A simple procedure for directly obtaining haplotype sequences of diploid genomes.

Background: Almost all genome sequencing projects neglect the fact that diploid organisms contain two genome copies and consequently what is published is a composite of the two. This means that the relationship between alternate alleles at two or more linked loci is lost. We have developed a simplified method of directly obtaining the haploid sequences of each genome copy from an individual organism.

Bilateral hand transplantation: Functional benefits assessment in five patients with a mean follow-up of 7.6 years (range 4-13 years).

Between January 2000 and July 2009, five adults who had suffered bilateral traumatic below-elbow amputations, received bilateral hand-forearm allografts performed by the Lyon team. We report the functional benefits achieved over a mean follow-up period of 7.6 years (range 4-13 years), up to December 31st, 2013.

Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis.

The circadian clock in Arabidopsis exerts a critical role in timing multiple biological processes and stress responses through the regulation of up to 80% of the transcriptome. As a key component of the clock, the Myb-like transcription factor CIRCADIAN CLOCK ASSOCIATED1 (CCA1) is able to initiate and set the phase of clock-controlled rhythms and has been shown to regulate gene expression by binding directly to the evening element (EE) motif found in target gene promoters. However, the precise molecular mechanisms underlying clock regulation of the rhythmic transcriptome, specifically how clock components connect to clock output pathways, is poorly understood.

On the Design and Implementation of a Highly Accurate Pulse Predictor for Exercise Equipment.

Goal: This study aims to develop highly accurate heart rate monitoring from the hand-held contact signal within a noisy environment during exercise.

Methods: The periodic pattern and uncertainties of a physiological signal are modeled by a Laplacian random process. Based on this statistical model, a highly accurate pulse predictor (HAPPEE) is derived and implemented in real-time on a Cypress PSoC 5LP development board.

Identification of Open Stomata1-Interacting Proteins Reveals Interactions with Sucrose Non-fermenting1-Related Protein Kinases2 and with Type 2A Protein Phosphatases That Function in Abscisic Acid Responses.

The plant hormone abscisic acid (ABA) controls growth and development and regulates plant water status through an established signaling pathway. In the presence of ABA, pyrabactin resistance/regulatory component of ABA receptor proteins inhibit type 2C protein phosphatases (PP2Cs). This, in turn, enables the activation of Sucrose Nonfermenting1-Related Protein Kinases2 (SnRK2).

Development of Small-Molecule Cryptochrome Stabilizer Derivatives as Modulators of the Circadian Clock.

Small-molecule probes have been playing prominent roles in furthering our understanding of the molecular underpinnings of the circadian clock. We previously discovered a carbazole derivative, KL001 (N-(3-(9H-carbazol-9-yl)-2-hydroxypropyl)-N-(furan-2-ylmethyl)methanesulfonamide), as a stabilizer of the clock protein cryptochrome (CRY). Herein we describe an extensive structure-activity relationship analysis of KL001 derivatives leading to the development of a highly active derivative: 2-(9H-carbazol-9-yl)-N-(2-chloro-6-cyanophenyl)acetamide (KL044).

Spatial and temporal regulation of biosynthesis of the plant immune signal salicylic acid.

The plant hormone salicylic acid (SA) is essential for local defense and systemic acquired resistance (SAR). When plants, such as Arabidopsis, are challenged by different pathogens, an increase in SA biosynthesis generally occurs through transcriptional induction of the key synthetic enzyme isochorismate synthase 1 (ICS1). However, the regulatory mechanism for this induction is poorly understood.

Modelling the increased frequency of extreme sea levels in the Ganges-Brahmaputra-Meghna delta due to sea level rise and other effects of climate change.

Coastal flooding due to storm surge and high tides is a serious risk for inhabitants of the Ganges-Brahmaputra-Meghna (GBM) delta, as much of the land is close to sea level. Climate change could lead to large areas of land being subject to increased flooding, salinization and ultimate abandonment in West Bengal, India, and Bangladesh. IPCC 5th assessment modelling of sea level rise and estimates of subsidence rates from the EU IMPACT2C project suggest that sea level in the GBM delta region may rise by 0.

Measurement of lymphocyte aggregation by flow cytometry-physiological implications in chronic lymphocytic leukemia.

Background: Cellular aggregation is a physiological response of lymphocytes to various extracellular stimuli. Currently, lymphocytes aggregation is only evaluated qualitatively or by semiquantitative methods. In this study, we assessed the capacity of flow cytometry to measure lymphocytes aggregation in a quantitative, accurate, and reproducible manner, and examined the significance of aggregation responses in various lymphoproliferative diseases.

C-H activation generates period-shortening molecules that target cryptochrome in the mammalian circadian clock.

The synthesis and functional analysis of KL001 derivatives, which are modulators of the mammalian circadian clock, are described. By using cutting-edge C-H activation chemistry, a focused library of KL001 derivatives was rapidly constructed, which enabled the identification of the critical sites on KL001 derivatives that induce a rhythm-changing activity along with the components that trigger opposite modes of action. The first period-shortening molecules that target the cryptochrome (CRY) were thus discovered.

Ovarian Hormones Regulate SP-D Expression in the Mouse Uterus During Estrous Cycle and Early Pregnancy.

Problem: Differential expression of SP-D in the cycling human and mouse endometrium suggests its regulation by ovarian hormones.

Method Of Study: SP-D expression in the mouse uterus was analyzed across the estrous cycle and during early pregnancy. Effect of exogenous ovarian hormones on the uterine expression of SP-D was analyzed.

Identification of small-molecule modulators of the circadian clock.

Chemical biology or chemical genetics has emerged as an interdisciplinary research area applying chemistry to understand biological systems. The development of combinatorial chemistry and high-throughput screening technologies has enabled large-scale investigation of the biological activities of diverse small molecules to discover useful chemical probes. This approach is applicable to the analysis of the circadian clock mechanisms through cell-based assays to monitor circadian rhythms using luciferase reporter genes.

The Hd, Hj, and Hz66 flagella variants of Salmonella enterica serovar Typhi modify host responses and cellular interactions.

Salmonella Typhi, the causative agent of typhoid fever, is a monophyletic, human-restricted bacterium that exhibits limited phenotypic variation. S. Typhi from Indonesia are a notable exception, with circulating strains expressing diverse flagella antigens including Hj, Hd and Hz66.

A parametric classification rule based on the exponentially embedded family.

In this paper, we extend the exponentially embedded family (EEF), a new approach to model order estimation and probability density function construction originally proposed by Kay in 2005, to multivariate pattern recognition. Specifically, a parametric classifier rule based on the EEF is developed, in which we construct a distribution for each class based on a reference distribution. The proposed method can address different types of classification problems in either a data-driven manner or a model-driven manner.

Equivalency between emulated disc electrodes and conventional disc electrode human electroencephalography.

We have previously shown that tripolar concentric ring electrode (TCRE) Laplacian electroencephalography (tEEG) has significantly better signal-to-noise ratio, spatial resolution, and mutual information than disc electrode electroencephalography (EEG). This paper compares the EEG signals acquired simultaneously from the outer ring of the TCRE (oTCRE), shorting all three elements of the TCRE (sTCRE) and disc electrode (disc) concurrently from nearly the same location on the human scalp. We calculated the average correlation for the time series between each pair of signals and average coherence over the pass-band frequencies between all pairs of signals as well.

Two decades of experience with thoracoscopic lobectomy in infants and children: standardizing techniques for advanced thoracoscopic surgery.

Objectives: This study evaluates the safety and efficacy of thoracoscopic lobectomy in infants and children.

Materials And Methods: From January 1994 to November 2013, 347 patients underwent video-assisted thoracoscopic lobe resection at two institutions. All procedures were performed by or under the direct guidance of a single surgeon.

Predicting future thermal habitat suitability of competing native and invasive fish species: from metabolic scope to oceanographic modelling.

Global increase in sea temperatures has been suggested to facilitate the incoming and spread of tropical invaders. The increasing success of these species may be related to their higher physiological performance compared with indigenous ones. Here, we determined the effect of temperature on the aerobic metabolic scope (MS) of two herbivorous fish species that occupy a similar ecological niche in the Mediterranean Sea: the native salema (Sarpa salpa) and the invasive marbled spinefoot (Siganus rivulatus).

An Arabidopsis gene regulatory network for secondary cell wall synthesis.

The plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and vital to cell function.

Relationship between indices of obesity obtained by anthropometry and dual-energy X-ray absorptiometry: The Fourth and Fifth Korea National Health and Nutrition Examination Survey (KNHANES IV and V, 2008-2011).

Background: Body mass index (BMI), waist circumference (WC), and even dual-energy X-ray absorptiometry (DXA) are used for obesity diagnosis. However, it is not known which DXA-derived index of obesity correlates best with BMI and/or WC and it is not clear whether such an index is accurate or not.

Objectives: The aim of this study is to show the relationship between anthropometric measurements (BMI, WC) and body fat indices from DXA and to determine which DXA indices are strongly related to BMI and WC.

Traditional cardiovascular risk factors and coronary artery calcification in adults with polymyositis and dermatomyositis: a Danish multicenter study.

Objective: To determine the occurrence of traditional cardiovascular (CV) risk factors and coronary artery calcification (CAC) in adults with polymyositis (PM) or dermatomyositis (DM) compared to healthy controls and to assess the association between CV risk factors, PM/DM, and CAC score.

Methods: Traditional CV risk factors were assessed in a cross-sectional, observational study of 76 patients with PM/DM and in 48 sex- and age-matched healthy controls. CAC was quantified by means of cardiac computed tomography scan and expressed in Agatston units.

Content discovery and retrieval services at the European Nucleotide Archive.

The European Nucleotide Archive (ENA; http://www.ebi.ac.

Control of plant stem cell function by conserved interacting transcriptional regulators.

Plant stem cells in the shoot apical meristem (SAM) and root apical meristem are necessary for postembryonic development of aboveground tissues and roots, respectively, while secondary vascular stem cells sustain vascular development. WUSCHEL (WUS), a homeodomain transcription factor expressed in the rib meristem of the Arabidopsis SAM, is a key regulatory factor controlling SAM stem cell populations, and is thought to establish the shoot stem cell niche through a feedback circuit involving the CLAVATA3 (CLV3) peptide signalling pathway. WUSCHEL-RELATED HOMEOBOX 5 (WOX5), which is specifically expressed in the root quiescent centre, defines quiescent centre identity and functions interchangeably with WUS in the control of shoot and root stem cell niches.

Tissue-specific clocks in Arabidopsis show asymmetric coupling.

Many organisms rely on a circadian clock system to adapt to daily and seasonal environmental changes. The mammalian circadian clock consists of a central clock in the suprachiasmatic nucleus that has tightly coupled neurons and synchronizes other clocks in peripheral tissues. Plants also have a circadian clock, but plant circadian clock function has long been assumed to be uncoupled.