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 94.8% was obtained by aligning contigs to Nr, SwissProt, and TrEMBL, with 27,281 sequences that simultaneously mapped on the three databases. A total of 14,966 ORFs were also functionally annotated by using the eggNOG database. Among them, we identified ORF sequences of the main gene families involved in insecticide resistance. Therefore, this resource stands as a valuable reference for further studies of differential gene expression as well as to identify genes of interest for genetic-based control tools.

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. D is a marine parasite able to survive and thrive both at very cold and warm temperatures within the environment and its hosts. Here, a de novo transcriptome of C. osculatum sp. D was generated for the first time, by performing RNA-Seq experiments on a set of individuals exposed to temperatures experienced by the nematode during its life cycle. The analysis generated 425,954,724 reads, which were assembled and then annotated. The high-quality assembly was validated, achieving over 88% mapping against the transcriptome. The transcriptome of this parasite will represent a valuable genomic resource for future studies aimed at disentangling the genomic architecture of thermal tolerance and metabolic pathways related to temperature stress.

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. Unlike traditional static analysis tools, MDLR goes beyond simply taking a snapshot of ligand-receptor binding interactions (lrbi), uncovering long-lasting molecular interactions and predicting the time-dependent inhibitory activity of specific drugs. With MDLR, researchers can gain insights into the dynamic behavior of complex ligand-receptor systems. Our pipeline is optimized for high-performance computing, capable of efficiently processing vast molecular dynamics trajectories on multicore Linux servers or even multinode HPC clusters. In the latter case, MDLR allows the user to analyze large trajectories in a very short time. To facilitate the exploration and visualization of lrbi, we provide an intuitive Python notebook (Jupyter), which allows users to examine and interpret the results through various graphical representations.

De novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stage.

Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Attitude to disperse is unevenly distributed among individuals within populations, and that individual personality can have pivotal roles in the shaping of this attitude. Here, we assembled and annotated the first de novo transcriptome of the head tissues of Salamandra salamandra from individuals, representative of distinct behavioral profiles. We obtained 1,153,432,918 reads, which were successfully assembled and annotated. The high-quality of the assembly was confirmed by three assembly validators. The alignment of contigs against the de novo transcriptome led to a mapping percentage higher than 94%. The homology annotation with DIAMOND led to 153,048 (blastx) and 95,942 (blastp) shared contigs, annotated on NR, Swiss-Prot and TrEMBL. The domain and site protein prediction led to 9850 GO-annotated contigs. This de novo transcriptome represents reliable reference for comparative gene expression studies between alternative behavioral types, for comparative gene expression studies within Salamandra, and for whole transcriptome and proteome studies in amphibians.

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. PARTICIPANTS/SETTING: Parents (n = 640; mean age = 35.9 y; 70.8% female) consented and agreed to provide their child's PW for digital imaging, across 11 QSRs in Massachusetts in areas with low socioeconomic status and ethnically diverse populations. OUTCOME MEASURES: Outcome measures were interrater reliability for DIs, correspondence between methods for energy consumed and left over, and correspondence between methods across varying quantities of PW. ANALYSES PERFORMED: Intraclass correlations, percent agreement, Spearman correlations, Wilcoxon signed rank tests, and Bland-Altman plots were used. RESULTS: Interrater reliability ratings for DIs had substantial intraclass correlations (ICC = 0.94) but not acceptable exact percent agreement (80.2%); DI and PW energy consumed were significantly correlated (r = 0.96, P < 0.001); DI slightly underestimated energy consumed compared with PW (Mdiff = -1.61 kcals, P < 0.001). Bland-Altman plots showed high DI-PW correspondence across various energy amounts and revealed few outliers. Energy left over by BC was highly correlated with DI (r = 0.87, P < 0.001) and PW (r = 0.90, P < 0.001); and mean differences were not significantly different from DI (Mdiff = 9.77 kcal, P = 0.06) or PW (Mdiff = -2.84 kcal, P = 0.20). CONCLUSIONS: Correspondence was high between PW and DI assessments of energy consumed, and high with BC energy left over. Results demonstrate reliability and practical validity of digital images for assessing child meal consumption in QSR settings.

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. These simulations are focused on the stability and conformational changes of two DNA/TOP1-DV complexes in solution, the data being compared with the biomimetic thymine dimer counterparts. Results from root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) analyses unequivocally confirmed increased stability of the DNA/TOP1-DV complexes throughout the simulation duration. Detailed interaction analyses, uncovering the presence of salt bridges, hydrogen bonds, water-mediated interactions, and hydrophobic interactions, as well as pinpointing the non-covalent interactions within the complexes, enabled the identification of specific TOP1 residues involved in the interactions over time and suggested a potential TOP1 inhibition mechanism in action.

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. This gives hTop1p a central role in cancer therapy. Recently, two artesunic acid derivatives (compounds c6 and c7) have been proposed as promising inhibitors of hTop1p with possible antitumor activity. We used several computational approaches to obtain in silico confirmations of the experimental data and to form a comprehensive dynamic description of the ligand-receptor system. We performed molecular docking analyses to verify the ability of the two new derivatives to access the enzyme-DNA interface, and a classical molecular dynamics simulation was performed to assess the capacity of the two compounds to maintain a stable binding pose over time. Finally, we calculated the noncovalent interactions between the two new derivatives and the hTop1p receptor in order to propose a possible inhibitory mechanism like that adopted by CPT.

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. pegreffii was here generated aiming to provide a robust bulk of data to be used for a comprehensive "ready-to-use" resource for detecting functional studies on genes and gene products of A. pegreffii involved in the molecular mechanisms of parasite-host interaction. DATA DESCRIPTION: A RNA-seq library of A. pegreffii L3 was here newly generated by using Illumina TruSeq platform. It was combined with other five RNA-seq datasets previously gathered from L3 of the same species stored in SRA of NCBI. The final dataset was analyzed by launching three assembler programs and two validation tools. The use of a robust pipeline produced a high-confidence protein-coding transcriptome of A. pegreffii. These data represent a more robust and complete transcriptome of this species with respect to the actually existing resources. This is of importance for understanding the involved adaptive and immunomodulatory genes implicated in the "cross talk" between the parasite and its hosts, including the accidental one (humans).

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. The Heagerty's C-index for survival tested for discrimination of each model at different time points after nephrectomy. RESULTS: Three hundred and fifty-eight M0 ccRCC patients were included. RFS significantly differed among each risk category for all models (P < 0.001). SSIGN showed the highest c-index over time (from 0.89 at 6-month to 0.82 at 60-month), followed by Leibovich (from 0.89-0.82), AJCC/TNM stage (from 0.82-0.77), ASSURE (from 0.81 to 0.76), GRANT (from 0.83-0.73) and UISS (from 0.76-0.72). For all models, peak discriminatory ability was reached before 12 months. The most prominent decline occurred within 24 months and reaches the lowest discriminatory ability at 60 months. CONCLUSIONS: Predictive models, with preference for SSIGN and Leibovich scores, are reliable to predict recurrence after nephrectomy and should be recommended to tailor postoperative surveillance protocols.

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

Purpose: 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.Methods: 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.Results: Overall, there were 500 eligible respondents; the analysis focused on dietitians working in clinical care who were familiar with the NCP (n = 420). In total, 87.9% and 77.5% of respondents reported always/frequently using aspects of the NCP and NCPT in their practice, respectively. There were variations in use by province/territory (P < 0.001); use was more frequent in Alberta and Manitoba versus other provinces/territories. A main barrier to implementation was lack of time; main facilitators to implementation were peer support, management support, and required use of the NCP. The prevalence of many facilitators and barriers varied by province (P < 0.05). Attitudes regarding the NCP/NCPT were variable.Conclusions: Overall, most clinical care dietitians reported some type of use of the NCP/NCPT. There were provincial/territorial variations in use, barriers, and facilitators. These findings provide information to develop strategies to enhance use of the NCP/NCPT in Canada.

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. An open label, retrospective study was undertaken where PD patients had been undergoing LT, using polychromatic light, for four months to 15 years prior. It was found that 1 h exposure to light, just prior to retiring, significantly improved insomnia and reduced RSBD in as little as one month after commencing LT. In addition, the improvement was maintained as long as LT was continued over a four to six year period. The efficacy of LT in alleviating these sleep related conditions was not compromised by time since diagnosis or age of the patient. These results intimate the value of long term application of non-invasive techniques such as LT for treating sleep disorders in PD and justify further controlled trials on the long term efficacy of LT.

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. Fixation indices (FST) showed that populations in river valleys were significantly differentiated for both species (racers, FST = 0.096, P = 0.001; bullsnakes FST = 0.045-0.157, P = 0.001). Bayesian assignment (STRUCTURE) and ordination (DAPC) strongly supported genetically differentiated groups in the geographically distinct river valleys. Finer-scale subdivision of populations within river valleys was not apparent based on our data, but is a topic that should be investigated further. Our findings highlight the importance of major river valleys for snakes at the northern extent of their ranges, and raise the possibility that populations in each river valley may warrant separate management strategies.

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. The opposite of connection, social isolation, has a negative effect on health and can increase depressive symptoms as well as mortality. Counseling patients on increasing social connections, prescribing connection, and inquiring about quantity and quality of social interactions at routine visits are ways that lifestyle medicine specialists can use connection to help patients to add not only years to their life but also health and well-being to those years.

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. Niche metrics using δ13C and δ15N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearby reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (Fst, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Thus, future research should focus on the potential impacts of thermal emissions on development and recruitment.

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). We generated libraries using genomic DNA serially extracted from the muscle tissue of 8 individual lake whitefish (Coregonus clupeaformis) following 0-, 12-, 48- and 96-h incubation at room temperature posteuthanasia. This treatment of the tissue resulted in input DNA that ranged in quality from nearly intact to highly sheared. All samples were sequenced as a multiplexed pool on an Illumina MiSeq. Libraries created from low to moderately degraded DNA (12-48 h) performed well. In contrast, the number of RADtags per individual, number of variable sites, and percentage of identical RADtags retained were all dramatically reduced when libraries were made using highly degraded DNA (96-h group). This reduction in performance was largely due to a significant and unexpected loss of raw reads as a result of poor quality scores. Our findings remained consistent after changes in restriction enzymes, modified fold coverage values (2- to 16-fold), and additional read-length trimming. We conclude that starting DNA quality is an important consideration for RADSeq; however, the approach remains robust until genomic DNA is extensively degraded.

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. Although radiologists are responsible for the final reading of chest radiographs, very often the clinicians, and in particular the emergency physicians, are alone in the emergency room facing this task. In literature many studies have demonstrated how important and essential is an accurate direct interpretation by the clinician without the need of an immediate reading by the radiologist. Moreover, the sensitivity of CXR is much impaired when the study is performed at bedside by portable machines, particularly in the diagnosis of some important causes of acute dyspnoea, such as pulmonary embolism, pneumothorax, and pulmonary edema. In these cases, a high inter-observer variability of bedside CXR reading limits the diagnostic usefulness of the methodology and complicates the differential diagnosis. The aim of this review is to analyze the radiologic signs and the correct use of CXR in the most important conditions that cause cardiac and pulmonary dyspnoea, as acute exacerbation of chronic obstructive pulmonary disease, acute pulmonary oedema, acute pulmonary trombo-embolism, pneumothorax and pleural effusion, and to focus indications and limitations of this diagnostic tool.