Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost

BACKGROUND: Multiple sequence alignment (MSA) is a useful tool in bioinformatics. Although many MSA algorithms have been developed, there is still room for improvement in accuracy and speed. In the alignment of a family of protein sequences, global MSA algorithms perform better than local ones in many cases, while local ones perform better than global ones when some sequences have long insertions or deletions (indels) relative to others. Many recent leading MSA algorithms have incorporated pairwise alignment information obtained from a mixture of sources into their scoring system to improve accuracy of alignment containing long indels. RESULTS: We propose a novel group-to-group sequence alignment algorithm that uses a piecewise linear gap cost. We developed a program called PRIME, which employs our proposed algorithm to optimize the well-defined sum-of-pairs score. PRIME stands for Profile-based Randomized Iteration MEthod. We evaluated PRIME and some recent MSA programs using BAliBASE version 3.0 and PREFAB version 4.0 benchmarks. The results of benchmark tests showed that PRIME can construct accurate alignments comparable to the most accurate programs currently available, including L-INS-i of MAFFT, ProbCons, and T-Coffee. CONCLUSION: PRIME enables users to construct accurate alignments without having to employ pairwise alignment information. PRIME is available at

Fine structure and magneto-optics of exciton, trion, and charged biexciton states in single InAs quantum dots emitting at 1.3 um

We present a detailed investigation into the optical characteristics of individual InAs quantum dots (QDs) grown by metalorganic chemical vapor deposition, with low temperature emission in the telecoms window around 1300 nm. Using micro-photoluminescence (PL) spectroscopy we have identified neutral, positively charged, and negatively charged exciton and biexciton states. Temperature-dependent measurements reveal dot-charging effects due to differences in carrier diffusivity. We observe a pronounced linearly polarized splitting of the neutral exciton and biexciton lines (~250 ueV) resulting from asymmetry in the QD structure. This asymmetry also causes a mixing of the excited trion states which is manifested in the fine structure and polarization of the charged biexciton emission; from this data we obtain values for the ratio between the anisotropic and isotropic electron-hole exchange energies of (Delta1)/(Delta0)= 0.2--0.5. Magneto-PL spectroscopy has been used to investigate the diamagnetic response and Zeeman splitting of the various exciton complexes. We find a significant variation in g-factor between the exciton, the positive biexciton, and the negative biexciton; this is also attributed to anisotropy effects and the difference in lateral extent of the electron and hole wavefunctions.Comment: 7 pages, 6 figures, submitted to Phys. Rev.

Study on Behavioral Decision Making by Power Generation Companies Regarding Energy Transitions under Uncertainty

With respect to decision making by companies, normative approaches such as the net present value (NPV) method are widely applied, even though it is known that investors may make non-normative decisions. This study aimed to obtain new information on the decision-making behavior of renewable energy (RE) companies under uncertainty in the energy market, which is not provided by the conventional normative approach. In this study, we designed a novel framework that expressed both normative and non-normative perspectives of decision making, and developed a behavioral decision-making model of a power generation company investing in large-scale RE (RE company). We also examined the decisions of the RE company under uncertainty in the energy market using the developed model, considering the Kansai region in Japan as an example study area. As a result, compared to the conventional NPV method, we obtained the following information: (i) heavy investments in either photovoltaics (PV) or wind resulted in decreased variable renewable energy (VRE) capacity, even though financial support was sufficient; (ii) balanced investments in both PV and wind yielded a larger VRE capacity in cases where financial support was sufficient; and (iii) co-worker’s suggestions that lowered the decision-makers’ reference point (RFP) encouraged VRE investments despite insufficient financial support

Viscous Instanton for Burgers' Turbulence

We consider the tails of probability density functions (PDF) for different characteristics of velocity that satisfies Burgers equation driven by a large-scale force. The saddle-point approximation is employed in the path integral so that the calculation of the PDF tails boils down to finding the special field-force configuration (instanton) that realizes the extremum of probability. We calculate high moments of the velocity gradient $\partial_xu$ and find out that they correspond to the PDF with $\ln[{\cal P}(\partial_xu)]\propto-(-\partial_xu/{\rm Re})^{3/2}$ where ${\rm Re}$ is the Reynolds number. That stretched exponential form is valid for negative $\partial_xu$ with the modulus much larger than its root-mean-square (rms) value. The respective tail of PDF for negative velocity differences $w$ is steeper than Gaussian, $\ln{\cal P}(w)\sim-(w/u_{\rm rms})^3$, as well as single-point velocity PDF $\ln{\cal P}(u)\sim-(|u|/u_{\rm rms})^3$. For high velocity derivatives $u^{(k)}=\partial_x^ku$, the general formula is found: $\ln{\cal P}(|u^{(k)}|)\propto -(|u^{(k)}|/{\rm Re}^k)^{3/(k+1)}$.Comment: 15 pages, RevTeX 3.

L-arginine uptake, the citrulline-NO cycle and arginase II in the rat brain: an in situ hybridization study

Nitric oxide (NO) is synthesized from a unique precursor, arginine, by nitric oxide synthase (NOS). In brain cells, arginine is supplied by protein breakdown or extracted from the blood through cationic amino acid transporters (CATs). Arginine can also be recycled from the citrulline produced by NOS activity, through argininosuccinate synthetase (AS) and argininosuccinate lyase (AL) activities, and metabolized by arginase. NOS, AS and AL constitute the so-called citrulline-NO cycle. In order to better understand arginine transport, recycling and degradation, we studied the regional distribution of cells expressing CAT1, CAT3, AS, AL, neuronal NOS (nNOS) and arginase II (AII) in the adult rat brain by non-radioisotopic in situ hybridization (ISH). CAT1, AL and AII presented an ubiquitous neuronal and glial expression, whereas CAT3 and AS were confined to neurons. nNOS was restricted to scattered neurons and a few brain nuclei and layers. We demonstrate by this study that cells expressing nNOS all appear to express the entire citrulline-NO cycle, whereas numerous cells expressing AL do not express AS. The differential expression of these genes within the same anatomical structure could indicate that intercellular exchanges of citrulline-NO cycle metabolites are relevant. Thus vicinal interactions should be taken into account to study their regulatory mechanisms

Differential expression of the cationic amino acid transporter 2(B) in the adult rat brain

L-Arginine is a substrate for the synthesis of proteins, nitric oxide (NO), creatine, urea, proline, glutamate, polyamines and agmatine. In the central nervous system (CNS), arginine is extracted from the blood and exchanged by cells through carriers called cationic amino acid transporters (CAT) and belonging to the so-called system y+. In order to better understand the arginine transport in the CNS, we studied in detail the regional distribution of the cells expressing the CAT2(B) transcript in the adult rat brain by non-radioisotopic in situ hybridization. We show that CAT2(B) is expressed in neurons and oligodendrocytes throughout the brain, but is not detected in astrocytes. The pattern of localization of CAT2(B) in the normal adult rat brain fits closely that of CRT1, a specific creatine transporter. Our study demonstrates that the in vivo expression of CAT2(B) differs from that reported in vitro, implying that local cellular interactions should be taken into account in studies of gene regulation of the CAT2(B) gene. Our work suggests that CAT2(B) may play a role in case of increased NO production as well as arginine or creatine deficiency in the brain

An inertial range length scale in structure functions

It is shown using experimental and numerical data that within the traditional inertial subrange defined by where the third order structure function is linear that the higher order structure function scaling exponents for longitudinal and transverse structure functions converge only over larger scales, $r>r_S$, where $r_S$ has scaling intermediate between $\eta$ and $\lambda$ as a function of $R_\lambda$. Below these scales, scaling exponents cannot be determined for any of the structure functions without resorting to procedures such as extended self-similarity (ESS). With ESS, different longitudinal and transverse higher order exponents are obtained that are consistent with earlier results. The relationship of these statistics to derivative and pressure statistics, to turbulent structures and to length scales is discussed.Comment: 25 pages, 9 figure

Superdiffusivity of the 1D lattice Kardar-Parisi-Zhang equation

The continuum Kardar-Parisi-Zhang equation in one dimension is lattice discretized in such a way that the drift part is divergence free. This allows to determine explicitly the stationary measures. We map the lattice KPZ equation to a bosonic field theory which has a cubic anti-hermitian nonlinearity. Thereby it is established that the stationary two-point function spreads superdiffusively.Comment: 21 page

Multiple sequence alignment based on set covers

We introduce a new heuristic for the multiple alignment of a set of sequences. The heuristic is based on a set cover of the residue alphabet of the sequences, and also on the determination of a significant set of blocks comprising subsequences of the sequences to be aligned. These blocks are obtained with the aid of a new data structure, called a suffix-set tree, which is constructed from the input sequences with the guidance of the residue-alphabet set cover and generalizes the well-known suffix tree of the sequence set. We provide performance results on selected BAliBASE amino-acid sequences and compare them with those yielded by some prominent approaches