Driven activation versus thermal activation

Activated dynamics in a glassy system undergoing steady shear deformation is studied by numerical simulations. Our results show that the external driving force has a strong influence on the barrier crossing rate, even though the reaction coordinate is only weakly coupled to the nonequilibrium system. This "driven activation" can be quantified by introducing in the Arrhenius expression an effective temperature, which is close to the one determined from the fluctuation-dissipation relation. This conclusion is supported by analytical results for a simplified model system.Comment: 5 pages, 3 figure

Tagged particle in a sheared suspension: effective temperature determines density distribution in a slowly varying external potential beyond linear response

We consider a sheared colloidal suspension under the influence of an external potential that varies slowly in space in the plane perpendicular to the flow and acts on one selected (tagged) particle of the suspension. Using a Chapman-Enskog type expansion we derive a steady state equation for the tagged particle density distribution. We show that for potentials varying along one direction only, the tagged particle distribution is the same as the equilibrium distribution with the temperature equal to the effective temperature obtained from the violation of the Einstein relation between the self-diffusion and tagged particle mobility coefficients. We thus prove the usefulness of this effective temperature for the description of the tagged particle behavior beyond the realm of linear response. We illustrate our theoretical predictions with Brownian dynamics computer simulations.Comment: Accepted for publication in Europhys. Let

Diffusion-jump model for the combined Brownian and Neel relaxation dynamics of ferrofluids in the presence of external fields and flow

Relaxation of suspended magnetic nanoparticles occurs via Brownian rotational diffusion of the particle as well as internal magnetization dynamics. The latter is often modeled by the stochastic Landau-Lifshitz equation, but its numerical treatment becomes prohibitively expensive in many practical applications due to a time-scale separation between fast, Larmor-type precession and slow, barrier-crossing dynamics. Here, a diffusion-jump model is proposed to take advantage of the time-scale separation and to approximate barrier-crossings as thermally activated jump processes that occur alongside rotational diffusion. The predictions of our diffusion-jump model are compared to reference results obtained by solving the stochastic Landau-Lifshitz equation coupled to rotational Brownian motion. Good agreement is found in the regime of high energy barriers where Neel relaxation can be considered a thermally activated rare event. While many works in the field have neglected N\'eel relaxation altogether, our approach opens the possibility to efficiently include Neel relaxation also into interacting many-particle models

Karakterisasi Keragaman Genetik Populasi Jabon Putih Menggunakan Penanda Random Amplified Polymorphism Dna

Anthocepalus cadamba (white jabon) has high economical value for furniture. White jabon forests severely degraded due to intensive exploitation and land conversion. Genetic diversity is one of important consideration to design conservation and improvement strategies. Aim of this study was to access the genetic diversity values within and among population of white jabon. Leaf samples of white jabon were collected from conservation plots originated from West Lombok, Sumbawa, South Sumatera and West Sumatera. Red jabon was included as an outgroup population. Based on 37 polymorphic RAPD loci, the results showed comparable value of genetic diversity between white jabon and red jabon. Number of detected and rare alleles was highest founded in Sumbawa population among the other three populations of white jabon. As consequence, value of expected heterozygosity in the population was highest (HE=0.315). Private allele was only detected in South Sumatera population. Principal coordinate analysis (PCA) showed that integrating between genetic and geographical distance was inconsistent; similar gene resources or human impact might be responsible for this result. The populations that have high value of genetic diversity and private allele are recommended to be selected for the conservation strategies, i.e. Sumbawa and South Sumatera

RepSeq-A database of amino acid repeats present in lower eukaryotic pathogens

BACKGROUND Amino acid repeat-containing proteins have a broad range of functions and their identification is of relevance to many experimental biologists. In human-infective protozoan parasites (such as the Kinetoplastid and Plasmodium species), they are implicated in immune evasion and have been shown to influence virulence and pathogenicity. RepSeq http://repseq.gugbe.com is a new database of amino acid repeat-containing proteins found in lower eukaryotic pathogens. The RepSeq database is accessed via a web-based application which also provides links to related online tools and databases for further analyses. RESULTS The RepSeq algorithm typically identifies more than 98% of repeat-containing proteins and is capable of identifying both perfect and mismatch repeats. The proportion of proteins that contain repeat elements varies greatly between different families and even species (3 - 35% of the total protein content). The most common motif type is the Sequence Repeat Region (SRR) - a repeated motif containing multiple different amino acid types. Proteins containing Single Amino Acid Repeats (SAARs) and Di-Peptide Repeats (DPRs) typically account for 0.5 - 1.0% of the total protein number. Notable exceptions are P. falciparum and D. discoideum, in which 33.67% and 34.28% respectively of the predicted proteomes consist of repeat-containing proteins. These numbers are due to large insertions of low complexity single and multi-codon repeat regions. CONCLUSION The RepSeq database provides a repository for repeat-containing proteins found in parasitic protozoa. The database allows for both individual and cross-species proteome analyses and also allows users to upload sequences of interest for analysis by the RepSeq algorithm. Identification of repeat-containing proteins provides researchers with a defined subset of proteins which can be analysed by expression profiling and functional characterisation, thereby facilitating study of pathogenicity and virulence factors in the parasitic protozoa. While primarily designed for kinetoplastid work, the RepSeq algorithm and database retain full functionality when used to analyse other species

The ATLAS inner detector trigger performance in pp collisions at 13 TeV during LHC Run 2

The design and performance of the inner detector trigger for the high level trigger of the ATLAS experiment at the Large Hadron Collider during the 2016–2018 data taking period is discussed. In 2016, 2017, and 2018 the ATLAS detector recorded 35.6 fb−1, 46.9 fb−1, and 60.6 fb−1 respectively of proton–proton collision data at a centre-of-mass energy of 13 TeV. In order to deal with the very high interaction multiplicities per bunch crossing expected with the 13 TeV collisions the inner detector trigger was redesigned during the long shutdown of the Large Hadron Collider from 2013 until 2015. An overview of these developments is provided and the performance of the tracking in the trigger for the muon, electron, tau and b-jet signatures is discussed. The high performance of the inner detector trigger with these extreme interaction multiplicities demonstrates how the inner detector tracking continues to lie at the heart of the trigger performance and is essential in enabling the ATLAS physics programme

Cavalier King Charles Spaniels with Chiari-like malformation and Syringomyelia have increased variability of spatio-temporal gait characteristics

Abstract Background Chiari-like malformation in the Cavalier King Charles Spaniel is a herniation of the cerebellum and brainstem into or through the foramen magnum. This condition predisposes to Syringomyelia; fluid filled syrinxes within the spinal cord. The resulting pathology in spinal cord and cerebellum create neuropathic pain and changes in gait. This study aims to quantify the changes in gait for Cavalier King Charles Spaniel with Chiari-like malformation and Syringomyelia. Methods We compared Cavalier King Charles Spaniel with Chiari-like malformation with (n = 9) and without (n = 8) Syringomyelia to Border Terriers (n = 8). Two video cameras and manual tracking was used to quantify gait parameters. Results and conclusions We found a significant increase in coefficient of variation for the spatio-temporal characteristics and ipsilateral distance between paws and a wider base of support in the thoracic limbs but not in the pelvic limbs for Cavalier King Charles Spaniels compared with the border terrier

Internal Insulation of Historic Buildings: A Stochastic Approach to Life Cycle Costing Within RIBuild EU Project

The application of internal insulation is a widespread and effective solution for energy renovation of historic buildings.However, it entails quite high installation costs and a certain risk of failure due to moisture-related problems. A probabilistic risk assessment of both hygrothermal performance and life cycle costs can be used to address internal insulation issue, in order to support riskmanagement and decisionmaking. This paper presents the application of a probabilistic approach to Life Cycle Costing developed within the EU project RIBuild (Robust Internal Thermal Insulation of Historic Buildings), to five internal insulations solutions widely used in Italy. The method provides estimates of the range and likelihood of global costs and payback periods, also considering alternative energy and future economic scenarios. The impact of insulation systems service life on global costs is also addressed, in order to highlight the possible connection of the method to a stochastic estimation of insulation systems durability based on hygrothermal and damage assessments

Exercise and Physical Therapy Interventions for Children with Ataxia: a systematic review

The effectiveness of exercise and physical therapy for children with ataxia is poorly understood. The aim of this systematic review was to critically evaluate the range, scope and methodological quality of studies investigating the effectiveness of exercise and physical therapy interventions for children with ataxia. The following databases were searched: AMED, CENTRAL, CDSR, CINAHL, ClinicalTrials.gov, EMBASE, Ovid MEDLINE, PEDro and Web of Science. No limits were placed on language, type of study or year of publication. Two reviewers independently determined whether the studies met the inclusion criteria, extracted all relevant outcomes, and conducted methodological quality assessments. A total of 1988 studies were identified, and 124 full texts were screened. Twenty studies were included in the review. A total of 40 children (aged 5-18 years) with ataxia as a primary impairment participated in the included studies. Data were able to be extracted from eleven studies with a total of 21 children (aged 5-18 years), with a range of cerebellar pathology. The studies reported promising results but were of low methodological quality (no RCTs), used small sample sizes and were heterogeneous in terms of interventions, participants and outcomes. No firm conclusions can be made about the effectiveness of exercise and physical therapy for children with ataxia. There is a need for further high-quality child-centred research

Immunohistochemical analysis of brain lesions using S100B and glial fibrillary acidic protein antibodies in arundic acid- (ONO-2506) treated stroke-prone spontaneously hypertensive rats

Stroke-prone spontaneously hypertensive rats (SHRSP) used as a model of essential hypertension cause a high incidence of brain stroke on the course of hypertension. Incidences and sizes of brain lesions are known to relate to the astrocyte activities. Therefore, relation between brain damage and the expression profile of the astrocytes was investigated with morphometric and immunohistochemical analyses using astrocyte marker antibodies of S100B and glial fibrillary acidic protein (GFAP) with or without arundic acid administration, a suppressor on the activation of astrocytes. Arundic acid extended the average life span of SHRSP. An increase in brain tissue weight was inhibited concomitant with a lower rate of gliosis/hemosiderin deposit/scarring in brain lesions. S100B- or GFAP-positive dot and filamentous structures were decreased in arundic acid-treated SHRSP, and this effect was most pronounced in the cerebral cortex, white matter, and pons, and less so in the hippocampus, diencephalon, midbrain, and cerebellum. Blood pressure decreased after administration of arundic acid in the high-dose group (100 mg/kg/day arundic acid), but not in the low-dose group (30 mg/kg/day). These data indicate that arundic acid can prevent hypertension-induced stroke, and may inhibit the enlargement of the stroke lesion by preventing the inflammatory changes caused by overproduction of the S100B protein in the astrocytes