The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation.

MOTIVATION: Pangenomes provide novel insights for population and quantitative genetics, genomics and breeding not available from studying a single reference genome. Instead, a species is better represented by a pangenome or collection of genomes. Unfortunately, managing and using pangenomes for genomically diverse species is computationally and practically challenging. We developed a trellis graph representation anchored to the reference genome that represents most pangenomes well and can be used to impute complete genomes from low density sequence or variant data. RESULTS: The Practical Haplotype Graph (PHG) is a pangenome pipeline, database (PostGRES & SQLite), data model (Java, Kotlin or R) and Breeding API (BrAPI) web service. The PHG has already been able to accurately represent diversity in four major crops including maize, one of the most genomically diverse species, with up to 1000-fold data compression. Using simulated data, we show that, at even 0.1× coverage, with appropriate reads and sequence alignment, imputation results in extremely accurate haplotype reconstruction. The PHG is a platform and environment for the understanding and application of genomic diversity. AVAILABILITY AND IMPLEMENTATION: All resources listed here are freely available. The PHG Docker used to generate the simulation results is https://hub.docker.com/ as maizegenetics/phg:0.0.27. PHG source code is at https://bitbucket.org/bucklerlab/practicalhaplotypegraph/src/master/. The code used for the analysis of simulated data is at https://bitbucket.org/bucklerlab/phg-manuscript/src/master/. The PHG database of NAM parent haplotypes is in the CyVerse data store (https://de.cyverse.org/de/) and named/iplant/home/shared/panzea/panGenome/PHG_db_maize/phg_v5Assemblies_20200608.db. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Development and feasibility of quantitative dynamic cardiac imaging for mice using µSPECT.

BACKGROUND: Despite growing interest in coronary microvascular disease (CMVD), there is a dearth of mechanistic understanding. Mouse models offer opportunities to understand molecular processes in CMVD. We have sought to develop quantitative mouse imaging to assess coronary microvascular function. METHODS: We used 99mTc-sestamibi to measure myocardial blood flow in mice with MILabs U-SPECT+ system. We determined recovery and crosstalk coefficients, the influx rate constant from blood to myocardium (K1), and, using microsphere perfusion, constraints on the extraction fraction curve. We used 99mTc and stannous pyrophosphate for red blood cell imaging to measure intramyocardial blood volume (IMBV) as an alternate measure of microvascular function. RESULTS: The recovery coefficients for myocardial tissue (RT) and left ventricular arterial blood (RA) were 0.81 ± 0.16 and 1.07 ± 0.12, respectively. The assumption RT = 1 - FBV (fraction blood volume) does not hold in mice. Using a complete mixing matrix to fit a one-compartment model, we measured K1 of 0.57 ± 0.08 min-1. Constraints on the extraction fraction curve for 99mTc-sestamibi in mice for best-fit Renkin-Crone parameters were α = 0.99 and ß = 0.39. Additionally, we found that wild-type mice increase their IMBV by 22.9 ± 3.3% under hyperemic conditions. CONCLUSIONS: We have developed a framework for measuring K1 and change in IMBV in mice, demonstrating non-invasive µSPECT-based quantitative imaging of mouse microvascular function.

Determining the effect of cardiac blood volume on accuracy of uptake rate constants by simulation.

Objective. There is great interest in better understanding coronary microvascular disease using mouse models. Typical quantification requires dynamic imaging to estimate the rate constantK1of the tracer moving from the blood into the myocardium. In addition toK1, it is also desirable to determine blood volume fractionV, which if known allows for more accurate fitting ofK1. Our previously published kinetic modeling software did not consider the effect ofV. To ensure a better fit of experimental data to the model for myocardialµSPECT imaging, in this work we updated our kinetic modeling software to include a blood volume fractionV, which adds a fraction of the arterial activity concentration into the tissue concentration.Approach. The tissue and blood time-activity curves (TACs) used for fit input were generated using ideal equations with known values in MATLAB. This allowed post-fit results to be compared to known values to determine fit errors. Parameters that were varied in generating the TACs included blood volume fraction (0, 0.05, 0.1, 0.2 and 0.3),K1(0.5, 1.5, 2.5 ml min-1g-1), frame length (1, 2, 5, 10, 15, 20 s), FWHM of the input Gaussian (10, 20, 40 s), and time of the injection peak relative to frame duration. Blood volume-fraction results have low error when blood volume is lowest, but results worsen as frame length andK1increase.Main results. We demonstrated that blood volume can be accurately determined, and also show how fit accuracy varies across TACs with different input properties.Significance. This information allows for robust use of the fitting algorithm and aids in understanding fit performance when used in animal studies.

Anabolic steroid: effects on strength development.

Twelve matched pairs of subjects, fed a high protein diet, were trained with weights for 6 weeks. In the final 3 weeks twelve subjects received 5 milligrams of methandrostenolone (Dianabol) twice daily. Maximum weight lifting, thickness of skin folds, oxygen uptake, blood chemistry profile, and concentration of blood lipids were determined. Also used were cable tensiometry and anthropometric measurements. The strength of treated subjects increased significantly; their mean weight gain was 2.48 kilograms with no significant change in skin fold thickness. Several anthropometric measurements increased significantly, as did oxygen uptake ability and nitrogen retention by the blood.

Bispectrum analysis of electroencephalogram signals during waking and sleeping.

The degree of interaction of component waves making up a single electroencephalogram trace was strongly correlated with alpha activity, lead placement, and state of consciousness. Significant quadratic coupling of the waves was found only for awake subjects with high alpha activity. For these subjects about 50 percent of beta activity can be attributed to harmonic coupling with the alpha peak. During sleep, the degree of interaction was of borderline significance and did not follow a consistent pattern with respect to subject, frequency, state, or lead.

Human growth hormone release: relation to slow-wave sleep and sleep-walking cycles.

Release of human growth hormone during sleep is significantly related to slow, synchronized stages of sleep and therefore would seem to be controlled by related neural mechanisms. When sleep-waking cycles are reversed by 12 hours, the release of growth hormone with sleep is reversed; thus release does not follow an inherent circadian rhythm independent of sleep.

Ecological genomics: understanding gene and genome function in the natural environment.

The field of ecological genomics seeks to understand the genetic mechanisms underlying responses of organisms to their natural environments. This is being achieved through the application of functional genomic approaches to identify and characterize genes with ecological and evolutionary relevance. By its very nature, ecological genomics is an interdisciplinary field. In this review, we consider the significance of this new area of study from both an ecological and genomic perspective using examples from the recent literature. We submit that by considering more fully an ecological context, researchers may gain additional insights into the underlying genetic basis of ecologically relevant phenotypic variation. Likewise, genomic approaches are beginning to offer new insights into higher-level biological phenomena that previously occupied the realm of ecological investigation only. We discuss various approaches that are likely to be useful in ecological genomic studies and offer thoughts on where this field is headed in the future.

Effect of pinhole shape on projection resolution.

We are designing a dual-resolution pre-clinical SPECT system based on square-pinhole apertures for use in applications with a small field-of-view (FOV), such as cardiac imaging of mice. Square pinholes allow for increased sensitivity due to more efficient projection tiling on the detector compared to circular pinholes. Aperture fabrication techniques cannot produce a perfect square, giving the square pinholes some amount of roundedness at the corners. This work investigates how this roundedness affects the physical properties of projection images in terms of spatial resolution. Different pinhole full-acceptance angles and roundedness values were simulated. To facilitate a fair comparison, properties of the non-square pinholes were manipulated to yield pinholes with approximately the same sensitivity (to within 0.1%) and FOV (to within 0.5%) as those of the square pinholes, subsequently referred to as matched apertures. The aperture size (flat-to-flat edge length) of each non-square aperture was increased until its sensitivity was approximately equal to that of the square pinhole. Next, the full acceptance angle was increased until the FOV of each non-square aperture was approximately equivalent to that of the square pinhole. Sensitivity was calculated to include both the geometric and penetrative sensitivity of a point source, as well as the packing faction of the multi-pinhole collimator. Using the sensitivity-matched and FOV-matched apertures, spatial resolution was estimated. For the 0.3 mm, 0.5 mm, and 1 mm edge-length square apertures studied, the full-width at half-maximum widened as pinhole shape changed from square to circle, while full-width tenth-maximum showed little change. These results indicate that a perfect square pinhole shape is more desirable than a rounded-square pinhole with regard to spatial resolution when sensitivity and FOV-matched pinholes are compared.

The REM cycle is a sleep-dependent rhythm.

Two studies, using data from fragmented sleep studies from three sleep laboratories, are reviewed. These studies indicate that the REM cycle is primarily governed by a sleep-dependent oscillator. These data, however, do not rule out the potential influence of endogenous or environmental variables as factors influencing the REM cycle. Further, acceptance of the REM cycle as a sleep-dependent rhythm does not lead to the denial of the basic rest-activity cycle (BRAC) proposed by Kleitman. It is questioned, however, whether the BRAC measured during waking is an extension of the REM cycle recorded during sleep.

Relationship of arousal threshold to sleep stage distribution and subjective estimates of depth and quality of sleep.

The relationship of arousal threshold, amounts of various sleep stages, and subjective rating of sleep was studied in two separate experiments involving 7 and 26 young adult subjects, respectively. Electroencephalographic sleep stage data, subjective response data, and arousal threshold data were collected over a series of nights in the sleep laboratory. Only nonsignificant relationships were found between magnitude of arousal threshold and amounts of various sleep stages or subjective rating of sleep quality in between-subjects analyses. However, when the nights representing extremes in arousal threshold were examined within-subject, it was found that nights of high threshold were accompanied by subjective reports of significantly better sleep in both studies and by a significant decrease in the amount of stage W in one study. Arousal threshold was not related to subjective depth of sleep in either study. Rather, subjective ratings of depth of sleep were significantly related to the amount of EEG-defined wakefulness and stage 1.

Benzodiazepine hypnotics increase heart rate during sleep.

The cardiovascular effects of benzodiazepines administered intravenously as preoperative sedatives have received considerable study, but sleep laboratory research on benzodiazepines administered orally as hypnotics has not focused on assessment of cardiovascular changes. Analysis of heart rate (HR) data collected in sleep laboratory studies on the effects of 0.5 mg of triazolam (Halcion) and 30 mg of flurazepam (Dalmane) demonstrated that both benzodiazepine hypnotics produced a significant HR elevation that was present for up to 4 h during sleep. By the 3rd night of bedtime administration of triazolam, the HR increase was no longer statistically significant, but on the 5th night of flurazepam administration, HR was still significantly elevated over baseline levels. The HR elevation does not appear to be of clinical significance for most patients. However, this finding indicates that benzodiazepines administered at hypnotic-dose levels have peripheral as well as central effects.

REM-NREM cycle in the cat may be sleep-dependent.

The periodicity of the rapid eye movement-nonrapid eye movement (REM-NREM) cycle in real time versus compressed sleep was determined by autocorrelation, computed on the sequence of sleep stages in recordings from spontaneously sleeping cats. The resulting autocorrelation function was correlated to damped cosine waves, and the highest squared correlation coefficient (r2) was taken as indicating the most likely periodicity in the data entered for each animal. The periodicity of REM sleep was stronger (significantly higher r2) in the compressed sleep data than in the real-time data, indicating sleep dependency of the REM-NREM cycle. The REM-NREM cycle lengths determined by the autocorrelation technique were not significantly different for the real-time and compressed sleep data. The REM sleep episode interval, defined as the average interval between the start of successive REM sleep episodes, was significantly shorter for real-time sustained sleep than the cycle lengths as determined by the autocorrelation technique. A model is proposed which explains this phenomenon as due to fragmentation of REM sleep within the time periods with high probability for REM sleep. When such fragmentation occurs, the average REM sleep episode interval will not reflect an ultradian REM sleep periodicity.

Relative and combined effects of heat and noise exposure on sleep in humans.

In a counter-balanced design, the effects of daytime and/or nighttime exposure to heat and/or traffic noise on night sleep were studied in eight healthy young men. During the day, the subjects were exposed to baseline condition (ambient temperature = 20 degrees C; no noise) or to both heat (35 degrees C) and noise. The duration of the daytime exposure was 8 h ending 5 h before sleep onset. The following nights, the subjects slept either in undisturbed (20 degrees C; no noise) or in noise, heat, or noise plus heat-disturbed environments. During the day, the various types of traffic noise were distributed at a rate of 48/h with peak intensities ranging between 79 and 86 dB(A). The background noise level was at 45 dB(A). At night, the peak intensities were reduced by 15 dB(A), the rate was diminished to 9/h, and the background noise was at 30 dB(A). Electrophysiological measures of sleep and esophageal and mean skin temperatures were continuously recorded. The results showed that both objective and subjective measures of sleep were more disturbed by heat than by noise. The thermal load had a larger impact on sleep quality than on sleep architecture. In the nocturnal hot condition, total sleep time decreased while duration of wakefulness, number of sleep stage changes, stage 1 episodes, number of awakenings, and transitions toward waking increased. An increase in the frequency of transient activation phases was also found in slow-wave sleep and in stage 2. In the nocturnal noise condition, only total number of sleep stage changes, changes to waking, and number of stage 1 episodes increased.(ABSTRACT TRUNCATED AT 250 WORDS)

Daytime sleepiness, performance, mood, nocturnal sleep: the effect of benzodiazepine and caffeine on their relationship.

The present study was part of a larger 3-day, 2-night double-blind parallel group design in which 80 young adult men were divided into eight treatment groups to examine the effects of benzodiazepines and caffeine on nocturnal sleep and daytime sleepiness, performance, and mood. The present study was done to examine further the relationship among daytime sleepiness, performance, mood, and nocturnal sleep and to determine if and how these relationships were affected by the nighttime use of benzodiazepine and the ingestion of caffeine in the morning. Subjects received 15 or 30 mg of flurazepam, 0.25 or 0.50 mg of triazolam, or placebo at bedtime and 250 mg of caffeine or placebo in the morning for two treatment days. Two objective (Multiple Sleep Latency Test and lapses) and two subjective (Stanford Sleepiness Scale and Visual Analog Scale) measures of sleepiness, five performance tests, and two mood measures (Profile of Mood Scale and Visual Analog Scale) were administered repeatedly on both days. Electroencephalogram sleep was recorded on both nights. Objective sleep measures of daytime sleepiness were not significantly related to either performance or mood, but subjects with greater daytime sleepiness had significantly longer and more efficient nocturnal sleep. Neither benzodiazepine or caffeine influenced these relationships. In contrast, higher estimates of subjective sleepiness were significantly associated with poorer mood and tended to be related to poorer performance. Caffeine significantly reduced these relationships. Nocturnal sleep measures were not related to subjective estimates of daytime sleepiness.

Effect of continuous heat exposure on sleep during partial sleep deprivation.

This study examined the effects of continuous heat exposure on sleep structure during a partial sleep-deprivation regime. The experimental protocol was divided into three periods. After a baseline period (5 days and nights at 20 degrees C), the sleep of the subjects was restricted to the second half of the night (3 a.m.-7 a.m.) for four consecutive nights. The restricted-sleep period was followed by two recovery days and nights. During the deprivation and recovery periods, the ambient temperature was 20 degrees C for six of the 12 subjects and 35 degrees C for the others. Sleep, esophageal and mean skin temperatures were continuously recorded. At 20 degrees C, the expected effect of sleep debt was apparent. There were significant reductions in time spent awake and in latencies for sleep and stage 4 sleep. The duration of stage 4 sleep significantly increased during the four successive restricted-sleep nights, whereas esophageal temperature significantly decreased over the successive days. When heat was added, esophageal temperature decrease was weakened, and the significant increase in stage 4 duration seen at 20 degrees C was not found. The findings suggest that the heat load imposed in our experimental condition has a suppressive effect on sleep stage 4 increase, which is induced by sleep restriction. The hypothesis that an increase in this sleep stage serves as a mechanism for energy conservation should be also considered.

Auditory arousal thresholds of good sleepers and poor sleepers with and without flurazepam.

Auditory arousal thresholds of good (N = 12) and poor (N = 12) sleepers (sleep onset insomniacs) were obtained during stage 2, stage 4, and REM sleep at various times of the night. Despite claims of being "light" sleepers who are easily awakened by noise, poor sleeper auditory arousal thresholds were the same as those of good sleepers. Flurazepam (30 mg) increased the auditory arousal thresholds of poor sleepers (N = 6), but the increase was statistically significant only during the period of peak effect which occurred 1--2 hr after ingestion. Consistent with poor sleeper complaints of trouble falling asleep, the return to sleep (i.e., sleep latency) was significantly longer for poor than for good sleepers following stimulus arousals during the first stage 2 and first stage 4 periods of the night. Sleep latencies for good and poor sleepers did not differ significantly following subsequent arousals. The sleep latency following the first stage 2 stimulus arousal was significantly reduced in poor sleepers during flurazepam-induced sleep.

Lipoma of the frontal bone.

A 61-hear-old man was followed up for more than 17 years with what was thought to be fibrous dysplasia of the frontal bone. Postmortem microscopic examination of the lesion showed an intraosseous lipoma with myxomatous foci and bony metaplasia involving the frontal and orbital portions of the frontal bone.

Sedative-hypnotics and human performance.

In 52 studies, performance data were obtained the next day following bedtime ingestion of a sedative-hypnotic or a placebo. Only eight of these studies used insomniac patients. Most studies used young adult males. Benzodiazepine hypnotics were most frequently administered and psychomotor performance was most often measured. Little consistent data are available on cognitive functioning and more complex behavior. Drug-related improvement in performance was not found, and, in comparing active drug to placebo, it is clear that all hypnotics, at some doses, produce decrements in performance the next day. Higher doses consistently showed a decrement, and this decrement was usually persistent over the entire day. Although long-acting drugs generally showed more performance decrement, half-life data were not consistent.

Effects of triazolam (0.5 mg) on sleep, performance, memory, and arousal threshold.

The effects of a short-acting benzodiazepine hypnotic, triazolam (0.5 mg), on sleep, performance, and arousal threshold were assessed in 20 male poor sleepers (age 21 +/- 2.37 years). Following in a laboratory screening night, all subjects received placebo for 3 nights (single-blind), ten received triazolam and ten placebo for 6 nights (double-blind), and all received placebo on 2 withdrawal nights (single-blind). All effects described below were statistically significant. Triazolam reduced sleep latency and increased total sleep time and sleep efficiency. Percent Stage 2 was increased and percent Stage 4 was reduced during treatment. Morning performance, measured 8.25 h post-drug, showed no decrements. Acute effects were assessed on treatment night 6 during arousals from sleep at 1.5, 3, and 5 h post-administration: performance was impaired in triazolam subjects on the Wilkinson 4-Choice Reaction Time Test, Digit Symbol Substitution Test, Williams Word Memory Test, and Card Sorting Task. In the morning following treatment night 6, long-term memory was tested using a recognition task requiring subjects to identify words presented during night-time test batteries: triazolam subjects correctly identified fewer target words. Triazolam administration produced anterograde amnesic effects. However, in a Paired Associates Test learned prior to drug ingestion on the previous evening, triazolam did not impair morning recall of word pairs. Threshold for arousal from slow wave sleep was elevated during treatment, and triazolam subjects did not show increased sensitivity to the arousing tone over nights as did placebo subjects.

Benzodiazepines and caffeine: effect on daytime sleepiness, performance, and mood.

In a double-blind parallel group design, 80 young adult males were divided into eight treatment groups. Subjects received 15 or 30 mg flurazepam, 0.25 or 0.50 mg triazolam, or placebo at bedtime, and 250 mg caffeine or placebo in the morning for 2 treatment days. Two objective (Multiple Sleep Latency Test and lapses) and two subjective (Stanford Sleepiness Scale and Visual Analog Scale) measures of sleepiness, five performance tests, and two mood measures (Profile of Mood Scale and Visual Analog Mood Scale) were administered repeatedly on both days. Significant treatment effects were found for sleepiness but not for performance or mood. Early morning caffeine significantly antagonized next day hypnotic-induced drowsiness and enhanced alertness in the subjects who received bed-time placebo. Flurazepam, 30 mg, subjects were more sleepy than all other groups. Although not significantly different, the flurazepam, 30 mg, group demonstrated a trend toward poorer performance and a more negative mood than all other groups. Caffeine most improved performance of this group. In all groups, sleepiness was greatest and performance and mood poorest in early morning trials and caffeine was most effective at this time.