Local alignment is an important task in molecular biology to see if two sequences contain regions that are similar. The most popular approach to local alignment is the use of dynamic programming due to Smith and Waterman, but the alignment reported by the Smith-Waterman algorithm has some undesirable properties. The recent approach to fix these problems is to use the notion of normalized scores for local alignments by Arslan, Egecioglu and Pevzner. In this paper we consider the problem of finding all local alignments whose normalized scores are above a given threshold, and present a fast heuristic algorithm. Our algorithm is 180-330 times faster than Arslan et al.''s for sequences of length about 120 kbp and about 40-50 times faster for sequences of length about 30 kbp.
Molecular Biology

Objective: The primary objective of this study was to investigate the effect of methylphenidate (MPH) on height, weight, and body mass index (BMI) in drug-naive children and adolescents with attention deficit hyperactivity disorder (ADHD) over 24 months. The secondary objective was to investigate whether the age of MPH initiation and sex act as risk factors for growth retardation. Methods: A total of 82 patients with ADHD were included. Weight, height, and BMI were measured at baseline and every 6 months up to 24 months. Weight, height, and BMI data were converted to z-scores and analyzed using two-way repeated-measures ANOVA and multiple linear regression. Results: The z-score of height, weight and BMI decreased from the baseline values. The z-scores of height were at baseline 0.002; 6 months -0.100; 12 months -0.159; 18 months -0.159; 24 months -0.186. The z-scores of weight were at baseline 0.104; 6 months -0.155; 12 months -0.256; 18 months -0.278; 24 months -0.301. Here were no age and sex differences of height, weight, and BMI. Conclusion The use of MPH was associated with attenuation of weight and height gain rates in children and adolescents with ADHD.

Tumor peptides associated with MHC class I molecules or their synthetic variants have attracted great attention for their potential use as vaccines to induce tumor-specific CTLs. However, the outcome of clinical trials of peptide-based tumor vaccines has been disappointing. There are various reasons for this lack of success, such as difficulties in delivering the peptides specifically to professional Ag-presenting cells, short peptide halflife in vivo, and limited peptide immunogenicity. We report here a novel peptide vaccination strategy that efficiently induces peptide-specific CTLs. Nanoparticles (NPs) were fabricated from a biodegradable polymer, poly(D,L-lactic-co-glycolic acid), attached to H-2Kb molecules, and then the natural peptide epitopes associated with the H-2K b molecules were exchanged with a model tumor peptide, SIINFEKL (OVA 257-268 ). These NPs were efficiently phagocytosed by immature dendritic cells (DCs), inducing DC maturation and activation. In addition, the DCs that phagocytosed SIINFEKL-pulsed NPs potently activated SIINFEKL-H-2K b complex-specific CD8 + T cells via cross-presentation of SIINFEKL. In vivo studies showed that intravenous administration of SIINFEKL-pulsed NPs effectively generated SIINFEKLspecific CD8 + T cells in both normal and tumor-bearing mice. Furthermore, intravenous administration of SIINFEKL-pulsed NPs into EG7.OVA tumor-bearing mice almost completely inhibited the tumor growth. These results demonstrate that vaccination with polymeric NPs coated with tumor peptide-MHC-I complexes is a novel strategy for efficient induction of tumor-specific CTLs.

PURPOSE: To determine the reliability of edema grading of the psoas and paraspinal muscles on axial T2-weighted magnetic resonance (MR) image (T2WI) for the detection of lumbar transverse process (TP) fractures. MATERIALS AND METHODS: A retrospective review of lumbar spine MR images of 56 patients (mean age = 56.1 years, age range = 17–87 years, male:female = 28:28) was conducted by 2 radiologists. Based on the axial T2WI at the disc level, the paraspinal muscles were classified into 4 compartments and muscle edema (increased signal intensity on axial T2WI) grading performed for each quadrant. RESULTS: A total of 486 TPs (with fracture: 24, without fracture: 462) of 56 patients were evaluated. Muscle edema grade showed moderate correlation with the presence of TP fracture (ρ = 0.466). When the total score of muscle edema was 2.50, the receiver operating characteristic curve showed a sensitivity of 72.7% and a specificity of 90.7%. A higher edema grade had a significantly higher probability of concomitant TP fracture [any sided (total): odds ratio = 1.704 (95% confidence interval = 1.410–2.060)]. CONCLUSION Edema grading of the psoas and paraspinal muscles on axial T2WI of lumbar spine can be helpful in the detection of TP fracture.

Background and Objectives: Injection laryngoplasty is a common method for treatment of unilateral vocal fold paralysis. Unilateral vocal fold paralysis has various causes, including idiopathic, infection, stroke, neurologic condition, surgery and nerve invasion by cancer. To the knowledge of the authors, there was no study on the relationship between the causes of vocal cord paralysis and the outcome of injection laryngoplasty. Therefore, we tried to investigate the difference in the outcomes of injection laryngoplasty between vocal cord paralysis after surgery group and nerve invasion by cancer group.Materials and Method A retrospective analysis was performed for 24 patients who underwent vocal cord injection due to unilateral vocal cord paralysis caused by surgery or nerve invasion by cancer. The objective quality of the voice was assessed by acoustic voice analysis with the Multi-Dimensional Voice Program. Results: Both group showed an improvement of fundamental frequemcy (F0), jitter percent, shimmer (percent), and noise to hearmonic ratio (NHR) after injection laryngoplasty. The vocal cord paralysis due to nerve invasion group showed more improvement in both the mean and median value of F0, shimmer percent and NHR than the vocal cord paralysis due to surgery group, but there was not statistically significant. Conclusion Our study did not show a statistically significant difference in outcome between vocal cord paralysis due to cancer invasion group and surgery group, but statistically tendency was suggested. The vocal cord paralysis due to nerve invasion group showed more improvement in both the mean and median value of acoustic voice analysis than surgery group.

Asian-lineage H5 highly pathogenic avian influenza (HPAI) viruses have caused continuous outbreaks in poultry and wild birds. Development of rapid and accurate diagnostic methods is needed for preventing further spread of the virus and reducing the time required for eradication of the virus. We developed a low-density microarray for the rapid detection and identification of avian influenza virus subtypes H5, H7, and H9 and their pathotypes in a previous study. In the present study, we evaluated previously developed diagnostic microarray using avian influenza viruses isolated in Mongolia, including H5 HPAI viruses. All H5 HPAI viruses isolated in Mongolia were shown as H5-specific and highly pathogenic pattern in the microarray. H2, H3 and H12 viruses isolated in Mongolia used in this study did not show any H5, H7 and H9 patterns. These results indicated that this diagnostic microarray has enormous potential for the rapid subtyping and pathotyping of influenza viruses, including viruses isolated in Mongolia.
Animals ; Birds ; Disease Outbreaks ; Influenza in Birds* ; Mongolia* ; Orthomyxoviridae ; Poultry

OBJECTIVE: To investigate whether the polymorphisms of CASP3 gene (rs4647602, intron A/C and rs1049216, UTR C/T) and CASP9 gene (rs1052576, Gln/Arg G/A and rs1052571, Ser/Val T/C) were associated with the development, and clinical severity of ischemic stroke and functional consequences after stroke. METHODS: Genomic DNA from 121 ischemic stroke patients and 201 healthy control subjects were extracted, and polymerase chain reaction products were sequenced. To investigate the association of polymorphisms and the development, and National Institutes of Health Stroke Scale (K-NIHSS), logistic regression models were analyzed. RESULTS: Polymorphism of the untranslational region of CASP3 (rs1049216, UTR C/T) has been associated with the development of ischemic stroke—in codominant1 model (odds ratio [OR], 0.51; 95% confidence interval [CI], 0.29–0.88; p=0.017), in dominant model (OR, 0.57; 95% CI, 0.34–0.97; p=0.034), and in the overdominant model (OR, 0.50; 95% CI, 0.29–0.87; p=0.011). A missense SNP of CASP9 gene (rs1052571, Ser/Val T/C) was associated with the development of ischemic stroke (OR, 1.93; 95% CI, 1.05–3.55; p=0.034 in recessive model). CONCLUSION: These results indicate the possibility that CASP3 and CASP9 genes are markers for the development of ischemic stroke.
Activities of Daily Living ; Brain Infarction ; Caspase 3* ; DNA ; Humans ; Introns ; Logistic Models ; National Institutes of Health (U.S.) ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Stroke*

Background: Rotational thromboelastometry (ROTEM; TEM International GmbH, Munich, Germany) is a global coagulation test that guides evidence-based platelet transfusion in trauma patients. We evaluated ROTEM parameters for predicting mid-term (five days) platelet transfusion in trauma patients. Methods: Maximum clot firmness and clot amplitudes after 5, 10, and 15 mins (A5, A10, and A15, respectively) of fibrin-specific ROTEM (FIBTEM) and extrinsically activated ROTEM (EXTEM) were retrospectively collected from 82 hospitalized, stable, non-bleeding trauma patients after successful initial resuscitation. Platelet-specific ROTEM (PLTEM) was calculated by subtracting FIBTEM from EXTEM. Platelet transfusions were reviewed for five days after ROTEM. Results: The areas under the curve for FIBTEM, EXTEM, and PLTEM predicting platelet concentrate transfusion of > 12 U at mid-term were 0.915–0.923, 0.878–0.896, and 0.551–0.735, respectively. FIBTEM and EXTEM parameters were comparable to those of fibrinogen, fibrin/fibrinogen degradation products, D-dimer, and antithrombin III. Strong correlations (r > 0.7) were noted between platelet count and EXTEM (A5, A10, and A15) or PLTEM (A5), platelet function (per platelet count) and EXTEM (A10 and A15), and fibrinogen levels and all FIBTEM parameters. Conclusions FIBTEM and EXTEM can reliably predict mid-term platelet transfusion in trauma patients. FIBTEM, EXTEM, and PLTEM parameters correlate with conventional coagulation tests (platelets and fibrinogen).