A Bayesian Hierarchical Model to Derive Novel Gene Networks from Gene Ontology Fingerprints

We developed a Bayesian hierarchical model to identify gene networks based on the similarity score generated from comparing the gene ontology fingerprints of gene pairs. Genes in this network were assumed to have similar biological functions that can be indicated by their ontology fingerprints. Our results indicate that different pathways show consistent score threshold that allow us to distinguish biological relevant gene—gene connections in the network

Ultraviolet LED Biofouling Mitigation

The goal is to determine if low-cost UV LEDs can mitigate marine biofouling on small glass or acrylic camera lenses. A microprocessor-controlled experimental setup to control the illumination of low-cost UV LEDs of various wavelength and packaging was fashioned. The system consists of a programmed microcontroller, a manufactured LED breakout interface, and a submergible UV LED array enclosed in a borosilicate glass tube. A preliminary qualitative assessment of four different UV LEDs was conducted during a three-week deployment of the experimental setup in the raw seawater system at the Cal Poly Center for Costal and Marine Sciences in Avila Beach, California. Although some evidence from testing suggests that UV LEDS can mitigate biofouling, a longer qualitative test and an additional quantitative test would have to be conducted for conclusive findings

Co-design for not-for-profit urganization

Co-design has potential to help community-based organizations deliver better services to their beneficiaries, since it encourages users to get involved in designing services that will be delivered to them. Good use of co-design could bring several benefits, e.g. ensuring that services match users’ needs. However, the extent of co-design knowledge among community-based organizations is currently unknown. Hence, this study aimed at investigating their current state of co-design knowledge in order to develop guidance to help them effectively co-design services with their beneficiaries. This project employed a mix-method approach including a survey, interviews, case studies, and a creative workshop. This paper will discuss results of case studies conducted with five organizations, which involved observations and interviews with key staff and users. The results revealed that the level of understanding of co-design among community-based organizations varied greatly. While most organizations have the right mindset for adopting co-design, since they are keen to listen to users’ ideas, only the minority actually involves users in designing services. The lack of awareness may be the main reason of the slow adoption of codesign. Thus, it is important to help them understand the value of co-design and how it can be used to suit their needs.</p

Cardiopulmonary exercise testing for predicting early outcomes after major cancer resection: A systematic review

Background: Postoperative complications after major surgery are thought to be associated with reduced fitness. Surgical cancer patients are often malnourished, cachexic and subject to neoadjuvant chemotherapy resulting in low preoperative fitness levels. This review examined the associations between aerobic fitness, as determined objectively by preoperative cardiopulmonary exercise testing (CPEX), and short-term morbidity after cancer surgery. Methods: A literature search using databases of PubMed, Medline, Embase, Cumulative Index to Nursing and Allied Health Literature (CINAHL) and the Cochrane Library for studies that examined associations between preoperative CPEX variables and postoperative complications following surgery for the ten commonest cancers. Results: A total of 21 observational studies were identified with 4957 patients that underwent CPEX testing prior to lung, colorectal, liver, oesophagogastric, bladder and pancreas resections. The median sample size was 105 patients (range 64 - 1684). No studies were found for breast or brain cancers or lymphoma. In lung cancer patients undergoing thoracotomy, a VO2peak ≤ 15ml/kg/min was associated with an increased risk of respiratory complications and death. None of the studies in other cancer types had adequate sample sizes to report on mortality. CPEX testing had mostly poor to average discriminatory accuracy to predict postoperative morbidity in other cancer resection surgeries. Findings across studies were inconsistent, and detection and selective reporting biases were likely to be significant. Conclusion: The utility of CPEX testing prior to cancer surgery is questionable and currently should not be used as a discriminatory tool, except in patients undergoing lung cancer resection by thoracotomy. Larger studies with more robust methodologies are currently required to determine the utility of CPEX

Does physical activity protect against the development of gastroesophageal reflux disease, Barrett’s oesophagus and oesophageal adenocarcinoma?:A review of the literature with a meta-analysis

Physical activity affects the functioning of the gastrointestinal system through both local and systemic effects and may play an important role in reducing the risk of esophageal adenocarcinoma. This review assesses the biological mechanisms and epidemiological evidence for the relationship between physical activity and the development of esophageal adenocarcinoma and its precursor diseases: gastroesophageal reflux disease (GORD) and Barrett's esophagus. A search of PubMed, Medline, Embase, and CINAHL was conducted from their inceptions to 25th March 2017 for analytical studies that examined associations between recreational and/or occupational levels of physical activity and the risk of GORD, Barrett's esophagus, and esophageal adenocarcinoma. Where appropriate, a meta-analysis of effects was undertaken. Seven studies were included (2 cohort, 5 case control). For GORD, there were three case-control studies with 10 200 cases among 78 034 participants, with a pooled estimated OR of 0.67 (95% CI 0.57–0.78) for high versus low levels of recreational physical activity. In Barrett's esophagus, there was a single case-control study, which reported no association, OR 1.19 (95% CI 0.82–1.73). For esophageal adenocarcinoma, there were three studies (two prospective cohort, one case control) with 666 cases among 910 376 participants. The largest cohort study reported an inverse association for high versus low levels of recreational physical activity, RR 0.68, 95% CI 0.48–0.96. The remaining two studies reported no associations with either occupational or combined recreational and occupational activity. Heterogeneity in the measurement of exposure (recreational, occupational, and both) made a pooled estimate for esophageal adenocarcinoma inappropriate. Although limited, there is some evidence that higher levels of recreational physical activity may reduce the risk of both GORD and esophageal adenocarcinoma, but further large cohort studies examining the type, intensity and duration of activities that may be beneficial are needed

Black lives matter: On the denial of systemic racism, White liberals, and polite racism

Systemic discrimination, racism, and inequality have garnered renewed and intense attention following the George Floyd murder and demonstrations of Black Lives Matter (BLM) around the world. In sharing our anger and sorrow, we reached out to several colleagues and scholars in the Black community. We wanted to provide a forum [1] for them to express their grief, share their experiences and help us move forward. The response to our invitation to write was overwhelming, but also heartbreaking. Our colleagues were devastated and broken. They expressed immense difficulty in writing because of anger, despair, and sadness. Stella Nkomo (personal correspondence) asked if “the burst of recognition of systemic racism for real this time?” It is our hope that their collective voices, captured in this collection of essays, will help us find a way forward as academics, researchers, and mentors. We need to refocus our efforts to combat anti-Black racism, dismantle systemic discrimination, restore racial justice, and enable Blacks and other racially oppressed groups to fully participate in society and life

Parallel developmental genetic features underlie stickleback gill raker evolution.

BackgroundConvergent evolution, the repeated evolution of similar phenotypes in independent lineages, provides natural replicates to study mechanisms of evolution. Cases of convergent evolution might have the same underlying developmental and genetic bases, implying that some evolutionary trajectories might be predictable. In a classic example of convergent evolution, most freshwater populations of threespine stickleback fish have independently evolved a reduction of gill raker number to adapt to novel diets. Gill rakers are a segmentally reiterated set of dermal bones important for fish feeding. A previous large quantitative trait locus (QTL) mapping study using a marine × freshwater F2 cross identified QTL on chromosomes 4 and 20 with large effects on evolved gill raker reduction.ResultsBy examining skeletal morphology in adult and developing sticklebacks, we find heritable marine/freshwater differences in gill raker number and spacing that are specified early in development. Using the expression of the Ectodysplasin receptor (Edar) gene as a marker of raker primordia, we find that the differences are present before the budding of gill rakers occurs, suggesting an early change to a lateral inhibition process controlling raker primordia spacing. Through linkage mapping in F2 fish from crosses with three independently derived freshwater populations, we find in all three crosses QTL overlapping both previously identified QTL on chromosomes 4 and 20 that control raker number. These two QTL affect the early spacing of gill raker buds.ConclusionsCollectively, these data demonstrate that parallel developmental genetic features underlie the convergent evolution of gill raker reduction in freshwater sticklebacks, suggesting that even highly polygenic adaptive traits can have a predictable developmental genetic basis

LDL receptor-related protein-1 regulates NFκB and microRNA-155 in macrophages to control the inflammatory response

LDL receptor-related protein-1 (LRP1) is an endocytic and cell-signaling receptor. In mice in which LRP1 is deleted in myeloid cells, the response to lipopolysaccharide (LPS) was greatly exacerbated. LRP1 deletion in macrophages in vitro, under the control of tamoxifen-activated Cre-ER(T) fusion protein, robustly increased expression of proinflammatory cytokines and chemokines. In LRP1-expressing macrophages, proinflammatory mediator expression was regulated by LRP1 ligands in a ligand-specific manner. The LRP1 agonists, α2-macroglobulin and tissue-type plasminogen activator, attenuated expression of inflammatory mediators, even in the presence of LPS. The antagonists, receptor-associated protein (RAP) and lactoferrin (LF), and LRP1-specific antibody had the entirely opposite effect, promoting inflammatory mediator expression and mimicking LRP1 deletion. NFκB was rapidly activated in response to RAP and LF and responsible for the initial increase in expression of proinflammatory mediators. RAP and LF also significantly increased expression of microRNA-155 (miR-155) after a lag phase of about 4 h. miR-155 expression reflected, at least in part, activation of secondary cell-signaling pathways downstream of TNFα. Although miR-155 was not involved in the initial induction of cytokine expression in response to LRP1 antagonists, miR-155 was essential for sustaining the proinflammatory response. We conclude that LRP1, NFκB, and miR-155 function as members of a previously unidentified system that has the potential to inhibit or sustain inflammation, depending on the continuum of LRP1 ligands present in the macrophage microenvironment