cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7116992
title: Supplementary Material for: Utility of Rapid On-Site Cytologic Evaluation during Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration in Malignant and Nonmalignant Disease

description: <b><i>Background:</i></b> Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is an accurate procedure to sample mediastinal tissue. Rapid on-site cytologic evaluation (ROSE) has been advocated to improve the performance of this procedure, but its benefit remains controversial. Our objective is to assess the utility of ROSE for EBUS-TBNA diagnostic accuracy among unselected patients. <b><i>Methods:</i></b> We prospectively collected data from all consecutive EBUS-TBNA procedures performed between 2008 and 2014. ROSE was introduced since 2011 in our daily practice. The accuracy of EBUS-TBNA with and without ROSE was compared in a univariate and multivariate model accounting for confounding factors. The impact of ROSE was then analyzed according to the etiology and size of the lesions. <b><i>Results:</i></b> Among 348 EBUS-TBNA procedures analyzed, 213 were performed with ROSE. The overall accuracy tended to be better with ROSE than without (90.6 vs. 84.4%; <i>p</i> = 0.082). After adjustment in a multivariate model, the benefit of ROSE still did not reach statistical significance (adjusted odds ratio 1.86; 95% confidence interval 0.79–4.41). Similar results were obtained in subgroups of patients with malignant disease or sarcoidosis. The size of the lesion did not influence the impact of ROSE on accuracy. <b><i>Conclusions:</i></b> ROSE was associated with a moderate increase in the accuracy of EBUS-TBNA, but the difference was not statistically significant. The same effect of ROSE was observed in malignant and nonmalignant lesions and this effect was not influenced by the lesion’s size.
DOI: 10.6084/m9.figshare.7117001.v1
title: Supplementary Material for: Allergen Immunization Induces Major Changes in Microbiota Composition and Short-Chain Fatty Acid Production in Different Gut Segments in a Mouse Model of Lupine Food Allergy

description: <b><i>Background:</i></b> The incidence of food allergies in western countries has increased in recent decades. <b><i>Objectives:</i></b> To study the association between gut bacterial microbiota composition, short-chain fatty acids (SCFAs) and food allergy in a mouse model. <b><i>Methods:</i></b> After oral immunizations with the human food allergen lupine with the adjuvant cholera toxin (CT) (or buffer in controls), sensitization and anaphylactic responses were determined. Gastrointestinal content was collected from the distal ileum, cecum, colon, and fecal pellets, and the bacterial diversity and composition was determined by deep sequencing of the 16S rRNA gene. SCFAs in gastrointestinal content supernatants were determined by gas chromatography. <b><i>Results:</i></b> The microbiota signatures were profoundly affected by allergen immunization. Ten operational taxonomic units (OTUs) were significantly different between immunized and control animals for at least one of the intestinal segments; eight of these OTUs belonged to the Clostridia class. Although consistent across all four gut segments, the colon showed the highest number of OTUs significantly associated with allergic immunization. SCFA levels in the cecum were also altered by immunization. <b><i>Conclusions:</i></b> Allergen immunization with CT in the present food allergy model induced profound changes in the microbiome composition and SCFA production. The result suggests that the colon may be the most sensitive gut segment for investigating changes in the gut microbiome.
DOI: 10.6084/m9.figshare.7116977
title: Knowledge and awareness of hepatitis B among households in Malaysia: A community-based cross-sectional survey

description: This data is part of submission to BMC Public Health.
DOI: 10.6084/m9.figshare.7116977.v1
title: Knowledge and awareness of hepatitis B among households in Malaysia: A community-based cross-sectional survey

description: This data is part of submission to BMC Public Health.
DOI: 10.6084/m9.figshare.7116992.v1
title: Supplementary Material for: Utility of Rapid On-Site Cytologic Evaluation during Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration in Malignant and Nonmalignant Disease

description: <b><i>Background:</i></b> Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is an accurate procedure to sample mediastinal tissue. Rapid on-site cytologic evaluation (ROSE) has been advocated to improve the performance of this procedure, but its benefit remains controversial. Our objective is to assess the utility of ROSE for EBUS-TBNA diagnostic accuracy among unselected patients. <b><i>Methods:</i></b> We prospectively collected data from all consecutive EBUS-TBNA procedures performed between 2008 and 2014. ROSE was introduced since 2011 in our daily practice. The accuracy of EBUS-TBNA with and without ROSE was compared in a univariate and multivariate model accounting for confounding factors. The impact of ROSE was then analyzed according to the etiology and size of the lesions. <b><i>Results:</i></b> Among 348 EBUS-TBNA procedures analyzed, 213 were performed with ROSE. The overall accuracy tended to be better with ROSE than without (90.6 vs. 84.4%; <i>p</i> = 0.082). After adjustment in a multivariate model, the benefit of ROSE still did not reach statistical significance (adjusted odds ratio 1.86; 95% confidence interval 0.79–4.41). Similar results were obtained in subgroups of patients with malignant disease or sarcoidosis. The size of the lesion did not influence the impact of ROSE on accuracy. <b><i>Conclusions:</i></b> ROSE was associated with a moderate increase in the accuracy of EBUS-TBNA, but the difference was not statistically significant. The same effect of ROSE was observed in malignant and nonmalignant lesions and this effect was not influenced by the lesion’s size.
DOI: 10.25377/sussex.7116842
title: Research data for paper: 'The Role of Emergent Shared Identity in Psychosocial Support among Refugees of Conflict in Developing Countries'. Jordan survey data-set.

description: Data from survey of 156 Syrian refugees in Jordan, collected 2016, as part of Alfadhli's thesis and forming part of a paper published in International Review of Social Psychology, January 2019. (Expected date of publication)<br><br><b>Abstract</b>In spite of the harsh conditions that refugees of conflicts experience for many years in exile in developing countries, there is evidence showing that refugees of conflict help each other. This study aimed to explore one possible mechanism underlying such support and sought to answer three main research questions: Do refugees share an emergent identity that facilitates support among them (similar to people affected by disasters)? Does this identity-based support have an impact on their health? If so, does this positive impact help to mitigate the negative effect of exile stressors on refugees’ health? We carried out two questionnaire surveys among Syrian refugees, first in Turkey (n = 234) and then in Jordan (n = 156). The data were analysed using path analysis to test hypotheses and build a theoretical model. We found evidence suggesting a process of shared social identity-based support among the refugees. We found that the general health of refugees to be predicted mainly by stress, but we also found that collective efficacy has a positive association with health, which suggests a buffering effect. These results shed light on the process of social support among refugees of war and suggest the role of shared identity, which can have a limited buffering effect on the health of the refugees, though not enough to fully mitigate the negative effect of secondary stressors. However, we suggest that such a process can be utilised as base for interventions that approach refugees of war as a group (i.e., at community rather than individual level).<br>
DOI: 10.6084/m9.figshare.7116836.v1
title: ZHAOv18-M2-mode-2.mat

description: An empirical internal tide model for the mode-2 M2 internal tide, constructed using 25 years of satellite altimetry data. The mapping method is described in a paper under review by JGR-Oceans. The model covers the global ocean from -65 to 65 in latitude and 0-360 in longitude. The regular grid is 0.1 degrees by 0.1 degrees. The SSH amplitude is in cm and the phase is in Greenwich.
DOI: 10.6084/m9.figshare.7116824
title: Disruption of the RNA exosome reveals the hidden face of the malaria parasite transcriptome

description: Antisense transcription emerges as a key regulator of important biological processes in the human malaria parasite <i>Plasmodium falciparum</i>. RNA-processing factors, however, remain poorly characterized in this pathogen. Here, we purified the multiprotein RNA exosome complex of malaria parasites by affinity chromatography, using HA-tagged PfRrp4 and PfDis3 as the ligands. Seven distinct core exosome subunits (PfRrp41, PfMtr3, PfRrp42, PfRrp45, PfRrp4, PfRrp40, PfCsl4) and two exoribonuclease proteins PfRrp6 and PfDis3 are identified by mass spectrometry. Western blot analysis detects Dis3 and Rrp4 predominantly in the cytoplasmic fraction during asexual blood stage development. An inducible gene knock out of the PfDis3 subunit reveals the upregulation of structural and coding RNA, but the vast majority belongs to antisense RNA. Furthermore, we detect numerous types of cryptic unstable transcripts (CUTs) linked to virulence gene families including antisense RNA in the <i>rif</i> gene family. Our work highlights the limitations of steady-state RNA analysis to predict transcriptional activity and link the RNA surveillance machinery directly with post-transcriptional control and gene expression in malaria parasites.
DOI: 10.6084/m9.figshare.7116833
title: Calculation of LDs and their ratios.xlsx

description: Caculation of LDs and their potency ratio by probit-logdose regression (Lei and Sun, 2018, BMC Pharmacology & Toxicology).
DOI: 10.6084/m9.figshare.7116821
title: Karakosta et al - Cord leptin predicts child neurposychological development - Supplementary Tables

description: <b>Supplementary </b><b>Table S1:</b>Data for the trajectory model selection<b></b><i></i><sub></sub><sup></sup><br><b>Supplementary Table S2: </b>Background characteristics of the study population (subjects with available cord leptin levels and at least one assessment of neuropsychological development of cognition from birth to 6 years) based on cord leptin status; Rhea birth cohort, Crete Greece (n=429).<b>Supplementary Table S3: </b>Background characteristics of the study population included in the analysis and lost to follow up.<br><b>Supplementary Table S4:</b>Association of cord leptin with child neuropsychological development, after i. excluding preterm and/or low birth weight neonates, and iii. additional adjusting for ponderal index.<br>
DOI: 10.6084/m9.figshare.7116833.v2
title: Calculation of LDs and their ratios.xlsx

description: Caculation of LDs and their potency ratio by probit-logdose regression (Lei and Sun, 2018, BMC Pharmacology & Toxicology).
DOI: 10.6084/m9.figshare.7116833.v1
title: Calculation of LDs and their ratios.xlsx

description: Caculation of LDs and their potency ratio by probit-logdose regression (Lei and Sun, 2018).
DOI: 10.6084/m9.figshare.7116821.v1
title: Karakosta et al - Cord leptin predicts child neurposychological development - Supplementary Tables

description: <b>Supplementary Table S1: </b>Background characteristics of the study population (subjects with available cord leptin levels and at least one assessment of neuropsychological development of cognition from birth to 6 years) based on cord leptin status; Rhea birth cohort, Crete Greece (n=429).<br><br><b>Supplementary Table S2: </b>Background characteristics of the study population included in the analysis and lost to follow up.<br><br><b>Supplementary Table S3:</b>Association of cord leptin with child neuropsychological development, after i. excluding preterm and/or low birth weight neonates, and iii. additional adjusting for ponderal index.<br><b>Supplementary </b><b>Table S4:</b>Data for the trajectory model selection
DOI: 10.26180/5ba4800bca2a2
title: Using Alma Mobile - Photo competition

description: Photo entries for the use and advertising of Alma Mobile. One photo was awarded as the first prize.<br>https://www.exlibrisgroup.com/alma-mobile-photo-competition-winner/<br>Photo concept: Rachelle Orodio<br>Photographer: Beth Pearson<br><br>
DOI: 10.6084/m9.figshare.7116710
title: ANALISIS PÁGINA INICIO YOUTUBE .xlsx

description: Resultados del análisis del artículo: <b>Entre el “Broadcast Yourself” y “Broadcast Whatever”: la página de inicio de <i>YouTube </i>como síntesis de su estrategia empresarial.</b><b></b>
DOI: 10.6084/m9.figshare.7116560
title: Additional file 2: of Epidemiology of Taenia saginata taeniosis/cysticercosis: a systematic review of the distribution in the Americas

description: Table S1. Identified literature supporting the presence of Taenia saginata in the Americas during 1990-2017. Table S2. States in Brazil with bovine cysticercosis in 1990â 2017. Table S3. Countries in the Americas with Taenia saginata occurrence in 1990-2017. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.7116560.v1
title: Additional file 2: of Epidemiology of Taenia saginata taeniosis/cysticercosis: a systematic review of the distribution in the Americas

description: Table S1. Identified literature supporting the presence of Taenia saginata in the Americas during 1990-2017. Table S2. States in Brazil with bovine cysticercosis in 1990â 2017. Table S3. Countries in the Americas with Taenia saginata occurrence in 1990-2017. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.7116392
title: Additional file 2: of Transcriptomic response of female adult moths to host and non-host plants in two closely related species

description: Table S1. Details on sequencing reads and contaminants per library. Table S2. Top hit species after BLAST analysis, for the ECB-ref transcripts (sheet 1) and ABB-ref transcripts (sheet 2). Table S3. Read mapping against ABB-ref transcripts for ABB and ECB samples. Table S4. Sequencing characteristics of the RNA pools. Table S5. Detailed information for DE genes homologous with virus (A) and retrovirus-like transposon sequences (B). Table S6. Detailed information for genes DE between ECB and ABB species. Table S7. Fisherâ s test of enrichment in GO term categories between the DE transcripts (test set) and the whole transcriptome (reference set). Table S8. Detailed information for genes DE between experimental environments (maize, choice, mugwort). Table S9. Detailed information for genes involved in ECB-pref, ECB-avoid and ABB-pref. Table S10. Detailed information for genes specific to ABB-pref, ECB-pref and ECB-avoid contrasts in HT and ABDO tissues. Table S11. Published chemosensory Ostrinia spp. genes. Table S12. Detailed information for DE chemosensory genes.
DOI: 10.6084/m9.figshare.7116392.v1
title: Additional file 2: of Transcriptomic response of female adult moths to host and non-host plants in two closely related species

description: Table S1. Details on sequencing reads and contaminants per library. Table S2. Top hit species after BLAST analysis, for the ECB-ref transcripts (sheet 1) and ABB-ref transcripts (sheet 2). Table S3. Read mapping against ABB-ref transcripts for ABB and ECB samples. Table S4. Sequencing characteristics of the RNA pools. Table S5. Detailed information for DE genes homologous with virus (A) and retrovirus-like transposon sequences (B). Table S6. Detailed information for genes DE between ECB and ABB species. Table S7. Fisherâ s test of enrichment in GO term categories between the DE transcripts (test set) and the whole transcriptome (reference set). Table S8. Detailed information for genes DE between experimental environments (maize, choice, mugwort). Table S9. Detailed information for genes involved in ECB-pref, ECB-avoid and ABB-pref. Table S10. Detailed information for genes specific to ABB-pref, ECB-pref and ECB-avoid contrasts in HT and ABDO tissues. Table S11. Published chemosensory Ostrinia spp. genes. Table S12. Detailed information for DE chemosensory genes.
DOI: 10.6084/m9.figshare.7116386
title: Additional file 4: of Integrated genomic analyses in PDX model reveal a cyclin-dependent kinase inhibitor Palbociclib as a novel candidate drug for nasopharyngeal carcinoma

description: Table S2. Summary of 282 SNV mutations in 5 NPC-PDX tumors. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.7116386.v1
title: Additional file 4: of Integrated genomic analyses in PDX model reveal a cyclin-dependent kinase inhibitor Palbociclib as a novel candidate drug for nasopharyngeal carcinoma

description: Table S2. Summary of 282 SNV mutations in 5 NPC-PDX tumors. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.7116353
title: MOESM9 of Genetic repertoires of anaerobic microbiomes driving generation of biogas

description: Additional file 9. Summary of EC numbers with assignments to metabolic modules.
DOI: 10.6084/m9.figshare.7116353.v1
title: MOESM9 of Genetic repertoires of anaerobic microbiomes driving generation of biogas

description: Additional file 9. Summary of EC numbers with assignments to metabolic modules.
DOI: 10.6084/m9.figshare.7116332
title: Additional file 9: of Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance

description: Table S8. RNA-seq and expression microarray data showing genes differentially expressed in heterozygous E8.5Â day embryos sired by Eedhypo/hypo fathers compared to E8.5-day embryos sired by Eedhypo/wt fathers. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7116332.v1
title: Additional file 9: of Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance

description: Table S8. RNA-seq and expression microarray data showing genes differentially expressed in heterozygous E8.5Â day embryos sired by Eedhypo/hypo fathers compared to E8.5-day embryos sired by Eedhypo/wt fathers. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7116320
title: MOESM6 of Genetic repertoires of anaerobic microbiomes driving generation of biogas

description: Additional file 6. Annotated list of top 500 differentially expressed transcripts.
DOI: 10.6084/m9.figshare.7116320.v1
title: MOESM6 of Genetic repertoires of anaerobic microbiomes driving generation of biogas

description: Additional file 6. Annotated list of top 500 differentially expressed transcripts.
DOI: 10.6084/m9.figshare.7116317
title: Additional file 8: of Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance

description: Table S7. ChIP-seq data showing regions with decreased H3K27me3 in Eedhypo/hypo compared Eedwt/wt to germ cells identified using EdgeR. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7116317.v1
title: Additional file 8: of Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance

description: Table S7. ChIP-seq data showing regions with decreased H3K27me3 in Eedhypo/hypo compared Eedwt/wt to germ cells identified using EdgeR. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7116302
title: Additional file 7: of Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance

description: Table S6. ChIP-seq data from E15.5 male Eedhypo/hypo compared to Eedwt/wt germ cells: Peaks with increased H3K27me3 in Eedhypo/hypo germ cells. (XLSX 83 kb)
DOI: 10.6084/m9.figshare.7116302.v1
title: Additional file 7: of Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance

description: Table S6. ChIP-seq data from E15.5 male Eedhypo/hypo compared to Eedwt/wt germ cells: Peaks with increased H3K27me3 in Eedhypo/hypo germ cells. (XLSX 83 kb)
DOI: 10.6084/m9.figshare.7116296
title: MOESM4 of Genetic repertoires of anaerobic microbiomes driving generation of biogas

description: Additional file 4. List of GO terms from top 500 expressed transcripts.
DOI: 10.6084/m9.figshare.7116296.v1
title: MOESM4 of Genetic repertoires of anaerobic microbiomes driving generation of biogas

description: Additional file 4. List of GO terms from top 500 expressed transcripts.
DOI: 10.6084/m9.figshare.7116290
title: Additional file 2: of Progression-specific genes identified in microdissected formalin-fixed and paraffin-embedded tissue containing matched ductal carcinoma in situ and invasive ductal breast cancers

description: Overlapping genes, Description: Comparison of WG-DASL results with the data from the FF investigation. 124 of the transcripts were found to show differential expression in both investigations (Pâ
DOI: 10.6084/m9.figshare.7116290.v1
title: Additional file 2: of Progression-specific genes identified in microdissected formalin-fixed and paraffin-embedded tissue containing matched ductal carcinoma in situ and invasive ductal breast cancers

description: Overlapping genes, Description: Comparison of WG-DASL results with the data from the FF investigation. 124 of the transcripts were found to show differential expression in both investigations (Pâ
DOI: 10.6084/m9.figshare.7116281
title: Additional file 6: of Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance

description: Table S5. ChIP-seq data from E15.5 male Eedhypo/hypo compared to Eedwt/wt germ cells: Peaks with decreased H3K27me3 in Eedhypo/hypo germ cells. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.7116281.v1
title: Additional file 6: of Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance

description: Table S5. ChIP-seq data from E15.5 male Eedhypo/hypo compared to Eedwt/wt germ cells: Peaks with decreased H3K27me3 in Eedhypo/hypo germ cells. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.7116272
title: Additional file 1: of Progression-specific genes identified in microdissected formalin-fixed and paraffin-embedded tissue containing matched ductal carcinoma in situ and invasive ductal breast cancers

description: WG-DASL analysis resulted in 1784 transcripts that were differentially expressed between DCIS and IBC in the FFPE breast cancer tissue samples (Pâ
DOI: 10.6084/m9.figshare.7116269
title: MOESM2 of Genetic repertoires of anaerobic microbiomes driving generation of biogas

description: Additional file 2. Summary of genomic bins including estimated profile completeness, number of deduced coding sequences and EC numbers.
DOI: 10.6084/m9.figshare.7116272.v1
title: Additional file 1: of Progression-specific genes identified in microdissected formalin-fixed and paraffin-embedded tissue containing matched ductal carcinoma in situ and invasive ductal breast cancers

description: WG-DASL analysis resulted in 1784 transcripts that were differentially expressed between DCIS and IBC in the FFPE breast cancer tissue samples (Pâ
DOI: 10.6084/m9.figshare.7116269.v1
title: MOESM2 of Genetic repertoires of anaerobic microbiomes driving generation of biogas

description: Additional file 2. Summary of genomic bins including estimated profile completeness, number of deduced coding sequences and EC numbers.
DOI: 10.6084/m9.figshare.7116260
title: Additional file 5: of Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance

description: Table S4. Relative representation of annotated repeat categories in H3K27me3 peaks in Eedwt/wt and Eedhypo/hypo germ cells. (XLSX 1124 kb)
DOI: 10.6084/m9.figshare.7116260.v1
title: Additional file 5: of Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance

description: Table S4. Relative representation of annotated repeat categories in H3K27me3 peaks in Eedwt/wt and Eedhypo/hypo germ cells. (XLSX 1124 kb)
DOI: 10.6084/m9.figshare.7116245
title: Additional file 4: of Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance

description: Table S3. Comparison of known PRC target genes in ES cells with H3K27me3 peaks in foetal germ cells, ES cells and spermatocytes. (XLSX 1161 kb)