Le rôle de la collaboration et du mentorat dans la publication des recherches des résidents en chirurgie

Background: Research is an integral part of surgical training and a mandated competency by national accreditation bodies. Most residents engage in research, but the conversion of this research into peer-reviewed publications is unknown. The objectives of this study were to assess the conversion rate of resident research into published manuscripts and determine what variables predict publication. Methods: Through a retrospective design, 99 resident research abstracts were identified from the Surgery Research Day at the University of Saskatchewan 2008-2018. Publication status was verified using Google Scholar and PubMed. Variables associated with resident-specific, mentor-specific, and project-specific variables were assessed for their role in predicting publication. Results: Fifty-two (53%) of the 99 abstracts were published in a peer-reviewed journal, and 43 (43%) were presented at a national conference. Logistic regression analysis revealed multidisciplinary research (OR 4.46, CI 1.8-11.4, p = 0.002), projects involving multiple resident researchers (OR 2.56, CI 1.02-6.43, p = 0.045), and faculty supervisor having > 25 publications (OR 2.46, CI 1.03-5.88, p = 0.042) as significant predictors of publication. Conclusions: Our study identifies 3 variables related to collaboration and mentorship that can serve as potential starting points to increase research productivity amongst medical trainees.Contexte : La recherche fait partie intégrante de la formation en chirurgie et elle est définie comme une compétence obligatoire par les organismes d’agrément nationaux. La plupart des résidents font de la recherche, mais la portion de ces travaux qui donne lieu à des publications évaluées par les pairs demeure inconnue. Les objectifs de cette étude étaient d’évaluer le taux de recherches de résidents qui se traduisent par une publication et de déterminer les variables permettant de prédire la publication. Méthodes : Aux fins de cette étude rétrospective, nous avons repéré 99 résumés de recherche présentés par des résidents dans le cadre de la Journée de recherche en chirurgie à l’Université de Saskatchewan entre 2008 et 2018. Le statut de publication a été vérifié en utilisant Google Scholar et PubMed. Les variables liées aux variables du résident, du mentor et du projet ont été évaluées pour déterminer leur rôle dans la prédiction de la publication. Résultats : Cinquante-deux (53 %) des 99 résumés ont été publiés dans une revue évaluée par les pairs, et 43 (43 %) ont été présentés à une conférence nationale. L’analyse de régression logistique a révélé que la recherche multidisciplinaire (OR 4,46, CI 1,8-11,4, p=0,002), les projets regroupant plusieurs chercheurs résidents (OR 2,56, CI 1,02-6,43, p=0,045) et ceux supervisés par un membre du corps professoral ayant > 25 publications (OR 2,46, CI 1,03-5,88, p=0,042) étaient des prédicteurs significatifs de la publication. Conclusions : Notre étude fait ressortir trois variables liées à la collaboration et au mentorat qui peuvent servir de points de départ pour stimuler la recherche par les médecins résidents

UC-318 Capstone Cybersecurity Website Hardening Group 2-01

The project we were given by Professor Privitera is to secure a web server that is a simulation of a genuine business with our case being a restaurant known as Akwaaba. The business website is hosted on Apache, MariaDB, Red Hat Linux, and PHP. We will first need to explore the network we were given to determine the system’s weaknesses to evaluate the risks and create a proper security policies plan with the help of the National Institute of Standards and Technology (NIST) standards. Following the security plan we created, our group will implement these changes into the network, hardening them to these standards. Finally, we will participate in a red/blue team cybersecurity ethical hacking procedure with our network and the two other teams. We will use white hat hacker skills to gain access to other groups’ networks while protecting our own network by patching up weaknesses if they have been breached

Partial Covering Arrays: Algorithms and Asymptotics

A covering array $\mathsf{CA}(N;t,k,v)$ is an $N\times k$ array with entries in $\{1, 2, \ldots , v\}$, for which every $N\times t$ subarray contains each $t$-tuple of $\{1, 2, \ldots , v\}^t$ among its rows. Covering arrays find application in interaction testing, including software and hardware testing, advanced materials development, and biological systems. A central question is to determine or bound $\mathsf{CAN}(t,k,v)$, the minimum number $N$ of rows of a $\mathsf{CA}(N;t,k,v)$. The well known bound $\mathsf{CAN}(t,k,v)=O((t-1)v^t\log k)$ is not too far from being asymptotically optimal. Sensible relaxations of the covering requirement arise when (1) the set $\{1, 2, \ldots , v\}^t$ need only be contained among the rows of at least $(1-\epsilon)\binom{k}{t}$ of the $N\times t$ subarrays and (2) the rows of every $N\times t$ subarray need only contain a (large) subset of $\{1, 2, \ldots , v\}^t$. In this paper, using probabilistic methods, significant improvements on the covering array upper bound are established for both relaxations, and for the conjunction of the two. In each case, a randomized algorithm constructs such arrays in expected polynomial time

Extensive sequence-influenced DNA methylation polymorphism in the human genome

Background: Epigenetic polymorphisms are a potential source of human diversity, but their frequency and relationship to genetic polymorphisms are unclear. DNA methylation, an epigenetic mark that is a covalent modification of the DNA itself, plays an important role in the regulation of gene expression. Most studies of DNA methylation in mammalian cells have focused on CpG methylation present in CpG islands (areas of concentrated CpGs often found near promoters), but there are also interesting patterns of CpG methylation found outside of CpG islands. Results: We compared DNA methylation patterns on both alleles between many pairs (and larger groups) of related and unrelated individuals. Direct observation and simulation experiments revealed that around 10% of common single nucleotide polymorphisms (SNPs) reside in regions with differences in the propensity for local DNA methylation between the two alleles. We further showed that for the most common form of SNP, a polymorphism at a CpG dinucleotide, the presence of the CpG at the SNP positively affected local DNA methylation in cis. Conclusions: Taken together with the known effect of DNA methylation on mutation rate, our results suggest an interesting interdependence between genetics and epigenetics underlying diversity in the human genome

Use of partial least squares regression to impute SNP genotypes in Italian Cattle breeds

Background The objective of the present study was to test the ability of the partial least squares regression technique to impute genotypes from low density single nucleotide polymorphisms (SNP) panels i.e. 3K or 7K to a high density panel with 50K SNP. No pedigree information was used. Methods Data consisted of 2093 Holstein, 749 Brown Swiss and 479 Simmental bulls genotyped with the Illumina 50K Beadchip. First, a single-breed approach was applied by using only data from Holstein animals. Then, to enlarge the training population, data from the three breeds were combined and a multi-breed analysis was performed. Accuracies of genotypes imputed using the partial least squares regression method were compared with those obtained by using the Beagle software. The impact of genotype imputation on breeding value prediction was evaluated for milk yield, fat content and protein content. Results In the single-breed approach, the accuracy of imputation using partial least squares regression was around 90 and 94% for the 3K and 7K platforms, respectively; corresponding accuracies obtained with Beagle were around 85% and 90%. Moreover, computing time required by the partial least squares regression method was on average around 10 times lower than computing time required by Beagle. Using the partial least squares regression method in the multi-breed resulted in lower imputation accuracies than using single-breed data. The impact of the SNP-genotype imputation on the accuracy of direct genomic breeding values was small. The correlation between estimates of genetic merit obtained by using imputed versus actual genotypes was around 0.96 for the 7K chip. Conclusions Results of the present work suggested that the partial least squares regression imputation method could be useful to impute SNP genotypes when pedigree information is not available

Stereotactic body radiotherapy in the treatment of Pancreatic Adenocarcinoma in elderly patients

Background: Treatment of pancreatic adenocarcinoma in the elderly is often complicated by comorbidities that preclude surgery, chemotherapy and/or conventional external beam radiation therapy (EBRT). Stereotactic body radiotherapy (SBRT) has thus garnered interest in this setting.Methods: A retrospective review of 26 patients of age ≥ 80 with pancreatic adenocarcinoma treated with definitive SBRT+/-chemotherapy from 2007-2011 was performed. Twenty-seven percent of patients were stage I, 38% were stage II, 27% were stage III and 8% were stage IV. Patients most commonly received 24 Gy/1 fraction or 30-36 Gy/3 fractions. Kaplan-Meier was used to estimate overall survival (OS), local control (LC), cause specific survival (CSS) and freedom-from-metastatic disease (FFMD).Results: The median age was 86 (range 80-91), and median follow-up was 11.6 months (3.5-24.6). The median planning target volume was 21.48 cm3 (6.1-85.09). Median OS was 7.6 months with 6/12 month OS rates of 65.4%/34.6%, respectively. Median LC was 11.5 months, 6-month and 12-month actuarial LC rates were 60.1% and 41.2%, respectively. There were no independent predictors for LC, but there was a trend for improved LC with prescription dose greater than 20 Gy (p = 0.063). Median CSS was 6.3 months, and 6-month and 12-month actuarial CSS were 53.8% and 23.1%, respectively. Median FFMD was 8.4 months, and 6-month and 12-month actuarial rates were 62.0% and 41.4%, respectively. Nine patients (47%) had local failures, 11 (58%) had distant metastasis, and 7 (37%) had both. There were no acute or late grade 3+ toxicities.Conclusions: Definitive SBRT is feasible, safe and effective in elderly patients who have unresectable disease, have comorbidities precluding surgery or decline surgery. © 2013 Kim et al.; licensee BioMed Central Ltd

Genomic-Bioinformatic Analysis of Transcripts Enriched in the Third-Stage Larva of the Parasitic Nematode Ascaris suum

Differential transcription in Ascaris suum was investigated using a genomic-bioinformatic approach. A cDNA archive enriched for molecules in the infective third-stage larva (L3) of A. suum was constructed by suppressive-subtractive hybridization (SSH), and a subset of cDNAs from 3075 clones subjected to microarray analysis using cDNA probes derived from RNA from different developmental stages of A. suum. The cDNAs (n = 498) shown by microarray analysis to be enriched in the L3 were sequenced and subjected to bioinformatic analyses using a semi-automated pipeline (ESTExplorer). Using gene ontology (GO), 235 of these molecules were assigned to ‘biological process’ (n = 68), ‘cellular component’ (n = 50), or ‘molecular function’ (n = 117). Of the 91 clusters assembled, 56 molecules (61.5%) had homologues/orthologues in the free-living nematodes Caenorhabditis elegans and C. briggsae and/or other organisms, whereas 35 (38.5%) had no significant similarity to any sequences available in current gene databases. Transcripts encoding protein kinases, protein phosphatases (and their precursors), and enolases were abundantly represented in the L3 of A. suum, as were molecules involved in cellular processes, such as ubiquitination and proteasome function, gene transcription, protein–protein interactions, and function. In silico analyses inferred the C. elegans orthologues/homologues (n = 50) to be involved in apoptosis and insulin signaling (2%), ATP synthesis (2%), carbon metabolism (6%), fatty acid biosynthesis (2%), gap junction (2%), glucose metabolism (6%), or porphyrin metabolism (2%), although 34 (68%) of them could not be mapped to a specific metabolic pathway. Small numbers of these 50 molecules were predicted to be secreted (10%), anchored (2%), and/or transmembrane (12%) proteins. Functionally, 17 (34%) of them were predicted to be associated with (non-wild-type) RNAi phenotypes in C. elegans, the majority being embryonic lethality (Emb) (13 types; 58.8%), larval arrest (Lva) (23.5%) and larval lethality (Lvl) (47%). A genetic interaction network was predicted for these 17 C. elegans orthologues, revealing highly significant interactions for nine molecules associated with embryonic and larval development (66.9%), information storage and processing (5.1%), cellular processing and signaling (15.2%), metabolism (6.1%), and unknown function (6.7%). The potential roles of these molecules in development are discussed in relation to the known roles of their homologues/orthologues in C. elegans and some other nematodes. The results of the present study provide a basis for future functional genomic studies to elucidate molecular aspects governing larval developmental processes in A. suum and/or the transition to parasitism

Acyl Homoserine Lactones from Culture Supernatants of Pseudomonas aeruginosa Accelerate Host Immunomodulation

The virulence of Pseudomonas aeruginosa is multifactorial and under the control of quorum sensing signals, such as acyl homoserine lactones (AHLs). The importance of these molecules in the establishment of infection has been previously reported. These molecules either improve the virulence potential of P. aeruginosa or modulate the host immune response. To establish the immune modulating potential of quorum sensing signal molecules, previous studies have only used synthetic AHLs. However, there can be differences in the biological properties of synthetic and natural AHLs. The use of naturally extracted AHLs from the culture supernatant of P. aeruginosa is likely to simulate natural conditions more than the use of synthetic AHLs. Therefore, in the present study, the immune modulating potential of synthetic and naturally extracted AHLs was compared using a thymidine uptake assay, immunophenotyping and sandwich ELISA in order to assess mouse T-cell proliferation and production of Th1 and Th2 cytokines. Natural AHLs were able to suppress T-cell proliferation, even at low concentrations, compared to synthetic AHLs. The majority of cells undergoing proliferation were CD4+, as revealed by immunophenotyping. The inhibition of T-cells was stronger with natural AHLs compared to synthetic AHLs. Moreover, the natural AHLs were also able to shift immune responses away from host protective Th1 responses to pathogen protective Th2 responses

The role of chaotic resonances in the solar system

Our understanding of the Solar System has been revolutionized over the past decade by the finding that the orbits of the planets are inherently chaotic. In extreme cases, chaotic motions can change the relative positions of the planets around stars, and even eject a planet from a system. Moreover, the spin axis of a planet-Earth's spin axis regulates our seasons-may evolve chaotically, with adverse effects on the climates of otherwise biologically interesting planets. Some of the recently discovered extrasolar planetary systems contain multiple planets, and it is likely that some of these are chaotic as well.Comment: 28 pages, 9 figure