cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11466351
title: MOESM2 of Network analysis exposes core functions in major lifestyles of fungal and oomycete plant pathogens

description: Additional file 2 : Table S1. Organisms used in this study. Table S2. Frequency of annotated core families and their proteins (see sections “Core components” and “Construction of the pan-proteome network”, Methods). Table S3. Significantly enriched annotations in core components of Biotroph (B), Hemibiotroph (H) and Necrotroph (N). * Annotations starting with: K, KEGG ortholog; IPR, InterPro domain; MER, MEROPS proteases. ** Functional categories: N, nucleic acid related; L, light responsive; A, amino acid metabolism; T, transporters; C, carbohydrate metabolism; P, protease and peptidases; SM, secondary metabolites (including toxins); O, oxidoreductases (with no other function); Tf, trafficking; E, energy; ST, signal transduction. *** Following procedure described in methods, and subsequent manual curation. Table S4. Selected organisms used in KAAS analysis for identififcation of KEGG orthologs. Table S5. Normalized counts of gene families (components) connecting a pair of lifestyles. Numbers in parenthesis are the normalized mean values obtained from random 10,000 simulations for each lifestyle. A single asterisk indicates nonsignificant values (P &gt; 0.01, non-parametric rank test, see Methods) (XLS 3237 kb)
DOI: 10.6084/m9.figshare.11466351.v1
title: MOESM2 of Network analysis exposes core functions in major lifestyles of fungal and oomycete plant pathogens

description: Additional file 2 : Table S1. Organisms used in this study. Table S2. Frequency of annotated core families and their proteins (see sections “Core components” and “Construction of the pan-proteome network”, Methods). Table S3. Significantly enriched annotations in core components of Biotroph (B), Hemibiotroph (H) and Necrotroph (N). * Annotations starting with: K, KEGG ortholog; IPR, InterPro domain; MER, MEROPS proteases. ** Functional categories: N, nucleic acid related; L, light responsive; A, amino acid metabolism; T, transporters; C, carbohydrate metabolism; P, protease and peptidases; SM, secondary metabolites (including toxins); O, oxidoreductases (with no other function); Tf, trafficking; E, energy; ST, signal transduction. *** Following procedure described in methods, and subsequent manual curation. Table S4. Selected organisms used in KAAS analysis for identififcation of KEGG orthologs. Table S5. Normalized counts of gene families (components) connecting a pair of lifestyles. Numbers in parenthesis are the normalized mean values obtained from random 10,000 simulations for each lifestyle. A single asterisk indicates nonsignificant values (P &gt; 0.01, non-parametric rank test, see Methods) (XLS 3237 kb)
DOI: 10.6084/m9.figshare.11466300
title: MOESM5 of Genetic perturbations of disease risk genes in mice capture transcriptomic signatures of late-onset Alzheimer’s disease

description: Additional file 5: Table S5. Transcriptional factor annotations in LOAD mouse modules. The attached table illustrate transcriptional factor enriched in each 26 mouse modules of co-expressed genes.
DOI: 10.6084/m9.figshare.11466300.v1
title: MOESM5 of Genetic perturbations of disease risk genes in mice capture transcriptomic signatures of late-onset Alzheimer’s disease

description: Additional file 5: Table S5. Transcriptional factor annotations in LOAD mouse modules. The attached table illustrate transcriptional factor enriched in each 26 mouse modules of co-expressed genes.
DOI: 10.6084/m9.figshare.11466294
title: MOESM4 of Genetic perturbations of disease risk genes in mice capture transcriptomic signatures of late-onset Alzheimer’s disease

description: Additional file 4: Table S4. Jaccard indices between Mouse and AMP-AD modules. The attached table contains Jaccard indices and its significance (p-value) for each mouse-human module pair.
DOI: 10.6084/m9.figshare.11466294.v1
title: MOESM4 of Genetic perturbations of disease risk genes in mice capture transcriptomic signatures of late-onset Alzheimer’s disease

description: Additional file 4: Table S4. Jaccard indices between Mouse and AMP-AD modules. The attached table contains Jaccard indices and its significance (p-value) for each mouse-human module pair.
DOI: 10.6084/m9.figshare.11466285
title: MOESM3 of Genetic perturbations of disease risk genes in mice capture transcriptomic signatures of late-onset Alzheimer’s disease

description: Additional file 3: Table S3. Mouse modules of co-expressed genes. Summaries of the 26 mouse modules of co-expressed genes. In sheet 1, genes in each mouse modules were listed. Sheet 2 depicts mouse modules were observed to be significantly (p
DOI: 10.6084/m9.figshare.11466285.v1
title: MOESM3 of Genetic perturbations of disease risk genes in mice capture transcriptomic signatures of late-onset Alzheimer’s disease

description: Additional file 3: Table S3. Mouse modules of co-expressed genes. Summaries of the 26 mouse modules of co-expressed genes. In sheet 1, genes in each mouse modules were listed. Sheet 2 depicts mouse modules were observed to be significantly (p
DOI: 10.6084/m9.figshare.11466276
title: MOESM2 of Genetic perturbations of disease risk genes in mice capture transcriptomic signatures of late-onset Alzheimer’s disease

description: Additional file 2: Table S2. KEGG pathway annotation in LOAD mouse strains. The attached table depicts the KEGG pathway annotations for the up and down-regulated genes in LOAD mouse strains compared to C7BL/6 J mice.
DOI: 10.6084/m9.figshare.11466276.v1
title: MOESM2 of Genetic perturbations of disease risk genes in mice capture transcriptomic signatures of late-onset Alzheimer’s disease

description: Additional file 2: Table S2. KEGG pathway annotation in LOAD mouse strains. The attached table depicts the KEGG pathway annotations for the up and down-regulated genes in LOAD mouse strains compared to C7BL/6 J mice.
DOI: 10.6084/m9.figshare.11466267
title: MOESM1 of Genetic perturbations of disease risk genes in mice capture transcriptomic signatures of late-onset Alzheimer’s disease

description: Additional file 1: Table S1. Differentially expressed genes in LOAD mouse strains. The attached table depicts the differentially expressed genes in LOAD mouse strains compared to C7BL/6 J mice.
DOI: 10.6084/m9.figshare.11466267.v1
title: MOESM1 of Genetic perturbations of disease risk genes in mice capture transcriptomic signatures of late-onset Alzheimer’s disease

description: Additional file 1: Table S1. Differentially expressed genes in LOAD mouse strains. The attached table depicts the differentially expressed genes in LOAD mouse strains compared to C7BL/6 J mice.
DOI: 10.6084/m9.figshare.11466042
title: Milosavljevic Biological Control

description: Dataset associated with Milosavljevic et al., submitted in 2019 to Biological Control
DOI: 10.6084/m9.figshare.11466042.v1
title: Milosavljevic Biological Control

description: Dataset associated with Milosavljevic et al., submitted in 2019 to Biological Control
DOI: 10.6084/m9.figshare.11465925
title: Data and Network Generator

description: In this study, we proposed a method for indoor navigation networks of indoor spaces based on a indoor environment analysis. we shared data and network generator tool in the figshare repository.
DOI: 10.6084/m9.figshare.11466012.v1
title: The influence of surface stress fluctuation on saltation sand transport around threshold

description: This dataset includes data used in the original research article, "The influence of surface stress fluctuation on saltation sand transport around threshold" by Xiaojing Zheng, Ting Jin, Ping Wang.
DOI: 10.6084/m9.figshare.11465913
title: Table of numerical simulation results of improved triple-porosity model for calculating the porosity exponent-m

description: We have established an improved triple-porosity model to calculate the porosity exponent of fractured-vuggy reservoirs, based on the Maxwell-Garnett mixing rule. The improved model can be used to calculate the porosity exponent of three types of reservoir spaces: nonconnected vugs, fractures and matrix pores. This is the table of numerical simulation results of improved triple-porosity model for calculating the porosity exponent-m.
DOI: 10.6084/m9.figshare.11465925.v2
title: Data and Network Generator

description: In this study, we proposed a method for indoor navigation networks of indoor spaces based on a indoor environment analysis. we shared data and network generator tool in the figshare repository.
DOI: 10.6084/m9.figshare.11465925.v1
title: Data and Network Generator

description: In this study, we proposed a method for indoor navigation networks of indoor spaces based on a indoor environment analysis. we shared data and network generator tool in the figshare repository.
DOI: 10.6084/m9.figshare.11465877
title: sacramento2

description: Dataset for testing pysal.tobler<br>
DOI: 10.6084/m9.figshare.11465877.v1
title: sacramento2

description: Dataset for testing pysal.tobler<br>
DOI: 10.6084/m9.figshare.11465565
title: Metanephrops_challengeri_CO1.fasta

description: FASTA file containing partial mitochondrial cytochrome c oxidase subunit one DNA sequences isolated from New Zealand scampi (<i>Metanephrops challengeri</i>).<br>Lot numbers within sequence names refer to lots taken during the KAH1501 NZ scampi survey. <br><br>
DOI: 10.6084/m9.figshare.11465535
title: tracts

description: Dataset for demonstrating Tobler areal interpolation package<br>
DOI: 10.6084/m9.figshare.11465565.v1
title: Metanephrops_challengeri_CO1.fasta

description: FASTA file containing partial mitochondrial cytochrome c oxidase subunit one DNA sequences isolated from New Zealand scampi (<i>Metanephrops challengeri</i>).<br>Lot numbers within sequence names refer to lots taken during the KAH1501 NZ scampi survey. <br><br>
DOI: 10.6084/m9.figshare.11465481
title: Diao et al 2020.rar

description: This file includes the postseismic data inferred from Zhao et al. (2017) and Wang and Fialko, (2018), interseismic GPS data inferred from Zheng et al. (2017), the interseismic leveling data inferred from Jackson and Bilham (1994), and model results supporting the conclusions of Diao et al.(2020).
DOI: 10.6084/m9.figshare.11465535.v1
title: tracts

description: Dataset for demonstrating Tobler areal interpolation package<br>
DOI: 10.6084/m9.figshare.11465460
title: Example files of processed GLDS-200 subsample

description: Example files of what a "processed" directory might hold.<br>
DOI: 10.6084/m9.figshare.11465466
title: precincts

description: Dataset used for demonstration of Tobler areal interpolation.<br>
DOI: 10.6084/m9.figshare.11465481.v1
title: Diao et al 2020.rar

description: This file includes the postseismic data inferred from Zhao et al. (2017) and Wang and Fialko, (2018), interseismic GPS data inferred from Zheng et al. (2017), the interseismic leveling data inferred from Jackson and Bilham (1994), and model results supporting the conclusions of Diao et al.(2020).
DOI: 10.6084/m9.figshare.11465466.v1
title: precincts

description: Dataset used for demonstration of Tobler areal interpolation.<br>
DOI: 10.6084/m9.figshare.11465460.v1
title: Example files of processed GLDS-200 subsample

description: Example files of what a "processed" directory might hold.<br>
DOI: 10.6084/m9.figshare.11465460.v2
title: Example files of processed GLDS-200 subsample

description: Example files of what a "processed" directory might hold.<br>
DOI: 10.6084/m9.figshare.11462583
title: Implicit task switching in Parkinson’s disease is preserved when on medication

description: The "pat" folder contains all the raw patient data
DOI: 10.6084/m9.figshare.11462421
title: Lianas in subtropical montane forests (Tucuman, Argentina).xlsx

description: Community ecology data of lianas in secondary and mature forests, dominated by native tree species, from Northwestern Argentina. Addittionally, the dataset includes information on lianas in secondary forests invaded by the exotic tree species Ligustrum lucidum and Morus alba.<br>
DOI: 10.6084/m9.figshare.11462469.v1
title: Untitled Item

description: Unimputed genotype datasets for each chromosome are in the vcf format. User can redo the quality control on their own purposes. The imputed genotype data was in hapmap format including all the chromosomes which is ready for conducting GWAS. The beagle was used for the imputation.
DOI: 10.6084/m9.figshare.11462274
title: Raw data for revised ver.

description: Raw data of subject title "Necroptosis in pancreatic cancer promotes cancer cell migration and invasion by release of CXCL5"
DOI: 10.6084/m9.figshare.11462274.v1
title: Raw data for revised ver.

description: Raw data of subject title "Necroptosis in pancreatic cancer promotes cancer cell migration and invasion by release of CXCL5"
DOI: 10.6084/m9.figshare.11462118
title: Fiber Optic Ground Deformation Supporting Data

description: Supporting Data for 2019JB018878
DOI: 10.6084/m9.figshare.11462118.v1
title: Fiber Optic Ground Deformation Supporting Data

description: Supporting Data for 2019JB018878
DOI: 10.6084/m9.figshare.11462004
title: Immune stimulatory effect of anti-EpCAM immunotoxin – improved overall survival of metastatic colorectal cancer patients

description: <b>Introduction:</b> In a recent phase I trial in a heterogeneous group of carcinoma patients with advanced disease, we did not observe objective responses by CT at 8 weeks in patients treated with either the anti-EpCAM immunotoxin MOC31PE alone or administered in combination with the immunosuppressor cyclosporin (CsA). We have now assessed overall survival (OS) data for the two groups to reveal potential differences, and to elucidate putative underlying mechanisms. <b>Material and methods:</b> The OS time of MOC31PE monotherapy (34 patients) and MOC31PE in combination with CsA (23 patients), was assessed. Pre- and post-treatment patient sera were analyzed in a multiplex immunoassay, and the immunogenic effects of MOC31PE were studied <i>in vitro</i> and in a dendritic cell maturation assay. <b>Results:</b> When the data were analyzed for all treated patients regardless of cancer type, the MOC31PE alone group had a median OS of 12.7 months (95% CI = 5.6–19.8 months) compared to 6.2 months (95% CI = 5.6–6.8 months) (<i>p</i>=.066) for the patients treated with MOC31PE + CsA group. For the subgroup of patients with colorectal cancer, the median OS survival was 16.3 months (95% CI = 5.6–27.0) for the MOC31PE only cohort (<i>n</i> = 15), compared to 6.0 months (CI = 5.8–6.2) (<i>p</i> in vitro immunological studies indicate that MOC31PE induced an immunogenic response leading to T-cell activation; a response that was suppressed in patients treated with MOC31PE + CsA. <b>Conclusions:</b> The results reveal a promising clinical benefit of anti-EpCAM immunotoxin treatment in patients with advanced disease, an effect apparently explained by a previously unknown immunogenic effect of MOC31PE.
DOI: 10.6084/m9.figshare.11462004.v1
title: Immune stimulatory effect of anti-EpCAM immunotoxin – improved overall survival of metastatic colorectal cancer patients

description: <b>Introduction:</b> In a recent phase I trial in a heterogeneous group of carcinoma patients with advanced disease, we did not observe objective responses by CT at 8 weeks in patients treated with either the anti-EpCAM immunotoxin MOC31PE alone or administered in combination with the immunosuppressor cyclosporin (CsA). We have now assessed overall survival (OS) data for the two groups to reveal potential differences, and to elucidate putative underlying mechanisms. <b>Material and methods:</b> The OS time of MOC31PE monotherapy (34 patients) and MOC31PE in combination with CsA (23 patients), was assessed. Pre- and post-treatment patient sera were analyzed in a multiplex immunoassay, and the immunogenic effects of MOC31PE were studied <i>in vitro</i> and in a dendritic cell maturation assay. <b>Results:</b> When the data were analyzed for all treated patients regardless of cancer type, the MOC31PE alone group had a median OS of 12.7 months (95% CI = 5.6–19.8 months) compared to 6.2 months (95% CI = 5.6–6.8 months) (<i>p</i>=.066) for the patients treated with MOC31PE + CsA group. For the subgroup of patients with colorectal cancer, the median OS survival was 16.3 months (95% CI = 5.6–27.0) for the MOC31PE only cohort (<i>n</i> = 15), compared to 6.0 months (CI = 5.8–6.2) (<i>p</i> in vitro immunological studies indicate that MOC31PE induced an immunogenic response leading to T-cell activation; a response that was suppressed in patients treated with MOC31PE + CsA. <b>Conclusions:</b> The results reveal a promising clinical benefit of anti-EpCAM immunotoxin treatment in patients with advanced disease, an effect apparently explained by a previously unknown immunogenic effect of MOC31PE.
DOI: 10.6084/m9.figshare.11461407
title: Evaluating the impact of information and support for people with nystagmus in the digital age: A patient and carer questionnaire study

description: <b>Background</b>: Nystagmus is a disorder of rhythmic, involuntary oscillations of the eyes and can be classified as either infantile or acquired. Whether it occurs in isolation or as a part of other visual or neurological disorders, it causes significant visual dysfunction and problems with social functioning. In this study, we seek to understand ways in which people with nystagmus are currently supported across the UK and identify any geographical variations or disconnects between current practice and best practice, as judged by patients and their carers. <b>Methods</b>: A nationwide, qualitative, cross-sectional, questionnaire study of people with nystagmus and their carers. Recruitment was achieved through specialist clinics, charity events, online advertisements and social media calls. Data was gathered using five, age-appropriate questionnaires which were completed and returned to the research team between November 2016 and August 2018. <b>Results</b>: 184 respondents were included (89 carers, 47 patients aged 4–10 years, 5 aged 11–14 years, 4 aged 15–17 years and 39 &gt; 18 years). Notably, respondents rated social media as the best source of information they have received, even compared with face-to-face consultation with medical professionals. Additionally, only 33% of the respondents had been offered visual impairment support. Notably, patterns of clinical practice and patient experience emerged according to geographical location, particularly provision of initial information and ongoing VI support. <b>Conclusions</b>: This study highlights a significant variation in the support and information received by people in the UK with nystagmus. It also supports the role of charities and increasingly, social media in the provision of patient information. The study also highlights the need for standardized guidelines for the management of patients with nystagmus, particularly with regard to support and information.
DOI: 10.6084/m9.figshare.11461407.v1
title: Evaluating the impact of information and support for people with nystagmus in the digital age: A patient and carer questionnaire study

description: <b>Background</b>: Nystagmus is a disorder of rhythmic, involuntary oscillations of the eyes and can be classified as either infantile or acquired. Whether it occurs in isolation or as a part of other visual or neurological disorders, it causes significant visual dysfunction and problems with social functioning. In this study, we seek to understand ways in which people with nystagmus are currently supported across the UK and identify any geographical variations or disconnects between current practice and best practice, as judged by patients and their carers. <b>Methods</b>: A nationwide, qualitative, cross-sectional, questionnaire study of people with nystagmus and their carers. Recruitment was achieved through specialist clinics, charity events, online advertisements and social media calls. Data was gathered using five, age-appropriate questionnaires which were completed and returned to the research team between November 2016 and August 2018. <b>Results</b>: 184 respondents were included (89 carers, 47 patients aged 4–10 years, 5 aged 11–14 years, 4 aged 15–17 years and 39 &gt; 18 years). Notably, respondents rated social media as the best source of information they have received, even compared with face-to-face consultation with medical professionals. Additionally, only 33% of the respondents had been offered visual impairment support. Notably, patterns of clinical practice and patient experience emerged according to geographical location, particularly provision of initial information and ongoing VI support. <b>Conclusions</b>: This study highlights a significant variation in the support and information received by people in the UK with nystagmus. It also supports the role of charities and increasingly, social media in the provision of patient information. The study also highlights the need for standardized guidelines for the management of patients with nystagmus, particularly with regard to support and information.
DOI: 10.6084/m9.figshare.11461023
title: Lower urinary tract symptoms (LUTS) are not associated with an increased risk of prostate cancer in men 50–69 years with PSA ≥3 ng/ml

description: <b>Background:</b> There is conflicting evidence about the association between prostate cancer and Lower Urinary Tract Symptoms (LUTS). We aimed to describe the prevalence of LUTS and its association with prostate cancer risk. <b>Methods:</b> We studied the association between International Prostate Symptom Score (IPSS) and prostate cancer in a population-based sample of men (<i>n</i> = 45,595) aged 50–69 years from the Stockholm3 study. Men with PSA ≥3 ng/ml (<i>n</i> = 4579) underwent systematic prostate biopsies. We used the International Society of Urological Pathology Gleason Grading (ISUP grade) and performed regression analysis for risk of any cancer (<i>n</i> = 1797), ISUP grade ≥2 (<i>n</i> = 840) and advanced cancer, defined as ISUP grade ≥3 or cT ≥3 (<i>n</i> = 353). <b>Results:</b> 74.6% of all men had no or mild LUTS (IPSS ≤7) and 3.2% had severe LUTS (IPSS &gt;19). Men with any, ISUP grade ≥2 or advanced cancer had lower median IPSS compared to men with benign biopsy (any cancer: 4 (IQR 2–9); ISUP grade ≥2: 4 (2–8); advanced cancer: 4 (2–8); benign biopsy: 6 (3–11); <i>p</i> <b>Conclusions:</b> Three-quarters of men aged 50–69 years report no or mild LUTS. Our data do not support any clinically meaningful association between LUTS and prostate cancer. Specifically, men with advanced prostate cancer did not exhibit more urinary symptoms than men without cancer.
DOI: 10.6084/m9.figshare.11461023.v1
title: Lower urinary tract symptoms (LUTS) are not associated with an increased risk of prostate cancer in men 50–69 years with PSA ≥3 ng/ml

description: <b>Background:</b> There is conflicting evidence about the association between prostate cancer and Lower Urinary Tract Symptoms (LUTS). We aimed to describe the prevalence of LUTS and its association with prostate cancer risk. <b>Methods:</b> We studied the association between International Prostate Symptom Score (IPSS) and prostate cancer in a population-based sample of men (<i>n</i> = 45,595) aged 50–69 years from the Stockholm3 study. Men with PSA ≥3 ng/ml (<i>n</i> = 4579) underwent systematic prostate biopsies. We used the International Society of Urological Pathology Gleason Grading (ISUP grade) and performed regression analysis for risk of any cancer (<i>n</i> = 1797), ISUP grade ≥2 (<i>n</i> = 840) and advanced cancer, defined as ISUP grade ≥3 or cT ≥3 (<i>n</i> = 353). <b>Results:</b> 74.6% of all men had no or mild LUTS (IPSS ≤7) and 3.2% had severe LUTS (IPSS &gt;19). Men with any, ISUP grade ≥2 or advanced cancer had lower median IPSS compared to men with benign biopsy (any cancer: 4 (IQR 2–9); ISUP grade ≥2: 4 (2–8); advanced cancer: 4 (2–8); benign biopsy: 6 (3–11); <i>p</i> <b>Conclusions:</b> Three-quarters of men aged 50–69 years report no or mild LUTS. Our data do not support any clinically meaningful association between LUTS and prostate cancer. Specifically, men with advanced prostate cancer did not exhibit more urinary symptoms than men without cancer.