Short communication: Identification of the pseudoautosomal region in the Hereford bovine reference genome assembly ARS-UCD1.2

In cattle, the X chromosome accounts for approximately 3 and 6% of the genome in bulls and cows, respectively. In spite of the large size of this chromosome, very few studies report analysis of the X chromosome in genome-wide association studies and genomic selection. This lack of genetic interrogation is likely due to the complexities of undertaking these studies given the hemizygous state of some, but not all, of the X chromosome in males. The first step in facilitating analysis of this gene-rich chromosome is to accurately identify coordinates for the pseudoautosomal boundary (PAB) to split the chromosome into a region that may be treated as autosomal sequence (pseudoautosomal region) and a region that requires more complex statistical models. With the recent release of ARS-UCD1.2, a more complete and accurate assembly of the cattle genome than was previously available, it is timely to fine map the PAB for the first time. Here we report the use of SNP chip genotypes, short-read sequences, and long-read sequences to fine map the PAB (X chromosome:133,300,518) and simultaneously determine the neighboring regions of reduced homology and true pseudoautosomal region. These results greatly facilitate the inclusion of the X chromosome in genome-wide association studies, genomic selection, and other genetic analysis undertaken on this reference genome.

Underappreciation of non-alcoholic fatty liver disease by primary care clinicians: limited awareness of surrogate markers of fibrosis

BACKGROUND

Non-alcoholic fatty liver disease (NAFLD) is a common cause of incidental liver test abnormalities. General practitioners (GP) have a key role in identifying people with NAFLD at risk of significant liver disease. Recent specialist guidelines emphasise the use of fibrosis algorithms or serum biomarkers rather than routine liver tests, to assess advanced fibrosis.

AIM

To evaluate primary care clinicians' current approach to diagnosis, management and referral of NAFLD.

METHODS

A cross-sectional survey of primary care clinicians was undertaken through a structured questionnaire about NAFLD. A convenience sample of general practice clinics and general practice conferences in Metropolitan Brisbane and regional south east Queensland was selected.

RESULTS

A total of 108 primary care clinicians completed the survey (participation rate 100%). Fifty-one percent of respondents considered the prevalence of NAFLD in the general population to be ≤10%. Twenty-four percent of respondents felt that liver enzymes were sufficiently sensitive to detect underlying NAFLD. Most respondents were unsure whether the Fibrosis 4 score (62.7% unsure) or Enhanced Liver Fibrosis score (63.7% unsure) could help to identify advanced fibrosis or cirrhosis. Although 47% of respondents said they would refer a patient to a Gastroenterologist/Hepatologist if they suspect the patient has NAFLD, 44.1% do not make any referrals. Of concern, 70.6% of clinicians said they were unlikely to refer a patient to Hepatology unless liver function tests are abnormal.

CONCLUSION

Our findings demonstrate that many primary care clinicians underestimate the prevalence of NAFLD and under-recognise the clinical spectrum of NAFLD and how this is assessed.

A Pragmatic Approach Identifies a High Rate of Nonalcoholic Fatty Liver Disease With Advanced Fibrosis in Diabetes Clinics and At-Risk Populations in Primary Care

Noninvasive serum biomarkers (nonalcoholic fatty liver disease fibrosis score [NFS], fibrosis 4 score [FIB‐4], or enhanced liver fibrosis [ELF] test) are recommended as first‐line tools to determine the risk of advanced fibrosis in nonalcoholic fatty liver disease. We aimed to assess the utility of a pragmatic approach to screening for clinically significant fibrosis in primary care and diabetes clinics. We recruited 252 patients from an endocrine clinic or primary care facility. Anthropometric measurements, ELF test, ultrasound, and liver stiffness measurements (LSMs) were performed. Clinically significant fibrosis was defined as LSM ≥8.2 kPa or ELF ≥9.8. A subgroup of patients underwent liver biopsy (n = 48) or had imaging diagnostic of cirrhosis (n = 14). Patients were 57.3 ± 12.3 years old with a high prevalence of metabolic syndrome (84.5%), type 2 diabetes (82.5%), and body mass index (BMI) ≥40 kg/m² (21.8%). LSM met quality criteria in 230 (91.3%) patients. NFS and FIB‐4 combined had a high negative predictive value (90.0%) for excluding LSM ≥8.2 kPa. However, 84.1% of patients had indeterminate or high NFS or FIB‐4 scores requiring further assessment. LSM ≥8.2 kPa and ELF ≥9.8 were present in 31.3% and 28.6% of patients, respectively. Following adjustment for age, BMI, sex, and presence of advanced fibrosis, older age was independently associated with ELF ≥9.8 (adjusted odds ratio, 1.14; 95% confidence interval, 1.06‐1.24), whereas increasing BMI was independently associated with LSM ≥8.2 kPa (adjusted odds ratio, 1.15; 95% confidence interval, 1.01‐1.30). Concordant LSM <8.2 kPa and ELF <9.8 and concordant LSM ≥8.2 kPa and ELF ≥9.8 had a high negative predictive value (91.7%) and positive predictive value (95.8%) for excluding and identifying clinically significant fibrosis, respectively. Conclusion: Simple scoring tools alone lack accuracy. LSM accuracy is influenced by severe obesity, whereas age impacts the ELF test. Further studies are required to confirm whether combining LSM and ELF may enhance accuracy and confidence in identifying clinically significant fibrosis. (Hepatology Communications 2018; 00:000‐000)

Controlled attenuation parameter in NAFLD identifies risk of suboptimal glycaemic and metabolic control

AIMS

To examine the relationship between steatosis quantified by controlled attenuation parameter (CAP) values and glycaemic/metabolic control.

METHODS

230 patients, recruited from an Endocrine clinic or primary care underwent routine Hepatology assessment, with liver stiffness measurements and simultaneous CAP. Multivariable logistic regression was performed to identify potential predictors of Metabolic Syndrome (MetS), HbA1c ≥ 7%, use of insulin, hypertriglyceridaemia and CAP ≥ 300 dB/m.

RESULTS

Patients were 56.7 ± 12.3 years of age with a high prevalence of MetS (83.5%), T2DM (81.3%), and BMI ≥ 40 kg/m² (18%). Median CAP score was 344 dB/m, ranging from 128 to 400 dB/m. BMI (aOR 1.140 95% CI 1.068-1.216), requirement for insulin (aOR 2.599 95% CI 1.212-5.575), and serum ALT (aOR 1.018 95% CI 1.004-1.033) were independently associated with CAP ≥ 300 dB/m. Patients with CAP interquartile range < 40 (68%) had a higher median serum ALT level (p = 0.029), greater prevalence of BMI ≥ 40 kg/m² (p = 0.020) and higher median CAP score (p < 0.001). Patients with higher CAP scores were more likely to have MetS (aOR 1.011 95% CI 1.003-1.019), HBA1c ≥ 7 (aOR 1.010 95% CI 1.003-1.016), requirement for insulin (aOR 1.007 95% CI 1.002-1.013) and hypertriglyceridemia (aOR 1.007 95% CI 1.002-1.013).

CONCLUSIONS

Our data demonstrate that an elevated CAP reflects suboptimal metabolic control. In diabetic patients with NAFLD, CAP may be a useful point-of-care test to identify patients at risk of poorly controlled metabolic comorbidities or advanced diabetes.

A Qualitative Study on the Usage of a Learning Management System by Allied Health Faculty

Learning management systems (LMSs) are available to faculty in many higher education institutions; however, not all faculty members take advantage of the tools LMSs offer in facilitating their face-to-face classes. To deepen understanding of this gap, this study explored faculty's experiences in LMS usage and factors that affected faculty's use of LMS to facilitate classroom learning. For this qualitative study, data were collected through interviews with various allied health faculty (n=10), and content analysis was used to identify themes. Two types of LMS user groups were identified in the study: high LMS users, who used three or more LMS tools, and low LMS users, who used fewer tools. Data analysis for the high LMS users identified four themes: adopted andragogy, perceived usefulness, perceived ease of use, and enhances adopted andragogy. For low LMS users, five themes were developed: no adopted andragogy, perceived usefulness, perceived ease of use, work enhancement, and barriers for further use. Both groups had the themes of perceived usefulness and perceived ease of use, but to various degrees. The emergent themes imply that high LMS users had an adopted andragogy framework from which they worked in designing their face-to-face courses, but low LMS users did not. Having an adopted andragogy appears to motivate faculty to use LMSs beyond the basic tools. The results of this qualitative study extended the technology acceptance model, an information systems theory explaining how users accept and use technology by adding a pivotal preceding construct, adopted andragogy, which is faculty embracing methods for teaching adult learners.

Diabetic patient adherence to pathology request completion in primary care

Objective Little research exists regarding the prevalence of patient non-adherence with completing pathology requests for chronic disease monitoring. The aims of the present study were to determine the extent to which this exists in diabetic patients and to identify possible reasons contributing to this behaviour. Methods Patients diagnosed with type 2 diabetes mellitus were recruited from three general practices with different demographics. Data were collected by recording demographic patient information at the time of visit. In addition, information regarding patient pathology request adherence and the reasons provided when this was not achieved were also noted. These reasons were compared with preconceptions by medical staff in each practice. Results General practitioner perceptions of poor patient adherence to pathology requests were confirmed, with rates of non-adherence up to 31% at one practice site. The primary reasons preventing completion of pathology testing included forgetfulness, time poorness, poor health literacy and, in some cases, language barriers. Conclusion A high proportion of patients do not prioritise the monitoring of their diabetes, potentially because of a lack of understanding of the importance such management has on their health. Further research should be conducted to determine the effect of the implementation of point-of-care testing on patient outcomes in such areas of low non-adherence with disease management. What is known about the topic? Little quantitative information exists regarding the adherence rate of patients to pathology request completion. Without up-to-date pathology results, a barrier is created, preventing accurate medical treatment of the patient's condition because the doctor cannot ascertain a full picture of the patient's current disease state at the time of consultation. What does this paper add? This paper quantifies the rate of non-adherence among three diabetic patient groups at different practice sites, taking into account patient and site demographics. It also confirms patient non-adherence to timely pathology request completion as a prevalent issue of concern at all practice sites recruited. In addition, it looks at reasons why this issue exists as a means of addressing the problem in the future. What are the implications for practitioners? This research may aid practitioners in addressing such issues at a local level within general practice, because reasons creating barriers to successful completion of pathology requests have been identified and potential solutions suggested.

Advanced anaerobic digestion of municipal sludge using a novel and energy-efficient radio frequency pretreatment system

Microwave (MW) sludge pretreatment systems are usually limited to a frequency of 2.45 GHz and the heating frequency is constrained by commercially available hardware. Studies using MW heating at this frequency have reported negative net energy balance (output energy as methane minus input electrical energy). This necessitates further research into more efficient thermal pretreatment technologies. In this research, a novel and highly efficient radio frequency (RF) pretreatment system at a frequency of 13.56 MHz was designed, implemented, and tested for the first time. The system was custom-designed based on the dielectric characteristics of thickened waste activated sludge (TWAS) to achieve a very efficient and uniform heating system. The effects of three factors including pretreatment method (RF vs. MW), final temperature (60, 90 and 120 °C), and stationary (holding) time (0, 1 and 2 h) on sludge solubilization and performance of mesophilic batch anaerobic digestion were evaluated simultaneously. Energy measurements were also made to compare the efficiency of the custom-designed RF and conventional MW heating systems. The differences in sludge disintegration (solubilization) using the RF and MW pretreatment systems were negligible (P > 0.05). No statistically significant difference was also observed between the two pretreatment systems in terms of mesophilic biogas production rate and extent (P > 0.05). The energy efficiency of the RF pretreatment system was measured between 67.3 and 95.5% for the temperature range of 25-120 °C which was significantly higher than that of the MW system efficiency which varied from 37 to 43%. Overall, the average input energy of the RF system was less than half of the energy consumed during the operation of the MW system to achieve a same target temperature. Considering the results of this research, the RF heating at a frequency of 13.56 MHz is suggested as an effective and energy-efficient technique for thermal hydrolysis of TWAS.

Effects of functional endoscopic sinus surgery on the acoustics of the sinonasal tract

BACKGROUND

Nasal and paranasal cavities are supposed to contribute substantially to the vocal tract resonator properties. However, their acoustical effects as well as the effects of sinus surgery on the voice remain unclear. In this work we investigate resonance phenomena of paranasal sinuses prior to and after various rhinosurgical procedures in cadaveric human sinonasal tracts and corresponding 3D casts.

METHODOLOGY

Nasal and paranasal cavities of formalin-preserved cadavers and corresponding 3D replicas were excited by sine-tone sweeps from an earphone placed in the epipharynx. The response was picked up by a microphone at the nostrils. Different FESS procedures were performed and the acoustical responses following excitation were recorded. The measured acoustical changes in the obtained transfer functions were then evaluated.

RESULTS

Marked low frequency dips were detected in the transfer functions when sinus cavities were included in the nasal resonator system. These dips showed a significant correlation with sinus volumes. Following FESS procedures they moved upwards in frequency depending on the extent of the surgical intervention.

CONCLUSIONS

The transfer functions obtained in cadaveric situs and 3D replicas showed dips at the resonance frequencies of the paranasal cavities. Marked acoustic effects in terms of increase in dip frequency following FESS procedures were reproducibly documented.

Multimorbidity and polypharmacy in diabetic patients with NAFLD: Implications for disease severity and management

An observational study describing the number and type of chronic conditions and medications taken by diabetic patients with NAFLD and identifying characteristics that may impact liver disease severity or clinical management.Adults with type 2 diabetes have a high prevalence of nonalcoholic fatty liver disease (NAFLD) and increased risk of developing advanced liver disease. Appropriate management should consider the characteristics of the diabetic NAFLD population, as comorbid conditions and medications may increase the complexity of treatment strategies.Diabetic patients with NAFLD at risk of clinically significant liver disease (as assessed by the FIB-4 or NAFLD fibrosis scores) were recruited consecutively from the Endocrine clinic or primary care. Medical conditions, medication history, anthropometric measurements, and laboratory tests were obtained during assessment. NAFLD severity was classified by transient elastography and liver ultrasound into "no advanced disease" (LSM < 8.2 kPa) or "clinically significant liver disease" (LSM ≥ 8.2 kPa).The most common coexistent chronic conditions were metabolic syndrome (94%), self-reported "depression" (44%), ischaemic heart disease (32%), and obstructive sleep apnoea (32%). Polypharmacy or hyperpolypharmacy was present in 59% and 31% of patients respectively. Elevated LSM (≥ 8.2 kPa) suggesting significant liver disease was present in 37% of this at-risk cohort. Increasing obesity and abdominal girth were both independently associated with likelihood of having significant liver disease.There is a high burden of multimorbidity and polypharmacy in diabetic NAFLD patients, highlighting the importance of multidisciplinary management to address their complex health care needs and ensure optimal medical treatment.

Evaluation of the Safety of Drugs and Biological Products Used During Lactation: Workshop Summary

This report serves as a summary of a 2-day public workshop sponsored by the US Food and Drug Administration (FDA) to discuss the safety of drugs and biological products used during lactation. The aim of the workshop was to provide a forum to discuss the collection of data to inform the potential risks to breastfed infants with maternal use of medications during lactation. Discussions included the review of current approaches to collect data on medications used during lactation, and the considerations for future approaches to design and guide clinical lactation studies. This workshop is part of continuing efforts to raise the awareness of the public for women who choose to breastfeed their infants.

Bovine mammary gland X chromosome inactivation

X chromosome inactivation (XCI) is a process by which 1 of the 2 copies of the X chromosomes present in female mammals is inactivated. The transcriptional silencing of one X chromosome achieves dosage compensation between XX females and XY males and ensures equal expression of X-linked genes in both sexes. Although all mammals use this form of dosage compensation, the complex mechanisms that regulate XCI vary between species, tissues, and development. These mechanisms include not only varying levels of inactivation, but also the nature of inactivation, which can range from being random in nature to driven by parent of origin. To date, no data describing XCI in calves or adult cattle have been reported and we are reliant on data from mice to infer potential mechanisms and timings for this process. In the context of dairy cattle breeding and genomic prediction, the implications of X chromosome inheritance and XCI in the mammary gland are particularly important where a relatively small number of bulls pass their single X chromosome on to all of their daughters. We describe here the use of RNA-seq, whole genome sequencing and Illumina BovineHD BeadChip (Illumina, San Diego, CA) genotypes to assess XCI in lactating mammary glands of dairy cattle. At a population level, maternally and paternally inherited copies of the X chromosome are expressed equally in the lactating mammary gland consistent with random inactivation of the X chromosome. However, average expression of the paternal chromosome ranged from 10 to 90% depending on the individual animal. These results suggest that either the mammary gland arises from 1 or 2 stem cells, or a nongenetic mechanism that skews XCI exists. Although a considerable amount of future work is required to fully understand XCI in cattle, the data reported here represent an initial step in ensuring that X chromosome variation is captured and used in an appropriate manner for future genomic selection.

Detection and assessment of copy number variation using PacBio long-read and Illumina sequencing in New Zealand dairy cattle

Single nucleotide polymorphisms have been the DNA variant of choice for genomic prediction, largely because of the ease of single nucleotide polymorphism genotype collection. In contrast, structural variants (SV), which include copy number variants (CNV), translocations, insertions, and inversions, have eluded easy detection and characterization, particularly in nonhuman species. However, evidence increasingly shows that SV not only contribute a substantial proportion of genetic variation but also have significant influence on phenotypes. Here we present the discovery of CNV in a prominent New Zealand dairy bull using long-read PacBio (Pacific Biosciences, Menlo Park, CA) sequencing technology and the Sniffles SV discovery tool (version 0.0.1; https://github.com/fritzsedlazeck/Sniffles). The CNV identified from long reads were compared with CNV discovered in the same bull from Illumina sequencing using CNVnator (read depth-based tool; Illumina Inc., San Diego, CA) as a means of validation. Subsequently, further validation was undertaken using whole-genome Illumina sequencing of 556 cattle representing the wider New Zealand dairy cattle population. Very limited overlap was observed in CNV discovered from the 2 sequencing platforms, in part because of the differences in size of CNV detected. Only a few CNV were therefore able to be validated using this approach. However, the ability to use CNVnator to genotype the 557 cattle for copy number across all regions identified as putative CNV allowed a genome-wide assessment of transmission level of copy number based on pedigree. The more highly transmissible a putative CNV region was observed to be, the more likely the distribution of copy number was multimodal across the 557 sequenced animals. Furthermore, visual assessment of highly transmissible CNV regions provided evidence supporting the presence of CNV across the sequenced animals. This transmission-based approach was able to confirm a subset of CNV that segregates in the New Zealand dairy cattle population. Genome-wide identification and validation of CNV is an important step toward their inclusion in genomic selection strategies.

Ferrule-Effect Dominates Over Use of a Fiber Post When Restoring Endodontically Treated Incisors: An In Vitro Study

OBJECTIVES

 The aim of this study was to investigate the restoration of broken-down endodontically treated incisors with the ferrule effect using glass ceramic crowns bonded to composite resin core buildups with or without a fiber post. A no-ferrule group with post was also included for comparison.

METHODS AND MATERIALS

 Thirty decoronated endodontically treated bovine incisors with a 2-mm ferrule were restored with a direct buildup using a nanohybrid direct composite resin (Miris 2 and Optibond FL) with or without a glass-fiber-reinforced post. An additional group of 15 teeth without a ferrule were restored with buildup and a fiber post. All teeth were prepared to receive bonded glass ceramic crowns (e.max CAD luted with Variolink Esthetic DC) and were subjected to accelerated fatigue testing. Cyclic isometric loading was applied to the incisal edge at an angle of 30° and a frequency of 5 Hz, beginning with a load of 100 N (×5000 cycles). A 100 N load increase was applied each 15,000 cycles. Specimens were loaded until failure or to a maximum of 1000 N (×140,000 cycles). Groups were compared using the Kaplan Meier survival analysis (log rank test at p=0.05).

RESULTS

 None of the tested specimens withstood all 140,000 load cycles. Specimens with posts but without a ferrule were affected by an initial failure phenomenon (wide gap at the lingual margin between the buildup/crown assembly and the root). There was a significant difference in mean survived cycles between the ferrule groups (Fp=73,332× and FNp=73,244×) and the no-ferrule group (50,121×; p=0.001). The addition of a fiber post was not significant in the presence of the ferrule (p=0.884). In both groups with posts, 100% of failures were unrestorable. The no-post group had 47% of restorable and possibly restorable failures.

CONCLUSIONS

 The survival of broken-down nonvital incisors was improved by the presence of the ferrule but not by the fiber-reinforced post. Fiber posts were always detrimental to the failure mode and were not able to compensate for the absence of a ferrule.

Patterns of service utilisation within Australian hepatology clinics: high prevalence of advanced liver disease

BACKGROUND

Liver diseases in Australia are estimated to affect 6 million people with a societal cost of $51 billion annually. Information about utilisation of specialist hepatology care is critical in informing policy makers about the requirements for delivery of hepatology-related healthcare.

AIMS

This study examined the aetiology and severity of liver disease seen in a tertiary hospital hepatology clinic, as well as the resource utilisation patterns.

METHODS

A longitudinal cohort study included consecutive patients booked in hepatology outpatient clinics during a 3-month period. Subsequent outpatient appointments for these patients over the following 12 months were then recorded.

RESULTS

During the initial 3-month period, 1471 appointments were scheduled with a hepatologist, 1136 of which were attended. Twenty-one per cent of patients were 'new cases'. Hepatitis B virus (HBV) was the most common disease aetiology for new cases (37%). Advanced disease at presentation varied between aetiology; only 5% of HBV cases had advanced liver disease at presentation, in contrast with HCV, NAFLD and ALD, in which advanced disease was identified at presentation in 31%, 46% and 72% of cases, respectively. Most patients (83%) attended multiple hepatology appointments, and a range of referral patterns for procedures, investigations and other specialty assessments were observed.

CONCLUSIONS

There is a high prevalence of HBV in new case referrals. Patients with HCV infection, NAFLD and ALD have a high prevalence of advanced liver disease at referral, requiring ongoing surveillance for development of decompensated liver disease and liver cancer. These findings that describe the patterns of health service utilisation among patients with liver disease provide useful information for planning sustainable health service provision for this clinical population.

Environmental stress in the Gulf of Mexico and its potential impact on public health

The Deepwater Horizon (DWH) oil spill in the Gulf of Mexico was the largest maritime oil spill in history resulting in the accumulation of genotoxic substances in the air, soil, and water. This has potential far-reaching health impacts on cleanup field workers and on the populations living in the contaminated coastal areas. We have employed portable airborne particulate matter samplers (SKC Biosampler Impinger) and a genetically engineered bacterial reporter system (umu-ChromoTest from EBPI) to determine levels of genotoxicity of air samples collected from highly contaminated areas of coastal Louisiana including Grand Isle, Port Fourchon, and Elmer's Island in the spring, summer and fall of 2011, 2012, 2013 and 2014. Air samples collected from a non-contaminated area, Sea Rim State Park, Texas, served as a control for background airborne genotoxic particles. In comparison to controls, air samples from the contaminated areas demonstrated highly significant increases in genotoxicity with the highest values registered during the month of July in 2011, 2013, and 2014, in all three locations. This seasonal trend was disrupted in 2012, when the highest genotoxicity values were detected in October, which correlated with hurricane Isaac landfall in late August of 2012, about five weeks before a routine collection of fall air samples. Our data demonstrate: (i) high levels of air genotoxicity in the monitored areas over last four years post DWH oil spill; (ii) airborne particulate genotoxicity peaks in summers and correlates with high temperatures and high humidity; and (iii) this seasonal trend was disrupted by the hurricane Isaac landfall, which further supports the concept of a continuous negative impact of the oil spill in this region.

MODELING STREAMFLOW AND WATER QUALITY SENSITIVITY TO CLIMATE CHANGE AND URBAN DEVELOPMENT IN 20 U.S. WATERSHEDS

Watershed modeling in 20 large, United States (U.S.) watersheds addresses gaps in our knowledge of streamflow, nutrient (nitrogen and phosphorus), and sediment loading sensitivity to mid-21st Century climate change and urban/residential development scenarios. Use of a consistent methodology facilitates regional scale comparisons across the study watersheds. Simulations use the Soil and Water Assessment Tool. Climate change scenarios are from the North American Regional Climate Change Assessment Program dynamically downscaled climate model output. Urban and residential development scenarios are from U.S. Environmental Protection Agency's Integrated Climate and Land Use Scenarios project. Simulations provide a plausible set of streamflow and water quality responses to mid-21st Century climate change across the U.S. Simulated changes show a general pattern of decreasing streamflow volume in the central Rockies and Southwest, and increases on the East Coast and Northern Plains. Changes in pollutant loads follow a similar pattern but with increased variability. Ensemble mean results suggest that by the mid-21st Century, statistically significant changes in streamflow and total suspended solids loads (relative to baseline conditions) are possible in roughly 30-40% of study watersheds. These proportions increase to around 60% for total phosphorus and total nitrogen loads. Projected urban/residential development, and watershed responses to development, are small at the large spatial scale of modeling in this study.

Immunological control of virus-induced tumors in primates

Cells infected by oncogenic viruses may transform, may develop a latent carrier state, or may be destroyed but understanding of the control of the results of infection is incomplete. Even if cells transform, ultimate development of a tumor may be immunologically controlled. For example, cells of some marmoset species transform after infection with RNA tumor viruses, and animals react to the transformed cells with cell-mediated and humoral immune responses. Both virus specific and cross-reacting cell membrane antigens have been demonstrated. Immune deficiency accelerates tumor growth or causes recurrence of a regressing tumor. In contrast certain simian herpesvirus (Herpesvirus saimiri, HVS and Herpesvirus ateles, HVA), which cause no or minor disease in their natural hosts, induce lymphomas or lymphoblastic leukemias in other primate species. The immune response of the natural host species to HVS is greater than that of animals developing malignancies after experimental infection. HVS and HVA share many properties with Epstein-Barr virus (EBV) of man, including antigens appearing early and late during infection and their related antibody responses but no evidence exists that they induce malignancies in their natural hosts. However, if induction is as infrequent as that with EBV and Burkitt's lymphoma (BL), we have not observed sufficient numbers of squirrel or spider monkeys to have seen a BL-like tumor. Interference with the immune systems of animals carrying HVS or HVA may induce tumor development, and clarify our understanding of the relationships between EBV and BL.

IL8 polymorphisms and overall survival in pazopanib- or sunitinib-treated patients with renal cell carcinoma

BACKGROUND

We evaluated germline single nucleotide polymorphisms (SNPs) for association with overall survival (OS) in pazopanib- or sunitinib-treated patients with advanced renal cell carcinoma (aRCC).

METHODS

The discovery analysis tested 27 SNPs within 13 genes from a phase III pazopanib trial (N=241, study 1). Suggestive associations were then pursued in two independent datasets: a phase III trial (COMPARZ) comparing pazopanib vs sunitinib (N=729, study 2) and an observational study of sunitinib-treated patients (N=89, study 3).

RESULTS

In study 1, four SNPs showed nominally significant association (P≤0.05) with OS; two of these SNPs (rs1126647, rs4073) in IL8 were associated (P≤0.05) with OS in study 2. Because rs1126647 and rs4073 were highly correlated, only rs1126647 was evaluated in study 3, which also showed association (P≤0.05). In the combined data, rs1126647 was associated with OS after conservative multiple-test adjustment (P=8.8 × 10(-5); variant vs reference allele hazard ratio 1.32, 95% confidence interval: 1.15-1.52), without evidence for heterogeneity of effects between studies or between pazopanib- and sunitinib-treated patients.

CONCLUSIONS

Variant alleles of IL8 polymorphisms are associated with poorer survival outcomes in pazopanib- or sunitinib-treated patients with aRCC. These findings provide insight in aRCC prognosis and may advance our thinking in development of new therapies.