RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays

<p>Abstract</p> <p>Background</p> <p>Reverse Phase Protein Arrays (RPPA) are convenient assay platforms to investigate the presence of biomarkers in tissue lysates. As with other high-throughput technologies, substantial amounts of analytical data are generated. Over 1000 samples may be printed on a single nitrocellulose slide. Up to 100 different proteins may be assessed using immunoperoxidase or immunoflorescence techniques in order to determine relative amounts of protein expression in the samples of interest.</p> <p>Results</p> <p>In this report an RPPA Information Management System (RIMS) is described and made available with open source software. In order to implement the proposed system, we propose a metadata format known as reverse phase protein array markup language (RPPAML). RPPAML would enable researchers to describe, document and disseminate RPPA data. The complexity of the data structure needed to describe the results and the graphic tools necessary to visualize them require a software deployment distributed between a client and a server application. This was achieved without sacrificing interoperability between individual deployments through the use of an open source semantic database, S3DB. This data service backbone is available to multiple client side applications that can also access other server side deployments. The RIMS platform was designed to interoperate with other data analysis and data visualization tools such as Cytoscape.</p> <p>Conclusion</p> <p>The proposed RPPAML data format hopes to standardize RPPA data. Standardization of data would result in diverse client applications being able to operate on the same set of data. Additionally, having data in a standard format would enable data dissemination and data analysis.</p

Honey bee foraging distance depends on month and forage type

To investigate the distances at which honey bee foragers collect nectar and pollen, we analysed 5,484 decoded waggle dances made to natural forage sites to determine monthly foraging distance for each forage type. Firstly, we found significantly fewer overall dances made for pollen (16.8 %) than for non-pollen, presumably nectar (83.2 %; P < 2.2 × 10−23). When we analysed distance against month and forage type, there was a significant interaction between the two factors, which demonstrates that in some months, one forage type is collected at farther distances, but this would reverse in other months. Overall, these data suggest that distance, as a proxy for forage availability, is not significantly and consistently driven by need for one type of forage over the other

Limb-shaking transient ischemic attacks: case report and review of literature

BACKGROUND: Limb shaking Transient Ischemic Attack is a rare manifestation of carotid-occlusive disease. The symptoms usually point towards a seizure like activity and misdiagnosed as focal seizures. On careful history the rhythmic seizure like activity reveals no Jacksonian march mainly precipitated by maneuvers which lead to carotid compression. We here present a case of an elderly gentleman who was initially worked up as suffering from epileptic discharge and then later on found to have carotid occlusion. CASE PRESENTATION: Elderly gentleman presented with symptoms of rhythmic jerky movements of the left arm and both the lower limbs. Clinical suspicion of focal epilepsy was made and EEG, MRI-Brain with MRA were done. EEG and MRI-Brain revealed normal findings but the MRA revealed complete occlusion of right internal carotid artery. On a follow-up visit jerky movements of the left arm were precipitated by hyperextension and a tremor of 3–4 Hz was revealed. Based on this the diagnosis of low flow TIA was made the patient was treated conservatively with adjustment of his anti-hypertensive and anti-platelet medications. CONCLUSION: Diagnosis of limb-shaking TIA is important and should be differentiated from other disorders presenting as tremors. Timely diagnosis is important as these patients are shown to benefit from reperfusion procedures either surgical or radiological reducing their risk of stroke

Attaining the canopy in dry and moist tropical forests: strong differences in tree growth trajectories reflect variation in growing conditions

Availability of light and water differs between tropical moist and dry forests, with typically higher understorey light levels and lower water availability in the latter. Therefore, growth trajectories of juvenile trees—those that have not attained the canopy—are likely governed by temporal fluctuations in light availability in moist forests (suppressions and releases), and by spatial heterogeneity in water availability in dry forests. In this study, we compared juvenile growth trajectories of Cedrela odorata in a dry (Mexico) and a moist forest (Bolivia) using tree rings. We tested the following specific hypotheses: (1) moist forest juveniles show more and longer suppressions, and more and stronger releases; (2) moist forest juveniles exhibit wider variation in canopy accession pattern, i.e. the typical growth trajectory to the canopy; (3) growth variation among dry forest juveniles persists over longer time due to spatial heterogeneity in water availability. As expected, the proportion of suppressed juveniles was higher in moist than in dry forest (72 vs. 17%). Moist forest suppressions also lasted longer (9 vs. 5 years). The proportion of juveniles that experienced releases in moist forest (76%) was higher than in dry forest (41%), and releases in moist forests were much stronger. Trees in the moist forest also had a wider variation in canopy accession patterns compared to the dry forest. Our results also showed that growth variation among juvenile trees persisted over substantially longer periods of time in dry forest (>64 years) compared to moist forest (12 years), most probably because of larger persistent spatial variation in water availability. Our results suggest that periodic increases in light availability are more important for attaining the canopy in moist forests, and that spatial heterogeneity in water availability governs long-term tree growth in dry forests

Discovery of New Molecular Subtypes in Oesophageal Adenocarcinoma

A large number of patients suffering from oesophageal adenocarcinomas do not respond to conventional chemotherapy; therefore, it is necessary to identify new predictive biomarkers and patient signatures to improve patient outcomes and therapy selections. We analysed 87 formalin-fixed and paraffin-embedded (FFPE) oesophageal adenocarcinoma tissue samples with a reverse phase protein array (RPPA) to examine the expression of 17 cancer-related signalling molecules. Protein expression levels were analysed by unsupervised hierarchical clustering and correlated with clinicopathological parameters and overall patient survival. Proteomic analyses revealed a new, very promising molecular subtype of oesophageal adenocarcinoma patients characterised by low levels of the HSP27 family proteins and high expression of those of the HER family with positive lymph nodes, distant metastases and short overall survival. After confirmation in other independent studies, our results could be the foundation for the development of a Her2-targeted treatment option for this new patient subgroup of oesophageal adenocarcinoma

Hereditary leiomyomatosis and renal cell cancer presenting as metastatic kidney cancer at 18 years of age: implications for surveillance

Hereditary leiomyomatosis and renal cell cancer (HLRCC) is an autosomal dominant syndrome characterized by skin piloleiomyomas, uterine leiomyomas and papillary type 2 renal cancer caused by germline mutations in the fumarate hydratase (FH) gene. Previously, we proposed renal imaging for FH mutation carriers starting at the age of 20 years. However, recently an 18-year-old woman from a Dutch family with HLRCC presented with metastatic renal cancer. We describe the patient and family data, evaluate current evidence on renal cancer risk and surveillance in HLRCC and consider the advantages and disadvantages of starting surveillance for renal cancer in childhood. We also discuss the targeted therapies administered to our patient

Day-to-Day Test–Retest Variability of CBF, CMRO2, and OEF Measurements Using Dynamic 15O PET Studies

Contains fulltext : 169592.pdf (publisher's version ) (Open Access)PURPOSE: We assessed test-retest variability of cerebral blood flow (CBF), cerebral blood volume (CBV), cerebral metabolic rate of oxygen (CMRO(2)), and oxygen extraction fraction (OEF) measurements derived from dynamic (15)O positron emission tomography (PET) scans. PROCEDURES: In seven healthy volunteers, complete test-retest (15)O PET studies were obtained; test-retest variability and left-to-right ratios of CBF, CBV, OEF, and CMRO(2) in arterial flow territories were calculated. RESULTS: Whole-brain test-retest coefficients of variation for CBF, CBV, CMRO(2), and OEF were 8.8%, 13.8%, 5.3%, and 9.3%, respectively. Test-retest variability of CBV left-to-right ratios was <7.4% across all territories. Corresponding values for CBF, CMRO(2), and OEF were better, i.e., <4.5%, <4.0%, and <1.4%, respectively. CONCLUSIONS: The test-retest variability of CMRO(2) measurements derived from dynamic (15)O PET scans is comparable to within-session test-retest variability derived from steady-state (15)O PET scans. Excellent regional test-retest variability was observed for CBF, CMRO(2), and OEF. Variability of absolute CBF and OEF measurements is probably affected by physiological day-to-day variability of CBF

Colonial America

The first permanent British settlement in what became the United States was established in 1607, nearly 170 years prior to the American declaration of independence. This chapter examines the economic development of the British North American colonies that became the United States. As it describes, abundant natural resources and scarce labor and capital contributed to the remarkable growth in the size of the colonial economy, and allowed the free white colonial population to enjoy a relatively high standard of living. There was not, however, much improvement over time in living standards. Patterns of factor abundance also played an important role in shaping colonial institutions, encouraging reliance on indentured and enslaved labor as well as the development of representative government. For most of the colonial era, the colonists happily accepted their relationship to Britain. After 1763, however, changes in British policies following the end of the Seven Years War created growing tensions with the colonists and ultimately led to the colonies to declare their independence