Water Quality of Stoney Creek and its Effects on Salmon Spawning

Runoff water in urban streams possesses a major threat in salmon spawning. This has been the effect on Burnaby BC\u27s, Stoney Creek. Sample water was retrieved at four sites, with two along Stoney Creek (sites 1 and 4) and two tributaries further upstream (sites 2 and 3). To begin our research we had formulated the hypothesis that tributaries would have lower dissolved oxygen content due to no remediation efforts being applied and downstream sample sites would have higher levels of pollutants due to road runoff accumulation. Multiple means in determining water quality of Stoney Creek were employed; in-stream water quality tests for dissolved oxygen (DO), pH, and temperature were determined using a DO, and pocket pH meter. Water samples were also obtained from each site and were further analyzed for phosphorous, ammonium and chemical oxygen demand levels (COD) using the Hach DR5000 spectrophotometer. Our last means of water quality testing was through the Water Quality TestKit on samples brought from site 1 and 3. In-stream testing resulted in pH levels ranging between 6.4 and 6.7, dissolved oxygen contents of 10.60mg/L and greater, and temperatures of 9.2°C and below. Accordingly, levels in pH, DO and temperature measured are all suitable for salmon spawning. Samples further tested in the lab showed higher ammonium, and phosphate levels that can effect spawning negatively. Lastly the Water Quality TestKit did not demonstrate very good accuracy, and was ruled to be unreliable. Our results indicate that Stoney Creek\u27s conditions are favorable for salmon spawning, and that there is a strong correlation between temperature, pH and dissolved oxygen

Exploration of cloud computing late start LDRD #149630 : Raincoat. v. 2.1.

This report contains documentation from an interoperability study conducted under the Late Start LDRD 149630, Exploration of Cloud Computing. A small late-start LDRD from last year resulted in a study (Raincoat) on using Virtual Private Networks (VPNs) to enhance security in a hybrid cloud environment. Raincoat initially explored the use of OpenVPN on IPv4 and demonstrates that it is possible to secure the communication channel between two small 'test' clouds (a few nodes each) at New Mexico Tech and Sandia. We extended the Raincoat study to add IPSec support via Vyatta routers, to interface with a public cloud (Amazon Elastic Compute Cloud (EC2)), and to be significantly more scalable than the previous iteration. The study contributed to our understanding of interoperability in a hybrid cloud

A 7-year review of clinical characteristics, predisposing factors and outcomes of post-keratoplasty infectious keratitis: the Nottingham infectious keratitis study

Background/objectives: Post-keratoplasty infectious keratitis (PKIK) is a unique sight-threatening clinical entity which often poses significant therapeutic challenges. This study aimed to examine the clinical presentation, risk factors, management, and clinical outcomes of PKIK. Methods: This was a retrospective study of all patients who presented to the Queen’s Medical Centre, Nottingham, with PKIK between September 2015 and August 2022 (a 7-year period). Relevant data on types of keratoplasty, clinical presentations, causative microorganisms, management, and outcome were analyzed. Results: Forty-nine PKIK cases, including four cases of interface infectious keratitis, were identified during the study period. The most common graft indications for PKP, DALK and EK were failed grafts (9, 37.5%), keratoconus (6, 54.5%) and Fuchs endothelial corneal dystrophy (FECD; 8, 57.1%), respectively. Staphylococcus spp. were the most commonly identified organisms (15, 50.0%). Bullous keratopathy (18, 36.7%), ocular surface disease (18, 36.7%), and broken/loose sutures (15, 30.6%) were the most common risk factors. Concurrent use of topical steroids was identified in 25 (51.0%) cases. Of 31 functioning grafts at presentation, 12 (38.7%) grafts failed at final follow-up with 15 (48.4%) patients retaining a CDVA of ≥1.0 logMAR. The overall estimated 5-year survival rate post-PKIK was 55.9% (95% CI, 35.9%-75.9%), with DALK having the highest survival rate [63.6% (95% CI, 28.9%-98.3%)], followed by EK [57.1% (95% CI, 20.4%-93.8%)] and PKP [52.7% (95% CI, 25.1%-80.3%)], though no statistical difference was observed (p=0.48). Conclusions: PKIK represents an important cause of IK and graft failure. Bullous keratopathy, OSD and suture-related complications are the commonest risk factors, highlighting the potential benefit of prophylactic topical antibiotics (for unhealthy ocular surface) and early suture removal (where possible) in reducing the risk of PKIK. Graft survival may be higher in lamellar keratoplasty following PKIK but larger studies are required to elucidate this observation

Rethinking physical activity communication: using focus groups to understand women’s goals, values, and beliefs to improve public health

Abstract Background Communication about physical activity (PA) frames PA and influences what it means to people, including the role it plays in their lives. To the extent that PA messages can be designed to reflect outcomes that are relevant to what people most value experiencing and achieving in their daily lives, the more compelling and effective they will be. Aligned with self-determination theory, this study investigated proximal goals and values that are salient in everyday life and how they could be leveraged through new messaging to better support PA participation among women. The present study was designed to examine the nature of women’s daily goals and priorities and investigate women’s PA beliefs, feelings, and experiences, in order to identify how PA may compete with or facilitate women’s daily goals and priorities. Preliminary recommendations are proposed for designing new PA messages that align PA with women’s daily goals and desired experiences to better motivate participation. Methods Eight focus groups were conducted with White, Black, and Hispanic/Latina women aged 22–49, stratified by amount of self-reported PA (29 low active participants, 11 high active participants). Respondents discussed their goals, values, and daily priorities along with beliefs, feelings about and experiences being physically active. Data were collected, coded, and analyzed using a thematic analysis strategy to identify emergent themes. Results Many of the goals and values that both low and high active participants discussed as desiring and valuing map on to key principles of self-determination theory. However, the discussions among low active participants suggested that their beliefs, feelings, experiences, and definitions of PA were in conflict with their proximal goals, values, and priorities, also undermining their psychological needs for autonomy, competence, and relatedness. Conclusions Findings from this study can be used to inform and evaluate new physical activity communication strategies that leverage more proximal goals, values, and experiences of happiness and success to better motivate PA among ethnically diverse low active women. Specifically, this research suggests a need to address how women’s daily goals and desired experiences may undermine PA participation, in addition to framing PA as facilitating rather than competing with their daily priorities and desired leisure-time experiences.https://deepblue.lib.umich.edu/bitstream/2027.42/136775/1/12889_2017_Article_4361.pd

A method to improve protein subcellular localization prediction by integrating various biological data sources

<p>Abstract</p> <p>Background</p> <p>Protein subcellular localization is crucial information to elucidate protein functions. Owing to the need for large-scale genome analysis, computational method for efficiently predicting protein subcellular localization is highly required. Although many previous works have been done for this task, the problem is still challenging due to several reasons: the number of subcellular locations in practice is large; distribution of protein in locations is imbalanced, that is the number of protein in each location remarkably different; and there are many proteins located in multiple locations. Thus it is necessary to explore new features and appropriate classification methods to improve the prediction performance.</p> <p>Results</p> <p>In this paper we propose a new predicting method which combines two key ideas: 1) Information of neighbour proteins in a probabilistic gene network is integrated to enrich the prediction features. 2) Fuzzy k-NN, a classification method based on fuzzy set theory is applied to predict protein locating in multiple sites. Experiment was conducted on a dataset consisting of 22 locations from Budding yeast proteins and significant improvement was observed.</p> <p>Conclusion</p> <p>Our results suggest that the neighbourhood information from functional gene networks is predictive to subcellular localization. The proposed method thus can be integrated and complementary to other available prediction methods.</p

Detecting and removing sample contamination in phylogenomic data: an example and its implications for Cicadidae phylogeny (Insecta Hemiptera).

Contamination of a genetic sample with DNA from one or more nontarget species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and next-generation sequencing studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on the detection of bimodal distributions of patristic distances across gene trees. When contamination occurs between samples within a data set, a comparison between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a data set generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN