Benchmarking

Text mining of scientific libraries and social media has already proven itself as a reliable tool for drug repurposing and hypothesis generation. The task of mapping a disease mention to a concept in a controlled vocabulary, typically to the standard thesaurus in the Unified Medical Language System (UMLS), is known as medical concept normalization. This task is challenging due to the differences in the use of medical terminology between health care professionals and social media texts coming from the lay public...

OBJECTIVE: Automatic text summarization offers an efficient solution to access the ever-growing amounts of both scientific and clinical literature in the biomedical domain by summarizing the source documents while maintaining their most informative contents. In this paper, we propose a novel graph-based summarization method that takes advantage of the domain-specific knowledge and a well-established data mining technique called frequent itemset mining. METHODS: Our summarizer exploits the Unified Medical Language System (UMLS) to construct a concept-based model of the source document and mapping the document to the concepts...

We present a thorough investigation of the errors in results obtained with the combination of Frozen-Density Embedding Theory and the Algebraic Diagrammatic Construction Scheme for the polarization propagator of second order (FDE-ADC(2)). The study was carried out on a set of 52 intermolecular complexes with varying interaction strength, each consisting of a chromophore of fundamental interest and a few small molecules in its environment. The errors emerging in Frozen-Density Embedding Theory based methods originate from: (a) the solver of the quantum many body problem used to obtain the embedded wavefunction (Ψemb), (b) the approximation for the explicit density functional for the embedding potential, and (c) the choice of the density representing the environment (ρB(r))...

The variational reduced density matrix theory has been recently applied with great success to models within the truncated doubly-occupied configuration interaction space, which corresponds to the seniority zero subspace. Conservation of the seniority quantum number restricts the Hamiltonians to be based on the SU(2) algebra. Among them there is a whole family of exactly solvable Richardson-Gaudin pairing Hamiltonians. We benchmark the variational theory against two different exactly solvable models, the Richardson-Gaudin-Kitaev and the reduced BCS Hamiltonians...

Strongly correlated vanadium dioxide (VO2) is one of the most promising materials to exhibit temperature-driven, metal-insulator transition (MIT) near room temperature. The ability to manipulate the MIT at nanoscale offers both an insight to understand the energetics of phase transition and a promising potential for nanoelectronic devices. In this work, we study nanoscale electrical modifications of the MIT in epitaxial VO2 thin films using a combined approach with scanning probe microscopy (SPM) and theoretical calculations...

Mixed-solvent molecular dynamics (MixMD) is a cosolvent simulation technique for identifying binding hotspots and specific favorable interactions on a protein's surface. MixMD studies have the ability to identify these biologically relevant sites by examining the occupancy of the cosolvent over the course of the simulation. However, previous MixMD analysis required a great deal of manual inspection to identify relevant sites. To address this limitation, we have developed MixMD Probeview as a plugin for the freely available, open-source version of the molecular visualization program PyMOL...

Photoelectrochemical (PEC) reduction of CO2 with H2 O not only provides an opportunity for reducing net CO2 emissions but also produces value-added chemical feedstocks and fuels. Syngas, a mixture of CO and H2 , is a key feedstock for the production of methanol and other commodity hydrocarbons in industry. However, it is challenging to achieve efficient and stable PEC CO2 reduction into syngas with controlled composition owing to the difficulties associated with the chemical inertness of CO2 and complex reaction network of CO2 conversion...

We have redesigned a tried-and-true laboratory exercise into an inquiry-based team activity exploring microbial growth control, and implemented this activity as the basis for preparing a scientific poster in a large, multi-section laboratory course. Spanning most of the semester, this project culminates in a poster presentation of data generated from a student-designed experiment. Students use and apply the scientific method and improve written and verbal communication skills. The guided inquiry format of this exercise provides the opportunity for student collaboration through cooperative learning...

Background: The aim of the study was to determine the optimal set point for the critical event benchmarks described in stroke guidelines and validate the ability of these goals to predict successful administration of intravenous thrombolysis within 60 min of hospital arrival. Methods: This was a retrospective cohort analysis of patients with acute ischemic stroke who received intravenous thrombolysis following presentation to the emergency department. The national benchmarks for time intervals associated with the completion of critical events required to determine candidacy for thrombolysis were evaluated for the ability to predict successful administration of thrombolysis within 60 min of hospital arrival...

We develop a quantitative methodology to characterize vulnerability among 132 U.S. urban centers ('cities') to terrorist events, applying a place-based vulnerability index to a database of terrorist incidents and related human casualties. A centered autologistic regression model is employed to relate urban vulnerability to terrorist outcomes and also to adjust for autocorrelation in the geospatial data. Risk-analytic 'benchmark' techniques are then incorporated into the modeling framework, wherein levels of high and low urban vulnerability to terrorism are identified...

Secreted proteins are widely spread in living organisms and cells. Since secreted proteins are easy to be detected in body fluids, urine, and saliva in clinical diagnosis, they play important roles in biomarkers for disease diagnosis and vaccine production. In this study, we propose a novel predictor for accurate high-throughput identification of mammalian secreted proteins that is based on sequence-derived features. We combine the features of amino acid composition, sequence motifs, and physicochemical properties to encode collected proteins...

Single-stranded (ss) oligonucleotide aptamers are emerging as the promising substitutes for monoclonal antibodies because of their low production cost and good batch-to-batch consistency. Aptamers vividly bind to a variety of cellular targets and alter their functions with a remarkable degree of specificities. In this study, the positive clones of human epidermal growth factor receptor 2 (HER2) specific binding ssDNA aptamers which were previously identified by in vitro Systematic Evolution of Ligands by EXponential enrichment (SELEX) process, hitherto lacking the putative binding site information and residues crucial for aptamer recognition are studied...

PURPOSE: There is ample evidence that single fraction radiation therapy (SFRT) is equally efficacious as more costly and morbid multi-fraction regimens. We previously demonstrated that an audit-based intervention increased the use of SFRT in all regional cancer centers the year following. However, other investigators have demonstrated interventions were only associated with a transient one-year change in prescribing practices. We sought to determine if our intervention resulted in a more lasting impact...

BACKGROUND: To determine national benchmarks and assess variability across centers, the STS Congenital Heart Surgery Database (CHSD) was analyzed to document proportions of patients receiving intraoperative blood transfusion during open heart surgery. METHODS: Index CPB operations reported in the STS CHSD (2014-2015) were potentially eligible for inclusion. Data from centers with > 15% missing data for packed red blood cell (PRBC) transfusion were excluded, as were individual records missing information about PRBC transfusion...

Oil sand operations in Alberta, Canada will eventually include returning treated process-affected waters to the environment. Organic constituents in oil sand process-affected water (OSPW) represent complex mixtures of nonionic and ionic (e.g. naphthenic acids) compounds, and compositions can vary spatially and temporally, which has impeded development of water quality benchmarks. To address this challenge, it was hypothesized that solid phase microextraction fibers coated with polydimethylsiloxane (PDMS) could be used as a biomimetic extraction (BE) to measure bioavailable organics in OSPW...

Cyclic voltammetry (CV) and in-situ attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy were used to investigate the effect of major urine compounds on the electrooxidation activity of urea using a nickel cobaltite (NiCo2O4) catalyst. As a substrate, carbon paper exhibited better benchmark potential and current values compared to stainless steel and fluorine-doped tin oxide glass, which was attributed to its greater active surface area per electrode geometric area. CV analysis of a synthetic urine showed that phosphate, creatinine, and gelatin (i...

Long-term functional outcomes in young adults with facial burns remain poorly studied. This 5-year (2003-2008) prospective multicenter study includes burn survivors (age 19-30 years) who completed the Young Adult Burn Outcome Questionnaire (YABOQ) from 0 to 36 months after baseline survey administration. A composite canonical score was developed from 15 YABOQ domains using discriminant analysis, maximizing the difference at the baseline between burn-injured patients with face involved and not involved. A generalized linear model with the generalized estimation equation technique was used to track the changing pattern of the composite score over time...

The main purpose of this paper is to analyse the activities for Radon Risk Communication under the National Radon Program and to outline the main objectives in the new Radon Action Plan for developing a communication strategy. The preliminary activities were implemented under the National Radon Program. Survey via the Internet for assessment of perceptions and the level of knowledge regarding radon was conducted as a benchmark for evaluation of public awareness. The main channels which were used to inform the population were publications on websites, magazines, in TV interviews and radio (local), seminars, from which the most widely used were local seminars...

Pembrolizumab is the only programmed cell death 1/programmed death-ligand 1 inhibitor for treatment of patients with non-small cell lung cancer, with a companion diagnostic assay, the 22C3 PharmDx. Although in many studies 22C3 and Ventana's SP263 appear to yield overlapping results, they show discrepancies at clinically relevant cutoffs (1% and 50%). We provide a solid comparison between 22C3 and SP263 assays in a large cohort of non-small cell lung cancer cases taking into account interobserver variability between trained pathologists who are used to either clone in their clinical practice...

This data article contains data related to the research article entitled, "Solving the multi-vehicle multi-covering tour problem" (Pham et al., 2017) [4]. All data of this article was generated from instances kroA100, kroB100, kroC100, kroD100, kroA200, and kroB200 from TSPLIB. It can be downloaded from public repository. This data can be used as benchmarks for the covering tour problem (CTP) variants, such as m -CTP- p , m -CTP, mm -CTP- p , mm -CTP, mm -CTP-o, mm -CTP-wo. We tested our algorithm on these data and results are shown in Pham et al...