Dynamic Stability and Thermodynamic Characterization in an Enzymatic Reaction at the Single Molecule Level

In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability distribution, the reaction velocity, and its efficiency of energy conversion depend on the system parameters. We employ in this study a recently introduced formalism for performing a multiscale thermodynamic analysis in continuous-time discrete-state stochastic systems.Comment: In Press in Physica

Morphometricity as a measure of the neuroanatomical signature of a trait

Complex physiological and behavioral traits, including neurological and psychiatric disorders, often associate with distributed anatomical variation. This paper introduces a global metric, called morphometricity, as a measure of the anatomical signature of different traits. Morphometricity is defined as the proportion of phenotypic variation that can be explained by macroscopic brain morphology. We estimate morphometricity via a linear mixed-effects model that uses an anatomical similarity matrix computed based on measurements derived from structural brain MRI scans. We examined over 3,800 unique MRI scans from nine large-scale studies to estimate the morphometricity of a range of phenotypes, including clinical diagnoses such as Alzheimer’s disease, and nonclinical traits such as measures of cognition. Our results demonstrate that morphometricity can provide novel insights about the neuroanatomical correlates of a diverse set of traits, revealing associations that might not be detectable through traditional statistical techniques.National Institute for Biomedical Imaging and Bioengineering (U.S.) (R01EB006758)National Institute for Biomedical Imaging and Bioengineering (U.S.) (P41EB015896)National Institute for Biomedical Imaging and Bioengineering (U.S.) (R21EB018907)National Institute for Biomedical Imaging and Bioengineering (U.S.) (R01EB019956)National Institute on Aging (5R01AG008122)National Institute on Aging (R01AG016495)National Institute of Neurological Diseases and Stroke (U.S.) (R01NS0525851)National Institute of Neurological Diseases and Stroke (U.S.) (R21NS072652)National Institute of Neurological Diseases and Stroke (U.S.) (R01NS070963)National Institute of Neurological Diseases and Stroke (U.S.) (R01NS083534)National Institute of Neurological Diseases and Stroke (U.S.) (5U01NS086625)United States. National Institutes of Health (5U01-MH093765)United States. National Institutes of Health (R01NS083534)United States. National Institutes of Health (R01NS070963)United States. National Institutes of Health (R41AG052246)United States. National Institutes of Health (1K25EB013649-01

Metagenomic study of the viruses of African straw-coloured fruit bats: detection of a chiropteran poxvirus and isolation of a novel adenovirus

Viral emergence as a result of zoonotic transmission constitutes a continuous public health threat. Emerging viruses such as SARS coronavirus, hantaviruses and henipaviruses have wildlife reservoirs. Characterising the viruses of candidate reservoir species in geographical hot spots for viral emergence is a sensible approach to develop tools to predict, prevent, or contain emergence events. Here, we explore the viruses of Eidolon helvum, an Old World fruit bat species widely distributed in Africa that lives in close proximity to humans. We identified a great abundance and diversity of novel herpes and papillomaviruses, described the isolation of a novel adenovirus, and detected, for the first time, sequences of a chiropteran poxvirus closely related with Molluscum contagiosum. In sum, E. helvum display a wide variety of mammalian viruses, some of them genetically similar to known human pathogens, highlighting the possibility of zoonotic transmission

Multidimensional heritability analysis of neuroanatomical shape

In the dawning era of large-scale biomedical data, multidimensional phenotype vectors will play an increasing role in examining the genetic underpinnings of brain features, behaviour and disease. For example, shape measurements derived from brain MRI scans are multidimensional geometric descriptions of brain structure and provide an alternate class of phenotypes that remains largely unexplored in genetic studies. Here we extend the concept of heritability to multidimensional traits, and present the first comprehensive analysis of the heritability of neuroanatomical shape measurements across an ensemble of brain structures based on genome-wide SNP and MRI data from 1,320 unrelated, young and healthy individuals. We replicate our findings in an extended twin sample from the Human Connectome Project (HCP). Our results demonstrate that neuroanatomical shape can be significantly heritable, above and beyond volume, and can serve as a complementary phenotype to study the genetic determinants and clinical relevance of brain structure.National Institute for Biomedical Imaging and Bioengineering (U.S.) (P41EB015896)United States. National Institutes of Health (S10RR023043)United States. National Institutes of Health (S10RR023401)United States. National Institutes of Health (K25CA181632)United States. National Institutes of Health (K01MH099232)United States. National Institutes of Health (K99MH101367)United States. National Institutes of Health (R21AG050122-01A1)United States. National Institutes of Health (R41AG052246-01)United States. National Institutes of Health (1K25EB013649-01)United States. National Institutes of Health (K24MH094614)United States. National Institutes of Health (R01MH101486

Strange Attractors in Dissipative Nambu Mechanics : Classical and Quantum Aspects

We extend the framework of Nambu-Hamiltonian Mechanics to include dissipation in $R^{3}$ phase space. We demonstrate that it accommodates the phase space dynamics of low dimensional dissipative systems such as the much studied Lorenz and R\"{o}ssler Strange attractors, as well as the more recent constructions of Chen and Leipnik-Newton. The rotational, volume preserving part of the flow preserves in time a family of two intersecting surfaces, the so called {\em Nambu Hamiltonians}. They foliate the entire phase space and are, in turn, deformed in time by Dissipation which represents their irrotational part of the flow. It is given by the gradient of a scalar function and is responsible for the emergence of the Strange Attractors. Based on our recent work on Quantum Nambu Mechanics, we provide an explicit quantization of the Lorenz attractor through the introduction of Non-commutative phase space coordinates as Hermitian $N \times N$ matrices in $R^{3}$. They satisfy the commutation relations induced by one of the two Nambu Hamiltonians, the second one generating a unique time evolution. Dissipation is incorporated quantum mechanically in a self-consistent way having the correct classical limit without the introduction of external degrees of freedom. Due to its volume phase space contraction it violates the quantum commutation relations. We demonstrate that the Heisenberg-Nambu evolution equations for the Quantum Lorenz system give rise to an attracting ellipsoid in the $3 N^{2}$ dimensional phase space.Comment: 35 pages, 4 figures, LaTe

Single-photon emission from isolated monolayer islands of InGaN

We identify and characterize a novel type of quantum emitter formed from InGaN monolayer islands grown using molecular beam epitaxy and further isolated via the fabrication of an array of nanopillar structures. Detailed optical analysis of the characteristic emission spectrum from the monolayer islands is performed, and the main transmission is shown to act as a bright, stable, and fast single-photon emitter with a wavelength of ~400 nm. © 2020, The Author(s)

The host metabolite D-serine contributes to bacterial niche specificity through gene selection

Escherichia coli comprise a diverse array of both commensals and niche-specific pathotypes. The ability to cause disease results from both carriage of specific virulence factors and regulatory control of these via environmental stimuli. Moreover, host metabolites further refine the response of bacteria to their environment and can dramatically affect the outcome of the host–pathogen interaction. Here, we demonstrate that the host metabolite, D-serine, selectively affects gene expression in E. coli O157:H7. Transcriptomic profiling showed exposure to D-serine results in activation of the SOS response and suppresses expression of the Type 3 Secretion System (T3SS) used to attach to host cells. We also show that concurrent carriage of both the D-serine tolerance locus (dsdCXA) and the locus of enterocyte effacement pathogenicity island encoding a T3SS is extremely rare, a genotype that we attribute to an ‘evolutionary incompatibility’ between the two loci. This study demonstrates the importance of co-operation between both core and pathogenic genetic elements in defining niche specificity

Deliquescence of NaCl–NaNO(3), KNO(3)–NaNO(3), and NaCl–KNO(3 )salt mixtures from 90 to 120°C

We conducted reversed deliquescence experiments in saturated NaCl–NaNO(3)–H(2)O, KNO(3)–NaNO(3)–H(2)O, and NaCl–KNO(3)–H(2)O systems from 90 to 120°C as a function of relative humidity and solution composition. NaCl, NaNO(3), and KNO(3 )represent members of dust salt assemblages that are likely to deliquesce and form concentrated brines on high-level radioactive waste package surfaces in a repository environment at Yucca Mountain, NV. Discrepancy between model prediction and experiment can be as high as 8% for relative humidity and 50% for dissolved ion concentration. The discrepancy is attributed primarily to the use of 25°C models for Cl–NO(3 )and K–NO(3 )ion interactions in the current Yucca Mountain Project high-temperature Pitzer model to describe the nonideal behavior of these highly concentrated solutions

Interoperability of Statistical Models in Pandemic Preparedness: Principles and Reality

We present "interoperability" as a guiding framework for statistical modelling to assist policy makers asking multiple questions using diverse datasets in the face of an evolving pandemic response. Interoperability provides an important set of principles for future pandemic preparedness, through the joint design and deployment of adaptable systems of statistical models for disease surveillance using probabilistic reasoning. We illustrate this through case studies for inferring spatial-temporal coronavirus disease 2019 (COVID-19) prevalence and reproduction numbers in England

Preventing intrusive memories after trauma via a brief intervention involving Tetris computer game play in the emergency department: a proof-of-concept randomized controlled trial.

After psychological trauma, recurrent intrusive visual memories may be distressing and disruptive. Preventive interventions post trauma are lacking. Here we test a behavioural intervention after real-life trauma derived from cognitive neuroscience. We hypothesized that intrusive memories would be significantly reduced in number by an intervention involving a computer game with high visuospatial demands (Tetris), via disrupting consolidation of sensory elements of trauma memory. The Tetris-based intervention (trauma memory reminder cue plus c. 20 min game play) vs attention-placebo control (written activity log for same duration) were both delivered in an emergency department within 6 h of a motor vehicle accident. The randomized controlled trial compared the impact on the number of intrusive trauma memories in the subsequent week (primary outcome). Results vindicated the efficacy of the Tetris-based intervention compared with the control condition: there were fewer intrusive memories overall, and time-series analyses showed that intrusion incidence declined more quickly. There were convergent findings on a measure of clinical post-trauma intrusion symptoms at 1 week, but not on other symptom clusters or at 1 month. Results of this proof-of-concept study suggest that a larger trial, powered to detect differences at 1 month, is warranted. Participants found the intervention easy, helpful and minimally distressing. By translating emerging neuroscientific insights and experimental research into the real world, we offer a promising new low-intensity psychiatric intervention that could prevent debilitating intrusive memories following trauma