cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15131/shef.data.5783001.v1
title: Data set for Journal of Aircraft paper: Using the Reynolds Stress Turbulence Model to Predict Shock-Induced Separation on Transport Aircraft

description: This item contains the following:<br><br><b>grids : </b>ICEM CFD files *.tin and *.blk for the multi-block structured meshes about the NASA CRM deformed at various angles of attack. ICEM CFD is required to rebuild the grids. We are now considering uploading the fully built grids as well.<br><br><b>crm-wb-case-setup-template.txt: </b>setup of Fluent Case file<b><br></b><b>cp : </b>Pressure Coefficient data on the deformed CRM at different angles of attack<br>If any other data is needed that is not available here or in the paper, do not hesitate to contact us and will do our best to make it available. <br>
DOI: 10.6084/m9.figshare.5782998
title: Supplementary Material for: Epigenetic Silencing of the MLH1 Promoter in Relation to the Development of Gastric Cancer and its use as a Biomarker for Patients with Microsatellite Instability: a Systematic Analysis

description: <b><i>Background/Aims:</i></b> Human mutL homolog 1 (<i>MLH1</i>) promoter methylation was reported in gastric cancer (GC). This study determined the clinicopathological, prognostic, and diagnostic effects of <i>MLH1</i> promoter methylation in GC. <b><i>Methods:</i></b> The combined odds ratio (OR) or hazard ratio (HR) and their corresponding 95% confidence intervals (95% CI) were calculated. The pooled sensitivity, specificity, and area under the curve (AUC) were analyzed. <b><i>Results:</i></b> A total of 4654 GC patients and 3669 non-malignant controls were identified in this systematic analysis. <i>MLH1</i> promoter methylation was significantly higher in GC samples than in gastric adenomas, chronic gastritis, adjacent tissues, normal gastric mucosa, and normal healthy blood samples, but it exhibited a similar frequency in GC vs. intestinal metaplasia and dysplasia samples. <i>MLH1</i> promoter methylation correlated with age and microsatellite instability (MSI), but it was not associated with gender, <i>H. pylori</i> infection, smoking, drinking behaviors, pathological histology, tumor differentiation, clinical stage, lymph node status, distant metastasis, or overall survival of GC. <i>MLH1</i> promoter methylation exhibited a poor sensitivity value (&lt; 0.5) in patients with GC compared with adjacent tissues, gastric adenomas, chronic gastritis, normal gastric mucosa, and normal healthy blood samples. The pooled sensitivity, specificity, and AUC of <i>MLH1</i> promoter methylation in GC with MSI vs. GC with microsatellite stability (MSS) samples were 0.64, 0.96, and 0.90, respectively. <b><i>Conclusions:</i></b> Our results suggest that the detection of <i>MLH1</i> promoter methylation may be a potential prognostic biomarker for GC patients with MSI.
DOI: 10.6084/m9.figshare.5782992
title: Evaluation of supervised multimodal prehabilitation programme in cancer patients undergoing colorectal resection: a randomized control trial

description: <b>Background:</b> Prehabilitation has been previously shown to be more effective in enhancing postoperative functional capacity than rehabilitation alone. The purpose of this study was to determine whether a weekly supervised exercise session could provide further benefit to our current prehabilition program, when comparing to standard post-surgical rehabilitation. <b>Methods:</b> A parallel-arm single-blind randomized control trial was conducted in patients scheduled for non-metastatic colorectal cancer resection. Patients were assigned to either a once weekly supervised prehabilitation (PREHAB+, <i>n</i> = 41) or standard rehabilitation (REHAB, <i>n</i> = 39) program. Both multimodal programs were home-based program and consisted of moderate intensity aerobic and resistance exercise, nutrition counseling with daily whey protein supplementation and anxiety-reduction strategies. Perioperative care was standardized for both groups as per enhanced recovery after surgery (ERAS<sup>®</sup>) guidelines. Functional exercise capacity, as determined by the 6-minute walk test distance (6MWD), was the primary outcome. Exercise quantity, intensity and energy expenditure was determined by the CHAMPS questionnaire. <b>Results:</b> Both groups were comparable for baseline walking capacity (PREHAB+: 448 m [IQR 375–525] vs. REHAB: 461 m [419–556], <i>p</i>=.775) and included a similar proportion of patients who improved walking capacity (&gt;20 m) during the preoperative period (PREHAB+: 54% vs. REHAB: 38%, <i>p</i> = .222). After surgery, changes in 6MWD were also similar in both groups. In PREHAB+, however, there was a significant association between physical activity energy expenditure and 6MWD (<i>p</i> <b>Conclusions:</b> The addition of a weekly supervised exercise session to our current prehabilitation program did not further enhance postoperative walking capacity when compared to standard REHAB care. Sedentary patients, however, seemed more likely to benefit from PREHAB+. An association was found between energy spent in physical activity and 6MWD. This information is important to consider when designing cost-effective prehabilitation programs.
DOI: 10.6084/m9.figshare.5782992.v1
title: Evaluation of supervised multimodal prehabilitation programme in cancer patients undergoing colorectal resection: a randomized control trial

description: <b>Background:</b> Prehabilitation has been previously shown to be more effective in enhancing postoperative functional capacity than rehabilitation alone. The purpose of this study was to determine whether a weekly supervised exercise session could provide further benefit to our current prehabilition program, when comparing to standard post-surgical rehabilitation. <b>Methods:</b> A parallel-arm single-blind randomized control trial was conducted in patients scheduled for non-metastatic colorectal cancer resection. Patients were assigned to either a once weekly supervised prehabilitation (PREHAB+, <i>n</i> = 41) or standard rehabilitation (REHAB, <i>n</i> = 39) program. Both multimodal programs were home-based program and consisted of moderate intensity aerobic and resistance exercise, nutrition counseling with daily whey protein supplementation and anxiety-reduction strategies. Perioperative care was standardized for both groups as per enhanced recovery after surgery (ERAS<sup>®</sup>) guidelines. Functional exercise capacity, as determined by the 6-minute walk test distance (6MWD), was the primary outcome. Exercise quantity, intensity and energy expenditure was determined by the CHAMPS questionnaire. <b>Results:</b> Both groups were comparable for baseline walking capacity (PREHAB+: 448 m [IQR 375–525] vs. REHAB: 461 m [419–556], <i>p</i>=.775) and included a similar proportion of patients who improved walking capacity (&gt;20 m) during the preoperative period (PREHAB+: 54% vs. REHAB: 38%, <i>p</i> = .222). After surgery, changes in 6MWD were also similar in both groups. In PREHAB+, however, there was a significant association between physical activity energy expenditure and 6MWD (<i>p</i> <b>Conclusions:</b> The addition of a weekly supervised exercise session to our current prehabilitation program did not further enhance postoperative walking capacity when compared to standard REHAB care. Sedentary patients, however, seemed more likely to benefit from PREHAB+. An association was found between energy spent in physical activity and 6MWD. This information is important to consider when designing cost-effective prehabilitation programs.
DOI: 10.6084/m9.figshare.5782983
title: Supplementary Material for: The <b><i>von Hippel-Lindau</i></b> Gene Is Required to Maintain Renal Proximal Tubule and Glomerulus Integrity in Zebrafish Larvae

description: <b><i>Background:</i></b> <i>von Hippel-Lindau</i> (<i>VHL</i>) disease is characterized by the development of benign and malignant tumours in many organ systems, including renal cysts and clear cell renal cell carcinoma. It is not completely understood what underlies the development of renal pathology, and the use of murine <i>Vhl</i> models has been challenging due to limitations in disease conservation. We previously described a zebrafish model bearing inactivating mutations in the orthologue of the human <i>VHL</i> gene. <b><i>Methods:</i></b> We used histopathological and functional assays to investigate the pronephric and glomerular developmental defects in <i>vhl</i> mutant zebrafish, supported by human cell culture assays. <b><i>Results:</i></b> Here, we report that <i>vhl</i> is required to maintain pronephric tubule and glomerulus integrity in zebrafish embryos. <i>vhl</i> mutant glomeruli are enlarged, <i>cxcr4a+</i> capillary loops are dilated and the Bowman space is widened. While we did not observe pronephric cysts, the cells of the proximal convoluted and anterior proximal straight tubule are enlarged, periodic acid schiff (PAS) and Oil Red O positive, and display a clear cytoplasm after hematoxylin and eosine staining. Ultrastructural analysis showed the <i>vhl</i><sup>–/–</sup> tubule to accumulate large numbers of vesicles of variable size and electron density. Microinjection of the endocytic fluorescent marker AM1–43 in zebrafish embryos revealed an accumulation of endocytic vesicles in the <i>vhl</i> mutant pronephric tubule, which we can recapitulate in human cells lacking <i>VHL.</i> <b><i>Conclusions:</i></b> Our data indicates that <i>vhl</i> is required to maintain pronephric tubule and glomerulus integrity during zebrafish development, and suggests a role for VHL in endocytic vesicle trafficking.
DOI: 10.6084/m9.figshare.5782983.v1
title: Supplementary Material for: The <b><i>von Hippel-Lindau</i></b> Gene Is Required to Maintain Renal Proximal Tubule and Glomerulus Integrity in Zebrafish Larvae

description: <b><i>Background:</i></b> <i>von Hippel-Lindau</i> (<i>VHL</i>) disease is characterized by the development of benign and malignant tumours in many organ systems, including renal cysts and clear cell renal cell carcinoma. It is not completely understood what underlies the development of renal pathology, and the use of murine <i>Vhl</i> models has been challenging due to limitations in disease conservation. We previously described a zebrafish model bearing inactivating mutations in the orthologue of the human <i>VHL</i> gene. <b><i>Methods:</i></b> We used histopathological and functional assays to investigate the pronephric and glomerular developmental defects in <i>vhl</i> mutant zebrafish, supported by human cell culture assays. <b><i>Results:</i></b> Here, we report that <i>vhl</i> is required to maintain pronephric tubule and glomerulus integrity in zebrafish embryos. <i>vhl</i> mutant glomeruli are enlarged, <i>cxcr4a+</i> capillary loops are dilated and the Bowman space is widened. While we did not observe pronephric cysts, the cells of the proximal convoluted and anterior proximal straight tubule are enlarged, periodic acid schiff (PAS) and Oil Red O positive, and display a clear cytoplasm after hematoxylin and eosine staining. Ultrastructural analysis showed the <i>vhl</i><sup>–/–</sup> tubule to accumulate large numbers of vesicles of variable size and electron density. Microinjection of the endocytic fluorescent marker AM1–43 in zebrafish embryos revealed an accumulation of endocytic vesicles in the <i>vhl</i> mutant pronephric tubule, which we can recapitulate in human cells lacking <i>VHL.</i> <b><i>Conclusions:</i></b> Our data indicates that <i>vhl</i> is required to maintain pronephric tubule and glomerulus integrity during zebrafish development, and suggests a role for VHL in endocytic vesicle trafficking.
DOI: 10.6084/m9.figshare.5782941
title: Unconscious response inhibition differences between table tennis athletes and non-athletes

description: We share ERP raw data, behavioural raw data of this article.
DOI: 10.6084/m9.figshare.5782938
title: Supplementary Material for: Low-Dose Oral Immunotherapy Using Low-Egg-Allergen Cookies for Severe Egg-Allergic Children Reduces Allergy Severity and Affects Allergen-Specific Antibodies in Serum

description: <b><i>Background:</i></b> We evaluated the safety and efficacy of low-egg-allergen cookies (LAC) as low-dose oral immunotherapy (OIT) in children with severe egg allergy. We also examined the relationship between mild desensitization by low-dose OIT and serum biomarkers of allergy. <b><i>Methods:</i></b> We enrolled 13 children with egg allergy who could not receive OIT with hard-boiled egg white (EW). For 11 participants, OIT was carried out using LAC for 3-4 months. Open food challenges with hard-boiled EW and blood samplings were performed before and after OIT. Participants were divided into 2 groups: high effect (H-E) and no/low effect (N/L-E). Serum levels of total IgE and egg yolk-, EW-, and ovomucoid (OM)-specific IgE, ovalbumin (OVA)- and OM-specific IgG<sub>4</sub>, IgA<sub>1</sub>, and IgA<sub>2</sub>, and the percentage of CD 203c<sup>+</sup> were measured. <b><i>Results:</i></b> Allergic severity was reduced in 7 patients, who were assigned to the H-E group. Moreover, no study participants were taken off the intake of LAC during OIT. In the H-E group, OVA-specific IgA<sub>2</sub> levels after OIT were significantly higher than before OIT. The ratios of OM-specific IgG<sub>4</sub>/OM-specific IgE and OM-specific IgA<sub>2</sub>/OM-specific IgE in the H-E group after OIT were significantly higher than before OIT. <b><i>Conclusion:</i></b> Our findings suggest that low-dose OIT using LAC is an effective and safe treatment for patients with severe egg allergy.
DOI: 10.6084/m9.figshare.5782938.v1
title: Supplementary Material for: Low-Dose Oral Immunotherapy Using Low-Egg-Allergen Cookies for Severe Egg-Allergic Children Reduces Allergy Severity and Affects Allergen-Specific Antibodies in Serum

description: <b><i>Background:</i></b> We evaluated the safety and efficacy of low-egg-allergen cookies (LAC) as low-dose oral immunotherapy (OIT) in children with severe egg allergy. We also examined the relationship between mild desensitization by low-dose OIT and serum biomarkers of allergy. <b><i>Methods:</i></b> We enrolled 13 children with egg allergy who could not receive OIT with hard-boiled egg white (EW). For 11 participants, OIT was carried out using LAC for 3-4 months. Open food challenges with hard-boiled EW and blood samplings were performed before and after OIT. Participants were divided into 2 groups: high effect (H-E) and no/low effect (N/L-E). Serum levels of total IgE and egg yolk-, EW-, and ovomucoid (OM)-specific IgE, ovalbumin (OVA)- and OM-specific IgG<sub>4</sub>, IgA<sub>1</sub>, and IgA<sub>2</sub>, and the percentage of CD 203c<sup>+</sup> were measured. <b><i>Results:</i></b> Allergic severity was reduced in 7 patients, who were assigned to the H-E group. Moreover, no study participants were taken off the intake of LAC during OIT. In the H-E group, OVA-specific IgA<sub>2</sub> levels after OIT were significantly higher than before OIT. The ratios of OM-specific IgG<sub>4</sub>/OM-specific IgE and OM-specific IgA<sub>2</sub>/OM-specific IgE in the H-E group after OIT were significantly higher than before OIT. <b><i>Conclusion:</i></b> Our findings suggest that low-dose OIT using LAC is an effective and safe treatment for patients with severe egg allergy.
DOI: 10.6084/m9.figshare.5782881
title: Results of interview about voluntary initiation HAL-Tsukuba

description: Results of interviewing 20 HAL patients about theit experience and subjective control strategies while using HAL for lower limb movement rehabilitation<br>
DOI: 10.6084/m9.figshare.5782839
title: Trends and themes in African ornithology

description: Ornithology in Africa has a long history. I review trends in the ornithological literature since 1990 within the context of the 14th Pan-African Ornithological Congress. Using full text searches of papers on PubMed® and abstracts from main ornithological journals I found that most papers referencing African bird species are focused on medical-related research questions. Restricting the literature search to journals African ornithologists are most likely to publish in, I found 2 279 relevant papers. These describe work on 29% of African bird species from 82% of African bird families, in all but two African countries. Overall output has increased slightly over time, with more papers tackling more research topics. Most popular research topics were demography, conservation and climate, with disease ecology, physiology and ecological processes the least researched topics. I found that while many authors with African affiliations publish papers, outside of South Africa very few African-based authors reliably publish in the international research literature, perhaps indicating difficulties in establishing a productive research career in much of Africa. I conclude with a call to overseas ornithologists working in Africa and to organisations funding research in Africa to work together to build capacity outside of the few established research centres.
DOI: 10.6084/m9.figshare.5782839.v1
title: Trends and themes in African ornithology

description: Ornithology in Africa has a long history. I review trends in the ornithological literature since 1990 within the context of the 14th Pan-African Ornithological Congress. Using full text searches of papers on PubMed® and abstracts from main ornithological journals I found that most papers referencing African bird species are focused on medical-related research questions. Restricting the literature search to journals African ornithologists are most likely to publish in, I found 2 279 relevant papers. These describe work on 29% of African bird species from 82% of African bird families, in all but two African countries. Overall output has increased slightly over time, with more papers tackling more research topics. Most popular research topics were demography, conservation and climate, with disease ecology, physiology and ecological processes the least researched topics. I found that while many authors with African affiliations publish papers, outside of South Africa very few African-based authors reliably publish in the international research literature, perhaps indicating difficulties in establishing a productive research career in much of Africa. I conclude with a call to overseas ornithologists working in Africa and to organisations funding research in Africa to work together to build capacity outside of the few established research centres.
DOI: 10.6084/m9.figshare.5782824
title: The image of Fig.4 and partial orginal data

description: Fig. 4 Variations in hydrological conditions inferred from peat-containing profiles since the LD, and selected environmental proxies. (a) Synthesis of reconstructed Holocene temperature in China [Fang and Hou, 2011]. (b) Annual mean temperature record based on pollen analysis from the Dajiuhu, Shennongjia peat section [Zhu et al., 2008]. (c) Annual precipitation record from Gonghai Lake, Northern China [Chen et al., 2015]. (d) Monsoonal precipitation record from the Daihai Lake region [Peng et al., 2005]. (e) Summer monsoon index reconstructed from the sediments of Qinghai Lake [An et al., 2012]. (f) Dongge Cave stalagmite D4 oxygen isotope record [Dykoski et al., 2005]. (g) Relative Holocene water level variations from the DSGL section in the Southeastern Mu Us Desert [Liu et al., 2017a]. (h) Northern Hemisphere summer insolation at 30°N [Berger and Loutre, 1991]. (i) Synthesis of variations in hydrological conditions inferred from peat-containing profiles (this study).
DOI: 10.6084/m9.figshare.5782785
title: MOESM9 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes

description: Additional file 9. Genomic SNVs used for phylogenetic analysis. List of SNVs used for construction of phylogenetic trees. Only SNVs detected in all analyzed genomes (i.e., positions with the “N” base in any of the compared genomes were not considered) were used in the analysis. Genes tp0433 (arp), tp0470, and tp0897 (tprK) were excluded from analyses. Altogether, 2444 unique SNV positions were identified when the TPE Fribourg-Blanc genome sequence was used as an outgroup. Coordinates (positions) and gene annotations according to the SS14 genome (CP04011.1); “NA” = not annotated (IGR, intergenic region); “.” = deletion.
DOI: 10.6084/m9.figshare.5782785.v1
title: MOESM9 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes

description: Additional file 9. Genomic SNVs used for phylogenetic analysis. List of SNVs used for construction of phylogenetic trees. Only SNVs detected in all analyzed genomes (i.e., positions with the “N” base in any of the compared genomes were not considered) were used in the analysis. Genes tp0433 (arp), tp0470, and tp0897 (tprK) were excluded from analyses. Altogether, 2444 unique SNV positions were identified when the TPE Fribourg-Blanc genome sequence was used as an outgroup. Coordinates (positions) and gene annotations according to the SS14 genome (CP04011.1); “NA” = not annotated (IGR, intergenic region); “.” = deletion.
DOI: 10.6084/m9.figshare.5782749
title: MOESM4 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes

description: Additional file 4. A Genome coverage statistics—number of non-covered bases for individual Chinese strains. SS14 genome (CP004011.1) [6] was used as a reference for mapping; coordinates according to the CP004011.1. The list includes all positions without any coverage by mapped reads. B Genome covearge statistics—number of zero covered bases for individual Chinese strains. Nichols genome (CP004010.2) [6] was used as a reference for mapping; coordinates according to the CP004010.2. The list includes all positions without any coverage by mapped reads.
DOI: 10.6084/m9.figshare.5782749.v1
title: MOESM4 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes

description: Additional file 4. A Genome coverage statistics—number of non-covered bases for individual Chinese strains. SS14 genome (CP004011.1) [6] was used as a reference for mapping; coordinates according to the CP004011.1. The list includes all positions without any coverage by mapped reads. B Genome covearge statistics—number of zero covered bases for individual Chinese strains. Nichols genome (CP004010.2) [6] was used as a reference for mapping; coordinates according to the CP004010.2. The list includes all positions without any coverage by mapped reads.
DOI: 10.6084/m9.figshare.5782716
title: Additional file 5: Table S5. of Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome

description: Paralogs identified in the pangenome of Zymoseptoria tritici. (XLSX 68Â kb)
DOI: 10.6084/m9.figshare.5782716.v1
title: Additional file 5: Table S5. of Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome

description: Paralogs identified in the pangenome of Zymoseptoria tritici. (XLSX 68Â kb)
DOI: 10.6084/m9.figshare.5782701
title: Additional file 4: Table S4. of Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome

description: Protein clusterization and functional annotation of the pangenome of Zymoseptoria tritici. (XLSX 5334Â kb)
DOI: 10.6084/m9.figshare.5782701.v1
title: Additional file 4: Table S4. of Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome

description: Protein clusterization and functional annotation of the pangenome of Zymoseptoria tritici. (XLSX 5334Â kb)
DOI: 10.6084/m9.figshare.5782677
title: Additional file 5: Table S4. of Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses

description: Sample OTU table. (XLSX 1629Â kb)