Twinning hierarchy, shape memory, and superelasticity demonstrated by molecular dynamics

A martensitic phase transition exhibiting shape memory, transformation-induced plasticity, or superelasticity typically involves a transformation between a high temperature, high symmetry phase and a low temperature, low symmetry phase. There have been numerous attempts using molecular dynamics to simulate the shape memory behavior, where the memory is stored in a twinned martensite and deformation occurs by motion of twin boundaries. However, the 3D case has always proved elusive, because suitable interatomic potentials to produce a unique low temperature phase are difficult to obtain. Here we present a study in which the binary Morse potential is tuned specifically to maximize the difference between L1_{0} and B19 (Strukturbericht notation, spacegroups P4/mmm and Pmma) structures. The twinned structure of martensite has been induced by gradually cooling the sample below the transition temperature. A bar-shaped sample was plastically deformed in the martensite phase, and on reheating above the transition temperature the initial shape was recovered. The effect of the shear-induced phase transition on the nanostructure of resulting martensite has also been investigated. An unusual discovery is that of a hierarchy of twins: nanotwins accommodate the mismatch between austenite and martensite at the habit plane, while dynamically created macrotwins are responsible for the deformation behavior and shape memory

Toward detailed prominence seismology - I. Computing accurate 2.5D magnetohydrodynamic equilibria

Context. Prominence seismology exploits our knowledge of the linear eigenoscillations for representative magnetohydro- dynamic models of filaments. To date, highly idealized models for prominences have been used, especially with respect to the overall magnetic configurations. Aims. We initiate a more systematic survey of filament wave modes, where we consider full multi-dimensional models with twisted magnetic fields representative of the surrounding magnetic flux rope. This requires the ability to compute accurate 2.5 dimensional magnetohydrodynamic equilibria that balance Lorentz forces, gravity, and pressure gradients, while containing density enhancements (static or in motion). Methods. The governing extended Grad-Shafranov equation is discussed, along with an analytic prediction for circular flux ropes for the Shafranov shift of the central magnetic axis due to gravity. Numerical equilibria are computed with a finite element-based code, demonstrating fourth order accuracy on an explicitly known, non-trivial test case. Results. The code is then used to construct more realistic prominence equilibria, for all three possible choices of a free flux-function. We quantify the influence of gravity, and generate cool condensations in hot cavities, as well as multi- layered prominences. Conclusions. The internal flux rope equilibria computed here have the prerequisite numerical accuracy to allow a yet more advanced analysis of the complete spectrum of linear magnetohydrodynamic perturbations, as will be demonstrated in the companion paper.Comment: Accepted by Astronomy & Astrophysics, 15 pages, 15 figure

Chronic Invasive Aspergillosis caused by Aspergillus viridinutans

Aspergillus viridinutans, a mold phenotypically resembling A. fumigatus, was identified by gene sequence analyses from 2 patients. Disease was distinct from typical aspergillosis, being chronic and spreading in a contiguous manner across anatomical planes. We emphasize the recognition of fumigati-mimetic molds as agents of chronic or refractory aspergillosis

Magnetohydrodynamic equilibria of a cylindrical plasma with poloidal mass flow and arbitrary cross section shape

The equilibrium of a cylindrical plasma with purely poloidal mass flow and cross section of arbitrary shape is investigated within the framework of the ideal MHD theory. For the system under consideration it is shown that only incompressible flows are possible and, conscequently, the general two dimensional flow equilibrium equations reduce to a single second-order quasilinear partial differential equation for the poloidal magnetic flux function $\psi$, in which four profile functionals of $\psi$ appear. Apart from a singularity occuring when the modulus of Mach number associated with the Alfv\'en velocity for the poloidal magnetic field is unity, this equation is always elliptic and permits the construction of several classes of analytic solutions. Specific exact equlibria for a plasma confined within a perfectly conducting circular cylindrical boundary and having i) a flat current density and ii) a peaked current density are obtained and studied.Comment: Accepted to Plasma Physics & Controlled Fusion, 14 pages, revte

Barley plasma membrane intrinsic proteins (PIP aquaporins) as water and CO2 transporters

We identified barley aquaporins and demonstrated that one, HvPIP2;1, transports water and CO2. Regarding water homeostasis in plants, regulations of aquaporin expression were observed in many plants under several environmental stresses. Under salt stress, a number of plasma membrane-type aquaporins were down-regulated, which can prevent continuous dehydration resulting in cell death. The leaves of transgenic rice plants that expressed the largest amount of HvPIP2;1 showed a 40% increase in internal CO2 conductance compared with leaves of wild-type rice plants. The rate of CO2 assimilation also increased in the transgenic plants. The goal of our plant aquaporin research is to determine the key aquaporin species responsible for water and CO2 transport, and to improve plant water relations, stress tolerance, CO2 uptake or assimilation, and plant productivity via molecular breeding of aquaporins.</p

A Novel Bacterium Associated with Lymphadenitis in a Patient with Chronic Granulomatous Disease

Chronic granulomatous disease (CGD) is a rare inherited disease of the phagocyte NADPH oxidase system causing defective production of toxic oxygen metabolites, impaired bacterial and fungal killing, and recurrent life-threatening infections. We identified a novel gram-negative rod in excised lymph nodes from a patient with CGD. Gram-negative rods grew on charcoal-yeast extract, but conventional tests could not identify it. The best 50 matches of the 16S rRNA (using BLAST) were all members of the family Acetobacteraceae, with the closest match being Gluconobacter sacchari. Patient serum showed specific band recognition in whole lysate immunoblot. We used mouse models of CGD to determine whether this organism was a genuine CGD pathogen. Intraperitoneal injection of gp91(phox) (−/−) (X-linked) and p47 (phox −/−) (autosomal recessive) mice with this bacterium led to larger burdens of organism recovered from knockout compared with wild-type mice. Knockout mouse lymph nodes had histopathology that was similar to that seen in our patient. We recovered organisms with 16S rRNA sequence identical to the patient's original isolate from the infected mice. We identified a novel gram-negative rod from a patient with CGD. To confirm its pathogenicity, we demonstrated specific immune reaction by high titer antibody, showed that it was able to cause similar disease when introduced into CGD, but not wild-type mice, and we recovered the same organism from pathologic lesions in these mice. Therefore, we have fulfilled Koch's postulates for a new pathogen. This is the first reported case of invasive human disease caused by any of the Acetobacteraceae. Polyphasic taxonomic analysis shows this organism to be a new genus and species for which we propose the name Granulobacter bethesdensis

Cluster randomized controlled trial protocol: addressing reproductive coercion in health settings (ARCHES)

Background\ud Women ages 16–29 utilizing family planning clinics for medical services experience higher rates of intimate partner violence (IPV) and reproductive coercion (RC) than their same-age peers, increasing risk for unintended pregnancy and related poor reproductive health outcomes. Brief interventions integrated into routine family planning care have shown promise in reducing risk for RC, but longer-term intervention effects on partner violence victimization, RC, and unintended pregnancy have not been examined.\ud \ud Methods/Design\ud The ‘Addressing Reproductive Coercion in Health Settings (ARCHES)’ Intervention Study is a cluster randomized controlled trial evaluating the effectiveness of a brief, clinician-delivered universal education and counseling intervention to reduce IPV, RC and unintended pregnancy compared to standard-of-care in family planning clinic settings. The ARCHES intervention was refined based on formative research. Twenty five family planning clinics were randomized (in 17 clusters) to either a three hour training for all family planning clinic staff on how to deliver the ARCHES intervention or to a standard-of-care control condition. All women ages 16–29 seeking care in these family planning clinics were eligible to participate. Consenting clients use laptop computers to answer survey questions immediately prior to their clinic visit, a brief exit survey immediately after the clinic visit, a first follow up survey 12–20 weeks after the baseline visit (T2), and a final survey 12 months after the baseline (T3). Medical record chart review provides additional data about IPV and RC assessment and disclosure, sexual and reproductive health diagnoses, and health care utilization. Of 4009 women approached and determined to be eligible based on age (16–29 years old), 3687 (92 % participation) completed the baseline survey and were included in the sample.\ud \ud Discussion\ud The ARCHES Intervention Study is a community-partnered study designed to provide arigorous assessment of the short (3-4 months) and long-term (12 months) effects of a brief, clinician-delivered universal education and counseling intervention to reduce IPC, RC and unintended pregnancy in family planning clinic settings. The trial features a cluster randomized controlled trial design, a comprehensive data collection schedule and a large sample size with excellent retention.\ud \ud Trial Registration\ud ClinicialTrials.gov NCT01459458. Registered 10 October 2011

Viability and Burden of Leishmania in Extralesional Sites during Human Dermal Leishmaniasis

Understanding of the dynamics and distribution of Leishmania in the human host is fundamental to the targeting of control measures and their evaluation. Amplification of parasite gene sequences in clinical samples from cutaneous leishmaniasis patients has provided evidence of Leishmania in blood, other tissues and sites distinct from the lesion and of persistence of infection after clinical resolution of disease. However, there is uncertainty about the interpretation of the presence of Leishmania DNA as indicative of viable parasites. Because RNA is short-lived and labile, its presence provides an indicator of viability. We amplified Leishmania 7SLRNA, a molecule involved in intracellular protein translocation, to establish viability and estimate parasite load in blood monocytes, tonsil swab samples, and tissue fluid from healthy skin of patients with dermal leishmaniasis. Results showed that during active dermal leishmaniasis, viable Leishmania are present in blood monocytes, tonsils and normal skin in quantities similar to that in lesions, demonstrating widespread dissemination of infection and subclinical involvement of tissues beyond the lesion site. Leishmania 7SLRNA will be useful in deciphering the role of human infection in transmission