GenomeScope is an open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate and repeat content from unprocessed short reads. These ...features are essential for studying genome evolution, and help to choose parameters for downstream analysis. We demonstrate its accuracy on 324 simulated and 16 real datasets with a wide range in genome sizes, heterozygosity levels and error rates.
http://genomescope.org , https://github.com/schatzlab/genomescope.git .
mschatz@jhu.edu.
Supplementary data are available at Bioinformatics online.
Electrical and chemical synapses coexist in circuits throughout the CNS. Yet, it is not well understood how electrical and chemical synaptic transmission interact to determine the functional output ...of networks endowed with both types of synapse. We found that release of glutamate from bipolar cells onto retinal ganglion cells (RGCs) was strongly shaped by gap-junction-mediated electrical coupling within the bipolar cell network of the mouse retina. Specifically, electrical synapses spread signals laterally between bipolar cells, and this lateral spread contributed to a nonlinear enhancement of bipolar cell output to visual stimuli presented closely in space and time. Our findings thus (1) highlight how electrical and chemical transmission can work in concert to influence network output and (2) reveal a previously unappreciated circuit mechanism that increases RGC sensitivity to spatiotemporally correlated input, such as that produced by motion.
•Gap junctions mediate lateral interactions across parallel ON bipolar cell circuits•These lateral interactions nonlinearly shape glutamate release from bipolar cells•Bipolar cell synaptic output is preferentially enhanced for low contrast stimuli•Nonlinear lateral interactions increase retinal ganglion cell sensitivity to motion
Kuo et al. find that electrical and chemical synaptic transmission work in concert to control glutamate release from retinal ON cone bipolar cells. This interaction enhances retinal ganglion cell sensitivity to visual inputs with strong spatiotemporal correlations, such as motion.
Sensory neurons downstream of primary receptors are selective for specific stimulus features, and they derive their selectivity both from excitatory and inhibitory synaptic inputs from other neurons ...and from their own intrinsic properties. Electrical synapses, formed by gap junctions, modulate sensory circuits. Retinal ganglion cells (RGCs) are diverse feature detectors carrying visual information to the brain, and receive excitatory input from bipolar cells and inhibitory input from amacrine cells (ACs). Here we describe a RGC that relies on gap junctions, rather than chemical synapses, to convey its selectivity for the orientation of a visual stimulus. This represents both a new functional role of electrical synapses as the primary drivers of feature selectivity and a new circuit mechanism for orientation selectivity in the retina.
A new 5-stage cardiogenic shock (CS) classification scheme was recently proposed by the Society for Cardiovascular Angiography and Intervention (SCAI) for the purpose of risk stratification.
This ...study sought to apply the SCAI shock classification in a cardiac intensive care unit (CICU) population.
The study retrospectively analyzed Mayo Clinic CICU patients admitted between 2007 and 2015. SCAI CS stages A through E were classified retrospectively using CICU admission data based on the presence of hypotension or tachycardia, hypoperfusion, deterioration, and refractory shock. Hospital mortality in each SCAI shock stage was stratified by cardiac arrest (CA).
Among the 10,004 unique patients, 43.1% had acute coronary syndrome, 46.1% had heart failure, and 12.1% had CA. The proportion of patients in SCAI CS stages A through E was 46.0%, 30.0%, 15.7%, 7.3%, and 1.0% and unadjusted hospital mortality in these stages was 3.0%, 7.1%, 12.4%, 40.4%, and 67.0% (p < 0.001), respectively. After multivariable adjustment, each higher SCAI shock stage was associated with increased hospital mortality (adjusted odds ratio: 1.53 to 6.80; all p < 0.001) compared with SCAI shock stage A, as was CA (adjusted odds ratio: 3.99; 95% confidence interval: 3.27 to 4.86; p < 0.001). Results were consistent in the subset of patients with acute coronary syndrome or heart failure.
When assessed at the time of CICU admission, the SCAI CS classification, including presence or absence of CA, provided robust hospital mortality risk stratification. This classification system could be implemented as a clinical and research tool to identify, communicate, and predict the risk of death in patients with, and at risk for, CS.
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Intracranial pressure (ICP) monitoring is now viewed as integral to the clinical care of many life-threatening brain insults, such as severe traumatic brain injury, subarachnoid hemorrhage, and ...malignant stroke. It serves to warn of expanding intracranial mass lesions, to prevent or treat herniation events as well as pressure elevation which impedes nutrient delivery to the brain. It facilitates the calculation of cerebral perfusion pressure (CPP) and the estimation of cerebrovascular autoregulatory status. Despite advancements in our knowledge emanating from a half century of experience with this technology, important controversies remain related even to fundamental aspects of ICP measurements, including indications for monitoring, ICP treatment thresholds, and management of intracranial hypertension. Here, we review the history of ICP monitoring, the underlying pathophysiology as well as current perspectives on why, when and how ICP monitoring is best used. ICP is typically assessed invasively but a number of emerging, non-invasive technologies with inherently lower risk are showing promise. In selected cases, additional neuromonitoring can be used to assist in the interpretation of ICP monitoring information and adapt directed treatment accordingly. Additional efforts to expand the evidence base relevant to ICP monitoring, related technologies and management remain a high priority in neurosurgery and neurocritical care.
Upcoming experimental programs, including the Beam Energy Scan at RHIC, will look for signatures of a possible critical point in the QCD phase diagram in fluctuation observables. To understand and ...predict these signatures, one must account for the fact that the dynamics of any critical fluctuations must be out-of-equilibrium: because of critical slowing down, the fluctuations cannot stay in equilibrium as the droplet of quark gluon plasma produced in a collision expands and cools. Furthermore, their out-of-equilibrium dynamics must also influence the hydrodynamic evolution of the cooling droplet. The recently developed Hydro+ formalism allows for a consistent description of both the hydrodynamics and the out-of-equilibrium fluctuations, including the feedback between them. We shall provide an explicit demonstration of how this works, setting up a Hydro+ simulation in a simplified setting: a rapidity-independent fireball undergoing radial flow with an equation of state in which we imagine a critical point close to the μB = 0 axis of the phase diagram. Within this setup, we show that we can quantitatively capture nonequilibrium phenomena, including critical fluctuations over a range of scales and memory effects. Furthermore, we illustrate the interplay between the dynamics of the fluctuations and the hydrodynamic flow of the fireball: as the fluid cools and flows, the dynamical fluctuations lag relative to how they would evolve if they stayed in equilibrium; there is then a backreaction on the flow itself due to the out-of-equilibrium fluctuations; and, in addition, the radial flow transports fluctuations outwards by advection. Within our model, we find that the backreaction from the out-of-equilibrium fluctuations does not yield dramatically large effects in the hydrodynamic variables. Further work will be needed in order to check this quantitative conclusion in other settings but, if it persists, this will considerably simplify future modeling.
Biogeographic disjunction patterns, where multiple taxa are shared between isolated geographic areas, represent excellent systems for investigating the historical assembly of modern biotas and ...fundamental biological processes such as speciation, diversification, niche evolution, and evolutionary responses to climate change. Studies on plant genera disjunct across the northern hemisphere, particularly between eastern North America (ENA) and eastern Asia (EAS), have yielded tremendous insight on the geologic history and assembly of rich temperate floras. However, one of the most prevalent disjunction patterns involving ENA forests has been largely overlooked: that of taxa disjunct between ENA and cloud forests of Mesoamerica (MAM), with examples including Acer saccharum, Liquidambar styraciflua, Cercis canadensis, Fagus grandifolia, and Epifagus virginiana. Despite the remarkable nature of this disjunction pattern, which has been recognized for over 75 years, there have been few recent efforts to empirically examine its evolutionary and ecological origins. Here I synthesize previous systematic, paleobotanical, phylogenetic, and phylogeographic studies to establish what is known about this disjunction pattern to provide a roadmap for future research. I argue that this disjunction pattern, and the evolution and fossil record of the Mexican flora more broadly, represents a key missing piece in the broader puzzle of northern hemisphere biogeography. I also suggest that the ENA–MAM disjunction represents an excellent system for examining fundamental questions about how traits and life history strategies mediate plant evolutionary responses to climate change and for predicting how broadleaf temperate forests will respond to the ongoing climatic pressures of the Anthropocene.
Abstract
When the fourth edition of the Brain Trauma Foundation's Guidelines for the Management of Severe Traumatic Brain Injury were finalized in late 2016, it was known that the results of the ...RESCUEicp (Trial of Decompressive Craniectomy for Traumatic Intracranial Hypertension) randomized controlled trial of decompressive craniectomy would be public after the guidelines were released. The guideline authors decided to proceed with publication but to update the decompressive craniectomy recommendations later in the spirit of “living guidelines,” whereby topics are updated more frequently, and between new editions, when important new evidence is published. The update to the decompressive craniectomy chapter presented here integrates the findings of the RESCUEicp study as well as the recently published 12-mo outcome data from the DECRA (Decompressive Craniectomy in Patients With Severe Traumatic Brain Injury) trial. Incorporation of these publications into the body of evidence led to the generation of 3 new level-IIA recommendations; a fourth previously presented level-IIA recommendation remains valid and has been restated. To increase the utility of the recommendations, we added a new section entitled Incorporating the Evidence into Practice. This summary of expert opinion provides important context and addresses key issues for practitioners, which are intended to help the clinician utilize the available evidence and these recommendations.
The full guideline can be found at: https://braintrauma.org/guidelines/guidelines-for-the-management-of-severe-tbi-4th-ed#/.
In recent decades, the prevalence of overweight and obesity has become increasingly common such that it is now the major nutritional problem worldwide. Obesity occurs when dietary energy intake ...exceeds energy expenditure and has arisen in many societies due to an increasingly “obesogenic” environment in which physical activity has declined and yet children continue to be exposed to unhealthy, energy-dense diets. Additional risks for the development of obesity also include psychological issues and genetic factors. Obesity has many adverse health consequences including development of insulin resistance, Type 2 diabetes, and the metabolic syndrome. There are also important genetic influences on the likelihood of developing insulin resistance. Given the limited success of therapeutic interventions to treat obesity and the metabolic syndrome, there has been an increased interest in preventative strategies. These are likely to be most successful when targeting the young and will require a combination of approaches which will need inter-disciplinary collaborations across health and local government to target families, schools, and local environments to facilitate behavior changes which influence young people's eating behaviors and habitual levels of physical activity.
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