K-Mer-Based Genome Size Estimation in Theory and Practice.

Recent advances in sequencing technologies have made genome sequencing of non-model organisms with very large and complex genomes possible. The data can be used to estimate diverse genome characteristics, including genome size, repeat content, and levels of heterozygosity. K-mer analysis is a powerful biocomputational approach with a wide range of applications, including estimation of genome sizes.

Establishing MinION Sequencing and Genome Assembly Procedures for the Analysis of the Rooibos () Genome.

While plant genome analysis is gaining speed worldwide, few plant genomes have been sequenced and analyzed on the African continent. Yet, this information holds the potential to transform diverse industries as it unlocks medicinally and industrially relevant biosynthesis pathways for bioprospecting. Considering that South Africa is home to the highly diverse Cape Floristic Region, local establishment of methods for plant genome analysis is essential.

Intraoperative conversion and complications in robotic assisted primary and redo gastric bypass surgery.

The rise of robotic assisted surgery in the treatment of morbidly obese patients has enlarged the armamentarium for surgeons involved in bariatric surgery. This in particular is of great advantage not only in primary cases, but also in patients undergoing revisional procedures following preceding upper GI surgery. In the following, our experience with intraoperative conversions and complications in revisional robotic surgery using the Da Vinci robotic system will be reported and compared to primary robotic bypass surgery and the literature.

Minimally Invasive Conversion of a Gastric Bypass into Sleeve Gastrectomy for Postprandial Hyperinsulinemic Hypoglycemia.

The treatment of postprandial hyperinsulinemic hypoglycemia following gastric bypass surgery for obesity can be challenging despite dietetic and medical treatment and eventually surgical treatment remains the exclusive treatment to resolve the problem for the patient. In the following, the experience with a conversion surgery from a complicated Roux-en-Y gastric bypass to sleeve gastrectomy using the Da Vinci robotic system will be reported.

Transcriptomics of the Rooibos () Species Complex.

Rooibos (), widely known as a herbal tea, is endemic to the Cape Floristic Region of South Africa (SA). It produces a wide range of phenolic compounds that have been associated with diverse health promoting properties of the plant. The species comprises several growth forms that differ in their morphology and biochemical composition, only one of which is cultivated and used commercially.

Rooibos () Genome Size Estimation Using Flow Cytometry and K-Mer Analyses.

Plant genomes provide information on biosynthetic pathways involved in the production of industrially relevant compounds. Genome size estimates are essential for the initiation of genome projects. The genome size of rooibos ( species complex) was estimated using DAPI flow cytometry and k-mer analyses.

Visualization of Aspalathin in Rooibos () Plant and Herbal Tea Extracts Using Thin-Layer Chromatography.

Aspalathin, the main polyphenol of rooibos (), is associated with diverse health promoting properties of the tea. During fermentation, aspalathin is oxidized and concentrations are significantly reduced. Standardized methods for quality control of rooibos products do not investigate aspalathin, since current techniques of aspalathin detection require expensive equipment and expertise.

[Minimally invasive robot-assisted gastric bypass after open Mason reduction gastroplasty].

Background: The introduction of robot-assisted surgery in the treatment of morbidly obese patients has enlarged the armamentarium for surgeons involved in bariatric surgery. This article describes the experiences with a conversion surgery from a complicated open Mason gastroplasty to a Roux en Y gastric bypass using the da Vinci Xi robotic system.

Case: A 29-year-old female patient underwent a Mason reduction gastroplasty by laparotomy in 1995 (body mass index BMI 53.

Gastric carcinoma after sleeve gastrectomy for obesity.

Obesity is associated with an increased risk of cancer development in the upper gastrointestinal tract. We present the case of a female patient with gastric carcinoma after sleeve gastrectomy. Before bariatric surgery, one rationale for performing routine endoscopy is to detect clinically relevant conditions with the potential to change the surgical procedure.

Virome Assembly and Annotation: A Surprise in the Namib Desert.

Sequencing, assembly, and annotation of environmental virome samples is challenging. Methodological biases and differences in species abundance result in fragmentary read coverage; sequence reconstruction is further complicated by the mosaic nature of viral genomes. In this paper, we focus on biocomputational aspects of virome analysis, emphasizing latent pitfalls in sequence annotation.

Body surface area determined by whole-body CT scanning: need for new formulae?

Calculation of the estimated body surface area (BSA) by body height and weight has been a challenge in the past centuries due to lack of a well-documented gold standard. More recently, available techniques such as 3D laser surface scanning and CT scanning may be expected to quantify the BSA in an easier and more accurate way. This study provides the first comparison between BSA obtained from post-mortem whole-body CT scans and BSA calculated by nine predictive formulae.

Prevalence of antibiotic use: a comparison across various European health care data sources.

Purpose: There is widespread concern about increases in antibiotic use, but comparative data from different European countries on rates of use are lacking. This study was designed to measure and understand the variation in antibiotic utilization across five European countries.

Methods: Seven European healthcare databases with access to primary care data from Denmark, Germany, the Netherlands, Spain and the UK were used to measure and compare the point and 1-year-period prevalence of antibiotic use between 2004 and 2009.

Exposure to benzodiazepines (anxiolytics, hypnotics and related drugs) in seven European electronic healthcare databases: a cross-national descriptive study from the PROTECT-EU Project.

Purpose: Studies on drug utilization usually do not allow direct cross-national comparisons because of differences in the respective applied methods. This study aimed to compare time trends in BZDs prescribing by applying a common protocol and analyses plan in seven European electronic healthcare databases.

Methods: Crude and standardized prevalence rates of drug prescribing from 2001-2009 were calculated in databases from Spain, United Kingdon (UK), The Netherlands, Germany and Denmark.

Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms.

Background: De novo transcriptome assembly of short transcribed fragments (transfrags) produced from sequencing-by-synthesis technologies often results in redundant datasets with differing levels of unassembled, partially assembled or mis-assembled transcripts. Post-assembly processing intended to reduce redundancy typically involves reassembly or clustering of assembled sequences. However, these approaches are mostly based on common word heuristics and often create clusters of biologically unrelated sequences, resulting in loss of unique transfrags annotations and propagation of mis-assemblies.

Time trends of period prevalence rates of patients with inhaled long-acting beta-2-agonists-containing prescriptions: a European comparative database study.

Background: Inhaled, long-acting beta-2-adrenoceptor agonists (LABA) have well-established roles in asthma and/or COPD treatment. Drug utilisation patterns for LABA have been described, but few studies have directly compared LABA use in different countries. We aimed to compare the prevalence of LABA-containing prescriptions in five European countries using a standardised methodology.

Different initiatives across Europe to enhance losartan utilization post generics: impact and implications.

Introduction: There is an urgent need for health authorities across Europe to fully realize potential savings from increased use of generics to sustain their healthcare systems. A variety of strategies were used across Europe following the availability of generic losartan, the first angiotensin receptor blocker (ARB) to be approved and marketed, to enhance its prescribing vs. single-sourced drugs in the class.

Tracing the maternal roots of the domestic Red Mountain Cattle.

The Red Mountain Cattle (RHV) is an important native ancient breed from the lower mountain ranges of Central Europe, which was originally raised for milk and meat production and as draught animal. In the 1980s, the RHV was close to extinction and only the sperm of a single purebreed bull and a few cows were available for breed formation. In this study the mitogenomes were sequenced of RHV from six maternal founder lineages.

Patient characteristics among users of analgesic over-the-counter aspirin in a Danish pharmacy setting.

Background: Use of over-the-counter (OTC) high-dose acetylsalicylic acid (ASA) is a risk factor for experiencing gastric bleeding. However, more detailed knowledge on the characteristics of users of OTC ASA is needed.

Objective: To characterise users of OTC high-dose ASA in a Danish pharmacy setting.

Antidepressant prescribing in five European countries: application of common definitions to assess the prevalence, clinical observations, and methodological implications.

Purpose: Drug utilization studies have applied different methods to various data types to describe medication use, which hampers comparisons across populations. The aim of this study was to describe the time trends in antidepressant prescribing in the last decade and the variation in the prevalence, calculated in a uniform manner, in seven European electronic healthcare databases.

Methods: Annual prevalence per 10,000 person-years (PYs) was calculated for 2001-2009 in databases from Spain, Germany, Denmark, the United Kingdom (UK), and the Netherlands.

Incidence rates and trends of hip/femur fractures in five European countries: comparison using e-healthcare records databases.

Hip fractures represent a major public health challenge worldwide. Multinational studies using a common methodology are scarce. We aimed to estimate the incidence rates (IRs) and trends of hip/femur fractures over the period 2003-2009 in five European countries.

Antiepileptic drug use in seven electronic health record databases in Europe: a methodologic comparison.

Objective: The annual prevalence of antiepileptic drug (AED) prescribing reported in the literature differs considerably among European countries due to use of different type of data sources, time periods, population distribution, and methodologic differences. This study aimed to measure prevalence of AED prescribing across seven European routine health care databases in Spain, Denmark, The Netherlands, the United Kingdom, and Germany using a standardized methodology and to investigate sources of variation.

Methods: Analyses on the annual prevalence of AEDs were stratified by sex, age, and AED.

A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads.

Downstream analyses of short-reads from next-generation sequencing platforms are often preceded by a pre-processing step that removes uncalled and wrongly called bases. Standard approaches rely on their associated base quality scores to retain the read or a portion of it when the score is above a predefined threshold. It is difficult to differentiate sequencing error from biological variation without a reference using quality scores.

Bridging differences in outcomes of pharmacoepidemiological studies: design and first results of the PROTECT project.

Background: Observational pharmacoepidemiological (PE) studies on drug safety have produced discrepant results that may be due to differences in design, conduct and analysis.

Purpose: The pharmacoepidemiology work-package (WP2) of the Pharmacoepidemiological Research on Outcomes of Therapeutics by a European ConsorTium (PROTECT) project aims at developing, testing and disseminating methodological standards for design, conduct and analysis of pharmacoepidemiological studies applicable to different safety issues using different databases across European countries. This article describes the selection of the safety issues and the description of the databases to be systematically studied.