[Chaotic artificial bee colony algorithm: a new approach to the problem of minimization of energy of the 3D protein structure]

Frediction of the three-dimensional structure of a protein from its amino acid sequence can be considered as a global optimization problem. In this paper, the Chaotic Artificial Bee Colony (CABC) algorithm was introduced and applied to 3D protein structure prediction. Based on the 3D off-lattice AB model, the CABC algorithm combines global search and local search of the Artificial Bee Colony (ABC) algorithm with the Chaotic search algorithm to avoid the problem of premature convergence and easily trapping the local optimum solution. The experiments carried out with the popular Fibonacci sequences demonstrate that the proposed algorithm provides an effective and high-performance method for protein structure prediction.

Impaired prefronto-thalamic functional connectivity as a key feature of treatment-resistant depression: a combined MEG, PET and rTMS study

Prefrontal left-right functional imbalance and disrupted prefronto-thalamic circuitry are plausible mechanisms for treatment-resistant depression (TRD). Add-on repetitive transcranial magnetic stimulation (rTMS), effective in treating antidepressant-refractory TRD, was administered to verify the core mechanisms underlying the refractoriness to antidepressants. Thirty TRD patients received a 2-week course of 10-Hz rTMS to the left dorsolateral prefrontal cortex (DLPFC). Depression scores were evaluated at baseline (W0), and the ends of weeks 1, 2, and 14 (W14). Responders were defined as those who showed an objective improvement in depression scores ≥50% after rTMS. Left-right frontal alpha asymmetry (FAA) was measured by magnetoencephalography at each time point as a proxy for left-right functional imbalance. Prefronto-thalamic connections at W0 and W14 were assessed by studying couplings between prefrontal alpha waves and thalamic glucose metabolism (PWTMC, reflecting intact thalamo-prefrontal connectivity). A group of healthy control subjects received magnetoencephalography at W0 (N = 50) to study whether FAA could have a diagnostic value for TRD, or received both magnetoencephalography and positron-emission-tomography at W0 (N = 10) to confirm the existence of PWTMC in the depression-free state. We found that FAA changes cannot differentiate between TRD and healthy subjects or between responders and non-responders. No PWTMC were found in the TRD group at W0, whereas restitution of the PWTMC was demonstrated only in the sustained responders at W14 and euthymic healthy controls. In conclusion, we affirmed impaired prefronto-thalamic functional connections, but not frontal functional imbalance, as a core deficit in TRD.

A comparison of complex sleep behaviors with two short-acting Z-hypnosedative drugs in nonpsychotic patients

OBJECTIVE

Complex sleep behaviors (CSBs) are classified as "parasomnias" in the International Classifcation of Sleep Disorders, Second Edition (ICSD-2). To realize the potential danger after taking two short-acting Z-hypnosedative drugs, we estimated the incidence of CSBs in nonpsychotic patients in Taiwan.

METHODS

Subjects (N = 1,220) using zolpidem or zopiclone were enrolled from the psychiatric outpatient clinics of a medical center in Taiwan over a 16-month period in 2006-2007. Subjects with zolpidem (N = 1,132) and subjects with zopiclone (N = 88) were analyzed. All subjects completed a questionnaire that included demographic data and complex sleep behaviors after taking hypnotics.

RESULTS

Among zolpidem and zopiclone users, 3.28% of patients reported incidents of somnambulism or amnesic sleep-related behavior problems. The incidence of CSBs with zolpidem and zopiclone were 3.27%, and 3.41%, respectively, which was signifcantly lower than other studies in Taiwan.

CONCLUSION

These results serve as a reminder for clinicians to make inquiries regarding any unusual performance of parasomnic activities when prescribing zolpidem or zopiclone.

Regional cortical thinning in patients with major depressive disorder: a surface-based morphometry study

This study uses surfaced-based morphometry to investigate cortical thinning and its functional correlates in patients with major depressive disorder (MDD). Subjects with MDD (N=36) and healthy control subjects (N=36) were enrolled in the study. Each subject received T1 structural magnetic resonance imaging (MRI), clinical evaluations, and neuropsychological examinations of executive functions with the Color Trail Test (CTT) and the Wisconsin Card Sorting Test (WCST). This study used an automated surface-based method (FreeSurfer) to measure cortical thickness and to generate the thickness maps for each subject. Statistical comparisons were performed using a general linear model. Compared with healthy controls, subjects with MDD showed the largest area of cortical thinning in the prefrontal cortex. This study also noted smaller areas of cortical thinning in the bilateral inferior parietal cortex, left middle temporal gyrus, left entorhinal cortex, left lingual cortex, and right postcentral gyrus. Regression analysis demonstrated cortical thinning in several frontoparietal regions, predicting worse executive performance measured by CTT 2, though the patterns of cortical thickness/executive performance correlation differed in healthy controls and MDD subjects. In conclusion, the results provide further evidence for the significant role of a prefrontal structural deficit and an aberrant structural/functional relationship in patients with MDD.

Maximum multiple-correlation beamformer for estimating source connectivities in electromagnetic brain activities

Synchrony is a phenomenon of local-scale and long-range integrations within a brain circuit. Synchronous activities manifest themselves in similar temporal structures that can be statistically quantified by temporal correlation. In previous studies, synchronous activities were estimated by calculating the correlation coefficient or coherence between a single reference signal and the activity in a brain region. However, a brain circuit may involve multiple brain regions and these regions may communicate to each other through different temporal patterns. Therefore, temporal correlation to multiple reference signals is effective in quantify the source connectivities in the brain. This paper proposes a novel algorithm to calculate the maximum multiple-correlation for each brain region which has an activity estimated by a beamformer. Furthermore, this algorithm can accommodate various latencies of activities in a circuit. Experimental results demonstrate that the proposed method can accurately detect source activities correlated to the given multiple reference signals, even when unknown latencies exist between the source and references.

A 24.2-Mb deletion of 4q12 --> q21.21 characterized by array CGH in a 131/2-year-old girl with short stature, mental retardation, developmental delay, hyperopia, exotropia, enamel defects, delayed tooth eruption and delayed puberty

We report molecular and cytogenetic characterization of proximal deletion of chromosome 4q, del(4)(q12 --> q21.21) in a 131/2-year-old girl with short stature, mental retardation, developmental delay, hyperopia, exotropia, enamel defects, delayed tooth eruption and delayed puberty. We speculate that haploinsufficiency of the AMTN, ENAM and AMBN genes is most likely responsible for dental disorders, haploinsufficiency of the BMP2K genes is most likely responsible for ocular disorders, and haploinsufficiency of the EREG, AREG and BTC genes is most likely responsible for delayed puberty in this patient.

Differences in white matter abnormalities between bipolar I and II disorders

BACKGROUND

Although patients with bipolar I and II disorders exhibit heterogeneous clinical presentations and cognitive functions, it remains unclear whether these two subtypes have distinct neural substrates. This study aimed to differentiate the fiber abnormalities between bipolar I and II patients using diffusion tensor images.

METHOD

Fourteen bipolar I patients, thirteen bipolar II patients, and twenty-one healthy subjects were recruited. Fractional anisotropy (FA) values calculated from diffusion tensor images were compared among groups using two-sample t-test analysis in a voxel-wise manner. Correlations between the mean FA value of each survived area and the clinical characteristics as well as the scores of neuropsychological tests were further analyzed.

RESULTS

Patients of both subtypes manifested fiber impairments in the thalamus, anterior cingulate, and inferior frontal areas, whereas the bipolar II patients showed more fiber alterations in the temporal and inferior prefrontal regions. The FA values of the subgenual anterior cingulate cortices for both subtypes correlated with the performance of working memory. The FA values of the right inferior frontal area of bipolar I and the left middle temporal area of bipolar II both correlated with executive function. For bipolar II patients, the left middle temporal and inferior prefrontal FA values correlated with the scores of YMRS and hypomanic episodes, respectively.

CONCLUSIONS

Our findings suggest distinct neuropathological substrates between bipolar I and II subtypes. The fiber alterations observed in the bipolar I patients were majorly associated with cognitive dysfunction, whereas those in the bipolar II patients were related to both cognitive and emotional processing.

Production of Ethanol from d-Xylose by Using d-Xylose Isomerase and Yeasts

d-Xylulose, an intermediate of d-xylose catabolism, was observed to be fermentable to ethanol and carbon dioxide in a yield of greater than 80% by yeasts (including industrial bakers' yeast) under fermentative conditions. This conversion appears to be carried out by many yeasts known for d-glucose fermentation. In some yeasts, xylitol, in addition to ethanol, was produced from d-xylulose. Fermenting yeasts are also able to produce ethanol from d-xylose when d-xylose isomerizing enzyme is present. The results indicate that ethanol could be produced from d-xylose in a yield of greater than 80% by a two-step process. First, d-xylose is converted to d-xylulose by xylose isomerase. d-Xylulose is then fermented to ethanol by yeasts.

d-Xylulose Fermentation to Ethanol by Saccharomyces cerevisiae

We used commercial bakers' yeast (Saccharomyces cerevisiae) to study the conversion of d-xylulose to ethanol in the presence of d-xylose. The rate of ethanol production increased with an increase in yeast cell density. The optimal temperature for d-xylulose fermentation was 35 degrees C, and the optimal pH range was 4 to 6. The fermentation of d-xylulose by yeast resulted in the production of ethanol as the major product; small amounts of xylitol and glycerol were also produced. The production of xylitol was influenced by pH as well as temperature. High pH values and low temperatures enhanced xylitol production. The rate of d-xylulose fermentation decreased when the production of ethanol yielded concentrations of 4% or more. The slow conversion rate of d-xylulose to ethanol was increased by increasing the yeast cell density. The overall production of ethanol from d-xylulose by yeast cells under optimal conditions was 90% of the theoretical yield.

Distinct neuronal oscillatory responses between patients with bipolar and unipolar disorders: a magnetoencephalographic study

BACKGROUND

Bipolar disorder (BD) and major depressive disorder (MDD) have distinct pathophysiologies but similar depressive appearances. The present study aimed at the differentiation of the brain responses between BD and MDD patients. We hypothesized that different affective disorder patients may have distinct patterns of oscillatory cortical activities in response to negative emotional stimuli.

METHODS

Twenty BD patients, twenty MDD patients, and twenty age- and gender-matched healthy normal subjects were recruited. We adopted an implicit emotional task with facial image stimuli. The acquired event-related magnetoencephalographic signals were processed by the time-frequency analysis and beamformer-based source imaging techniques followed by statistical inference.

RESULTS

We found that there were gamma oscillation decreases in the frontal regions of both BD and MDD patients, gamma oscillation increases in the bilateral temporal regions of MDD, and alpha-beta rhythm increases in BD patients. Relative to the cortical activation in the control group, the BD patients displayed more widely increased oscillatory activities over the fronto-parieto-occipital regions than MDD patients.

CONCLUSIONS

Our results demonstrate the distinct neuropathological patterns of emotional responses in BD and MDD patients. The findings suggest that the dysfunction of emotion regulation in BD may result from the increased sensitivity to emotionally salient information, implicating the potential cause of the emotion lability. The present study also suggests that the implicit emotional task is an effective approach to differentiate bipolar from unipolar disorders and their distinct neuropathological patterns to emotional stimuli may provide objective and quantitative measures for potential diagnostic significance.

First-principles investigation of Ge doping effects on the structural, electronic and magnetic properties in antiperovskite Mn(3)CuN

We have investigated the structural, electronic, and magnetic properties of Mn(3)Cu(1 - x)Ge(x)N (x = 0, 0.125, 0.25) using first-principles density-functional theory within the generalized gradient approximation (GGA) + U schemes. The crystal structure of the compounds is a tetragonal crystal for x = 0 while it is a cubic crystal for x = 0.125, 0.25. The unit cell volume increases as the Ge doping increases. Our GGA + U calculations give a metallic ground state from x = 0 to 0.25 in agreement with experiments. The magnetic structure for x = 0 is found to be the ferromagnetic state while for x = 0.125, 0.25 it is the Γ(5g)-type antiferromagnetic state. From the density of states (DOS), the coupling between Ge 4p and Mn 3d is the main reason for magnetic transition in Mn(3)Cu(1 - x)Ge(x)N.

First Report of Tomato yellow leaf curl virus Infecting Tomato, Tomatillo, and Peppers in Guatemala

In Guatemala and other Central American countries, whitefly-transmitted geminiviruses (begomoviruses) cause economically important diseases of tomato (Solanum lycopersicum) and pepper (Capsicum annuum). Disease symptoms include stunted and distorted growth and leaf curling, crumpling, light green to yellow mosaic, purpling, and vein swelling. In Guatemala, at least eight bipartite begomovirus species infect tomato or peppers (1), but their role and relative importance is unclear. As part of an Integrated Pest Management strategy to manage these diseases, surveys for begomovirus symptoms in pepper and tomato have been conducted in the Salama Valley, Sanarate, and other locations since 2003, and begomoviruses were identified by squash blot hybridization, PCR and DNA sequencing. Beginning in 2006, a new type of symptom, stunted upright growth and upcurled leaves with yellowing of the margins and interveinal areas, was observed in tomato and tomatillo plants in the Salama Valley and Sanarate. These symptoms were similar to those induced by the exotic monopartite begomovirus Tomato yellow leaf curl virus (TYLCV). Evidence that TYLCV caused these symptoms came from positive results in high stringency squash blot hybridization tests with a TYLCV probe, and amplification of the expected size of ~0.3- and 2.8-kb fragments in PCR tests with TYLCV capsid protein (CP) gene and full-length component primer pairs, respectively (3). Sequence analyses of PCR-amplified CP fragments and portions of full-length fragments revealed 97 to 99% identity with isolates of TYLCV-Israel (TYLCV-IL). The complete nucleotide sequence of an isolate from the Salama Valley (GenBank Accession No. GU355941) was >99% identical to those of TYLCV-IL isolates from the Dominican Republic, Florida, and Cuba and ~97% identical to those of isolates from Mexico and California. Thus, this TYLCV-IL isolate (TYLCV-IL[GT:06]) was probably introduced from the Caribbean Region. To further characterize begomoviruses in the Salama Valley, leaf samples were collected from 44 and 118 tomato plants showing symptoms of begomovirus infection in March 2006 and 2007, respectively, and from 106 symptomatic pepper plants in March 2007. Begomovirus infection was confirmed in 42 of 44 and 93 of 118 of the tomato samples and 100 of 106 of the pepper samples based on PCR amplification of the expected size of ~0.6- and 1.1-kb DNA fragments with the begomovirus degenerate primers pairs AV494/AC1048 and PAL1v1978/PAR1c496, respectively (2,4). Sequence analyses of cloned PCR-amplified fragments revealed that 3 of the 44 and 16 of the 118 tomato samples collected in 2006 and 2007, respectively, and 9 of the 106 pepper samples were infected with TYLCV based on >97% identity with TYLCV-IL. In all samples, TYLCV was present in mixed infections with other begomoviruses. The introduction of TYLCV adds to the already high level of genetic complexity of bipartite begomovirus infection of tomatoes and peppers in Guatemala and will undoubtedly complicate disease management efforts. References: (1) M. K. Nakhla et al. Acta Hortic. 695:277, 2005. (2) M. R. Rojas et al. Plant Dis. 77:340, 1993. (3) R. Salati et al. Phytopathology 92:487, 2002. (4) S. D. Wyatt and J. Brown. Phytopathology 86:1288, 1996.

First-principles investigation of the structural, magnetic and electronic properties of perovskite SrRu(1-x)Mn(x)O(3)

We have investigated the structural, magnetic and electronic properties of single-crystal SrRu(1-x)Mn(x)O(3), using first-principles density functional theory within the generalized gradient approximation (GGA)+U schemes. The entire series of SrRu(1-x)Mn(x)O(3) (x = 0, 0.25, 0.5 and 1) is stabilized in the single-crystal perovskite structure which is in agreement with experimental findings. Our spin-polarized calculations give a metallic ground state for the x<0.5 regime and an insulator ground state for the x≥0.5 regime. The magnetic structure for x = 0 is found to be the ferromagnetic state while the magnetic structures for 0<x<0.5 are the ferrimagnetic state where any Mn ions are coupled antiparallel to the Ru at the near sites. The magnetic structures for x≥0.5 are found to be the antiferromagnetic states. The substitution of itinerant Ru ions by localized Mn ions enhances the p-d coupling between O and the transition metal. It also strongly drives the system from the ferromagnetic metal to the antiferromagnetic insulator.

Ab initio molecular-dynamics simulation of liquid As(x)Te(1-x) alloys

Ab initio molecular-dynamics simulations have been used to investigate the structure and dynamics properties of the liquid alloy As(x)Te(1-x) at 800 K and at the five compositions x = 0.2, 0.3, 0.4, 0.5 and 0.6. We present results for the static structure factors, diffusion coefficients and frequency spectra, in addition to the electronic density of states. Both the results for the structural and dynamic properties are in relatively good agreement with the experimental data available. The results also indicate that the increase in the number of As atoms reduces the metallic character of the sample in close connection with a corresponding disruption of the Te chain structure.

Accurate and robust extraction of brain regions using a deformable model based on radial basis functions

Brain extraction from head magnetic resonance (MR) images is a classification problem of segmenting image volumes into brain and non-brain regions. It is a difficult task due to the convoluted brain surface and the inapparent brain/non-brain boundaries in images. This paper presents an automated, robust, and accurate brain extraction method which utilizes a new implicit deformable model to well represent brain contours and to segment brain regions from MR images. This model is described by a set of Wendland's radial basis functions (RBFs) and has the advantages of compact support property and low computational complexity. Driven by the internal force for imposing the smoothness constraint and the external force for considering the intensity contrast across boundaries, the deformable model of a brain contour can efficiently evolve from its initial state toward its target by iteratively updating the RBF locations. In the proposed method, brain contours are separately determined on 2D coronal and sagittal slices. The results from these two views are generally complementary and are thus integrated to obtain a complete 3D brain volume. The proposed method was compared to four existing methods, Brain Surface Extractor, Brain Extraction Tool, Hybrid Watershed Algorithm, and Model-based Level Set, by using two sets of MR images as well as manual segmentation results obtained from the Internet Brain Segmentation Repository. Our experimental results demonstrated that the proposed approach outperformed these four methods when jointly considering extraction accuracy and robustness.