Deciphering the metabolic response of Mycobacterium tuberculosis to nitrogen stress.

© 2015 John Wiley & Sons Ltd.A key component to the success of Mycobacterium tuberculosis as a pathogen is the ability to sense and adapt metabolically to the diverse range of conditions encountered in vivo, such as oxygen tension, environmental pH and nutrient availability. Although nitrogen is an essential nutrient for every organism, little is known about the genes and pathways responsible for nitrogen assimilation in M. tuberculosis. In this study we have used transcriptomics and chromatin immunoprecipitation and high-throughput sequencing to address this. In response to nitrogen starvation, a total of 185 genes were significantly differentially expressed (96 up-regulated and 89 down regulated; 5% genome) highlighting several significant areas of metabolic change during nitrogen limitation such as nitrate/nitrite metabolism, aspartate metabolism and changes in cell wall biosynthesis. We identify GlnR as a regulator involved in the nitrogen response, controlling the expression of at least 33 genes in response to nitrogen limitation. We identify a consensus GlnR binding site and relate its location to known transcriptional start sites. We also show that the GlnR response regulator plays a very different role in M. tuberculosis to that in non-pathogenic mycobacteria, controlling genes involved in nitric oxide detoxification and intracellular survival instead of genes involved in nitrogen scavenging

Secure pseudo-random linear binary sequences generators based on arithmetic polynoms

We present a new approach to constructing of pseudo-random binary sequences (PRS) generators for the purpose of cryptographic data protection, secured from the perpetrator's attacks, caused by generation of masses of hardware errors and faults. The new method is based on use of linear polynomial arithmetic for the realization of systems of boolean characteristic functions of PRS' generators. "Arithmetizatio" of systems of logic formulas has allowed to apply mathematical apparatus of residue systems for multisequencing of the process of PRS generation and organizing control of computing errors, caused by hardware faults. This has guaranteed high security of PRS generator's functioning and, consequently, security of tools for cryptographic data protection based on those PRSs

Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules.

Background The ability to adapt to environments with fluctuating nutrient availability is vital for bacterial survival. Although essential for growth, few nitrogen metabolism genes have been identified or fully characterised in mycobacteria and nitrogen stress survival mechanisms are unknown. Results A global transcriptional analysis of the mycobacterial response to nitrogen stress, showed a significant change in the differential expression of 16% of the Mycobacterium smegmatis genome. Gene expression changes were mapped onto the metabolic network using Active Modules for Bipartite Networks (AMBIENT) to identify metabolic pathways showing coordinated transcriptional responses to the stress. AMBIENT revealed several key features of the metabolic response not identified by KEGG enrichment alone. Down regulated reactions were associated with the general reduction in cellular metabolism as a consequence of reduced growth rate. Up-regulated modules highlighted metabolic changes in nitrogen assimilation and scavenging, as well as reactions involved in hydrogen peroxide metabolism, carbon scavenging and energy generation. Conclusions Application of an Active Modules algorithm to transcriptomic data identified key metabolic reactions and pathways altered in response to nitrogen stress, which are central to survival under nitrogen limiting environments

Fluctuations in measured radioactive decay rates inside a modified Faraday cage: Correlations with space weather

[EN] For several years, reports have been published about fluctuations in measured radioactive decay time-series and in some instances linked to astrophysical as well as classical environmental influences. Anomalous behaviors of radioactive decay measurement and measurement of capacitance inside and outside a modified Faraday cage were documented by our group in previous work. In the present report, we present an in-depth analysis of our measurement with regard to possible correlations with space weather, i.e. the geomagnetic activity (GMA) and cosmic-ray activity (CRA). Our analysis revealed that the decay and capacitance time-series are statistically significantly correlated with GMA and CRA when specific conditions are met. The conditions are explained in detail and an outlook is given on how to further investigate this important finding. Our discovery is relevant for all researchers investigating radioactive decay measurements since they point out that the space weather condition during the measurement is relevant for partially explaining the observed variability.This work has been partially financed by: grant no. 20170764 (Equipos de deteccion, regulacion e informacion en el sector de los sistemas inteligentes de transporte (ITS). Nuevos modelos y ensayos de compatibilidad y verificacion de funcionamiento) (Spain), by grant no. RTI2018-102256-B-I00 (Spain), by the Generalitat Valenciana (Spain) under project Bioingenieria de las Radiaciones Ionizantes. Biorad (PROMETEO/2018/035) and the project MEMO RADION (IDIFEDER/2018/038) co-financed by the Programa Operativo del Fondo Social Europeo 2014-2020", and by grant No.075-00845-20-01 (Russia).Milián-Sánchez, V.; Scholkmann, F.; Fernández De Córdoba, P.; Mocholí Salcedo, A.; Mocholí-Belenguer, F.; Iglesias-Martínez, ME.; Castro-Palacio, JC.... (2020). 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Sexual functioning in 4,418 postmenopausal women participating in UKCTOCS: a qualitative free-text analysis

OBJECTIVE: Sexual well-being can contribute significantly to the overall quality of women's lives. This qualitative study aimed to examine sexual activity, functioning, and satisfaction in a large sample of postmenopausal women from the UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS) METHODS:: Thematic analysis was used to evaluate the free-text data of the Fallowfield Sexual Activity Questionnaire (FSAQ) completed by UKCTOCS participants at baseline before annual screening. RESULTS: A total of 24,305 women completed the baseline FSAQ and 4,525 (19%) provided free-text data, with 4,418 comments eligible for analysis. Median age was 64 years; 65% had a partner and 22.5% were sexually active. Four interrelated themes were derived: partner availability, physical and sexual health, mental well-being, and interpersonal relationships. Primary reason for absence of sexual activity was lack of a partner, mainly due to widowhood (n = 1,000). Women discussed how partner's medical condition (27%) or sexual dysfunction (13.5%), their own physical health (18%) or menopause-related symptoms (12.5%), and prescribed medication (7%) affected sexual activity. Impact of low libido in self (16%) or partner (7%), relationship problems (10.5%) or logistics (6%), and perceptions of ageing (9%) were also mentioned. Few (3%) referred to positive sexual experiences or had sought medical help for sexual problems (6%). CONCLUSIONS: This qualitative analysis explored postmenopausal women's perspective on their sexual functioning. Having an intimate partner and good physical health are key factors for continuation of sexual activity and satisfaction. Further sexual education for healthcare professionals is needed to raise awareness about sexuality and sexual difficulties in later life. : Video Summary: Supplemental Digital Content 1, http://links.lww.com/MENO/A426

Reasons for accepting or declining to participate in randomized clinical trials for cancer therapy

This paper reports on the reasons why patients agreed to or declined entry into randomized trials of cancer following discussions conducted by clinicians in both District General and University Hospitals. Two hundred and four patients completed a 16-item questionnaire following the consultation, of these 112 (55%) were women with breast cancer. Overall results showed that 147 (72.1%) patients accepted entry to a randomized clinical trial (RCT). The main reasons nominated for participating in a trial were that ‘others will benefit’ (23.1%) and ‘trust in the doctor’ (21.1%). One of the main reasons for declining trial entry was that patients were ‘worried about randomization’ (19.6%). There was a significantly higher acceptance rate for trials providing active treatment in every arm 98 (80.6%) compared with those trials with a no treatment arm 46 (60.5%), χ2test P = 0.003. The study outlines a number of factors that appear to influence a patient’s decision to accept or decline entry into an RCT of cancer therapy. An important factor is whether or not the trial offers active treatment in all arms of the study. Communication that promotes trust and confidence in the doctor is also a powerful motivating influence. © 2000 Cancer Research Campaig

The Cosmology of Composite Inelastic Dark Matter

Composite dark matter is a natural setting for implementing inelastic dark matter - the O(100 keV) mass splitting arises from spin-spin interactions of constituent fermions. In models where the constituents are charged under an axial U(1) gauge symmetry that also couples to the Standard Model quarks, dark matter scatters inelastically off Standard Model nuclei and can explain the DAMA/LIBRA annual modulation signal. This article describes the early Universe cosmology of a minimal implementation of a composite inelastic dark matter model where the dark matter is a meson composed of a light and a heavy quark. The synthesis of the constituent quarks into dark mesons and baryons results in several qualitatively different configurations of the resulting dark matter hadrons depending on the relative mass scales in the system.Comment: 31 pages, 4 figures; references added, typos correcte

Viral population estimation using pyrosequencing

The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response as well as for vaccine design and antiviral drug therapy. Recently developed pyrophosphate based sequencing technologies (pyrosequencing) can be used for quantifying this diversity by ultra-deep sequencing of virus samples. We present computational methods for the analysis of such sequence data and apply these techniques to pyrosequencing data obtained from HIV populations within patients harboring drug resistant virus strains. Our main result is the estimation of the population structure of the sample from the pyrosequencing reads. This inference is based on a statistical approach to error correction, followed by a combinatorial algorithm for constructing a minimal set of haplotypes that explain the data. Using this set of explaining haplotypes, we apply a statistical model to infer the frequencies of the haplotypes in the population via an EM algorithm. We demonstrate that pyrosequencing reads allow for effective population reconstruction by extensive simulations and by comparison to 165 sequences obtained directly from clonal sequencing of four independent, diverse HIV populations. Thus, pyrosequencing can be used for cost-effective estimation of the structure of virus populations, promising new insights into viral evolutionary dynamics and disease control strategies.Comment: 23 pages, 13 figure

Can user testing of a clinical trial patient information sheet make it fit-for-purpose? - a randomized controlled trial

Background: The participant information sheet (PIS) provided to potential trial participants is a critical part of the process of valid consent. However, there is long-standing concern that these lengthy and complex documents are not fit-for-purpose. This has been supported recently through the application of a performance-based approach to testing and improving readability called user testing. This method is now widely used to improve patient medicine leaflets - determining whether people can find and understand key facts. This study applied for the first time a controlled design to determine whether a PIS developed through user testing had improved readability over the original, using a sheet from a UK trial in acute myeloid leukemia (AML16). Methods: In the first phase the performance of the original PIS was tested on people in the target group for the trial. There were three rounds of testing including 50 people in total - with the information revised according to its performance after each of the first 2 rounds. In the second phase, the revised PIS was compared with the original in a parallel groups randomised controlled trial (RCT) A total of 123 participants were recruited and randomly allocated to read one version of the PIS to find and show understanding of 21 key facts. Results: The first, developmental phase produced a revised PIS significantly altered in its wording and layout. In the second, trial phase 66% of participants who read the revised PIS were able to show understanding of all aspects of the trial, compared with 15% of those reading the original version (Odds Ratio 11.2; Chi-square = 31.5 p < .001). When asked to state a preference, 87.1% participants chose the revised PIS (Sign test p < .001). Conclusions: The original PIS for the AML16 trial may not have enabled valid consent. Combining performance-based user testing with expertise in writing for patients and information design led to a significantly improved and preferred information sheet. User testing is an efficient method for indicating strengths and weaknesses in trial information, and Research Ethics Committees and Institutional Review Boards should consider requesting such testing, to ensure that PIS are fit-for-purpose