Faculty Bibliography

Many important model organisms for biomedical and evolutionary research have sequenced genomes, but occupy a phylogenetically isolated position, evolutionarily distant from other sequenced genomes. This phylogenetic isolation is exemplified for zebrafish, a vertebrate model for cis-regulation, development and human disease, whose evolutionary distance to all other currently sequenced fish exceeds the distance between human and chicken. Such large distances make it difficult to align genomes and use them for comparative analysis beyond gene-focused questions. In particular, detecting conserved non-genic elements (CNEs) as promising cis-regulatory elements with biological importance is challenging. Here, we develop a general comparative genomics framework to align isolated genomes and to comprehensively detect CNEs. Our approach integrates highly sensitive and quality-controlled local alignments and uses alignment transitivity and ancestral reconstruction to bridge large evolutionary distances. We apply our framework to zebrafish and demonstrate substantially improved CNE detection and quality compared with previous sets. Our zebrafish CNE set comprises 54 533 CNEs, of which 11 792 (22%) are conserved to human or mouse. Our zebrafish CNEs (http://zebrafish.stanford.edu) are highly enriched in known enhancers and extend existing experimental (ChIP-Seq) sets. The same framework can now be applied to the isolated genomes of frog, amphioxus, Caenorhabditis elegans and many others.

BACKGROUND:Immediate-use steam sterilization (IUSS) is a safe method to sterilize emergently contaminated instruments, but inappropriate use may lead to an increased risk for surgical site infection. This study aimed to identify risk factors, rationale, and variability in procedural adherence in cases of IUSS. METHODS:This retrospective, case-control study compared adult patients undergoing hip and knee arthroplasty in which IUSS was (n = 104) and was not (n = 81) performed. RESULTS:Multivariate analysis revealed 4 predictive risk factors for IUSS: history of malignancy (odds ratio [OR], 3.2 [95% confidence interval (CI) 1.1-9.3]), obesity (OR, 2.3 [95% CI: 1.02-5.2]), procedure performed in operating room 13 (OR, 2.5 [95% CI: 1.2-5.4]), and Monday procedure (OR, 3.6 [95% CI: 1.4-9.1]). The only factor that protected against IUSS was performing the procedure in the morning (OR, 0.4 [95% CI: 0.2-0.96]). Only 9.5% of cases of IUSS involved an acceptable indication. Documented adherence to core practices was also variable. CONCLUSION/CONCLUSIONS:Several patient- and case-specific factors can help predict the incidence of IUSS. Furthermore, practices should be hardwired to ensure IUSS is utilized for the correct indication. Documentation must be improved to allow institutions to accurately track IUSS.

BACKGROUND:Two evidence-based therapies exist for the treatment of high-risk prostate cancer (PCA): external-beam radiotherapy (RT) with hormone therapy (H) (RT + H) and radical prostatectomy (S) with adjuvant radiotherapy (S + RT). Each of these strategies is associated with different rates of local control, distant metastasis (DM), and toxicity. By using decision analysis, the authors of this report compared the quality-adjusted life expectancy (QALE) between men with high-risk PCA who received RT + H versus S + RT versus a hypothetical trimodality therapy (S + RT + H). METHODS:The authors developed a Markov model to describe lifetime health states after treatment for high-risk PCA. Probabilities and utilities were extrapolated from the literature. Toxicities after radiotherapy were based on intensity-modulated radiotherapy series, and patients were exposed to risks of diabetes, cardiovascular disease, and fracture for 5 years after completing H. Deterministic and probabilistic sensitivity analyses were performed to model uncertainty in outcome rates, toxicities, and utilities. RESULTS:RT + H resulted in a higher QALE compared with S + RT over a wide range of assumptions, nearly always resulting in an increase of >1 quality-adjusted life year with outcomes highly sensitive to the risk of increased all-cause mortality from H. S + RT + H typically was superior to RT + H, albeit by small margins (<0.5 quality-adjusted life year), with results sensitive to assumptions about toxicity and radiotherapy efficacy. CONCLUSIONS:For men with high-risk PCA, RT + H was superior to S + RT, and the result was sensitive to the risk of all-cause mortality from H. Moreover, trimodality therapy may offer local and distant control benefits that lead to optimal outcomes in a meaningful population of men.

BACKGROUND:Presumptive treatment for malaria is common in resource-limited settings, yet controversial given the imprecision of clinical diagnosis. The researchers compared costs of diagnosis and drugs for two strategies: (1) empirical treatment of malaria via clinical diagnosis; and (2) empirical diagnosis followed by treatment only with Giemsa smear confirmation. METHODS:Patients with a diagnosis of clinical malaria were recruited from a mission/university teaching hospital in southwestern Nigeria. The patients underwent free Giemsa thick (diagnosis) and thin (differentiation) smears, but paid for all anti-malarial drugs. Clinical diagnosis was made on clinicians' judgments based on symptoms, including fever, diarrhoea, headache, and body aches. The paediatric regimen was artesunate (6-9 tablets of 3 mg/kg on day one and 1.5 mg/kg for the next four days) plus amodiaquine (10 mg/kg day 1-2 and 5 mg/kg on day three in suspension). Adults were given two treatment options: option one (four and one-half 50 mg artesunate tablets on day one and nine tablets for the next four days, plus three 500 mg sulphadoxine/25 mg pyrimethamine tablets) and option two (same artesunate regimen plus nine 200 mg tablets of amodiaquine at 10 mg/kg day 1-2 and 5 mg/kg on day three). The researchers calculated the costs of smears/drugs from standard hospital charges. RESULTS:Doctors diagnosed 304 patients (170 adults ages >16 years and 134 pediatric) with clinical malaria, prescribing antimalarial drugs to all. Giemsa thick smears were positive in 115/304 (38%). The typical patient cost for a Giemsa smear was 550 Naira (US$3.74 in 2009). For children, the cost of testing all, but treating only Giemsa positives was N888 ($6.04)/child; the cost of empiric treatment of all who were clinically diagnosed was lower, N660 ($4.49)/child. For adults, the cost of testing all, but treating only Giemsa positives was N711 ($4.84)/adult for treatment option one (artesunate and sulphadoxine/pyrimethamine) and N730 ($4.97)/adult for option two (artesunate and amodiaquine). This contrasts to lower costs of empiric treatment for both options one (N610 = $4.14/adult) and two (N680=$4.63/adult). CONCLUSIONS:Empiric treatment of all suspected cases of malaria was cheaper (at the end of the dry to the beginning of the rainy season) than only treating those who had microscopy-confirmed diagnoses of malaria, even though the majority of patients suspected to have malaria were negative via microscopy. One can acknowledge that giving many malaria-uninfected Nigerians anti-malarial drugs is undesirable for both their personal health and fears of drug resistance with overuse. Therefore, funding of rapid diagnostic tests whose performance exceeds the Giemsa smear is needed to achieve an ideal of diagnostic confirmation before treatment.

BACKGROUND:This study is a randomized controlled trial comparing skin closure time between coaptive film and subcuticular monocryl sutures in children undergoing identical single session, bilateral limb multiple soft tissue releases. METHODS:Eight children less than 18 years of age (mean 14.5) with cerebral palsy underwent identical, single session bilateral multiple soft tissue releases in the lower limb from August 2005 to March 2007. There were 50 incisions in all in which 25 incisions were closed with 4-0 intracuticular monocryl sutures and 25 were closed with coaptive film (Steri Strip S; 3M company). Time taken for closure using either technique was recorded. A blinded plastic surgeon used a visual analog scale to assess the cosmetic results at the end of a 3 month follow-up. RESULTS:The average length of incisions closed with coaptive film was almost identical to the corresponding incision on the contralateral limb that was closed with subcuticular monocryl suture (4.45 and 4.81 cm, P=0.66). The average time for skin closure using monocryl sutures was 167.04 seconds compared with the average time of 79.36 seconds when using coaptive film (P <0.0001). There was no significant difference in the cosmetic results or the number of wound complications using either technique. CONCLUSION/CONCLUSIONS:Coaptive film is an attractive and cost-effective option for skin closure after pediatric surgery. CLINICAL RELEVANCE/CONCLUSIONS:The time saved, comparable cosmetic results and lack of complications makes coaptive film an attractive option for skin closure in the pediatric age group.

Following facial nerve resection in the mouse, a substantial number of neurons reside in an atrophied state (characterized by cell shrinkage and decreased ability to uptake Nissl stain), which can be reversed by re-injury. The mechanisms mediating the reversal of neuronal atrophy remain unclear. Although T cells have been shown to prevent neuronal loss following peripheral nerve injury, it was unknown whether T cells play a role in mediating the reversal of axotomy-induced neuronal atrophy. Thus, we used a facial nerve re-injury model to test the hypothesis that the reversal of neuronal atrophy would be impaired in recombinase activating gene-2 knockout (RAG-2 KO) mice, which lack functional T and B cells. Measures of neuronal survival were compared in the injured facial motor nucleus (FMN) of RAG-2 KO and wild-type (WT) mice that received a resection of the right facial nerve followed by re-injury of the same nerve 10 weeks later ("chronic resection+re-injury") or a resection of the right facial nerve followed by sham re-injury of the same nerve 10 weeks later ("chronic resection+sham"). We recently demonstrated that prior exposure to neuronal injury elicited a marked increase in T cell trafficking indicative of a T cell memory response when the contralateral FMN was injured later in adulthood. We examined if such a T cell memory response would also occur in the current re-injury model. RAG-2 KO mice showed no reversal of neuronal atrophy whereas WT mice showed a robust response. The reversal of atrophy in WT mice was not accompanied by a T cell memory response. Although the number of CD4(+) and CD8(+) T cells in the injured FMN did not differ from each other, double-negative T cells appear to be recruited in response to neuronal injury. Re-injury did not result in increased expression of MHC2 by microglia. Our findings suggest that T cells may be involved in reversing the axotomy-induced atrophy of injured neurons.