Human-mouse alignments with BLASTZ

The Mouse Genome Analysis Consortium aligned the human and mouse genome sequences for a variety of purposes, using alignment programs that suited the various needs. For investigating issues regarding genome evolution, a particularly sensitive method was needed to permit alignment of a large proportion of the neutrally evolving regions. We selected a program called BLASTZ, an independent implementation of the Gapped BLAST algorithm specifically designed for aligning two long genomic sequences. BLASTZ was subsequently modified, both to attain efficiency adequate for aligning entire mammalian genomes and to increase its sensitivity. This work describes BLASTZ, its modifications, the hardware environment on which we run it, and several empirical studies to validate its results.     

The extended latissimus dorsi muscle island flap for flexion or extension of the fingers

We describe the technique of transferring the latissmus dorsi muscle as an island flap for the restoration of digital flexion or extension in 28 patients. The latissmus dorsi muscle is raised down to the posterior iliac crest and prolonged with the gluteal superficial facia. We believe that this method is particularly suitable for extensive and prolonged paralysis of the lower elements of brachial plexus. It can be used also for severe Volkmann's contracture or the loss of flexor or extensor muscles of the fingers due to extensive debridement. The technique does not require microsurgery and there is no delay in reinnervation of the muscle.     

Tomonaga–Luttinger Spin Liquid and Kosterlitz–Thouless Transition in the Spin-1/2 Branched Chains: The Study of Topological Phase Transition

In the present work, we provide a comprehensive numerical investigation of the magnetic properties and phase spectra of three types of spin-1/2 branched chains consisting of one, two and three side spins per unit block with intra-chain interaction and a uniform inter-chain interaction in the presence of an external magnetic field. In a specific magnetic field interval, the low-temperature magnetization of these chains shows a step-like behavior with a pronounced plateau depending on the strength and the type of intra-chain interaction being ferromagnetic or antiferromagnetic. We demonstrate that when inter-chain interaction J1 is antiferromagnetic and intra-chain interaction J2 is ferromagnetic, the magnetization of the models manifests a smooth increase without a plateau, which is evidence of the existence of a Luttinger-like spin liquid phase before reaching its saturation value. On the other hand, when J1 is ferromagnetic and J2 is antiferromagnetic, the low-temperature magnetization of the chain with two branches shows an intermediate plateau at one-half of the saturation magnetization that breaks a quantum spin liquid phase into two regions. The magnetization of the chain with three branches exhibits two intermediate plateaus and two regions of a quantum spin liquid. We demonstrate that the chains with more than one side spin illustrate in their ground-state phase diagram a Kosterlitz–Thouless transition from a gapful phase to a gapless spin liquid phase.     

Pregnancy in the Sickle Cell Disease and Fetomaternal Outcomes in Different Sickle cell Genotypes: A Systematic Review and Meta-Analysis

BackgroundPregnancy is a major concern among women with the sickle cell disease (SCD), and it is associated with increased adverse outcomes. The aim of the present meta-analysis is to report the fetomaternal outcomes in different sickle cell genotypes.MethodsIn this systematic review and meta-analysis, a comprehensive search of databases and search engines such as PubMed, Scopus, Web of Science, ProQuest, Cochrane Library, Science Direct and Google Scholar were performed. Any observational studies that had compared at least one outcome such as maternal outcomes, fetal outcomes, and morbidity between two groups of pregnant women with different types of sickle cell genotypes and pregnant women without SCD were evaluated.ResultsA total number of 9,827 pregnant women with SCD were examined. The results showed that pregnancy in SCD increased the risk of adverse outcomes for the mothers (including postpartum hemorrhage, prematurity, pregnancy-induced hypertension, pre-eclampsia, eclampsia, cesarean section, lower segment cesareansection, maternal death), fetus (including live births, low birth weight, intrauterine growth restriction, APGAR score at 5 min <7, stillbirth, neonatal death, perinatal mortality, acute fetal distress, intrauterine fetal death) and morbidity among the SCD(severe anemia, urinary tract infection, blood transfusion, painful crisis, acute chest syndrome, vaso-occlusive crises).ConclusionAccording to the results of this meta-analysis, pregnancy in the SCD is associated with an increased risk of maternal outcomes, fetal outcomes, and morbidity among SCD patients with different genotypes. Pregnancy in sickle cell hemoglobinopathies needs careful multidisciplinary management and cautious caring so as to decrease maternal and fetal morbidity and mortality.     

Effect of nutritional counseling on low-density lipoprotein cholesterol among Thai HIV-infected adults receiving antiretroviral therapy

HIV-infected patients receiving antiretroviral therapy have increased risk of metabolic syndrome, including dyslipidemia. In this study, we determined whether individual nutritional counseling reduced dyslipidemia, particularly low-density lipoprotein (LDL) cholesterol, among HIV-infected patients with dyslipidemia not currently taking lipid-lowering medication. We conducted a randomized 24-week trial among HIV-infected patients with dyslipidemia who were on antiretroviral therapy and were eligible to initiate therapeutic lifestyle changes according to the Thai National Cholesterol Education Program. Participants were randomly assigned to an intervention group that received individual counseling with a nutritionist for seven sessions (baseline, weeks 2, 4, 8, 12, 18, and 24) and a control group that received standard verbal diet information at baseline and nutritional counseling only at week 24. A 24-h recall technique was used to assess dietary intake for both groups at baseline and week 24. Lipid profile (total cholesterol, LDL, high-density lipoprotein (HDL), and triglyceride) was measured at baseline and after 12 and 24 weeks of therapy. An intention-to-treat and linear mixed model were used. Seventy-two patients were randomly assigned, and 62 (86%) participants completed their lipid profile test. After 12 weeks of follow-up, there were significant reductions in the intervention group for total cholesterol (?14.4?±?4.6?mg/dL, P?=?.002), LDL cholesterol (?13.7?±?4.1?mg/dL, P?=?.001), and triglyceride (?30.4?±?13.8?mg/dL, P?=?.03). A significant reduction in LDL cholesterol was also observed in the control group (?7.7?±?3.8?mg/dL, P?=?.04), but there were no significant differences in change of mean lipid levels between the groups at 12 weeks of follow-up. After 24 weeks, participants assigned to the intervention group demonstrated significantly greater decreases in serum total cholesterol (?19.0?±?4.6?vs. 0.2?±?4.3?mg/dL, P?=?.003) and LDL cholesterol (?21.5?±?4.1?vs. ?6.8?±?3.8?mg/dL, P?=?.009). There were no significant changes in HDL cholesterol or triglyceride levels in either group.     

Epidemiologic Evidence on Coffee and Cancer

Coffee consumption is a major and frequent dietary exposure in diverse cultures around the globe whose safety has been questioned. A substantial body of epidemiologic evidence, consisting of over 500 papers relating the consumption of coffee to cancer of various sites, has accumulated to date. Numerous individual, site-specific meta analyses have been undertaken at various times. However, there is no comprehensive, up-to-date overview of the entirety of the knowledge base. To address this need, this review summarized the findings of the meta analyses and recent papers on site-specific human cancers among coffee consumers. For hepatocellular and endometrial cancers, there appears to be a strong and consistent protective association; for colorectal cancer, the direction of association is borderline protective. There appears to be no association with breast, pancreatic, kidney, ovarian, prostate, or gastric cancer. Risk of bladder cancer appears to be associated with heavy coffee consumption in some populations and among men. The associations with childhood leukemia and mother's consumption of coffee were ambiguous—with some suggestion of risk at high levels of daily consumption.     

miRNA-binding site polymorphism in IL-15RA gene in rheumatoid arthritis and systemic lupus erythematosus: correlation with disease risk and clinical characteristics

Clinical Rheumatology - MiRSNPs may interfere with mRNA stability through effects on microRNAs (miRNAs)-mRNA interactions via direct changes in miRNA binding site or effect on the secondary...