On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei

Background: Although technical advances in genomics and proteomics research have yielded a better understanding of the coding capacity of a genome, one major challenge remaining is the identification of all expressed proteins, especially those less than 100 amino acids in length. Such information can be particularly relevant to human pathogens, such as Trypanosoma brucei, the causative agent of African trypanosomiasis, since it will provide further insight into the parasite biology and life cycle. Results: Starting with 993 T. brucei transcripts, previously shown by RNA-Sequencing not to coincide with annotated coding sequences (CDS), homology searches revealed that 173 predicted short open reading frames in these transcripts are conserved across kinetoplastids with 13 also conserved in representative eukaryotes. Mining mass spectrometry data sets revealed 42 transcripts encoding at least one matching peptide. RNAi-induced down-regulation of these 42 transcripts revealed seven to be essential in insect-form trypanosomes with two also required for the bloodstream life cycle stage. To validate the specificity of the RNAi results, each lethal phenotype was rescued by co-expressing an RNAi-resistant construct of each corresponding CDS. These previously non-annotated essential small proteins localized to a variety of cell compartments, including the cell surface, mitochondria, nucleus and cytoplasm, inferring the diverse biological roles they are likely to play in T. brucei. We also provide evidence that one of these small proteins is required for replicating the kinetoplast (mitochondrial) DNA. Conclusions: Our studies highlight the presence and significance of small proteins in a protist and expose potential new targets to block the survival of trypanosomes in the insect vector and/or the mammalian host

Integrin regulated differentiation and apoptosis in normal keratinocytes and squamous cell carcinomas

Integrins are cell surface receptors, consisting of a heterodimer of an α and β subunit. The extracellular domains confer binding specificity to ligands such as extracellular matrix proteins and cellular counter-receptors. The short intracellular portion is associated with molecules that are known to play a role in signal transduction; hence integrin ligation provides a mechanism by which cells can respond to their immediate environment and profoundly affect cell functions such as survival, proliferation and commitment to differentiation. Normal stratified epithelia express the αvβ5 integrin, but in squamous cell carcinomas (SCCs) there is a downregulation of αvβ5 and an upregulation of αvβ6. To investigate the significance of this change we studied a human SCC cell line, H357, that lacks av integrins. Transduction of H357 cells with an αv expressing retrovirus resulted in cell surface expression of αvβ5. Unlike the parental cells αvβ5 expressing cells underwent suspension-induced apoptosis (anoikis), which could be inhibited by αvβ5 ligation. Introduction of the β6 subunit resulted in replacement of the αvβ5 with αvβ6 and suppressed anoikis. Cells that were resistant to anoikis activated PI3-kinase signalling in suspension, as measured by PKB/Akt phosphorylation, whereas αvβ5 expressing cells did not. Anoikis could be induced in parent and αvβ6 cells by inhibition of PI3-kinase. Conversely, activation of Akt in αvβ5 expressing cells suppressed anoikis. Anoikis required the cytoplasmic domain of β5 and was independent of the death receptor pathway. These results suggest that downregulation of αvβ5 and upregulation of αvβ6 may protect SCCs from anoikis by activating a PI3-kinase survival signal. Normal primary kertinocytes differentiate rather than apoptose when placed in suspension. It appears that caspases are also activated within 2 hours of the onset of epidermal cell differentiation and that caspase activation and differentiation are inhibited by a PI3-kinase inhibitor while an active Akt construct drives differentiation

Hearing Women’s Voices: Understanding Women\u27s Stories of Violence from the Perspective of Strength

The purpose of this study was to understand women\u27s experiences of violence from the perspective of strength. Women who had experienced woman abuse participated, identifying common themes that emerged relating to their strengths and resilience that helped them survive their traumatic experiences, as well as their posttraumatic growth. Interviews were conducted with women who were involved in an adult education program for women who had experienced woman abuse. All of the women in this study were suffering distress and mental health concerns related to their experiences of violence; however all of them showed resilience and posttraumatic growth in areas of their life as well. Four themes emerged from the women\u27s narratives that related to their resilience and posttraumatic growth: hope, ability to display vulnerability, a sense of identity, and a desire for a new life. These results are discussed in relation to the context of abuse these women endured, the theoretical frameworks used in this study (Relational Cultural Theory, Ecological Theory and the notion of self), and the implications for practice and future research

British Fascism in the 1930s in Life and Literature

Political and economic turmoil in 1930s Britain gave rise to a home-grown fascist movement led by the controversial Oswald Mosley. Literature of this period by Joseph O’Neill and Rex Warner mirrored the internal nature of the British fascist movement by depicting fascist-like societies embedded under or entrenched within the English countryside. Their metaphors of fascism rising as a solution to fear and disorder conjure the threat of fascism that was rising in Europe in that period. The metaphors are made more particularly relevant by the fact that the forces of Italian, German, and British fascism were not invasions from without, but growths from within. Furthermore, the recipe of severe political and economic downturn combined with the rise of a charismatic group leading their distressed people toward fascism is still relevant today in Greece and other European countries

Phase and amplitude scintillations of microwave signals over an elevated atmospheric path

Phase and amplitude scintillations of microwave signals over elevated atmospheric path for obtaining atmospheric density profile

Automated test-based learning and verification of performance models for microservices systems

Effective and automated verification techniques able to provide assurances of performance and scalability are highly demanded in the context of microservices systems. In this paper, we introduce a methodology that applies specification-driven load testing to learn the behavior of the target microservices system under multiple deployment configurations. Testing is driven by realistic workload conditions sampled in production. The sampling produces a formal description of the users' behavior through a Discrete Time Markov Chain. This model drives multiple load testing sessions that query the system under test and feed a Bayesian inference process which incrementally refines the initial model to obtain a complete specification from run-time evidence as a Continuous Time Markov Chain. The complete specification is then used to conduct automated verification by using probabilistic model checking and to compute a configuration score that evaluates alternative deployment options. This paper introduces the methodology, its theoretical foundation, and the toolchain we developed to automate it. Our empirical evaluation shows its applicability, benefits, and costs on a representative microservices system benchmark. We show that the methodology detects performance issues, traces them back to system-level requirements, and, thanks to the configuration score, provides engineers with insights on deployment options. The comparison between our approach and a selected state-of-the-art baseline shows that we are able to reduce the cost up to 73% in terms of number of tests. The verification stage requires negligible execution time and memory consumption. We observed that the verification of 360 system-level requirements took ~1 minute by consuming at most 34 KB. The computation of the score involved the verification of ~7k (automatically generated) properties verified in ~72 seconds using at most ~50 KB. (C)& nbsp;2022 The Author(s). Published by Elsevier Inc.& nbsp

Accommodating Covariates in ROC Analysis

Classification accuracy is the ability of a marker or diagnostic test to discriminate between two groups of individuals, cases and controls, and is commonly summarized using the receiver operating characteristic (ROC) curve. In studies of classification accuracy, there are often covariates that should be incorporated into the ROC analysis. We describe three different ways of using covariate informa- tion. For factors that affect marker observations among controls, we present a method for covariate adjustment. For factors that affect discrimination (ie the ROC curve), we describe methods for mod- elling the ROC curve as a function of covariates. Finally, for factors that contribute to discrimination, we propose combining the marker and covariate information, and ask how much discriminatory accu- racy improves with the addition of the marker to the covariates (incremental value). These methods follow naturally when representing the ROC curve as a summary of the distribution of case marker observations, standardized with respect to the control distribution

Estimation and Comparison of Receiver Operating Characteristic Curves

The receiver operating characteristic (ROC) curve displays the capacity of a marker or diagnostic test to discriminate between two groups of subjects, cases versus controls. We present a comprehensive suite of Stata commands for performing ROC analysis. Non-parametric, semiparametric and parametric estimators are calculated. Comparisons between curves are based on the area or partial area under the ROC curve. Alternatively pointwise comparisons between ROC curves or inverse ROC curves can be made. Options to adjust these analyses for covariates, and to perform ROC regression are described in a companion article. We use a unified framework by representing the ROC curve as the distribution of the marker in cases after standardizing it to the control reference distribution