Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data

Background DNA methylation is an important epigenetic modification involved in many biological processes. Reduced representation bisulfite sequencing (RRBS) is a cost-effective method for studying DNA methylation at single base resolution. Although several tools are available for RRBS data processing and analysis, it is not clear which strategy performs the best and there has not been much attention to the contamination issue from artificial cytosines incorporated during the end repair step of library preparation. To address these issues, we describe a new method, Targeted Alignment and Artificial Cytosine Elimination for RRBS (TRACE-RRBS), which aligns bisulfite sequence reads to MSP1 digitally digested reference and specifically removes the end repair cytosines. We compared this approach on a simulated and a real dataset with 7 other RRBS analysis tools and Illumina 450 K microarray platform. Results TRACE-RRBS aligns sequence reads to a small fraction of the genome where RRBS protocol targets on and was demonstrated as the fastest, most sensitive and specific tool for the simulated dataset. For the real dataset, TRACE-RRBS took about the same time as RRBSMAP, a third to a sixth of time needed for BISMARK and NOVOALIGN. TRACE-RRBS aligned more reads uniquely than other tools and achieved the highest correlation with 450 k microarray data. The end repair artificial cytosine removal increased correlation between nearby CpGs and accuracy of methylation quantification. Conclusions TRACE-RRBS is fast and more accurate tool for RRBS data analysis. It is freely available for academic use at http://​bioinformaticsto​ols.​mayo.​edu/​

Sex hormones influence survival of patients with metastatic urothelial carcinoma undergoing immune checkpoint therapy

Introduction Clinical trials investigating efficacy of immune checkpoint inhibitors (ICI) revealed sex-specific divergent outcomes in urothelial cancer (UC), suggesting that sex hormones might play an important role in gender-specific dimorphisms of response upon ICI. However, further clinical investigations are still needed to understand the influence of sex hormones in UC. The aim of this study was to get further insights on the prognostic and predictive value of sex hormone levels in patients with metastatic UC (mUC) who underwent ICI. Material and methods Sex hormone levels of patients with mUC including luteinizing hormone (LH), follicle-stimulating hormone (FSH), LH/FSH ratio, prolactin, testosterone and 17β-estradiol (E2) were evaluated at baseline and during ICI at 6/8 weeks and 12/14 weeks. Results Twenty-eight patients (10 women, 18 men) with a median age of 70 years were included. Metastatic disease was confirmed in 21 patients (75%) after radical cystectomy while seven patients showed mUC at first diagnosis. Twelve patients (42.8%) received first line and 16 patients second line pembrolizumab. The objective response rate (ORR) was 39% (CR in 7%). The median progression-free survival (PFS) and overall survival (OS) was 5.5 and 20 months. Focusing on changes of sex hormone levels during ICI, a significant increase in FSH levels and decrease of the LH/FSH ratio was noticed in responders (p = 0.035), yet without sex-specific significance. When adjusted for sex and treatment line, a significant increase of FSH levels was confirmed in men during second line pembrolizumab. Focusing on baseline levels, LH/FSH ratio was significantly higher in female responders (p = 0.043) compared to non-responders. In women, increased LH levels and LH/FSH ratio were associated with better PFS (p = 0.014 for LH, p = 0.016 for LH/FSH ratio) and OS (p = 0.026 and p = 0.018). In male patients, increased E2 levels were linked with improved PFS (p < 0.001) and OS (p = 0.039). Conclusion Increased LH and LH/FSH values in women as well as high E2 levels in men were significant predictors of better survival. Elevated LH/FSH ratio was predictive of better response to ICI in women. These results show first clinical evidence of the potential role of sex hormones as prognostic and predictive biomarker in mUC. Further prospective analyses are needed to corroborate our findings

Thoracic Outlet Syndrome: Single Center Experience on Robotic Assisted First Rib Resection and Literature Review.

Background Thoracic outlet syndrome (TOS) is a pathological condition caused by a narrowing between the clavicle and first rib leading to a compression of the neurovascular bundle to the upper extremity. The incidence of TOS is probably nowadays underestimated because the diagnosis could be very challenging without a thorough clinical examination along with appropriate clinical testing. Beside traditional supra-, infraclavicular or transaxillary approaches, the robotic assisted first rib resection has been gaining importance in the last few years. Methods We conducted a retrospective cohort analysis of all patients who underwent robotic assisted first rib resection due to TOS at Lucerne Cantonal Hospital and then we performed a narrative review of the English literature using PubMed, Cochrane Database of Systematic Reviews and Scopus. Results Between June 2020 and November 2021, eleven robotic assisted first rib resections were performed due to TOS at Lucerne Cantonal Hospital. Median length of stay was 2 days (Standard Deviation: +/- 0.67 days). Median surgery time was 180 min (Standard Deviation: +/- 36.5). No intra-operative complications were reported. Conclusions Robotic assisted first rib resection could represent a safe and feasible option in expert hands for the treatment of thoracic outlet syndrome

Altering broiler gut development, morphology, microbiology and function by manipulating feed grain type, particle size and milling method affects life-long performance

The modern broiler chicken increases its bodyweight by 5000% in the first six weeks of life. Even so, the genetic potential of the bird is ever increasing. The intensive nature of the modern broiler meat production system also potentially increases risk of transmissible diseases. Thus, the stresses on the bird's physiological systems; skeletal/muscular, digestive, immune and cardiovascular, are also increasing. Augmentation of suitable husbandry practices with appropriate nutrition will allow improved broiler production and health, by helping the birds’ physiological systems serve their respective intended purposes. That is, nutritionists need to present a feed to the broiler that more accurately meets its needs, not only on a nutritional level, but also on a physiological level, such that the bird is more able to effectively digest and absorb the feed due to improved physiological responses to the feed itself. The nutritionist can only do so much when it comes to feeding for profit. Aside from the nutritional needs of the bird, economic constraint is the largest factor that must be considered when formulating a broiler diet. It is therefore important that feed production costs are reduced, and at the other end, feed efficiency is improved, essentially enabling a more profitable product per unit cost of feed

A chemokine network of T cell exhaustion and metabolic reprogramming in renal cell carcinoma

Renal cell carcinoma (RCC) is frequently infiltrated by immune cells, a process which is governed by chemokines. CD8+ T cells in the RCC tumor microenvironment (TME) may be exhausted which most likely influence therapy response and survival. The aim of this study was to evaluate chemokine-driven T cell recruitment, T cell exhaustion in the RCC TME, as well as metabolic processes leading to their functional anergy in RCC. Eight publicly available bulk RCC transcriptome collectives (n=1819) and a single cell RNAseq dataset (n=12) were analyzed. Immunodeconvolution, semi-supervised clustering, gene set variation analysis and Monte Carlo-based modeling of metabolic reaction activity were employed. Among 28 chemokine genes available, CXCL9/10/11/CXCR3, CXCL13/CXCR5 and XCL1/XCR1 mRNA expression were significantly increased in RCC compared to normal kidney tissue and also strongly associated with tumor-infiltrating effector memory and central memory CD8+ T cells in all investigated collectives. M1 TAMs, T cells, NK cells as well as tumor cells were identified as the major sources of these chemokines, whereas T cells, B cells and dendritic cells were found to predominantly express the cognate receptors. The cluster of RCCs characterized by high chemokine expression and high CD8+ T cell infiltration displayed a strong activation of IFN/JAK/STAT signaling with elevated expression of multiple T cell exhaustion-associated transcripts. Chemokinehigh RCCs were characterized by metabolic reprogramming, in particular by downregulated OXPHOS and increased IDO1-mediated tryptophan degradation. None of the investigated chemokine genes was significantly associated with survival or response to immunotherapy. We propose a chemokine network that mediates CD8+ T cell recruitment and identify T cell exhaustion, altered energy metabolism and high IDO1 activity as key mechanisms of their suppression. Concomitant targeting of exhaustion pathways and metabolism may pose an effective approach to RCC therapy

MicroWalk: A Framework for Finding Side Channels in Binaries

Microarchitectural side channels expose unprotected software to information leakage attacks where a software adversary is able to track runtime behavior of a benign process and steal secrets such as cryptographic keys. As suggested by incremental software patches for the RSA algorithm against variants of side-channel attacks within different versions of cryptographic libraries, protecting security-critical algorithms against side channels is an intricate task. Software protections avoid leakages by operating in constant time with a uniform resource usage pattern independent of the processed secret. In this respect, automated testing and verification of software binaries for leakage-free behavior is of importance, particularly when the source code is not available. In this work, we propose a novel technique based on Dynamic Binary Instrumentation and Mutual Information Analysis to efficiently locate and quantify memory based and control-flow based microarchitectural leakages. We develop a software framework named \tool~for side-channel analysis of binaries which can be extended to support new classes of leakage. For the first time, by utilizing \tool, we perform rigorous leakage analysis of two widely-used closed-source cryptographic libraries: \emph{Intel IPP} and \emph{Microsoft CNG}. We analyze $15$ different cryptographic implementations consisting of $112$ million instructions in about $105$ minutes of CPU time. By locating previously unknown leakages in hardened implementations, our results suggest that \tool~can efficiently find microarchitectural leakages in software binaries

Response to a sexual risk reduction intervention provided in combination with hepatitis C treatment by HIV/HCV co-infected men who have sex with men: a reflexive thematic analysis.

BACKGROUND: Hepatitis C virus reinfections in HIV-positive men-who-have-sex-with-men (MSM) challenge the effectiveness of antiviral treatment. To fight this problem, an adapted sexual risk reduction intervention was implemented within a hepatitis C treatment trial. Following this, the current study had two aims and describes 1) how the program was received by participants; and 2) their responses to the program regarding sexual risk taking. Based on the participants' input, we hoped to judge the intervention's potential for scale-up. METHODS: Seventeen participants who received the sexual risk reduction intervention in addition to hepatitis C treatment were recruited for semi-structured interviews six to 12 months post-intervention. We evaluated the responses via reflexive thematic analysis and applied the concept of sense-making. RESULTS: Giving hepatitis C a place and living without it again illustrates how participants received the program and how their experiences were altered by the impact of sense-making. Based on their responses, we allocated participants to three groups: 1. Avoid risks: get rid of hepatitis C for life. For these men, hepatitis C remained a life-threatening disease: they actively modified their risk behavior and felt supported by the intervention in maintaining their behavioral changes. 2. Minimize risks: live as long as possible without hepatitis C. In contrast to group 1, these men saw hepatitis C as a manageable disease. The intervention facilitated reflection on risks and how to develop behavioral changes that suited them individually. 3. Accept risks; live with the risk of hepatitis C. These men perceived behavioral changes as much more difficult than "easy" medical treatment. They expected to either undergo repeated rounds of treatment or stay HCV re-infected. CONCLUSION: These results illustrate the diversity of men's responses and their decisions regarding sexual risk behavior after participating in a combination of antiviral treatment and a sexual risk reduction intervention. Two major aspects were identified: 1) Teachable moments, particularly at the time of diagnosis/treatment, could offer an opportunity to develop openness for behavioral change; 2) adapting sexual risk reduction interventions to sense-making patterns could help to improve its effectiveness. Support for reducing infection risk and raising awareness of preventative measures are additional benefits. TRIAL REGISTRATION: Clinical Trial Number: NCT02785666 , 30.05.2016

Giovanni Boccaccio. Italienisch-deutscher Kulturtransfer von der Frühen Neuzeit bis zur Gegenwart

Italien und Deutschland – kaum zwei andere Kulturen in Europa sind so stark miteinander verbunden wie diese beiden, sei es geschichtlich oder kulturell. Am wirkmächtigsten war sicherlich die Übernahme des Gedankenguts der italienischen Renaissance, in deren Folge Wissen aus gesellschaftlichen, wissenschaftlichen und kulturellen Bereichen den Weg nach Deutschland fand, darunter auch die Kenntnis von Giovanni Boccaccios Werken, die sich auf deutschsprachige Kontexte auswirkten. Der vorliegende Tagungsband versammelt die Beiträge zur gleichnamigen Tagung „Giovanni Boccaccio. Italienisch-deutscher Kulturtransfer von der Frühen Neuzeit bis zur Gegenwart“ (Bamberg, 21. bis 23. November 2013), die sich mit vielfältigen Aspekten der Boccaccio-Rezeption auseinandersetzen