Galaxy LIMS for next-generation sequencing.

Summary: We have developed a laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform. The system provides lab technicians standard and customizable sample information forms, barcoded submission forms, tracking of input sample quality, multiplex-capable automatic flow cell design and automatically generated sample sheets to aid physical flow cell preparation. In addition, the platform provides the researcher with a user-friendly interface to create a request, submit accompanying samples, upload sample quality measurements and access to the sequencing results.

Inequalities in perinatal and maternal health.

Purpose Of Review: To describe inequalities in perinatal and maternal mortality, and morbidity from an international high-income country perspective. Measures of inequalities are socioeconomic status, ethnic background, and living area.

Recent Findings: Despite decreasing overall perinatal and maternal mortality in high-income countries, perinatal and maternal health inequalities persist.

Results of a cosmetovigilance survey in The Netherlands.

Background: Cosmetic products contribute considerably to the incidence of contact dermatitis. In response to a resolution of the Council of Europe, the National Institute for Public Health and the Environment (RIVM) in The Netherlands set up a pilot project to report undesirable effects attributed to cosmetic products.

Objectives: To provide an overview of undesirable effects attributed to cosmetic products and to identify the ingredients involved.

Structural and functional brain connectivity in presymptomatic familial frontotemporal dementia.

Objective: We aimed to investigate whether cognitive deficits and structural and functional connectivity changes can be detected before symptom onset in a large cohort of carriers of microtubule-associated protein tau and progranulin mutations.

Methods: In this case-control study, 75 healthy individuals (aged 20-70 years) with 50% risk for frontotemporal dementia (FTD) underwent DNA screening, neuropsychological assessment, and structural and functional MRI. We used voxel-based morphometry and tract-based spatial statistics for voxelwise analyses of gray matter volume and diffusion tensor imaging measures.

Does neonatal morphine use affect neuropsychological outcomes at 8 to 9 years of age?

Morphine is widely used to treat severe pain in neonatal intensive care unit patients. Animal studies suggest adverse long-term side effects of neonatal morphine, but a follow-up study of 5-year-old children who participated in a morphine-placebo controlled trial as newborns found no such effects on the child's general functioning. This study indicated that morphine may negatively affect response inhibition, a domain of executive functions.

Plasma proprotein convertase subtilisin kexin type 9 levels are related to markers of cholesterol synthesis in familial combined hyperlipidemia.

Background And Aims: Two recent independent studies showed that patients with familial combined hyperlipidemia (FCHL) have elevated plasma levels of proprotein convertase subtilisin kexin type 9 (PCSK9) and markers of cholesterol synthesis. Both PCSK9 expression and cholesterol synthesis are downstream effects of hepatic activation of sterol regulatory element binding protein 2 (SREBP2). The present study was conducted to study the relationship between plasma PCSK9 and markers of cholesterol synthesis in FCHL.

HLA typing from RNA-Seq sequence reads.

We present a method, seq2HLA, for obtaining an individual's human leukocyte antigen (HLA) class I and II type and expression using standard next generation sequencing RNA-Seq data. RNA-Seq reads are mapped against a reference database of HLA alleles, and HLA type, confidence score and locus-specific expression level are determined. We successfully applied seq2HLA to 50 individuals included in the HapMap project, yielding 100% specificity and 94% sensitivity at a P-value of 0.

A gene-centric study of common carotid artery remodelling.

Background: Expansive remodelling is the process of compensatory arterial enlargement in response to atherosclerotic stimuli. The genetic determinants of this process are poorly characterized.

Methods: Genetic association analyses of inter-adventitial common carotid artery diameter (ICCAD) in the IMPROVE study (n = 3427) using the Illumina 200k Metabochip was performed.

Crystal-structure prediction via the floppy-box Monte Carlo algorithm: method and application to hard (non)convex particles.

In this paper, we describe the way to set up the floppy-box Monte Carlo (FBMC) method [L. Filion, M. Marechal, B.

Low-dimensional semiconductor superlattices formed by geometric control over nanocrystal attachment.

Oriented attachment, the process in which nanometer-sized crystals fuse by atomic bonding of specific crystal facets, is expected to be more difficult to control than nanocrystal self-assembly that is driven by entropic factors or weak van der Waals attractions. Here, we present a study of oriented attachment of PbSe nanocrystals that counteract this tuition. The reaction was studied in a thin film of the suspension casted on an immiscible liquid at a given temperature.

The effect of frequent whole blood donation on ferritin, hepcidin, and subclinical atherosclerosis.

Background: Iron catalyzes the formation of free radicals, which could lead to damaged vascular walls and subsequent atherosclerosis. Blood donation decreases iron stores and can thus decrease cardiovascular risk. Even within blood donors, differences in stored iron are observed.

Living in deprived urban districts increases perinatal health inequalities.

Objective: Analyses of the effects of place of residence, socioeconomic status and ethnicity on perinatal mortality and morbidity in the Netherlands.

Methods: Epidemiological analysis of all singleton deliveries > 22 gestational weeks (871,889 live born and 5927 stillborn) from the Dutch National Perinatal Registry 2002-2006. Multiple logistic regression analysis was used to determine whether place of residence (deprived neighborhood, or not) contributed to the adverse perinatal outcome (defined as perinatal mortality, preterm birth, small for gestational age, congenital abnormalities or Apgar score <7, 5 min after birth), additional to individual pregnancy characteristics, demographic characteristics, ethnic background and socioeconomic class.

Confidence-based somatic mutation evaluation and prioritization.

Next generation sequencing (NGS) has enabled high throughput discovery of somatic mutations. Detection depends on experimental design, lab platforms, parameters and analysis algorithms. However, NGS-based somatic mutation detection is prone to erroneous calls, with reported validation rates near 54% and congruence between algorithms less than 50%.

Phenotypes of hypertriglyceridemia caused by excess very-low-density lipoprotein.

Objective: To characterize the composition of very-low-density lipoprotein (VLDL) particles and the proportion of VLDL to total apolipoprotein B (apoB) particles in patients with hypertriglyceridemia caused by excess VLDL.

Methods: Subjects were selected from 2023 consecutive patients attending the Lipid Clinic at the Laval University Centre. Plasma lipids, apoB, and apoA-I were measured and chylomicron lipids and VLDL and LDL lipids and apoB determined after ultracentrifugation.

Electrostatic interactions between Janus particles.

In this paper we study the electrostatic properties of "Janus" spheres with unequal charge densities on both hemispheres. We introduce a method to compare primitive-model Monte Carlo simulations of the ionic double layer with predictions of (mean-field) nonlinear Poisson-Boltzmann theory. We also derive practical Derjaguin Landau Verwey Overbeek (DLVO)-like expressions that describe the Janus-particle pair interactions by mean-field theory.

Ordered two-dimensional superstructures of colloidal octapod-shaped nanocrystals on flat substrates.

We studied crystal structures in a monolayer consisting of anisotropic branched colloidal (nano)octapods. Experimentally, octapods were observed to form a monolayer on a substrate with a square-lattice crystal structure by drop-casting and fast evaporation of solvent. The experimental results were analyzed by Monte Carlo simulations using a hard octapod model consisting of four interpenetrating spherocylinders.

Common carotid intima-media thickness measurements in cardiovascular risk prediction: a meta-analysis.

Context: The evidence that measurement of the common carotid intima-media thickness (CIMT) improves the risk scores in prediction of the absolute risk of cardiovascular events is inconsistent.

Objective: To determine whether common CIMT has added value in 10-year risk prediction of first-time myocardial infarctions or strokes, above that of the Framingham Risk Score.

Data Sources: Relevant studies were identified through literature searches of databases (PubMed from 1950 to June 2012 and EMBASE from 1980 to June 2012) and expert opinion.

Low-density lipoprotein-lowering strategies: target versus maximalist versus population percentile.

Purpose Of Review: Maximalist low-density lipoprotein (LDL)-lowering strategies such as lowering LDL as much as possible or, alternatively, using the most potent LDL-lowering regimens have become increasingly popular. Almost all attention has focused on the potential advantages of these approaches with little focus on their potential disadvantages. Moreover, it is increasingly assumed that the lower and lower is better and better approach is supported by unassailable evidence.

Long-term results of maxillomandibular advancement surgery in patients with obstructive sleep apnoea syndrome.

This article describes the eight-year follow-up results of maxillomandibular advancement (MMA) in a cohort of patients with obstructive sleep apnea syndrome (OSAS). Results are promising by means of Apnoea Hypopnoea Index (AHI) and Epworth Sleepiness Scale (ESS).

Increase in serum brain-derived neurotrophic factor in met allele carriers of the BDNF Val66Met polymorphism is specific to males.

Background: Association studies of the Val66Met polymorphism and serum brain-derived neurotrophic factor (BDNF) levels have yielded conflicting results. Recently, sex-specific differences in BDNF levels were demonstrated. As these might explain the reported inconsistencies, we tested sex interactions with the Val66Met genotype on serum BDNF level.

A newly developed scavenging system for administration of nitrous oxide during labour: safe occupational use.

Objective: Nitrous oxide (N(2) O) is routinely used as an analgesic in obstetrics during labour. Epidemiological studies have linked chronic occupational exposure to N(2) O to specific health problems, including reproductive risks. Occupational exposure limits (OELs) allow the use of N(2) O once appropriate preventive and safety measures have been taken.

Investigating phosphorus limitation in a fixed bed filter with phosphorus and nitrogen profile measurements.

In 2000, the European Union adopted the European Water Framework Directive (WFD) (European Commission, 2000). The WFD focuses on increasingly stringent nutrient standards including ultra low nitrogen (< 2.2 mg N-total/L) and phosphorus concentrations (< 0.

Minimising the risk on phosphorus limitation; an optimised coagulant dosage system.

In the near future the WWTP Horstermeer will be confronted with more stringent requirements. Important factor in this respect is the European Water Framework Directive 2000/60/EC. Within the WFD approach the focus is more and more on low nitrogen (<2.

The genetics of familial combined hyperlipidaemia.

Almost 40 years after the first description of familial combined hyperlipidaemia (FCHL) as a discrete entity, the genetic and metabolic basis of this prevalent disease has yet to be fully unveiled. In general, two strategies have been applied to elucidate its complex genetic background, the candidate-gene and the linkage approach, which have yielded an extensive list of genes associated with FCHL or its related traits, with a variable degree of scientific evidence. Some genes influence the FCHL phenotype in many pedigrees, whereas others are responsible for the affected state in only one kindred, thereby adding to the genetic and phenotypic heterogeneity of FCHL.