PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data.

Although the majority of bacteria are harmless or even beneficial to their host, others are highly virulent and can cause serious diseases, and even death. Due to the constantly decreasing cost of high-throughput sequencing there are now many completely sequenced genomes available from both human pathogenic and innocuous strains. The data can be used to identify gene families that correlate with pathogenicity and to develop tools to predict the pathogenicity of newly sequenced strains, investigations that previously were mainly done by means of more expensive and time consuming experimental approaches. We describe PathogenFinde

In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

Background: The increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a potentially attractive source of novel antibiotics due to their broad spectrum of antimicrobial activities. We specifically focus on a computational analysis of the distinctive biosynthetic potential of Bacillus paralicheniformis strains isolated from the Red Sea, an ecosystem exposed to adverse, highly saline and hot conditions. Results: We report the complete circular and annotated genomes of two Red Sea strains, B. paralicheniformis Bac48 isolated from mangrove mud and B. paralicheniformis Bac84 isolated from microbial mat collected from Rabigh Harbor Lagoon in Saudi Arabia. Comparing the genomes of B. paralicheniformis Bac48 and B. paralicheniformis Bac84 with nine publicly available complete genomes of B. licheniformis and three genomes of B. paralicheniformis, revealed that all of the B. paralicheniformis strains in this study are more enriched in nonribosomal peptides (NRPs). We further report the first computationally identified trans-acyltransferase (trans-AT) nonribosomal peptide synthetase/polyketide synthase (PKS/ NRPS) cluster in strains of this species. Conclusions:B. paralicheniformis species have more genes associated with biosynthesis of antimicrobial bioactive compounds than other previously characterized species of B. licheniformis, which suggests that these species are better potential sources for novel antibiotics. Moreover, the genome of the Red Sea strain B. paralicheniformis Bac48 is more enriched in modular PKS genes compared to B. licheniformis strains and other B. paralicheniformis strains. This may be linked to adaptations that strains surviving in the Red Sea underwent to survive in the relatively hot and saline ecosystems

Enabling large-scale design, synthesis and validation of small molecule protein-protein antagonists

Although there is no shortage of potential drug targets, there are only a handful known low-molecular-weight inhibitors of protein-protein interactions (PPIs). One problem is that current efforts are dominated by low-yield high-throughput screening, whose rigid framework is not suitable for the diverse chemotypes present in PPIs. Here, we developed a novel pharmacophore-based interactive screening technology that builds on the role anchor residues, or deeply buried hot spots, have in PPIs, and redesigns these entry points with anchor-biased virtual multicomponent reactions, delivering tens of millions of readily synthesizable novel compounds. Application of this approach to the MDM2/p53 cancer target led to high hit rates, resulting in a large and diverse set of confirmed inhibitors, and co-crystal structures validate the designed compounds. Our unique open-access technology promises to expand chemical space and the exploration of the human interactome by leveraging in-house small-scale assays and user-friendly chemistry to rationally design ligands for PPIs with known structure. © 2012 Koes et al

Induction chemotherapy followed by chemoradiation in locally advanced cervical cancer: Quality of life outcomes of the GCIG INTERLACE trial

Aim: Induction chemotherapy (IC) added to chemoradiation (CRT) in locally advanced cervical cancer (LACC) improves survival at the expense of adverse events (AEs), 99 % with IC/CRT vs 95 % CRT alone, 59 % vs 48 % G3/4 AEs. We investigated the impact of this on quality of life (QoL).// Methods: 500 women with FIGO 2008 stage IB1 node positive, IB2, II, IIIB and IVA cervical carcinoma were randomised to CRT alone or IC (6 weeks carboplatin AUC2 paclitaxel 80mg/m2) followed by CRT. QoL questionnaires (EORTC QLQ-C30 v3, QLQ-CX24) were completed at baseline, D1 week 4 IC, D1 CRT, D1 week 3 CRT, 4 weeks post CRT and all follow up visits. Mixed modelling for repeated measures was used to compare the groups during trial treatment to 2 years follow up (adjusting for baseline).// Results: QoL (global health status, physical and social functioning) slightly worsened during IC and symptom experience slightly improved. Emotional functioning improved during IC. Peripheral neuropathy was slightly worse with IC/CRT. Fatigue and nausea/vomiting worsened from baseline to week 4 IC whilst pain and diarrhoea improved, consistent with reported AEs. Over the whole period, mean differences for these symptoms between the treatment groups was small and not clinically significant and resolved by 12–18 months. In all cases, mean score differences during trial treatment until 2 years post CRT showed only small differences (<5 units) not meeting the threshold for clinical relevance. Conclusion: IC added to CRT does not adversely impact QoL compared to CRT, either during IC, during CRT or later

Using death to one's advantage: HIV modulation of apoptosis

Infection by human immunodeficiency virus (HIV) is associated with an early immune dysfunction and progressive destruction of CD4+ T lymphocytes. This progressive disappearance of T cells leads to a lack of immune control of HIV replication and to the development of immune deficiency resulting in the increased occurrence of opportunistic infections associated with acquired immune deficiency syndrome (AIDS). The HIV-induced, premature destruction of lymphocytes is associated with the continuous production of HIV viral proteins that modulate apoptotic pathways. The viral proteins, such as Tat, Env, and Nef, are associated with chronic immune activation and the continuous induction of apoptotic factors. Viral protein expression predisposes lymphocytes, particularly CD4+ T cells, CD8+ T cells, and antigen-presenting cells, to evolve into effectors of apoptosis and as a result, to lead to the destruction of healthy, non-infected T cells. Tat and Nef, along with Vpu, can also protect HIV-infected cells from apoptosis by increasing anti-apoptotic proteins and down- regulating cell surface receptors recognized by immune system cells. This review will discuss the validity of the apoptosis hypothesis in HIV disease and the potential mechanism(s) that HIV proteins perform in the progressive T cell depletion observed in AIDS pathogenesis. Originally published Leukemia, Vol. 15, No. 3, Mar 200

Vulvar Carcinoma:Diagnosis, Staging, and Treatment

Vulvar cancer accounts for only 5% of all gynecologic cancers with an incidence rate of 2.4 per 100, 000 women. The most common histological type of vulvar cancer is vulvar squamous cell carcinoma (VSCC). There are two different types of VSCC with their own associated premalignant lesions. The most common type occurs in elderly women and leads to mostly differentiated keratinizing VSCC in a background of lichen sclerosus and often differentiated vulvar intraepithelial neoplasia. The second type of VSCC consists of mainly nonkeratinizing carcinomas, primarily affecting younger women, and is associated with high-grade squamous intraepithelial lesions. The diagnosis VSCC should be confirmed histologically, preferably by a punch biopsy. The method of treatment for VSCC depends on the extent of the disease. In general, surgery is the first choice of treatment in patients with primary VSCC. The inguinofemoral lymph node status at initial diagnosis reflected in stage is of critical prognostic importance for patients with VSCC. The treatment of VSCC consists of radical local excision of the tumor combined with the sentinel node procedure in patients with early-stage unifocal tumors of less than 4 cm and without clinically suspicious groin lymph nodes. In case of a metastatic sentinel node, a larger or multifocal tumor, or clinically suspicious lymph nodes, an inguinofemoral lymphadenectomy is indicated. There is a limited role for primary radio- and/or chemotherapy. Overall survival for early-stage VSCC patients is good with 75% at 5 years.</p

The regulation of IL-10 expression

Interleukin (IL)-10 is an important immunoregulatory cytokine and an understanding of how IL-10 expression is controlled is critical in the design of immune intervention strategies. IL-10 is produced by almost all cell types within the innate (including macrophages, monocytes, dendritic cells (DCs), mast cells, neutrophils, eosinophils and natural killer cells) and adaptive (including CD4(+) T cells, CD8(+) T cells and B cells) immune systems. The mechanisms of IL-10 regulation operate at several stages including chromatin remodelling at the Il10 locus, transcriptional regulation of Il10 expression and post-transcriptional regulation of Il10 mRNA. In addition, whereas some aspects of Il10 gene regulation are conserved between different immune cell types, several are cell type- or stimulus-specific. Here, we outline the complexity of IL-10 production by discussing what is known about its regulation in macrophages, monocytes, DCs and CD4(+) T helper cells

Uptake and 4-week outcomes of an ‘opt-out’ smoking cessation referral strategy in a London-based lung cancer screening setting

INTRODUCTION: Lung cancer screening (LCS) enables the delivery of smoking cessation interventions to a population experiencing long-term tobacco dependence, but the optimal delivery method remains unclear. Here, we report uptake and short-term outcomes of an ‘opt-out’ smoking cessation referral strategy in an LCS cohort. METHODS: Individuals currently smoking tobacco who attended a face-to-face lung health check in the SUMMIT study (NCT03934866) were offered very brief advice on smoking cessation and where possible, an ‘opt-out’ referral to their local stop smoking service (SSS). Aggregate data on referral outcomes were obtained from each SSS individually. RESULTS: 33.7% (n=2090/6203) of individuals currently smoking tobacco consented to a practitioner-made ‘opt-out’ smoking cessation referral. 42.7% (n=893/2090) of these individuals resided in boroughs where SSS were not present or required self-referral. Males (adjusted OR (aOR) 1.16), younger individuals (55–59: aOR 1.70, 60–64: aOR 1.71 and 65–69: aOR 1.78) and those of ethnic minority backgrounds (Asian: aOR 1.31, Black: aOR 1.71 and Mixed: aOR 1.72) were more likely to consent, while individuals from the most deprived socioeconomic quintile were less likely to do so (aOR 0.65). High level of motivation to quit within a defined time frame (aOR 1.92), previous quit attempts in the past 12 months (1–4: aOR 1.65 and ≥5: aOR 1.54) and time to first cigarette of ≤60 min (<5: aOR 2.07, 6–30: aOR 1.55 and 31–60: aOR 1.56) were measures of tobacco dependence associated with a higher likelihood of providing consent. Outcomes were available for 742 referrals. An appointment with the service was accepted by 47.3% (n=351/742) of individuals, following which 65.5% (n=230/351) set a quit date. The 4-week quit rate among those setting a quit date and all individuals referred was 57.4% (n=132/230) and 17.8% (n=132/742), respectively. CONCLUSION: A proactive, ‘opt-out’ smoking cessation referral strategy for individuals currently smoking tobacco who interact with an LCS programme may be beneficial

Social geography of AIDS in Brazil: identifying patterns of regional inequalities

The trend towards decline and stabilization of the AIDS epidemic in Brazil should be analyzed carefully, since aggregate data can mask regional or local inequalities in such a large and diverse country. The current study reevaluates the epidemic’s spatial dissemination and the AIDS-related mortality pattern in Brazil. The study considered all AIDS cases diagnosed in individuals over 18 years of age and living in Brazil, as well as AIDS deaths recorded in 1998-2008. Three-year moving average rates were estimated, and a spatial analysis was conducted using a local empirical Bayesian method. The epidemic was only found to be expanding in the North and Northeast regions, while declining in the rest of the country, especially in the Southeast. According to the findings, the apparent stabilization of AIDS mortality tends to mask regional disparities. Social determinants of health and regional disparities should be taken into account in program development and policymaking

A review of a strategic roadmapping exercise to advance clinical translation of photoacoustic imaging: From current barriers to future adoption

Photoacoustic imaging (PAI), also referred to as optoacoustic imaging, has shown promise in early-stage clinical trials in a range of applications from inflammatory diseases to cancer. While the first PAI systems have recently received regulatory approvals, successful adoption of PAI technology into healthcare systems for clinical decision making must still overcome a range of barriers, from education and training to data acquisition and interpretation. The International Photoacoustic Standardisation Consortium (IPASC) undertook an community exercise in 2022 to identify and understand these barriers, then develop a roadmap of strategic plans to address them. Here, we outline the nature and scope of the barriers that were identified, along with short-, medium- and long-term community efforts required to overcome them, both within and beyond the IPASC group