A class representative model for Pure Parsimony Haplotyping under uncertain data

The Pure Parsimony Haplotyping (PPH) problem is a NP-hard combinatorial optimization problem that consists of finding the minimum number of haplotypes necessary to explain a given set of genotypes. PPH has attracted more and more attention in recent years due to its importance in analysis of many fine-scale genetic data. Its application fields range from mapping complex disease genes to inferring population histories, passing through designing drugs, functional genomics and pharmacogenetics. In this article we investigate, for the first time, a recent version of PPH called the Pure Parsimony Haplotype problem under Uncertain Data (PPH-UD). This version mainly arises when the input genotypes are not accurate, i.e., when some single nucleotide polymorphisms are missing or affected by errors. We propose an exact approach to solution of PPH-UD based on an extended version of Catanzaro et al.[1] class representative model for PPH, currently the state-of-the-art integer programming model for PPH. The model is efficient, accurate, compact, polynomial-sized, easy to implement, solvable with any solver for mixed integer programming, and usable in all those cases for which the parsimony criterion is well suited for haplotype estimation.     

Peter Brian Medawar

Patients with coccidioidomycosis manifest a wide variety of severity of infection. Patients with unifocal and particularly multifocal dissemination manifest a defect in host defense mechanisms. This study focuses on the in vitro response to PHA as an indicator of immunoregulatory mechanisms. Study subjects are divided into four groups: Group I—17, patients with active disseminated coccidioidomycosis and lesions in multiple organs; Group II—15, patients with active disseminated coccidioidomycosis and a single lesion; Group III—16, patients with active coccidioidomycosis confined to the lungs; and Group IV—18, patients in whom coccidioidomycosis is inactive. The response to PHA was heterogeneous, even within groups. When cells were cultured in the presence of indomethacin or R020-5720, Group I cells demonstrated highly significant augmentation of the response to PHA (P < 0.002), whereas cells from Groups II to IV were unaffected. When adherent cells were removed by passage through a nylon wool column, the effect of indomethacin could no longer be demonstrated. Direct measurement of prostaglandin production (PGE₂ and PGF_2α) and thromboxane suggest that there is no difference in the quantity of these compounds produced by unstimulated or PHA-stimulated cells by Group I versus Group IV cells (P = 0.2-0.4). Indomethacin or R020-5720 markedly inhibit the production of these compounds. Studies of the effect of exogenous prostaglandin on PHA-stimulated cells suggest that Group I cells may be more inhibited by PGF_1α and PGF_2α compared to Group IV cells. The data demonstrate that PHA cultures of cells from Group I patients are suppressed. The suppressor cell can be removed by adherence to nylon wool and is inhibited by indomethacin or R020-5720.     

Kallikrein and amylase contents in tissues from a mutant mouse model for human cystic fibrosis

Kallikrein and amylase activities are decreased in the pancreas and salivary glands from $\text{cri/cri}$ homozygote mutant mice. Kallikrein is decreased in the $\text{cri/cri}$ kidney too. With reference to nucleic acid concentrations there is no difference between control and mutant mice. The previously described electrolyte abnormalities of the cribriform degeneration $\text{(cri)}$ mutant mouse, could be due to the abnormal activity of the kallikrein-kinin system on the transport mechanism of tubular cells in the organs mentioned. These findings represent a new step on our efforts to develop a useful animal model for human cystic fibrosis research.     

The Low-Affinity Receptor for Neurotrophins p75NTR Plays a Key Role for Satellite Cell Function in Muscle Repair Acting via RhoA

Regeneration of muscle fibers, lost during pathological muscle degeneration or after injuries, is mediated by the production of new myofibres. This process, sustained by the resident stem cells of the muscle, the satellite cells, is finely regulated by local cues, in particular by cytokines and growth factors. Evidence in the literature suggests that nerve growth factor (NGF) is involved in muscle fiber regeneration; however, its role and mechanism of action were unclear. We have investigated this issue in in vivo mouse models of muscle regeneration and in primary myogenic cells. Our results demonstrate that NGF acts through its low-affinity receptor p75^NTR in a developmentally regulated signaling pathway necessary to myogenic differentiation and muscle repair in vivo. We also demonstrate that this action of NGF is mediated by the down-regulation of RhoA-GTP signaling in myogenic cells.     

Anandamide Suppresses Proliferation and Cytokine Release from Primary Human T-Lymphocytes Mainly via CB2 Receptors

Background

Anandamide (AEA) is an endogenous lipid mediator that exerts several effects in the brain as well as in peripheral tissues. These effects are mediated mainly by two types of cannabinoid receptors, named CB₁R and CB₂R, making AEA a prominent member of the “endocannabinoid” family. Also immune cells express CB₁ and CB₂ receptors, and possess the whole machinery responsible for endocannabinoid metabolism. Not surprisingly, evidence has been accumulated showing manifold roles of endocannabinoids in the modulation of the immune system. However, details of such a modulation have not yet been disclosed in primary human T-cells.

Methodology/Significance

In this investigation we used flow cytometry and ELISA tests, in order to show that AEA suppresses proliferation and release of cytokines like IL-2, TNF-α and INF-γ from activated human peripheral T-lymphocytes. However, AEA did not exert any cytotoxic effect on T-cells. The immunosuppression induced by AEA was mainly dependent on CB₂R, since it could be mimicked by the CB₂R selective agonist JWH-015, and could be blocked by the specific CB₂R antagonist SR144528. Instead the selective CB₁R agonist ACEA, or the selective CB₁R antagonist SR141716, were ineffective. Furthermore, we demonstrated an unprecedented immunosuppressive effect of AEA on IL-17 production, a typical cytokine that is released from the unique CD4+ T-cell subset T-helper 17.

Conclusions/Significance

Overall, our study investigates for the first time the effects of the endocannabinoid AEA on primary human T-lymphocytes, demonstrating that it is a powerful modulator of immune cell functions. In particular, not only we clarify that CB₂R mediates the immunosuppressive activity of AEA, but we are the first to describe such an immunosuppressive effect on the newly identified Th-17 cells. These findings might be of crucial importance for the rational design of new endocannabinoid-based immunotherapeutic approaches.     

Comparative Treatment of Helicobacter pylori–Positive Duodenal Ulcer Using Pantoprazole at Low and High Doses Versus Omeprazole in Triple Therapy

Background. Helicobacter pylori eradication has become the standard treatment for peptic ulcer disease. H. pylori –eradicating triple therapy with omeprazole plus two antibiotics has been used until recently; however, the efficacy of pantoprazole and antibiotics for H. pylori eradication has not been researched thoroughly until now. The aim of this randomized clinical trial was to verify the efficacy of triple oral therapy comparing the effects of pantoprazole using two different doses versus omeprazole twice daily in H. pylori eradication, in ulcer healing and relapses, and in gastritis improvement.
Materials and Methods. We enrolled 243 patients with H. pylori– positive duodenal ulcer and randomized them into three treatment groups: 84 patients (group Ome40) were assigned to receive omeprazole, 20 mg twice daily, plus amoxicillin, 1 gm twice daily, and clarithromycin, 500 mg twice daily for 10 days; 79 patients (group Pan40) were treated with pantoprazole, 40 mg daily, plus amoxicillin and clarithromycin at the same doses as those of group Ome40; and 80 patients (group Pan80) were treated with pantoprazole, 40 mg twice daily, plus amoxicillin and clarithromycin at the same doses as those of group Ome40.
Results. Ulcer healing was observed in 81 of 84 patients (96.4%) in group Ome40; in 66 of 79 patients (83.5%) in group Pan40; and in 77 of 80 patients (96.2%) in group Pan80. H. pylori was eradicated in 79 of 84 patients (94%) in group Ome40; in 63 of 79 patients (79.7%) in group Pan40; and in 75 of 80 patients (93.7%) in group Pan80.
Conclusions. We found that 10-day triple therapy with amoxicillin, clarithromycin, and either pantoprazole, 80 mg daily, or omeprazole, 40 mg daily, is highly effective in ulcer healing and is very well tolerated, achieving the 90% cure recommended for an ideal first-line anti– H. pylori positive duodenal ulcer treatment regimen.     

Detection of Low-Level Mixed-Population Drug Resistance in Mycobacterium tuberculosis Using High Fidelity Amplicon Sequencing

Undetected and untreated, low-levels of drug resistant (DR) subpopulations in clinical Mycobacterium tuberculosis (Mtb) infections may lead to development of DR-tuberculosis, potentially resulting in treatment failure. Current phenotypic DR susceptibility testing has a theoretical potential for 1% sensitivity, is not quantitative, and requires several weeks to complete. The use of “single molecule-overlapping reads” (SMOR) analysis with next generation DNA sequencing for determination of ultra-rare target alleles in complex mixtures provides increased sensitivity over standard DNA sequencing. Ligation free amplicon sequencing with SMOR analysis enables the detection of resistant allele subpopulations at ≥0.1% of the total Mtb population in near real-time analysis. We describe the method using standardized mixtures of DNA from resistant and susceptible Mtb isolates and the assay’s performance for detecting ultra-rare DR subpopulations in DNA extracted directly from clinical sputum samples. SMOR analysis enables rapid near real-time detection and tracking of previously undetectable DR sub-populations in clinical samples allowing for the evaluation of the clinical relevance of low-level DR subpopulations. This will provide insights into interventions aimed at suppressing minor DR subpopulations before they become clinically significant.