Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination.

Next-generation sequencing (NGS) is a valuable tool for the detection and quantification of HIV-1 variants in vivo. However, these technologies require detailed characterization and control of artificially induced errors to be applicable for accurate haplotype reconstruction. To investigate the occurrence of substitutions, insertions, and deletions at the individual steps of RT-PCR and NGS, 454 pyrosequencing was performed on amplified and non-amplified HIV-1 genomes. Artificial recombination was explored by mixing five different HIV-1 clonal strains (5-virus-mix) and applying different RT-PCR conditions followed by 454 pyrosequencing. Error rates ranged from 0.04-0.66% and were similar in amplified and non-amplified samples. Discrepancies were observed between forward and reverse reads, indicating that most errors were introduced during the pyrosequencing step. Using the 5-virus-mix, non-optimized, standard RT-PCR conditions introduced artificial recombinants in a fraction of at least 30% of the reads that subsequently led to an underestimation of true haplotype frequencies. We minimized the fraction of recombinants down to 0.9-2.6% by optimized, artifact-reducing RT-PCR conditions. This approach enabled correct haplotype reconstruction and frequency estimations consistent with reference data obtained by single genome amplification. RT-PCR conditions are crucial for correct frequency estimation and analysis of haplotypes in heterogeneous virus populations. We developed an RT-PCR procedure to generate NGS data useful for reliable haplotype reconstruction and quantification.

Why do humans make antisaccade errors?

Antisaccade errors are attributed to failure to inhibit the habitual prosaccade. We investigated whether the amount of information about the required response the patient has before the trial begins also contributes to error rate. Participants performed antisaccades in five conditions. The traditional design had two goals on the left and right horizontal meridians. In the second condition, stimulus-goal confusability between trials was eliminated by displacing one goal upward. In the third, hemifield uncertainty was eliminated by placing both goals in the same hemifield. In the fourth, goal uncertainty was eliminated by having only one goal, but interspersed with no-go trials. The fifth condition eliminated all uncertainty by having the same goal on every trial. Antisaccade error rate increased by 2% with each additional source of uncertainty, with the main effect being hemifield information, and a trend for stimulus-goal confusability. A control experiment for the effects of increasing angular separation between targets without changing these types of prior response information showed no effects on latency or error rate. We conclude that other factors besides prosaccade inhibition contribute to antisaccade error rates in traditional designs, possibly by modulating the strength of goal activation.

Trial history biases the spatial programming of antisaccades

The historical context in which saccades are made influences their latency and error rates, but less is known about how context influences their spatial parameters. We recently described a novel spatial bias for antisaccades, in which the endpoints of these responses deviate towards alternative goal locations used in the same experimental block, and showed that expectancy (prior probability) is at least partly responsible for this 'alternate-goal bias'. In this report we asked whether trial history also plays a role. Subjects performed antisaccades to a stimulus randomly located on the horizontal meridian, on a 40° angle downwards from the horizontal meridian, or on a 40° upward angle, with all three locations equally probable on any given trial. We found that the endpoints of antisaccades were significantly displaced towards the goal location of not only the immediately preceding trial (n - 1) but also the penultimate (n - 2) trial. Furthermore, this bias was mainly present for antisaccades with a short latency of <250 ms and was rapidly corrected by secondary saccades. We conclude that the location of recent antisaccades biases the spatial programming of upcoming antisaccades, that this historical effect persists over many seconds, and that it influences mainly rapidly generated eye movements. Because corrective saccades eliminate the historical bias, we suggest that the bias arises in processes generating the response vector, rather than processes generating the perceptual estimate of goal location.

Reduced perception of the motion-induced blindness illusion in schizophrenia

Motion-induced blindness (MIB) occurs when target stimuli are presented together with a moving distractor pattern. Most observers experience the targets disappearing and reappearing repeatedly for periods of up to several seconds. MIB can be viewed as a striking marker for the organization of cognitive functioning. In the present study, MIB rates and durations were assessed in 34 schizophrenia-spectrum disorder patients and matched controls. The results showed that positive symptoms and excitement enhanced MIB, whereas depression and negative symptoms attenuated the illusion. MIB was more frequently found in normal subjects. The results remained consistent after adjusting for reaction time and error rates. Hence, MIB may provide a valid and reliable measure of cognitive organization in schizophrenia.

Visual exploration in Parkinson's disease and Parkinson's disease dementia

Parkinson's disease, typically thought of as a movement disorder, is increasingly recognized as causing cognitive impairment and dementia. Eye movement abnormalities are also described, including impairment of rapid eye movements (saccades) and the fixations interspersed between them. Such movements are under the influence of cortical and subcortical networks commonly targeted by the neurodegeneration seen in Parkinson's disease and, as such, may provide a marker for cognitive decline. This study examined the error rates and visual exploration strategies of subjects with Parkinson's disease, with and without cognitive impairment, whilst performing a battery of visuo-cognitive tasks. Error rates were significantly higher in those Parkinson's disease groups with either mild cognitive impairment (P = 0.001) or dementia (P < 0.001), than in cognitively normal subjects with Parkinson's disease. When compared with cognitively normal subjects with Parkinson's disease, exploration strategy, as measured by a number of eye tracking variables, was least efficient in the dementia group but was also affected in those subjects with Parkinson's disease with mild cognitive impairment. When compared with control subjects and cognitively normal subjects with Parkinson's disease, saccade amplitudes were significantly reduced in the groups with mild cognitive impairment or dementia. Fixation duration was longer in all Parkinson's disease groups compared with healthy control subjects but was longest for cognitively impaired Parkinson's disease groups. The strongest predictor of average fixation duration was disease severity. Analysing only data from the most complex task, with the highest error rates, both cognitive impairment and disease severity contributed to a predictive model for fixation duration [F(2,76) = 12.52, P ≤ 0.001], but medication dose did not (r = 0.18, n = 78, P = 0.098, not significant). This study highlights the potential use of exploration strategy measures as a marker of cognitive decline in Parkinson's disease and reveals the efficiency by which fixations and saccades are deployed in the build-up to a cognitive response, rather than merely focusing on the outcome itself. The prolongation of fixation duration, present to a small but significant degree even in cognitively normal subjects with Parkinson's disease, suggests a disease-specific impact on the networks directing visual exploration, although the study also highlights the multi-factorial nature of changes in exploration and the significant impact of cognitive decline on efficiency of visual search.

Traffic-Adaptive and Link-Quality-Aware Communication in Wireless Sensor Networks

This paper is a summary of the main contribu- tions of the PhD thesis published in [1]. The main research contributions of the thesis are driven by the research question how to design simple, yet efficient and robust run-time adaptive resource allocation schemes within the commu- nication stack of Wireless Sensor Network (WSN) nodes. The thesis addresses several problem domains with con- tributions on different layers of the WSN communication stack. The main contributions can be summarized as follows: First, a a novel run-time adaptive MAC protocol is intro- duced, which stepwise allocates the power-hungry radio interface in an on-demand manner when the encountered traffic load requires it. Second, the thesis outlines a metho- dology for robust, reliable and accurate software-based energy-estimation, which is calculated at network run- time on the sensor node itself. Third, the thesis evaluates several Forward Error Correction (FEC) strategies to adap- tively allocate the correctional power of Error Correcting Codes (ECCs) to cope with timely and spatially variable bit error rates. Fourth, in the context of TCP-based communi- cations in WSNs, the thesis evaluates distributed caching and local retransmission strategies to overcome the perfor- mance degrading effects of packet corruption and trans- mission failures when transmitting data over multiple hops. The performance of all developed protocols are eval- uated on a self-developed real-world WSN testbed and achieve superior performance over selected existing ap- proaches, especially where traffic load and channel condi- tions are suspect to rapid variations over time.

Models for intensive care training. A European perspective.

The diversity of European culture is reflected in its healthcare training programs. In intensive care medicine (ICM), the differences in national training programs were so marked that it was unlikely that they could produce specialists of equivalent skills. The Competency-Based Training in Intensive Care Medicine in Europe (CoBaTrICE) program was established in 2003 as a Europe-based worldwide collaboration of national training organizations to create core competencies for ICM using consensus methodologies to establish common ground. The group's professional and research ethos created a social identity that facilitated change. The program was easily adaptable to different training structures and incorporated the voice of patients and relatives. The CoBaTrICE program has now been adopted by 15 European countries, with another 12 countries planning to adopt the training program, and is currently available in nine languages, including English. ICM is now recognized as a primary specialty in Spain, Switzerland, and the UK. There are still wide variations in structures and processes of training in ICM across Europe, although there has been agreement on a set of common program standards. The combination of a common "product specification" for an intensivist, combined with persisting variation in the educational context in which competencies are delivered, provides a rich source of research inquiry. Pedagogic research in ICM could usefully focus on the interplay between educational interventions, healthcare systems and delivery, and patient outcomes, such as including whether competency-based program are associated with lower error rates, whether communication skills training is associated with greater patient and family satisfaction, how multisource feedback might best be used to improve reflective learning and teamworking, or whether increasing the proportion of specialists trained in acute care in the hospital at weekends results in better patient outcomes.

Influence of credibility, warnings, and source-monitoring questions on the misinformation effect.

Introduction. Erroneous answers in studies on the misinformation effect (ME) can be reduced in different ways. In some studies, ME was reduced by SM questions, warnings, or a low credibility of the source of post-event information (PEI). Results are inconsistent, however. Of course, a participant can deliberately decide to refrain from reporting a critical item only when the difference between the original event and the PEI is distinguishable in principle. We were interested in the question to what extent the influence of erroneous information on a central aspect of the original event can be reduced by different means applied singly or in combination. Method. With a 2 (credibility; high vs. low) x 2 (warning; present vs. absent) between subjects design and an additional control group that received neither misinformation nor a warning (N = 116), we examined the above-mentioned factors’ influence on the ME. Participants viewed a short video of a robbery. The critical item suggested in the PEI was that the victim was given a kick by the perpetrator (which he was actually not). The memory test consisted of a two-forced-choice recognition test followed by a SM test. Results. To our surprise, neither a main effect of erroneous PEI nor a main effect of credibility was found. The error rates for the critical item in the control group (50%) as well as in the high (65%) and low (52%) credibility condition without warning did not significantly differ. A warning about possible misleading information in the PEI significantly reduced the influence of misinformation in both credibility conditions by 32-37%. Using a SM question significantly reduced the error rate too, but only in the high credibility no warning condition. Conclusion and Future Research. Our results show that, contrary to a warning or the use of a SM question, low source credibility did not reduce the ME. The most striking finding was, however, the absence of a main effect of erroneous PEI. Due to the high error rate in the control group, we suspect that the wrong answers might have been caused either by the response format (recognition test) or by autosuggestion possibly promoted by the high schema-consistency of the critical item. First results of a post-study in which we used open-ended questions before the recognition test support the former assumption. Results of a replication of this study using open-ended questions prior to the recognition test will be available by June.

Cue Recognition and Integration - Eye Tracking Evidence of Processing Differences in Sentence Comprehension in Aphasia

PURPOSE: We aimed at further elucidating whether aphasic patients' difficulties in understanding non-canonical sentence structures, such as Passive or Object-Verb-Subject sentences, can be attributed to impaired morphosyntactic cue recognition, and to problems in integrating competing interpretations. METHODS: A sentence-picture matching task with canonical and non-canonical spoken sentences was performed using concurrent eye tracking. Accuracy, reaction time, and eye tracking data (fixations) of 50 healthy subjects and 12 aphasic patients were analysed. RESULTS: Patients showed increased error rates and reaction times, as well as delayed fixation preferences for target pictures in non-canonical sentences. Patients' fixation patterns differed from healthy controls and revealed deficits in recognizing and immediately integrating morphosyntactic cues. CONCLUSION: Our study corroborates the notion that difficulties in understanding syntactically complex sentences are attributable to a processing deficit encompassing delayed and therefore impaired recognition and integration of cues, as well as increased competition between interpretations.