cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5789004
title: Tobacco exposure-related alterations in DNA methylation and gene expression in human monocytes: the Multi-Ethnic Study of Atherosclerosis (MESA)

description: Alterations in DNA methylation and gene expression in blood leukocytes are potential biomarkers of harm and mediators of the deleterious effects of tobacco exposure. However, methodological issues, including the use of self-reported smoking status and mixed cell types have made previously identified alterations in DNA methylation and gene expression difficult to interpret. In this study, we examined associations of tobacco exposure with DNA methylation and gene expression, utilizing a biomarker of tobacco exposure (urine cotinine) and CD14+ purified monocyte samples from 934 participants of the community-based Multi-Ethnic Study of Atherosclerosis (MESA). Urine cotinine levels were measured using an immunoassay. DNA methylation and gene expression were measured with microarrays. Multivariate linear regression was used to test for associations adjusting for age, sex, race/ethnicity, education, and study site. Urine cotinine levels were associated with methylation of 176 CpGs [false discovery rate (FDR)&lt;0.01]. Four CpGs not previously identified by studies of non-purified blood samples nominally replicated (<i>P</i> value&lt;0.05) with plasma cotinine-associated methylation in 128 independent monocyte samples. Urine cotinine levels associated with expression of 12 genes (FDR&lt;0.01), including increased expression of <i>P2RY6</i> (Beta ± standard error = 0.078 ± 0.008, <i>P</i> = 1.99 × 10<sup>−22</sup>), a gene previously identified to be involved in the release of pro-inflammatory cytokines. No cotinine-associated (FDR&lt;0.01) methylation profiles significantly (FDR&lt;0.01) correlated with cotinine-associated (FDR&lt;0.01) gene expression profiles. In conclusion, our findings i) identify potential monocyte-specific smoking-associated methylation patterns and ii) suggest that alterations in methylation may not be a main mechanism regulating gene expression in monocytes in response to cigarette smoking.
DOI: 10.6084/m9.figshare.5789004.v1
title: Tobacco exposure-related alterations in DNA methylation and gene expression in human monocytes: the Multi-Ethnic Study of Atherosclerosis (MESA)

description: Alterations in DNA methylation and gene expression in blood leukocytes are potential biomarkers of harm and mediators of the deleterious effects of tobacco exposure. However, methodological issues, including the use of self-reported smoking status and mixed cell types have made previously identified alterations in DNA methylation and gene expression difficult to interpret. In this study, we examined associations of tobacco exposure with DNA methylation and gene expression, utilizing a biomarker of tobacco exposure (urine cotinine) and CD14+ purified monocyte samples from 934 participants of the community-based Multi-Ethnic Study of Atherosclerosis (MESA). Urine cotinine levels were measured using an immunoassay. DNA methylation and gene expression were measured with microarrays. Multivariate linear regression was used to test for associations adjusting for age, sex, race/ethnicity, education, and study site. Urine cotinine levels were associated with methylation of 176 CpGs [false discovery rate (FDR)&lt;0.01]. Four CpGs not previously identified by studies of non-purified blood samples nominally replicated (<i>P</i> value&lt;0.05) with plasma cotinine-associated methylation in 128 independent monocyte samples. Urine cotinine levels associated with expression of 12 genes (FDR&lt;0.01), including increased expression of <i>P2RY6</i> (Beta ± standard error = 0.078 ± 0.008, <i>P</i> = 1.99 × 10<sup>−22</sup>), a gene previously identified to be involved in the release of pro-inflammatory cytokines. No cotinine-associated (FDR&lt;0.01) methylation profiles significantly (FDR&lt;0.01) correlated with cotinine-associated (FDR&lt;0.01) gene expression profiles. In conclusion, our findings i) identify potential monocyte-specific smoking-associated methylation patterns and ii) suggest that alterations in methylation may not be a main mechanism regulating gene expression in monocytes in response to cigarette smoking.
DOI: 10.6084/m9.figshare.5788980
title: Supplementary Material for: Oral Immunotherapy in Japanese Children with Anaphylactic Peanut Allergy

description: <b><i>Background:</i></b> Reports on oral immunotherapy (OIT) for anaphylactic food allergy are lacking. We investigated the efficacy and safety of peanut OIT for anaphylactic patients. <b><i>Methods:</i></b> We enrolled 22 peanut anaphylactic patients who underwent OIT between 2011 and 2013, all of whom demonstrated anaphylaxis during a baseline double-blind, placebo-controlled food challenge. After starting in-hospital OIT, participants gradually increased ingestion to 795 mg of peanut protein per day at home and then took a maintenance dose (795 mg) daily. After 3 asymptomatic months, participants underwent an oral food challenge (OFC) of 795 mg after 2 weeks of peanut avoidance to confirm sustained unresponsiveness. The historical control group consisted of 11 patients with anaphylaxis by OFC and underwent the second OFC after 2 years. <b><i>Results:</i></b> All patients (22/22) achieved desensitization by 8 months after starting OIT and completed the protocol within 2 years. Two years later, 15/22 patients (68.1%) in the OIT group achieved sustained unresponsiveness, whereas only 2 (18.1%) in the control group passed the second OFC. After 2 years, the median peanut-specific IgE had significantly decreased (from 38.5 to 12.4 kUA/L) in the OIT group, but not in the control group. Median peanut- and Ara h 2-specific IgG4 in the OIT group had significantly increased from baseline after 1 month. The adverse reaction rate per ingestion was 43% in hospital and 5% at home. Three patients received adrenaline at the hospital and 2 at home. <b><i>Conclusions:</i></b> These data suggest that for patients with peanut anaphylaxis, OIT can increase the threshold and support achieving sustained unresponsiveness with relative safety.
DOI: 10.6084/m9.figshare.5788980.v1
title: Supplementary Material for: Oral Immunotherapy in Japanese Children with Anaphylactic Peanut Allergy

description: <b><i>Background:</i></b> Reports on oral immunotherapy (OIT) for anaphylactic food allergy are lacking. We investigated the efficacy and safety of peanut OIT for anaphylactic patients. <b><i>Methods:</i></b> We enrolled 22 peanut anaphylactic patients who underwent OIT between 2011 and 2013, all of whom demonstrated anaphylaxis during a baseline double-blind, placebo-controlled food challenge. After starting in-hospital OIT, participants gradually increased ingestion to 795 mg of peanut protein per day at home and then took a maintenance dose (795 mg) daily. After 3 asymptomatic months, participants underwent an oral food challenge (OFC) of 795 mg after 2 weeks of peanut avoidance to confirm sustained unresponsiveness. The historical control group consisted of 11 patients with anaphylaxis by OFC and underwent the second OFC after 2 years. <b><i>Results:</i></b> All patients (22/22) achieved desensitization by 8 months after starting OIT and completed the protocol within 2 years. Two years later, 15/22 patients (68.1%) in the OIT group achieved sustained unresponsiveness, whereas only 2 (18.1%) in the control group passed the second OFC. After 2 years, the median peanut-specific IgE had significantly decreased (from 38.5 to 12.4 kUA/L) in the OIT group, but not in the control group. Median peanut- and Ara h 2-specific IgG4 in the OIT group had significantly increased from baseline after 1 month. The adverse reaction rate per ingestion was 43% in hospital and 5% at home. Three patients received adrenaline at the hospital and 2 at home. <b><i>Conclusions:</i></b> These data suggest that for patients with peanut anaphylaxis, OIT can increase the threshold and support achieving sustained unresponsiveness with relative safety.
DOI: 10.6084/m9.figshare.5788974
title: Supplementary Material for: Multiple Sclerosis Mortality by Race/Ethnicity, Age, Sex, and Time Period in the United States, 1999–2015

description: <b><i>Background:</i></b> Multiple sclerosis (MS) carries high morbidity and shortens life span. While there is recent recognition of other US minority populations such as blacks and Hispanics being affected with MS, examination of MS-specific mortality trends by race/ethnicity has been lacking.<b><i> Objective:</i></b> To investigate MS mortality rates and trends in the United States by sex, age, and race/ethnicity. <b><i>Methods:</i></b> We used the Compressed Mortality data file for 1999–2015 in the Wide-ranging online Data for Epidemiological Research system developed by the Center for Disease Control and Prevention to calculate the age-adjusted (US 2000 standard population) and age-specific MS mortality rate (per 100,000) by race/ethnicity and sex over time. Five mutually exclusive racial/ethnic groups were included in the analysis: non-Hispanic (NH) white, NH black, NH Asian or Pacific Islander (API), NH American Indian or Alaska Native, and Hispanic. <b><i>Results:</i></b> The average annual age-adjusted MS mortality rate was highest among NH whites (0.90 for males and 1.50 for females) immediately followed by NH blacks (0.75 for males and 1.42 for females), and lowest among APIs (0.05 for males and 0.12 for females). Statistically significant, increasing trend in age-adjusted MS mortality was observed during 1999–2015 among NH whites and NH blacks regardless of sex, more substantially in the latter. Age-specific MS mortality patterns showed NH blacks had the highest rate under age 55 and NH whites had the highest rate after that age point. For these 2 groups, MS mortality increased with age in both sexes and peaked at ages 55–64 for NH blacks and 65–74 for NH whites before declining substantially, while for Hispanic and API groups the risk plateaued after age 55. <b><i>Conclusion:</i></b> MS-specific mortality trends demonstrate distinctive differences by race/ethnicity and age. The observations that whites and females are more likely to die from MS is in line with the overall understanding that these groups are affected more by MS. However, the findings of blacks dying at an earlier age and having more substantially increasing mortality trends than whites suggest that MS burden weighs unequally by race. Further investigation into these trends may provide additional evidence into risk or protective factors within each group.
DOI: 10.6084/m9.figshare.5788974.v1
title: Supplementary Material for: Multiple Sclerosis Mortality by Race/Ethnicity, Age, Sex, and Time Period in the United States, 1999–2015

description: <b><i>Background:</i></b> Multiple sclerosis (MS) carries high morbidity and shortens life span. While there is recent recognition of other US minority populations such as blacks and Hispanics being affected with MS, examination of MS-specific mortality trends by race/ethnicity has been lacking.<b><i> Objective:</i></b> To investigate MS mortality rates and trends in the United States by sex, age, and race/ethnicity. <b><i>Methods:</i></b> We used the Compressed Mortality data file for 1999–2015 in the Wide-ranging online Data for Epidemiological Research system developed by the Center for Disease Control and Prevention to calculate the age-adjusted (US 2000 standard population) and age-specific MS mortality rate (per 100,000) by race/ethnicity and sex over time. Five mutually exclusive racial/ethnic groups were included in the analysis: non-Hispanic (NH) white, NH black, NH Asian or Pacific Islander (API), NH American Indian or Alaska Native, and Hispanic. <b><i>Results:</i></b> The average annual age-adjusted MS mortality rate was highest among NH whites (0.90 for males and 1.50 for females) immediately followed by NH blacks (0.75 for males and 1.42 for females), and lowest among APIs (0.05 for males and 0.12 for females). Statistically significant, increasing trend in age-adjusted MS mortality was observed during 1999–2015 among NH whites and NH blacks regardless of sex, more substantially in the latter. Age-specific MS mortality patterns showed NH blacks had the highest rate under age 55 and NH whites had the highest rate after that age point. For these 2 groups, MS mortality increased with age in both sexes and peaked at ages 55–64 for NH blacks and 65–74 for NH whites before declining substantially, while for Hispanic and API groups the risk plateaued after age 55. <b><i>Conclusion:</i></b> MS-specific mortality trends demonstrate distinctive differences by race/ethnicity and age. The observations that whites and females are more likely to die from MS is in line with the overall understanding that these groups are affected more by MS. However, the findings of blacks dying at an earlier age and having more substantially increasing mortality trends than whites suggest that MS burden weighs unequally by race. Further investigation into these trends may provide additional evidence into risk or protective factors within each group.
DOI: 10.6084/m9.figshare.5788968
title: Supplementary Material for: Survey Results of the Expert Meeting on Laparoscopic Surgery for Gallbladder Cancer and a Review of Relevant Literature

description: <b><i>Background:</i></b> Favorable outcomes of laparoscopic surgery for gallbladder cancer (GBC) have been reported; yet consensus on the indications and surgical techniques for laparoscopic surgery for GBC is lacking. <b><i>Objective:</i></b> To evaluate the current status of laparoscopic surgery for GBC by analyzing the results of a survey of experts and by reviewing the relevant published literature. <b><i>Methods:</i></b> Before an expert meeting was held on September 10, 2016 in Seoul, Korea, an international survey was undertaken of expert surgeons in the field of GBC surgery. <b><i>Results:</i></b> The majority of surgeons who responded agreed that laparoscopic surgery has an acceptable role for suspicious or early GBC, and that laparoscopic extended cholecystectomy has a value comparable to that of open surgery in selected patients with GBC. However, the selection criteria for laparoscopic surgery for overt GBC and the details of the surgical techniques varied among surgeons. <b><i>Conclusions:</i></b> This survey and literature review revealed that laparoscopic surgery for GBC is performed in highly selected cases. However, the favorable outcomes in the published reports and the positive view of experienced surgeons for this operative procedure suggest a high likelihood that laparoscopic surgery will be more frequently performed for GBC in the future.
DOI: 10.6084/m9.figshare.5788959
title: Supplementary Material for: The Practical Management of Chronic Pancreatitis: A Multidisciplinary Symposium Held at the Annual Meeting of the Pancreatic Society of Great Britain and Ireland, Manchester 2016

description: <b><i>Aim:</i></b> This study is about a questionnaire survey of delegates attending the chronic pancreatitis symposium at the 2016 meeting of the Pancreatic Society of Great Britain and Ireland and seeks a multidisciplinary “snapshot” overview of practice. <b><i>Methods:</i></b> A questionnaire was developed with multidisciplinary input. Questions on access to specialist care, methods of diagnosis and treatment including specific scenarios were incorporated. Eighty-three (66%) of 125 delegates effectively participated in this survey. <b><i>Results:</i></b> Twenty-four (29%) had neither a chronic pancreatitis MDT in their hospital nor a chronic pancreatitis referral MDT. Most frequently utilised diagnostic modalities were CT, MR and EUS with no respondents utilising duodenal intubation tests. Initial treatment was provided through non-opiate analgesia by 69 (93%), through the use of opiates by 56 (76%) and through the use of co-analgesics by 49 (66%). Fifty two (68%) routinely referred patients with alcohol-related disease for counselling. Preferred treatment for large duct disease without mass was endoscopic therapy. In older patients with a mass, pancreaticoduodenectomy was preferred. <b><i>Conclusion:</i></b> This is a small study likely to be skewed by sampling bias but is thought to be the first multidisciplinary survey of the management of chronic pancreatitis in the United Kingdom and Ireland. The results show a need for comprehensive access to specialist pancreatitis MDT care and there remains substantial variation in management.
DOI: 10.6084/m9.figshare.5788959.v1
title: Supplementary Material for: The Practical Management of Chronic Pancreatitis: A Multidisciplinary Symposium Held at the Annual Meeting of the Pancreatic Society of Great Britain and Ireland, Manchester 2016

description: <b><i>Aim:</i></b> This study is about a questionnaire survey of delegates attending the chronic pancreatitis symposium at the 2016 meeting of the Pancreatic Society of Great Britain and Ireland and seeks a multidisciplinary “snapshot” overview of practice. <b><i>Methods:</i></b> A questionnaire was developed with multidisciplinary input. Questions on access to specialist care, methods of diagnosis and treatment including specific scenarios were incorporated. Eighty-three (66%) of 125 delegates effectively participated in this survey. <b><i>Results:</i></b> Twenty-four (29%) had neither a chronic pancreatitis MDT in their hospital nor a chronic pancreatitis referral MDT. Most frequently utilised diagnostic modalities were CT, MR and EUS with no respondents utilising duodenal intubation tests. Initial treatment was provided through non-opiate analgesia by 69 (93%), through the use of opiates by 56 (76%) and through the use of co-analgesics by 49 (66%). Fifty two (68%) routinely referred patients with alcohol-related disease for counselling. Preferred treatment for large duct disease without mass was endoscopic therapy. In older patients with a mass, pancreaticoduodenectomy was preferred. <b><i>Conclusion:</i></b> This is a small study likely to be skewed by sampling bias but is thought to be the first multidisciplinary survey of the management of chronic pancreatitis in the United Kingdom and Ireland. The results show a need for comprehensive access to specialist pancreatitis MDT care and there remains substantial variation in management.
DOI: 10.6084/m9.figshare.5788947
title: SuggestedMetadataClassification.xlsx

description: A suggested update to the Metabolomics Standards Initiative (MSI) metadata reporting standards. The existing standards are classified as either Mandatory (should be reported for all studies), Required (should be reported for all studies where used e.g. treatment) or Optional (reporting is down to the authors discretion). The standards are also classified as whether they should be reported on a per sample or per study basis.
DOI: 10.6084/m9.figshare.5788947.v1
title: SuggestedMetadataClassification.xlsx

description: A suggested update to the Metabolomics Standards Initiative (MSI) metadata reporting standards. The existing standards are classified as either Mandatory (should be reported for all studies), Required (should be reported for all studies where used e.g. treatment) or Optional (reporting is down to the authors discretion). The standards are also classified as whether they should be reported on a per sample or per study basis.
DOI: 10.6084/m9.figshare.5788938
title: DVS tracking dataset and resulted video

description: 1. The DVS recordings for event-stream pattern tracking:"DAVIS recordings and groundtruth.zip" and "DVS recordings and groundtruth.zip"<br>2. results displayed by videos
DOI: 10.6084/m9.figshare.5788905
title: bandt-pompe-master.zip

description: In this work, we propose a technique for the extraction and selection of relevant and non-redundant multivariate ordinal patterns from the high-dimensional combinatorial search space. Our proposed approach $ordex$, simultaneously extracts and scores the relevance and redundancy of ordinal patterns without training a classifier. As a filter-based approach, ordex aims to select a set of relevant patterns with complementary information. <br> Hence, using our scoring function based on the principles of Chebyshev's inequality, we maximize the relevance of the patterns and minimize the correlation between them. Our experiments on real-world datasets show that ordinality in time series contains valuable information for classification in several applications.
DOI: 10.6084/m9.figshare.5788905.v1
title: bandt-pompe-master.zip

description: In this work, we propose a technique for the extraction and selection of relevant and non-redundant multivariate ordinal patterns from the high-dimensional combinatorial search space. Our proposed approach $ordex$, simultaneously extracts and scores the relevance and redundancy of ordinal patterns without training a classifier. As a filter-based approach, ordex aims to select a set of relevant patterns with complementary information. <br> Hence, using our scoring function based on the principles of Chebyshev's inequality, we maximize the relevance of the patterns and minimize the correlation between them. Our experiments on real-world datasets show that ordinality in time series contains valuable information for classification in several applications.
DOI: 10.6084/m9.figshare.5788896
title: <i>Biecheleria tirezensis</i> sp. nov. (Dinophyceae, Suessiales), a new halotolerant dinoflagellate species isolated from the athalassohaline Tirez natural pond in Spain

description: A new euryhaline and eurythermal dinoflagellate species, <i>Biecheleria tirezensis</i> sp. nov., is described based on samples taken from an extreme environment, the athalassohaline and particularly sulphate-rich Tirez natural pond (Spain). This species is able to survive in salinities from almost fresh water up to 56 and over a 5–25°C temperature range. Thus, the ecological characteristics of this isolate differentiate it from other species of the same genus. Its morphology, as examined by light, scanning and transmission electron microscopy, shows that the cells are almost spherical, with several series of amphiesmal vesicles. It also has a single elongate amphiesmal vesicle (EAV) observed by SEM and the eyespot has a type E structure, typical of <i>Biecheleria</i>. Spherical and smooth cysts were observed in old cultures. The pigment composition is typical of a peridinin-containing dinoflagellate. Phylogeny inferred from nuclear rDNA SSU, ITS and LSU sequences showed the isolate belongs to the genus <i>Biecheleria</i>, closest to <i>B. cincta</i> and <i>B. brevisulcata</i>. Modelling and analysis of the secondary structure of its ITS2 region, and that of other species of the same genus and some representatives of the most closely related genera, indicated that the isolate represents a new species clearly separated from but related to <i>B. cincta</i>. The criterion of the presence of Compensatory Base Changes (CBCs) in the secondary structure of the ITS2 region as an indicator of species differentiation confirmed this, supporting the establishment of the Tirez pond isolate as a new species of <i>Biecheleria</i>.