iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE.

Acinetobacter baumannii has become an urgent clinical threat due to the recent emergence of multi-drug resistant strains. There is thus a significant need to discover new therapeutic targets in this organism. One means for doing so is through the use of high-quality genome-scale reconstructions. Well-curated and accurate genome-scale models (GEMs) of A. baumannii would be useful for improving treatment options. We present an updated and improved genome-scale reconstruction of A. baumannii AYE, named iCN718, that improves and standardizes previous A. baumannii AYE reconstructions. iCN718 has 80% accuracy for predicting gene essentiality data and additionally can predict large-scale phenotypic data with as much as 89% accuracy, a new capability for an A. baumannii reconstruction. We further demonstrate that iCN718 can be used to analyze conserved metabolic functions in the A. baumannii core genome and to build strain-specific GEMs of 74 other A. baumannii strains from genome sequence alone. iCN718 will serve as a resource to integrate and synthesize new experimental data being generated for this urgent threat pathogen

Developing body estimation in adolescence is associated with neural regions that support self-concept

Both self-concept, the evaluation of who you are, and the physical body undergo changes throughout adolescence. These two processes might affect the development of body image, a complex construct that comprises one's thoughts, feelings, and perception of one's body. This study aims to better understand the development of body image in relation to self-concept development and its neural correlates. Adolescents (aged 11-24) from the longitudinal Leiden Self-Concept study were followed for three consecutive years (NT1 = 160, NT2 = 151, and NT3 = 144). Their body image was measured using a figure rating scale and body dissatisfaction questionnaire. Body estimation was calculated based on figure ratings relative to their actual body mass index (BMI). Additionally, participants evaluated their physical appearance traits in an functional magnetic resonance imaging (fMRI) task. Results revealed that body estimation and body dissatisfaction increased with age. Heightened inferior parietal lobe (IPL) activation during physical self-evaluation was associated with lower body estimation, meaning that the neural network involved in thinking about one's physical traits is more active for individuals who perceive themselves as larger than they are. IPL activity showed continued development during adolescence, suggesting an interaction between neural development and body perception. These findings highlight the complex interplay between affective, perceptual, and biological factors in shaping body image.</p

Comparison of Shiga toxin-encoding bacteriophages in highly pathogenic strains of Shiga toxin-producing Escherichia coli O157:H7 in the UK

Over the last 35 years in the UK, the burden of Shiga toxin-producing Escherichia coli (STEC) O157:H7 infection has, during different periods of time, been associated with five different sub-lineages (1983-1995, Ia, I/IIa and I/IIb; 1996-2014, Ic; and 2015-2018, IIb). The acquisition of a stx2a-encoding bacteriophage by these five sub-lineages appears to have coincided with their respective emergences. The Oxford Nanopore Technologies (ONT) system was used to sequence, characterize and compare the stx-encoding prophages harboured by each sub-lineage to investigate the integration of this key virulence factor. The stx2a-encoding prophages from each of the lineages causing clinical disease in the UK were all different, including the two UK sub-lineages (Ia and I/IIa) circulating concurrently and causing severe disease in the early 1980s. Comparisons between the stx2a-encoding prophage in sub-lineages I/IIb and IIb revealed similarity to the prophage commonly found to encode stx2c, and the same site of bacteriophage integration (sbcB) as stx2c-encoding prophage. These data suggest independent acquisition of previously unobserved stx2a-encoding phage is more likely to have contributed to the emergence of STEC O157:H7 sub-lineages in the UK than intra-UK lineage to lineage phage transmission. In contrast, the stx2c-encoding prophage showed a high level of similarity across lineages and time, consistent with the model of stx2c being present in the common ancestor to extant STEC O157:H7 and maintained by vertical inheritance in the majority of the population. Studying the nature of the stx-encoding bacteriophage contributes to our understanding of the emergence of highly pathogenic strains of STEC O157:H7

Norovirus whole genome sequencing by SureSelect target enrichment: a robust and sensitive method

Norovirus full genome sequencing is challenging due to sequence heterogeneity between genomes. Previous methods have relied on PCR amplification, which is problematic due to primer design, and RNASeq which non-specifically sequences all RNA in a stool specimen, including host and bacterial RNA.Target enrichment uses a panel of custom-designed 120-mer RNA baits which are complementary to all publicly available norovirus sequences, with multiple baits targeting each position of the genome, thus overcoming the challenge of primer design. Norovirus genomes are enriched from stool RNA extracts to minimise sequencing non-target RNA.SureSelect target enrichment and Illumina sequencing was used to sequence full genomes from 507 norovirus positive stool samples with RT-qPCR Ct values 10-43. Sequencing on an Illumina MiSeq in batches of 48 generated on average 81% on-target-reads per sample and 100% genome coverage with >12,000-fold read depth. Samples included genotypes GI.1, GI.2, GI.3, GI.6, GI.7, GII.1, GII.2, GII.3, GII.4, GII.5, GII.6, GII.7, GII.13, GII.14 and GII.17. Once outliers are accounted for, we generate over 80% genome coverage for all positive samples, regardless of Ct value.164 samples were tested in parallel with conventional PCR genotyping of the capsid shell domain. 164/164 samples were successfully sequenced, compared to 158/164 that were amplified by PCR. Four of the samples that failed capsid PCR had low titres, suggesting target enrichment is more sensitive than gel-based PCR. Two samples failed PCR due to primer mismatches; target enrichment uses multiple baits targeting each position, thus accommodating sequence heterogeneity between norovirus genomes

Plasmonic Gadolinium Oxide Nanomatryoshkas: Bifunctional Magnetic Resonance Imaging Enhancers for Photothermal Cancer Therapy

Nanoparticle-assisted laser-induced photothermal therapy (PTT) is a promising method for cancer treatment; yet, visualization of nanoparticle uptake and photothermal response remain a critical challenge. Here, we report a magnetic resonance imaging-active nanomatryoshka (Gd2O3-NM), a multilayered (Au core/Gd2O3 shell/Au shell) sub-100 nm nanoparticle capable of combining T1 MRI contrast with PTT. This bifunctional nanoparticle demonstrates an r1 of 1.28 × 108 mM-1 s-1, an MRI contrast enhancement per nanoparticle sufficient for T1 imaging in addition to tumor ablation. Gd2O3-NM also shows excellent stability in an acidic environment, retaining 99% of the internal Gd(3). This report details the synthesis and characterization of a promising system for combined theranostic nanoparticle tracking and PTT

Problems with Sleep Do Not Predict Self-Reported Driving Factors and Perception in Older Drivers: Evidences from the Candrive II Prospective Cohort

Given that sleep problems and serious motor vehicle collisions are increasingly prevalent in older adults, even minor drowsiness could potentially contribute to driving patterns in older drivers. To date, it is unknown whether less serious problems with sleep influence driving frequency and ability in older adults. We investigated the influence of everyday sleep disturbances on driving practices and driver perceptions in a large cohort of healthy older drivers. Selfreported measures of sleep problems were used to investigate the influence of sleep disturbance on self-reported driving practices and perceived driving abilities. On two measures of self-reported driving outcomes, participants with problems with rated themselves more poorly. However, this relationship disappeared when health and demographic variables were entered prior in hierarchical regression analyses. Our results show that the relationship between sleep problems, driving frequency and perceived abilities is better explained by mediating demographic, health, and cognitive factors

Avaliação da eficácia do aluminosilicato de sódio hidratado na prevenção de câncer hepático induzido por aflatoxina em truta arco-íris

The use of aluminum silicates for decontaminating animal feed containing aflatoxins has yielded encouraging results in chicken and turkey poults. In contrast, very few studies have tested these substances in aquaculture. In this work, we investigated the efficacy of a trout diet containing 0.5% hydrated sodium aluminosilicate (HSAS) in protecting against contamination with aflatoxin B1. Trout were reared on these diets for one year and the experimental groups were examined monthly for hepatic presumptive preneoplastic and neoplastic lesions. Regardless of the presence of HSAS, all of the fish that received aflatoxin in their diet have shown hepatic lesions indicative of a carcinogenic process, presenting also the development of cancer in some fish. The concentration of HSAS used in this study was ineffective in preventing the onset of hepatic lesions induced by aflatoxin B1 in rainbow trout.Resultados encorajadores têm sido observados com o emprego de aluminosilicatos para descontaminação de ração contendo aflatoxina destinada à avicultura. No entanto, raros estudos têm sido destinados a testar essa substância em aqüicultura. Assim, no presente trabalho, foi investigada a eficácia do aluminosilicato de sódio hidratado (HSAS, 0,5%) em proteger a truta arco-íris dos danos hepáticos causados por ração contaminada com aflatoxina B1. Os grupos experimentais foram alimentados com suas respectivas dietas durante 12 meses, mensalmente cada grupo foi amostrado para análises anatomopatológica e histopatológica para verificação da presença de lesões hepáticas. Apesar da presença de HSAS, todos os grupos que receberam dieta contaminada com aflatoxina B1 apresentaram lesões hepáticas indicativas do processo carcinogênico, sendo que exemplares alimentados com essas dietas por mais longo prazo apresentaram hepatocarcinoma ou colangiocarcinoma. Estes resultados indicaram que a concentração de HSAS usada no presente estudo não foi efetiva em prevenir o desenvolvimento de lesões hepáticas induzidas por aflatoxina B1 em truta arco-íris.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundo de Apoio ao Ensino, Pesquisa e Extensão da Universidade Estadual de Campina

Identifying Potential Risks and Benefits of Using Cloud in Distributed Software Development

Cloud-based infrastructure has been increasingly adopted by the industry in distributed software development (DSD) environments. Its proponents claim that its several benefits include reduced cost, increased speed and greater productivity in software development. Empirical evaluations, however, are in the nascent stage of examining both the benefits and the risks of cloud-based in-frastructure. The objective of this paper is to identify potential benefits and risks of using cloud in a DSD project conducted by teams based in Helsinki and Ma-drid. A cross-case qualitative analysis is performed based on focus groups con-ducted at the Helsinki and Madrid sites. Participants’ observations are used to supplement the analysis. The results of the analysis indicated that the main ben-efits of using cloud are rapid development, continuous integration, cost savings, code sharing, and faster ramp-up. The key risks determined by the project are dependencies, unavailability of access to the cloud, code commitment and inte-gration, technical debt, and additional support costs. The results revealed that if such environments are not planned and set up carefully, the benefits of using cloud in DSD projects might be overshadowed by the risks associated with it.Peer reviewe