Phased nanopore assembly with Shasta and modular graph phasing with GFAse.

Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive regions of the genome, long-read sequencing technologies are often used to perform phased de novo assembly. As a step toward reducing the cost and complexity of this type of analysis, we describe new methods for accurately phasing Oxford Nanopore Technologies (ONT) sequence data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome scale called GFAse. We test using new variants of ONT PromethION sequencing, including those using proximity ligation, and show that newer, higher accuracy ONT reads substantially improve assembly quality.

Modeling the Evolution of Rates of Continuous Trait Evolution.

Rates of phenotypic evolution vary markedly across the tree of life, from the accelerated evolution apparent in adaptive radiations to the remarkable evolutionary stasis exhibited by so-called "living fossils." Such rate variation has important consequences for large-scale evolutionary dynamics, generating vast disparities in phenotypic diversity across space, time, and taxa. Despite this, most methods for estimating trait evolution rates assume rates vary deterministically with respect to some variable of interest or change infrequently during a clade's history. These assumptions may cause underfitting of trait evolution models and mislead hypothesis testing. Here, we develop a new trait evolution model that allows rates to vary gradually and stochastically across a clade. Further, we extend this model to accommodate generally decreasing or increasing rates over time, allowing for flexible modeling of "early/late bursts" of trait evolution. We implement a Bayesian method, termed "evolving rates" (evorates for short), to efficiently fit this model to comparative data. Through simulation, we demonstrate that evorates can reliably infer both how and in which lineages trait evolution rates varied during a clade's history. We apply this method to body size evolution in cetaceans, recovering substantial support for an overall slowdown in body size evolution over time with recent bursts among some oceanic dolphins and relative stasis among beaked whales of the genus Mesoplodon. These results unify and expand on previous research, demonstrating the empirical utility of evorates. [cetacea; macroevolution; comparative methods; phenotypic diversity; disparity; early burst; late burst].

Regional soundscape modeling of the Atlantic Outer Continental Shelfa).

The ocean soundscape is a complex superposition of sound from natural and anthropogenic sources. Recent advances in acoustic remote sensing and marine bioacoustics have highlighted how animals use their soundscape and how the background sound levels are influenced by human activities. In this paper, developments in computational ocean acoustics, remote sensing, and oceanographic modeling are combined to generate modelled sound fields at multiple scales in time and space. Source mechanisms include surface shipping, surface wind, and wave fields. A basin scale model is presented and applied to the United States Atlantic Outer Continental Shelf (OCS). For model-data comparison at a single hydrophone location, the model is run for a single receiver position. Environmental and source model uncertainty is included in the site-specific modeling of the soundscape. An inversion of the local sediment type is made for a set of sites in the OCS. After performing this inversion, the qualitative comparison of the modelled sound pressure level (SPL) time series and observed SPL is excellent. The quantitative differences in the mean root mean square error between the model and data is less than 3 dB for most sites and frequencies above 90 Hz.

Observed transmissions and ocean-ice-acoustic coupled modelling in the Beaufort Sea.

An ocean-ice-acoustic coupled model is configured for the Beaufort Sea. The model uses outputs from a data assimilating global scale ice-ocean-atmosphere forecast to drive a bimodal roughness algorithm for generating a realistic ice canopy. The resulting range-dependent ice cover obeys observed roughness, keel number density, depth, and slope, and floe size statistics. The ice is inserted into a parabolic equation acoustic propagation model as a near-zero impedance fluid layer along with a model defined range-dependent sound speed profile. Year-long observations of transmissions at 35 Hz from the Coordinated Arctic Acoustic Thermometry Experiment and 925 Hz from the Arctic Mobile Observing System source were recorded over the winter of 2019-2020 on a free-drifting, eight-element vertical line array designed to vertically span the Beaufort duct. The ocean-ice-acoustic coupled model predicts receive levels that reasonably agree with the measurements over propagation ranges of 30-800 km. At 925 Hz, seasonal and sub-seasonal ocean and ice driven variations of propagation loss are captured in the data and reproduced in the model.

Clinical impact of whole-genome sequencing in patients with early-onset dementia.

BACKGROUND: In the clinical setting, identification of the genetic cause in patients with early-onset dementia (EOD) is challenging due to multiple types of genetic tests required to arrive at a diagnosis. Whole-genome sequencing (WGS) has the potential to serve as a single diagnostic platform, due to its superior ability to detect common, rare and structural genetic variation. METHODS: WGS analysis was performed in 50 patients with EOD. Point mutations, small insertions/deletions, as well as structural variants (SVs) and short tandem repeats (STRs), were analysed. An Alzheimer's disease (AD)-related polygenic risk score (PRS) was calculated in patients with AD. RESULTS: Clinical genetic diagnosis was achieved in 7 of 50 (14%) of the patients, with a further 8 patients (16%) found to have established risk factors which may have contributed to their EOD. Two pathogenic variants were identified through SV analysis. No expanded STRs were found in this study cohort, but a blinded analysis with a positive control identified a C9orf72 expansion accurately. Approximately 37% (7 of 19) of patients with AD had a PRS equivalent to >90th percentile risk. DISCUSSION: WGS acts as a single genetic test to identify different types of clinically relevant genetic variations in patients with EOD. WGS, if used as a first-line clinical diagnostic test, has the potential to increase the diagnostic yield and reduce time to diagnosis for EOD.

Challenges of antithrombotic therapy in the management of cardiovascular disease in patients with inherited bleeding disorders: A single-centre experience.

INTRODUCTION: Cardiovascular events in patients with inherited bleeding disorders are challenging to manage. The risk of bleeding secondary to antithrombotic treatment must be balanced against the risk of thrombosis secondary to haemostatic therapy. METHODS: Patients with inherited bleeding disorders with coronary artery bypass grafting (CABG), percutaneous coronary intervention (PCI) or atrial fibrillation (AF) from a single centre (2010-2018) are included. RESULTS: A total of 11 patients undergoing CABG (n = 3), PCI (n = 5) or with AF (n = 3) and a diagnosis of haemophilia A (n = 8), haemophilia B (n = 1), factor XI deficiency (n = 1) and von Willebrand disease (n = 1) managed by a multidisciplinary team are reported. In patients undergoing CABG, factor levels were normalized for 7-10 days with trough levels of 70-80% with severe patients continuing high-dose factor prophylaxis (trough 20-30%) three weeks post-operatively with daily aspirin. In a patient with mild haemophilia A and an inhibitor, recombinant factor VIIa dosing was monitored with thromboelastometry. For PCI, a 3rd-generation drug-eluting stent with one month of dual antiplatelet therapy in addition to high-dose prophylaxis as needed was preferred. Patients with AF and severe haemophilia did not receive antithrombotic treatment, and a thrombin generation assay was used to guide heparin dosing in mild haemophilia. CONCLUSION: Our experience demonstrates the importance of interdisciplinary communication to identify strategies that decrease the risk of bleeding and thrombosis. The use of extended, increased intensity prophylaxis facilitated antiplatelet therapy. Global assays may help balance the intensity of haemostatic and antithrombotic treatment.

North Sea soundscapes from a fish perspective: Directional patterns in particle motion and masking potential from anthropogenic noise.

The aquatic world of animals is an acoustic world as sound is the most prominent sensory capacity to extract information about the environment for many aquatic species. Fish can hear particle motion, and a swim bladder potentially adds the additional capacity to sense sound pressure. Combining these capacities allows them to sense direction, distance, spectral content, and detailed temporal patterns. Both sound pressure and particle motion were recorded in a shallow part of the North Sea before and during exposure to a full-scale airgun array from an experimental seismic survey. Distinct amplitude fluctuations and directional patterns in the ambient noise were found to be fluctuating in phase with the tidal cycles and coming from distinct directions. It was speculated that the patterns may be determined by distant sources associated with large rivers and nearby beaches. Sounds of the experimental seismic survey were above the ambient conditions for particle acceleration up to 10 km from the source, at least as detectable for the measurement device, and up to 31 km for the sound pressure. These results and discussion provide a fresh perspective on the auditory world of fishes and a shift in the understanding about potential ranges over which they may have access to biologically relevant cues and be masked by anthropogenic noise.

Exploring movement patterns and changing distributions of baleen whales in the western North Atlantic using a decade of passive acoustic data.

Six baleen whale species are found in the temperate western North Atlantic Ocean, with limited information existing on the distribution and movement patterns for most. There is mounting evidence of distributional shifts in many species, including marine mammals, likely because of climate-driven changes in ocean temperature and circulation. Previous acoustic studies examined the occurrence of minke (Balaenoptera acutorostrata) and North Atlantic right whales (NARW; Eubalaena glacialis). This study assesses the acoustic presence of humpback (Megaptera novaeangliae), sei (B. borealis), fin (B. physalus), and blue whales (B. musculus) over a decade, based on daily detections of their vocalizations. Data collected from 2004 to 2014 on 281 bottom-mounted recorders, totaling 35,033 days, were processed using automated detection software and screened for each species' presence. A published study on NARW acoustics revealed significant changes in occurrence patterns between the periods of 2004-2010 and 2011-2014; therefore, these same time periods were examined here. All four species were present from the Southeast United States to Greenland; humpback whales were also present in the Caribbean. All species occurred throughout all regions in the winter, suggesting that baleen whales are widely distributed during these months. Each of the species showed significant changes in acoustic occurrence after 2010. Similar to NARWs, sei whales had higher acoustic occurrence in mid-Atlantic regions after 2010. Fin, blue, and sei whales were more frequently detected in the northern latitudes of the study area after 2010. Despite this general northward shift, all four species were detected less on the Scotian Shelf area after 2010, matching documented shifts in prey availability in this region. A decade of acoustic observations have shown important distributional changes over the range of baleen whales, mirroring known climatic shifts and identifying new habitats that will require further protection from anthropogenic threats like fixed fishing gear, shipping, and noise pollution.

Assessing auditory masking for management of underwater anthropogenic noise.

Masking is often assessed by quantifying changes, due to increasing noise, to an animal's communication or listening range. While the methods used to measure communication or listening ranges are functionally similar if used for vocalizations, they differ in their approaches: communication range is focused on the sender's call, while the listening range is centered on the listener's ability to perceive any signal. How these two methods differ in their use and output is important for management recommendations. Therefore it was investigated how these two methods may alter the conclusions of masking assessments based on Atlantic cod calls in the presence of a commercial air gun array. The two methods diverged with increasing distance from the masking noise source with maximum effects lasting longer between air gun pulses in terms of communication range than listening range. Reductions in the cod's communication ranges were sensitive to fluctuations in the call's source level. That instability was not observed for the listening range. Overall, changes to the cod's communication range were more conservative but very sensitive to the call source level. A high level of confidence in the call is therefore required, while confidence in the receiver's audiogram and soundscape is required for the listening range method.

Displaying bioacoustic directional information from sonobuoys using "azigrams".

The AN/SSQ-53 Directional Frequency Analysis and Recording (DIFAR) sonobuoy is an expendable device that can derive acoustic particle velocity along two orthogonal horizontal axes, along with acoustic pressure. This information enables computation of azimuths of low-frequency acoustic sources from a single compact sensor. The standard approach for estimating azimuth from these sensors is by conventional beamforming (i.e., adding weighted time series), but the resulting "cardioid" beampattern is imprecise, computationally expensive, and vulnerable to directional noise contamination for weak signals. Demonstrated here is an alternative multiplicative processing scheme that computes the "active intensity" of an acoustic signal to obtain the dominant directionality of a noise field as a function of time and frequency. This information is conveniently displayed as an "azigram," which is analogous to a spectrogram, but uses color to indicate azimuth instead of intensity. Data from several locations demonstrate this approach, which can be computed without demultiplexing the raw signal. Azigrams have been used to help diagnose sonobuoy issues, improve detectability, and estimate bearings of low signal-to-noise ratio signals. Azigrams may also enhance the detection and potential classification of signals embedded in directional noise fields.

Evaluation of Three Sensor Types for Particle Motion Measurement.

All fish sense acoustic particle motion; some species also sense pressure. Concern over the effects of anthropogenic sounds is increasing the need to monitor acoustic particle motion. Particle motion can be measured directly using vector sensors or calculated from pressure gradients. This article compares three devices that measure particle motion: a three-axis accelerometer, a three-axis velocity sensor, and two 4-element hydrophone arrays. A series of sounds (constant-wave tones, white noise, and Ricker wavelets) were played from a fixed-position projector. The particle motion of sounds from imploding light bulbs was also measured.

Methods for Predicting Potential Impacts of Pile-Driving Noise on Endangered Sturgeon During Bridge Construction.

The potential impacts of pile-driving noise on Hudson River sturgeon during construction of the New NY Bridge were predicted. Abundance data for shortnose and Atlantic sturgeon derived from fisheries sampling were combined with data about the spatial extent of pile-driving noise. This approach was used to calculate the number of sturgeon that could occur within sound level isopleths exceeding peak and cumulative noise criteria used by the National Marine Fisheries Service to determine the incidental take of sturgeon. The number of sturgeon subject to the potential onset of physiological effects during pile driving was predicted to be 35-41 fish for each species.

Pile Driving at the New Bridge at Tappan Zee: Potential Environmental Impacts.

A new bridge will be constructed to replace the aging Tappan Zee Bridge over the Hudson River in New York. Construction will potentially result in hydroacoustic impacts to the local fish fauna. As a consequence, a substantial environmental impact analysis had to be conducted to obtain construction permits. This paper describes the process of environmental analysis and some of the results of the studies that led up to the final permitting. The process included modeling of pile-driving acoustics, analysis of river ambient noise, analysis of test piling, and observations on fish behavior during these tests.

Use of Z-scores to rank applicants to professional degree programs.

Criteria for assessing suitability of applicants for professional degree programs such as veterinary medicine are usually treated as distinct components of a composite scoring procedure that determines applicant ranking. Some components are valued more than others, which is reflected in the relative weights assigned to each component. However, the patterns of dispersal of individual components have the potential to alter the assigned relative weights. Components with larger variances can have greater influences on composite scores than intended. Such unintended altered weighting can be avoided through standardization. Yet non-standardized approaches continue to be used for admissions ranking in several programs. In this study, we documented the potential for differential selection of applicants when non-standardized scoring approaches are applied to admissions assessment components. At our medical school, applicants' component scores with differing variances are standardized by determining Z-scores with a mean of 0 and standard deviation of 1 before mathematically combining to calculate composite scores and admissions ranking. We retrospectively and hypothetically ranked one applicant cohort using non-standardized methods and identified differences in ranking between the standardized and non-standardized approaches. Most differences were observed for applicants in the second, third, and fourth quintiles of the admissions rank list, that is, those for whom admissions cut-off decisions make a marked difference. Observations were supported by lower Spearman's rank correlation coefficients in these quintiles. Although standardization of component scores is not a novel topic, we document the implications of using non-standardized scoring approaches for applicant ranking and underscore the importance of standardization of component scores.

Utility of a writing station in the multiple mini-interview.

The multiple mini-interview (MMI) is a reliable and valid method of selecting applicants for admission to health professional schools on the basis of non-cognitive traits. Because the MMI is a series of short interview stations that applicants rotate through in coordinated sequence, it can potentially be resource intensive. However, the MMI design has room for innovation and efficiency. At the University of Manitoba Faculty of Medicine, a 10-minute unsupervised writing station (WS) was incorporated into the MMI to obtain a writing sample from each applicant, to increase the number of independent scores per applicant, and to increase the number of applicants interviewed per circuit without increasing interviewer numbers. One assessor evaluated all the writing samples and assigned a score ranging from 1 to 7. With the inclusion of a WS into an 11-station MMI, the faculty's capacity to interview applicants increased by 9% (from 297 to 324) without substantially increasing interviewer hours needed per day. For 1,257 applicants interviewed in 2008-2011, the mean WS score was 4.03 (SD=1.36), whereas applicants' mean of 10 oral station (OS) scores was 4.62 (SD=0.69). Correlations between WS score and mean OS score ranged from .16 to .27 (p<.01) over the four years. Because inter-station correlations for OS ranged from .01 to .37, the correlation of .21 between WS and mean OS scores for all four years combined appears reasonable. Institutions that want to effectively increase the capacity of their MMI process might consider adding a WS.

Multiple mini-interview scores of medical school applicants with and without rural attributes.

INTRODUCTION: Students from rural areas are under-represented in medical schools. Concerns have been raised about rural applicants' qualifications relative to those of their urban counterparts, and the impact such potential differences in competitiveness may have on their under-representation. Although studies have reported no differences in Grade Point Average (GPA) and Medical College Admission Test (MCAT) scores between applicants with and without rural attributes, to date no study has assessed if performance on the multiple mini-interview (MMI) varies between the two groups. METHODS: The MMI scores of 1257 interviewees for admission to the MD program at the Faculty of Medicine, University of Manitoba, in years 2008 to 2011, were studied for an association with graduation from a rural high school and attributes in the following three domains: rural connections, employment in rural areas, and rural community service. RESULTS: There were 205 (16.3%) rural high school graduates among interviewed applicants. Rural high school graduates scored significantly lower (mean of 4.4 on a scale of 1 to 7; p < 0.05) than urban high school graduates (4.6). Among rural-attribute domains, those with rural community service alone had the highest MMI scores (4.9) while those with rural connections alone had the lowest scores (4.3; p = 0.016). After adjusting for demographics, GPA, and MCAT scores in a multiple linear regression model, rural-attribute domains were not significant predictors of an applicant's MMI score. However, graduation from a rural high school was significantly associated with decreased MMI scores (a 0.122 decrease in predicted MMI scores on a scale of 1 to 7). CONCLUSION: Despite graduates from rural and urban high schools having comparable GPA, there exists a rural-urban divide in MMI scores that could exacerbate the under-representation of rural students in medical schools. Aboriginal applicants can also potentially be disproportionately affected, as they were more often from rural high schools than from urban high schools. Future studies need to determine systematic and institutional reasons, if any, for the differential in MMI scoring that can affect admission decisions for some rural applicants. It is also to be noted that the magnitude of difference is small enough that it may ultimately be irrelevant for future physician performance and practitioner outcomes.

Fluid balance during physical work in the heat is not modified by the menstrual cycle when fluids are freely available.

We tested the hypothesis that women may be more at risk of becoming dehydrated during physical work in the heat in the early follicular phase (EF), compared with the late follicular (LF) and mid-luteal (ML) phases of the menstrual cycle when allowed free access to drink. Twelve healthy, eumenorrheic, unacclimated women (26 ± 5 yr) completed three trials (EF, LF, and ML phases) involving 4 h of exposure to 33.8 ± 0.8 °C, 54 ± 1% relative humidity. Each hour, participants walked on a treadmill for 30 min at a rate of metabolic heat production of 338 ± 9 W. Participants drank a cool, flavor-preferred non-caloric sport drink ad libitum. Nude body weight was measured pre- and post-exposure, and percent changes in body weight loss were interpreted as an index of changes in total body water. Total fluid intake and urine output were measured and sweat rate was estimated from changes in body mass corrected for fluid intake and urine output. Fluid intake was not different between phases (EF: 1,609 ± 919 mL; LF: 1,902 ± 799 mL; ML: 1,913 ± 671; P = 0.202). Total urine output (P = 0.543) nor sweat rate (P = 0.907) differed between phases. Percent changes in body mass were not different between phases (EF: -0.5 ± 0.9%; LF: -0.3 ± 0.9%; ML: -0.3 ± 0.7%; P = 0.417). This study demonstrates that the normal hormonal fluctuations that occur throughout the menstrual cycle do not alter fluid balance during physical work in the heat.NEW & NOTEWORTHY The effect of the menstrual cycle on fluid balance during physical work in the heat when fluids are freely available is unknown. This study demonstrates that fluid balance is not modified in women across three distinct phases of the menstrual cycle during physical work in the heat These results indicate that when women have free access to cool fluid during physical work in the heat, they respond similarly across all three phases to maintain fluid homeostasis across the menstrual cycle.

Phased nanopore assembly with Shasta and modular graph phasing with GFAse.

As a step towards simplifying and reducing the cost of haplotype resolved de novo assembly, we describe new methods for accurately phasing nanopore data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome scale called GFAse. We test using new variants of Oxford Nanopore Technologies' (ONT) PromethION sequencing, including those using proximity ligation and show that newer, higher accuracy ONT reads substantially improve assembly quality.

A study of the efficacy and safety of ciclesonide hydrofluoroalkane nasal aerosol in patients with seasonal allergic rhinitis from mountain cedar pollen.

A nasal aerosol formulation of ciclesonide with a hydrofluoroalkane propellant (CIC-HFA) is currently in development for treatment of allergic rhinitis (AR). This study evaluated the efficacy and safety of once-daily administration of CIC-HFA 74 or 148 micrograms compared with placebo in patients with seasonal AR (SAR) from mountain cedar pollen. Patients ≥12 years of age with a ≥2-year history of SAR from mountain cedar pollen were randomized in a placebo-controlled, double-blind, parallel group, multicenter study to CIC-HFA 74 micrograms, CIC-HFA 148 micrograms, or placebo once daily in the morning for 2 weeks. Change from baseline in reflective total nasal symptom score (rTNSS), instantaneous TNSS (iTNSS), and reflective total ocular symptom score (rTOSS) in patients with baseline rTOSS ≥5.00 were evaluated. Adverse events (AEs) were monitored throughout the study. A statistically significant improvement in rTNSS (least squares [LS] mean change from baseline 1.04 and 1.02 respectively; p < 0.0001 versus placebo for both) and iTNSS (LS mean change from baseline 0.90 and 0.83 respectively; p < 0.001 vs placebo for both) was observed after treatment with CIC-HFA 74- or 148-microgram doses. Only the CIC-HFA 74-micrograms treatment group showed a statistically significant improvement in rTOSS (LS mean change from baseline 0.52; p = 0.0124) compared with placebo. The overall incidence of AEs was low and comparable between the treatment groups. In this study, statistically significant improvements in nasal symptoms of SAR were observed after treatment with CIC-HFA 74-microgram or CIC-HFA 148-microgram doses. Both active treatments were well tolerated. Clinical trial registry URL and registration number: www.clinicaltrials.gov/ct2/show/NCT01010971.

Tracking of Pacific walruses in the Chukchi Sea using a single hydrophone.

The vocal repertoire of Pacific walruses includes underwater sound pulses referred to as knocks and bell-like calls. An extended acoustic monitoring program was performed in summer 2007 over a large region of the eastern Chukchi Sea using autonomous seabed-mounted acoustic recorders. Walrus knocks were identified in many of the recordings and most of these sounds included multiple bottom and surface reflected signals. This paper investigates the use of a localization technique based on relative multipath arrival times (RMATs) for potential behavior studies. First, knocks are detected using a semi-automated kurtosis-based algorithm. Then RMATs are matched to values predicted by a ray-tracing model. Walrus tracks with vertical and horizontal movements were obtained. The tracks included repeated dives between 4.0 m and 15.5 m depth and a deep dive to the sea bottom (53 m). Depths at which bell-like sounds are produced, average knock production rate and source levels estimates of the knocks were determined. Bell sounds were produced at all depths throughout the dives. Average knock production rates varied from 59 to 75 knocks/min. Average source level of the knocks was estimated to 177.6 ± 7.5 dB re 1 µPa peak @ 1 m.