HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation.

Background: The availability of transcriptomic data for species without a reference genome enables the construction of de novo transcriptome assemblies as alternative reference resources from RNA-Seq data. A transcriptome provides direct information about a species' protein-coding genes under specific experimental conditions. The de novo assembly process produces a unigenes file in FASTA format, subsequently targeted for the annotation.

Integrated de novo transcriptome of Culex pipiens mosquito larvae as a resource for genetic control strategies.

We present a de novo transcriptome of the mosquito vector Culex pipiens, assembled by sequences of susceptible and insecticide resistant larvae. The high quality of the assembly was confirmed by TransRate and BUSCO. A mapping percentage until 94.

Molecular Dynamics Investigations of Human DNA-Topoisomerase I Interacting with Novel Dewar Valence Photo-Adducts: Insights into Inhibitory Activity.

Chronic exposure to ultraviolet (UV) radiation is known to induce the formation of DNA photo-adducts, including cyclobutane pyrimidine dimers (CPDs) and Dewar valence derivatives (DVs). While CPDs usually occur at higher frequency than DVs, recent studies have shown that the latter display superior selectivity and significant stability in interaction with the human DNA/topoisomerase 1 complex (TOP1). With the aim to deeply investigate the mechanism of interaction of DVs with TOP1, we report here four all-atom molecular dynamic simulations spanning one microsecond.

De novo transcriptome assembly of an Antarctic nematode for the study of thermal adaptation in marine parasites.

Understanding the genomic underpinnings of thermal adaptation is a hot topic in eco-evolutionary studies of parasites. Marine heteroxenous parasites have complex life cycles encompassing a free-living larval stage, an ectothermic intermediate host and a homeothermic definitive host, thus representing compelling systems for the study of thermal adaptation. The Antarctic anisakid Contracaecum osculatum sp.

MD-Ligand-Receptor: A High-Performance Computing Tool for Characterizing Ligand-Receptor Binding Interactions in Molecular Dynamics Trajectories.

Molecular dynamics simulation is a widely employed computational technique for studying the dynamic behavior of molecular systems over time. By simulating macromolecular biological systems consisting of a drug, a receptor and a solvated environment with thousands of water molecules, MD allows for realistic ligand-receptor binding interactions (lrbi) to be studied. In this study, we present MD-ligand-receptor (MDLR), a state-of-the-art software designed to explore the intricate interactions between ligands and receptors over time using molecular dynamics trajectories.

Molecular Docking and Dynamics Simulation Revealed the Potential Inhibitory Activity of New Drugs against Human Topoisomerase I Receptor.

Human Topoisomerase I (hTop1p) is a ubiquitous enzyme that relaxes supercoiled DNA through a conserved mechanism involving transient breakage, rotation, and binding. Htop1p is the molecular target of the chemotherapeutic drug camptothecin (CPT). It causes the hTop1p-DNA complex to slow down the binding process and clash with the replicative machinery during the S phase of the cell cycle, forcing cells to activate the apoptotic response.

Reliability and Validity of Digital Images to Assess Child Dietary Intake in a Quick-Service Restaurant Setting.

Background: Development of methods to accurately measure dietary intake in free-living situations-restaurants or otherwise-is critically needed to understand overall dietary patterns.

Objective: This study aimed to develop and test reliability and validity of digital images (DI) for measuring children's dietary intake in quick-service restaurants (QSRs), validating against weighed plate waste (PW) and bomb calorimetry (BC).

Design: In 2016, cross-sectional data were collected at two time points within a randomized controlled trial assessing children's leftovers in QSRs from parents of 4- to 12-year-old children.

De novo transcriptome assembly and annotation of the third stage larvae of the zoonotic parasite Anisakis pegreffii.

Objectives: Anisakis pegreffii is a zoonotic parasite requiring marine organisms to complete its life-history. Human infection (anisakiasis) occurs when the third stage larvae (L3) are accidentally ingested with raw or undercooked infected fish or squids. A new de novo transcriptome of A.

Risk of recurrence after nephrectomy: Comparison of predictive ability of validated risk models.

Objective: To assess accuracy of University of California Los Angeles Integrated Staging System (UISS), Stage, Size, Grade and Necrosis (SSIGN) score, Leibovich score and GRade, Age, Nodes and Tumor (GRANT) score, the ASSURE (Adjuvant Sunitinib or Sorafenib vs. placebo in resected Unfavorable REnal cell carcinoma) score models and seventh American Joint Committee on Cancer (AJCC)/TNM staging system in predicting recurrence-free survival (RFS) in surgically-treated non-metastatic clear cell renal cell carcinoma (ccRCC) patients.

Materials And Methods: Kaplan-Meier curves and the log-rank test tested RFS according to risk groups among the UISS, SSIGN, Leibovich and GRANT models and the AJCC/TNM system.

Use of the Nutrition Care Process and Terminology in Canada: A National and Regional Update.

The purpose of this paper is to understand Canadian dietitians' use of the Nutrition Care Process (NCP) and terminology (NCPT) nationally and by province/territory as well as facilitators, barriers, and attitudes regarding the NCP/NCPT. Canadian dietitians were invited to complete an online survey (SurveyMonkey) on the NCP/NCPT from February to April 2017 through multiple channels. Data were analyzed using descriptive statistics and nonparametric tests.

The effect of light exposure on insomnia and nocturnal movement in Parkinson's disease: an open label, retrospective, longitudinal study.

Insomnia, hypersomnia and REM Sleep Behavior Disorder (RSBD) during sleep are major problems for patients suffering from Parkinson's disease (PD) but they are also used to predict its onset. While these secondary symptoms detract from the quality of life in PD patients, few treatment options are available due to limited efficacy or risk of complicating the treatment regimen. Light therapy (LT) has been suggested as a strategy for sleep disorders but it has only been implemented recently for use in PD.

Conservation genetics of the eastern yellow-bellied racer (Coluber constrictor flaviventris) and bullsnake (Pituophis catenifer sayi): River valleys are critical features for snakes at northern range limits.

On the North American Great Plains, several snake species reach their northern range limit where they rely on sparsely distributed hibernacula located in major river valleys. Independent colonization histories for the river valleys and barriers to gene flow caused by the lack of suitable habitat between them may have produced genetically differentiated snake populations. To test this hypothesis, we used 10 microsatellite loci to examine the population structure of two species of conservation concern in Canada: the eastern yellow-bellied racer (Coluber constrictor flaviventris) and bullsnake (Pituophis catenifer sayi) in 3 major river valleys in southern Saskatchewan.

Fine-Scale Ecological and Genetic Population Structure of Two Whitefish (Coregoninae) Species in the Vicinity of Industrial Thermal Emissions.

Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species (Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation.

The Connection Prescription: Using the Power of Social Interactions and the Deep Desire for Connectedness to Empower Health and Wellness.

Social connection is a pillar of lifestyle medicine. Humans are wired to connect, and this connection affects our health. From psychological theories to recent research, there is significant evidence that social support and feeling connected can help people maintain a healthy body mass index, control blood sugars, improve cancer survival, decrease cardiovascular mortality, decrease depressive symptoms, mitigate posttraumatic stress disorder symptoms, and improve overall mental health.

Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq).

Degraded DNA from suboptimal field sampling is common in molecular ecology. However, its impact on techniques that use restriction site associated next-generation DNA sequencing (RADSeq, GBS) is unknown. We experimentally examined the effects of in situDNA degradation on data generation for a modified double-digest RADSeq approach (3RAD).

Revisiting signs, strengths and weaknesses of Standard Chest Radiography in patients of Acute Dyspnea in the Emergency Department.

Dyspnoea, defined as an uncomfortable awareness of breathing, together with thoracic pain are two of the most frequent symptoms of presentation of thoracic diseases in the Emergency Department (ED). Causes of dyspnoea are various and involve not only cardiovascular and respiratory systems. In the emergency setting, thoracic imaging by standard chest X-ray (CXR) plays a crucial role in the diagnostic process, because it is of fast execution and relatively not expensive.