Protein structure prediction is one of the most challenging problems in computational biology and remains unsolved for many decades. In a simplified version of the problem, the task is to find a ...self-avoiding walk with the minimum free energy assuming a discrete lattice and a given energy matrix. Genetic algorithms currently produce the state-of-the-art results for simplified protein structure prediction. However, performance of the genetic algorithms largely depends on the encodings they use in representing protein structures and the twin removal technique they use in eliminating duplicate solutions from the current population. In this paper, we present a new efficient encoding for protein structures. Our encoding is nonisomorphic in nature and results into efficient twin removal. This helps the search algorithm diversify and explore a larger area of the search space. In addition to this, we also propose an approximate matching scheme for removing near-similar solutions from the population. Our encoding algorithm is generic and applicable to any lattice type. On the standard benchmark proteins, our techniques significantly improve the state-of-the-art genetic algorithm for hydrophobic-polar (HP) energy model on face-centered-cubic (FCC) lattice.
Background African-American ancestry, hypokalemia, and QT interval prolongation on the electrocardiogram are all risk factors for sudden cardiac death (SCD), but their interactions remain to be ...characterized. SCN5A -1103Y is a common missense variant, of African ancestry, of the cardiac sodium channel gene. SCN5A -1103Y is known to interact with QT-prolonging factors to promote ventricular arrhythmias in persons at high risk for SCD, but its clinical impact in the general African-American population has not been established. Methods We genotyped SCN5A -S1103Y in 4,476 participants of the Jackson Heart Study, a population-based cohort of African Americans. We investigated the effect of SCN5A -1103Y, including interaction with hypokalemia, on QT interval prolongation, a widely-used indicator of prolonged myocardial repolarization and predisposition to SCD. We then evaluated the two sub-components of the QT interval: QRS duration and JT interval. Results The carrier frequency for SCN5A -1103Y was 15.4%. SCN5A -1103Y was associated with QT interval prolongation (2.7 milliseconds; P < .001) and potentiated the effect of hypokalemia on QT interval prolongation (14.6 milliseconds; P = .02). SCN5A -1103Y had opposing effects on the two sub-components of the QT interval, with shortening of QRS duration (−1.5 milliseconds; P = .001) and prolongation of the JT interval (3.4 milliseconds; P < .001). Hypokalemia was associated with diuretic use (78%; P < .001). Conclusions SCN5A -1103Y potentiates the effect of hypokalemia on prolonging myocardial repolarization in the general African-American population. These findings have clinical implications for modification of QT prolonging factors, such as hypokalemia, in the 15% of African Americans who are carriers of SCN5A -1103Y.
Benign Partial Seizures of Adolescence King, Mark A.; Newton, Mark R.; Berkovic, Samuel F.
Epilepsia (Copenhagen),
September 1999, Volume:
40, Issue:
9
Journal Article
Peer reviewed
Purpose: A benign syndrome of partial seizures in adolescents (BPSA) was described by Loiseau et al. in 1978, but confirmation of this syndrome has been lacking. We sought to identify BPSA among ...teenagers with new‐onset focal seizures enrolled in our prospective first‐seizure study and to assess the EEG and magnetic resonance imaging (MRI) findings.
Methods: We searched the study database for patients aged between 10 and 20 years with focal seizures who did not have idiopathic partial epilepsies, epileptogenic lesions on MRI, or recurrent tonic‐clonic seizures during 2 years of follow‐up.
Results: The database contained 92 adolescents, including 37 with partial epilepsy, of whom eight (22%) patients matched the description of BPSA. All eight patients had seizures with a sensory/motor “march.” Six had a secondarily generalized seizure and two had simple partial seizures alone. Epileptiform abnormalities were documented in five cases but lacked a distinctive morphology or distribution. No lesions were seen on MRI.
Conclusions: BPSA can be provisionally diagnosed in teenagers with unprovoked focal seizures characterized by a march of sensory/motor symptoms, whose MRI is normal. The psychosocial consequences of chronic epilepsy in adolescence are considerable, so early recognition of this benign syndrome is important.
Anger Proneness, Gender, and the Risk of Heart Failure Kucharska-Newton, Anna M., PhD, MPH; Williams, Janice E., PhD, MPH; Chang, Patricia P., MD, MPH ...
Journal of cardiac failure,
12/2014, Volume:
20, Issue:
12
Journal Article
Peer reviewed
Open access
Abstract Background Evidence regarding the association of anger proneness with incidence of heart failure is lacking. Methods and Results Anger proneness was ascertained among 13,171 black and white ...participants of the Atherosclerosis Risk in Communities (ARIC) study cohort with the use of the Spielberger Trait Anger Scale. Incident heart failure events, defined as occurrence of ICD-9-CM code 428.x, were ascertained from participants' medical records during follow-up in the years 1990–2010. Relative hazard of heart failure across categories of trait anger was estimated with the use of Cox proportional hazard models. Study participants (mean age 56.9 SD 5.7 years) experienced 1,985 incident HF events during 18.5 (SD 4.9) years of follow-up. Incidence of HF was greater among those with high, as compared to those with low or moderate trait anger, with higher incidence observed for men than for women. The relative hazard of incident HF was modestly high among those with high trait anger, compared with those with low or moderate trait anger (age-adjusted hazard ratio for men: 1.44 (95% confidence interval CI 1.23–1.69). Adjustment for comorbidities and depressive symptoms attenuated the estimated age-adjusted relative hazard in men to 1.26 (95% CI 1.00–1.60). Conclusions Assessment of anger proneness may be necessary in successful prevention and clinical management of heart failure, especially in men.
No single algorithm suits the best for the protein structure prediction problem. Therefore, researchers have tried hybrid techniques to mix the power of different strategies to gain improvements. In ...this paper, we present a hybrid search framework that embeds a tabu-based local search within a population based genetic algorithm. We applied our hybrid algorithm on simplified protein structure prediction problem. We use a low-resolution ab initio search method with the hydrophobic-polar energy model and face-centred-cubic lattice. Within the genetic algorithm, we apply local search in two different situations: i) only once at the beginning and ii) every time at search stagnation. At the beginning, we apply local search to improve the randomly generated individuals and use them as an initial population for the genetic algorithm. Later, we apply local search after applying a random-walk at situations where the genetic algorithm gets stuck. In both cases, the use of local search is to improve the randomised solutions quickly. We experimentally show that our hybrid approach outperforms the state-of-the-art approaches.
On sites with shallow soil in semi-arid climate conditions, whiteleaf manzanita (Arctostaphyllos viscida) and Pacific madrone (Arbutus menziesii) utilize water from the bedrock. Roots of these plants ...occupy rock fissures as small as 100 µm Although the root stele remains cylindrical in shape without visible mechanical stress, the cortex may become flat, creating "wing-like" structures on the sides of the stele. Fine particles of soil and rock that fill the space between root cortex and rock matrices create good contact for water flow.
We analyze in-plane and out-of-plane texture and terahertz analysis of a YBa
2
Cu
3
O
7-δ
(YBCO) film deposited by chemical solution deposition technique onto LaAlO
3
(100) substrate. X-ray ...diffraction reveals the presence of (00l) reflections for the YBCO phase. The out-of-plane texture, measured by a rocking curve, shows two sub-layers with Δω = 0.45° and 1.8°. The value of the c-axis fraction of the crystallites is 81%. Also, the in-plane texture was studied by ϕ-scan measurements of the (102) reflection, displaying mostly a colony of c-axis oriented grains, and two colonies of a-axis oriented grains onto the YBCO surface. In addition, the temperature dependence of the magnetization measurement revealed a critical temperature of 90 K, typical for YBCO superconductor material. From the temperature-dependent optical conductivity of YBCO, we observe an absorption feature at ≈1.57 THz, which redshifts with increasing temperature.
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