An Optimal Algorithm for the Maximum-Density Segment Problem

We address a fundamental problem arising from analysis of biomolecular sequences. The input consists of two numbers $w_{\min}$ and $w_{\max}$ and a sequence $S$ of $n$ number pairs $(a_i,w_i)$ with $w_i>0$. Let {\em segment} $S(i,j)$ of $S$ be the consecutive subsequence of $S$ between indices $i$ and $j$. The {\em density} of $S(i,j)$ is $d(i,j)=(a_i+a_{i+1}+...+a_j)/(w_i+w_{i+1}+...+w_j)$. The {\em maximum-density segment problem} is to find a maximum-density segment over all segments $S(i,j)$ with $w_{\min}\leq w_i+w_{i+1}+...+w_j \leq w_{\max}$. The best previously known algorithm for the problem, due to Goldwasser, Kao, and Lu, runs in $O(n\log(w_{\max}-w_{\min}+1))$ time. In the present paper, we solve the problem in O(n) time. Our approach bypasses the complicated {\em right-skew decomposition}, introduced by Lin, Jiang, and Chao. As a result, our algorithm has the capability to process the input sequence in an online manner, which is an important feature for dealing with genome-scale sequences. Moreover, for a type of input sequences $S$ representable in $O(m)$ space, we show how to exploit the sparsity of $S$ and solve the maximum-density segment problem for $S$ in $O(m)$ time.Comment: 15 pages, 12 figures, an early version of this paper was presented at 11th Annual European Symposium on Algorithms (ESA 2003), Budapest, Hungary, September 15-20, 200

Anti-inflammatory effect of low intensity ultrasound (LIUS) on complete Freund's adjuvant-induced arthritis synovium

SummaryObjectivesArthritis with intra-articular inflammation was accompanied by joint pain, swelling, and stiffness leading to significant functional impairment. Thus, regulation of joint inflammation is a good therapeutic approach for patients with arthritis. In this study, the effect of low intensity ultrasound (LIUS) applied to an adjuvant-induced arthritic rat model on the synovium was investigated.DesignSynovial inflammation was induced by complete Freund's adjuvant (CFA)-injection into the rat knee joint. LIUS (200 mW/cm2) was applied on the ipsilateral knee everyday for 10 min beginning 1 day after inflammation induction. The expression of proinflammatory factors and immunohistochemical staining pattern of the synovium were assessed.ResultsCFA induced an increase of the knee circumference that was significantly diminished by LIUS. Synovial membrane hyperplasia in the ipsilateral joint was also affected by LIUS. The inflammatory mediators, COX-1/2, IL-1β, and iNOS, but not TNF-α, in the synovial membrane were induced after 3 days, and they closely correlated with the degree of edema. In the synovial membrane, the expression of inflammatory mediators was reduced by LIUS. The chemoattractant chemokine receptor CCR5 also was involved. On immunohistochemical analysis, CFA caused increased infiltration of CD11b-positive cells in the synovium. After 3 days, neutrophils, myeloperoxidase (MPO)-positive cells filled the inflammatory core; later, monocytes and macrophages, ionized calcium binding adaptor molecule 1 (Iba1)-positive cells in the periphery infiltrated the core by day 5. LIUS markedly reduced CFA-induced inflammatory cells infiltration.ConclusionLIUS showed a potent anti-inflammatory effect in this animal arthritis model with reduced infiltration of inflammatory cells into the synovium

Relationship between Obesity-related Hormone Peptides and Quality of Life in Obese Women among Different Traditional Chinese Medicine Syndrome Groups

AbstractThe aim of this study was to explore the relationship between obesity-related hormone peptides and quality of life in obese women among different traditional Chinese medicine (TCM) syndrome groups (證型 zhèng xíng). 260 obese women met with age between 20 and 65years old and body mass index (BMI) ≧ 27kg/m2, were recruited. The participants filled out a questionnaire on obese TCM syndrome groups, which was designed by professional TCM doctors, and two questionnaires on quality of life (QOL), WHOQOL-BREF Taiwan version and MOS Short Form-12 (SF-12). Data of biochemical characteristics and obesity-related hormone peptides were collected at the same time. According to the responses provided, the obese subjects were classified into spleen deficiency with dampness encumbrance syndrome (脾虛濕阻證 pí xū shī zǔ zhèng; SDD), stomach heat with dampness encumbrance syndrome (胃熱濕阻證 wèi rè shī zǔ zhèng; SHD), liver depression and qi stagnation syndrome (肝鬱氣滯證 gān yù qì zhì zhèng; LDQ), dual spleen-kidney deficiency syndrome (脾腎兩虛證 pí shèn liǎng xū zhèng; SKD), yin deficiency with internal heat syndrome (陰虛內熱證 yīn xū nèi rè zhèng; YDI) and a control group. For physical conditions, SDD group had significantly higher means in weight and BMI compared with the control group. The insulin and leptin levels in SHD group were significantly higher than those in the control group. The LDQ group showed marked decrease in mental condition scores compared with the control group. This study found that obese women in the SDD group were fatter than those in the control group. SHD group might have greater influence on the regulation of obesity-related hormone peptides. The LDQ group had poor QOL than the control group. Analysis of TCM syndrome groups among obese women merits further investigation

Blow to the northeast? Intraspecific differentiation of populus davidiana suggests a northeastward skew of a phylogeographic break boundary in East Asia

Aim There is increasing interest in the role that biological traits, and historical and biogeographic processes, play in the formation of phylogeographic patterns. An arid belt that once existed in northern China might have affected many plants, but this has yet to be tested in an arid-tolerant, wind-dispersed species. Here, we tested how intrinsic and extrinsic factors have affected the phylogeography of Populus davidiana. Location East Asia. Methods Genetic variation was surveyed across 40 populations (555 individuals) covering the Chinese range of P. davidiana, using 16 nuclear microsatellite loci (nSSRs) and four chloroplast fragments (cpDNA). Demographic and migration hypotheses were tested using coalescent-based approaches, and the present and past potential distributions were predicted using species distribution modelling. Results Molecular data divide P. davidiana into two lineages, north-eastern China (NECR) and central and northern China (CNCR); however, the dividing line is around 118ºE for nSSRs, but 122ºE for cpDNA. The range and habitat of the two lineages barely overlap at present, and their ecological separation may have initiated around the Pliocene-Quaternary boundary, when major intraspecific cpDNA clades diverged. NECR and CNCR experienced post-glacial north-eastward and northward range shifts respectively. Bi-directional historical gene flow was detected between NECR and CNCR for both bi-parentally inherited nSSRs and maternally inherited cpDNA. Demographic inferences suggest a severe bottleneck for CNCR and especially NECR, around the latest Pleistocene. Main conclusions The phylogeographic break within P. davidiana reflects the impacts of biogeographic history, climate and biological traits. Its plumed, wind-dispersed seeds might be especially significant because prevailing south-western spring winds may have moved the NECR-CNCR boundary further east than similar phylogenetic breaks in other species, and also moved the cpDNA boundary relative to that for nuclear markers. Biological traits, therefore, should also be considered when examining the genetic and ecological differentiation between closely related taxa

Combined Effects of Interleukin-7 and Stem Cell Factor Administration on Lymphopoiesis after Murine Bone Marrow Transplantation

The decreased ability of the thymus to generate T cells after bone marrow transplantation (BMT) is a clinically significant problem. Interleukin (IL)-7 and stem cell factor (SCF) induce proliferation, differentiation, and survival of thymocytes. Although previous studies have shown that administration of recombinant human IL-7 (rhIL-7) after murine and human BMT improves thymopoiesis and immune function, whether administration of SCF exerts similar effects is unclear. To evaluate independent or combinatorial effects of IL-7 and SCF in post-BMT thymopoiesis, bone marrow (BM)-derived mesenchymal stem cells transduced ex vivo with the rhIL-7 or murine SCF (mSCF) genes were cotransplanted with T cell–depleted BM cells into lethally irradiated mice. Although rhIL-7 and mSCF each improved immune reconstitution, the combination treatment had a significantly greater effect than either cytokine alone. Moreover, the combination treatment significantly increased donor-derived common lymphoid progenitors (CLPs) in BM, suggesting that transplanted CLPs expand more rapidly in response to IL-7 and SCF and may promote immune reconstitution. Our findings demonstrate that IL-7 and SCF might be therapeutically useful for enhancing de novo T cell development. Furthermore, combination therapy may allow the administration of lower doses of IL-7, thereby decreasing the likelihood of IL-7–mediated expansion of mature T cells

Fidelity approach to Gaussian transitions

The fidelity approach to the Gaussian transitions in spin-one XXZ spin chains with three different values of Ising-like anisotropy lambda is analyzed by means of the density matrix renormalization group (DMRG) technique for systems of large sizes. We find that, despite the success in the cases of lambda=2.59 and 1, the fidelity susceptibility fails to detect the Gaussian transition for lambda=0.5. Thus our results demonstrate the limitation of the fidelity susceptibility in characterizing quantum phase transitions, which was proposed recently in general frameworks.Comment: 9 pages, 9 figure

Replica theory for learning curves for Gaussian processes on random graphs

Statistical physics approaches can be used to derive accurate predictions for the performance of inference methods learning from potentially noisy data, as quantified by the learning curve defined as the average error versus number of training examples. We analyse a challenging problem in the area of non-parametric inference where an effectively infinite number of parameters has to be learned, specifically Gaussian process regression. When the inputs are vertices on a random graph and the outputs noisy function values, we show that replica techniques can be used to obtain exact performance predictions in the limit of large graphs. The covariance of the Gaussian process prior is defined by a random walk kernel, the discrete analogue of squared exponential kernels on continuous spaces. Conventionally this kernel is normalised only globally, so that the prior variance can differ between vertices; as a more principled alternative we consider local normalisation, where the prior variance is uniform

Electronic properties of bilayer and multilayer graphene

We study the effects of site dilution disorder on the electronic properties in graphene multilayers, in particular the bilayer and the infinite stack. The simplicity of the model allows for an easy implementation of the coherent potential approximation and some analytical results. Within the model we compute the self-energies, the density of states and the spectral functions. Moreover, we obtain the frequency and temperature dependence of the conductivity as well as the DC conductivity. The c-axis response is unconventional in the sense that impurities increase the response for low enough doping. We also study the problem of impurities in the biased graphene bilayer.Comment: 36 pages, 42 figures, references adde