cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5123956
title: Supplementary Material for: <b><i>Francisella tularensis </i></b>Alters Human Neutrophil Gene Expression: Insights into the Molecular Basis of Delayed Neutrophil Apoptosis

description: We demonstrated recently that <i>Francisella tularensis</i> profoundly impairs human neutrophil apoptosis, but how this is achieved is largely unknown. Herein we used human oligonucleotide microarrays to test the hypothesis that changes in neutrophil gene expression contribute to this phenotype, and now demonstrate that <i>F. tularensis</i> live vaccine strain (LVS) caused significant changes in neutrophil gene expression over a 24-hour time period relative to the uninfected controls. Of approximately 47,000 genes analyzed, 3,435 were significantly up- or downregulated by LVS, including 365 unique genes associated with apoptosis and cell survival. Specific targets in this category included genes asso-ciated with the intrinsic and extrinsic apoptotic pathways (<i>CFLAR</i>, <i>TNFAIP3</i>, <i>TNFRSF10D</i>, <i>SOD2, BCL2A1</i>, <i>BIRC4</i>, <i>PIM2</i>, <i>TNFSF10</i>, <i>TNFRSF10C</i>, <i>CASP2</i> and <i>CASP8</i>) and genes that act via the NFĸB pathway and other mechanisms to prolong cell viability (<i>NFKB1</i>, <i>NFKB2</i> and <i>RELA</i>, <i>IL1B</i>, <i>CAST, CDK2,</i><i>GADD45B</i>, <i>BCL3</i>, <i>BIRC3</i>, <i>CDK2</i>, <i>IL1A</i>, <i>PBEF1</i>, <i>IL6</i>, <i>CXCL1</i>, <i>CCL4</i> and <i>VEGF</i>). The microarray data were confirmed by qPCR and pathway analysis. Moreover, we demonstrate that the X-linked inhibitor of apoptosis protein remained abundant in polymorphonuclear leukocytes over 48 h of LVS infection, whereas BAX mRNA and protein were progressively downregulated. These data strongly suggest that antiapoptotic and prosurvival mechanisms collaborate to sustain the viability of <i>F. tularensis</i>--infected neutrophils.
DOI: 10.6084/m9.figshare.5123959.v1
title: Supplementary Material for: Identification of Interstitial Cajal-Like Cells in the Human Thoracic Duct

description: Interstitial Cajal-like cells (ICLCs) are speculated to be pacemakers in smooth muscle tissues. While the human thoracic duct (TD) is spontaneously active, the origin of this activity is unknown. We hypothesized that ICLCs could be present in the TD and using histological techniques, immunohistochemistry and immunofluorescence we have investigated the presence of ICLCs, protein markers for ICLCs and the cellular morphology of the human TD. Transmission electron microscopy was employed to investigate ultrastructure. Methylene blue staining, calcium-dependent fluorophores and confocal microscopy were used to identify ICLCs in live tissue. Methylene blue stained cells with morphology suggestive of ICLCs in the TD. Immunoreactivity localized the ICLC protein markers c-kit, CD34 and vimentin to many cells and processes associated with smooth muscle cells (SMCs): coexpression of c-kit with vimentin or CD34 was observed in some cells. Electron microscopy analysis confirmed ICLCs as a major cell type of the human TD. Lymphatic ICLCs possess caveolae, dense bands, a patchy basal lamina, intermediate filaments and specific junctions to SMCs. ICLCs were ultrastructurally differentiable from other interstitial cells observed: fibroblasts, mast cells, macrophages and pericytes. Lymphatic ICLCs were localized to the subendothelial region of the wall as well as in intimate association with smooth muscle bundles throughout the media. ICLCs were morphologically distinct with multiple processes and also spindle shapes. Confocal imaging with calcium-dependent fluorophores corroborated cell morphology and localization observed in fixed tissues. Lymphatic ICLCs thus constitute a significant cell type of the human TD and physically interact with lymphatic SMCs.
DOI: 10.6084/m9.figshare.5123956.v1
title: Supplementary Material for: <b><i>Francisella tularensis </i></b>Alters Human Neutrophil Gene Expression: Insights into the Molecular Basis of Delayed Neutrophil Apoptosis

description: We demonstrated recently that <i>Francisella tularensis</i> profoundly impairs human neutrophil apoptosis, but how this is achieved is largely unknown. Herein we used human oligonucleotide microarrays to test the hypothesis that changes in neutrophil gene expression contribute to this phenotype, and now demonstrate that <i>F. tularensis</i> live vaccine strain (LVS) caused significant changes in neutrophil gene expression over a 24-hour time period relative to the uninfected controls. Of approximately 47,000 genes analyzed, 3,435 were significantly up- or downregulated by LVS, including 365 unique genes associated with apoptosis and cell survival. Specific targets in this category included genes asso-ciated with the intrinsic and extrinsic apoptotic pathways (<i>CFLAR</i>, <i>TNFAIP3</i>, <i>TNFRSF10D</i>, <i>SOD2, BCL2A1</i>, <i>BIRC4</i>, <i>PIM2</i>, <i>TNFSF10</i>, <i>TNFRSF10C</i>, <i>CASP2</i> and <i>CASP8</i>) and genes that act via the NFĸB pathway and other mechanisms to prolong cell viability (<i>NFKB1</i>, <i>NFKB2</i> and <i>RELA</i>, <i>IL1B</i>, <i>CAST, CDK2,</i><i>GADD45B</i>, <i>BCL3</i>, <i>BIRC3</i>, <i>CDK2</i>, <i>IL1A</i>, <i>PBEF1</i>, <i>IL6</i>, <i>CXCL1</i>, <i>CCL4</i> and <i>VEGF</i>). The microarray data were confirmed by qPCR and pathway analysis. Moreover, we demonstrate that the X-linked inhibitor of apoptosis protein remained abundant in polymorphonuclear leukocytes over 48 h of LVS infection, whereas BAX mRNA and protein were progressively downregulated. These data strongly suggest that antiapoptotic and prosurvival mechanisms collaborate to sustain the viability of <i>F. tularensis</i>--infected neutrophils.
DOI: 10.6084/m9.figshare.5123944
title: Supplementary Material for: Cross-Sectional Association between Polyfluoroalkyl Chemicals and Cognitive Limitation in the National Health and Nutrition Examination Survey

description: <b><i>Background/Aims:</i></b> Our limited understanding of how polyfluoroalkyl chemicals (PFCs) may impact on human health suggests the potential for a protective impact on brain health. This study was designed to explore the association between PFCs and cognitive ability in older adults. <b><i>Methods:</i></b> We assessed the association between four PFCs, perfluorooctanoic acid (PFOA), perfluorooctane sulfonic acid (PFOS), perfluorononanoic acid (PFNA) and perfluorohexane sulfonic acid (PFHxS), and self-reported limitation due to difficulty remembering or periods of confusion using data from participants aged 60–85 years from the 1999–2000 and 2003–2008 National Health and Nutrition Examination Surveys. We also considered whether diabetic status or diabetic medication use modifies this association in light of in vitro evidence that PFCs may act on the same receptors as some diabetic medications. <b><i>Results:</i></b> In multivariable adjusted models, point estimates suggest a protective association between PFCs and self-reported cognitive limitation (odds ratio, OR; 95% confidence interval, CI) for a doubling in PFC concentration: PFOS (OR, 0.90; 95% CI, 0.78, 1.03), PFOA (OR, 0.92; 95% CI, 0.78, 1.09), PFNA (OR, 0.91; 95% CI, 0.79, 1.04) and PFHxS (OR, 0.93; 95% CI, 0.82, 1.06). The protective association was concentrated in diabetics, with strong, significant protective associations in nonmedicated diabetics. <b><i>Conclusions:</i></b> This cross-sectional study suggests that there may be a protective association between exposure to PFCs and cognition in older adults, particularly diabetics.
DOI: 10.6084/m9.figshare.5123947
title: Supplementary Material for: Negative Symptoms and Executive Function in Schizophrenia: Does Their Relationship Change with Illness Duration?

description: <b><i>Background:</i></b> Negative symptoms and cognitive dysfunction are of crucial functional and prognostic importance in schizophrenia. However, the nature of the relationship between them and the factors that may influence it have not been well established. <b><i>Aims:</i></b> To investigate whether the relationship between negative symptoms and executive function changes according to the duration of illness in schizophrenia. <b><i>Methods:</i></b> The Positive and Negative Syndrome Scale was used to assess psychopathology and the Wisconsin Card Sorting Test (WCST) to evaluate executive function in a sample of 200 schizophrenic patients who were classified in 3 groups according to their duration of illness: up to 5 years (short duration group), 6-20 years (intermediate duration group) and over 20 years of illness (long duration group). <b><i>Results:</i></b> Medium-sized correlations were found between negative symptoms and WCST performance as assessed by the number of completed categories in all 3 groups. However, differences were found according to the duration of schizophrenia. For patients in the short duration group, negative symptoms correlated with WCST nonperseverative errors, but for those in the long duration group the correlation was with perseverative errors. <b><i>Conclusion:</i></b> We found a differential relationship between negative and cognitive symptoms in different stages of schizophrenia. Illness duration should be considered when studying the relationship between negative symptoms and cognition.
DOI: 10.6084/m9.figshare.5123950
title: Supplementary Material for: Genetic Variation in the Scavenger Receptor MARCO and Its Association with Chronic Obstructive Pulmonary Disease and Lung Infection in 10,604 Individuals

description: <b><i>Background:</i></b> MARCO (macrophage receptor with collagenous structure) is a dominant receptor for unopsonized particles and bacteria in the lungs. Reduced function of this receptor due to genetic variation may be associated with susceptibility to chronic obstructive pulmonary disease (COPD) and lung infection. <b><i>Objectives:</i></b> To identify novel genetic variants in <i>MARCO</i> that are associated with reduced lung function, or increased risk of COPD or lung infection. <b><i>Methods:</i></b> We first screened 760 individuals with extreme lung phenotypes in a large general population study to identify novel variants in the <i>MARCO</i> gene. We next genotyped the entire cohort consisting of 10,604 individuals to assess the clinical relevance of these variants. <b><i>Results:</i></b> We identified 4 novel (R124H, K201N, P303L and G340W) and 5 previously described (H101Q, F282S, G319V, K387Q and E511D) non-synonymous variants. When screening the entire cohort for these variants, we found low minor allele frequencies ranging from 0.005 to 5%. None of the individual <i>MARCO</i> genotypes were associated with reduced lung function, or risk of COPD or lung infection. H101Q heterozygotes had an increased odds ratio for sepsis of 2.2 (95% CI: 1.1–4.4) compared to non-carriers, but none of the other <i>MARCO</i> genotypes were associated with the risk of sepsis. <b><i>Conclusions:</i></b> We identified 9 non-synonymous variants in the <i>MARCO</i> gene and showed that these variants are not major risk factors for COPD or lung infection in the Danish population. H101Q heterozygotes had increased sepsis risk, but further research is required to confirm this finding. This study is the first to examine genetic variants in <i>MARCO</i> and the risk of COPD and infections in humans.
DOI: 10.6084/m9.figshare.5123953.v1
title: Supplementary Material for: A Problem Shared Is a Problem Reduced: Seeking Efficiency in the Conservation of Felids and Primates

description: Threats faced by mammalian species can be grouped into one of a handful of categories, such as habitat loss, unsustainable hunting and persecution. Insofar as they face common threats, diverse species may benefit from the same conservation intervention, thereby offering efficiencies in conservation action. We explore this proposition for primates and felids by examining coarse scale overlaps in geographical distributions, using IUCN Red List assessments of the primary threats posed to each species. A global analysis of primates and felids that face common threats reveals the greatest overlap is in Central and South Asia, where up to 14 primates and felids co-occur. More than 80% of the land where at least 1 threatened species of either primate or felid occurs also contains at least one threatened species of the other taxon, yet over 60% of these grid cells containing both threatened primates and felids lie outside Conservation International’s hot spots. A review of IUCN Action Plans of the threats to felids and primates strongly supports the hypothesis that they are often the same and occur in the same place. In principle, steps to conserve big cats have the potential to benefit several species of threatened primates, and vice versa.
DOI: 10.6084/m9.figshare.5123941
title: Supplementary Material for: Cognition and Incident Dementia Hospitalization: Results from the Atherosclerosis Risk in Communities Study

description: <b><i>Background/Aims:</i></b> Cognitive decline is a defining feature of dementia. We sought to determine if a single baseline cognitive test score or change in test score over time is more strongly associated with risk of dementia hospitalization. We also sought to compare short- and long-term dementia risk. <b><i>Methods:</i></b> Prospective cohort study of 9,399 individuals from the Atherosclerosis Risk in Communities Study (median 10 years of follow-up). Cognition was assessed at two time points (6 years apart) using three tests: Delayed Word Recall Test (DWRT), Digit Symbol Substitution Test (DSST), and Word Fluency Test. Dementia hospitalizations were determined using ICD-9 codes. <b><i>Results:</i></b> Baseline cognitive test scores were associated with both short-term and long-term risk of dementia. The association of 6-year change in cognitive test score with dementia risk was stronger than that of individual test scores at a single visit [change from highest to lowest tertile, DWRT: hazard ratio = 6.45 (95% confidence interval = 1.80–23.08); DSST: hazard ratio = 10.94 (95% confidence interval = 3.07–38.97)]. <b><i>Conclusions:</i></b> In this community-based population, 6-year changes in cognitive scores were more strongly associated with risk of incident dementia hospitalization than baseline scores, although single DWRT and DSST scores were predictive. Our findings support the contention that cognitive changes may precede clinical dementia by a decade or more.
DOI: 10.6084/m9.figshare.5123947.v1
title: Supplementary Material for: Negative Symptoms and Executive Function in Schizophrenia: Does Their Relationship Change with Illness Duration?

description: <b><i>Background:</i></b> Negative symptoms and cognitive dysfunction are of crucial functional and prognostic importance in schizophrenia. However, the nature of the relationship between them and the factors that may influence it have not been well established. <b><i>Aims:</i></b> To investigate whether the relationship between negative symptoms and executive function changes according to the duration of illness in schizophrenia. <b><i>Methods:</i></b> The Positive and Negative Syndrome Scale was used to assess psychopathology and the Wisconsin Card Sorting Test (WCST) to evaluate executive function in a sample of 200 schizophrenic patients who were classified in 3 groups according to their duration of illness: up to 5 years (short duration group), 6-20 years (intermediate duration group) and over 20 years of illness (long duration group). <b><i>Results:</i></b> Medium-sized correlations were found between negative symptoms and WCST performance as assessed by the number of completed categories in all 3 groups. However, differences were found according to the duration of schizophrenia. For patients in the short duration group, negative symptoms correlated with WCST nonperseverative errors, but for those in the long duration group the correlation was with perseverative errors. <b><i>Conclusion:</i></b> We found a differential relationship between negative and cognitive symptoms in different stages of schizophrenia. Illness duration should be considered when studying the relationship between negative symptoms and cognition.
DOI: 10.6084/m9.figshare.5123932
title: Supplementary Material for: Lung Function of Infants with Congenital Lung Lesions in the First Year of Life

description: <b><i>Background:</i></b> Several studies have evaluated short-term neonatal outcome in infants with congenital lung lesions (CLL) but clinical course and lung function in the longer term have not yet been documented. We hypothesized that clinical course and lung function would be negatively affected by surgical resection. <b><i>Objective:</i></b> To evaluate respiratory symptoms and lung function longitudinally in the first year of life in infants with CLL, and to analyse differences herein between infants managed by observation only and infants whose affected lung parts were resected. <b><i>Methods:</i></b> We evaluated respiratory symptoms and lung function at 6 and 12 months in 30 patients with CLL. Functional residual capacity (FRC<sub>p</sub>) and maximal expiratory flow at functional residual capacity (V′<sub>max</sub>frc) were measured with body plethysmography. SD scores were calculated for V′<sub>max</sub>frc. <b><i>Results:</i></b> Prevalence of respiratory symptoms did not differ between the groups. Mean FRC<sub>p</sub> (95% CI) was 25.3 (23.3–27.3) in the group managed by observation versus 27.3 (25.1–29.6) in the group managed by surgery (p = 0.149). Mean (95% CI) SDS V′<sub>max</sub>frc was –1.45 (–1.84 to –1.06) versus –1.41 (–1.90 to –0.91) (p = 0.892). Lung function did not change significantly over the 6-month period. <b><i>Conclusion:</i></b> Surgical resection did not seem to have negatively affected the clinical course and lung function. We recommend pulmonary follow-up of all CLL patients into adulthood to further identify any long-term effects of CLL and observation or surgery.
DOI: 10.6084/m9.figshare.5123935
title: Supplementary Material for: Staging of Mental Disorders: Systematic Review

description: <b><i>Background:</i></b> The staging method, whereby a disorder is characterized according to its seriousness, extension, development and features, is attracting increasing attention in clinical psychology and psychiatry. The aim of this systematic review was to critically summarize the tools that are available for reproducing and standardizing the clinical intuitions that are involved in a staging formulation. <b><i>Methods:</i></b> A comprehensive research was conducted on the MEDLINE, PsycINFO, EMBASE and Cochrane databases from inception to May 2012. The following search terms were used: ‘stage/staging’ AND ‘psychiatric disorder/mental disorder/schizophrenia/mood disorder/anxiety disorder/substance use disorder/eating disorder’. <b><i>Results:</i></b> A total of 78 studies were identified for inclusion in the review. We discussed studies addressing or related to the issue of staging in a number of mental disorders (schizophrenia, unipolar depression, bipolar disorder, panic disorder, substance use disorders, anorexia and bulimia nervosa). The literature indicates that disorders have a longitudinal development or a treatment history that can be categorized according to stages. We proposed staging formulations for the above-mentioned psychiatric disorders. <b><i>Conclusion:</i></b> Staging models offer innovative assessment tools for clinical psychologists and psychiatrists. Characterizing each stage of an illness demarcates major prognostic and therapeutic differences among patients who otherwise seem to be deceptively similar since they share the same psychiatric diagnosis. A stage 0 to denote an at-risk condition does not appear to be warranted at the current state of research.
DOI: 10.6084/m9.figshare.5123938
title: Supplementary Material for: AGO Recommendations for Diagnosis and Treatment of Patients with Early and Metastatic Breast Cancer: Update 2012

description: Medicine
DOI: 10.6084/m9.figshare.5123929
title: Supplementary Material for: Decline in Gait Performance Detected by an Electronic Walkway System in 907 Older Adults of the Population-Based KORA-Age Study

description: <b><i>Background:</i></b> Gait changes at older ages are a strong predictor of a decline in lower extremity functions. However, large population-based studies assessing gait parameters in various gait tasks are lacking. <b><i>Objective:</i></b> We investigated the relationship of age, the use of mobility aids and being fitted with an endoprosthesis with selected gait parameters, assessed in different walking tasks. <b><i>Methods:</i></b> In the population-based KORA-Age study, data from 907 men and women aged 65-91 years were obtained using the validated electronic walkway system GAITRite, which quantifies spatiotemporal gait parameters in the measurement range of a 488 × 61 cm walkway mat. Participants completed three walking tasks at different speeds (normal, slow and fast) and a fourth walking task at normal speed with the additional task of counting backwards (dual-task walking). Additionally, the impact of endoprostheses (hip or knee) and mobility aids was assessed. <b><i>Results:</i></b> The highest relative age-related decline for velocity was observed during dual-task walking (26.1% for men and 23.4% for women) and for step length during fast walking (20.2 and 14.4%) when comparing participants aged &lt;70 years with those aged ≥85 years. Weaker performances for velocity, cadence and step length were observed among women with knee or hip endoprostheses (fast walking speed) (p &lt; 0.05). Across all walking tasks, significant differences between mobility aid users and nonusers were observed for velocity and step length among both men and women (p &lt; 0.05). <b><i>Conclusion:</i></b> A decline in gait performance is most notable in fast speed and dual-task walking, in age-related endoprosthesis and mobility aid analyses. The marked relative decrease in gait parameters in these difficult gait tasks may be attributed to lacking resources for compensation among the elderly.
DOI: 10.6084/m9.figshare.5123932.v1
title: Supplementary Material for: Lung Function of Infants with Congenital Lung Lesions in the First Year of Life

description: <b><i>Background:</i></b> Several studies have evaluated short-term neonatal outcome in infants with congenital lung lesions (CLL) but clinical course and lung function in the longer term have not yet been documented. We hypothesized that clinical course and lung function would be negatively affected by surgical resection. <b><i>Objective:</i></b> To evaluate respiratory symptoms and lung function longitudinally in the first year of life in infants with CLL, and to analyse differences herein between infants managed by observation only and infants whose affected lung parts were resected. <b><i>Methods:</i></b> We evaluated respiratory symptoms and lung function at 6 and 12 months in 30 patients with CLL. Functional residual capacity (FRC<sub>p</sub>) and maximal expiratory flow at functional residual capacity (V′<sub>max</sub>frc) were measured with body plethysmography. SD scores were calculated for V′<sub>max</sub>frc. <b><i>Results:</i></b> Prevalence of respiratory symptoms did not differ between the groups. Mean FRC<sub>p</sub> (95% CI) was 25.3 (23.3–27.3) in the group managed by observation versus 27.3 (25.1–29.6) in the group managed by surgery (p = 0.149). Mean (95% CI) SDS V′<sub>max</sub>frc was –1.45 (–1.84 to –1.06) versus –1.41 (–1.90 to –0.91) (p = 0.892). Lung function did not change significantly over the 6-month period. <b><i>Conclusion:</i></b> Surgical resection did not seem to have negatively affected the clinical course and lung function. We recommend pulmonary follow-up of all CLL patients into adulthood to further identify any long-term effects of CLL and observation or surgery.