Adobe Flash as a medium for online experimentation: a test of reaction time measurement capabilities

Adobe Flash can be used to run complex psychological experiments over the Web. We examined the reliability of using Flash to measure reaction times (RTs) using a simple binary-choice task implemented both in Flash and in a Linux-based system known to record RTs with millisecond accuracy. Twenty-four participants were tested in the laboratory using both implementations; they also completed the Flash version on computers of their own choice outside the lab. RTs from the trials run on Flash outside the lab were approximately 20 msec slower than those from trials run on Flash in the lab, which in turn were approximately 10 msec slower than RTs from the trials run on the Linux-based system (baseline condition). RT SDs were similar in all conditions, suggesting that although Flash may overestimate RTs slightly, it does not appear to add significant noise to the data recorded

Using Adobe Flash Lite on mobile phones for psychological research: reaction time measurement reliability and inter-device variability

Mobile telephones have significant potential for use in psychological research, possessing unique characteristics—not least their ubiquity—that may make them useful tools for psychologists. We examined whether it is possible to measure reaction times (RTs) accurately using Adobe Flash Lite on mobile phones. We ran simple and choice RT experiments on two widely available mobile phones, a Nokia 6110 Navigator and a Sony Ericsson W810i, using a wireless application protocol (WAP) connection to access the Internet from the devices. RTs were compared within subjects with those obtained using a Linux-based millisecond-accurate measurement system. Results show that measured RTs were significantly longer on mobile devices, and that overall RTs and distribution of RTs varied across device

Good Learning and Implicit Model Enumeration

MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation

The packing of granular polymer chains

Rigid particles pack into structures, such as sand dunes on the beach, whose overall stability is determined by the average number of contacts between particles. However, when packing spatially extended objects with flexible shapes, additional concepts must be invoked to understand the stability of the resulting structure. Here we study the disordered packing of chains constructed out of flexibly-connected hard spheres. Using X-ray tomography, we find long chains pack into a low-density structure whose mechanical rigidity is mainly provided by the backbone. On compaction, randomly-oriented, semi-rigid loops form along the chain, and the packing of chains can be understood as the jamming of these elements. Finally we uncover close similarities between the packing of chains and the glass transition in polymers.Comment: 11 pages, 4 figure

SBML models and MathSBML

MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation

Validity of the diagnosis of pneumonia in hospitalised patients with COPD.

Rationale: Exacerbations of chronic obstructive pulmonary disease (COPD) and pneumonia are two of the most common reasons for acute hospital admissions. Acute exacerbations and pneumonia present with similar symptoms in COPD patients, representing a diagnostic challenge with a significant impact on patient outcomes. The objectives of this study were to compare the prevalence of radiographic consolidation with the discharge diagnoses of hospitalised COPD patients. Methods: COPD patients admitted to three UK hospitals over a 3-year period were identified. Participants were included if they were admitted with an acute respiratory illness, COPD was confirmed by spirometry and a chest radiograph was performed within 24 h of admission. Pneumonia was defined as consolidation on chest radiograph reviewed by two independent observers. Results: There were 941 admissions in 621 patients included in the final analysis. In 235 admissions, consolidation was present on chest radiography and there were 706 admissions without consolidation. Of the 235 admissions with consolidation, only 42.9% had a discharge diagnosis of pneumonia; 90.7% of patients without consolidation had a discharge diagnosis of COPD exacerbation. The presence of consolidation was associated with increased rate of high-dependency care admission, increased mortality and prolonged length of stay. Inhaled corticosteroid use was associated with recurrent pneumonia. Conclusions: Pneumonia is underdiagnosed in patients with COPD. Radiographic consolidation is associated with worse outcomes and prolonged length of stay. Incorrect diagnosis could result in inappropriate use of inhaled corticosteroids. Future guidelines should specifically address the diagnosis and management of pneumonia in COPD

Millisecond accuracy video display using OpenGL under Linux

To measure people’s reaction times to the nearest millisecond, it is necessary to know exactly when a stimulus is displayed. This article describes how to display stimuli with millisecond accuracy on a normal CRT monitor, using a PC running Linux. A simple C program is presented to illustrate how this may be done within X Windows using the OpenGL rendering system. A test of this system is reported that demonstrates that stimuli may be consistently displayed with millisecond accuracy. An algorithm is presented that allows the exact time of stimulus presentation to be deduced, even if there are relatively large errors in measuring the display time

A PC parallel port button box provides millisecond response time accuracy under Linux

For psychologists, it is sometimes necessary to measure people's reaction times to the nearest millisecond. This article describes how to use the PC parallel port to receive signals from a button box to achieve millisecond response time accuracy. The workings of the parallel port, the corresponding port addresses, and a simple Linux program for controlling the port are described. A test of the speed and reliability of button box signal detection is reported. If the reader is moderately familiar with Linux, this article should provide sufficient instruction for him or her to build and test his or her own parallel port button box. This article also describes how the parallel port could be used to control an external apparatus

Intra-alveolar neutrophil-derived microvesicles are associated with disease severity in COPD

Despite advances in the pathophysiology of Chronic Obstructive Pulmonary Disease (COPD), there is a distinct lack of biochemical markers to aid clinical management. Microvesicles (MVs) have been implicated in the pathophysiology of inflammatory diseases including COPD but their association to COPD disease severity remains unknown. We analysed different MV populations in plasma and bronchoalveolar lavage fluid (BALF) taken from sixty-two patients with mild to very severe COPD (51% male; mean age: 65.9 years). These patients underwent comprehensive clinical evaluation (symptom scores, lung function, exercise testing) and the capacity of MVs to be clinical markers of disease severity was assessed. We successfully identified various MV subtype populations within BALF (leukocyte, PMN (polymorphonuclear leukocyte i.e. neutrophil), monocyte, epithelial and platelet MVs) and plasma (leukocyte, PMN, monocyte and endothelial MVs), and compared each MV population to disease severity. BALF neutrophil MVs were the only population to significantly correlate with the clinical evaluation scores including FEV1, mMRC dyspnoea score, 6-minute walk test, hyperinflation and gas transfer. BALF neutrophil MVs, but not neutrophil cell numbers, also strongly correlated with BODE index. We have undertaken, for the first time, a comprehensive evaluation of MV profiles within BALF/plasma of COPD patients. We demonstrate that BALF levels of neutrophil-derived MVs are unique in correlating with a number of key functional and clinically-relevant disease severity indices. Our results show the potential of BALF neutrophil MVs for a COPD biomarker that tightly links a key pathophysiological mechanism of COPD (intra-alveolar neutrophil activation) with clinical severity/outcome