Accuracy of identification of tissue types in endoscopic esophageal mucosal biopsies used for molecular biology studies

Open Access Initiativ

Why Do Developers Get Password Storage Wrong? A Qualitative Usability Study

Passwords are still a mainstay of various security systems, as well as the cause of many usability issues. For end-users, many of these issues have been studied extensively, highlighting problems and informing design decisions for better policies and motivating research into alternatives. However, end-users are not the only ones who have usability problems with passwords! Developers who are tasked with writing the code by which passwords are stored must do so securely. Yet history has shown that this complex task often fails due to human error with catastrophic results. While an end-user who selects a bad password can have dire consequences, the consequences of a developer who forgets to hash and salt a password database can lead to far larger problems. In this paper we present a first qualitative usability study with 20 computer science students to discover how developers deal with password storage and to inform research into aiding developers in the creation of secure password systems

Pulmonary rehabilitation in idiopathic pulmonary fibrosis and COPD: a propensity matched real-world study

BACKGROUND: The adherence to and clinical efficacy of pulmonary rehabilitation in idiopathic pulmonary fibrosis (IPF), particularly in comparison to people with chronic obstructive pulmonary disease (COPD), remains uncertain. The objectives of this real-world study were to compare the responses of patients with IPF with a matched group of patients with COPD undergoing the same supervised, outpatient pulmonary rehabilitation program, and to determine whether pulmonary rehabilitation is associated with survival in IPF. RESEARCH QUESTION: Do people with IPF improve to the same extent with pulmonary rehabilitation as a matched group of individuals with COPD, and are non-completion of and/or non-response to pulmonary rehabilitation associated with one-year all-cause mortality in IPF? STUDY DESIGN AND METHODS: Using propensity score matching, 163 patients with IPF were matched 1:1 with a control group of 163 patients with COPD referred to pulmonary rehabilitation. We compared between-group pulmonary rehabilitation completion rates and response. Survival status in the IPF cohort was recorded over one-year following pulmonary rehabilitation discharge. Cox proportional-hazards regression explored the association between pulmonary rehabilitation status and all-cause mortality. RESULTS: Similar pulmonary rehabilitation completion rates (IPF: 69%; COPD: 63%; p=0.24) and improvements in exercise response were observed in both groups with no significant mean (95% confidence interval (CI)) between-group differences in incremental shuttle walk (ISW) change (2 (-18 to 22) meters). Pulmonary rehabilitation non-completion (hazard ratio (HR) (95%CI) 5.62 (2.24 to 14.08)) and non-response (HR (95%CI) 3.91 (1.54 to 9.93)) were independently associated with increased one-year all-cause mortality in IPF. INTERPRETATION: Compared with a matched group of patients with COPD, this real-word study demonstrates that patients with IPF have similar completion rates and magnitude of response to pulmonary rehabilitation. In IPF, non-completion of and non-response to pulmonary rehabilitation were associated with increased all-cause mortality. These data reinforce the benefits of pulmonary rehabilitation in patients with IPF

Nemo: a computational tool for analyzing nematode locomotion

The nematode Caenorhabditis elegans responds to an impressive range of chemical, mechanical and thermal stimuli and is extensively used to investigate the molecular mechanisms that mediate chemosensation, mechanotransduction and thermosensation. The main behavioral output of these responses is manifested as alterations in animal locomotion. Monitoring and examination of such alterations requires tools to capture and quantify features of nematode movement. In this paper, we introduce Nemo (nematode movement), a computationally efficient and robust two-dimensional object tracking algorithm for automated detection and analysis of C. elegans locomotion. This algorithm enables precise measurement and feature extraction of nematode movement components. In addition, we develop a Graphical User Interface designed to facilitate processing and interpretation of movement data. While, in this study, we focus on the simple sinusoidal locomotion of C. elegans, our approach can be readily adapted to handle complicated locomotory behaviour patterns by including additional movement characteristics and parameters subject to quantification. Our software tool offers the capacity to extract, analyze and measure nematode locomotion features by processing simple video files. By allowing precise and quantitative assessment of behavioral traits, this tool will assist the genetic dissection and elucidation of the molecular mechanisms underlying specific behavioral responses.Comment: 12 pages, 2 figures. accepted by BMC Neuroscience 2007, 8:8

Change in gait speed and adverse outcomes in patients with idiopathic pulmonary fibrosis: a prospective cohort study.

BACKGROUND AND OBJECTIVE: Gait speed is associated with survival in individuals with idiopathic pulmonary fibrosis (IPF). The extent to which four-metre gait speed (4MGS) decline predicts adverse outcome in IPF remains unclear. We aimed to examine longitudinal 4MGS change and identify a cut-point associated with adverse outcome. METHODS: In a prospective cohort study, we recruited 132 individuals newly diagnosed with IPF and measured 4MGS change over 6 months. Death/first hospitalization at 6 months were composite outcome events. Complete data (paired 4MGS plus index event) were available in 85 participants; missing 4MGS data were addressed using multiple imputation. Receiver-Operating Curve plots identified a 4MGS change cut-point. Cox proportional-hazard regression assessed the relationship between 4MGS change and time to event. RESULTS: 4MGS declined over 6 months (mean [95% CI] change: -0.05 [-0.09 to -0.01] m/s; p = 0.02). A decline of 0.07 m/s or more in 4MGS over 6 months had better discrimination for the index event than change in 6-minute walk distance, forced vital capacity, Composite Physiologic Index or Gender Age Physiology index. Kaplan-Meier curves demonstrated a significant difference in time to event between 4MGS groups (substantial decline: >-0.07 m/s versus minor decline/improvers: ≤-0.07 m/s; p = 0.007). Those with substantial decline had an increased risk of hospitalization/death (adjusted hazard ratio [95% CI] 4.61 [1.23-15.83]). Similar results were observed in multiple imputation analysis. CONCLUSION: In newly diagnosed IPF, a substantial 4MGS decline over 6 months is associated with shorter time to hospitalization/death at 6 months. 4MGS change has potential as a surrogate endpoint for interventions aimed at modifying hospitalization/death

De novo assembly of the cattle reference genome with single-molecule sequencing.

BackgroundMajor advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.ResultsWe present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.ConclusionsWe demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species

Isothermal by Design: An Accelerated Approach to the Prediction of the Crystallizability of Slowly Nucleating Systems

A route to the accelerated nucleation of α-para-aminobenzoic acid in ethanol/water (EtOH/H2O) mixed solvent solutions, using antisolvent crystallization, is presented. An isothermal by design approach is adopted, whereby the exothermic enthalpy of mixing associated with antisolvent addition is offset by the control of the temperature of the antisolvent added. Induction times (τ) are found to be reduced by 4 orders of magnitude using this methodology, consistent with the use of this approach as a nucleation acceleration technique. Calculation of the nucleation kinetic parameters for a range of solution concentrations, compositions, and supersaturations (S) reveal that effective interfacial tensions (γeff) vary from 8.4 to 2.3 mJ m–2 from solutions in H2O solvent and EtOH solvent, respectively, in line with the trend in solubility. The critical nucleus radius (r*) decreases from 1.98 to 0.40 nm associated with a decrease in the number of molecules in the critical nucleus (i*) from 196 to 2 molecules. A change in nucleation mechanism from heterogeneous nucleation to homogeneous nucleation is observed to take place at S ≈ 1.5. Limitations, particularly with focus toward larger-scale operation, are highlighted together with potential solutions to overcome such aspects

Influence of solution chemistry on the solubility, crystallisability and nucleation behaviour of eicosane in toluene : acetone mixed-solvents

The interplay between the solution chemistry and crystallisability of eicosane in mixed toluene : acetone solutions is examined over the full compositional range from pure toluene to pure acetone, using a combination of polythermal crystallisation experiments and molecular modelling. Enthalpies of dissolution and mixing, as well as metastable zone widths increase with increasing acetone content, up to a mol fraction of 0.85 acetone, followed by a decrease in values to pure acetone solutions. Nucleation is found to occur via an instantaneous pathway for the pure solvent systems and also when toluene is in excess, in contrast to solutions where acetone is in excess, which are found to nucleate progressively. Rationalisation through molecular modelling highlights likely changes in the solution structure, whereby eicosane can be expected to be preferentially solvated by toluene, with this solvated cluster being surrounded by a ‘cage’ of acetone molecules. This proposed structure is consistent with a model whereby solute diffusion and hence clustering is hindered when acetone is in excess, decreasing the crystallisability of the solution and effecting a change in the mechanism of nucleation. However, above a critical acetone composition, the potential for complete toluene solvation is restricted and easier crystallisation is enabled