Shrimp MultiPath™ multiplexed PCR white spot syndrome virus detection in penaeid shrimp.

White spot syndrome virus (WSSV), which causes white spot disease, is one of the notoriously feared infectious agents in the shrimp industry, inflicting estimated production losses world-wide of up to US$1 billion annually. Cost-effective accessible surveillance testing and targeted diagnosis are key to alerting shrimp industries and authorities worldwide early about WSSV carrier status in targeted shrimp populations. Here we present key validation pathway metrics for the Shrimp MultiPathTM (SMP) WSSV assay as part of the multi-pathogen detection platform. With superior throughput, fast turn-around time, and extremely low cost per test, the SMP WSSV assay achieves a high level of analytical sensitivity (~2.9 copies), perfect analytical specificity (~100%), and good intra- and inter-run repeatability (coefficient of variation <5%). The diagnostic metrics were estimated using Bayesian latent class analysis on data from 3 experimental shrimp populations from Latin America with distinct WSSV prevalence and yielded a diagnostic sensitivity of 95% and diagnostic specificity of 99% for SMP WSSV, which was higher than these parameters for the TaqMan quantitative PCR (qPCR) assays currently recommended by the World Organisation for Animal Health and the Commonwealth Scientific and Industrial Research Organisation. This paper additionally presents compelling data for the use of synthetic double-stranded DNA analyte spiked into pathogen-naïve shrimp tissue homogenate as a means to substitute clinical samples for assay validation pathways targeting rare pathogens. SMP WSSV shows analytical and diagnostic metrics comparable to qPCR-based assays and demonstrates fit-for-purpose performance for detection of WSSV in clinically diseased and apparently healthy animals.

Detection and genetic diversity of porcine rotavirus A, B and C in eastern Australian piggeries.

Rotaviruses (RV) have a high prevalence in piggeries worldwide and are one of the major pathogens causing severe diarrhoea in young pigs. RV species A, B, and C have been linked to piglet diarrhoea in Australian pig herds, but their genetic diversity has not been studied in detail. Based on sequencing of the structural viral protein 7 (VP7) RVA G genotypes G3, G4 and G5, and RVC types G1, G3, G5, and G6 have been identified in Australian piggeries in previous studies. Although occurrence of RVB was reported in Australia in 1988, no further genetic analysis has been conducted. To improve health management decisions in Australian pig herds, more information on RV prevalence and genetic diversity is needed. Here, 243 enteric samples collected from 20 pig farms within Eastern Australia were analysed for the presence of RV in different age groups using a novel PCR-based multiplex assay (Pork MultiPath™ enteric panel). RVA, RVB, and RVC were detected in 10, 14, and 14 farms, respectively. Further sequencing of VP7 in selected RV-positive samples revealed G genotypes G2, G5, G9 (RVA), G6, G8, G14, G16, G20 (RVB), and G1, G3, G5, G6 (RVC) present. RVA was only detected in young (<10 weeks old) pigs whereas RVB and RVC were also detected in older animals (>11 weeks old). Interestingly, RVB and RVC G-type occurrence differed between age groups. In conclusion, this study provides new insights on the prevalence and diversity of different RV species in pig herds of Eastern Australia whilst demonstrating the ability of the Pork MultiPath™ technology to accurately differentiate between these RV species.

Enterocytozoon hepatopenaei real-time and Shrimp MultiPathTM PCR assay validation for South-East Asian and Latin American strains of Penaeid shrimp.

Enterocytozoon hepatopenaei (EHP) infections are a global challenge for the Penaeid shrimp industry with a sharp rise in prevalence over the last 10 yr. EHP is known to cause sub-optimal growth, large size variation and reduced survival of shrimp. Molecular methods development has mainly focussed on 18S rRNA or spore wall protein 1 (SWP1). Due to the specificity and sensitivity issues with previously designed assays for both targets, new molecular assays are needed by the global shrimp industry and regulators to help manage the risks posed by EHP. This paper describes new real-time PCR (qPCR) methods developed for the novel EHP gene targets polar tube protein 2 (PTP2) and spore wall protein 26 (SWP26), whilst also presenting performance metrics of the new Shrimp MultiPathTM technology EHP assay. qPCR assays PTP2G and SWP26G show high amplification efficiency, a limit of detection (LOD) of between 1 and 4 copies, low assay variation and high diagnostic sensitivity (DSe) and specificity (DSp) compared to imperfect reference assays. Similar performance is seen with Shrimp MultiPathTM EHP showing an LOD of 8 copies, low assay variation and high DSe and DSp. These novel molecular targets for EHP and Shrimp MultiPathTM EHP strengthen global efforts to monitor and mitigate risks of EHP infections and outbreaks. Moreover, this study presents novel data on distribution of EHP in shrimp populations from South-East Asia and Latin America, and how sequence variations need to be considered when monitoring EHP in different geographies.

Safety evaluation of calcium L-methylfolate.

Calcium L-methylfolate (L-5-MTHF-Ca; CAS Number 151533-22-1) is a source of folate and an alternative to folic acid for use in human food and food supplements. The safety of L-5-MTHF-Ca was evaluated by testing for genotoxicity, subchronic and prenatal developmental toxicity. In in vitro assays L-5-MTHF-Ca was not mutagenic and did not induce other chromosomal events. Additionally, L-5-MTHF-Ca was not genotoxic in the in vivo micronucleus test nor did it induce DNA damage in rat liver cells. In a subchronic toxicity study, rats administered up to 400 mg/kg bw/day of L-5-MTHF-Ca via oral gavage for 13 weeks had no treatment-related mortalities, and no treatment-related effects were identified on behaviour, body weight, food consumption, ophthalmology, haematology, or organ weights. No treatment-related macroscopic or histopathological findings were observed. Calcium and sodium levels increased with increasing dosage, however the slight increases were within historical control ranges and reversible after the recovery period. L-5-MTHF-Ca is neither teratogenic nor embryotoxic. Based on the results of the in vitro and in vivo studies, the safe use of L-5-MTHF-Ca as an ingredient in foods is supported. The no observed adverse effect level was the highest dose in the subchronic toxicity study, i.e. 400 mg/kg bw/day for male and female rats.

Structure, property, and function of sheepshead (Archosargus probatocephalus) teeth.

OBJECTIVES: This paper studies A. probatocephalus teeth and investigates the mechanical properties and chemical composition of the enameloid and dentin. DESIGN: Nanoindentation tests with a max load of 1000 µN and X-ray Energy Dispersive Spectroscopy (EDS) were performed along the diameter of the polished sample. Microstructural analysis of the dentin tubules was performed from SEM images. RESULTS: From nanoindentation testing, the dentin of the sheepshead teeth has a nanoindentation hardness of 0.89 ±â€¯0.21 (mean ±â€¯S.D.) GPa and a reduced Young's modulus of 23.29 ±â€¯5.30 GPa. The enameloid of A. probatocephalus has a hardness of 4.36 ±â€¯0.44 GPa and a mean reduced Young's modulus of 98.14 ±â€¯6.91 GPa. Additionally, nanoindentation tests showed that the enameloid's hardness and modulus increased closer to the surface of the tooth. X-ray Energy Dispersive Spectroscopy (EDS) data further suggests that the gradient may be a result of the wt% fluoride within the enameloid, where an increase in fluoride results in an increase in reduced Young's modulus and hardness. CONCLUSION: The microstructural characterization of the number density and area of the dentin tubules were used to address the porosity effect in the dentin to achieve the experimentally validated microhardness. The mechanical properties of the sheepshead teeth were also compared with previous nanoindentation tests from other aquatic species. The sheepshead teeth exhibit a greater reduced Young's modulus and hardness compared to shark and piranha teeth.

Classics revisited. Raissa Nitabuch, on the uteroplacental circulation and the fibrinous membrane.

The adaptive conversion of spiral arteries is essential for pregnancy physiology and incomplete conversion is associated with preeclampsia and intrauterine growth restriction. The anatomy of the uteroplacental circulation as well as the basic concept of nutrition of the foetus had been a matter of dispute among scientists for a long time. Based on the study of an autopsy of a pregnant uterus, Raissa Nitabuch was the first to give an accurate description of the uteroplacental circulation in her doctoral thesis in 1887. In this thesis, the fibrinous layer in the decidua was identified as site of detachment of the placenta from the uterine wall after delivery of the baby. Although this was only an accidental finding, as "Nitabuch membrane" this fibrinous layer up to this day is associated with her name. It is unclear, why the much more important findings on the uteroplacental circulation never were published in a scientific journal. Today the basic anatomy of the uteroplacental circulation is unquestioned. However, it remains largely unknown, that the first accurate description appeared as a doctoral thesis. In view of the ongoing investigations on function and regulation of uteroplacental circulation, there can be no doubt, that an original publication of the findings of Raissa Nitabuch in a scientific journal today would be a "Classic" deserving to be revisited.

A hierarchical Bayesian framework for force field selection in molecular dynamics simulations.

We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different environmental conditions with the corresponding variability in experimental data. The high computational cost associated with the hierarchical Bayesian framework is reduced by orders of magnitude through a parallelized Transitional Markov Chain Monte Carlo method combined with the Laplace Asymptotic Approximation. The suitability of the hierarchical approach is demonstrated by performing MD simulations with prescribed parameters to obtain data for transport coefficients under different conditions, which are then used to infer and evaluate the parameters of the MD model. We demonstrate the selection of MD models based on experimental data and verify that the hierarchical model can accurately quantify the uncertainty across experiments; improve the posterior probability density function estimation of the parameters, thus, improve predictions on future experiments; identify the most plausible force field to describe the underlying structure of a given dataset. The framework and associated software are applicable to a wide range of nanoscale simulations associated with experimental data with a hierarchical structure.

LGR5 rs17109924 is a predictive genetic biomarker for time to recurrence in patients with colon cancer treated with 5-fluorouracil-based adjuvant chemotherapy.

We recently found variants in cancer stem cell genes (CD44, ALCAM and LGR5) significantly associated with increased time to recurrence (TTR) in patients with stage III and high-risk stage II colon cancer treated with 5-fluorouracil (5-FU)-based chemotherapy. In this study, we validated these genetic biomarkers in a large and independent patient cohort (n=599). Patients who received 5-FU-based adjuvant chemotherapy (n=391) carrying at least one C allele in LGR5 rs17109924 had a significantly increased TTR compared with patients carrying the homozygous T/T variant (HR 0.38, 95%CI 0.19-0.79; P=0.006). In patients treated with surgery alone (n=208), no association between LGR rs17109924 and TTR was found (P=0.728). In the multivariate Cox-analysis, LGR5 rs17109924 remained statistically significant (HR 0.38, 95%CI 0.18-0.78; P=0.008) for patients who received adjuvant chemotherapy. We confirmed in a large and independent study cohort that LGR5 rs17109924 is a predictive genetic biomarker for TTR in patients with colon cancer treated with 5-FU-based adjuvant chemotherapy.

Race and health profiles in the United States: an examination of the social gradient through the 2009 CHIS adult survey.

OBJECTIVE: To examine the role of the social gradient on multiple health outcomes and behaviors. It was predicted that higher levels of SES, measured by educational attainment and family income, would be associated with positive health behaviors (i.e., smoking, drinking, physical activity, and diet) and health status (i.e., limited physical activity due to chronic condition, blood pressure, obesity, diabetes, BMI, and perceived health condition). The study also examined the differential effects of the social gradient in health among different racial/ethnic groups (i.e., non-Hispanic Whites, Blacks, Asian, Hispanics, and American Indians). STUDY DESIGN: Cross-sectional study. METHODS: The data were from the adult 2009 California Health Interview Survey (CHIS). Weighted multivariable linear and logistic regression models were conducted to examine trends found between SES and health conditions and health behaviors. Polynomial trends were examined for all linear and logistic models to test for the possible effects (linear, quadratic, and cubic) of the social gradient on health behaviors and outcomes stratified by race/ethnicity. RESULTS: Findings indicated that, in general, Whites had more favorable health profiles in comparison to other racial/ethnic groups with the exception of Asians who were likely to be as healthy as or healthier than Whites. Predicted marginals indicated that Asians in the upper two strata of social class display the healthiest outcomes of health status among all other racial/ethnic groups. Also, the social gradient was differentially associated with health outcomes across race/ethnicity groups. While the social gradient was most consistently observed for Whites, education did not have the same protective effect on health among Blacks and American Indians. Also, compared to other minority groups, Hispanics and Asians were more likely to display curvilinear trends of the social gradient: an initial increase from low SES to mid-level SES was associated with worse health outcomes and behaviors; however, continued increase from mid-SES to high SES saw returns to healthy outcomes and behaviors. CONCLUSION: The study contributes to the literature by illustrating unique patterns and trends of the social gradient across various racial/ethnic populations in a nationally representative sample. Future studies should further explore temporal trends to track the impact of the social gradient for different racial and ethnic populations in tandem with indices of national income inequalities.

An integrated approach to safety-driven and ICT-enabled process reengineering: methodological advice and a case study.

Patient safety is a central concern inside any healthcare environment. With the progress of Information and Communication Technologies (ICTs), new solutions have become available to support care and management processes. Analyzing process risks helps identifying areas of improvement and provides ICT-solutions design with indications on what portions of the process need primary interventions. Understanding the link between process reengineering, technology assessment of enabling technologies and risk management allows user acceptance and patient safety improvements. Fondazione IRCCS Istituto Nazionale dei Tumori (INT), offers a good example of process reengineering driven by the purpose of increasing patient safety, enabled by new technologies. A pillar of the evolution of ICT process support at INT is based on Radio Frequency Identification technologies, implemented to identify and trace items and people across processes. This paper will present an integrated approach, based on process reengineering methodologies and risk assessment studies, and methodological advice applied to a case of surgical kits management procedures.

ARF inhibits the growth and malignant progression of non-small-cell lung carcinoma.

Non-small-cell lung carcinoma (NSCLC) is among the deadliest of human cancers. The CDKN2A locus, which houses the INK4a and ARF tumor suppressor genes, is frequently altered in NSCLC. However, the specific role of ARF in pulmonary tumorigenesis remains unclear. KRAS and other oncogenes induce the expression of ARF, thus stabilizing p53 activity and arresting cell proliferation. To address the role of ARF in Kras-driven NSCLC, we compared the susceptibility of NIH/Ola strain wild-type and Arf-knockout mice to urethane-induced lung carcinogenesis. Lung tumor size, malignancy and associated morbidity were significantly increased in Arf(-/-) compared with Arf(+/+) animals at 25 weeks after induction. Pulmonary tumors from Arf-knockout mice exhibited increased cell proliferation and DNA damage compared with wild-type mice. A subgroup of tumors in Arf(-/-) animals presented as dedifferentiated and metastatic, with many characteristics of pulmonary sarcomatoid carcinoma, a neoplasm previously undocumented in mouse models. Our finding of a role for ARF in NSCLC is consistent with the observation that benign adenomas from Arf(+/+) mice robustly expressed ARF, while ARF expression was markedly reduced in malignant adenocarcinomas. ARF expression also frequently colocalized with the expression of p21(CIP1), a transcriptional target of p53, arguing that ARF induces the p53 checkpoint to arrest cell proliferation in vivo. Taken together, these findings demonstrate that induction of ARF is an early response in lung tumorigenesis that mounts a strong barrier against tumor growth and malignant progression.

Validation of C-reactive protein levels as a prognostic indicator for survival in a large cohort of pancreatic cancer patients.

BACKGROUND: Recent evidence indicates that the host inflammatory response has an important role in the tumour progression. Elevated C-reactive protein (CRP) levels have been previously associated with poor prognosis in several cancer types including small-scale studies in pancreatic cancer (PC) patients. The purpose of the present study was to validate the prognostic impact of plasma CRP levels at date of diagnosis on cancer-specific survival (CSS) in a large cohort of PC patients. METHODS: Data from 474 consecutive patients with adenocarcinoma of the pancreas, treated between 2004 and 2012 at a single centre, were evaluated retrospectively. CSS was analysed using the Kaplan-Meier method. To evaluate the prognostic significance of plasma CRP levels, univariate and multivariate Cox analyses were applied. RESULTS: High plasma CRP levels at diagnosis were significantly associated with well-established prognostic factors, including high tumour stage and tumour grade and the administration of chemotherapy (P<0.05). In univariate analysis, we observed that a high plasma CRP level was a consistent factor for poor CSS in PC patients (hazard ratio (HR)=2.21; 95% confidence interval (CI)=1.68-2.92, P<0.001). In multivariate analysis, tumour stage, grade, administration of chemotherapy, a high neutrophil-lymphocyte ratio and the highest quartile of CRP levels (HR=1.60, 95% CI=1.16-2.21; P=0.005) were identified as independent prognostic factors in PC patients. CONCLUSION: In conclusion, we confirmed a significant association of elevated CRP levels with poor clinical outcome in PC patients. Our results indicate that the plasma CRP level might represent a useful marker for patient stratification in PC management.

The preoperative lymphocyte to monocyte ratio predicts clinical outcome in patients with stage III colon cancer.

BACKGROUND: Inflammation has a critical role in the pathogenesis and progression of cancer. The lymphocyte to monocyte ratio (LMR) could be shown to be prognostic in haematologic neoplasia. In this study, we analysed the LMR with clinical outcome in stage II and III colon cancer patients. METHODS: Three hundred and seventy-two patients with stage II and III colon cancer were included in this retrospective study. Kaplan-Meier curves and multivariate Cox-regression analyses were calculated for time to recurrence (TTR) and overall survival (OS). RESULTS: Including all patients, the elevated preoperative LMR was significantly associated with increased TTR and OS in multivariate analysis (HR: 0.47, 95%CI: 0.29-0.76, P=0.002; HR: 0.51, 95%CI: 0.31-0.83, P=0.007; respectively). In subanalyses, the association was limited to patients with stage III (HR: 0.40, 95%CI: 0.22-0.72, P=0.002), in contrast to patients with stage II (HR: 0.40, 95%CI: 0.28-1.66, P=0.397). When the subgroup of patients with 'high-risk' LMR≤2.83 was analysed, no benefit of adjuvant 5-FU-based chemotherapy could be found (HR: 0.99; 95%CI: 0.60-1.63; P=0.953). CONCLUSION: The LMR might be an independent prognostic marker for TTR in stage III colon cancer patients. Our results further suggest that high-risk patients based on the LMR do not benefit from adjuvant chemotherapy. Independent validation of our findings is warranted.

A derived neutrophil to lymphocyte ratio predicts clinical outcome in stage II and III colon cancer patients.

BACKGROUND: Inflammation has a critical role in the pathogenesis and progression of cancer. Recently, the derived neutrophil to lymphocyte ratio (absolute count of neutrophils divided by the absolute white cell count minus the absolute count of neutrophils; dNLR) has been shown to influence clinical outcome in various cancer entities. In this study, we analysed the dNLR with clinical outcome in stage II and III colon cancer patients. METHODS: Three-hundred and seventy-two patients with stage II and III colon cancer were included in this retrospective study. Kaplan-Meier curves and multivariate Cox proportion analyses were calculated for time to recurrence (TTR) and overall survival (OS). RESULTS: In univariate analysis, the elevated preoperative dNLR was significantly associated with decreased TTR (hazard ratio (HR) 2.38, 95% confidence interval (CI) 1.57-3.6, P<0.001) and remained significant in multivariate analysis. Patients with dNLR >3 had a median TTR of 83 months, and patients with dNLR ≤ 3 showed a median TTR of 132 months. In OS analysis, a dNLR >2.2 was significantly associated with decreased OS in univariate (HR 1.85, 95% CI 1.11-3.08, P=0.018) and multivariate analysis. Patients with dNLR >2.2 showed a median OS of 121 months, and patients with dNLR ≤ 2.2 had a median OS of 147 months. CONCLUSION: The dNLR may be an independent prognostic marker for TTR and OS in patients with stage II and III colon cancer. Independent validation of our findings is warranted.

The effect of a Bacillus-based direct-fed microbial supplemented to sows on the gastrointestinal microbiota of their neonatal piglets.

Direct-fed microbials (DFM) supplemented in sow diets may confer health benefits to the host and their piglets by reducing pathogens in the sow and environment. In this study we evaluated the effect of a Bacillus-based DFM on the gastrointestinal microbiota of neonatal piglets. A total of 208 sows were divided into 2 treatments: a control diet and the control diet supplemented with a Bacillus subtilis-based DFM (3.75 × 10(5) cfu/g feed). Twenty-one piglets sampled from each sow treatment group were euthanized on d 3 of lactation followed by an additional 15 piglets per treatment on d 10 of lactation. Litters from DFM-supplemented sows had greater (P = 0.02) weaning weights and a tendency (P = 0.09) for improvement in litter ADG. Sows supplemented with the DFM weaned more pigs (P = 0.06) than control sows which was reflected in numerically lower but not statistically different (P = 0.12) decrease in piglet mortality in DFM litters. Terminal RFLP was used to characterize gastrointestinal (GI) microbial populations in the ileum and colon of the piglets. Terminal restriction fragments (T-RF) were compared between control and DFM treatments. There was a greater incidence and quantity of T-RF B423 and H330 (binary P = 0.01, 0.08; quantitative P = 0.01, 0.05, respectively), putatively identified as Lactobacillus gasseri/johnsonii, in the ileum of pigs nursing sows supplemented with DFM at d 3. Terminal restriction fragment peaks B423 and H330 were also greater (binary P = 0.01, 0.08; quantitative P = 0.01, 0.01, respectively) in the colon of pigs nursing sows supplemented with DFM at d 3. Peaks M495 and B394, putatively identified as E. coli, were greater (binary P = 0.01, 0.04; quantitative P = 0.01, 0.01, respectively) in the colon of the control pigs at d 3. At d 10, both the presence and quantity of Lactobacillus species were greater (P < 0.05) in the colon of pigs with the DFM treatment. Additionally, there was a tendency for T-RF B227 and H257 (binary P = 0.07, 0.07, respectively), putatively identified as Clostridium perfringens, to be present in the ileum of the control pigs at d 10 compared with treated pigs. Results of this study reveal that the developing gastrointestinal microbiota of a neonatal piglet can be affected by DFM supplementation to the sow.

Finding the striatum in sheep: use of a multi-modal guided approach for convection enhanced delivery.

Our goal is delivery of a long-term treatment for Huntington's disease. We administer intracerebrally in sheep adeno-associated virus (AAV) to establish optimal safety, spread and neuronal uptake of AAV based therapeutics. Sheep have large gyrencephalic brains and offer the opportunity to study a transgenic Huntington's disease model. However, lack of a relevant brain stereotactic atlas and the difficulty of skull fixation make conventional stereotaxy unreliable. We describe a multi-modal image-guidance technique to achieve accurate placement of therapeutics into the sheep striatum.

Mechanical properties and structure of the biological multilayered material system, Atractosteus spatula scales.

During recent decades, research on biological systems such as abalone shell and fish armor has revealed that these biological systems employ carefully arranged hierarchical multilayered structures to achieve properties of high strength, high ductility and light weight. Knowledge of such structures may enable pathways to design bio-inspired materials for various applications. This study was conducted to investigate the spatial distribution of structure, chemical composition and mechanical properties in mineralized fish scales of the species Atractosteus spatula. Microindentation tests were conducted, and cracking patterns and damage sites in the scales were examined to investigate the underlying protective mechanisms of fish scales under impact and penetration loads. A difference in nanomechanical properties was observed, with a thinner, stiffer and harder outer layer (indentation modulus ∼69 GPa and hardness ∼3.3 GPa) on a more compliant and thicker inner layer (indentation modulus ∼14.3 GPa and hardness ∼0.5 GPa). High-resolution scanning electron microscopy imaging of a fracture surface revealed that the outer layer contained oriented nanorods embedded in a matrix, and that the nanostructure of the inner layer contained fiber-like structures organized in a complex layered pattern. Damage patterns formed during microindentation show complex deformation mechanisms. Images of cracks identify growth through the outer layer, then deflection along the interface before growing and arresting in the inner layer. High-magnification images of the crack tip in the inner layer show void-linking and fiber-bridging exhibiting inelastic behavior. The observed difference in mechanical properties and unique nanostructures of different layers may have contributed to the resistance of fish scales to failure by impact and penetration loading.