Benchmarking

BACKGROUND: Vitamin D is an environmental and dietary agent with known anticarcinogenic effects, but protection against breast cancer has not been established. OBJECTIVE: We evaluated the association between baseline serum 25-hydroxyvitamin D [25(OH)D] levels, supplemental vitamin D use, and breast cancer incidence over the subsequent 5 y of follow-up. METHODS: From 2003-2009, the Sister Study enrolled 50,884 U.S. women 35-74 y old who had a sister with breast cancer but had never had breast cancer themselves...

A novel method for exploring macrocycle conformational space, Prime Macrocycle Conformational Sampling (Prime-MCS), is introduced and evaluated in the context of other available algorithms (Molecular Dynamics, LowModeMD in MOE, and MacroModel Baseline Search). The algorithms were benchmarked on a dataset of 208 macrocycles which was curated for diversity from the Cambridge Structural Database, the Protein Databank, and the Biologically Interesting Molecule Reference Dictionary. The algorithms were evaluated in terms of accuracy (ability to reproduce the crystal structure), diversity (coverage of conformational space), and computational speed...

Kalman filtering methods have long been regarded as efficient adaptive Bayesian techniques for estimating hidden states in models of linear dynamical systems under Gaussian uncertainty. Recent advents of the Cubature Kalman filter (CKF) have extended this efficient estimation property to nonlinear systems, and also to hybrid nonlinear problems where by the processes are continuous and the observations are discrete (continuous-discrete CD-CKF). Employing CKF techniques, therefore, carries high promise for modeling many biological phenomena where the underlying processes exhibit inherently nonlinear, continuous, and noisy dynamics and the associated measurements are uncertain and time-sampled...

BACKGROUND: It is the gold standard to use a placebo treatment as the control group in prospective randomized controlled trials (RCTs). Although placebo-controlled trials can reveal an effect of an active treatment, the pure effect of a placebo treatment alone has never been presented or evaluated. No evidence-based, placebo-therapeutic options are currently available, and no placebo-controlled trials have been performed to elucidate the pure placebo effect. OBJECTIVES: To analyze the pure placebo effect on clinical, chronic pain through a blinded RCT...

No abstract text is available yet for this article.

Deep neural networks (NNs) are the state-of-the-art models for understanding the content of images and videos. However, implementing deep NNs in embedded systems is a challenging task, e.g., a typical deep belief network could exhaust gigabytes of memory and result in bandwidth and computational bottlenecks. To address this challenge, this paper presents an algorithm and hardware codesign for efficient deep neural computation. A hardware-oriented deep learning algorithm, named the deep adaptive network, is proposed to explore the sparsity of neural connections...

In this paper, we present and analyze an event distribution system for brain-computer interfaces (BCIs). Events are commonly used to mark and describe incidents during an experiment and are therefore critical for later data analysis or immediate real-time processing. The presented approach, called TiD (Tools for brain-computer interaction - interface D), delivers messages in XML format via a bus-like system using TCP (transmission control protocol) connections or shared memory. A dedicated server dispatches TiD messages to distributed or local clients...

Transition metal dichalcogenides (TMDs) are a group of layered 2D semiconductors that have shown many intriguing electrical and optical properties. However, the thermal transport properties in TMDs are not well understood due to the challenges in characterizing anisotropic thermal conductivity. Here, a variable-spot-size time-domain thermoreflectance approach is developed to simultaneously measure both the in-plane and the through-plane thermal conductivity of four kinds of layered TMDs (MoS2 , WS2 , MoSe2 , and WSe2 ) over a wide temperature range, 80-300 K...

The National Beef Quality Audit (NBQA)-2016 used in-plant cooler assessments to benchmark the current status of the fed steer and heifer beef industry in the United States. In-plant cooler assessments ( = 9,106 carcasses) were conducted at 30 facilities, where approximately 10% of a single day's production were evaluated for USDA quality grade (QG) and yield grade (YG) factors. Frequencies of evaluated traits were 66.5% steer and 33.4% heifer sex classes and 82.9% native, 15.9% dairy-type, and 1.2% estimated breed types...

PURPOSE: Palliative care referral is primarily based on clinician judgment, contributing to highly variable access. Standardized criteria to trigger automatic referral have been proposed, but it remains unclear how best to apply them in practice. We conducted a Delphi study of international experts to identify a consensus for the use of standardized criteria to trigger automatic referral. METHODS: Sixty international experts stated their level of agreement for 14 statements regarding the use of clinician-based referral and automatic referral over two Delphi rounds...

Halophilic bacteria were isolated from oil spill samples collected from West-coast of Goa. Bacteria were isolated from oil studded soil, salt marsh and offshore samples (A, A7, CSM, CB and CM) collected along the West coastline in Goa (India) i.e. Arambol beach, Calanguate beach, Candolim beach and Colva beach on Zobell Marine agar, R2A agar, Mannitol salt agar and Blood agar at temperature 22 to 24 °C. Isolates showed growth in the presence of hydrocarbons (1% phenanthrene and 2% bitumen). Diverse profiles of pigments were observed on different nutrient medium...

Several available online tools provide network growing functions where an algorithm utilizing different data sources suggests additional genes/proteins that should connect an input gene set into functionally meaningful networks. Using the well-studied system of influenza host interactions, we compare the network growing function of two free tools GeneMANIA and STRING and the commercial IPA for their performance of recovering known influenza A virus host factors previously identified from siRNA screens. The result showed that given small (~30 genes) or medium (~150 genes) input sets all three network growing tools detect significantly more known host factors than random human genes with STRING overall performing strongest...

In an effort to reduce the frequency and severity of adverse reactions seen from the use of mineral oil adjuvants in salmonid fish, the effects of two alternative adjuvants were assessed, focusing on the induction of adverse effects as well as protection. Using rainbow trout (Oncorhynchus mykiss) as recipients, injection vaccines based on formalin-inactivated Aeromonas salmonicida subspecies salmonicida were formulated with CpG oligodeoxynucleotides, the liposomal cationic adjuvant formulation 01 (CAF01) or with Freund's incomplete adjuvant and administered intraperitoneally...

We describe a new reproducibility-optimization method ROPECA for statistical analysis of proteomics data with a specific focus on the emerging data-independent acquisition (DIA) mass spectrometry technology. ROPECA optimizes the reproducibility of statistical testing on peptide-level and aggregates the peptide-level changes to determine differential protein-level expression. Using a 'gold standard' spike-in data and a hybrid proteome benchmark data we show the competitive performance of ROPECA over conventional protein-based analysis as well as state-of-the-art peptide-based tools especially in DIA data with consistent peptide measurements...

A key determinant of population health is the behavioral profile of a population. Nearly 80 percent of Americans reach their fifties having smoked cigarettes, been obese, or both. It is unknown to what extent risky behaviors (for example, smoking, having a poor diet, being physically inactive, and consuming an excessive amount of alcohol) collectively are reducing the health and life expectancy of the US population, or what improvements might be achievable in their absence. Using data from the Health and Retirement Study, we studied people ages fifty and older who had never smoked, who were not obese, and who consumed alcohol moderately...

OBJECTIVE: Clinical guidelines provide recommendations for diagnosis and treatment of attention-deficit hyperactivity disorder (ADHD), with specific guidance on caring for children younger than 6 years. This exploratory study describes ADHD diagnosis and treatment patterns among young children in the United States using 2 nationally representative parent surveys. METHODS: The National Survey of Children's Health (2007-2008, 2011-2012) was used to produce weighted prevalence estimates of current ADHD and ADHD medication treatment among US children aged 2 to 5 years...

No abstract text is available yet for this article.

Strongly correlated materials are now under intense development, and Natural Orbital Functional (NOF) methods seem to be able to capture the physics of these systems. We present a benchmark based on the Hubbard model for a class of commonly used NOF approximations (also known as reduced density matrix functional approximations). Our findings highlight the importance of imposing ensemble N -representability conditions in order to obtain consistent results in systems with either weak or strong electronic correlation, such as the Hubbard system with a varying two-particle interaction parameter...

Current benchmarking methods in quantum chemistry rely on databases that are built using a chemist's intuition. It is not fully understood how diverse or representative these databases truly are. Multivariate statistical techniques like archetypal analysis and K-means clustering have previously been used to summarise large sets of nanoparticles however molecules are more diverse and not as easily characterised by descriptors. In this work we compare three sets of descriptors based on the one-, two- and three-dimensional structure of a molecule...

PURPOSE: A joint working group was created by the American Association of Physicists in Medicine (AAPM), the European Society for Radiotherapy and Oncology (ESTRO), and the Australasian Brachytherapy Group (ABG) with the charge, among others, to develop a set of well-defined test case plans and perform model-based dose calculation algorithms (MBDCA) dose calculations and comparisons. Its main goal is to facilitate a smooth transition from the AAPM Task Group No. 43 (TG-43) dose calculation formalism, widely being used in clinical practice for brachytherapy, to the one proposed by Task Group No...