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Single-cell RNA-sequencing has great potential to discover cell types, identify cell states, trace development lineages, and reconstruct the spatial organization of cells. However, dimension reduction to interpret structure in single-cell sequencing data remains a challenge. Existing algorithms are either not able to uncover the clustering structures in the data or lose global information such as groups of clusters that are close to each other. We present a robust statistical model, scvis, to capture and visualize the low-dimensional structures in single-cell gene expression data. Simulation results demonstrate that low-dimensional representations learned by scvis preserve both the local and global neighbor structures in the data. In addition, scvis is robust to the number of data points and learns a probabilistic parametric mapping function to add new data points to an existing embedding. We then use scvis to analyze four single-cell RNA-sequencing datasets, exemplifying interpretable two-dimensional representations of the high-dimensional single-cell RNA-sequencing data. Although single-cell transcriptome data are increasingly available, their interpretation remains a challenge. Here, the authors present a dimensionality reduction approach that preserves both the local and global neighbourhood structures in the data thus enhancing its interpretability.

Activating mutations in FLT3 occur in ~30% of adult acute myeloid leukemia, primarily consisting of internal tandem duplication (ITD) mutations (~25%) and point mutations in the tyrosine kinase domain (~5%), commonly at the activation loop residue D835. Secondary kinase domain mutations in FLT3-ITD, particularly at the D835 residue are frequently associated with acquired clinical resistance to effective FLT3 tyrosine kinase inhibitors (TKIs). Molecular docking studies have suggested that D835 mutations primarily confer resistance by stabilizing an active Asp-Phe-Gly in (‘DFG-in’) kinase conformation unfavorable to the binding of type II FLT3 TKIs, which target a ‘DFG-out’ inactive conformation. We profiled the activity of active type II FLT3 TKIs against D835 kinase domain mutants that have been clinically detected to date. We found that type II inhibitors (quizartinib, sorafenib, ponatinib and PLX3397) retain activity against specific D835 substitutions. Modeling studies suggest that bulky hydrophobic substitutions (D835Y/V/I/F) at this residue are particularly resistant, whereas mutations that preserve interactions between D835 and S838 are relatively sensitive (D835E/N). All mutants retain sensitivity to the type I inhibitor crenolanib. These results suggest that patients with relatively sensitive D835 mutations should be included in clinical trials of type II FLT3 TKIs.

Purpose of ReviewThe objectives of this article are to review the major changes in the staging of head and neck cancers and the rationale for the modifications.Recent FindingsInformation gathered from various institutional reports lead to a better understanding of the clinical and biological behavior of head and neck tumors, resulting in distinct outcomes, which were used to update the staging system.SummaryThis article reviews the changes in the staging of head and neck cancers published in the 8th edition of the AJCC/UICC TNM staging system.

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most successful modern pathogens. The same organism that lives as a commensal and is transmitted in both health-care and community settings is also a leading cause of bacteraemia, endocarditis, skin and soft tissue infections, bone and joint infections and hospital-acquired infections. Genetically diverse, the epidemiology of MRSA is primarily characterized by the serial emergence of epidemic strains. Although its incidence has recently declined in some regions, MRSA still poses a formidable clinical threat, with persistently high morbidity and mortality. Successful treatment remains challenging and requires the evaluation of both novel antimicrobials and adjunctive aspects of care, such as infectious disease consultation, echocardiography and source control. In this Review, we provide an overview of basic and clinical MRSA research and summarize the expansive body of literature on the epidemiology, transmission, genetic diversity, evolution, surveillance and treatment of MRSA.Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen both within hospitals and in the community. In this Review, Fowler and colleagues provide an overview of basic and clinical MRSA research and explore the epidemiology, transmission, genetic diversity, evolution, surveillance and treatment of MRSA.

The recently released eighth edition of the American Joint Committee on Cancer (AJCC) Staging Manual, Head and Neck Section, introduces significant modifications from the prior seventh edition. This article details several of the most significant modifications, and the rationale for the revisions, to alert the reader to evolution of the field. The most significant update creates a separate staging algorithm for high-risk human papillomavirus-associated cancer of the oropharynx, distinguishing it from oropharyngeal cancer with other causes. Other modifications include: the reorganizing of skin cancer (other than melanoma and Merkel cell carcinoma) from a general chapter for the entire body to a head and neck-specific cutaneous malignancies chapter; division of cancer of the pharynx into 3 separate chapters; changes to the tumor (T) categories for oral cavity, skin, and nasopharynx; and the addition of extranodal cancer extension to lymph node category (N) in all but the viral-related cancers and mucosal melanoma. The Head and Neck Task Force worked with colleagues around the world to derive a staging system that reflects ongoing changes in head and neck oncology; it remains user friendly and consistent with the traditional tumor, lymph node, metastasis (TNM) staging paradigm.

Chromosomal instability (CIN) and epigenetic alterations are characteristics of advanced and metastatic cancers 1 – 4 , but whether they are mechanistically linked is unknown. Here we show that missegregation of mitotic chromosomes, their sequestration in micronuclei 5 , 6 and subsequent rupture of the micronuclear envelope 7 profoundly disrupt normal histone post-translational modifications (PTMs), a phenomenon conserved across humans and mice, as well as in cancer and non-transformed cells. Some of the changes in histone PTMs occur because of the rupture of the micronuclear envelope, whereas others are inherited from mitotic abnormalities before the micronucleus is formed. Using orthogonal approaches, we demonstrate that micronuclei exhibit extensive differences in chromatin accessibility, with a strong positional bias between promoters and distal or intergenic regions, in line with observed redistributions of histone PTMs. Inducing CIN causes widespread epigenetic dysregulation, and chromosomes that transit in micronuclei experience heritable abnormalities in their accessibility long after they have been reincorporated into the primary nucleus. Thus, as well as altering genomic copy number, CIN promotes epigenetic reprogramming and heterogeneity in cancer. Missegregated chromosomes that are sequestrated in micronuclei are subject to changes in histone modifications leading to abnormalities in chromatin accessibility that remain long after the chromosomes have been reincorporated into the primary nucleus.

COVID-19 altered lifestyles and disrupted routine health care. Whether blood pressure (BP) control worsened during COVID-19 is unknown. To understand whether home BP control worsened during COVID-19 across the United States (US) . A population-based analysis of home BP data from 72,706 participants enrolled in a digital health hypertension control program. Data was compared before (January 2019 to March 2020) and during (April 2020 to August 2020) COVID-19. Monthly mean home BP readings, systolic blood pressure (SBP), diastolic blood pressure (DBP), and mean arterial pressure (MAP) were quantified before and during the pandemic. Multivariable adjustments were made for age, sex, race, region, and months enrolled. Home BP readings were also classified based on monthly averages and highest home BP readings into risk groups: Stage 2 HTN: BP> = 135 or DBP> = 85; Uncontrolled HTN: SBP> = 145 or DBP> = 95; or Severely uncontrolled HTN: SBP> = 160 or DBP> = 100). Overall, 72,706 participants were enrolled in a digital health hypertension program between 1/1/2019 and 8/31/2020. Compared with participants pre-COVID-19 (n = 33,440), those during COVID-19 (n = 39,266) were of similar age (mean 53.0 ± 10.7 years vs 53.3 ± 10.8 years); sex (46% vs 50.6% female) and race (29.1% vs 34.2% non-white). Relative to pre-Covid (Apr-Aug 2019) the mean monthly number of home BP readings rose during COVID-19 (Apr-Aug, 2020), from 7.3 to 9.3 per month (P < .001). During COVID-19, participants had higher monthly adjusted mean SBP (131.6 mmHg vs. 127.5 mmHg, P < .001); DBP (80.2 mmHg vs. 79.2 mmHg, P < .001); and MAP (97.4 mmHg vs. 95.3 mmHg; P < .001). Relative to the pre-pandemic period, during COVID-19 the proportion of participants with a mean monthly BP classified as uncontrolled or severely uncontrolled hypertension also rose, 15% vs 19% and 4% vs 5%, respectively Based on home BP readings, mean monthly BP rose modestly after COVID-19, despite increased utilization of home monitoring. Further studies are needed to examine the longitudinal effects of the pandemic on cardiovascular disease risk factors, the impact of these on long-term population health.

The treatment of chronic myeloid leukemia (CML) achieved a great leap forward with the development of imatinib, a BCR-ABL kinase inhibitor. Alterations in the chemical structure of the inhibitor have produced agents that are more potent in vitro. In these studies, two new second-generation BCR-ABL kinase inhibitors, nilotinib and dasatinib, are compared with imatinib; these new drugs produce more complete responses and do so faster than imatinib. Both also appear to reduce the rate of progression to accelerated-phase and blast-phase disease. Chronic myeloid leukemia (CML) in the chronic phase, a clonal myeloproliferative disorder, is caused by the constitutively active BCR-ABL tyrosine kinase resulting from the translocation that produces the Philadelphia (Ph) chromosome. 1 , 2 Imatinib (Gleevec, Novartis Pharmaceuticals), an inhibitor of the BCR-ABL kinase, is the standard first-line therapy for patients with chronic-phase CML. 3 – 6 Dasatinib (Sprycel, Bristol-Myers Squibb), a second-generation BCR-ABL kinase inhibitor, has been approved as a second-line treatment for patients with CML if imatinib therapy fails. 4 – 7 Dasatinib therapy induces a complete cytogenetic response in approximately 50% of patients who do not have a response to imatinib or cannot . . .

The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands—or even millions—of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven challenges that will be central to bringing this emerging field of single-cell data science forward. For each challenge, we highlight motivating research questions, review prior work, and formulate open problems. This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years.