Robustness and epistasis in mutation-selection models

We investigate the fitness advantage associated with the robustness of a phenotype against deleterious mutations using deterministic mutation-selection models of quasispecies type equipped with a mesa shaped fitness landscape. We obtain analytic results for the robustness effect which become exact in the limit of infinite sequence length. Thereby, we are able to clarify a seeming contradiction between recent rigorous work and an earlier heuristic treatment based on a mapping to a Schr\"odinger equation. We exploit the quantum mechanical analogy to calculate a correction term for finite sequence lengths and verify our analytic results by numerical studies. In addition, we investigate the occurrence of an error threshold for a general class of epistatic landscape and show that diminishing epistasis is a necessary but not sufficient condition for error threshold behavior.Comment: 20 pages, 14 figure

Do bilinguals have different concepts? The case of shape and material in Japanese L2 users of English

An experiment investigated whether Japanese speakers’ categorisation of objects and substances as shape or material is influenced by acquiring English, based on Imai and Gentner (1997). Subjects were presented with an item such as a cork pyramid and asked to choose between two other items that matched it for shape (plastic pyramid) or for material (piece of cork). The hypotheses were that for simple objects the number of shape-based categorisations would increase according to experience of English and that the preference for shape and material-based categorisations of Japanese speakers of English would differ from mono¬lingual speakers of both languages. Subjects were 18 adult Japanese users of English who had lived in English-speaking countries between 6 months and 3 years (short-stay group), and 18 who had lived in English-speaking countries for 3 years or more (long-stay group). Both groups achieved above criterion on an English vocabulary test. Results were: both groups preferred material responses for simple objects and substances but not for complex objects, in line with Japanese mono¬linguals, but the long-stay group showed more shape preference than the short-stay group and also were less different from Americans. These effects of acquiring a second language on categorisation have implications for conceptual representation and methodology

Definição lexicográfica em semântica descritiva

O autor analisa os vários aspectos do ato de definir uma palavra para um dicionário eos tipos de critério a serem adotados. Uma questão de relevância é a do tipo de meta/íngua que se deveadotar na redação de um dicionário e a metodologia empregada para definir o "definiendum", podendo-se empregar várias estratégias: o método analítico, o método sintético, o método denotativo,o método ostensivo ou de mostração, o método implicativo, ou contextual. O método escolhido dependeráda natureza do termo a ser definido: um referente concreto, uma noção abstrata, uma ação ou processoverbal, um instrumento gramatical etc. A sinonímia e a antonímia amplamente usadas nas definiçõestêm também grande importância lexicográfica. O lexicógrafo, ou a equipe de dicionaristas que tra-.balham na confecção de um dicionário, nunca se deve esquecer que as suas definições devem valer paratoda a comunidade lingüística a que ele se destina e assim usarem a linguagem comum a todos e não o(s)seu(s) idioleto(s) particular(es)

Evolutionary dynamics of the most populated genotype on rugged fitness landscapes

We consider an asexual population evolving on rugged fitness landscapes which are defined on the multi-dimensional genotypic space and have many local optima. We track the most populated genotype as it changes when the population jumps from a fitness peak to a better one during the process of adaptation. This is done using the dynamics of the shell model which is a simplified version of the quasispecies model for infinite populations and standard Wright-Fisher dynamics for large finite populations. We show that the population fraction of a genotype obtained within the quasispecies model and the shell model match for fit genotypes and at short times, but the dynamics of the two models are identical for questions related to the most populated genotype. We calculate exactly several properties of the jumps in infinite populations some of which were obtained numerically in previous works. We also present our preliminary simulation results for finite populations. In particular, we measure the jump distribution in time and find that it decays as $t^{-2}$ as in the quasispecies problem.Comment: Minor changes. To appear in Phys Rev

Atomic Layer Deposition of Textured Li4Ti5O12 A High Power and Long Cycle Life Anode for Lithium Ion Thin Film Batteries

The zero strain Li4Ti5O12 is an attractive anode material for 3D solid state thin film batteries TFB to power upcoming autonomous sensor systems. Herein, Li4Ti5O12 thin films fabricated by atomic layer deposition ALD are electrochemically evaluated for the first time. The developed ALD process with a growth per cycle of 0.6 cycle amp; 8722;1 at 300 C enables high quality and dense spinel films with superior adhesion after annealing. The short lithium ion diffusion pathways of the nanostructured 30 nm films result in excellent electrochemical properties. Planar films reveal 98 of the theoretical capacity with 588 mAh cm amp; 8722;3 at 1 C. Substrate dependent film texture is identified as a key tuning parameter for exceptional C rate performance. The highly parallel grains of a strong out of plane 111 texture allow capacities of 278 mAh cm amp; 8722;3 at extreme rates of 200 C. Outstanding cycle performance is demonstrated, resulting in 97.9 capacity retention of the initial 366 mAh cm amp; 8722;3 after 1000 cycles at 100 C. Compared to other deposition techniques, the superior performance of ALD Li4Ti5O12 is a breakthrough towards scalable high power 3D TFB

In the absence of ATPase activity, pre-RC formation is blocked prior to MCM2-7 hexamer dimerization

The origin recognition complex (ORC) of Saccharomyces cerevisiae binds origin DNA and cooperates with Cdc6 and Cdt1 to load the replicative helicase MCM2–7 onto DNA. Helicase loading involves two MCM2–7 hexamers that assemble into a double hexamer around double-stranded DNA. This reaction requires ORC and Cdc6 ATPase activity, but it is unknown how these proteins control MCM2–7 double hexamer formation. We demonstrate that mutations in Cdc6 sensor-2 and Walker A motifs, which are predicted to affect ATP binding, influence the ORC–Cdc6 interaction and MCM2–7 recruitment. In contrast, a Cdc6 sensor-1 mutant affects MCM2–7 loading and Cdt1 release, similar as a Cdc6 Walker B ATPase mutant. Moreover, we show that Orc1 ATP hydrolysis is not involved in helicase loading or in releasing ORC from loaded MCM2–7. To determine whether Cdc6 regulates MCM2–7 double hexamer formation, we analysed complex assembly. We discovered that inhibition of Cdc6 ATPase restricts MCM2–7 association with origin DNA to a single hexamer, while active Cdc6 ATPase promotes recruitment of two MCM2–7 hexamer to origin DNA. Our findings illustrate how conserved Cdc6 AAA+ motifs modulate MCM2–7 recruitment, show that ATPase activity is required for MCM2–7 hexamer dimerization and demonstrate that MCM2–7 hexamers are recruited to origins in a consecutive process

Genital tract lesions in sexually mature Göttingen minipigs during the initial stages of experimental vaginal infection with <em>Chlamydia trachomatis </em>serovar D

BACKGROUND: Chlamydia is one of the most common sexually transmitted diseases in humans worldwide, causing chronic lesions in the reproductive tract. Due to its often asymptomatic course, there is limited knowledge about the initial changes in the genital tract following infection. This study employs a novel sexually mature minipig model to investigate the initial histopathological changes following vaginal infection with Chlamydia trachomatis serovar D. RESULTS: A vaginal inoculation resulted in an infection primarily affecting the lower genital tract. The histopathological changes were characterized by a subepithelial inflammation consisting of neutrophils and mononuclear cells, followed by an increase in the number of plasma cells within the sub-epithelial stroma of the vagina. Detection of Chlamydia was associated with expression of cyclooxygenase-2 and interleukin-8 by superficial epithelial cells. The infection was self-limiting, with a duration of 7 days. CONCLUSION: Neutrophils, plasma cells and IL-8 have been linked with Chlamydia genital infection of unknown duration in human patients. In this study, we observe a similar pattern of local immune response/inflammation following experimental inoculation suggesting this porcine model shows promise as a model for translational chlamydia research. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12917-016-0793-6) contains supplementary material, which is available to authorized users

Return to work after COVID-19 infection – A Danish nationwide registry study

OBJECTIVES: This study aimed to explore return to work after COVID-19 and how disease severity affects this. STUDY DESIGN: This is a Nationwide Danish registry–based cohort study using a retrospective follow-up design. METHODS: Patients with a first-time positive SARS-CoV-2 polymerase chain reaction test between 1 January 2020 and 30 May 2020, including 18–64 years old, 30-day survivors, and available to the workforce at the time of the first positive test were included. Admission types (i.e. no admission, admission to non–intensive care unit [ICU] department and admission to ICU) and return to work was investigated using Cox regression standardised to the age, sex, comorbidity and education-level distribution of all included subjects with estimates at 3 months from positive test displayed. RESULTS: Among the 7466 patients included in the study, 81.9% (6119/7466) and 98.4% (7344/7466) returned to work within 4 weeks and 6 months, respectively, with 1.5% (109/7466) not returning. Of the patients admitted, 72.1% (627/870) and 92.6% (805/870) returned 1 month and 6 months after admission to the hospital, with 6.6% (58/870) not returning within 6 months. Of patients admitted to the ICU, 36% (9/25) did not return within 6 months. Patients with an admission had a lower chance of return to work 3 months from positive test (relative risk [RR] 0.95, 95% confidence interval [CI] 0.94–0.96), with the lowest chance in patients admitted to an ICU department (RR 0.54, 95% CI 0.35–0.72). Female sex, older age, and comorbidity were associated with a lower chance of returning to work. CONCLUSION: Hospitalised patients with COVID-19 infection have a lower chance of returning to work with potential implications for postinfection follow-up and rehabilitation