Burmese amber fossils bridge the gap in the Cretaceous record of polypod ferns

publisher: Elsevier articletitle: Burmese amber fossils bridge the gap in the Cretaceous record of polypod ferns journaltitle: Perspectives in Plant Ecology, Evolution and Systematics articlelink: http://dx.doi.org/10.1016/j.ppees.2016.01.003 content_type: article copyright: Copyright © 2016 Elsevier GmbH. All rights reserved.Copyright © 2016 Elsevier GmbH. All rights reserved. This document is the authors' final accepted version of the journal article. You are advised to consult the publisher's version if you wish to cite from it

Eco-reliable path finding in time-variant and stochastic networks

This paper addresses a route guidance problem for finding the most eco-reliable path in time-variant and stochastic networks such that travelers can arrive at the destination with the maximum on-time probability while meeting vehicle emission standards imposed by government regulators. To characterize the dynamics and randomness of transportation networks, the link travel times and emissions are assumed to be time-variant random variables correlated over the entire network. A 0–1 integer mathematical programming model is formulated to minimize the probability of late arrival by simultaneously considering the least expected emission constraint. Using the Lagrangian relaxation approach, the primal model is relaxed into a dualized model which is further decomposed into two simple sub-problems. A sub-gradient method is developed to reduce gaps between upper and lower bounds. Three sets of numerical experiments are tested to demonstrate the efficiency and performance of our proposed model and algorithm

CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data

Cancer is known to have abundant copy number alterations (CNAs) that greatly contribute to its pathogenesis and progression. Investigation of CNA regions could potentially help identify oncogenes and tumor suppressor genes and infer cancer mechanisms. Although single-nucleotide polymorphism (SNP) arrays have strengthened our ability to identify CNAs with unprecedented resolution, a comprehensive collection of CNA information from SNP array data is still lacking. We developed a web-based CaSNP (http://cistrome.dfci.harvard.edu/CaSNP/) database for storing and interrogating quantitative CNA data, which curated ∼11 500 SNP arrays on 34 different cancer types in 104 studies. With a user input of region or gene of interest, CaSNP will return the CNA information summarizing the frequencies of gain/loss and averaged copy number for each study, and provide links to download the data or visualize it in UCSC Genome Browser. CaSNP also displays the heatmap showing copy numbers estimated at each SNP marker around the query region across all studies for a more comprehensive visualization. Finally, we used CaSNP to study the CNA of protein-coding genes as well as LincRNA genes across all cancer SNP arrays, and found putative regions harboring novel oncogenes and tumor suppressors. In summary, CaSNP is a useful tool for cancer CNA association studies, with the potential to facilitate both basic science and translational research on cancer

Assessment of the Type D Personality Construct in the Korean Population: A Validation Study of the Korean DS14

This study aimed to develop a Korean version of the Type D Personality Scale-14 (DS14) and evaluate the psychiatric symptomatology of Korean cardiac patients with Type D personality. Healthy control (n = 954), patients with a coronary heart disease (n = 111) and patients with hypertension and no heart disease (n = 292) were recruited. All three groups completed DS14, the Eysenck Personality Questionnaire (EPQ), the state subscale of Spielberger State and Trait Anxiety Inventory (STAI-S), the Center for Epidemiologic Studies Short Depression Scale (CESD), and the General Health Questionnaire (GHQ). The Korean DS14 was internally consistent and stable over time. 27% of the subjects were classified as Type D. Type D individuals had significantly higher mean scores on the STAI-S, CESD, and GHQ compared to non-Type D subjects in each group. The Korean DS14 was a valid and reliable tool for identifying Type D personality. The general population and cardiovascular patients with Type D personality showed higher rate of depression, anxiety and psychological distress regarding their health. Therefore, identifying Type D personality is important in clinical research and practice in chronic medical disorders, especially cardiovascular disease, in Korea

Gender differences in patients with dizziness and unsteadiness regarding self-perceived disability, anxiety, depression, and its associations

BACKGROUND: It is known that anxiety and depression influence the level of disability experienced by persons with vertigo, dizziness or unsteadiness. Because higher prevalence rates of disabling dizziness have been found in women and some studies reported a higher level of psychiatric distress in female patients our primary aim was to explore whether women and men with vertigo, dizziness or unsteadiness differ regarding self-perceived disability, anxiety and depression. Secondly we planned to investigate the associations between disabling dizziness and anxiety and depression. METHOD: Patients were recruited from a tertiary centre for vertigo and balance disorders. Participants rated their global disability as mild, moderate or severe. They filled out the Dizziness Handicap Inventory and the two subscales of the Hospital Anxiety Depression Scale (HADS). The HADS was analysed 1) by calculating the median values, 2) by estimating the prevalence rates of abnormal anxiety/depression based on recommended cut-off criteria. Mann-Whitney U-tests, Chi-square statistics and odds ratios (OR) were calculated to compare the observations in both genders. Significance values were adjusted with respect to multiple comparisons. RESULTS: Two-hundred and two patients (124 women) mean age (standard deviation) of 49.7 (13.5) years participated. Both genders did not differ significantly in the mean level of self-perceived disability, anxiety, depression and symptom severity. There was a tendency of a higher prevalence of abnormal anxiety and depression in men (23.7%; 28.9%) compared to women (14.5%; 15.3%). Patients with abnormal depression felt themselves 2.75 (95% CI: 1.31-5.78) times more severely disabled by dizziness and unsteadiness than patients without depression. In men the OR was 8.2 (2.35-28.4). In women chi-square statistic was not significant. The ORs (95% CI) of abnormal anxiety and severe disability were 4.2 (1.9-8.9) in the whole sample, 8.7 (2.5-30.3) in men, and not significant in women. CONCLUSIONS: In men with vertigo, dizziness or unsteadiness emotional distress and its association with self-perceived disability should not be underestimated. Longitudinal surveys with specific pre-defined co-variables of self-perceived disability, anxiety and depression are needed to clarify the influence of gender on disability, anxiety and depression in patients with vertigo, dizziness or unsteadiness

Pharmacological agents for preventing morbidity associated with the haemodynamic response to tracheal intubation

Background: Several drugs have been used in attenuating or obliterating the response associated with laryngoscopy and tracheal intubation. These changes are of little concern in relatively healthy patients but can lead to morbidity and mortality in the high risk patient population.Objectives: The primary objective of this review was to determine the effectiveness of pharmacological agents in preventing the morbidity and mortality resulting from the haemodynamic changes in response to laryngoscopy and tracheal intubation in adult patients aged 18 years and above who were undergoing elective surgery in the operating room setting.SEARCH Methods: We searched the Cochrane Central Register of Controlled Trials (CENTRAL) (2011, Issue 6), MEDLINE (1950 to June 2011), EMBASE (1980 to June 2011), and the bibliographies of published studies. We reran our search from June 2011 to December 2012 and will deal with these studies when we update the review.SELECTION CRITERIA: We included randomized controlled trials (RCTs) that compared a drug used as an intervention for preventing or attenuating the haemodynamic response to tracheal intubation to a control group, and that mentioned mortality, major morbidity, arrhythmia or electrocardiogram (ECG) evidence of ischaemia in the methodology, results, or discussion section of the reports.DATA COLLECTION AND ANALYSIS: Two authors independently assessed trial quality and extracted the outcome data.MAIN Results: We included 72 RCTs. The included trials studied the effects of 32 drugs belonging to different pharmacological groups. Only two trials mentioned the primary outcome of morbidity and mortality related to the haemodynamic response to tracheal intubation. Of the secondary outcomes, 40 of the included trials observed arrhythmia only, 11 observed myocardial ischaemia only and 20 observed both arrhythmias and myocardial ischaemia. Arrhythmias were observed in 2932 participants and myocardial ischaemia in 1616 participants. Arrhythmias were observed in 134 out of 993 patients in the control group compared to 80 out of 1939 in the intervention group. The risk of arrhythmias was significantly reduced with pharmacological interventions in the pooled data (Peto odds ratio (OR) 0.19, 95% CI 0.14 to 0.26, P \u3c 0.00001, I(2)= 47%). Local anaesthetics, calcium channel blockers, beta blockers and narcotics reduced the risk of arrhythmia in the intervention group compared to the control group. Myocardial ischaemia was observed in 21 out of 604 patients in the control group compared to 10 out of 1012 in the treatment group; the result was statistically significant (Peto OR 0.45, 95% CI 0.22 to 0.92, P = 0.03, I(2) = 19%). However, in subgroup analysis only local anaesthetics significantly reduced the ECG changes indicating ischaemia, but this evidence came from one study. The majority of the studies had a negative outcome. Hypotension and bradycardia were reported with 40 g kg(-1) intravenous alfentanil, chest rigidity with 75 ug kg(-1) alfentanil, and increased bronchomotor tone with sympathetic blockers.There were 17 studies which included high risk patients. Pharmacological treatment in this group resulted in the reduction of arrhythmias when the data from nine trials looking at arrhythmias were pooled (Peto OR 0.18, 95% CI 0.05 to 0.59, P = 0.005, I(2) = 80%). The analysis from four studies was not included. Three of these trials looked at the effect of sympathetic blockers but arrhythmias or myocardial ischaemia was observed throughout the perioperative period in two studies and some patients had arrhythmias due to atropine premedication in the third study. In the fourth study the authors mentioned myocardial ischaemia in the objectives section but did not report it in the results.AUTHORS\u27 CONCLUSIONS: The risk of arrhythmias associated with tracheal intubation was significantly reduced with pre-induction administration of local anaesthetics, calcium channel blockers, beta blockers and narcotics compared to placebo. Pharmacological intervention also reduced the risk of ECG evidence of myocardial ischaemia in the pooled data. Lignocaine pretreatment showed a significant effect but evidence came from one study only. The data suggested that there may be a reduction in ECG evidence of myocardial ischaemia with beta blocker pretreatment but this difference was not statistically significant. There is a need to focus on outcomes rather than haemodynamic measurements alone when studying this response in future trials

arrayMap: A Reference Resource for Genomic Copy Number Imbalances in Human Malignancies

Background: The delineation of genomic copy number abnormalities (CNAs) from cancer samples has been instrumental for identification of tumor suppressor genes and oncogenes and proven useful for clinical marker detection. An increasing number of projects have mapped CNAs using high-resolution microarray based techniques. So far, no single resource does provide a global collection of readily accessible oncoge- nomic array data. Methodology/Principal Findings: We here present arrayMap, a curated reference database and bioinformatics resource targeting copy number profiling data in human cancer. The arrayMap database provides a platform for meta-analysis and systems level data integration of high-resolution oncogenomic CNA data. To date, the resource incorporates more than 40,000 arrays in 224 cancer types extracted from several resources, including the NCBI's Gene Expression Omnibus (GEO), EBIs ArrayExpress (AE), The Cancer Genome Atlas (TCGA), publication supplements and direct submissions. For the majority of the included datasets, probe level and integrated visualization facilitate gene level and genome wide data re- view. Results from multi-case selections can be connected to downstream data analysis and visualization tools. Conclusions/Significance: To our knowledge, currently no data source provides an extensive collection of high resolution oncogenomic CNA data which readily could be used for genomic feature mining, across a representative range of cancer entities. arrayMap represents our effort for providing a long term platform for oncogenomic CNA data independent of specific platform considerations or specific project dependence. The online database can be accessed at http://www.arraymap.org.Comment: 17 pages, 5 inline figures, 3 tables, supplementary figures/tables split into 4 PDF files; manuscript submitted to PLoS ON

How bold is blood oxygenation level dependent (BOLD) magnetic resonance imaging of the kidney? Opportunities, challenges and future directions

Renal tissue hypoperfusion and hypoxia are key elements in the pathophysiology of acute kidney injury and its progression to chronic kidney disease. Yet, in vivo assessment of renal haemodynamics and tissue oxygenation remains a challenge. Many of the established approaches are invasive, hence not applicable in humans. Blood oxygenation level dependent (BOLD) magnetic resonance imaging (MRI) offers an alternative. BOLD-MRI is non-invasive and indicative of renal tissue oxygenation. Nonetheless recent (pre-)clinical studies revived the question as to how bold renal BOLD-MRI really is. This review aims to deliver some answers. It is designed to inspire the renal physiology, nephrology, and imaging communities to foster explorations into the assessment of renal oxygenation and haemodynamics by exploiting the powers of MRI. For this purpose the specifics of renal oxygenation and perfusion are outlined. The fundamentals of BOLD-MRI are summarized. The link between tissue oxygenation and the oxygenation sensitive MR biomarker T2 * is outlined. The merits and limitations of renal BOLD-MRI in animal and human studies are surveyed together with their clinical implications. Explorations into detailing the relation between renal T2 * and renal tissue partial pressure of oxygen (pO2 ) are discussed with a focus on factors confounding the T2 * versus tissue pO2 relation. Multi-modality in vivo approaches suitable for detailing the role of the confounding factors that govern T2 * are considered. A schematic approach describing the link between renal perfusion, oxygenation, tissue compartments and renal T2 * is proposed. Future directions of MRI assessment of renal oxygenation and perfusion are explored