 1</b>. Plasma SNORD83A as a potential biomarker for early diagnosis of
 non-small cell lung cancer
 
 
 




<i>Characteristics of NSCLC patients for SNORD83A
in TCGA</i>
DOI: 10.6084/m9.figshare.21285897
title: Additional file 6 of Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus

description: Additional file 6. Common and unique EB regulated genes on GD 3 and GD 4.5.
DOI: 10.6084/m9.figshare.21285906
title: Additional file 9 of Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus

description: Additional file 9. 386 EB-regulated genes also regulated by progesterone compared between EB and EBP.
DOI: 10.6084/m9.figshare.21285888.v1
title: Additional file 3 of Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus

description: Additional file 3. 807 Common genes between estrogen-regulated in the OVX WT and dysregulated in the AF_FFF GD3.
DOI: 10.6084/m9.figshare.21285888
title: Additional file 3 of Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus

description: Additional file 3. 807 Common genes between estrogen-regulated in the OVX WT and dysregulated in the AF_FFF GD3.
DOI: 10.6084/m9.figshare.21285903
title: Additional file 8 of Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus

description: Additional file 8. 31 genes significantly regulated between EBP and EB.
DOI: 10.6084/m9.figshare.21285906.v1
title: Additional file 9 of Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus

description: Additional file 9. 386 EB-regulated genes also regulated by progesterone compared between EB and EBP.
DOI: 10.6084/m9.figshare.21285663
title: Additional file 11 of Hypoxia is fine-tuned by Hif-1α and regulates mesendoderm differentiation through the Wnt/β-Catenin pathway

description: Additional file 11. A compressed file that included our original uncropped gel/blot images
DOI: 10.6084/m9.figshare.21285891
title: Additional file 4 of Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus

description: Additional file 4. 1341 Differentially expressed genes between the WT and AF1_FFF uterus on GD4.5.
DOI: 10.6084/m9.figshare.21285900
title: Additional file 7 of Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus

description: Additional file 7. G2M_checkpoint and E2F_Targets are not in the Top 20 gene sets enriched in EBP group vs Ctrl.
DOI: 10.6084/m9.figshare.21285903.v1
title: Additional file 8 of Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus

description: Additional file 8. 31 genes significantly regulated between EBP and EB.
DOI: 10.6084/m9.figshare.21285885
title: Additional file 2 of Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus

description: Additional file 2. 1261 Differentially expressed genes between the WT and AF1_FFF uterus on GD3.
DOI: 10.6084/m9.figshare.10278209
title: MOESM1 of Transcriptome profiling of ‘Kyoho’ grape at different stages of berry development following 5-azaC treatment

description: Additional file 1. Summary of the read numbers aligned onto the grape reference genome.
DOI: 10.6084/m9.figshare.21285660
title: Additional file 10 of Hypoxia is fine-tuned by Hif-1α and regulates mesendoderm differentiation through the Wnt/β-Catenin pathway

description: Additional file 10. A excel file that includes the values of data points in all figures
DOI: 10.6084/m9.figshare.10278209.v1
title: MOESM1 of Transcriptome profiling of ‘Kyoho’ grape at different stages of berry development following 5-azaC treatment

description: Additional file 1. Summary of the read numbers aligned onto the grape reference genome.
DOI: 10.6084/m9.figshare.23383865.v1
title: Circulation of Lassa virus across the endemic Edo-Ondo axis, Nigeria, with cross-species transmission between multimammate mice

description: We phylogenetically compared sequences of the zoonotic Lassa virus (LASV) obtained from <i>Mastomys</i> rodents in seven localities across the highly endemic Edo and Ondo States within Nigeria. Sequencing 1641 nt from the S segment of the virus genome, we resolved clades within lineage II that were either limited to Ebudin and Okhuesan in Edo state (2g-beta) or along Owo-Okeluse-Ifon in Ondo state (2g-gamma). We also found clades within Ekpoma, a relatively large cosmopolitan town in Edo state, that extended into other localities within Edo (2g-alpha) and Ondo (2g-delta). LASV variants from <i>M. natalensis</i> within Ebudin and Ekpoma in Edo State (dated approximately 1961) were more ancient compared to those from Ondo state (approximately 1977), suggesting a broadly east-west virus migration across south-western Nigeria; a pattern not always consistent with LASV sequences derived from humans in the same localities. Additionally, in Ebudin and Ekpoma, LASV sequences between <i>M. natalensis</i> and <i>M. erythroleucus</i> were interspersed on the phylogenetic tree, but those from <i>M. erythroleucus</i> were estimated to emerge more recently (approximately 2005). Overall, our results show that LASV amplification in certain localities (reaching a prevalence as high as 76% in Okeluse), anthropogenically-aided spread of rodent-borne variants amidst the larger towns (involving communal accommodation such as student hostels), and virus-exchange between syntopic <i>M. natalensis</i> and <i>M. erythroleucus</i> rodents (as the latter, a savanna species, encroaches southward into the degraded forest) pose perpetual zoonotic hazard across the Edo-Ondo Lassa fever belt, threatening to accelerate the dissemination of the virus into non endemic areas.
DOI: 10.6084/m9.figshare.8179829.v1
title: MOESM1 of Using hyperspectral analysis as a potential high throughput phenotyping tool in GWAS for protein content of rice quality

description: Additional file 1: Table S1. Information of all rice accessions.
DOI: 10.6084/m9.figshare.21285897.v1
title: Additional file 6 of Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus

description: Additional file 6. Common and unique EB regulated genes on GD 3 and GD 4.5.
DOI: 10.6084/m9.figshare.8179844
title: MOESM3 of Using hyperspectral analysis as a potential high throughput phenotyping tool in GWAS for protein content of rice quality

description: Additional file 3:Â Table S2. SummaryÂ of re-sequencing results.
DOI: 10.6084/m9.figshare.17092355
title: Nucleo-cytoplasmic RNA distribution responsible for maintaining neuroinflammatory microenvironment

description: Subcellular localization of transcripts is highly associated with regulation of gene expression, synthesis of protein, and also the development of the human brain cortex. Although many mechanisms are prevalent in the occurrence of neuroinflammation, the mechanisms based on differences in subcellular localization of transcripts have not been explored. To characterize the dynamic profile of nuclear and cytoplasmic transcripts during the progress of haemorrhage-induced neuroinflammation, we isolated nucleo-cytoplasmic RNA fractions of oxyhaemoglobin (oxy-Hb) treated microglia cells and sequenced both fractions. We discovered that cytoplasmic retained genes were the major forces to maintain the neuroinflammatory microenvironment with 10 hub genes and 40 conserved genes were identified. Moreover, antisense RNA Gm44096 and lincRNA Gm47270, which co-expressed with a crowd of inflammatory genes in the cytoplasm, were discovered as regulatory strategies for sustaining the neuroinflammatory microenvironment. Thus, our study provides a new perspective on understanding haemorrhage-induced neuroinflammation and also reveals a mechanism of lncRNA responsible for maintaining the neuroinflammatory microenvironment.
DOI: 10.6084/m9.figshare.17092355.v1
title: Nucleo-cytoplasmic RNA distribution responsible for maintaining neuroinflammatory microenvironment

description: Subcellular localization of transcripts is highly associated with regulation of gene expression, synthesis of protein, and also the development of the human brain cortex. Although many mechanisms are prevalent in the occurrence of neuroinflammation, the mechanisms based on differences in subcellular localization of transcripts have not been explored. To characterize the dynamic profile of nuclear and cytoplasmic transcripts during the progress of haemorrhage-induced neuroinflammation, we isolated nucleo-cytoplasmic RNA fractions of oxyhaemoglobin (oxy-Hb) treated microglia cells and sequenced both fractions. We discovered that cytoplasmic retained genes were the major forces to maintain the neuroinflammatory microenvironment with 10 hub genes and 40 conserved genes were identified. Moreover, antisense RNA Gm44096 and lincRNA Gm47270, which co-expressed with a crowd of inflammatory genes in the cytoplasm, were discovered as regulatory strategies for sustaining the neuroinflammatory microenvironment. Thus, our study provides a new perspective on understanding haemorrhage-induced neuroinflammation and also reveals a mechanism of lncRNA responsible for maintaining the neuroinflammatory microenvironment.
DOI: 10.6084/m9.figshare.10278215
title: MOESM1 of Cooperation of Dnmt3a R878H with Nras G12D promotes leukemogenesis in knock-in mice: a pilot study

description: Additional file 1: Table S1. Primers for identifying genotypes of Knock-in mice.
DOI: 10.6084/m9.figshare.10278215.v1
title: MOESM1 of Cooperation of Dnmt3a R878H with Nras G12D promotes leukemogenesis in knock-in mice: a pilot study

description: Additional file 1: Table S1. Primers for identifying genotypes of Knock-in mice.
DOI: 10.6084/m9.figshare.19189413.v1
title: Characterization and pathogenicity of a novel avian nephritis virus isolated in China

description: Avian nephritis virus infections of chicken flocks cause enteric and kidney disease, uneven growth, and runting stunting syndrome, leading to economic losses in the poultry industry. In this study, one ANV strain, designated as AH202017, was isolated from a diseased broiler flock in Anhui province, China, in 2020. Virus production in LMH cell culture was confirmed by real-time RT–PCR and immunofluorescence assay. The complete genome sequencing analysis indicated that AH202017 shares 77.5–85.5% identity with 12 reference strains in GenBank. Phylogenetic analysis of the capsid protein revealed that AH202017 is more closely related to VIC-6a/Australia/2014 belonging to ANV genotype 2. However, the phylogenetic tree, based on the ORF1a protein and ORF1b protein, indicated that AH202017 manifests a close relationship with GXJL815/China/2017 belonging to genotype 8. In infection experiments, four infected chickens showed depression and one chicken died at 6 days post-infection, corresponding to 5% mortality. The virus was shed daily in the faeces of infected chickens, and was found distributed in multiple organs. Macroscopic and microscopic lesions in the kidneys were observed. This is the first paper that describes the genomic characteristics and pathogenicity of a novel ANV strain in China.
RESEARCH HIGHLIGHTSA novel ANV strain was isolated for the first time from diseased broilers in China.The ANV strain caused nephritis and 5% mortality rate in 1-day-old SPF chickens. A novel ANV strain was isolated for the first time from diseased broilers in China. The ANV strain caused nephritis and 5% mortality rate in 1-day-old SPF chickens.
DOI: 10.6084/m9.figshare.10278218
title: MOESM2 of Transcriptome profiling of ‘Kyoho’ grape at different stages of berry development following 5-azaC treatment

description: Additional file 2. Summary of the gene expression numbers in the control and the treatment.
DOI: 10.6084/m9.figshare.10278218.v1
title: MOESM2 of Transcriptome profiling of ‘Kyoho’ grape at different stages of berry development following 5-azaC treatment

description: Additional file 2. Summary of the gene expression numbers in the control and the treatment.
DOI: 10.6084/m9.figshare.7132496
title: Additional file 5: of Genes significantly associated with lineage II food isolates of Listeria monocytogenes

description: Chi-Square test for significant gene clusters in lineage II. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.8179844.v1
title: MOESM3 of Using hyperspectral analysis as a potential high throughput phenotyping tool in GWAS for protein content of rice quality

description: Additional file 3:Â Table S2. SummaryÂ of re-sequencing results.
DOI: 10.6084/m9.figshare.10278224
title: MOESM3 of Transcriptome profiling of ‘Kyoho’ grape at different stages of berry development following 5-azaC treatment

description: Additional file 3. The cluster information of the genes from TC-seq analysis.
DOI: 10.6084/m9.figshare.10278224.v1
title: MOESM3 of Transcriptome profiling of ‘Kyoho’ grape at different stages of berry development following 5-azaC treatment

description: Additional file 3. The cluster information of the genes from TC-seq analysis.
DOI: 10.6084/m9.figshare.10278227
title: MOESM2 of Cooperation of Dnmt3a R878H with Nras G12D promotes leukemogenesis in knock-in mice: a pilot study

description: Additional file 2: Table S2. Genes with Different Expression Patterns of Gr-1 Positive Cells Between DKI and WT Mice.
DOI: 10.6084/m9.figshare.10278227.v1
title: MOESM2 of Cooperation of Dnmt3a R878H with Nras G12D promotes leukemogenesis in knock-in mice: a pilot study

description: Additional file 2: Table S2. Genes with Different Expression Patterns of Gr-1 Positive Cells Between DKI and WT Mice.
DOI: 10.6084/m9.figshare.8179811
title: Additional file 1: of Rifampin resistance and its fitness cost in Riemerella anatipestifer

description: Table S1. Primers and descriptions used in this study (XLSX 10 kb)
DOI: 10.6084/m9.figshare.10278230
title: MOESM4 of Transcriptome profiling of ‘Kyoho’ grape at different stages of berry development following 5-azaC treatment

description: Additional file 4. GO function enrichment analysis of gene expression in C1 cluster from TC-seq analysis.
DOI: 10.6084/m9.figshare.8179721
title: Additional file 1: of MicroRNA-655-3p and microRNA-497-5p inhibit cell proliferation in cultured human lip cells through the regulation of genes related to human cleft lip

description: Table S1. PCR primer sets used in this study. Table S2. Summary of databases searched. Table S3. Genes with significant contribution to human CL/P (identified through single gene studies). Table S4. Genes with significant contribution to human CL/P (identified through multiple genes studies). Table S5. Genes with significant contribution to human CL/P (unknown coding genes). Table S6. Genes without significant contribution to human CL/P. Table S7. CL/P candidate genes with significant signals in GWAS. Table S8. CL/P candidate genes without significant signals in GWAS. Table S9. GO terms enriched with genes associated with cleft lip with/without cleft palate (CL/P) in humans. Table S10. GO Biological Process terms enriched with human CL/P genes (FDR &lt; 0.005). Table S11. GO Molecular Function terms enriched with human CL/P genes (FDR &lt; 0.005). Table S12. GO Cellular Component terms enriched with human CL/P genes (FDR &lt; 0.05). Table S13. Top 30 Human Phenotype Ontology Categories. Table S14. KEGG pathways enriched with genes associated with cleft lip with/without cleft palate (CL/P) in humans. (ZIP 292 kb)
DOI: 10.6084/m9.figshare.10278230.v1
title: MOESM4 of Transcriptome profiling of ‘Kyoho’ grape at different stages of berry development following 5-azaC treatment

description: Additional file 4. GO function enrichment analysis of gene expression in C1 cluster from TC-seq analysis.
DOI: 10.6084/m9.figshare.10278233
title: MOESM3 of Cooperation of Dnmt3a R878H with Nras G12D promotes leukemogenesis in knock-in mice: a pilot study

description: Additional file 3: Table S3. Primers for validating the results of RNA-seq analysis.
DOI: 10.6084/m9.figshare.10278233.v1
title: MOESM3 of Cooperation of Dnmt3a R878H with Nras G12D promotes leukemogenesis in knock-in mice: a pilot study

description: Additional file 3: Table S3. Primers for validating the results of RNA-seq analysis.
DOI: 10.6084/m9.figshare.10278239
title: MOESM5 of Transcriptome profiling of ‘Kyoho’ grape at different stages of berry development following 5-azaC treatment

description: Additional file 5. The information of DEGs for A5-C5.
DOI: 10.6084/m9.figshare.10278239.v1
title: MOESM5 of Transcriptome profiling of ‘Kyoho’ grape at different stages of berry development following 5-azaC treatment

description: Additional file 5. The information of DEGs for A5-C5.
DOI: 10.5281/zenodo.10670466
title: "Elucidating the photoprotective properties of natural UV screening agents: ZEKE-PFI spectroscopy of methyl sinapate" dataset
DOI: 10.5281/zenodo.10670467
title: "Elucidating the photoprotective properties of natural UV screening agents: ZEKE-PFI spectroscopy of methyl sinapate" dataset
DOI: 10.6084/m9.figshare.21285735.v1
title: Additional file 2 of Müller cell degeneration and microglial dysfunction in the Alzheimer’s retina

description: Additional file 2. All p-values.
DOI: 10.6084/m9.figshare.10278251
title: MOESM7 of Transcriptome profiling of ‘Kyoho’ grape at different stages of berry development following 5-azaC treatment

description: Additional file 7. The sequences of primer used in the qRT-PCR.
DOI: 10.6084/m9.figshare.10278251.v1
title: MOESM7 of Transcriptome profiling of ‘Kyoho’ grape at different stages of berry development following 5-azaC treatment

description: Additional file 7. The sequences of primer used in the qRT-PCR.
DOI: 10.6084/m9.figshare.7132532
title: Additional file 7: of Genes significantly associated with lineage II food isolates of Listeria monocytogenes

description: List of eight significant genes, their homologues, and sequence accessions. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.24434075
title: Metamorphosed mélange in eastern Himalayan syntaxis: constraint for the India-Asia collision in Eocene

description: Table S1. Geochronology data.
DOI: 10.6084/m9.figshare.24434075.v1
title: Metamorphosed mélange in eastern Himalayan syntaxis: constraint for the India-Asia collision in Eocene

description: Table S1. Geochronology data.
DOI: 10.6084/m9.figshare.24434078
title: Metamorphosed mélange in eastern Himalayan syntaxis: constraint for the India-Asia collision in Eocene

description: Table S3. Whole-rock major and trace element results.
DOI: 10.6084/m9.figshare.24434078.v1
title: Metamorphosed mélange in eastern Himalayan syntaxis: constraint for the India-Asia collision in Eocene

description: Table S3. Whole-rock major and trace element results.
DOI: 10.6084/m9.figshare.24434081
title: Metamorphosed mélange in eastern Himalayan syntaxis: constraint for the India-Asia collision in Eocene

description: Table S2. Zircon Lu–Hf isotopic data.
DOI: 10.6084/m9.figshare.24434081.v1
title: Metamorphosed mélange in eastern Himalayan syntaxis: constraint for the India-Asia collision in Eocene

description: Table S2. Zircon Lu–Hf isotopic data.
DOI: 10.15129/60af5807-790e-4a97-9a4b-b0861d8c5fe8
title: Free Electron Laser (FEL) superradiant spike saturation video

description: Puffin simulation in 1-D of the superradiant radiation spike saturation process. The parameters used were 4 pi rho = 1.0. The details are published in a paper by Pornthep Ponchalee and Brian W.J. McNeil entitled "Superradiant pulse saturation in a Free Electron Laser". The video is the property of the author.