ECONOMIC AND ENVIRONMENTAL BENEFITS OF SOIL/WATER NITROGEN TESTING: THE CASE OF CENTRAL NEBRASKA

This research presents a competitive dynamic model to evaluate the economic and groundwater quality benefits resulting from the adoption of soil/water nitrogen testing. The model is applied to an irrigated corn production county in the Nebraska Mid-State area where the groundwater contamination level from nitrates is reported to be, on average, 18.7 parts per million (ppm). Adoption of nutrient management practices would result in increased economic benefits to farmers and reduced nitrate stocks in groundwater.Environmental Economics and Policy,

Vitamin D levels in peanut allergic children

Background The prevalence of peanut allergy is increasing. The reasons for this are not entirely known. A factor may be vitamin D (Vit D). Methods This study was performed in a referral allergist’s office in Ontario. Prospectively, all patients (\u3c18 years old) with peanut allergy who were tested for peanut specific IgE (PN IgE) also had Vit D measured. All measurements were done between December 2010 and May 2011. The Vit D measure was 25-hydroxy vitamin D. Patients were divided into three groups: deficient (less than 25 nmol/L), insufficient (25-75 nmol/L) and sufficient (75-250 nmol/L). Vit D levels were compared to PN IgE, sex, age, body mass index (BMI) and other allergies. Results Fifty peanut allergic patients were included. The mean Vit D level of the patients was 73.8 nmol/L and the 95% confidence interval was 69.6 - 75.7 nmol/L. One patient (2%) had deficient and thirty-one (62%) of the patients had insufficient Vit D levels. Nineteen (38%) had Vit D levels in the sufficient range. There was no correlation between Vit D levels and PN IgE or BMI. Generalized linear modeling showed that vit D levels were predicted by age and sex (p=0.04 & p=0.002, respectively). Conclusions Two percent of our patients had deficient Vit D levels while 62% of our patients had insufficient Vit D levels. These levels were statistically associated with age and sex. Insufficiency of Vit D may play a role in peanut allergy

Omalizumab: Practical considerations regarding the risk of anaphylaxis

Omalizumab has demonstrated efficacy among patients with moderate to severe persistent allergic asthma, whose symptoms are inadequately controlled with other controller agents. This therapy is generally well tolerated, but there are some safety considerations, the most important of which is the rare, but potentially life-threatening, occurrence of omalizumab-associated anaphylaxis

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. TopHat2 can align reads of various lengths produced by the latest sequencing technologies, while allowing for variable-length indels with respect to the reference genome. In addition to de novo spliced alignment, TopHat2 can align reads across fusion breaks, which can occur after genomic translocations. TopHat2 combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes. TopHat2 is available at http://ccb.jhu.edu/software/tophat

Differential response of lymphatic, venous and arterial endothelial cells to angiopoietin-1 and angiopoietin-2

BACKGROUND: The lymphatic system complements the blood circulatory system in absorption and transport of nutrients, and in the maintenance of homeostasis. Angiopoietins 1 and 2 (Ang1 and Ang2) are regulators of both angiogenesis and lymphangiogenesis through the Tek/Tie-2 receptor tyrosine kinase. The response of endothelial cells to stimulation with either Ang1 or Ang2 is thought to be dependent upon the origin of the endothelial cells. In this study, we examined the effects of the angiopoietins on lymphatic, venous and arterial primary endothelial cells (bmLEC, bmVEC and bmAEC, respectively), which were isolated and cultured from bovine mesenteric vessels. RESULTS: BmLEC, bmVEC and bmAEC cell populations all express Tie-2 and were shown to express the appropriate cellular markers Prox-1, VEGFR3, and Neuropilin-1 that define the particular origin of each preparation. We showed that while bmLECs responded slightly more readily to angiopoietin-2 (Ang2) stimulation, bmVECs and bmAECs were more sensitive to Ang1 stimulation. Furthermore, exposure of bmLECs to Ang2 induced marginally higher levels of proliferation and survival than did exposure to Ang1. However, exposure to Ang1 resulted in higher levels of migration in bmLECs than did to Ang2. CONCLUSION: Our results suggest that although both Ang1 and Ang2 can activate the Tie-2 receptor in bmLECs, Ang1 and Ang2 may have distinct roles in mesenteric lymphatic endothelial cells

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay. The volume and complexity of data from RNA-seq experiments necessitate scalable, fast and mathematically principled analysis software. TopHat and Cufflinks are free, open-source software tools for gene discovery and comprehensive expression analysis of high-throughput mRNA sequencing (RNA-seq) data. Together, they allow biologists to identify new genes and new splice variants of known ones, as well as compare gene and transcript expression under two or more conditions. This protocol describes in detail how to use TopHat and Cufflinks to perform such analyses. It also covers several accessory tools and utilities that aid in managing data, including CummeRbund, a tool for visualizing RNA-seq analysis results. Although the procedure assumes basic informatics skills, these tools assume little to no background with RNA-seq analysis and are meant for novices and experts alike. The protocol begins with raw sequencing reads and produces a transcriptome assembly, lists of differentially expressed and regulated genes and transcripts, and publication-quality visualizations of analysis results. The protocol's execution time depends on the volume of transcriptome sequencing data and available computing resources but takes less than 1 d of computer time for typical experiments and ~1 h of hands-on time

RTOG 0518: Randomized Phase III Trial to Evaluate Zoledronic Acid for Prevention of Osteoporosis and Associated Fractures in Prostate Cancer Patients

Background: RTOG 0518 evaluated the potential benefit of zoledronic acid therapy in preventing bone fractures for patients with high grade and/or locally advanced, non-metastatic prostate adenocarcinoma receiving luteinizing hormone-releasing hormone (LHRH) agonist and radiotherapy (RT). Methods: Eligible patients with T-scores of the hip ( −2.5 vs. > −1.0) and negative bone scans were prospectively randomized to either zoledronic acid, 4 mg, concurrently with the start of RT and then every six months for a total of 6 infusions (Arm 1) or observation (Arm 2). Vitamin D and calcium supplements were given to all patients. Secondary objectives included quality of life (QOL) and bone mineral density (BMD) changes over a period of three years. Results: Of 109 patients accrued before early closure, 96 were eligible. Median follow-up was 36.3 months for Arm I and 34.8 months for Arm 2. Only two patients experienced a bone fracture (1 in each arm) resulting in no difference in freedom from any bone fracture (p=0.95), nor in QOL. BMD percent changes from baseline to 36 months were statistically improved with the use of zoledronic acid compared to observation for the lumbar spine (6% vs. −5%, p<0.0001), left total hip (1% vs. −8%, p=0.0002), and left femoral neck (3% vs. −8%, p=0.0007). Conclusions: For patients with advanced, non-metastatic prostate cancer receiving LHRH agonist and RT, the use of zoledronic acid was associated with statistically improved BMD percent changes. The small number of accrued patients resulted in decreased statistical power to detect any differences in the incidence of bone fractures or QOL

Skin prick testing with extensively heated milk or egg products helps predict the outcome of an oral food challenge: a retrospective analysis

<p>Abstract</p> <p>Background</p> <p>Cow’s milk and hen’s egg are the most frequently encountered food allergens in the pediatric population. Skin prick testing (SPT) with commercial extracts followed by an oral food challenge (OFC) are routinely performed in the diagnostic investigation of these children. Recent evidence suggests that milk-allergic and/or egg-allergic individuals can often tolerate extensively heated (EH) forms of these foods. This study evaluated the predictive value of a negative SPT with EH milk or egg in determining whether a child would tolerate an OFC to the EH food product.</p> <p>Methods</p> <p>Charts from a single allergy clinic were reviewed for any patient with a negative SPT to EH milk or egg, prepared in the form of a muffin. Data collected included age, sex, symptoms of food allergy, co-morbidities and the success of the OFC to the muffin.</p> <p>Results</p> <p>Fifty-eight patients had negative SPTs to the EH milk or egg in a muffin and underwent OFC to the appropriate EH food in the outpatient clinic. Fifty-five of these patients tolerated the OFC. The negative predictive value for the SPT with the EH food product was 94.8%.</p> <p>Conclusions</p> <p>SPT with EH milk or egg products was predictive of a successful OFC to the same food. Larger prospective studies are required to substantiate these findings.</p