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Mycoplasma gallisepticum causes disease in poultry and emerged as a novel pathogen in house finches resulting in a mycoplasmal conjunctivitis epidemic across North America after a single successful host jump from poultry to house finches. The rapid spread of the epidemic across eastern North America, causing a decline in host abundance, has been documented. Once established, disease prevalence showed regular seasonal variation: a late summer/early autumn peak, a mid-December minimum, followed by a late winter peak and a breeding season minimum, which requires seasonal reproduction (providing an autumn pulse of naïve hosts) and winter social aggregation as well as partial immunity of recovered birds. Virulence evolved rapidly: in eastern populations it increased once the disease had become endemic. In western North America the established strain was of much lower virulence, but once established also increased in virulence. We show that virulence may evolve in opposite directions depending on selection pressures. A detailed study showed that disease decreased survival and mobility and a high proportion of birds recovered; also that re-observation rates of clinically diseased birds are often different from those of asymptomatic birds; only calculations which include this effect allow an accurate estimate of disease prevalence.
Disasters are typically unforeseen, causing most social and behavioral studies about disasters to be reactive. Occasionally, predisaster data are available, for example, when disasters happen while a study is already in progress or where data collected for other purposes already exist, but planned pre-post designs are all but nonexistent. This gap fundamentally limits the quantification of disasters’ human toll. Anticipating, responding to, and managing public reactions require a means of tracking and understanding those reactions, collected using rigorous scientific methods. Oftentimes, self-reports from the public are the best or only source of information, such as perceived risk, behavioral intentions, and social learning. Significant advancement in disaster research, to best inform practice and policy, requires well-designed surveys with large probability-based samples and longitudinal assessment of individuals across the life-cycle of a disaster and across multiple disasters.
Englacial layers in Antarctica and Greenland are indicators of the dynamic, rheological and subglacial configuration of the ice sheets. Airborne radar sounder data is the primary remote sensing solution for directly observing englacial layers and structures at the glacier-catchment to ice-sheet scale. However, when traditional along-track synthetic aperture radar (SAR) processing is applied, steep layers can disappear, limiting the detectability and interpretability of englacial layer geometry. This study provides a reconstruction algorithm to address the problem of destructive phase interference during the radargram formation. We develop and apply a novel SAR processor optimized for layer detection that enhances the Signal-to-Noise ratio (SNR) of specular reflectors. The algorithm also enables the automatic estimation of layer slope. We demonstrate the algorithm using data acquired at the Institute Ice Stream, West Antarctica.
Quaternary processes and environmental changes are often difficult to assess in remote subantarctic islands due to high surface erosion rates and overprinting of sedimentary products in locations that can be a challenge to access. We present a set of high-resolution, multichannel seismic lines and complementary multibeam bathymetry collected off the eastern (leeward) side of the subantarctic Auckland Islands, about 465 km south of New Zealand's South Island. These data constrain the erosive and depositional history of the island group, and they reveal an extensive system of sediment-filled valleys that extend offshore to depths that exceed glacial low-stand sea level. Although shallow, marine, U-shaped valleys and moraines are imaged, the rugged offshore geomorphology of the paleovalley floors and the stratigraphy of infill sediments suggests that the valley floors were shaped by submarine fluvial erosion, and subsequently filled by lacustrine, fjord, and fluvial sedimentary processes.
The taxonomic and ecologic composition of Earth's biota has shifted dramatically through geologic time, with some clades going extinct while others diversified. Here, we derive a metric that quantifies the change in biotic composition due to extinction or origination and show that it equals the product of extinction/origination magnitude and selectivity (variation in magnitude among groups). We also define metrics that describe the extent to which a recovery (1) reinforced or reversed the effects of extinction on biotic composition and (2) changed composition in ways uncorrelated with the extinction. To demonstrate the approach, we analyzed an updated compilation of stratigraphic ranges of marine animal genera. We show that mass extinctions were not more selective than background intervals at the phylum level; rather, they tended to drive greater taxonomic change due to their higher magnitudes. Mass extinctions did not represent a separate class of events with respect to either strength of selectivity or effect. Similar observations apply to origination during recoveries from mass extinctions, and on average, extinction and origination were similarly selective and drove similar amounts of biotic change. Elevated origination during recoveries drove bursts of compositional change that varied considerably in effect. In some cases, origination partially reversed the effects of extinction, returning the biota toward the pre-extinction composition; in others, it reinforced the effects of the extinction, magnifying biotic change. Recoveries were as important as extinction events in shaping the marine biota, and their selectivity deserves systematic study alongside that of extinction.
The science of studying diamond inclusions for understanding Earth history has developed significantly over the past decades, with new instrumentation and techniques applied to diamond sample archives revealing the stories contained within diamond inclusions. This chapter reviews what diamonds can tell us about the deep carbon cycle over the course of Earth’s history. It reviews how the geochemistry of diamonds and their inclusions inform us about the deep carbon cycle, the origin of the diamonds in Earth’s mantle, and the evolution of diamonds through time.
This chapter reviews the systematics of partial melting of mantle lithologies – like peridotite and eclogite – in the presence of carbon dioxide. It discusses the composition of mantle-derived magmas generated in the presence of carbon dioxide and whether magmas erupted on Earth’s surface resemble carbonated magmas from the mantle. It reviews how the production of carbon dioxide-rich magma in the mantle varies as a function of tectonic settings – beneath continents and oceans and in subduction zones – and time.
Human and animal research both operate within established standards. In the United States, criticism of the human research environment and recorded abuses of human research subjects served as the impetus for the establishment of the National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research, and the resulting Belmont Report. The Belmont Report established key ethical principles to which human research should adhere: respect for autonomy, obligations to beneficence and justice, and special protections for vulnerable individuals and populations. While current guidelines appropriately aim to protect the individual interests of human participants in research, no similar, comprehensive, and principled effort has addressed the use of (nonhuman) animals in research. Although published policies regarding animal research provide relevant regulatory guidance, the lack of a fundamental effort to explore the ethical issues and principles that should guide decisions about the potential use of animals in research has led to unclear and disparate policies. Here, we explore how the ethical principles outlined in the Belmont Report could be applied consistently to animals. We describe how concepts such as respect for autonomy and obligations to beneficence and justice could be applied to animals, as well as how animals are entitled to special protections as a result of their vulnerability.
Major depressive disorder and neuroticism (Neu) share a large genetic basis. We sought to determine whether this shared basis could be decomposed to identify genetic factors that are specific to depression.
We analysed summary statistics from genome-wide association studies (GWAS) of depression (from the Psychiatric Genomics Consortium, 23andMe and UK Biobank) and compared them with GWAS of Neu (from UK Biobank). First, we used a pairwise GWAS analysis to classify variants as associated with only depression, with only Neu or with both. Second, we estimated partial genetic correlations to test whether the depression's genetic link with other phenotypes was explained by shared overlap with Neu.
We found evidence that most genomic regions (25/37) associated with depression are likely to be shared with Neu. The overlapping common genetic variance of depression and Neu was genetically correlated primarily with psychiatric disorders. We found that the genetic contributions to depression, that were not shared with Neu, were positively correlated with metabolic phenotypes and cardiovascular disease, and negatively correlated with the personality trait conscientiousness. After removing shared genetic overlap with Neu, depression still had a specific association with schizophrenia, bipolar disorder, coronary artery disease and age of first birth. Independent of depression, Neu had specific genetic correlates in ulcerative colitis, pubertal growth, anorexia and education.
Our findings demonstrate that, while genetic risk factors for depression are largely shared with Neu, there are also non-Neu-related features of depression that may be useful for further patient or phenotypic stratification.
The authors report on pulsed laser powder bed fusion fabrication of nitinol (NiTi) shape memory materials. The authors first performed single-track laser parameter sweeps to assess melt pool stability and determine energy parameters and hatch spacing for larger builds. The authors then assessed the melt pool chemistry as a function of laser energy density and build plate composition. Brittle intermetallics were found to form at the part/build plate interface for both N200 and Ti-6-4 substrates. The intermetallic formation was reduced by building on a 50Ni–50Ti substrate, but delamination still occurred due to thermal stresses upon cooling. The authors were able to overcome delamination on all substrates and fabricate macroscopic parts by building a lattice support structure, which is both compliant and controls heat transfer into the build plate. This approach will enable scalable fabrication of complex NiTi parts.
Compound-specific radiocarbon (14C) dating often requires working with small samples of < 100 µg carbon (µgC). This makes the radiocarbon dates of biomarker compounds very sensitive to biases caused by extraneous carbon of unknown composition, a procedural blank, which is introduced to the samples during the steps necessary to prepare a sample for radiocarbon analysis by accelerator mass spectrometry (i.e., isolating single compounds from a heterogeneous mixture, combustion, gas purification and graphitization). Reporting accurate radiocarbon dates thus requires a correction for the procedural blank. We present our approach to assess the fraction modern carbon (F14C) and the mass of the procedural blanks introduced during the preparation procedures of lipid biomarkers (i.e. n-alkanoic acids) and lignin phenols. We isolated differently sized aliquots (6–151 µgC) of n-alkanoic acids and lignin phenols obtained from standard materials with known F14C values. Each compound class was extracted from two standard materials (one fossil, one modern) and purified using the same procedures as for natural samples of unknown F14C. There is an inverse linear relationship between the measured F14C values of the processed aliquots and their mass, which suggests constant contamination during processing of individual samples. We use Bayesian methods to fit linear regression lines between F14C and 1/mass for the fossil and modern standards. The intersection points of these lines are used to infer F14Cblank and mblank and their associated uncertainties. We estimate 4.88 ± 0.69 μgC of procedural blank with F14C of 0.714 ± 0.077 for n-alkanoic acids, and 0.90 ± 0.23 μgC of procedural blank with F14C of 0.813 ± 0.155 for lignin phenols. These F14Cblank and mblank can be used to correct AMS results of lipid and lignin samples by isotopic mass balance. This method may serve as a standardized procedure for blank assessment in small-scale radiocarbon analysis.
Translocation and rehabilitation programmes are critical tools for wildlife conservation. These methods achieve greater impact when integrated in a combined strategy for enhancing population or ecosystem restoration. During 2002–2016 we reared 37 orphaned southern sea otter Enhydra lutris nereis pups, using captive sea otters as surrogate mothers, then released them into a degraded coastal estuary. As a keystone species, observed increases in the local sea otter population unsurprisingly brought many ecosystem benefits. The role that surrogate-reared otters played in this success story, however, remained uncertain. To resolve this, we developed an individual-based model of the local population using surveyed individual fates (survival and reproduction) of surrogate-reared and wild-captured otters, and modelled estimates of immigration. Estimates derived from a decade of population monitoring indicated that surrogate-reared and wild sea otters had similar reproductive and survival rates. This was true for males and females, across all ages (1–13 years) and locations evaluated. The model simulations indicated that reconstructed counts of the wild population are best explained by surrogate-reared otters combined with low levels of unassisted immigration. In addition, the model shows that 55% of observed population growth over this period is attributable to surrogate-reared otters and their wild progeny. Together, our results indicate that the integration of surrogacy methods and reintroduction of juvenile sea otters helped establish a biologically successful population and restore a once-impaired ecosystem.
We present a new method for large scale dynamic simulation of colloidal particles with hydrodynamic interactions and Brownian forces, which we call fast Stokesian dynamics (FSD). The approach for modelling the hydrodynamic interactions between particles is based on the Stokesian dynamics (SD) algorithm (J. Fluid Mech., vol. 448, 2001, pp. 115–146), which decomposes the interactions into near-field (short-ranged, pairwise additive and diverging) and far-field (long-ranged many-body) contributions. In FSD, the standard system of linear equations for SD is reformulated using a single saddle point matrix. We show that this reformulation is generalizable to a host of particular simulation methods enabling the self-consistent inclusion of a wide range of constraints, geometries and physics in the SD simulation scheme. Importantly for fast, large scale simulations, we show that the saddle point equation is solved very efficiently by iterative methods for which novel preconditioners are derived. In contrast to existing approaches to accelerating SD algorithms, the FSD algorithm avoids explicit inversion of ill-conditioned hydrodynamic operators without adequate preconditioning, which drastically reduces computation time. Furthermore, the FSD formulation is combined with advanced sampling techniques in order to rapidly generate the stochastic forces required for Brownian motion. Specifically, we adopt the standard approach of decomposing the stochastic forces into near-field and far-field parts. The near-field Brownian force is readily computed using an iterative Krylov subspace method, for which a novel preconditioner is developed, while the far-field Brownian force is efficiently computed by linearly transforming those forces into a fluctuating velocity field, computed easily using the positively split Ewald approach (J. Chem. Phys., vol. 146, 2017, 124116). The resultant effect of this field on the particle motion is determined through solution of a system of linear equations using the same saddle point matrix used for deterministic calculations. Thus, this calculation is also very efficient. Additionally, application of the saddle point formulation to develop high-resolution hydrodynamic models from constrained collections of particles (similar to the immersed boundary method) is demonstrated and the convergence of such models is discussed in detail. Finally, an optimized graphics processing unit implementation of FSD for mono-disperse spherical particles is used to demonstrated performance and accuracy of dynamic simulations of
particles, and an open source plugin for the HOOMD-blue suite of molecular dynamics software is included in the supplementary material.
To assess the feasibility, reliability, and validity of the Pictorial Fit-Frail Scale (PFFS) among patients, caregivers, nurses, and geriatricians in an outpatient memory clinic.
A Canadian referral-based outpatient memory clinic.
Fifty-one consecutive patients and/or their caregivers, as well as attending nurses and geriatricians.
Participants (patients, caregivers, nurses, and geriatricians) were asked to complete the PFFS based on the patient’s current level of functioning. Time-to-complete and level of assistance required was recorded. Participants also completed a demographic survey and patients’ medical history (including the Mini-Mental State Examination [MMSE], and Comprehensive Geriatric Assessment [CGA]) was obtained via chart review.
Patient participants had a mean age of 77.3±10.1 years, and average MMSE of 22.0±7.0, and 53% were female. Participants were able to complete the PFFS with minimal assistance, and their average times to completion were 4:38±2:09, 3:11±1:16, 1:05±0:19, and 0:57±0:30 (mins:sec) for patients, caregivers, nurses, and geriatricians, respectively. Mean PFFS scores as rated by patients, caregivers, nurses, and geriatricians were 9.0±5.7, 13.1±6.6, 11.2±4.5, 11.9±5.9, respectively. Patients with low MMSE scores (0–24) took significantly longer to complete the scale and had higher PFFS scores. Inter-rater reliability between nurses and geriatricians was 0.74, but it was lower when assessments were done for patients with low MMSE scores (0.47, p<0.05). The correlation between PFFS and a Frailty Index based on the CGA was moderately high and statistically significant for caregivers, nurses, and geriatricians (r=0.66, r=0.59, r=0.64, respectively), but not patients.
The PFFS is feasible, even among people with some slight cognitive impairment, though it may be less useful when patients with severe dementia administer it to themselves. Further, the PFFS may help inform clinicians about areas of concern as identified by patients, enabling them to contribute more to diagnostic and treatment decisions or helping with health tracking and care planning.
Whether maternal obesity and gestational weight gain (GWG) are associated with early-childhood development in low-income, urban, minority populations, and whether effects differ by child sex remain unknown. This study examined the impact of prepregnancy BMI and GWG on early childhood neurodevelopment in the Columbia Center for Children’s Environmental Health Mothers and Newborns study. Maternal prepregnancy weight was obtained by self-report, and GWG was assessed from participant medical charts. At child age 3 years, the Psychomotor Development Index (PDI) and Mental Development Index (MDI) of the Bayley Scales of Infant Intelligence were completed. Sex-stratified linear regression models assessed associations between prepregnancy BMI and pregnancy weight gain z-scores with child PDI and MDI scores, adjusting for covariates. Of 382 women, 48.2% were normal weight before pregnancy, 24.1% overweight, 23.0% obese, and 4.7% underweight. At 3 years, mean scores on the PDI and MDI were higher among girls compared to boys (PDI: 102.3 vs. 97.2, P = 0.0002; MDI: 92.8 vs. 88.3, P = 0.0001). In covariate-adjusted models, maternal obesity was markedly associated with lower PDI scores in boys [b = −7.81, 95% CI: (−13.08, −2.55), P = 0.004], but not girls. Maternal BMI was not associated with MDI in girls or boys, and GWG was not associated with PDI or MDI among either sex (all-P > 0.05). We found that prepregnancy obesity was associated with lower PDI scores at 3 years in boys, but not girls. The mechanisms underlying this sex-specific association remain unclear, but due to elevated obesity exposure in urban populations, further investigation is warranted.
While echocardiographic parameters are used to quantify ventricular function in infants with single ventricle physiology, there are few data comparing these to invasive measurements. This study correlates echocardiographic measures of diastolic function with ventricular end-diastolic pressure in infants with single ventricle physiology prior to superior cavopulmonary anastomosis.
Data from 173 patients enrolled in the Pediatric Heart Network Infant Single Ventricle enalapril trial were analysed. Those with mixed ventricular types (n = 17) and one outlier (end-diastolic pressure = 32 mmHg) were excluded from the analysis, leaving a total sample size of 155 patients. Echocardiographic measurements were correlated to end-diastolic pressure using Spearman’s test.
Median age at echocardiogram was 4.6 (range 2.5–7.4) months. Median ventricular end-diastolic pressure was 7 (range 3–19) mmHg. Median time difference between the echocardiogram and catheterisation was 0 days (range −35 to 59 days). Examining the entire cohort of 155 patients, no echocardiographic diastolic function variable correlated with ventricular end-diastolic pressure. When the analysis was limited to the 86 patients who had similar sedation for both studies, the systolic:diastolic duration ratio had a significant but weak negative correlation with end-diastolic pressure (r = −0.3, p = 0.004). The remaining echocardiographic variables did not correlate with ventricular end-diastolic pressure.
In this cohort of infants with single ventricle physiology prior to superior cavopulmonary anastomosis, most conventional echocardiographic measures of diastolic function did not correlate with ventricular end-diastolic pressure at cardiac catheterisation. These limitations should be factored into the interpretation of quantitative echo data in this patient population.
Medical residents are an important group for antimicrobial stewardship programs (ASPs) to target with interventions aimed at improving antibiotic prescribing. In this study, we compared antimicrobial prescribing practices of 2 academic medical teams receiving different ASP training approaches along with a hospitalist control group.
Retrospective cohort study comparing guideline-concordant antibiotic prescribing for 3 common infections among a family medicine (FM) resident service, an internal medicine (IM) resident service, and hospitalists.
Community teaching hospital.
Adult patients admitted between July 1, 2016, and June 30, 2017, with a discharge diagnosis of pneumonia, cellulitis, and urinary tract infections were reviewed.
All 3 medical teams received identical baseline ASP education and daily antibiotic prescribing audit with feedback via clinical pharmacists. The FM resident service received an additional layer of targeted ASP intervention that included biweekly stewardship-focused rounds with an ASP physician and clinical pharmacist leadership. Guideline-concordant prescribing was assessed based on the institution’s ASP guidelines.
Of 1,572 patients, 295 (18.8%) were eligible for inclusion (FM, 96; IM, 69; hospitalist, 130). The percentage of patients receiving guideline-concordant antibiotic selection empirically was similar between groups for all diagnoses (FM, 87.5%; IM, 87%; hospitalist, 83.8%; P = .702). No differences were observed in appropriate definitive antibiotic selection among groups (FM, 92.4%; IM, 89.1%; hospitalist, 89.9%; P = .746). The FM resident service was more likely to prescribe a guideline-concordant duration of therapy across all diagnoses (FM, 74%; IM, 56.5%; hospitalist, 44.6%; P < .001).
Adding dedicated stewardship-focused rounds into the graduate medical curriculum demonstrated increased guideline adherence specifically to duration of therapy recommendations.