A prediction-based resampling method for estimating the number of clusters in a dataset

BACKGROUND: Microarray technology is increasingly being applied in biological and medical research to address a wide range of problems, such as the classification of tumors. An important statistical problem associated with tumor classification is the identification of new tumor classes using gene-expression profiles. Two essential aspects of this clustering problem are: to estimate the number of clusters, if any, in a dataset; and to allocate tumor samples to these clusters, and assess the confidence of cluster assignments for individual samples. Here we address the first of these problems. RESULTS: We have developed a new prediction-based resampling method, Clest, to estimate the number of clusters in a dataset. The performance of the new and existing methods were compared using simulated data and gene-expression data from four recently published cancer microarray studies. Clest was generally found to be more accurate and robust than the six existing methods considered in the study. CONCLUSIONS: Focusing on prediction accuracy in conjunction with resampling produces accurate and robust estimates of the number of clusters

Pathways to Decarbonization of Residential Heating

Space and water heating are the largest consumers of energy in residential buildings, up to 85% in cold climates. In addition to conservation measures, improving the building thermal envelope and optimizing the heat and hot water distribution, improving the performance of the heating technology is critical to provide a pathway to significantly reduce carbon emissions, with a focus on existing buildings. Conventional fuel-fired heating systems that use existing infrastructure have approached their thermodynamic limit over the past 15-20 years. While the performance of electrically-driven heat pumps, that would use electricity produced at the margin in a fuel-switching scenario, have improved, their performance in cold climates is highly dependent on regional and seasonal characteristics of the supplied electricity and the capacity of the heat pump and the grid itself to support this peak winter demand. The Gas Absorption Heat Pump (GAHP) is a thermally driven technology that can serve as the next step in fuel-fired heating with Coefficient of Performance (COP) value of 1.4 at design conditions with sufficient capacity to meet peak heating loads. The GAHP would serve as a drop-in replacement for furnaces, boilers and other conventional technologies, significantly reduce emissions, require no updates to existing infrastructure, and provide optionality as delivered decarbonized fuels become more widely available. This study looked at several locations in North America and compared potential emission and economic savings versus several baseline technologies, including furnaces, boilers, electric heat pumps, and various water heating options. The results show that the GAHP provided the lowest operating cost and highest emissions reduction (CO2e). Based on the results, the use and pursuit of GAHPs as a pathway to decarbonization is necessary to meet climate goals

Deletion of chromosome 11q predicts response to anthracycline-based chemotherapy in early breast cancer

Despite the recent consensus on the eligibility of adjuvant systemic therapy in patients with lymph node–negative breast cancer (NNBC) based on clinicopathologic criteria, specific biological markers are needed to predict sensitivity to the different available therapeutic options.W e examined the feasibility of developing a genomic predictor of chemotherapy response and recurrence risk in 185 patients with NNBC using assembled arrays containing 2,460 bacterial artificial chromosome clones for scanning the genome for DNA copy number changes.Aft er surgery, 90 patients received anthracyclinebased chemotherapy, whereas 95 did not.T amoxifen was administered to patients with hormone receptor–positive tumors. The association of genomic and clinicopathologic data and outcome was computed using Cox proportional hazard models and multiple testing adjustment procedures.Analysis of NNBC genomes revealed a common genomic signature.Specific DNA copy number aberrations were associated with hormonal receptor status, but not with other clinicopathologic variables. In patients treated with chemotherapy, none of the genomic changes were significantly correlated with recurrence.In patients not receiving chemotherapy, deletion of eight bacterial artificial chromosome clones clustered to chromosome 11q was independently associated with relapse (disease-free survival at 10 years F SE, 40% F 14% versus 86% F 6%; P < 0.0001). The 54 patients with deletion of 11q (29%) did not present more aggressive clinicopathologic features than those without 11q loss.The adverse influence of 11q deletion on clinical outcome was confirmed in an independent validation series of 88 patients with NNBC.Our data suggests that patients with NNBC with the 11q deletion might benefit from anthracycline-based chemotherapy despite other clinical, pathologic, or genetic features.However , these initial findings should be evaluated in randomized clinical trials

Intersection between metabolic dysfunction, high fat diet consumption, and brain aging

Deleterious neurochemical, structural, and behavioral alterations are a seemingly unavoidable aspect of brain aging. However, the basis for these alterations, as well as the basis for the tremendous variability in regards to the degree to which these aspects are altered in aging individuals, remains to be elucidated. An increasing number of individuals regularly consume a diet high in fat, with high‐fat diet consumption known to be sufficient to promote metabolic dysfunction, although the links between high‐fat diet consumption and aging are only now beginning to be elucidated. In this review we discuss the potential role for age‐related metabolic disturbances serving as an important basis for deleterious perturbations in the aging brain. These data not only have important implications for understanding the basis of brain aging, but also may be important to the development of therapeutic interventions which promote successful brain aging.Fil: Uranga, Romina Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Investigaciones Bioquímicas de Bahía Blanca. Universidad Nacional del Sur. Instituto de Investigaciones Bioquímicas de Bahía Blanca; ArgentinaFil: Bruce Keller, Annadora J.. State University of Louisiana; Estados UnidosFil: Morrison, Christopher D.. State University of Louisiana; Estados UnidosFil: Fernandez Kim, Sun Ok. State University of Louisiana; Estados UnidosFil: Ebenezer, Philip J.. State University of Louisiana; Estados UnidosFil: Zhang, Le. State University of Louisiana; Estados UnidosFil: Dasuri, Kalavathi. State University of Louisiana; Estados UnidosFil: Keller, Jeffrey N.. State University of Louisiana; Estados Unido

Systems analysis of the CO2 concentrating mechanism in cyanobacteria

Cyanobacteria are photosynthetic bacteria with a unique CO2 concentrating mechanism (CCM), enhancing carbon fixation. Understanding the CCM requires a systems level perspective of how molecular components work together to enhance CO2 fixation. We present a mathematical model of the cyanobacterial CCM, giving the parameter regime (expression levels, catalytic rates, permeability of carboxysome shell) for efficient carbon fixation. Efficiency requires saturating the RuBisCO reaction, staying below saturation for carbonic anhydrase, and avoiding wasteful oxygenation reactions. We find selectivity at the carboxysome shell is not necessary; there is an optimal non-specific carboxysome shell permeability. We compare the efficacy of facilitated CO2 uptake, CO2 scavenging, and HCO3− transport with varying external pH. At the optimal carboxysome permeability, contributions from CO2 scavenging at the cell membrane are small. We examine the cumulative benefits of CCM spatial organization strategies: enzyme co-localization and compartmentalization. DOI: http://dx.doi.org/10.7554/eLife.02043.00

MERTK in cancer therapy: Targeting the receptor tyrosine kinase in tumor cells and the immune system

The receptor tyrosine kinase MERTK is aberrantly expressed in numerous human malignancies, and is a novel target in cancer therapeutics. Physiologic roles of MERTK include regulation of tissue homeostasis and repair, innate immune control, and platelet aggregation. However, aberrant expression in a wide range of liquid and solid malignancies promotes neoplasia via growth factor independence, cell cycle progression, proliferation and tumor growth, resistance to apoptosis, and promotion of tumor metastases. Additionally, MERTK signaling contributes to an immunosuppressive tumor microenvironment via induction of an anti-inflammatory cytokine profile and regulation of the PD-1 axis, as well as regulation of macrophage, myeloid-derived suppressor cell, natural killer cell and T cell functions. Various MERTK-directed therapies are in preclinical development, and clinical trials are underway. In this review we discuss MERTK inhibition as an emerging strategy for cancer therapy, focusing on MERTK expression and function in neoplasia and its role in mediating resistance to cytotoxic and targeted therapies as well as in suppressing anti-tumor immunity. Additionally, we review preclinical and clinical pharmacological strategies to target MERTK

Corrigendum to “MERTK in cancer therapy: Targeting the receptor tyrosine kinase in tumor cells and the immune system” [Pharmacology & Therapeutics 213 (2020) 107577]

Correction to "MERTK in cancer therapy: Targeting the receptor tyrosine kinase in tumor cells and the immune system

Improving Melanoma Classification by Integrating Genetic and Morphologic Features

Boris Bastian and colleagues present a refined morphological classification of primary melanomas that can be used to improve existing melanoma classifications by defining genetically homogeneous subgroups

Genome position and gene amplification

Genomic analyses of human cells expressing dihydrofolate reductase provide insight into the effects of genome position on the propensity for a drug-resistance gene to amplify in human cells