Search

The use of topical vancomycin in the reduction of sternal wound infection (SWI) risk has become a point of contention. The earlier literature consists of observational studies and 1 unblinded trial. Hence, the objective of this study was to assess whether vancomycin reduces the incidence of SWI in a double-blind randomized controlled trial.Patients were randomized 1:1 to either vancomycin-soaked (vancomycin) or saline-soaked (control) sponges. The sponges were applied once the sternum was opened and were removed just before sternal closure. Patients were followed up at 3 months and at 1 year postoperatively to determine the incidence of SWI in each group. Results were analyzed according to the modified intention-to-treat principle.This study assessed 1038 patients for eligibility and enrolled 1037 patients. There were 517 patients randomized to the vancomycin group and 520 patients randomized to the control group. Analysis was performed on 1021 patients. At 3 months postoperatively, there was no significant difference in the incidence of SWI between the vancomycin and control groups (2.7% vs 4.1%; P = .23). There was also no significant difference between the vancomycin and control groups in the risk of superficial, deep, and organ-space infections. Similar findings were observed 1 year postoperatively. The most common organism isolated was coagulase-negative Staphylococcus.The use of vancomycin applied to the sternum during cardiac surgery does not reduce the incidence of SWI.

The appropriate use of narcotics for postoperative pain control is controversial because of potential medication-induced complications. The authors sought to determine the effects of narcotics in the pediatric population following cranial vault remodeling operations.A retrospective review was performed on 160 consecutive patients who underwent cranial vault remodeling for craniosynostosis.There was a statistically significant difference in total morphine equivalents in the group that experienced no emesis and those with at least one episode of emesis (0.97 morphine equivalents/kg versus 1.44 morphine equivalents/kg; p = 0.05). There was a statistically significant difference in hospital morphine equivalents in the group with documented respiratory events (average, 2.3 morphine equivalents/kg versus 1.3 morphine equivalents/kg in the nonevent group; p = 0.006). The patients who received dexmedetomidine had a trend toward a decrease in hospital narcotic administration with equivalent pain control (1.2 morphine equivalents/kg versus 1.9 morphine equivalents/kg; p = 0.09). There was a statistically significant positive correlation between total morphine equivalents for the hospitalization and hospital stay ( r = 0.27, p = 0.001). The amount of morphine equivalents used in the first 24 hours was also found to be an independent predictor of a respiratory event ( p = 0.002 by multivariate logistic regression). Independent positive predictors of hospital stay were age ( p0.001), intensive care unit time ( p0.001), and total morphine equivalents for the hospitalization ( p = 0.001) by multivariate analysis with linear regression.The authors' study demonstrates improvement in outcomes with decreased use of narcotics, which establishes that there is a need to further explore postsurgical recovery outcomes with multimodal pain control.Therapeutic, III.

Climate change will likely intensify hurricane activity in coastal regions. A thorough understanding of hurricane impacts to marine fauna is necessary to prepare for and mitigate potential impacts to social systems dependent upon adjacent fauna. Yet, research attention, conservation funding, and policy all can be biased toward taxa of societal interest, potentially favoring a limited understanding of hurricane impacts. Here, we analyzed the frequency of mentions of taxa in newspaper articles in relation to hurricane activity at three coastal US locations coupled with analysis of long-term fisheries-independent data. While economically important taxa dominate media discourse, we observed long-term hurricane-related abundance declines in ecologically important taxa having little direct human utility. We conclude that there is a potential for research and policy biases related to hurricane impacts. Preparation and mitigation efforts will benefit from researchers and managers making directed efforts to identify and incorporate hurricane sensitive taxa into their work.

Introduction: Early treatment for hypertension (HTN) portends better outcomes. However, few real-world studies have assessed initial antiHTN regimens and how they differ by baseline blood pressure (BP). We sought to compare initial treatment patterns, stratified by BP, between Medicaid and Medicare recipients. Methods: We performed a cross-sectional study of adults with newly-treated HTN in the One Florida+ Consortium(2012-2020) who had linked claims-EHR data from the treatment initiation visit. Eligible patients were Floridians with Medicaid or Medicare aged ≥18 years, with diagnosed HTN, who filled ≥1 first-line antiHTN class with no evidence of anti HTN fills during the year prior (in which continuous insurance enrollment was required). Baseline BP was categorized per current HTN guidelines, and logistic regression was used to estimate age-adjusted odds of combination vs. monotherapy, per 10 mmHg increase in systolic BP (SBP) or diastolic BP (DBP). Results: We included 2,902 patients (47% Medicaid, 53% Medicare); mean age was 44 (Medicaid) and 67 yrs(Medicare); 60% (64% and 56%, respectively) were women and 42% (57% and 29%, respectively) were Black. Initial antiHTN classes were similar comparing cohorts: ACEI, ARB and thiazide initiation varied little by BP category, in contrast to CCBs and β-blockers (Figure, panels A-B). In age-adjusted analyses, use of initial combination therapy was 40% more likely (OR, 1.40; 95% CI, 1.11, 1.76) among Medicare recipients and inversely related to BP category (panels C-D) among Medicare patients, in which each 10mmHg greater SBP (OR, 0.93; 95% CI, 0.88, 0.97) and DBP (OR 0.82; 95% CI, 0.75, 0.90) had lower odds of combination therapy. Among Medicaid recipients, only SBP associated with combination therapy (OR1.11; 95% CI, 1.03, 1.20). Conclusions: We observed similar initial class patterns among Medicaid & Medicare recipients across baseline BP, but differential use of combination therapy was less likely at higher baseline BP in Medicare recipients, which contrasts current guidance.

Therapeutic aryl hydrocarbon receptor (AHR) modulating agents gained attention in dermatology as non-steroidal anti-inflammatory drugs that improve skin barrier properties. By exploiting AHR's known ligand promiscuity, we generated novel AHR modulating agents by lead optimization of a selective AHR modulator (SAhRM; SGA360). Twenty-two newly synthesized compounds were screened yielding two novel derivatives, SGA360f and SGA388, in which agonist activity led to enhanced keratinocyte terminal differentiation. SGA388 showed the highest agonist activity with potent normalization of keratinocyte hyperproliferation, restored expression of skin barrier proteins and dampening of chemokine expression by keratinocytes upon Th2-mediated inflammation in vitro. The topical application of SGA360f and SGA388 reduced acute skin inflammation in vivo by reducing cyclooxygenase levels, resulting in less neutrophilic dermal infiltrates. The minimal induction of cytochrome P450 enzyme activity, lack of cellular toxicity and mutagenicity classifies SGA360f and SGA388 as novel potential therapeutic AHR ligands and illustrates the potential of medicinal chemistry to fine-tune AHR signaling for the development of targeted therapies in dermatology and beyond.

The occurrence of induced earthquakes in crystalline rocks kilometres from deep wastewater injection wells poses questions about the influence nonconformity contacts have on the downward and lateral transmission of pore fluid pressure and poroelastic stresses. We hypothesize that structural and mineralogical heterogeneities at the sedimentary-crystalline rock nonconformity control the degree to which fluids, fluid pressure, and associated poroelastic stresses are transmitted over long distances across and along the nonconformity boundary. We examined the spatial distribution of physical and chemical heterogeneities in outcrops and whole-rock core samples of the great nonconformity in the midcontinent of the United States, capturing a range of tectonic settings and rock properties that we use to characterize the degree of historical fluid communication and the potential for future communication. We identify three end-member nonconformity types that represent a range of properties that will influence direct fluid pressure transmission and poroelastic responses far from the injection site. These nonconformity types vary depending on whether the contact is sharp and minimally altered, or if it is dominated by phyllosilicates or secondary non-phyllosilicate mineralization. We expect the rock properties associated with the presence or absence of secondary non-phyllosilicate mineralization and phyllosilicates to either allow or inhibit fractures to cross the nonconformity, thus impacting the permeability of the nonconformity zone. Our observations provide geologic constraints for modelling fluid migration and the associated pressure communication and poroelastic effects at large-scale disposal projects by providing relevant subsurface properties and much needed data regarding common alteration minerals that may interact readily with brines or reactive fluids.

Evaluating the impact of new teachers on student learning is a requirement for accredited teacher preparation programs. This article shares findings from a mixed methods, multiple case study investigating P-12 student learning in the classrooms of six graduates two-three years after completing a teacher preparation program. Data collection included student engagement surveys, de-identified student growth percentile scores, teacher selected pre-post assessment data, and structured phone interviews with each graduate. Results indicated a majority of students from participants’ classrooms demonstrated learning growth, and participants viewed their teaching as effective. Implications for programs include pre-service opportunities to identify and respond to authentic student engagement and opportunities to build collective teacher efficacy. Additional insights describe pre-service teacher training to measure student progress and measure impact based on classroom assessments. The investigation provides a replicable case study design for teacher educators to examine relationships between teacher preparation, program graduates, and P-12 student outcomes.

Proteins that oxidize extracellular substrates in Gram-positive bacteria are poorly understood. Ferrimicrobium acidiphilum is an actinobacterium that respires aerobically on extracellular ferrous ions at pH 1.5. In situ absorbance measurements were conducted on turbid suspensions of intact Fm. acidiphilum using an integrating cavity absorption meter designed for that purpose. Initial velocity kinetic studies monitored the appearance of product ferric ions in the presence of catalytic quantities of cells. Cell-catalyzed iron oxidation obeyed the Michaelis-Menten equation with Km and Vmax values of 71 μM and 0.29 fmol/min/cell, respectively. Limited-turnover kinetic studies were conducted with higher concentrations of cells to detect and monitor changes in the absorbance properties of cellular redox proteins when the cells were exposed to limited quantities of soluble reduced iron. A single a-type cytochrome with reduced absorbance peaks at 448 and 605 nm was the only redox-active chromophore that was visible as the cells respired aerobically on iron. The reduced cytochrome 605 exhibited mathematical and correlational properties that were consistent with the hypothesis that oxidation of the cytochrome constituted the rate-limiting step in the aerobic respiratory process, with a turnover number of 35 ± 2 s−1. Genomic and proteomic analyses showed that Fm. acidiphilum could and did express only two a-type heme copper terminal oxidases. Cytochrome 605 was associated with the terminal oxidase gene that is located between nucleotides 31,090 and 33,039, inclusive, in the annotated circular genome of this bacterium. IMPORTANCE The identities and functions of proteins involved in aerobic respiration on extracellular ferrous ions at acidic pH are poorly understood in the four phyla of Gram-positive eukaryotes and archaea where such activities occur. In situ absorbance measurements were conducted on Fm. acidiphilum as it respired on extracellular iron using an integrating cavity absorption meter that permitted accurate optical measurements in turbid suspensions of the intact bacterium under physiological conditions. The significance of these measurements is that they permitted a direct spectrophotometric examination of the extents and rates of biological electron transfer events in situ under noninvasive physiological conditions without disrupting the complexity of the live cellular environment. One thing is certain: one way to understand how a protein functions in an intact organism is to actually observe that protein as it functions in the intact organism. This paper provides an example of just such an observation.

Introduction The Allocation System Changes for Equity in Kidney Transplantation (ASCENT) trial was a cluster-randomized pragmatic, effectiveness-implementation study designed to test whether a multicomponent educational intervention targeting leadership, clinic staff, and patients in dialysis facilities improved knowledge and awareness of the 2014 Kidney Allocation System (KAS) change. Methods Participants included 690 dialysis facility medical directors, nephrologists, social workers, and other staff within 655 US dialysis facilities, with 51% (n = 334) in the intervention group and 49% (n = 321) in the control group. Intervention activities included a webinar targeting medical directors and facility staff, an approximately 10-minute educational video targeting dialysis staff, an approximately 10-minute educational video targeting patients, and a facility-specific audit and feedback report of transplant performance. The control group received a standard United Network for Organ Sharing brochure. Provider knowledge was a secondary outcome of the ASCENT trial and the primary outcome of this study; knowledge was assessed as a cumulative score on a 5-point Likert scale (higher score = greater knowledge). Intention-to-treat analysis was used. Results At baseline, nonintervention providers had a higher mean knowledge score (mean ± SD, 2.45 ± 1.43) than intervention providers (mean ± SD, 2.31 ± 1.46). After 3 months, the average knowledge score was slightly higher in the intervention (mean ± SD, 3.14 ± 1.28) versus nonintervention providers (mean ± SD, 3.07 ± 1.24), and the estimated mean difference in knowledge scores between the groups at follow-up minus the mean difference at baseline was 0.25 (95% confidence interval [CI], 0.11–0.48; P = 0.039). The effect size (0.41) was low to moderate. Conclusion Dialysis facility provider education could help extend the impact of a national policy change in organ allocation., Graphical abstract

Patient portals promote self-management, but require skills with electronic health information which can be measured by a patient's eHealth literacy. We aimed to describe eHealth literacy among a population of kidney transplant (KT) and liver transplant (LT) recipients and to investigate the relationship between eHealth literacy and Web-based patient portal utilization. We conducted phone surveys (August 2016-March 2017) among 178 KT and 110 LT recipients at two large transplant centers, including the eHealth Literacy Scale (eHEALS) and items assessing routine portal usage. Portal users were defined as routine if usage was every day, weekly, or monthly. The mean eHEALS score was 30.9 (SD: 5.4), and 45.4% routinely used the patient portal more than a few times per month. Routine users had higher eHealth literacy than non-routine users and non-users (31.97 vs. 29.97 vs. 28.20, p

This study compared teaching skill evaluations and professional disposition evaluations for candidates accepted and denied admission to an educator preparation program based upon GPA and testing requirements. The study sought to determine the relationship between academic and non-academic indicators and teaching skills. The data revealed academic indicators of GPA and test scores do not relate to teaching skills. A correlation was found between non-academic indicators, professional dispositions, and the teaching skills evaluation score. The results suggest professional dispositions may be a stronger indicator of success for admission to educator preparation programs and future licensure than GPA and test scores.

BACKGROUND AND OBJECTIVES: Barriers exist in access to kidney transplantation, where minority and patients with low socioeconomic status are less likely to complete transplant evaluation. The purpose of this study was to examine the effectiveness of a transplant center–based patient navigator in helping patients at high risk of dropping out of the transplant evaluation process access the kidney transplant waiting list. DESIGN, SETTING, PARTICIPANTS & MEASUREMENTS: We conducted a randomized, controlled trial of 401 patients (n=196 intervention and n=205 control) referred for kidney transplant evaluation (January 2013 to August 2014; followed through May 2016) at a single center. A trained navigator assisted intervention participants from referral to waitlisting decision to increase waitlisting (primary outcome) and decrease time from referral to waitlisting (secondary outcome). Time-dependent Cox proportional hazards models were used to determine differences in waitlisting between intervention and control patients. RESULTS: At study end, waitlisting was not significantly different among intervention (32%) versus control (26%) patients overall (P=0.17), and time from referral to waitlisting was 126 days longer for intervention patients. However, the effectiveness of the navigator varied from early (

It is unknown whether dialysis facility staff are aware of the new kidney allocation system implemented in December 2014, which changed how deceased donor kidneys are allocated and waiting time is calculated. U.S. dialysis facilities with low annual waitlisting (

The Ah receptor (AHR) has been shown to exhibit both inflammatory and anti-inflammatory activity in a context-specific manner. In vivo macrophage-driven acute inflammation models were utilized here to test whether the selective Ah receptor modulator 1-allyl-7-trifluoromethyl-1H-indazol-3-yl]-4-methoxyphenol (SGA360) would reduce inflammation. Exposure to SGA360 was capable of significantly inhibiting lipopolysaccharide (LPS)-mediated endotoxic shock in a mouse model, both in terms of lethality and attenuating inflammatory signaling in tissues. Topical exposure to SGA360 was also able to mitigate joint edema in a monosodium urate (MSU) crystal gout mouse model. Inhibition was dependent on the expression of the high-affinity allelic AHR variant in both acute inflammation models. Upon peritoneal MSU crystal exposure SGA360 pretreatment inhibited neutrophil and macrophage migration into the peritoneum. RNA-seq analysis revealed that SGA360 attenuated the expression of numerous inflammatory genes and genes known to be directly regulated by AHR in thioglycolate-elicited primary peritoneal macrophages treated with LPS. In addition, expression of the high-affinity allelic AHR variant in cultured macrophages was necessary for SGA360-mediated repression of inflammatory gene expression. Mechanistic studies revealed that SGA360 failed to induce nuclear translocation of the AHR and actually enhanced cytoplasmic localization. LPS treatment of macrophages enhanced the occupancy of the AHR and p65 to the Ptgs2 promoter, whereas SGA360 attenuated occupancy. AHR ligand activity was detected in peritoneal exudates isolated from MSU-treated mice, thus suggesting that the anti-inflammatory activity of SGA360 is mediated at least in part through AHR antagonism of endogenous agonist activity. These results underscore an important role of the AHR in participating in acute inflammatory signaling and warrants further investigations into possible clinical applications.

Introduction The United Network for Organ Sharing (UNOS) implemented a new Kidney Allocation System (KAS) in December 2014 that is expected to substantially reduce racial disparities in kidney transplantation among waitlisted patients. However, not all dialysis facility clinical providers and end-stage renal disease (ESRD) patients are aware of how the policy change could improve access to transplantation. Methods We describe the ASCENT (Allocation System Changes for Equity in Kidney Transplantation) study, a randomized, controlled effectiveness-implementation study designed to test the effectiveness of a multicomponent intervention to improve access to the early steps of kidney transplantation among dialysis facilities across the United States. The multicomponent intervention consists of an educational webinar for dialysis medical directors, an educational video for patients and an educational video for dialysis staff, and a dialysis facility−specific transplantation performance feedback report. Materials will be developed by a multidisciplinary dissemination advisory board and will undergo formative testing in dialysis facilities across the United States. Results This study is estimated to enroll ∼600 US dialysis facilities with low waitlisting in all 18 ESRD networks. The co-primary outcomes include change in waitlisting and waitlist disparity at 1 year; secondary outcomes include changes in facility medical director knowledge about KAS, staff training regarding KAS, patient education regarding transplantation, and the intent of the medical director to refer patients for transplantation evaluation. Discussion The results from the ASCENT study will demonstrate the feasibility and effectiveness of a multicomponent intervention designed to increase access to the deceased donor kidney waitlist and to reduce racial disparities in waitlisting.

Herein we present evidence of the first observation of YOY Paralichthys dentatus (Summer Flounder) in the Saco River estuary, ME, in June of 2012. A possible explanation for the occurrence of YOY summer flounder in this region could be range expansion, which may have destructive effects on southern Maine estuary systems. As active predators, Summer Flounder have the potential to exploit locally abundant fishes, including Pseudopleuronectes americanus (Winter Flounder) and Ammodytes americanus (American Sand Lance).

Chemokines are components of the skin microenvironment, which enable immune cell chemotaxis. Traditionally, transcription factors involved in inflammatory signaling (eg, NFκB) are important mediators of chemokine expression. To what extent xenobiotics and their associated receptors control chemokine expression is poorly understood. The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor known to mediate physiological responses in the skin through the regulation of genes involved in xenobiotic metabolism, epidermal differentiation, and immunity. Here, we demonstrate that AHR activation within primary mouse keratinocytes regulates the expression of a neutrophil directing chemokine (C-X-C motif) ligand 5 (Cxcl5). AHR-mediated regulation of Cxcl5 is because of direct transcriptional activity upon treatment with AHR agonists such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Additionally, AHR mediates enhanced induction of Cxcl5 upon exposure to an agonist and the inflammatory cytokine interleukin 1 beta. This synergy is confined primarily to keratinocytes, as dermal fibroblasts did not achieve the same level of combinatorial induction. AHR-specific antagonists were able to reduce basal and induced levels of Cxcl5, demonstrating the potential for pharmacological intervention. Exposure of C57BL/6 J mice to ultraviolet (UV) light followed by topical treatment with the AHR agonist formylindolo(3,2-b)carbazole (FICZ) significantly induced Cxcl5 expression in skin compared with UV alone, and this response was absent in Ahr-/- mice. These results establish AHR as an important mediator of Cxcl5, with implications for the treatment of inflammatory skin diseases.

Background and objectives Despite the important role that health care providers at dialysis facilities have in reducing racial disparities in access to kidney transplantation in the United States, little is known about provider awareness of these disparities. We aimed to evaluate health care providers’ awareness of racial disparities in kidney transplant waitlisting and identify factors associated with awareness. Design, setting, participants, & measurements We conducted a cross-sectional analysis of a survey of providers from low-waitlisting dialysis facilities (n=655) across all 18 ESRD networks administered in 2016 in the United States merged with 2014 US Renal Data System and 2014 US Census data. Awareness of national racial disparity in waitlisting was defined as responding “yes” to the question: “Nationally, do you think that African Americans currently have lower waitlisting rates than white patients on average?” The secondary outcome was providers’ perceptions of racial difference in waitlisting at their own facilities. Results Among 655 providers surveyed, 19% were aware of the national racial disparity in waitlisting: 50% (57 of 113) of medical directors, 11% (35 of 327) of nurse managers, and 16% (35 of 215) of other providers. In analyses adjusted for provider and facility characteristics, nurse managers (versus medical directors; odds ratio, 7.33; 95% confidence interval, 3.35 to 16.0) and white providers (versus black providers; odds ratio, 2.64; 95% confidence interval, 1.39 to 5.02) were more likely to be unaware of a national racial disparity in waitlisting. Facilities in the South (versus the Northeast; odds ratio, 3.05; 95% confidence interval, 1.04 to 8.94) and facilities with a low percentage of blacks (versus a high percentage of blacks; odds ratio, 1.86; 95% confidence interval, 1.02 to 3.39) were more likely to be unaware. One quarter of facilities had >5% racial difference in waitlisting within their own facilities, but only 5% were aware of the disparity. Conclusions Among a limited sample of dialysis facilities with low waitlisting, provider awareness of racial disparities in kidney transplant waitlisting was low, particularly among staff who may have more routine contact with patients.

The mouse strain SKH1 is widely used in skin research due to its hairless phenotype and intact immune system. Due to the complex nature of aryl hydrocarbon receptor (AHR) function in the skin, the development of additional in vivo models is necessary to study its role in cutaneous homeostasis and pathology. Variants of the Ah allele, exist among different mouse strains. The Ahb-1 and Ahd alleles express high and low affinity ligand binding forms of the AHR, respectively. The outbred SKH1 mice express the Ahb-2 and/or Ahd alleles. SKH1 mice were crossed with C57BL/6J mice, which harbor the Ahb-1 allele, to create useful models for studying endogenous AHR function. SKH1 mice were bred to be homozygous for either the Ahb-1 or Ahd allele to establish strains for use in comparative studies of the effects of differential ligand-mediated activation through gene expression changes upon UVB exposure. Ahb-1 or Ahd allelic status was confirmed by DNA sequence analysis. We tested the hypothesis that SKH1-Ahb-1 mice would display enhanced inflammatory signaling upon UVB exposure compared to SKH1-Ahd mice. Differential basal AHR activation between the strains was determined by assessing Cyp1a1 expression levels in the small intestine, liver, and skin of the SKH1-Ahb-1 mice compared to SKH1-Ahd mice. To determine whether SKH1-Ahb-1 mice are more prone to a pro-inflammatory phenotype in response to UVB, gene expression of inflammatory mediators was analyzed. SKH1-Ahb-1 mice expressed enhanced gene expression of the chemotactic factors Cxcl5, Cxcl1, and Ccl20, as well as the inflammatory signaling factors S100a9 and Ptgs2, compared to SKH1-Ahd mice in skin. These data supports a role for AHR activation and enhanced inflammatory signaling in skin.

Historically, multiple species of diadromous fishes served as a coastal food source for commercially valuable nearshore predators. However, severe declines in diadromous fish populations in the nearshore Gulf of Maine (GOM) have impacted trophic dynamics and increased pressure on other estuarine-dependent forage resources. The objective of this study was to compare the trophic positions and interspecific interactions of diadromous fishes as predators and prey in relation to current GOM forage fishes. Empirical biomass data along with diet compositions and vital rates were used to construct a static model of a representative GOM coastal food web: the Saco River estuary (SRE) in Maine. A series of sensitivity analyses based on model outputs was performed to determine the trophic role of diadromous fishes in this estuarine food web. Model results suggested that juvenile marine transients played a greater role as forage species for SRE predators than did the anadromous Blueback Herring Alosa aestivalis and Alewife Alosa pseudoharengus. Due to the abundant forage fish base, Atlantic Sturgeon Acipenser oxyrinchus and Shortnose Sturgeon Acipenser brevirostrum were estimated to have a greater trophic position than reported in past literature. Lower-trophic-level fishes functioned as keystone prey species for sturgeon. The use of holistic approaches to update the ecological data on predator–prey interactions among diadromous fishes and forage resources within coastal ecosystems is necessary for the future management of these ecologically significant and threatened species. Received January 4, 2016; accepted May 20, 2016

The aryl hydrocarbon receptor (AhR) has been shown to play a role in an increasing number of cellular processes. Recent reports have linked the AhR to cell proliferation, cytoskeletal arrangement, and tumor invasiveness in various tumor cell types. The AhR plays a role in the de-repression of the interleukin (IL)6 promoter in certain tumor cell lines, allowing for increased transcriptional activation by cytokines. Here, we show that there is a significant level of constitutive activation of the AhR in cells isolated from patients with head and neck squamous cell carcinoma (HNSCC). Constitutive activation of the AhR in HNSCCs was blocked by antagonist treatment, leading to a reduction in IL6 expression. In addition, the AhR exhibits a high level of expression in HNSCCs than in normal keratinocytes. These findings led to the hypothesis that the basal AhR activity in HNSCCs plays a role in the aggressive phenotype of these tumors and that antagonist treatment could mitigate this phenotype. This study provides evidence that antagonism of the AhR in HNSCC tumor cells, in the absence of exogenous receptor ligands, has a significant effect on tumor cell phenotype. Treatment of these cell lines with the AhR antagonists 6, 2′, 4′-trimethoxyflavone, or the more potent GNF351, decreased migration and invasion of HNSCC cells and prevented benzo[a]pyrene-mediated induction of the chemotherapy efflux protein ABCG2. Thus, an AhR antagonist treatment has been shown to have therapeutic potential in HNSCCs through a reduction in aggressive cell phenotype. Mol Cancer Res; 10(10); 1369–79. ©2012 AACR.

The reproductive cycle of Raja texana was determined from 63 females (510-630 mm total length, L(T)) and 81 males (355-546 mm L(T)) collected from the Gulf of Mexico. The results, based on follicle size, mature spermatocysts and gonadosomatic index (I(G)) suggests year-round reproductive activity.

The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for a wide variety of organisms. The Browser also has many tools for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets, aligning sequences and uploading user data. Among the features released this year are a gene search tool and annotation track drag-reorder functionality as well as support for BAM and BigWig/BigBed file formats. New display enhancements include overlay of multiple wiggle tracks through use of transparent coloring, options for displaying transformed wiggle data, a ‘mean+whiskers’ windowing function for display of wiggle data at high zoom levels, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks.

The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc.edu/) provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users' own annotation data. As of September 2009, genomic sequence and a basic set of annotation 'tracks' are provided for 47 organisms, including 14 mammals, 10 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms and a yeast. New data highlights this year include an updated human genome browser, a 44-species multiple sequence alignment track, improved variation and phenotype tracks and 16 new genome-wide ENCODE tracks. New features include drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats for large datasets (bigBed and bigWig), a new multiple alignment output tool, links to variation and protein structure tools, in silico PCR utility enhancements, and improved track configuration tools.

The rhesus macaque ( Macaca mulatta ) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.

Background The plastid maturase MatK has been implicated as a possible model for the evolutionary “missing link” between prokaryotic and eukaryotic splicing machinery. This evolutionary implication has sparked investigations concerning the function of this unusual maturase. Intron targets of MatK activity suggest that this is an essential enzyme for plastid function. The matK gene, however, is described as a pseudogene in many photosynthetic orchid species due to presence of premature stop codons in translations, and its high rate of nucleotide and amino acid substitution. Results Sequence analysis of the matK gene from orchids identified an out-of-frame alternative AUG initiation codon upstream from the consensus initiation codon used for translation in other angiosperms. We demonstrate translation from the alternative initiation codon generates a conserved MatK reading frame. We confirm that MatK protein is expressed and functions in sample orchids currently described as having a matK pseudogene using immunodetection and reverse-transcription methods. We demonstrate using phylogenetic analysis that this alternative initiation codon emerged de novo within the Orchidaceae, with several reversal events at the basal lineage and deep in orchid history. Conclusion These findings suggest a novel evolutionary shift for expression of matK in the Orchidaceae and support the function of MatK as a group II intron maturase in the plastid genome of land plants including the orchids.

The goal of the Encyclopedia Of DNA Elements (ENCODE) Project is to identify all functional elements in the human genome. The pilot phase is for comparison of existing methods and for the development of new methods to rigorously analyze a defined 1% of the human genome sequence. Experimental datasets are focused on the origin of replication, DNase I hypersensitivity, chromatin immunoprecipitation, promoter function, gene structure, pseudogenes, non-protein-coding RNAs, transcribed RNAs, multiple sequence alignment and evolutionarily constrained elements. The ENCODE project at UCSC website (http://genome.ucsc.edu/ENCODE) is the primary portal for the sequence-based data produced as part of the ENCODE project. In the pilot phase of the project, over 30 labs provided experimental results for a total of 56 browser tracks supported by 385 database tables. The site provides researchers with a number of tools that allow them to visualize and analyze the data as well as download data for local analyses. This paper describes the portal to the data, highlights the data that has been made available, and presents the tools that have been developed within the ENCODE project. Access to the data and types of interactive analysis that are possible are illustrated through supplemental examples.

The biological functions of the aryl hydrocarbon receptor (AHR) can be delineated into dioxin response element (DRE)-dependent or -independent activities. Ligands exhibiting either full or partial agonist activity, e.g., 2,3,7,8-tetrachlorodibenzo-p-dioxin and α-naphthoflavone, have been demonstrated to potentiate both DRE-dependent and -independent AHR function. In contrast, the recently identified selective AHR modulators (SAhRMs), e.g., 1-allyl-3-(3,4-dimethoxyphenyl)-7-(trifluoromethyl)-1H-indazole (SGA360), bias AHR toward DRE-independent functionality while displaying antagonism with regard to ligand-induced DRE-dependent transcription. Recent studies have expanded the physiological role of AHR to include modulation of hematopoietic progenitor expansion and immunoregulation. It remains to be established whether such physiological roles are mediated through DRE-dependent or -independent pathways. Here, we present evidence for a third class of AHR ligand, “pure” or complete antagonists with the capacity to suppress both DRE-dependent and -independent AHR functions, which may facilitate dissection of physiological AHR function with regard to DRE or non-DRE-mediated signaling. Competitive ligand binding assays together with in silico modeling identify N-(2-(1H-indol-3-yl)ethyl)-9-isopropyl-2-(5-methylpyridin-3-yl)-9H-purin-6-amine (GNF351) as a high-affinity AHR ligand. DRE-dependent reporter assays, in conjunction with quantitative polymerase chain reaction analysis of AHR targets, reveal GNF351 as a potent AHR antagonist that demonstrates efficacy in the nanomolar range. Furthermore, unlike many currently used AHR antagonists, e.g., α-naphthoflavone, GNF351 is devoid of partial agonist potential. It is noteworthy that in a model of AHR-mediated DRE-independent function, i.e., suppression of cytokine-induced acute-phase gene expression, GNF351 has the capacity to antagonize agonist and SAhRM-mediated suppression of SAA1. Such data indicate that GNF351 is a pure antagonist with the capacity to inhibit both DRE-dependent and -independent activity.

The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) comprises a suite of web-based tools to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of genome-wide experimental measurements for multiple samples alongside their associated clinical information. Multiple data sets can be viewed simultaneously as coordinated ‘heatmap tracks’ to compare across studies or different data modalities. Users can order, filter, aggregate, classify and display data interactively based on any given feature set including clinical features, annotated biological pathways and user-contributed collections of genes. Integrated standard statistical tools provide dynamic quantitative analysis within all available data sets. The browser hosts a growing body of publicly available cancer genomics data from a variety of cancer types, including data generated from the Cancer Genome Atlas project. Multiple consortiums use the browser on confidential prepublication data enabled by private installations. Many new features have been added, including the hgMicroscope tumor image viewer, hgSignature for real-time genomic signature evaluation on any browser track, and ‘PARADIGM’ pathway tracks to display integrative pathway activities. The browser is integrated with the UCSC Genome Browser; thus inheriting and integrating the Genome Browser’s rich set of human biology and genetics data that enhances the interpretability of the cancer genomics data.

The Encyclopedia of DNA Elements (ENCODE) project is an international consortium of investigators funded to analyze the human genome with the goal of producing a comprehensive catalog of functional elements. The ENCODE Data Coordination Center at The University of California, Santa Cruz (UCSC) is the primary repository for experimental results generated by ENCODE investigators. These results are captured in the UCSC Genome Bioinformatics database and download server for visualization and data mining via the UCSC Genome Browser and companion tools (Rhead et al. The UCSC Genome Browser Database: update 2010, in this issue). The ENCODE web portal at UCSC (http://encodeproject.org or http://genome.ucsc.edu/ENCODE) provides information about the ENCODE data and convenient links for access.

The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs.

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view about chromatin structure has emerged, including its interrelationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded novel mechanistic and evolutionary insights about the functional landscape of the human genome. Together, these studies are defining a path forward to pursue a more-comprehensive characterisation of human genome function.

Summary: Most genes in human, mouse and rat produce more than one transcript isoform. The Affymetrix Exon Array is a tool for studying the many processes that regulate RNA production, with separate probesets measuring RNA levels at known and putative exons. For insights on how exons levels vary between normal tissues, we constructed the Affy Exon Tissues track from tissue data published by Affymetrix. This track reports exon probeset intensities as log ratios relative to median values across the dataset and renders them as colored heat maps, to yield quick visual identification of exons with intensities that vary between normal tissues. Availability: Affy Exon Tissues track is freely available under the UCSC Genome Browser (http://genome.ucsc.edu/) for human (hg18), mouse (mm8 and mm9), and rat (rn4). Contact: cline@soe.ucsc.edu Supplementary information: Supplementary data are available at Bioinformatics online.