Mycobacterium tuberculosis and whole genome sequencing: a practical guide and online tools available for the clinical microbiologist

Whole genome sequencing (WGS) has the potential to revolutionize the diagnosis of Mycobacterium tuberculosis (MTB) but the lack of bioinformatic expertise among clinical microbiologists is a barrier for adoption. Software products for analysis should be simple, free of charge, able to accept data directly from the sequencer (FASTQ files) and to provide the basic functionalities all-in-one. The main aim of this narrative review is to provide a practical guide for the clinical microbiologist, with little or no practical experience of WGS analysis, with a specific focus on software products tailored made for MTB analysis. With sequencing performed by an external provider, it is now feasible to implement WGS analysis in the routine clinical practice of any microbiology laboratory, with the potential to detect resistance weeks before traditional phenotypic culture methods, but the clinical microbiologist should be aware of the limitations of this approach

Comparison of System Call Representations for Intrusion Detection

Over the years, artificial neural networks have been applied successfully in many areas including IT security. Yet, neural networks can only process continuous input data. This is particularly challenging for security-related non-continuous data like system calls. This work focuses on four different options to preprocess sequences of system calls so that they can be processed by neural networks. These input options are based on one-hot encoding and learning word2vec or GloVe representations of system calls. As an additional option, we analyze if the mapping of system calls to their respective kernel modules is an adequate generalization step for (a) replacing system calls or (b) enhancing system call data with additional information regarding their context. However, when performing such preprocessing steps it is important to ensure that no relevant information is lost during the process. The overall objective of system call based intrusion detection is to categorize sequences of system calls as benign or malicious behavior. Therefore, this scenario is used to evaluate the different input options as a classification task. The results show, that each of the four different methods is a valid option when preprocessing input data, but the use of kernel modules only is not recommended because too much information is being lost during the mapping process.Comment: 12 pages, 1 figure, submitted to CISIS 201

Multipurpose electric furnace system

A multipurpose electric furnace system of advanced design for space applications was developed and tested. This system is intended for use in the Apollo-Soyuz Test Program. It consists of the furnace, control package and a helium package for rapid cooldown

Influence of a montmorency cherry juice blend on indices of exercise-induced stress and upper respiratory tract symptoms following marathon running—a pilot investigation

Background: Prolonged exercise, such as marathon running, has been associated with an increase in respiratory mucosal inflammation. The aim of this pilot study was to examine the effects of Montmorency cherry juice on markers of stress, immunity and inflammation following a Marathon. Methods: Twenty recreational Marathon runners consumed either cherry juice (CJ) or placebo (PL) before and after a Marathon race. Markers of mucosal immunity secretory immunoglobulin A (sIgA), immunoglobulin G (IgG), salivary cortisol, inflammation (CRP) and self-reported incidence and severity of upper respiratory tract symptoms (URTS) were measured before and following the race. Results: All variables except secretory IgA and IgG concentrations in saliva showed a significant time effect (P < 0.01). Serum CRP showed a significant interaction and treatment effect (P < 0.01). The CRP increase at 24 and 48 h post-Marathon was lower (P < 0.01) in the CJ group compared to PL group. Mucosal immunity and salivary cortisol showed no interaction effect or treatment effect. The incidence and severity of URTS was significantly greater than baseline at 24 h and 48 h following the race in the PL group and was also greater than the CJ group (P < 0.05). No URTS were reported in the CJ group whereas 50 % of runners in the PL group reported URTS at 24 h and 48 h post-Marathon. Conclusions: This is the first study that provides encouraging evidence of the potential role of Montmorency cherries in reducing the development of URTS post-Marathon possibly caused by exercise-induced hyperventilation trauma, and/or other infectious and non-infectious factors

Tuning Magnetic Avalanches in Mn12-ac

Using micron-sized Hall sensor arrays to obtain time-resolved measurements of the local magnetization, we report a systematic study in the molecular magnet Mn$_{12}$-acetate of magnetic avalanches controllably triggered in different fixed external magnetic fields and for different values of the initial magnetization. The speeds of propagation of the spin-reversal fronts are in good overall agreement with the theory of magnetic deflagration of Garanin and Chudnovsky \cite{Garanin}.Comment: 8 pages, 7 figures; discussion expanded and revise

Identification of 2-Aminothiazole-4-Carboxylate Derivatives Active against Mycobacterium tuberculosis H37Rv and the β-Ketoacyl-ACP Synthase mtFabH

Background Tuberculosis (TB) is a disease which kills two million people every year and infects approximately over one-third of the world's population. The difficulty in managing tuberculosis is the prolonged treatment duration, the emergence of drug resistance and co-infection with HIV/AIDS. Tuberculosis control requires new drugs that act at novel drug targets to help combat resistant forms of Mycobacterium tuberculosis and reduce treatment duration. Methodology/Principal Findings Our approach was to modify the naturally occurring and synthetically challenging antibiotic thiolactomycin (TLM) to the more tractable 2-aminothiazole-4-carboxylate scaffold to generate compounds that mimic TLM's novel mode of action. We report here the identification of a series of compounds possessing excellent activity against M. tuberculosis H37Rv and, dissociatively, against the β-ketoacyl synthase enzyme mtFabH which is targeted by TLM. Specifically, methyl 2-amino-5-benzylthiazole-4-carboxylate was found to inhibit M. tuberculosis H37Rv with an MIC of 0.06 µg/ml (240 nM), but showed no activity against mtFabH, whereas methyl 2-(2-bromoacetamido)-5-(3-chlorophenyl)t​hiazole-4-carboxylateinhibited mtFabH with an IC50 of 0.95±0.05 µg/ml (2.43±0.13 µM) but was not active against the whole cell organism. Conclusions/Significance These findings clearly identify the 2-aminothiazole-4-carboxylate scaffold as a promising new template towards the discovery of a new class of anti-tubercular agents

Competition of moir\'e network sites to form electronic quantum dots in reconstructed MoX2{}_2/WX2{}_2 heterostructures

Twisted bilayers of two-dimensional semiconductors offer a versatile platform to engineer quantum states for charge carriers using moir\'e superlattice effects. Among the systems of recent interest are twistronic MoSe${}_{2}$/WSe${}_{2}$ and MoS${}_{2}$/WS${}_{2}$ heterostructures, which undergo reconstruction into preferential stacking domains and highly strained domain wall networks, determining the electron/hole localization across moir\'e superlattices. Here, we present a catalogue of options for the formation of self-organized quantum dots and wires in lattice-reconstructed marginally twisted MoSe${}_{2}$/WSe${}_{2}$ and MoS${}_{2}$/WS${}_{2}$ bilayers, fine tuned by the twist angle between the monolayers from perfect alignment to $\theta \sim 1^{\circ}$, and by choosing parallel or anti-parallel orientation of their unit cells. The proposed scenarios of the quantum dots and wires formation are found using multi-scale modelling that takes into account the features of strain textures caused by twirling of domain wall networks.Comment: 7 pages, 5 figure