Monitoring and controlling distributed applications using Lomita (position paper)

Over the last four years, the Meta toolkit was developed for controlling distributed applications. This toolkit has been publicly available as part of the academic ISIS release, and has been used for building various system monitoring and control applications. One major stumbling block with using Meta has been the language (called NPL) it supports. NPL is very low-level and using it is difficult, in the same way it is difficult to write machine language programs or raw Postscript programs. Hence, a higher level language was built along with a runtime environment. The hope is that with this higher-level approach, more complicated Meta applications will be written and thereby concentrate more on the use (and limitations) of Meta as an architecture. The Meta toolkit is reviewed with its intended use. Next, the goals with Lomita and an overview is given of its architecture and language syntax. A detailed example is given of Lomita's use by presenting a complete program for a load-adaptable service

Progesterone and Luteinizing hormone secretion patterns in early pregnant gilts

Abstract We studied luteinizing hormone (LH) pulsatility and episodic progesterone release of the corpus luteum (CL) on Day 11 and Day 21 in inseminated gilts and aimed to establish a relationship between these two hormones. Blood was collected at 15-minute intervals for 12 hours on Days 11, 16, and 21 from a vena cava caudalis catheter. At euthanasia eight gilts were pregnant and six gilts were not pregnant. Progesterone parameters (basal, mean, pulse frequency, and pulse amplitude) did not differ between pregnant and non-pregnant gilts on Day 11, LH pulse frequency and amplitude tended to differ (p = 0.07 and p = 0.079). In pregnant gilts basal and mean progesterone, progesterone pulse amplitude and frequency declined significantly from Day 11 to Day 21 (p <0.05). A significant decline was also seen in the LH pulse amplitude from Day 11 to Day 21 (p <0.05). None of the LH pulses was followed by a progesterone pulse within 1 hour on Day 21. On Day 11 and Day 21 appeared a synchronicity in the LH pulse pattern, as there were two or three LH pulses in 12 hours and these LH pulses appeared in the same time window. We conclude that on Day 11 and Day 21 of pregnancy in gilts progesterone pulses do not follow an LH pulse within one hour. Further we demonstrated that the successful or not successful formation of a CL of pregnancy is independent of progesterone release on Day 11 after insemination. We confirmed the decline of progesterone from Day 11 to Day 21 in the vena cava caudalis and could demonstrate that this decline is partly due to lower progesterone pulse amplitude and frequency and that the decline occurs simultaneously with a decline in LH pulse amplitude.Peer reviewe

Quantitative analysis methods for studying fenestrations in liver sinusoidal endothelial cells. A comparative study

Liver Sinusoidal Endothelial Cells (LSEC) line the hepatic vasculature providing blood filtration via transmembrane nanopores called fenestrations. These structures are 50−300 nm in diameter, which is below the resolution limit of a conventional light microscopy. To date, there is no standardized method of fenestration image analysis. With this study, we provide and compare three different approaches: manual measurements, a semi-automatic (threshold-based) method, and an automatic method based on user-friendly open source machine learning software. Images were obtained using three super resolution techniques – atomic force microscopy (AFM), scanning electron microscopy (SEM), and structured illumination microscopy (SIM). Parameters describing fenestrations such as diameter, area, roundness, frequency, and porosity were measured. Finally, we studied the user bias by comparison of the data obtained by five different users applying provided analysis methods

Methyl and T-Butyl Group Reorientation in Planar Aromatic Solids: Low-Frequency Nuclear Magnetic Resonance Relaxometry and X-Ray Diffraction

We have synthesized 3-t-butylchrysene and measured the Larmor frequency omega/2pi (= 8.50, 22.5, and 53.0 MHz) and temperature T (110-310 K) dependence of the proton spin-lattice relaxation rate R in the polycrystalline solid [low-frequency solid state nuclear magnetic resonance (NMR) relaxometry]. We have also determined the molecular and crystal structure in a single crystal of 3-t-butylchrysene using x-ray diffraction, which indicates the presence of a unique t-butyl group environment. The spin-1/2 protons relax as a result of the spin-spin dipolar interactions being modulated by the superimposed reorientation of the t-butyl groups and their constituent methyl groups. The reorientation is successfully modeled by the simplest motion; that of random hopping describable by Poisson statistics. The x-ray data indicate near mirror-plane symmetry that places one methyl group nearly in the aromatic plane and the other two almost equally above and below the plane. The NMR relaxometry data indicate that the nearly in-plane methyl group and the entire t-butyl group reorient with a barrier of 24.2 +/- 0.9 kJ mol(-1), and the two out-of-plane methyl groups reorient with a barrier of 14.2 +/- 0.6 kJ mol(-1). Following a brief review of methyl group rotation in simple ethyl-, and isopropyl-substituted one- and two-ring aromatic van der Waals molecular solids, the barriers for the out-of-plane methyl groups and the t-butyl group in 3-t-butylchrysene are compared with those barriers in three related molecular solids whose crystal structure is known: 4-methyl-2,6-di-t-butylphenol, 1,4-di-t-butylbenzene, and polymorph A of 2,6-di-t-butyl- naphthalene. A trend is observed in the reorientational barriers for the t-butyl and the out-of-plane methyl groups across this series of four compounds: as the t-butyl barriers decrease, the out-of-plane methyl barriers increase

MicroRNAs targeting oncogenes are down-regulated in pancreatic malignant transformation from benign tumors

BACKGROUND MicroRNA (miRNA) expression profiles have been described in pancreatic ductal adenocarcinoma (PDAC), but these have not been compared with pre-malignant pancreatic tumors. We wished to compare the miRNA expression signatures in pancreatic benign cystic tumors (BCT) of low and high malignant potential with PDAC, in order to identify miRNAs deregulated during PDAC development. The mechanistic consequences of miRNA dysregulation were further evaluated. METHODS Tissue samples were obtained at a tertiary pancreatic unit from individuals with BCT and PDAC. MiRNA profiling was performed using a custom microarray and results were validated using RT-qPCR prior to evaluation of miRNA targets. RESULTS Widespread miRNA down-regulation was observed in PDAC compared to low malignant potential BCT. We show that amongst those miRNAs down-regulated, miR-16, miR-126 and let-7d regulate known PDAC oncogenes (targeting BCL2, CRK and KRAS respectively). Notably, miR-126 also directly targets the KRAS transcript at a "seedless" binding site within its 3'UTR. In clinical specimens, miR-126 was strongly down-regulated in PDAC tissues, with an associated elevation in KRAS and CRK proteins. Furthermore, miR-21, a known oncogenic miRNA in pancreatic and other cancers, was not elevated in PDAC compared to serous microcystic adenoma (SMCA), but in both groups it was up-regulated compared to normal pancreas, implicating early up-regulation during malignant change. CONCLUSIONS Expression profiling revealed 21 miRNAs down-regulated in PDAC compared to SMCA, the most benign lesion that rarely progresses to invasive carcinoma. It appears that miR-21 up-regulation is an early event in the transformation from normal pancreatic tissue. MiRNA expression has the potential to distinguish PDAC from normal pancreas and BCT. Mechanistically the down-regulation of miR-16, miR-126 and let-7d promotes PDAC transformation by post-transcriptional up-regulation of crucial PDAC oncogenes. We show that miR-126 is able to directly target KRAS; re-expression has the potential as a therapeutic strategy against PDAC and other KRAS-driven cancers

MicroRNA-375 plays a dual role in prostate carcinogenesis

Background: Prostate cancer (PCa), a highly incident and heterogeneous malignancy, mostly affects men from developed countries. Increased knowledge of the biological mechanisms underlying PCa onset and progression are critical for improved clinical management. MicroRNAs (miRNAs) deregulation is common in human cancers, and understanding how it impacts in PCa is of major importance. MiRNAs are mostly downregulated in cancer, although some are overexpressed, playing a critical role in tumor initiation and progression. We aimed to identify miRNAs overexpressed in PCa and subsequently determine its impact in tumorigenesis. Results: MicroRNA expression profiling in primary PCa and morphological normal prostate (MNPT) tissues identified 17 miRNAs significantly overexpressed in PCa. Expression of three miRNAs, not previously associated with PCa, was subsequently assessed in large independent sets of primary tumors, in which miR-182 and miR-375 were validated, but not miR-32. Significantly higher expression levels of miR-375 were depicted in patients with higher Gleason score and more advanced pathological stage, aswellaswithregionallymph nodesmetastases. Forced expression of miR-375 in PC-3 cells, which display the lowest miR-375 levels among PCa cell lines, increased apoptosis and reduced invasion ability and cell viability. Intriguingly, in 22Rv1 cells, which displayed the highest miR-375 expression, knockdown experiments also attenuated the malignant phenotype. Gene ontology analysis implicated miR-375 in several key pathways deregulated in PCa, including cell cycle and cell differentiation. Moreover, CCND2 was identified as putative miR-375 target in PCa, confirmed by luciferase assay. Conclusions: A dual role for miR-375 in prostate cancer progression is suggested, highlighting the importance of cellular context on microRNA targeting.Research Center of Portuguese Oncology Institute - Porto (CI-IPOP 4–2012) and by the Federal funds through Programa Operacional Temático Factores de Competitividade (COMPETE) with co-participation from the European Community Fund (FEDER) and by the National funds through Fundação para a Ciência e Tecnología (FCT) under the projects EXPL/BIM-ONC/0556/2012. FQV and JRC were or are supported by FCT-Fundação para a Ciência e a Tecnologia grants (SFRH/BD/70564/2010 and SFRH/BD/71293/2010, respectively)

Diagnosis of Pancreatic Ductal Adenocarcinoma and Chronic Pancreatitis by Measurement of microRNA Abundance in Blood and Tissue

A solid process for diagnosis could have a substantial impact on the successful treatment of pancreatic cancer, for which currently mortality is nearly identical to incidence. Variations in the abundance of all microRNA molecules from peripheral blood cells and pancreas tissues were analyzed on microarrays and in part validated by real-time PCR assays. In total, 245 samples from two clinical centers were studied that were obtained from patients with pancreatic ductal adenocarcinoma or chronic pancreatitis and from healthy donors. Utilizing the minimally invasive blood test, receiver operating characteristic (ROC) curves and the corresponding area under the curve (AUC) analysis demonstrated very high sensitivity and specificity of a distinction between healthy people and patients with either cancer or chronic pancreatitis; respective AUC values of 0.973 and 0.950 were obtained. Confirmative and partly even more discriminative diagnosis could be performed on tissue samples with AUC values of 1.0 and 0.937, respectively. In addition, discrimination between cancer and chronic pancreatitis was achieved (AUC = 0.875). Also, several miRNAs were identified that exhibited abundance variations in both tissue and blood samples. The results could have an immediate diagnostic value for the evaluation of tumor reoccurrence in patients, who have undergone curative surgical resection, and for people with a familial risk of pancreatic cancer

Serum microrna biomarkers for detection of non-small cell lung cancer

Non small cell lung cancer (NSCLC) is the leading cause of cancer-related mortality world-wide and the majority of cases are diagnosed at late stages of disease. There is currently no cost-effective screening test for NSCLC, and the development of such a test is a public health imperative. Recent studies have suggested that chest computed tomography screening of patients at high risk of lung cancer can increase survival from disease, however, the cost effectiveness of such screening has not been established. In this Phase I/II biomarker study we examined the feasibility of using serum miRNA as biomarkers of NSCLC using RT-qPCR to examine the expression of 180 miRNAs in sera from 30 treatment naive NSCLC patients and 20 healthy controls. Receiver operating characteristic curves (ROC) and area under the curve were used to identify differentially expressed miRNA pairs that could distinguish NSCLC from healthy controls. Selected miRNA candidates were further validated in sera from an additional 55 NSCLC patients and 75 healthy controls. Examination of miRNA expression levels in serum from a multi-institutional cohort of 50 subjects (30 NSCLC patients and 20 healthy controls) identified differentially expressed miRNAs. A combination of two differentially expressed miRNAs miR-15b and miR-27b, was able to discriminate NSCLC from healthy controls with sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of 100% in the training set. Upon further testing on additional 130 subjects (55 NSCLC and 75 healthy controls), this miRNA pair predicted NSCLC with a specificity of 84% (95% CI 0.73-0.91), sensitivity of 100% (95% CI; 0.93-1.0), NPV of 100%, and PPV of 82%. These data provide evidence that serum miRNAs have the potential to be sensitive, cost-effective biomarkers for the early detection of NSCLC. Further testing in a Phase III biomarker study in is necessary for validation of these results. © 2012 Hennessey et al

Two additive mechanisms impair the differentiation of 'substrate-selective' p38 inhibitors from classical p38 inhibitors in vitro

<p>Abstract</p> <p>Background</p> <p>The success of anti-TNF biologics for the treatment of rheumatoid arthritis has highlighted the importance of understanding the intracellular pathways that regulate TNF production in the quest for an orally-available small molecule inhibitor. p38 is known to strongly regulate TNF production via MK2. The failure of several p38 inhibitors in the clinic suggests the importance of other downstream pathways in normal cell function. Recent work has described a 'substrate-selective' p38 inhibitor that is able to preferentially block the activity of p38 against one substrate (MK2) versus another (ATF2). Using a combined experimental and computational approach, we have examined this mechanism in greater detail for two p38 substrates, MK2 and ATF2.</p> <p>Results</p> <p>We found that in a dual (MK2 and ATF2) substrate assay, MK2-p38 interaction reduced the activity of p38 against ATF2. We further constructed a detailed kinetic mechanistic model of p38 phosphorylation in the presence of multiple substrates and successfully predicted the performance of classical and so-called 'substrate-selective' p38 inhibitors in the dual substrate assay. Importantly, it was found that excess MK2 results in a stoichiometric effect in which the formation of p38-MK2-inhibitor complex prevents the phosphorylation of ATF2, despite the preference of the compound for the p38-MK2 complex over the p38-ATF2 complex. MK2 and p38 protein expression levels were quantified in U937, Thp-1 and PBMCs and found that [MK2] > [p38].</p> <p>Conclusion</p> <p>Our integrated mechanistic modeling and experimental validation provides an example of how systems biology approaches can be applied to drug discovery and provide a basis for decision-making with limited chemical matter. We find that, given our current understanding, it is unlikely that 'substrate-selective' inhibitors of p38 will work as originally intended when placed in the context of more complex cellular environments, largely due to a stoichiometric excess of MK2 relative to p38.</p