Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth.

While a genetic component of preterm birth (PTB) has long been recognized and recently mapped by genome-wide association studies (GWASs), the molecular determinants underlying PTB remain elusive. This stems in part from an incomplete availability of functional genomic annotations in human cell types relevant to pregnancy and PTB. We generated transcriptome (RNA-seq), epigenome (ChIP-seq of H3K27ac, H3K4me1, and H3K4me3 histone modifications), open chromatin (ATAC-seq), and chromatin interaction (promoter capture Hi-C) annotations of cultured primary decidua-derived mesenchymal stromal/stem cells and in vitro differentiated decidual stromal cells and developed a computational framework to integrate these functional annotations with results from a GWAS of gestational duration in 56,384 women.

Pilot early phase II study of decitabine and carboplatin in patients with advanced melanoma.

Introduction: Resistance to targeted and immune checkpoint blockade treatment remains a major problem in patients with advanced metastatic melanoma. To overcome this problem, there needs to be a decrease in burden of disease as well as re-establishing of immune sensitivity. The aim of this early phase 2 clinical trial is to investigate a novel way of sequencing and combining decitabine and carboplatin to decrease methylation and increase DNA repair resulting in a decrease in the disease burden and to re-establish sensitivity to the immune response.

Publisher Correction: Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics.

Mendelian randomization (MR) is a valuable tool for detecting causal effects by using genetic variant associations. Opportunities to apply MR are growing rapidly with the increasing number of genome-wide association studies (GWAS). However, existing MR methods rely on strong assumptions that are often violated, leading to false positives.

Detailed modeling of positive selection improves detection of cancer driver genes.

Identifying driver genes from somatic mutations is a central problem in cancer biology. Existing methods, however, either lack explicit statistical models, or use models based on simplistic assumptions. Here, we present driverMAPS (Model-based Analysis of Positive Selection), a model-based approach to driver gene identification.

A Statistical Framework for Mapping Risk Genes from De Novo Mutations in Whole-Genome-Sequencing Studies.

Analysis of de novo mutations (DNMs) from sequencing data of nuclear families has identified risk genes for many complex diseases, including multiple neurodevelopmental and psychiatric disorders. Most of these efforts have focused on mutations in protein-coding sequences. Evidence from genome-wide association studies (GWASs) strongly suggests that variants important to human diseases often lie in non-coding regions.

Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue.

We investigate 71 single nucleotide polymorphisms (SNPs) identified in meta-analytic studies of genome-wide association studies (GWAS) of breast cancer, the majority of which are located in intergenic or intronic regions. To explore regulatory impacts of these variants we conducted expression quantitative loci (eQTL) analyses on tissue samples from 376 invasive postmenopausal breast cancer cases in the Nurses' Health Study (NHS) diagnosed from 1990-2004. Expression analysis was conducted on all formalin-fixed paraffin-embedded (FFPE) tissue samples (and on 264 adjacent normal samples) using the Affymetrix Human Transcriptome Array.

A Phase I Dose Escalation Study of the Triple Angiokinase Inhibitor Nintedanib Combined with Low-Dose Cytarabine in Elderly Patients with Acute Myeloid Leukemia.

Unlabelled: Nintedanib (BIBF 1120), a potent multikinase inhibitor of VEGFR-1/-2/-3, FGFR-1/-2/-3 and PDGFR-α/-β, exerts growth inhibitory and pro-apoptotic effects in myeloid leukemic cells, especially when used in combination with cytarabine. This phase I study evaluated nintedanib in combination with low-dose cytarabine (LDAC) in elderly patients with untreated or relapsed/refractory acute myeloid leukemia (AML) ineligible for intensive chemotherapy in a 3+3 design. Nintedanib (dose levels 100, 150, and 200 mg orally twice daily) and LDAC (20 mg subcutaneous injection twice daily for 10 days) were administered in 28-day cycles.

Statistical thermodynamics of non-stoichiometric ceria and ceria zirconia solid solutions.

The thermodynamic redox properties of ceria and ceria zirconia solid solutions are analysed with a new methodology for modelling such systems based on the statistical mechanics of lattice configurations. Experimental thermogravimetric equilibrium data obtained for small non-stoichiometry measurements are combined with literature data to cover a large range of non-stoichiometry (CeO2-δ, δ = 0.001-0.

Continuation versus discontinuation of oxytocin infusion during the active phase of labour: a randomised controlled trial.

Objective: To investigate whether discontinuation of oxytocin infusion increases the duration of the active phase of labour and reduces maternal and neonatal complications.

Design: Randomised controlled trial.

Setting: Department of Obstetrics and Gynaecology, Regional Hospital of Randers, Denmark.

Image-guided Coring for Large-scale Studies in Molecular Pathology.

Sampling of formalin-fixed paraffin-embedded (FFPE) tissue blocks is a critical initial step in molecular pathology. Image-guided coring (IGC) is a new method for using digital pathology images to guide tissue block coring for molecular analyses. The goal of our study is to evaluate the use of IGC for both tissue-based and nucleic acid-based projects in molecular pathology.

Extensive rewiring of epithelial-stromal co-expression networks in breast cancer.

Background: Epithelial-stromal crosstalk plays a critical role in invasive breast cancer pathogenesis; however, little is known on a systems level about how epithelial-stromal interactions evolve during carcinogenesis.

Results: We develop a framework for building genome-wide epithelial-stromal co-expression networks composed of pairwise co-expression relationships between mRNA levels of genes expressed in the epithelium and stroma across a population of patients. We apply this method to laser capture micro-dissection expression profiling datasets in the setting of breast carcinogenesis.

Surface controlled reduction kinetics of nominally undoped polycrystalline CeO2.

Ceria is an interesting material for high temperature redox applications like solar-thermal splitting of CO2 and H2O. Technical implementation and reactor design for solar-thermal redox-based fuel generation requires reliable data for the chemical surface exchange coefficient and the chemical diffusivity of oxygen. The results of thermogravimetric relaxation experiments and equilibrium oxygen isotope exchange experiments with subsequent depth profiling analysis suggest that the reduction reaction of even dense samples of pure ceria (1 mm thickness, 93% of theoretical density) with a grain size of about 20 μm is surface reaction controlled.

Crowdsourcing image annotation for nucleus detection and segmentation in computational pathology: evaluating experts, automated methods, and the crowd.

The development of tools in computational pathology to assist physicians and biomedical scientists in the diagnosis of disease requires access to high-quality annotated images for algorithm learning and evaluation. Generating high-quality expert-derived annotations is time-consuming and expensive. We explore the use of crowdsourcing for rapidly obtaining annotations for two core tasks in com- putational pathology: nucleus detection and nucleus segmentation.

Computational pathology to discriminate benign from malignant intraductal proliferations of the breast.

The categorization of intraductal proliferative lesions of the breast based on routine light microscopic examination of histopathologic sections is in many cases challenging, even for experienced pathologists. The development of computational tools to aid pathologists in the characterization of these lesions would have great diagnostic and clinical value. As a first step to address this issue, we evaluated the ability of computational image analysis to accurately classify DCIS and UDH and to stratify nuclear grade within DCIS.

Genome-wide association study identifies multiple loci associated with both mammographic density and breast cancer risk.

Mammographic density reflects the amount of stromal and epithelial tissues in relation to adipose tissue in the breast and is a strong risk factor for breast cancer. Here we report the results from meta-analysis of genome-wide association studies (GWAS) of three mammographic density phenotypes: dense area, non-dense area and percent density in up to 7,916 women in stage 1 and an additional 10,379 women in stage 2. We identify genome-wide significant (P<5 × 10(-8)) loci for dense area (AREG, ESR1, ZNF365, LSP1/TNNT3, IGF1, TMEM184B and SGSM3/MKL1), non-dense area (8p11.

Cancer-associated PTEN mutants act in a dominant-negative manner to suppress PTEN protein function.

PTEN dysfunction plays a crucial role in the pathogenesis of hereditary and sporadic cancers. Here, we show that PTEN homodimerizes and, in this active conformation, exerts lipid phosphatase activity on PtdIns(3,4,5)P3. We demonstrate that catalytically inactive cancer-associated PTEN mutants heterodimerize with wild-type PTEN and constrain its phosphatase activity in a dominant-negative manner.

The adherens junction protein afadin is an AKT substrate that regulates breast cancer cell migration.

Unlabelled: The PI3K-AKT signaling pathway regulates all phenotypes that contribute to progression of human cancers, including breast cancer. AKT mediates signal relay by phosphorylating numerous substrates, which are causally implicated in biologic responses such as cell growth, survival, metabolic reprogramming, migration, and invasion. Here a new AKT substrate is identified, the adherens junction protein Afadin, which is phosphorylated by AKT at Ser1718.

Estrogen receptor negative/progesterone receptor positive breast cancer is not a reproducible subtype.

Introduction: Estrogen receptor (ER) and progesterone receptor (PR) testing are performed in the evaluation of breast cancer. While the clinical utility of ER as a predictive biomarker to identify patients likely to benefit from hormonal therapy is well-established, the added value of PR is less well-defined. The primary goals of our study were to assess the distribution, inter-assay reproducibility, and prognostic significance of breast cancer subtypes defined by patterns of ER and PR expression.

Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers.

Analysis of 4,405 variants in 89,050 European subjects from 41 case-control studies identified three independent association signals for estrogen-receptor-positive tumors at 11q13. The strongest signal maps to a transcriptional enhancer element in which the G allele of the best candidate causative variant rs554219 increases risk of breast cancer, reduces both binding of ELK4 transcription factor and luciferase activity in reporter assays, and may be associated with low cyclin D1 protein levels in tumors. Another candidate variant, rs78540526, lies in the same enhancer element.

Significance analysis of prognostic signatures.

A major goal in translational cancer research is to identify biological signatures driving cancer progression and metastasis. A common technique applied in genomics research is to cluster patients using gene expression data from a candidate prognostic gene set, and if the resulting clusters show statistically significant outcome stratification, to associate the gene set with prognosis, suggesting its biological and clinical importance. Recent work has questioned the validity of this approach by showing in several breast cancer data sets that "random" gene sets tend to cluster patients into prognostically variable subgroups.

Sex differences in social interaction behavior following social defeat stress in the monogamous California mouse (Peromyscus californicus).

Stressful life experiences are known to be a precipitating factor for many mental disorders. The social defeat model induces behavioral responses in rodents (e.g.

Acupuncture in migraine: investigation of autonomic effects.

Objective: A dysregulation of the autonomic nervous system is discussed as a pathogenetic factor in migraine. As acupuncture has been shown to exhibit considerable autonomic effects, we tested whether the clinical effects of acupuncture in migraine prophylaxis are mediated by changes of the autonomic regulation.

Methods: We simultaneously monitored changes of heart-rate variability (HRV) as an index of cardiac autonomic control and clinical improvement during an acupuncture treatment in 30 migraineurs.

The effect of Gua Sha treatment on the microcirculation of surface tissue: a pilot study in healthy subjects.

Context: Gua Sha, therapeutic surface frictioning that intentionally raises transitory petechiae and ecchymosis, is a traditional East Asian healing technique also known as cao gio, coining, scraping, and spooning. There are case reports in Western literature but no studies on the physiological effects of Gua Sha.

Objective: To study the microcirculatory effects of Gua Sha on the skin and subcutis in humans to elucidate physiological mechanisms responsible for the clinically observed pain-relieving effect of this treatment

Design: Laser Doppler imaging (LDI) was used to make sequential measurements of the microcirculation of surface tissue before and after Gua Sha treatment in 11 healthy subjects.