Benchmarking

OBJECTIVES: To evaluate the pharmacokinetic and pharmacodynamic effects of two novel levonorgestrel (LNG)-only contraceptive patches. STUDY DESIGN: This multi-center Phase I/II trial randomized participants to use a 7-day transdermal patch designed to deliver a 40 mcg or 75 mcg daily LNG dose for 11 consecutive weeks; randomization was stratified by body mass index (BMI) <32 or 32-40kg/m2 . Evaluations occurred twice weekly for 5weeks, then once weekly with supplemental visits for participants reporting a urinary LH surge...

PURPOSE: To automatically generate radiation therapy plans for oropharynx patients by com-bining knowledge-based planning (KBP) predictions with an inverse optimization (IO) pipeline. METHODS: We developed two KBP approaches, the bagging query (BQ) method and the generalized principal component analysis-based (gPCA) method, to predict achievable dose volume histograms (DVHs). These approaches generalize existing methods by predicting physically feasible organ-at-risk (OAR) and target DVHs in sites with multiple targets...

INTRODUCTION: The Health of the Nation Outcome Scales (HoNOS) for adults, and equivalent measures for children and adolescents and older people, are widely used in clinical practice and research contexts to measure mental health and functional outcomes. Additional HoNOS measures have been developed for special populations and applications. Stakeholders require synthesised information about the measurement properties of these measures to assess whether they are fit for use with intended service settings and populations and to establish performance benchmarks...

The ability to tag proteins has boosted the emergence of generic molecular methods for protein functional analysis. Fluorescent protein tags are used to visualize protein localization and affinity tags enable the mapping of molecular interactions by, for example, tandem affinity purification (TAP) or chromatin immunoprecipitation (ChIP). To apply these widely used molecular techniques on a single transgenic plant line, we developed a multifunctional TAP tag, named GSyellow, which combines the streptavidin-binding peptide (SBP) tag with citrine yellow fluorescent protein (cYFP)...

OBJECTIVE: As operative experience in general surgery decreases and work hour limitations increase there is less exposure of surgical residents to advanced vascular and trauma exposures. Many institutions have demonstrated benefits of cadaver laboratory courses. We have incorporated a multimedia cadaver laboratory course into our general surgery residency didactics curriculum with the objective to demonstrate a benefit of the program as well as the feasibility of incorporation. STUDY DESIGN: This is a prospective study at a tertiary care institution including general surgery residents within our residency program...

BACKGROUND: Bioactive peptides, including biological sources-derived peptides with different biological activities, are protein fragments that influence the functions or conditions of organisms, in particular humans and animals. Conventional methods of identifying bioactive peptides are time-consuming and costly. To quicken the processes, several bioinformatics tools are recently used to facilitate screening of the potential peptides prior their activity assessment in vitro and/or in vivo...

We propose a new approach to clinical decision support with interpretable recommendations from multi-view data. We introduce a Bayesian network structure learning method to help identify the relevant factors and their relationships. Guided by minimal domain knowledge, this method highlights the significant associations among the demography, medical and family history, lifestyle, and biomarker data to facilitate informed clinical decisions. We demonstrate the effectiveness of the method for detecting mild neurocognitive disorder in the elderly from a real-life dataset in Singapore...

The ever-increasing number of bioinformatics software tools that are publicly available, is leading to greater expectations about its regular use in clinical practice. However, from the end-users' perspective, they face many time the challenge of choosing the right tool for each task, from a panoply of solutions that have been developed over the years. In this paper, we propose a benchmarking methodology, based on a set of performance indicators, which can be used to identify the best methods and tools for each particular use case, both in research as in clinical practice...

The Nordic eHealth Research Network, a subgroup of the Nordic Council of Ministers eHealth group, is working on developing indicators to monitor progress in availability, use and outcome of eHealth applications in the Nordic countries. This paper reports on the consecutive analysis of National eHealth policies in the Nordic countries from 2012 to 2016. Furthermore, it discusses the consequences for the development of indicators that can measure changes in the eHealth environment arising from the policies. The main change in policies is reflected in a shift towards more stakeholder involvement and intensified focus on clinical infrastructure...

In this manuscript, the compact potential model for double-gate (DG) Si1-xGex/Si heterojunction tunnel field-effect transistors (TFETs) is proposed by adopting several strategies to the previous model. Compared with the control model, the enhanced model can describe the effects of additional parameters such as electron permittivity and Si1-xGex affinity, doping dependent bandgap narrowing, temperature, built-in potential change due to degenerately doping condition and energy band off-sets. The model accuracy is examined by benchmarking against to the technology computeraided design (TCAD) device simulations in terms of electrostatic potential profiles, band diagrams and minimum tunneling barrier width (Wt, min)...

A new analytical protocol was developed to provide quantitative, single-particle identification of arsenic in heterogeneous nanoscale mineral phases in soil samples, with a view to establishing its potential risk to human health. Microscopic techniques enabled quantitative, single-particle identification of As-bearing phases in twenty soil samples collected in a gold mining district with arsenic concentrations in range of 8 to 6354 mg kg-1 . Arsenic is primarily observed in association with iron (hydr) oxides in fine intergrowth with phyllosilicates...

The amount of solid waste generated in developing countries is rising from time to time due to economic growth, change in consumer behavior and lifestyles of people. But it is hard to manage and handle the increase of solid waste with existing waste management infrastructure. Thus, the management system of solid waste is very poor and become a serious problem. The main purpose of this study is to quantify the volume of solid waste generated and investigate factors affecting generation and disposal of wastes in the study area...

A model was developed for a water resources recovery facility (WRRF) activated sludge process (ASP) in Modified Ludzack-Ettinger (MLE) configuration. Amplification of air requirements and its associated energy consumptions were observed as a result of concurrent circadian variations in ASP influent flow and carbonaceous/nitrogenous constituent concentrations. The indirect carbon emissions associated with the ASP aeration were further amplified due to the simultaneous variations in carbon emissions intensity (kgCO2,eq (kWh)-1 ) and electricity consumption (kWh)...

Glycation is chemical reaction by which sugar molecule bonds with a protein without the help of enzymes. This is often cause to many diseases and therefore the knowledge about glycation is very important. In this paper, we present iProtGly-SS, a protein lysine glycation site identification method based on features extracted from sequence and secondary structural information. In the experiments, we found the best feature groups combination: Amino Acid Composition, Secondary Structure Motifs and Polarity. We used support vector machine classifier to train our model and used an optimal set of features using a group based forward feature selection technique...

Objective: The bacterial composition and distribution were evaluated in acute standardized epidermal wounds and uninjured skin by a molecular in situ technology benchmarked to conventional culturing. This was done to reveal whether bacterial biofilm is present in acute wounds. Approach: On the buttock of 26 healthy volunteers, 28 suction blisters were made and de-roofed. Four wounds were biopsied immediately after wounding, whereas the remaining 24 wounds were treated daily with sterile deionized water and covered with a moisture-retaining dressing...

Particle swarm optimization (PSO) and fireworks algorithm (FWA) are two recently developed optimization methods which have been applied in various areas due to their simplicity and efficiency. However, when being applied to high-dimensional optimization problems, PSO algorithm may be trapped in the local optima owing to the lack of powerful global exploration capability, and fireworks algorithm is difficult to converge in some cases because of its relatively low local exploitation efficiency for noncore fireworks...

BACKGROUND: Insertions and deletions (indels) are a major class of genomic variation associated with human disease. Indels are primarily detected from DNA sequencing (DNA-seq) data but their transcriptional consequences remain unexplored due to challenges in discriminating medium-sized and large indels from splicing events in RNA-seq data. RESULTS: Here, we developed transIndel, a splice-aware algorithm that parses the chimeric alignments predicted by a short read aligner and reconstructs the mid-sized insertions and large deletions based on the linear alignments of split reads from DNA-seq or RNA-seq data...

Motivation: CRISPR/Cas9 system is a widely used genome editing tool. A prediction problem of great interests for this system is: how to select optimal single guide RNAs (sgRNAs) such that its cleavage efficiency is high meanwhile the off-target effect is low. Results: This work proposed a two-step averaging method (TSAM) for the regression of cleavage efficiencies of a set of sgRNAs by averaging the predicted efficiency scores of a boosting algorithm and those by a support vector machine (SVM)...

Spoken Language Identification (LID) is the process of determining and classifying natural language from a given content and dataset. Typically, data must be processed to extract useful features to perform LID. The extracting features for LID, based on literature, is a mature process where the standard features for LID have already been developed using Mel-Frequency Cepstral Coefficients (MFCC), Shifted Delta Cepstral (SDC), the Gaussian Mixture Model (GMM) and ending with the i-vector based framework. However, the process of learning based on extract features remains to be improved (i...

Women comprise a minority of the Science, Technology, Engineering, Mathematics, and Medicine (STEMM) workforce. Quantifying the gender gap may identify fields that will not reach parity without intervention, reveal underappreciated biases, and inform benchmarks for gender balance among conference speakers, editors, and hiring committees. Using the PubMed and arXiv databases, we estimated the gender of 36 million authors from >100 countries publishing in >6000 journals, covering most STEMM disciplines over the last 15 years, and made a web app allowing easy access to the data (https://lukeholman...