A Conjugate Gradient Algorithm with Function Value Information and N-Step Quadratic Convergence for Unconstrained Optimization

It is generally acknowledged that the conjugate gradient (CG) method achieves global convergence—with at most a linear convergence rate—because CG formulas are generated by linear approximations of the objective functions. The quadratically convergent results are very limited. We introduce a new PRP method in which the restart strategy is also used. Moreover, the method we developed includes not only n-step quadratic convergence but also both the function value information and gradient value information. In this paper, we will show that the new PRP method (with either the Armijo line search or the Wolfe line search) is both linearly and quadratically convergent. The numerical experiments demonstrate that the new PRP algorithm is competitive with the normal CG method.     

Memory and Fitness Optimization of Bacteria under Fluctuating Environments

Bacteria prudently regulate their metabolic phenotypes by sensing the availability of specific nutrients, expressing the required genes for their metabolism, and repressing them after specific metabolites are depleted. It is unclear, however, how genetic networks maintain and transmit phenotypic states between generations under rapidly fluctuating environments. By subjecting bacteria to fluctuating carbon sources (glucose and lactose) using microfluidics, we discover two types of non-genetic memory in Escherichia coli and analyze their benefits. First, phenotypic memory conferred by transmission of stable intracellular lac proteins dramatically reduces lag phases under cyclical fluctuations with intermediate timescales (1–10 generations). Second, response memory, a hysteretic behavior in which gene expression persists after removal of its external inducer, enhances adaptation when environments fluctuate over short timescales (<1 generation). Using a mathematical model we analyze the benefits of memory across environmental fluctuation timescales. We show that memory mechanisms provide an important class of survival strategies in biology that improve long-term fitness under fluctuating environments. These results can be used to understand how organisms adapt to fluctuating levels of nutrients, antibiotics, and other environmental stresses.     

Chondroitin Sulfate Synthase-2/Chondroitin Polymerizing Factor Has Two Variants with Distinct Function

Chondroitin sulfate (CS) is a polysaccharide consisting of repeating disaccharide units of N-acetyl-d-galactosamine and d-glucuronic acid residues, modified with sulfated residues at various positions. To date six glycosyltransferases for chondroitin synthesis have been identified, and the complex of chondroitin sulfate synthase-1 (CSS1)/chondroitin synthase-1 (ChSy-1) and chondroitin sulfate synthase-2 (CSS2)/chondroitin polymerizing factor is assumed to play a major role in CS biosynthesis. We found an alternative splice variant of mouse CSS2 in a data base that lacks the N-terminal transmembrane domain, contrasting to the original CSS2. Here, we investigated the roles of CSS2 variants. Both the original enzyme and the splice variant, designated CSS2A and CSS2B, respectively, were expressed at different levels and ratios in tissues. Western blot analysis of cultured mouse embryonic fibroblasts confirmed that both enzymes were actually synthesized as proteins and were localized in both the endoplasmic reticulum and the Golgi apparatus. Pulldown assays revealed that either of CSS2A, CSS2B, and CSS1/ChSy-1 heterogeneously and homogeneously interacts with each other, suggesting that they form a complex of multimers. In vitro glycosyltransferase assays demonstrated a reduced glucuronyltransferase activity in CSS2B and no polymerizing activity in CSS2B co-expressed with CSS1, in contrast to CSS2A co-expressed with CSS1. Radiolabeling analysis of cultured COS-7 cells overexpressing each variant revealed that, whereas CSS2A facilitated CS biosynthesis, CSS2B inhibited it. Molecular modeling of CSS2A and CSS2B provided support for their properties. These findings, implicating regulation of CS chain polymerization by CSS2 variants, provide insight in elucidating the mechanisms of CS biosynthesis.     

Design of Optical Filters with Flat-on-Top Transmission Lineshapes Based on Two Side-Coupled Metallic Grooves

We investigate theoretically and numerically the resonant transmission through side-coupled metallic grooves. In the framework of coupled mode theory (CMT), a single metallic groove can be considered as a lossy optical resonator and two metallic grooves coupled via tunneling effect can be treated as a second-order cascade resonator. The relationship between the transmission lineshape of the coupled grooves and the cross-coupling between the grooves is analyzed by CMT. It is found that a flat-on-top lineshape can be obtained when the cross-coupling is equal to the total decay rate of the groove mode. Predictions based on the CMT analysis are in good agreement with the simulation results based on the finite-difference time-domain technique.     

Microchromosomes Exhibit Distinct Features of Vertebrate Chromosome Structure and Function with Underappreciated Ramifications for Genome Evolution

Microchromosomes are common yet poorly understood components of many vertebrate genomes. Recent studies have revealed that microchromosomes contain a high density of genes and possess other distinct characteristics compared with macrochromosomes. Whether distinctive characteristics of microchromosomes extend to features of genome structure and organization, however, remains an open question. Here, we analyze Hi-C sequencing data from multiple vertebrate lineages and show that microchromosomes exhibit consistently high degrees of interchromosomal interaction (particularly with other microchromosomes), appear to be colocalized to a common central nuclear territory, and are comprised of a higher proportion of open chromatin than macrochromosomes. These findings highlight an unappreciated level of diversity in vertebrate genome structure and function, and raise important questions regarding the evolutionary origins and ramifications of microchromosomes and the genes that they house.     

Optimization Design of a Multi-slot Nanoantenna Based on Genetic Algorithm for Energy Harvesting

A new genetic algorithm (GA)-based multi-slot nanoantenna is proposed for energy harvesting, which consists of two element nanoantennas with rectangular shape and with double bowtie double ring (DBDR) slot. The DBDR slot structure can enhance the electric field to increase the absorptivity of nanoantennas; however, the larger parameter space of multi-slot is more hardly controlled. Therefore, we use GA to optimize the parameters of the DBDR slot nanoantenna and the Finite-Difference Time-Domain method to calculate the absorptivity. It is found that absorptivity of the optimized nanoantenna is over 77% in 400–1800 nm waveband. We attribute the better absorbing property of the nanoantenna to the synergistic effect of the localized surface plasmon resonance enhancement and coupling between slots.

     

A Solution to the Challenge of Optimization on 'Golf-Course'-Like Fitness Landscapes

Genetic algorithms (GAs) have been used to find efficient solutions to numerous fundamental and applied problems. While GAs are a robust and flexible approach to solve complex problems, there are some situations under which they perform poorly. Here, we introduce a genetic algorithm approach that is able to solve complex tasks plagued by so-called ''''golf-course''''-like fitness landscapes. Our approach, which we denote variable environment genetic algorithms (VEGAs), is able to find highly efficient solutions by inducing environmental changes that require more complex solutions and thus creating an evolutionary drive. Using the density classification task, a paradigmatic computer science problem, as a case study, we show that more complex rules that preserve information about the solution to simpler tasks can adapt to more challenging environments. Interestingly, we find that conservative strategies, which have a bias toward the current state, evolve naturally as a highly efficient solution to the density classification task under noisy conditions.     

Utilizing Repetitive Transcranial Magnetic Stimulation to Improve Language Function in Stroke Patients with Chronic Non-fluent Aphasia

Transcranial magnetic stimulation (TMS) has been shown to significantly improve language function in patients with non-fluent aphasia¹. In this experiment, we demonstrate the administration of low-frequency repetitive TMS (rTMS) to an optimal stimulation site in the right hemisphere in patients with chronic non-fluent aphasia. A battery of standardized language measures is administered in order to assess baseline performance. Patients are subsequently randomized to either receive real rTMS or initial sham stimulation. Patients in the real stimulation undergo a site-finding phase, comprised of a series of six rTMS sessions administered over five days; stimulation is delivered to a different site in the right frontal lobe during each of these sessions. Each site-finding session consists of 600 pulses of 1 Hz rTMS, preceded and followed by a picture-naming task. By comparing the degree of transient change in naming ability elicited by stimulation of candidate sites, we are able to locate the area of optimal response for each individual patient. We then administer rTMS to this site during the treatment phase. During treatment, patients undergo a total of ten days of stimulation over the span of two weeks; each session is comprised of 20 min of 1 Hz rTMS delivered at 90% resting motor threshold. Stimulation is paired with an fMRI-naming task on the first and last days of treatment. After the treatment phase is complete, the language battery obtained at baseline is repeated two and six months following stimulation in order to identify rTMS-induced changes in performance. The fMRI-naming task is also repeated two and six months following treatment. Patients who are randomized to the sham arm of the study undergo sham site-finding, sham treatment, fMRI-naming studies, and repeat language testing two months after completing sham treatment. Sham patients then cross over into the real stimulation arm, completing real site-finding, real treatment, fMRI, and two- and six-month post-stimulation language testing.     

A Parallel Implementation of the Wuchty Algorithm with Additional Experimental Filters to More Thoroughly Explore RNA Conformational Space

We present new modifications to the Wuchty algorithm in order to better define and explore possible conformations for an RNA sequence. The new features, including parallelization, energy-independent lonely pair constraints, context-dependent chemical probing constraints, helix filters, and optional multibranch loops, provide useful tools for exploring the landscape of RNA folding. Chemical probing alone may not necessarily define a single unique structure. The helix filters and optional multibranch loops are global constraints on RNA structure that are an especially useful tool for generating models of encapsidated viral RNA for which cryoelectron microscopy or crystallography data may be available. The computations generate a combinatorially complete set of structures near a free energy minimum and thus provide data on the density and diversity of structures near the bottom of a folding funnel for an RNA sequence. The conformational landscapes for some RNA sequences may resemble a low, wide basin rather than a steep funnel that converges to a single structure.     

A Human iPSC Double-Reporter System Enables Purification of Cardiac Lineage Subpopulations with Distinct Function and Drug Response Profiles

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Design of a Frequency Reconfigurable Broadband THz Antenna Based on the Vanadium Dioxide

In this article, the design of a frequency reconfigurable broadband THz antenna based on vanadium dioxide (VO₂) is investigated. Instead of being fed by the microstrip line directly, a windmill-shaped feeding structure is designed to provide a proximity-coupled feeding method. Many modes with contiguous resonant frequencies can be excited to obtain the wideband performance. The proposed antenna combines gold with metamaterial VO₂. Thanks to insulator-metal phase transition characteristic of VO₂ at phase transition temperature (68 °C), we can change the length of the resonant branches to realize frequency reconfiguration by changing the external temperature (T). The simulated results illustrate that when T = 50 °C (State I), such an antenna has a bandwidth of 35.2% (7.01–10 THz) with S₁₁ below − 10 dB, and a maximum gain of 6.62 dBic. When T = 80 °C (State II), it has a bandwidth of 21.8% (5.77–7.18 THz) with S₁₁ below − 10 dB, and a maximum gain of 4.49 dBic. Thus, we realize a design of a proximity-coupled antenna with reconfigurable wideband over the THz band.

     

彩超系统中壁滤波器设计和性能比较

本文首先介绍了多普勒原理和血流多普勒信号模型,推出了壁滤波器设计在彩色超声成像系统中具有极其重要的地位;其次分析了如何通过无限脉冲冲激响应（IIR）滤波器和回归型滤波器设计壁滤波器的原理,其中无限脉冲冲激响应（IIR）滤波器根据初始状态的不同又可以分为零初始化、阶跃初始化和投影初始化三种滤波器;然后根据上述原理分别对各种形式的壁滤波器进行设计,得到它们的频谱图;最后根据频谱图,对这几种壁滤波器进行性能比较,得到它们的优缺点,对从事壁滤波器设计相关的工作者有一定得借鉴意义。     

Distinct Effects of Protein Kinase C on the Barrier Function at Different Developmental Stages

We show here, that activation of protein kinase C by the phorbol ester PMA improves barrier function in colon carcinoma (HT 29) cells. By contrast, in canine kidney (MDCK I) cells it caused increased permeability and opening of tight junctions; the latter has also been noticed in other studies. Thus, with PMA confluent HT 29 cells responded with a reduced passage of 330 kDa sodium fluorescein, increased transepithelial electrical resistance, and a change in the cell shape of the HT 29 cells from an irregular to a regular, hexagonal form. Confocal imaging revealed parallel distinct changes in the staining of occludin and caludin-1, viz. a translocation from cytoplasmic clusters to apical cell–cell contacts. Interestingly, in both cell lines protein kinase A activation caused a decreased in the threonine phosphorylation of occludin that correlated with tight junction assembly in HT 29 cells and tight junction disassembly in MDCK I cells. We conclude that protein kinase C regulation of the epithelial barrier involves specific molecular mechanisms and achieves distinct effects at different developmental stages.     

Study About the Effects of Different Fitness Sports on Cognitive Function and Emotion of the Aged

The aim of the study was to explore the effects of different fitness sports on cognitive function and emotion of the aged people. A total of 150 subjects aged between 60 and 70 were recruited from Shenyang Aged University and elderly activity center. All subjects reported no fitness before this study. The aged subjects were divided into five groups, included swimming group (A group), running group (B group), square dancing group (C group), Tai Chi group (D group) and control group (E group) with 30 people in each group. Subjects in each group received exercise intervention continued for 18 months. At baseline, 6, 12 and 18 months after intervention, the P300 test, SECF, HAMD and HAMA scale evaluations were performed. Compared to E group, the P2, N2 and P3 latency and response time in the D group after intervention for 6 months, and in the A–C groups after intervention for 12 months were significantly prolonged. The anxiety symptom and depression levels in the A–D groups after intervention for 12 months were significantly decreased when compared to E group (P < 0. 01), where significantly improved compared with the E group (P < 0. 01). The effect of exercise intervention for Tai Chi group was the most significant. Different fitness sports have marked beneficial effect on cognitive function and emotion of the aged people, especially the Tai Chi exercise.     

缢蛏SRAP-PCR体系的正交优化

运用L16(45)正交设计对影响缢蛏SRAP-PCR反应的5个因素:Taq酶浓度、Mg2+浓度、模板DNA浓度、dNTPs浓度和引物浓度在4个水平上进行了优化试验,PCR结果采用SPSS v16.0软件分析.结果表明,各因素对SRAP-PCR反应的影响依次为:引物>Taq酶>模板DNA>Mg2+;缢蛏SRAP反应最佳体系为:在20μL PCR反应体系中,引物0.3 μmol/L、Taq 酶0.5 U、模板DNA 50 ng、dNTPs 0.2 mmol/L及Mg2+2 mmol/L.用不同缢蛏的基因组DNA两次SRAP-PCR扩增,8对引物均能扩增出清晰且重复性好的谱带.因而建立的缢蛏反应体系稳定可靠.     

A Conjugate Gradient Algorithm with a Trust Region for Molecular Geometry Optimization

An algorithm is presented for the optimization of molecular geometries and general nonquadratic functions using the nonlinear conjugate gradient method with a restricted step and restart procedure. The algorithm only requires the evaluation of the energy function and its gradient, therefor less memory storage is needed than for other conjugate gradient algorithms. Some numerical results are also presented and the efficiency and behaviour of the algorithm is compared with the standard conjugate gradient method. We also present comparisons of both conjugate gradient and variable metric methods with and without the trust region technique. One of the main conclusions of the present work is that a trust region always improves the converge of any optimization method. A sketch of the algorithm is also given.