In recent years, the well-known Infinite Sites Assumption (ISA) has been a fundamental feature of computational methods devised for reconstructing tumor phylogenies and inferring cancer progressions. However, recent studies leveraging Single-Cell Sequencing (SCS) techniques have shown evidence of the widespread recurrence and, especially, loss of mutations in several tumor samples. While there exist established computational methods that infer phylogenies with mutation losses, there remain some advancements to be made. We present SASC (Simulated Annealing Single-Cell inference) a new and robust approach based on simulated annealing for the inference of cancer progression from SCS data sets. In particular, we introduce an extension of the model of evolution where mutations are only accumulated, by allowing also a limited amount of mutation loss in the evolutionary history of the tumor the Dollo-k model. We demonstrate that SASC achieves high levels of accuracy when tested on both simulated and real data sets and in comparison with some other available methods. The Simulated Annealing Single-Cell inference (SASC) tool is open source and available at https//github.com/sciccolella/sasc. Supplementary data are available at Bioinformatics online.Supplementary data are available at Bioinformatics online.Marjolin's ulcer (MU) is a rare, aggressive entity with frequent delay in diagnosis for a variety of regions. Although well described and classically taught in medical school, aspects of its treatment remain ill-defined and controversial. A systematic review was performed according to PRISMA guidelines to identify studies discussing patients who underwent surgical treatment of Marjolin's Ulcer. A total of 31 papers, reporting on 1,016 patients, were included. Burns were the most common etiology of malignant degeneration (68%), followed by trauma. The lower extremity was most affected (51%) and Squamous Cell Carcinoma (SCC) was found in 94% of cases, with the majority being well differentiated. IMP-1088 purchase Basal cell Carcinoma and Melenoma composed a minority of cases. Melanoma occurred more frequently in previously skin grafted wounds and had a higher rate of metastases than SCC. Most patients did not have associated regional or distant metastases present at diagnosis. Wide local excision (71%) was performed in most cases, unless amputation was indicated for severe disease or bone involvement. Lymphadenectomy and sentinel lymph node biopsy (SLNB) were variably reported, with conflicting evidence on the efficacy. Lymphadenectomy was most commonly indicated for known lymph node involvement. In cases of metastatic disease chemotherapy and radiation were used in conjunction with surgical treatment. Despite numerous articles on this topic, controversy remains in the management of MU. Early diagnosis of suspicious chronic wounds and prompt surgical intervention remain imperative to its treatment.Misreporting of added sugar intake has been the major criticism of studies linking high added sugar consumption to adverse health outcomes. Despite the advancement in dietary assessment methodologies, the bias introduced by self-reporting can never be completely eliminated. The search for an objective biomarker for total added sugar intake has therefore been a topic of interest. In this article, the reasons this search may be a wild goose chase will be outlined and discussed. The limitations and inability of the 2 candidate biomarkers, namely urinary sucrose and fructose and δ¹³C isotope, which are based on the 2 only possible ways (i.e., difference in metabolism and plant sources) to identify added sugar based on current knowledge in human physiology and food and nutritional sciences, are discussed in detail. Validation studies have shown that these 2 candidate biomarkers are unlikely to be suitable for use as a predictive or calibration biomarker for total added sugar intake. Unless advancement in our understanding in human physiology and food and nutritional sciences leads to new potential ways to distinguish between naturally occurring and added sugars, it is extremely unlikely that any accurate objective added sugar biomarker could be found. It may be time to stop the futile effort in searching for such a biomarker, and resources may be better spent on further improving and innovating dietary assessment methods to minimize the bias introduced by self-reporting.Women with polycystic ovary syndrome (PCOS) exhibit cardiometabolic (e.g., insulin resistance) and associated reproductive disruptions. Lifestyle modification (e.g., diet) is recommended as the first-line therapy to manage PCOS; however, a favorable dietary regimen remains unclear beyond energy restriction. We conducted a systematic review and meta-analysis of randomized controlled trials (RCTs) to summarize evidence on impacts of dietary glycemic index (GI) or glycemic load (GL) on cardiometabolic and reproductive profiles to update the International Evidence-based Guideline for the Assessment and Management of PCOS. Databases of MEDLINE, Cochrane, Web of Science, and Scopus were searched through 30 October 2019, and confirmed on 25 March 2020, to identify RCTs (≥8 wk) comparing the effects of diets with lower (LGI/LGL) and higher (HGI/HGL) GI/GL on glucoregulatory outcomes, lipid profile, anthropometrics, and androgen status in PCOS. The primary outcome was HOMA-IR. Data were pooled by random-effects modelsting their inclusion for dietary management of PCOS. Further RCTs should confirm these observations and address whether LGI diets improve more patient-pressing complications, including ovulatory cyclicity, infertility, and cardiovascular disease risk in this high-risk population. This review was registered at www.crd.york.ac.uk/PROSPERO as CRD42020175300. ipDMR is an R software tool for identification of differentially methylated regions using auto-correlated P values for individual CpGs from epigenome-wide association analysis using array or bisulfite sequencing data. It summarizes p-values for adjacent CpGs, identifies association peaks, and then extends peaks to find boundaries of differentially methylated regions. ipDMR uses BED format files as input and is easy to use. Simulations guided by real data found that ipDMR outperformed current available methods and provided slightly higher true positive rates and much lower false discovery rates. ipDMR is available at https//bioconductor.org/packages/release/bioc/html/ENmix.html.ipDMR is available at https//bioconductor.org/packages/release/bioc/html/ENmix.html.