The bacterium Deinococcus radiodurans is known to efficiently and accurately reassemble its genome after hundreds of DNA double-strand breaks (DSBs). Only at very large amounts of radiation-induced DSBs is this accuracy affected in the wild-type D. radiodurans, causing rearrangements in its genome structure. However, changes in its genome structure may also be possible during the propagation and storage of cell cultures. We investigate this possibility by listing structural differences between three completely sequenced genomes of D. radiodurans strains with a recent common ancestor-the type strain stored and sequenced in two different laboratories (of the ATCC 13939 lineage) and the first sequenced strain historically used as the reference (ATCC BAA-816). We detected a number of structural differences and found the most likely mechanisms behind them: (i) transposition/copy number change in mobile interspersed repeats-insertion sequences and small non-coding repeats, (ii) variable number of monomers within tandem repeats, (iii) deletions between long direct DNA repeats, and (iv) deletions between short (4-10 bp) direct DNA repeats. The most surprising finding was the deletions between short repeats because it indicates the utilization of a less accurate DSB repair mechanism in conditions in which a more accurate one should be both available and preferred. The detected structural differences, as well as SNPs and short indels, while being important footprints of deinococcal DNA metabolism and repair, are also a valuable resource for researchers using these D. radiodurans strains.

Body mass index (BMI) is a crucial health indicator for obesity. With the progression of socio-economic status and alterations in lifestyle, an increasing number of global populations are at risk of obesity. Given the complexity and severity of neurological diseases, early identification of risk factors is vital for the diagnosis and prognosis of such diseases. In this study, we employed Mendelian randomization (MR) analysis utilizing the most comprehensive genome-wide association study (GWAS) data to date. We selected single nucleotide polymorphisms (SNPs) that are unaffected by confounding factors and reverse causality as instrumental variables. These variables were used to evaluate the genetic and causal relationships between Body Mass Index (BMI) and various neurological diseases, including Parkinson\'s Disease (PD), Alzheimer\'s Disease (AD), Amyotrophic Lateral Sclerosis (ALS), Multiple Sclerosis (MS), Ischemic Stroke (IS), and Epilepsy (EP). The Inverse Variance Weighted (IVW) analysis indicated that there was no significant causal relationship between Body Mass Index (BMI) indicators and PD (P-value = 0.511), AD (P-value = 0.076), ALS (P-value = 0.641), EP (P-value = 0.380). However, a causal relationship was found between BMI indicators and MS (P-value = 0.035), and IS (P-value = 0.000), with the BMI index positively correlated with the risk of both diseases. The Cochran\'s Q test for MR-IVW showed no heterogeneity in the MR analysis results between the BMI index and the neurological diseases (P > 0.05). The Egger intercept test for pleiotropy revealed no horizontal pleiotropy detected in any of the neurological diseases studied (P > 0.05). It was found that there was no causal relationship between BMI and PD, AD, ALS, EP, and a genetic causal association with MS, and IS. Meanwhile, the increase in BMI can lead to a higher risk of MS and IS, which reveals the critical role of obesity as a risk factor for specific neurological diseases in the pathogenesis of the diseases.

BACKGROUND: Staphylococcus haemolyticus belongs to the Coagulase-Negative Staphylococci (CoNS), exhibiting the highest levels of antibiotic resistance within this group of bacteria. This species has been increasingly implicated in nosocomial and animal infections worldwide, with a prevalence of methicillin-resistant Staphylococcus haemolyticus (MRSH). Most information about this organism comes from regional analyzes or with the absence of typing data, thus not revealing the real role of S. haemolyticus strains in world public health.
METHODS: Here, we performed an enhanced global epidemiological analysis considering all available S. haemolyticus genomes from all continents, including genomes of nosocomial, environmental, and animal origin (n = 310). Furthermore, we added original genomic information from a clinical MRSH from the Brazilian Amazon region. The resistome and virulome of the genomes were associated with their mobilome, being inferred based on the presence of specific genes and databases such as CARD, VFDB, and PlasmidFinder, respectively.
RESULTS: Phylogenetic analysis revealed three main groups, the main one covering most of the clinical clonal complex 3 (CC3) genomes in the world. The virulome of some genomes in this cluster showed the complete capsule operon (capA-capM). Importantly, this virulome trait could be associated with the mobilome, since the capsule operon, as well as a whole set of genes of the type VII secretion system, were observed in plasmids. In addition, the resistome of the main cluster (CC3) was larger, characterized mainly by the presence of the mecA gene, in addition to a set of other genes (aad, aac-aph, aph, erm), contrasting with the poor resistome of the other two clusters. Several insertion sequences were identified, some of them linked to specific clusters, and resistance genes, such as the rare cfrA (IS257).
CONCLUSIONS: Therefore, successful lineages of CC3 S. haemolyticus causing human infections are widespread worldwide, raising concern about the impact of this scenario on public health.

Epidemiological investigations have indicated a correlation between elevated plasma levels of Dickkopf-related protein 1 (DKK1) and the presence of atherosclerosis. However, the exact causal relationship of DKK1 with the development of coronary artery disease (CAD) and ischemic stroke (IS) remains unclear. To address this gap, our study aimed to explore their causal association using a two-sample Mendelian randomization (MR) approach. We obtained summary statistics from genome-wide association studies (GWAS) meta-analyses conducted by Folkersen et al. and Nikpay et al., which included data from 21,758 individuals for DKK1 and 42,096 cases of CAD. Additionally, we obtained data from the FinnGen biobank analysis round 5, which included 10,551 cases of IS. Eight MR methods were employed to estimate causal effects and detect directional pleiotropy. Our findings demonstrated that genetic liability to DKK1 was associated with increased risks of CAD (odds ratio [OR]: 1.087; 95% confidence interval [CI]: 1.024-1.154; P = 0.006) and IS (OR: 1.096; 95% CI: 1.004-1.195; P = 0.039). These results establish a causal link between genetic liability to DKK1 and elevated risks of CAD and IS. Consequently, DKK1 may represent a promising therapeutic target for the prevention and treatment of CAD and IS.

BACKGROUND: Emerging evidence suggests that uremic toxins, in particular trimethylamine-N-oxide(TMAO), indoxyl-sulfate(IS), and p-cresyl-sulfate(PCS), may associate with increased risk of cardiovascular events(CVe). However, whether uremic toxins increase after partial nephrectomy(PN) and their correlation with risk for CVe remains unknown.
METHODS: 100 patients managed with PN were retrospectively reviewed. TMAO/IS/PCS levels were examined by liquid chromatography-mass-spectrometry. Renal-parenchymal-volume-preservation(RPVP) was estimated from CT scans. Predicted risks for CVe were obtained using the Framingham score. Linear regression assessed association between uremic toxins, GFR and risk of CVe. Logistic regression evaluated factors associated with post-PN TMAO.
RESULTS: TMAO, IS and PCS increased from 1.7, 3.7 and 3.5 μmol/L before PN to 3.6, 5.4 and 7.4 μmol/L at latest follow-up, respectively, while GFR declined from 102 to 93 ml/min/1.73 m2 (all p<0.001). TMAO, IS and PCS levels all negatively correlated with GFR(all p<0.001). Predicted 10-year risk of CVe increased from 1.1% pre-PN to 1.7% post-PN(p<0.001), primarily due to increased age(p<0.001), blood pressure(p = 0.002) and total cholesterol(p = 0.003). TMAO(β = 0.038) and GFR (β = -0.02) were independent predictors for predicted 10-year CVe risk on multivariable-analysis. Increased TMAO was an early and sustained finding maintained through 5 years, unlike IS, PCS and eGFR. On multivariable analysis, increased pre-PN TMAO(OR = 2.79) and decreased RPVP(OR = 3.23) were identified as independent risk factors for higher post-PN TMAO, while ischemia type/duration failed to correlate.
CONCLUSIONS: Uremic toxin levels increased after PN correlating with reduced GFR. Higher TMAO independently associated with greater predicted 10-year CVe risk. Parenchymal mass preserved rather than ischemia time or type associated with increased TMAO.

Circulating uremic toxin indoxyl sulfate (IS), endothelial cell (EC) dysfunction, and decreased nitric oxide (NO) bioavailability are found in chronic kidney disease patients. NO nitrosylates/denitrosylates a specific protein\'s cysteine residue(s), forming S-nitrosothios (SNOs), and the decreased NO bioavailability could interfere with NO-mediated signaling events. We were interested in investigating the underlying mechanism(s) of the reduced NO and how it would regulate the S-nitrosylation of tissue transglutaminase (TG2) and its substrates on glycolytic, redox and inflammatory responses in normal and IS-induced EC injury. TG2, a therapeutic target for fibrosis, has a Ca2+-dependent transamidase (TGase) that is modulated by S-nitrosylation. We found IS increased oxidative stress, reduced NADPH and GSH levels, and uncoupled eNOS to generate NO. Immunoblot analysis demonstrated the upregulation of an angiotensin-converting enzyme (ACE) and significant downregulation of the beneficial ACE2 isoform that could contribute to oxidative stress in IS-induced injury. An in situ TGase assay demonstrated IS-activated TG2/TGase aminylated eNOS, NFkB, IkBα, PKM2, G6PD, GAPDH, and fibronectin (FN), leading to caspases activation. Except for FN, TGase substrates were all differentially S-nitrosylated either with or without IS but were denitrosylated in the presence of a specific, irreversible TG2/TGase inhibitor ZDON, suggesting ZDON-bound TG2 was not effectively transnitrosylating to TG2/TGase substrates. The data suggest novel roles of TG2 in the aminylation of its substrates and could also potentially function as a Cys-to-Cys S-nitrosylase to exert NO\'s bioactivity to its substrates and modulate glycolysis, redox, and inflammation in normal and IS-induced EC injury.

Chimeric Antigen Receptor (CAR)-mediated immunotherapy shows promising results for refractory blood cancers. Currently, six CAR-T drugs have been approved by U.S. Food and Drug Administration (FDA). Theoretically, CAR-T cells must form an effective immunological synapse (IS, an interface between effective cells and their target cells) with their susceptible tumor cells to eliminate tumor cells. Previous studies show that CAR IS quality can be used as a predictive functional biomarker for CAR-T immunotherapies. However, quantification of CAR-T IS quality is clinically challenging. Machine learning (ML)-based CAR-T IS quality quantification has been proposed previously.Here, we show an easy-to-use, step-by-step approach to predicting the efficacy of CAR-modified cells using ML-based CAR IS quality quantification. This approach will guide the users on how to use ML-based CAR IS quality quantification in detail, which include: how to image CAR IS on the glass-supported planar lipid bilayer, how to define the CAR IS focal plane, how to segment the CAR IS images, and how to quantify the IS quality using ML-based algorithms.This approach will significantly enhance the accuracy and proficiency of CAR IS prediction in research.

In recent years, considerable work has been conducted on the development of synthetic medical images, but there are no satisfactory methods for evaluating their medical suitability. Existing methods mainly evaluate the quality of noise in the images, and the similarity of the images to the real images used to generate them. For this purpose, they use feature maps of images extracted in different ways or distribution of images set. Then, the proximity of synthetic images to the real set is evaluated using different distance metrics. However, it is not possible to determine whether only one synthetic image was generated repeatedly, or whether the synthetic set exactly repeats the training set. In addition, most evolution metrics take a lot of time to calculate. Taking these issues into account, we have proposed a method that can quantitatively and qualitatively evaluate synthetic images. This method is a combination of two methods, namely, FMD and CNN-based evaluation methods. The estimation methods were compared with the FID method, and it was found that the FMD method has a great advantage in terms of speed, while the CNN method has the ability to estimate more accurately. To evaluate the reliability of the methods, a dataset of different real images was checked.

Privacy by design within a system for assisted living, personalised care, and wellbeing is crucial to protect users from misuse of the data collected about their health. Especially if the information is collected through audio-video devices, the question is even more delicate due to the nature of these data. In addition to guaranteeing a high level of privacy, it is necessary to reassure end users about the correct use of these streams. The evolution of data analysis techniques began to take on an important role and increasingly defined characteristics in recent years. The purpose of this paper is twofold: on the one hand, it presents a state of the art about privacy in European Active Healthy Ageing/Active Healthy Ageing projects, with a focus on those related to audio and video processing. On the other hand, it proposes a methodology, developed in the context of the European project PlatfromUptake.eu, to identify clusters of stakeholders and application dimensions (technical, contextual, and business), define their characteristics, and show how privacy constraints affect them. From this study, we then generated a Strengths, Weaknesses, Opportunities, and Threats analysis in which we aim to identify the critical features connected to the selection and involvement of relevant stakeholders for the success of a project. Applying this type of methodology to the initial stages of a project allows understanding of which privacy issues could be related to the various stakeholder groups and which problems can then affect the correct development of the project. The idea is, therefore, to suggest a privacy-by-design approach according to the categories of stakeholders and project dimensions. The analysis will cover technical aspects, legislative and policies-related aspects also regarding the point of view of the municipalities, and aspects related to the acceptance and, therefore, to the perception of the safety of these technologies by the final end users.

T cell-redirecting strategies have emerged as effective cancer immunotherapy approaches. Bispecific antibodies (bsAbs) are designed to specifically recruit T cells to the tumor microenvironment and induce the assembly of the immunological synapse (IS) between T cells and cancer cells or antigen-presenting cells. The way that the quality of the IS might predict the effectiveness of T cell-redirecting strategies, including those mediated by bsAbs or by chimeric antigen receptors (CAR)-T cells, is currently under discussion. Here we review the organization of the canonical IS assembled during natural antigenic stimulation through the T cell receptor (TCR) and to what extent different bsAbs induce T cell activation, canonical IS organization, and effector function. Then, we discuss how the biochemical parameters of different formats of bsAbs affect the effectivity of generating an antigen-induced canonical IS. Finally, the quality of the IS assembled by bsAbs and monoclonal antibodies or CAR-T cells are compared, and strategies to improve bsAb-mediated T cell-redirecting strategies are discussed.