Urban Roadway Runoff Is Lethal to Juvenile Coho, Steelhead, and Chinook Salmonids, But Not Congeneric Sockeye.

We compared the sensitivity of closely related Pacific salmon and steelhead (Oncorhynchus spp.) to untreated urban stormwater runoff across three storm events. Juvenile coho, sockeye, steelhead, and Chinook were exposed for 24 h to untreated urban runoff and then transferred to clean water for 48 h. As anticipated from previous studies, coho were highly susceptible to runoff toxicity, with cumulative mortality rates ranging from 92%-100% across the three storms. By contrast, juvenile sockeye were unaffected (100% survival), and cumulative mortality rates were intermediate for steelhead (4%-42%) and Chinook (0%-13%). Furthermore, coho died rapidly following the onset of stormwater exposure (generally <4 h), whereas mortality in Chinook and steelhead was delayed by 1-2 days. Similar to previous findings for coho, steelhead and Chinook did not recover when transferred to clean water. Lastly, significant mortality occurred in coho even when roadway runoff was diluted by 95% in clean water. Our findings extend the urban runoff mortality syndrome in salmonids and point to a near-term need for sublethal studies in steelhead and Chinook to more precisely understand stormwater risks to threatened species recovery efforts in the western United States.

A catalog of associations between rare coding variants and COVID-19 outcomes.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease-19 (COVID-19), a respiratory illness that can result in hospitalization or death. We investigated associations between rare genetic variants and seven COVID-19 outcomes in 543,213 individuals, including 8,248 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome-wide or when specifically focusing on (i) 14 interferon pathway genes in which rare deleterious variants have been reported in severe COVID-19 patients; (ii) 167 genes located in COVID-19 GWAS risk loci; or (iii) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, with results publicly browsable at https://rgc-covid19.regeneron.com.

Live surgery: highly educational or harmful?

PURPOSE: Live surgery (LS) is considered a useful teaching opportunity. The benefits must be balanced with patient safety concerns. To evaluate the rate of complications of a series of urologic LS performed by experts during the Congress Challenge in Laparoscopy and Robotics (CILR). METHODS: We present a large, multi-institution, multi-surgeon database that derives from 12 CILR events, from 2004 to 2015 with a total of 224 cases. Radical prostatectomy (RP) was the most common procedure and a selection of complex cases was noted. The primary measure was postoperative complications and use of a Postoperative Morbidity Index (PMI) to allow quantitative weighing of postoperative complications. RESULTS: From 12 events, the number of cases increased from 11 in 2004 to 27 in 2015 and a total of 27 surgeons. Of 224 cases (164 laparoscopic and 60 robotic), there were 26 (11.6%) complications: 5 grade I, 5 grade II, 3 grade IIIa, 12 grade IIIb and 1 grade V, the latter from laparoscopic cystectomy. Analysis of PMI was 23 times higher from cystectomy compared to RP. CONCLUSIONS: In the setting of live surgery, the overall rate of complications is low considering the complexity of surgeries. The PMI is not higher in more complex procedures, whereas RP seems very safe.

Seasonal Population Dynamics of Megacopta cribraria (Hemiptera: Plataspidae) in Kudzu and Soybean, and Implication for Insecticidal Management in Soybean.

Megacopta cribraria (F.), an invasive species introduced from Asia in 2009, is now prolific in the southeastern United States. Megacopta cribraria develops primarily on kudzu and soybean completing two generations. It is not well understood how this economic pest is affected by changes in geographic distribution in the United States or how population levels have changed since its establishment. The effect of insecticide application timing on field populations of M. cribraria is not well documented. These studies seek to understand how population dynamics of M. cribraria vary with geographic regions in Georgia. Effect of application timing on populations throughout the growing season was also examined. Weekly from 2012 to 2013, all life stages were enumerated from kudzu and soybean environments at several locations throughout Georgia from sweeps samples and flight intercept captures. Coordinates were recorded for locations, and classified as belonging to the Piedmont or Coastal Plain region of the state. Single spray trials were conducted from 2011-2014, and applications were made to soybean at intervals throughout the season. From 2012 to 2015, two kudzu patches near Griffin, GA, were monitored to detect population changes. Differences in population dynamics from locations around the state were found, but no clear effect of latitude, longitude, or region was observed. Insecticide applications applied in July suppressed nymph populations significantly better than treatments made earlier or later. Megacopta cribraria populations declined in 2014 and 2015 compared with 2012 and 2013. These studies provide the critical information for M. cribraria management in soybean in the southeastern United States.

Epigenetic analysis of the IFNλ3 gene identifies a novel marker for response to therapy in HCV-infected subjects.

Chronic hepatitis C virus (HCV) infection is characterized by high interindividual variability in response to pegylated interferon and ribavirin. A genetic polymorphism on chromosome 19 (rs12979860) upstream of interferon-λ3 (IFNλ3) is associated with a twofold change in sustained virologic response rate after 48 weeks of treatment with pegylated interferon/ribavirin in HCV genotype 1 (GT1) treatment-naïve patients. We conducted epigenetic analysis on the IFNλ3 promoter to investigate whether DNA methylation is associated with response to HCV therapy. DNA samples from HCV GT1-infected subjects receiving an interferon-free paritaprevir-containing combination regimen (N=540) and from HCV-uninfected, healthy controls (N=124) were analysed for IFNλ3 methylation levels. Methylation was strongly associated with rs12979860 allele status whether adjusting for HCV status (r=65.0%, 95% CI: [60.2%, 69.5%]), or not (r=64.4%), both with P<2.2×10-16 . In HCV GT1-infected subjects, C/C genotypes had significantly lower methylation levels relative to C/T or T/T genotypes (P<1×10-14 ), with each T allele resulting in a nine-unit increase in mean methylation level. Methylation levels did not correlate with response in subjects treated for 12 or 24 weeks. However, non-C/C subjects with higher methylation levels were more likely to relapse when treatment duration was 8 weeks. This analysis suggests that methylation status of the IFNλ3 promoter region may be a useful parameter that identifies patients more likely to relapse following HCV therapy; however, continuing therapy for a sufficient duration can overcome this difference. These findings may provide mechanistic insight into the role of IFNλ3 genetic variants in HCV treatment response.

Integrating chemohormonal therapy and surgery in known or suspected lymph node metastatic prostate cancer.

BACKGROUND: Prostate cancer persisting in the primary site after systemic therapy may contribute to emergence of resistance and progression. We previously demonstrated molecular characteristics of lethal cancer in the prostatectomy specimens of patients presenting with lymph node metastasis after chemohormonal treatment. Here we report the post-treatment outcomes of these patients and assess whether a link exists between surgery and treatment-free/cancer-free survival. METHODS: Patients with either clinically detected lymph node metastasis or primaries at high risk for nodal dissemination were treated with androgen ablation and docetaxel. Those responding with PSA concentration <1 ng ml(-1) were recommended surgery 1 year from enrollment. ADT was withheld postoperatively. The rate of survival without biochemical progression 1 year after surgery was measured to screen for efficacy. RESULTS: Forty patients were enrolled and 39 were evaluable. Three patients (7.7%) declined surgery. Of the remaining 36, 4 patients experienced disease progression during treatment and 4 more did not reach PSA <1. Twenty-six patients (67%) completed surgery, and 13 (33%) were also progression-free 1 year postoperatively (8 with undetectable PSA). With a median follow-up of 61 months, time to treatment failure was 27 months in the patients undergoing surgery. The most frequent patterns of first disease recurrence were biochemical (10 patients) and systemic (5). CONCLUSIONS: Half of the patients undergoing surgery were off treatment and progression-free 1 year following completion of all therapy. These results suggest that integration of surgery is feasible and may be superior to systemic therapy alone for selected prostate cancer patients presenting with nodal metastasis.

Soil bioretention protects juvenile salmon and their prey from the toxic impacts of urban stormwater runoff.

Green stormwater infrastructure (GSI), or low impact development, encompasses a diverse and expanding portfolio of strategies to reduce the impacts of stormwater runoff on natural systems. Benchmarks for GSI success are usually framed in terms of hydrology and water chemistry, with reduced flow and loadings of toxic chemical contaminants as primary metrics. Despite the central goal of protecting aquatic species abundance and diversity, the effectiveness of GSI treatments in maintaining diverse assemblages of sensitive aquatic taxa has not been widely evaluated. In the present study we characterized the baseline toxicity of untreated urban runoff from a highway in Seattle, WA, across six storm events. For all storms, first flush runoff was toxic to the daphniid Ceriodaphnia dubia, causing up to 100% mortality or impairing reproduction among survivors. We then evaluated whether soil media used in bioretention, a conventional GSI method, could reduce or eliminate toxicity to juvenile coho salmon (Oncorhynchus kisutch) as well as their macroinvertebrate prey, including cultured C. dubia and wild-collected mayfly nymphs (Baetis spp.). Untreated highway runoff was generally lethal to salmon and invertebrates, and this acute mortality was eliminated when the runoff was filtered through soil media in bioretention columns. Soil treatment also protected against sublethal reproductive toxicity in C. dubia. Thus, a relatively inexpensive GSI technology can be highly effective at reversing the acutely lethal and sublethal effects of urban runoff on multiple aquatic species.

Zebrafish and clean water technology: assessing soil bioretention as a protective treatment for toxic urban runoff.

Urban stormwater contains a complex mixture of contaminants that can be acutely toxic to aquatic biota. Green stormwater infrastructure (GSI) is a set of evolving technologies intended to reduce impacts on natural systems by slowing and filtering runoff. The extent to which GSI methods work as intended is usually assessed in terms of water quantity (hydrology) and quality (chemistry). Biological indicators of GSI effectiveness have received less attention, despite an overarching goal of protecting the health of aquatic species. Here we use the zebrafish (Danio rerio) experimental model to evaluate bioinfiltration as a relatively inexpensive technology for treating runoff from an urban highway with dense motor vehicle traffic. Zebrafish embryos exposed to untreated runoff (48-96h; six storm events) displayed an array of developmental abnormalities, including delayed hatching, reduced growth, pericardial edema, microphthalmia (small eyes), and reduced swim bladder inflation. Three of the six storms were acutely lethal, and sublethal toxicity was evident across all storms, even when stormwater was diluted by as much as 95% in clean water. As anticipated from exposure to cardiotoxic polycyclic aromatic hydrocarbons (PAHs), untreated runoff also caused heart failure, as indicated by circulatory stasis, pericardial edema, and looping defects. Bioretention treatment dramatically improved stormwater quality and reversed nearly all forms of developmental toxicity. The zebrafish model therefore provides a versatile experimental platform for rapidly assessing GSI effectiveness.

Incisional hernia recurrence through genomic profiling: a pilot study.

PURPOSE: Although situational risk factors for incisional hernia formation are known, the methods used to determine who would be most susceptible to develop one are unreliable. We hypothesized that patients with recurrent incisional hernias may possess unique gene expression profiles. METHODS: Skin and intact fascia were collected from 15 normal control (NC) patients with no hernia history and 18 patients presenting for recurrent incisional hernia (RH) repair. Microarray analysis was performed using whole genome microarray chips on NC (n = 8) and RH (n = 9). These samples were further investigated using a pathway-specific PCR array containing fibrosis-related genes. RESULTS: Microarray data revealed distinct differences in the gene expression profiles between RH and NC patients. One hundred and sixty-seven genes in the skin and 7 genes in the fascia were differentially expressed, including 8 directly involved in collagen synthesis. In particular, GREMLIN1, or bone morphogenetic protein antagonist 1, was under expressed in skin (fold = 0.49, p < 10(-7), q = 0.0009) and fascia (fold = 0.23, p < 10(-4), q = 0.095) of RH patients compared with NC. The PCR array data supported previous reports of decreased collagen I/III ratios in skin of RH versus NC (mean = 1.51 ± 0.73 vs. mean = 2.26 ± 0.99; one-sided t test, p = 0.058). CONCLUSION: To our knowledge, this is the first microarray-based analysis to show distinct gene expression profiles between the skin and fascia of RH and NC patients and the first report of an association between GREMLIN1 and incisional hernia formation. Our results suggest that gene expression profiles may act as surrogate markers that stratify patients into different groups at risk for hernia development prior to their initial surgery.

Inflammatory cytokines differentially up-regulate human endometrial haptoglobin production in women with endometriosis.

BACKGROUND: Evidence suggests that eutopic endometrium from women with endometriosis (US-E) has intrinsic functional anomalies compared with women without endometriosis (US-C). We hypothesized that differences in endometrial haptoglobin (eHp) mRNA and protein levels exist between eutopic endometrium from US-E and US-C and that inflammatory mediators may be involved. METHODS: Endometrial stromal cells and tissue explants from US-E (n = 18) and US-C (n = 18) were cultured (24 h/48 h for cells/explants) with interleukin (IL)-1alpha, -1beta, -6, -8 or tumor necrosis factor-alpha (TNF-alpha) at 0-100 ng/ml. eHp protein in media and mRNA levels were quantified by enzyme-linked immunosorbent assay and quantitative PCR. RESULTS: In eutopic endometrial stromal cells from US-E, IL-1beta, IL-6 and TNF-alpha (10 ng/ml) increased eHp mRNA levels (P = 0.002, P < 0.001 and P < 0.001, respectively) and eHp protein (P = 0.023, 0.031 and 0.006, respectively) versus control. In endometrial tissues from US-E, IL-1beta, IL-6 and TNF-alpha increased eHp mRNA (P < 0.001, P = 0.017 and P < 0.001, respectively) and eHp protein (P < 0.001, P = 0.007 and 0.039, respectively) versus control. IL-1alpha and IL-8 had small or no effects on isolated endometrial cells or tissues. In US-C, IL-1beta, IL-8 and TNF-alpha each reduced eHp mRNA in endometrial stromal cells (all P < 0.001) versus control; IL-1alpha and IL-6 had no effect. eHp mRNA increased in endometrial tissues from US-C in response to IL-1beta (P = 0.008), IL-6 (P = 0.015) and TNF-alpha (P = 0.031) versus control; IL-1alpha or IL-8 had no effect. CONCLUSIONS: Endometrium from US-E differentially responds to specific inflammatory cytokines by production of eHp. We propose that up-regulation of endometrial eHp by inflammatory mediators disrupts normal endometrial function and may facilitate the pathogenesis of endometriosis.

An exploratory study measuring verbal order content and context.

BACKGROUND: The use of verbal orders, while essential in some healthcare settings, has been identified as a potential contributor to poor quality and less safe care. Despite the widespread use of verbal orders, little research attention has been paid to understanding and measuring the content of verbal orders or variables related to the context in which verbal orders are made. AIM: This paper first identifies variables related to verbal order content and context, and then provides detailed analyses from two exploratory studies conducted in one community hospital. METHODS: The data presented were collected using both a paper-based manual audit, and an analysis of data generated from a computerised order entry system. DISCUSSION: Selected analyses focus of variations in types and timing of verbal orders hospital-wide as well as for specific inpatient units, changes in verbal order utilisation following implementation of a computerised provider order entry system, and an analysis of the presence of sound-alike and high-alert medications in verbal orders.

Porous plug gas injection systems for studies of hydrocarbon dissociation and transport in the DIII-D tokamak.

A probe has been designed, constructed, and successfully used to inject methane into the DIII-D lower divertor in a manner imitating natural release by chemical erosion. This porous plug injector (PPI) probe consists of a self-contained gas reservoir with an integrated pressure gauge and a 3 cm diameter porous surface through which gas is injected into the lower divertor of the tokamak. The probe is positioned flush with the divertor target surface by means of the divertor materials evaluation system. Two gas delivery systems were developed: in the first, gas flow is regulated by a remotely controlled microvalve and in the second by a fixed micro-orifice flow restrictor. Because of the large area of the porous surface through which gas is admitted, the injected hydrocarbon molecules see a local carbon surface (>90% carbon) similar to that seen by hydrocarbons being emitted by chemical sputtering from surrounding carbon tiles. The distributed gas source also reduces the disturbance to the local plasma while providing sufficient signal for spectroscopic detection. In situ spectroscopic measurements with the PPI in DIII-D allow the direct calibration of response for measured plasma conditions from a known influx of gas.

Differential DNA methylation patterns of small B-cell lymphoma subclasses with different clinical behavior.

Non-Hodgkin's lymphoma (NHL) is a group of malignancies of the immune system with variable clinical behaviors and diverse molecular features. Despite the progress made in classification of NHLs based on classical methods, molecular classifications are a work in progress. Toward this goal, we used an array-based technique called differential methylation hybridization (DMH) to study small B-cell lymphoma (SBCL) subtypes. A total of 43 genomic DMH experiments were performed. From these results, several statistical methods were used to generate a set of differentially methylated genes for further validation. Methylation of LHX2, POU3F3, HOXC10, NRP2, PRKCE, RAMP, MLLT2, NKX6.1, LRP1B and ARF4 was validated in cell lines and patient samples and demonstrated subtype-related preferential methylation patterns. For LHX2 and LRP1B, bisulfite sequencing, real-time reverse transcriptase-polymerase chain reaction and induction of gene expression following treatment with the demethylating agent, 5'-aza-2'-deoxycytidine, were confirmed. This new epigenetic information is helping to define molecular portraits of distinct subtypes of SBCL that are not recognized by current classification systems and provides valuable potential insights into the biology of these tumors.

The transformation of hexabromocyclododecane in aerobic and anaerobic soils and aquatic sediments.

The biological transformation of hexabromocyclododecane (HBCD), a brominated fire retardant commonly used in a variety of consumer goods, was investigated in aerobic and anaerobic soils and freshwater sediments. Soil, river water, and aquatic sediments were collected from several locations in the United States and transformation of HBCD was evaluated in the correspondingly composed microcosms based on the Organisation for Economic Co-Operation and Development (OECD) Test Guidelines 307 (Aerobic and Anaerobic Transformation in Soil) or 308 (Aerobic and Anaerobic Transformation in Aquatic Sediment Systems). Soil and sediment reaction mixtures, prepared under either aerobic or anoxic conditions, were dosed with HBCD at a concentration ranging from approximately 10 to 80 ng/g dry weight. The soils and sediments were then placed at 20 degrees C for approximately 4 months and the concentration of HBCD in the microcosms was determined at selected time intervals utilizing high-performance liquid chromatography-mass spectrometry (LC-MS). HBCD loss was observed in both the aerobic and anaerobic soils and sediments although the rates were appreciable faster under anoxic conditions. Biologically mediated transformation processes (i.e., biotransformation) accelerated the rate of loss of HBCD when compared to the biologically inhibited (i.e., autoclaved) soils and sediments. Biotransformation half-lives for HBCD were determined to be 63 and 6.9 days in the aerobic and anaerobic soils, respectively, while biotransformation half-lives for HBCD in the two river systems ranged from 11 to 32 days and 1.1 to 1.5 days under aerobic and anaerobic conditions, respectively. Brominated degradation products were not detected in any of the soils or sediments during the course of the study.

Relating induced in situ conditions of raw chicken breast meat to pinking.

Our objective was to simulate the pink color defect in cooked chicken breast meat with treatment combinations that would induce measurable changes in the conditions of raw meat. In addition, the feasibility of using induced raw meat conditions to develop a logistic regression model for prediction of pinking was studied. Approximately 960 breast fillets from 2 plants with 2 replications were used for inducing in situ conditions with 16 combinations of sodium chloride, sodium tripolyphosphate, sodium erythorbate, and sodium nitrite (present and not present). Muscles in all treatments were subjected to individual injections, followed by tumbling, cooking, and chilling. Raw samples were analyzed for pH, oxidation-reduction potential, and pigment evaluation. Results indicated a significant role of induced in situ conditions of raw meat in the occurrence of pinking. Presence of 1 ppm or more of sodium nitrite in raw meat produced significant pinking of cooked meat. The light muscle color group was least affected and the dark group was most affected by induced pH, oxidation-reduction potential conditions, and metmyoglobin and nitrosopigment content. The predictive ability of the logistic model was more than 90% with nitrosopigment, pH, and reducing conditions being the most important factors. Moreover, validation of the model was confirmed by close association between observed pink samples and those predicted as pink.

RAPD markers linked to eastern filbert blight resistance in Corylus avellana.

A total of 1,110 decamer primers were screened for RAPD markers linked to a dominant allele in hazelnut ( Corylus avellana) that confers resistance to eastern filbert blight caused by Anisogramma anomala. Twenty RAPD markers linked in coupling, and five markers linked in repulsion, were found. A seedling population was used to construct a linkage map of the region flanking the resistance locus. The map spans 46.6 cM, with 14 markers on one side of the resistance locus and eight on the other side. Eleven markers showed less than 3% recombination with resistance, including three that showed no recombination. Seven of these 11 markers are sufficiently robust to allow their use in marker-assisted selection. These include AA12(850) which shows no recombination, and six markers on one side of the resistance locus: 173(500), 152(800), 122(825), 275(1130), H19(650) and O16(1250). Marker 268(580), which flanks the resistance locus on the other side, is also suitable for use in marker-assisted selection, but shows 5.8% recombination with resistance. Other markers are less suitable for marker-assisted selection because of sensitivity to changes in primer or MgCl(2) concentration, or the long time required for electrophoresis to separate bands of similar size. The 16 markers closest to the resistance locus were cloned and sequenced. The W07(365) marker, which showed no recombination with the resistance locus but is difficult to score, includes a CT microsatellite repeat. The sequence information will allow the design of SCAR primers and eventual map-based cloning of the resistance allele.

Toxoplasma gondii, Neospora caninum, Sarcocystis neurona, and Sarcocystis canis-like infections in marine mammals.

Toxoplasma gondii, Neospora caninum, Sarcocystis neurona, and S. canis are related protozoans that can cause mortality in many species of domestic and wild animals. Recently, T. gondii and S. neurona were recognized to cause encephalitis in marine mammals. As yet, there is no report of natural exposure of N. caninum in marine mammals. In the present study, antibodies to T. gondii and N. caninum were assayed in sera of several species of marine mammals. For T. gondii, sera were diluted 1:25, 1:50, and 1:500 and assayed in the T. gondii modified agglutination test (MAT). Antibodies (MAT > or =1:25) to T. gondii were found in 89 of 115 (77%) dead, and 18 of 30 (60%) apparently healthy sea otters (Enhydra lutris), 51 of 311 (16%) Pacific harbor seals (Phoca vitulina), 19 of 45 (42%) sea lions (Eumetopias jubatus) [corrected] 5 of 32 (16%) ringed seals (Phoca hispida), 4 of 8 (50%) bearded seals (Erignathus barbatus), 1 of 9 (11.1%) spotted seals (Phoca largha), 138 of 141 (98%) Atlantic bottlenose dolphins (Tursiops truncatus), and 3 of 53 (6%) walruses (Odobenus rosmarus). For N. caninum, sera were diluted 1:40, 1:80, 1:160, and 1:320 and examined with the Neospora agglutination test (NAT) using mouse-derived tachyzoites. NAT antibodies were found in 3 of 53 (6%) walruses, 28 of 145 (19%) sea otters, 11 of 311 (3.5%) harbor seals, 1 of 27 (3.7%) sea lions, 4 of 32 (12.5%) ringed seals, 1 of 8 (12.5%) bearded seals, and 43 of 47 (91%) bottlenose dolphins. To our knowledge, this is the first report of N. caninum antibodies in any marine mammal, and the first report of T. gondii antibodies in walruses and in ringed, bearded, spotted, and ribbon seals. Current information on T. gondii-like and Sarcocystis-like infections in marine mammals is reviewed. New cases of clinical S. canis and T. gondii infections are also reported in sea lions, and T. gondii infection in an Antillean manatee (Trichechus manatus manatus).