Auditory presentation and synchronization in Adobe Flash and HTML5/JavaScript Web experiments

Substantial recent research has examined the accuracy of presentation durations and response time measurements for visually presented stimuli in Web-based experiments, with a general conclusion that accuracy is acceptable for most kinds of experiments. However, many areas of behavioral research use auditory stimuli instead of, or in addition to, visual stimuli. Much less is known about auditory accuracy using standard Web-based testing procedures. We used a millisecond-accurate Black Box Toolkit to measure the actual durations of auditory stimuli and the synchronization of auditory and visual presentation onsets. We examined the distribution of timings for 100 presentations of auditory and visual stimuli across two computers with difference specs, three commonly used browsers, and code written in either Adobe Flash or JavaScript. We also examined different coding options for attempting to synchronize the auditory and visual onsets. Overall, we found that auditory durations were very consistent, but that the lags between visual and auditory onsets varied substantially across browsers and computer systems

Integrable boundaries in AdS/CFT: revisiting the Z=0 giant graviton and D7-brane

We consider the worldsheet boundary scattering and the corresponding boundary algebras for the Z=0 giant graviton and the Z=0 D7-brane in the AdS/CFT correspondence. We consider two approaches to the boundary scattering, the usual one governed by the (generalized) twisted Yangians and the q-deformed model of these boundaries governed by the quantum affine coideal subalgebras. We show that the q-deformed approach leads to boundary algebras that are of a more compact form than the corresponding twisted Yangians, and thus are favourable to use for explicit calculations. We obtain the q-deformed reflection matrices for both boundaries which in the q->1 limit specialize to the ones obtained using twisted Yangians.Comment: 36 pages. v2: minor typos corrected, references updated; v3: published versio

A randomized trial of mailed questionnaires versus telephone interviews: Response patterns in a survey

<p>Abstract</p> <p>Background</p> <p>Data for health surveys are often collected using either mailed questionnaires, telephone interviews or a combination. Mode of data collection can affect the propensity to refuse to respond and result in different patterns of responses. The objective of this paper is to examine and quantify effects of mode of data collection in health surveys.</p> <p>Methods</p> <p>A stratified sample of 4,000 adults residing in Denmark was randomised to mailed questionnaires or computer-assisted telephone interviews. 45 health-related items were analyzed; four concerning behaviour and 41 concerning self assessment. Odds ratios for more positive answers and more frequent use of extreme response categories (both positive and negative) among telephone respondents compared to questionnaire respondents were estimated. Tests were Bonferroni corrected.</p> <p>Results</p> <p>For the four health behaviour items there were no significant differences in the response patterns. For 32 of the 41 health self assessment items the response pattern was statistically significantly different and extreme response categories were used more frequently among telephone respondents (Median estimated odds ratio: 1.67). For a majority of these mode sensitive items (26/32), a more positive reporting was observed among telephone respondents (Median estimated odds ratio: 1.73). The overall response rate was similar among persons randomly assigned to questionnaires (58.1%) and to telephone interviews (56.2%). A differential nonresponse bias for age and gender was observed. The rate of missing responses was higher for questionnaires (0.73 – 6.00%) than for telephone interviews (0 – 0.51%). The "don't know" option was used more often by mail respondents (10 – 24%) than by telephone respondents (2 – 4%).</p> <p>Conclusion</p> <p>The mode of data collection affects the reporting of self assessed health items substantially. In epidemiological studies, the method effect may be as large as the effects under investigation. Caution is needed when comparing prevalences across surveys or when studying time trends.</p

Anterior ankle arthroscopy, distraction or dorsiflexion?

Anterior ankle arthroscopy can basically be performed by two different methods; the dorsiflexion- or distraction method. The objective of this study was to determine the size of the anterior working area for both the dorsiflexion and distraction method. The anterior working area is anteriorly limited by the overlying anatomy which includes the neurovascular bundle. We hypothesize that in ankle dorsiflexion the anterior neurovascular bundle will move away anteriorly from the ankle joint, whereas in ankle distraction the anterior neurovascular bundle is pulled tight towards the joint, thereby decreasing the safe anterior working area. Six fresh frozen ankle specimens, amputated above the knee, were scanned with computed tomography. Prior to scanning the anterior tibial artery was injected with contrast fluid and subsequently each ankle was scanned both in ankle dorsiflexion and in distraction. A special device was developed to reproducibly obtain ankle dorsiflexion and distraction in the computed tomography scanner. The distance between the anterior border of the inferior tibial articular facet and the posterior border of the anterior tibial artery was measured. The median distance from the anterior border of the inferior tibial articular facet to the posterior border of the anterior tibial artery in ankle dorsiflexion and distraction was 0.9 cm (range 0.7–1.5) and 0.7 cm (range 0.5–0.8), respectively. The distance in ankle dorsiflexion significantly exceeded the distance in ankle distraction (P = 0.03). The current study shows a significantly increased distance between the anterior distal tibia and the overlying anterior neurovascular bundle with the ankle in a slightly dorsiflexed position as compared to the distracted ankle position. We thereby conclude that the distracted ankle position puts the neurovascular structures more at risk for iatrogenic damage when performing anterior ankle arthroscopy

X-ray Structures of the Signal Recognition Particle Receptor Reveal Targeting Cycle Intermediates

The signal recognition particle (SRP) and its conjugate receptor (SR) mediate cotranslational targeting of a subclass of proteins destined for secretion to the endoplasmic reticulum membrane in eukaryotes or to the plasma membrane in prokaryotes. Conserved active site residues in the GTPase domains of both SRP and SR mediate discrete conformational changes during formation and dissociation of the SRP·SR complex. Here, we describe structures of the prokaryotic SR, FtsY, as an apo protein and in two different complexes with a non-hydrolysable GTP analog (GMPPNP). These structures reveal intermediate conformations of FtsY containing GMPPNP and explain how the conserved active site residues position the nucleotide into a non-catalytic conformation. The basis for the lower specificity of binding of nucleotide in FtsY prior to heterodimerization with the SRP conjugate Ffh is also shown. We propose that these structural changes represent discrete conformational states assumed by FtsY during targeting complex formation and dissociation

Risk factors and prognosis of young stroke. The FUTURE study: A prospective cohort study. Study rationale and protocol

Contains fulltext : 98322.pdf (postprint version ) (Open Access)BACKGROUND: Young stroke can have devastating consequences with respect to quality of life, the ability to work, plan or run a family, and participate in social life. Better insight into risk factors and the long-term prognosis is extremely important, especially in young stroke patients with a life expectancy of decades. To date, detailed information on risk factors and the long-term prognosis in young stroke patients, and more specific risk of mortality or recurrent vascular events, remains scarce. METHODS/DESIGN: The FUTURE study is a prospective cohort study on risk factors and prognosis of young ischemic and hemorrhagic stroke among 1006 patients, aged 18-50 years, included in our study database between 1-1-1980 and 1-11-2010. Follow-up visits at our research centre take place from the end of 2009 until the end of 2011. Control subjects will be recruited among the patients' spouses, relatives or social environment. Information on mortality and incident vascular events will be retrieved via structured questionnaires. In addition, participants are invited to the research centre to undergo an extensive sub study including MRI. DISCUSSION: The FUTURE study has the potential to make an important contribution to increase the knowledge on risk factors and long-term prognosis in young stroke patients. Our study differs from previous studies by having a maximal follow-up of more than 30 years, including not only TIA and ischemic stroke but also hemorrhagic stroke, the addition of healthy controls and prospectively collect data during an extensive follow-up visit. Completion of the FUTURE study may provide better information for treating physicians and patients with respect to the prognosis of young stroke.8 p

Profiling allele-specific gene expression in brains from individuals with autism spectrum disorder reveals preferential minor allele usage.

One fundamental but understudied mechanism of gene regulation in disease is allele-specific expression (ASE), the preferential expression of one allele. We leveraged RNA-sequencing data from human brain to assess ASE in autism spectrum disorder (ASD). When ASE is observed in ASD, the allele with lower population frequency (minor allele) is preferentially more highly expressed than the major allele, opposite to the canonical pattern. Importantly, genes showing ASE in ASD are enriched in those downregulated in ASD postmortem brains and in genes harboring de novo mutations in ASD. Two regions, 14q32 and 15q11, containing all known orphan C/D box small nucleolar RNAs (snoRNAs), are particularly enriched in shifts to higher minor allele expression. We demonstrate that this allele shifting enhances snoRNA-targeted splicing changes in ASD-related target genes in idiopathic ASD and 15q11-q13 duplication syndrome. Together, these results implicate allelic imbalance and dysregulation of orphan C/D box snoRNAs in ASD pathogenesis

Biophysical Studies of the Membrane-Embedded and Cytoplasmic Forms of the Glucose-Specific Enzyme II of the E. coli Phosphotransferase System (PTS)

The glucose Enzyme II transporter complex of the Escherichia coli phosphotransferase system (PTS) exists in at least two physically distinct forms: a membrane-integrated dimeric form, and a cytoplasmic monomeric form, but little is known about the physical states of these enzyme forms. Six approaches were used to evaluate protein-protein and protein-lipid interactions in this system. Fluorescence energy transfer (FRET) using MBP-IIGlc-YFP and MBP-IIGlc-CFP revealed that the homodimeric Enzyme II complex in cell membranes is stable (FRET-) but can be dissociated and reassociated to the heterodimer only in the presence of Triton X100 (FRET+). The monomeric species could form a heterodimeric species (FRET+) by incubation and purification without detergent exposure. Formaldehyde cross linking studies, conducted both in vivo and in vitro, revealed that the dimeric MBP-IIGlc activity decreased dramatically with increasing formaldehyde concentrations due to both aggregation and activity loss, but that the monomeric MBP-IIGlc retained activity more effectively in response to the same formaldehyde treatments, and little or no aggregation was observed. Electron microscopy of MBP-IIGlc indicated that the dimeric form is larger than the monomeric form. Dynamic light scattering confirmed this conclusion and provided quantitation. NMR analyses provided strong evidence that the dimeric form is present primarily in a lipid bilayer while the monomeric form is present as micelles. Finally, lipid analyses of the different fractions revealed that the three lipid species (PE, PG and CL) are present in all fractions, but the monomeric micellar structure contains a higher percentage of anionic lipids (PG & CL) while the dimeric bilayer form has a higher percentage of zwitterion lipids (PE). Additionally, evidence for a minor dimeric micellar species, possibly an intermediate between the monomeric micellar and the dimeric bilayer forms, is presented. These results provide convincing evidence for interconvertible physical forms of Enzyme-IIGlc

High-resolution analysis of HLA class I alterations in colorectal cancer

BACKGROUND: Previous studies indicate that alterations in Human Leukocyte Antigen (HLA) class I expression are frequent in colorectal tumors. This would suggest serious limitations for immunotherapy-based strategies involving T-cell recognition. Distinct patterns of HLA surface expression might conceal different immune escape mechanisms employed by the tumors and are worth further study. METHOD: We applied four-color multiparameter flow cytometry (FCM), using a large panel of alloantigen-specific anti-HLA-A and -B monoclonal antibodies, to study membranous expression of individual HLA alleles in freshly isolated colorectal cancer cell suspensions from 21 patients. RESULTS: Alterations in HLA class I phenotype were observed in 8 (38%) of the 21 tumors and comprised loss of a single A or B alleles in 4 cases, and loss of all four A and B alleles in the other 4 cases. Seven of these 8 tumors were located on the right side of the colon, and those showing loss of both HLA-A and -B membranous expression were all of the MSI-H phenotype. CONCLUSION: FCM allows the discrimination of complex phenotypes related to the expression of HLA class I. The different patterns of HLA class I expression might underlie different tumor behavior and influence the success rate of immunotherapy