IVA: accurate de novo assembly of RNA virus genomes

Motivation: An accurate genome assembly from short read sequencing data is critical for downstream analysis, for example allowing investigation of variants within a sequenced population. However, assembling sequencing data from virus samples, especially RNA viruses, into a genome sequence is challenging due to the combination of viral population diversity and extremely uneven read depth caused by amplification bias in the inevitable reverse transcription and polymerase chain reaction amplification process of current methods.

Results: We developed a new de novo assembler called IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples from human immunodeficiency virus-1 or influenza-virus-infected people and demonstrated that IVA outperforms all other virus de novo assemblers.

Availability and implementation: The software runs under Linux, has the GPLv3 licence and is freely available from http://sanger-pathogens.github.io/iva

Contact:iva@sanger.ac.uk

Supplementary information:Supplementary data are available at Bioinformatics online.

Influence of beliefs about heart rate and actual heart rate on heartbeat counting

The heartbeat counting task is used widely to assess the ability to perceive cardiac sensations. However, performance on this task may be determined by processes other than sensitivity to cardiac stimuli. Beliefs about the effects of postural and exercise challenges on heart rate were assessed by questionnaire prior to performing the heartbeat counting task, and then actual heart rate was manipulated during the counting task by changes in posture and exercise. On average, counted heart rates were closer to beliefs about heart rate than to actual heart rate. Hierarchical multiple regression analyses indicated that (a) believed heart rates predicted counted heart rates while controlling for actual heart rates and (b) actual heart rates also predicted counted heart rate while controlling for heart rate beliefs. These data suggest that the rate of heartbeat counting is influenced by beliefs about heart rate and by the processing of cardiac sensations.

A method of constant stimuli for examining heartbeat detection: comparison with the Brener-Kluvitse and Whitehead methods

A method of constant stimuli (MCS) for measuring heartbeat detection was examined by comparing performance on this method with the Brener and Kluvitse (BK) method and a variant of the Whitehead (WH') method. All methods required subjects to judge the simultaneity of heartbeat sensations and tones, and each yielded measures of judgment precision and of the temporal location of heartbeat sensations relative to the electrocardiogram R-wave. Both measures were found to be significantly correlated across tasks. A greater proportion of subjects met criteria for classification as heartbeat detectors on the MCS (54%) and BK (50%) tasks than on the WH' task (33%). In the MCS and BK tasks, subjects judged tones presented 100-300 ms after the R-wave to be most simultaneous with heartbeat sensations. Intratask correlations showed that only the MCS procedure yielded stable measurements of both judgment precision and temporal location. The MCS procedure possesses commendable psychometric properties and provides a simpler means than the BK procedure of examining heartbeat detection.

The temporal locations of heartbeat sensations

This experiment examined individual differences in the temporal location of heartbeat sensations and the reliability of their detection. Following practice on a familiarization task in judging light-tone simultaneity, 50 subjects were studied for two sessions on a heartbeat detection task, which required judging the simultaneity of heartbeat sensations and tones presented at six intervals following the onset of ventricular contraction. Subjects inspected the heartbeat-tone intervals as frequently and for as long as desired before choosing the one in which heartbeat sensations and tones were most simultaneous. The temporal locations of heartbeat sensations in subjects classified as "good heartbeat perceivers" (n = 16) ranged from 131 and 363 ms following ventricular contraction (mean = 228 ms). Correlations between the familiarization and heartbeat detection tasks in the accuracy of simultaneity judgments and in the frequency and duration of interval inspections suggest that general perceptual abilities and strategies may underlie success in detecting heartbeat sensations.

Accurate awareness of heartbeat in hypochondriacal and non-hypochondriacal patients

We measured the accurate awareness of resting heartbeat in a sample of medical out-patients meeting DSM-III-R criteria for hypochondriasis (n = 60), and in a comparison group of non-hypochondriacal patients (n = 60) from the same general medical clinic. Patients also completed subjective self-report ratings of their sensitivity to benign bodily sensation and of functional somatic symptoms. Hypochondriacal patients did not differ significantly from non-hypochondriacal patients in their accurate awareness of heartbeat. They did, however, consider themselves more sensitive to benign bodily sensation and report more functional somatic symptoms. Within each sample, the only statistically significant association found was a negative correlation (r = -0.32, p = 0.025) between heartbeat awareness and the severity of hypochondriacal symptoms among the hypochondriacal patients. These results suggest that hypochondriacs may not be more accurately aware of normal cardiac activity, and therefore that hypochondriacal somatic complaints may not result from an unusually fine discriminative ability to detect normal physiological sensations that non-hypochondriacal individuals do not perceive.

Cardiac stimulus intensity and heartbeat detection: effects of tilt-induced changes in stroke volume

The effects of variations in stroke volume on the intensity of cardiac stimuli was examined in a series of three experiments that employed classical psychophysical methods to assess heartbeat detection. Stroke volume was manipulated by passive body tilt and recorded using impedance cardiography while subjects performed heartbeat detection tasks. The postural manipulation generated little or no change in contractility or momentum but did produce substantial changes in stroke volume. However, this potential source of variation in cardiac stimulus magnitude did not influence either the precision of heartbeat detection or the temporal location of heartbeat sensations. It is concluded that the intensity dimension of the heartbeat stimulus is not determined by stroke volume.

Palpitations and cardiac awareness after heart transplantation

OBJECTIVE

The aim of this study was to examine the awareness of resting heartbeat in heart transplantation recipients, compare it with that found in other medical populations, and determine whether clinical characteristics are associated with accurate heartbeat awareness.

METHODS

Eligible patients underwent a research battery consisting of a heartbeat detection task and self-report questionnaires assessing cardiac symptoms, psychosocial variables, and cognitive function. The accurate awareness of resting heartbeat was determined by presenting the patients with auditory stimuli at each of six different delays following the R wave on the ECG. Patients then selected the tones that they thought coincided with the sensation they had of their heart beating. The patients' physicians rated their cardiac morbidity. The results were contrasted with comparable data obtained in previous work with other ambulatory medical populations.

RESULTS

Forty-one consecutive heart transplantation recipients who survived for at least 3 months after surgery were eligible. Thirty-four (82.9%) of them were studied and complete data were obtained on 26 (63.4%). Nine patients (34.6%) were reliably able to detect their resting heartbeat. When compared with the 17 patients who were not accurately aware of their heartbeat, the two groups did not differ significantly in cardiac morbidity, cognitive brain dysfunction, generalized psychiatric distress, depression, somatization, or hypochondriacal attitudes. A significantly higher proportion of heart transplantation recipients were accurately aware of their heartbeat than was found in a sample of general medical outpatients and in asymptomatic, nonpatient volunteers.

CONCLUSIONS

One-third of heart transplant recipients are accurately aware of resting heartbeat, despite the absence of cardiac innervation.

Sensitivity to mechanical stimuli and the role of general sensory and perceptual processes in heartbeat detection

Sensitivity to heartbeat sensations is commonly assessed using tasks that require individuals to judge the simultaneity of heartbeats and tones. In two experiments, we investigated the suitability of this paradigm for examining cardioception. In the first experiment, participants judged the simultaneity of near-threshold vibrations and suprathreshold tones. Precision in judging vibration-tone simultaneity was directly related to the detectability of the mechanical stimuli, thereby supporting use of the simultaneity paradigm to assess heartbeat detection. In the second experiment, we examined the influences of sensitivity to mechanical stimuli and the ability to make intermodality simultaneity judgments on the precision of heartbeat detection. We measured participants' vibrotactile thresholds, precision in judging light-tone simultaneity, and precision in judging heartbeat-tone simultaneity. The ability to judge the simultaneity of lights and tones accounted for 24.3% of the variance in precision of heartbeat detection, and mechanical sensitivity accounted for a further 8.5%.

The perception of cardiac activity in medical outpatients

This study compared several measures of cardiac perception and related them to patient' spontaneous reports of palpitations. One hundred and forty-five ambulatory patients referred for Holter monitoring for the evaluation of palpitations were compared with 70 asymptomatic nonpatients. Reports of palpitations during monitoring were compared with the ECG to determine whether they coincided with an arrhythmia. Subjects also completed a heartbeat detection task to determine whether they were accurately aware of cardiac systole while at rest. 20.7% of palpitation patients and 4.7% of asymptomatic controls demonstrated an accurate awareness of resting heartbeat (p = 0.01). Performance was unrelated to bodily amplification, somatization, hypochondriacal symptoms, ECG findings, or psychiatric morbidity. 34.3% of palpitation patients reported symptoms that consistently coincided with arrhythmias on ECG. These accurate patients had significantly lower levels of amplification, somatization, hypochondriacal symptoms, and psychiatric morbidity. Accuracy of symptom reporting and accuracy of heartbeat awareness were not statistically associated.(ABSTRACT TRUNCATED AT 250 WORDS)

Role of HIV-specific CD8+ T cells in pediatric HIV cure strategies after widespread early viral escape

Recent studies have suggested greater HIV cure potential among infected children than adults. A major obstacle to HIV eradication in adults is that the viral reservoir is largely comprised of HIV-specific cytotoxic T lymphocyte (CTL) escape variants. We here evaluate the potential for CTL in HIV-infected slow-progressor children to play an effective role in "shock-and-kill" cure strategies. Two distinct subgroups of children were identified on the basis of viral load. Unexpectedly, in both groups, as in adults, HIV-specific CTL drove the selection of escape variants across a range of epitopes within the first weeks of infection. However, in HIV-infected children, but not adults, de novo autologous variant-specific CTL responses were generated, enabling the pediatric immune system to "corner" the virus. Thus, even when escape variants are selected in early infection, the capacity in children to generate variant-specific anti-HIV CTL responses maintains the potential for CTL to contribute to effective shock-and-kill cure strategies in pediatric HIV infection.