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The outputs consist of raw and normalized peak scores (multiple normalizations) in text format and scaled bigWig coverage tracks that are directly accessible to data visualization programs. BAMScale also includes a visualization module facilitating direct, on-demand quantitative peak comparisons that can be used by experimentalists. Our tool can effectively analyze large sequencing datasets (~ 100 Gb size) in minutes, outperforming currently available tools. CONCLUSIONS BAMscale accurately quantifies and normalizes identified peaks directly from BAM files, and creates coverage tracks for visualization in genome browsers. BAMScale can be implemented for a wide set of methods for calculating coverage tracks, including ChIP-seq and ATAC-seq, as well as methods that currently require specialized, separate tools for analyses, such as splice-aware RNA-seq, END-seq and OK-seq for which no dedicated software is available. BAMscale is freely available on github (https//github.com/ncbi/BAMscale).BACKGROUND Chromatin dysregulation is associated with developmental disorders and cancer. Numerous methods for measuring genome-wide chromatin accessibility have been developed in the genomic era to interrogate the function of chromatin regulators. A recent technique which has gained widespread use due to speed and low input requirements with native chromatin is the Assay for Transposase-Accessible Chromatin, or ATAC-seq. Biologists have since used this method to compare chromatin accessibility between two cellular conditions. However, approaches for calculating differential accessibility can yield conflicting results, and little emphasis is placed on choice of normalization method during differential ATAC-seq analysis, especially when global chromatin alterations might be expected. RESULTS Using an in vivo ATAC-seq data set generated in our recent report, we observed differences in chromatin accessibility patterns depending on the data normalization method used to calculate differential accessibility. This observation was further verified on published ATAC-seq data from yeast. We propose a generalized workflow for differential accessibility analysis using ATAC-seq data. We further show this workflow identifies sites of differential chromatin accessibility that correlate with gene expression and is sensitive to differential analysis using negative controls. CONCLUSIONS We argue that researchers should systematically compare multiple normalization methods before continuing with differential accessibility analysis. ATAC-seq users should be aware of the interpretations of potential bias within experimental data and the assumptions of the normalization method implemented.BACKGROUND Elderly patients represent a major fraction of non-small cell lung cancer (NSCLC) patients in routine clinical practice, but they are still underrepresented in clinical trials. In particular, data regarding efficacy and safety in frail or elderly patients with respect to immunotherapy are lacking. Importantly, immunosenescence in elderly patients might interfere with activities of immune-modulating drugs such as PD-1/PD-L1 inhibitors. Thus, there is an urgent need to assess safety and efficacy of such inhibitors in this group. METHODS/DESIGN This prospective, open label, treatment stratified, randomized phase II study will enroll 200 patients with stage IV NSCLC amenable at least to single-agent chemotherapy (CT). Eligible patients must be aged 70 years or older and/or "frail" (Charlson Comorbidity Index > 1) or have a restricted performance status (Eastern Cooperative Oncology Group, ECOG > 1). Patients are stratified according to modified Cancer and Age Research Group (CARG) score "fit" patients N The DURATION trial will prospectively investigate the safety and tolerability of anti-PD-L1 treatment with durvalumab after chemotherapy in elderly and frail patients and thereby provide new insights into the effect of PD-L1 blockade and the impact of immunosenescence in this cohort of patients. TRIAL REGISTRATION ClinicalTrials.gov, NCT03345810; initially registered on 17 November 2017. Eudra-CT, 2016-003963-20; initially registered on 3 January 2017.BACKGROUND The World Health Organization recommends exclusive breastfeeding for 6 months and total breastfeeding for at least 2 years. Despite this and multiple interventions promoting breastfeeding, early breastfeeding cessation remains high with little data as to the ongoing barriers contributing to early cessation. METHODS Two groups of Nicaraguan mothers in an urban hospital were approached to complete a questionnaire to determine what newborn, maternal, and socioeconomic factors contributed to early cessation of breastfeeding. Group 1 participants were mothers of newborns in the newborn units, while group 2 were mothers of children 5 years or younger in the emergency room and pediatric ward. Descriptive statistics summarized the data. Fisher's exact test evaluated factors associated with early breastfeeding cessation. RESULTS In group 1, 97 participants were enrolled with 81% of mothers planning to fulfill the guideline for exclusive breastfeeding for 6 months. In group 2, there were 139 mothers of which 58% reported they had exclusively breastfed for 6 months. Only 25 and 27% of mothers in group 1 and 2 respectively planned to breastfeed or breastfed for 2 years. In group 1, mothers reported lack of knowledge regarding breastfeeding techniques and older mothers tended to plan for early cessation of exclusive breastfeeding. In group 2, mothers reported feeling uncomfortable with breastfeeding in public or had difficulty with latching. Cessation of any breastfeeding prior to 12 months was associated with being uncomfortable breastfeeding in public and knowing the WHO guidelines. In both groups, social media represented an expanding platform for receiving breastfeeding information. CONCLUSIONS Interventions focusing on reaching younger mothers and addressing breastfeeding knowledge and techniques while leveraging the increasing influence of social media platforms may help improve compliance with breastfeeding recommendations.Medical tourism occupies different spaces within national policy frameworks depending on which side of the transnational paradigm countries belong to, and how they seek to leverage it towards their developmental goals. This article draws attention to this policy divide in transnational healthcare through a comparative bibliometric review of policy research on medical tourism in select source (Canada, United States and United Kingdom) and destination countries (Mexico, India, Thailand, Malaysia and Singapore), using a systematic search of the Web of Science (WoS) database and review of grey literature. We assess cross-national differences in policy and policy research on medical tourism against contextual policy landscapes and challenges, and examine the convergence between research and policy. Our findings indicate major disparities in development agendas and national policy concerns, both between and among source and destination countries. CX-5461 order Further, we find that research on medical tourism does not always address prevailing policy challenges, just as the policy discourse oftentimes neglects relevant policy research on the subject. Based on our review, we highlight the limited application of theoretical policy paradigms in current medical tourism research and make the case for a comparative policy research agenda for the field.BACKGROUND Recent studies demonstrate that insect-specific viruses can influence the ability of their mosquito hosts to become infected with and transmit arboviruses of medical and veterinary importance. The aim of this study was to evaluate the interactions between Anopheles gambiae densovirus (AgDNV) (Parvoviridae) (a benign insect-specific virus that infects An. gambiae mosquitoes) and Mayaro virus (MAYV) (Togaviridae) (an emerging human pathogen that can be transmitted by An. gambiae) in both insect cell culture and mosquitoes. METHODS For in vitro studies, An. gambiae Mos55 cells infected or uninfected with AgDNV were infected with MAYV. For in vivo studies, An. gambiae mosquitoes were injected intrathoracically with AgDNV and 4 days later orally infected with MAYV. Mosquitoes were dissected 10 days after MAYV infection, and MAYV titers in the body, legs and saliva samples quantified using focus-forming assay. RESULTS MAYV virus replication was reduced 10-100-fold in An. gambiae Mos55 cells infected with AgDNV. In mosquitoes, there was a significant negative correlation between AgDNV and MAYV body titers 10 days post-blood meal. CONCLUSIONS AgDNV infection was associated with reduced production of MAYV in cell culture, and reduced body titers of MAYV in An. gambiae mosquitoes. As densovirus infections are common in natural mosquito populations, these data suggest that they may affect the epidemiology of viruses of medical importance.BACKGROUND Inverted urothelial papilloma (IUP) of the upper urinary tract is an uncommon benign tumour that occasionally presents as a polypoid mass causing urinary obstruction. Histologically, IUP is characterised by a proliferating urothelium arranged in cords and trabeculae, in continuity with overlying intact epithelium, and extending into the lamina propria in a non-invasive, endophytic manner. Cytological atypia is minimal or absent. Top differential diagnoses include urothelial carcinoma with inverted growth pattern and florid ureteritis cystica. Although urothelial carcinomas of the upper urinary tract with prominent inverted growth pattern commonly harbour microsatellite instability, the role of the mutator phenotype pathway in IUP development is still unclear. The aim of this study was to describe two additional cases of IUP of the upper urinary tract, along with an extensive literature review. CASE PRESENTATION We observed two polypoid tumours originating in the renal pelvis and the distal ureter, respectively. Both patients, a 76-year-old woman and a 56-year-old man, underwent surgery because of the increased likelihood of malignancy. Histology was consistent with IUP and patients are alive and asymptomatic after long-term follow-up (6 years for the renal pelvis lesion and 5 years for the ureter lesion). The tumours retained the expression of the mismatch-repair protein MLH1, MSH2, and PMS2 whereas loss of MSH6 was found in both cases. CONCLUSIONS When completely resected, IUP does not require rigorous surveillance protocols, such as those for urothelial carcinoma and exophytic urothelial papilloma. It is therefore important for the surgical pathologist to be aware of this rare entity in order to ensure correct patient management.BACKGROUND The highest incidence of breast cancer is in the Western world. Several aspects of the Western lifestyle are known risk factors for breast cancer. In particular, previous studies have shown that cholesterol levels can play an important role in the regulation of tumor progression. METHODS In the present study, we modulated cholesterol metabolism in the human breast cancer cell lines MCF-7 and MDA-MB-231 using a genetic approach. Apolipoprotein A-I (apoA-I) and apolipoprotein E (apoE) were expressed in these cell lines to modulate cholesterol metabolism. The effects of these apolipoproteins on cancer cell properties were examined. RESULTS Our results show that both apolipoproteins can regulate cholesterol metabolism and can control the epithelial-to-mesenchymal transition process. However, these effects were different depending on the cell type. We show that expressing apoA-I or apoE stimulates proliferation, migration, and tumor growth of MCF-7 cells. However, apoA-I or apoE reduces proliferation and migration of MDA-MB-231 cells.
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