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

Bacteraemia caused by Weissella confusa at a university hospital in Taiwan, 1997–2007

AbstractHuman infections caused by Weissella confusa are rarely reported. Ten patients with bacteraemia caused by W. confusa who were treated at a tertiary-care hospital in Taiwan during 1997–2007 were studied. All isolates were initially misidentified as various Lactobacillus and Leuconostoc species by two commercial automated identification methods, and were confirmed to be W. confusa by 16S rRNA sequencing analysis. MICs of these isolates for ten antimicrobial agents were determined by the agar dilution method. The characteristics of these patients included underlying malignancy (n = 4), presence of a central catheter (n = 6), surgery within the previous 3 months (n = 4) and concomitant polymicrobial bacteraemia (n = 5, 50%). Mortality was directly attributed to bacteraemia in two patients. All isolates exhibited high trimethoprim–sulphamethoxazole and ceftazidime MICs (≥128 mg/L) and were inhibited by linezolid, daptomycin, ceftobiprole and tigecycline at 4, 0.12, 2 and 0.12 mg/L, respectively. In conclusion, W. confusa should be included in the list of organisms causing bacteraemia in immunocompromised hosts. Novel antibiotics, including daptomycin, moxifloxacin, doripenem and tigecycline, exert good activity against W. confusa

Impact of measurement backaction on nuclear spin qubits in silicon

Phosphorus donor nuclear spins in silicon couple weakly to the environment making them promising candidates for high-fidelity qubits. The state of a donor nuclear spin qubit can be manipulated and read out using its hyperfine interaction with the electron confined by the donor potential. Here we use a master equation-based approach to investigate how the backaction from this electron-mediated measurement affects the lifetimes of single and multi-donor qubits. We analyze this process as a function of electric and magnetic fields, and hyperfine interaction strength. Apart from single nuclear spin flips, we identify an additional measurement-related mechanism, the nuclear spin flip-flop, which is specific to multi-donor qubits. Although this flip-flop mechanism reduces qubit lifetimes, we show that it can be effectively suppressed by the hyperfine Stark shift. We show that using atomic precision donor placement and engineered Stark shift, we can minimize the measurement backaction in multi-donor qubits, achieving larger nuclear spin lifetimes than single donor qubits

The non-Verbal Structure of Patient Case Discussions in Multidisciplinary Medical Team Meetings

Meeting analysis has a long theoretical tradition in social psychology, with established practical rami?cations in computer science, especially in computer supported cooperative work. More recently, a good deal of research has focused on the issues of indexing and browsing multimedia records of meetings. Most research in this area, however, is still based on data collected in laboratories, under somewhat arti?cial conditions. This paper presents an analysis of the discourse structure and spontaneous interactions at real-life multidisciplinary medical team meetings held as part of the work routine in a major hospital. It is hypothesised that the conversational structure of these meetings, as indicated by sequencing and duration of vocalisations, enables segmentation into individual patient case discussions. The task of segmenting audio-visual records of multidisciplinary medical team meetings is described as a topic segmentation task, and a method for automatic segmentation is proposed. An empirical evaluation based on hand labelled data is presented which determines the optimal length of vocalisation sequences for segmentation, and establishes the competitiveness of the method with approaches based on more complex knowledge sources. The effectiveness of Bayesian classi?cation as a segmentation method, and its applicability to meeting segmentation in other domains are discusse

Stability of Solid State Reaction Fronts

We analyze the stability of a planar solid-solid interface at which a chemical reaction occurs. Examples include oxidation, nitridation, or silicide formation. Using a continuum model, including a general formula for the stress-dependence of the reaction rate, we show that stress effects can render a planar interface dynamically unstable with respect to perturbations of intermediate wavelength

A Genome-Wide Association Study Using a Custom Genotyping Array Identifies Variants in GPR158 Associated with Reduced Energy Expenditure in American Indians

Pima Indians living in Arizona have a high prevalence of obesity, and we have previously shown that a relatively lower energy expenditure (EE) predicts weight and fat mass gain in this population. EE is a familial trait (heritability = 0.52); therefore, in the current study, we aimed to identify genetic variants that affect EE and thereby influence BMI and body fatness in Pima Indians. Genotypic data from 491,265 variants were analyzed for association with resting metabolic rate (RMR) and 24-h EE assessed in a whole-room calorimeter in 507 and 419 Pima Indians, respectively. Variants associated with both measures of EE were analyzed for association with maximum BMI and percent body fat (PFAT) in 5,870 and 912 Pima Indians, respectively. rs11014566 nominally associated with both measures of EE and both measures of adiposity in Pima Indians, where the G allele (frequency: Pima Indians = 0.60, Europeans <0.01) associated with lower 24-h EE ( = -33 kcal/day per copy), lower RMR ( = -31 kcal/day), higher BMI ( = +0.6 kg/m(2)), and higher PFAT ( = +0.9%). However, the association of rs11014566 with BMI did not directionally replicate when assessed in other ethnic groups. rs11014566 tags rs144895904, which affected promoter function in an in vitro luciferase assay. These variants map to GPR158, which is highly expressed in the brain and interacts with two other genes (RGS7 and CACNA1B) known to affect obesity in knockout mice. Our results suggest that common ethnic-specific variation in GPR158 may influence EE; however, its role in weight gain remains controversial, as it either had no association with BMI or associated with BMI but in the opposite direction in other ethnic groups

SU(3) Breaking in Hyperon Beta Decays: a Prediction for Xi^0 -> Sigma^+ e nu-bar

On the basis of a previous analysis of hyperon semi-leptonic decay data, a prediction is presented for g_1/f_1 in the Xi^0 -> Sigma^+ e nu-bar beta-decay. The analysis takes into account SU(3) breaking in this sector via the inclusion of mass-driven corrections. A rather precise measurement of the above channel by the KTeV experiment at Fermilab will shortly be available. Since the dependence on the SU(3) parameters, F and D, is identical to that of the neutron beta-decay, such a measurement will provide a rather stringent test of SU(3) and the models used to describe its violation in these decays. The prediction given here for the above decay is g_1/f_1=1.17, which leads to a rate of 0.80 x 10^6 s^-1 and thus a branching fraction of 2.3 x 10^-4.Comment: LaTeX, 7 pages, uses acromake, cite and topcapt packages. Non-printing extended ascii characters replaced plus minor correction

On the Nucleon Distribution Amplitude: The Heterotic Solution

We present a new nucleon distribution amplitude which amalgamates features of the Chernyak-Ogloblin-Zhitnitsky model with those of the Gari-Stefanis model. This "heterotic" solution provides the possibility to have asymptotically a small ratio \hbox{$\vert G_{M}^{n}\vert/G_{M}^{p}\le 0.1$}, while fulfilling most of the sum-rule requirements up to the third order. Using this nucleon distribution amplitude we calculate the electromagnetic and weak nucleon form factors, the transition form factor $\gamma p \Delta^{+}$ and the decay widths of the charmonium levels $^3S_{1}$, $^3P_{1}$, and $^3P_{2}$ into $p\bar p$. The agreement with the available data is remarkable in all cases.Comment: 15 pages, RUB-TPII-21/92 Preprin

Nucleon Decay Matrix Elements from Lattice QCD

We present a model-independent calculation of hadron matrix elements for all dimension-six operators associated with baryon number violating processes using lattice QCD. The calculation is performed with the Wilson quark action in the quenched approximation at $\beta=6/g^2=6.0$ on a $28^2\times 48\times 80$ lattice. Our results cover all the matrix elements required to estimate the partial lifetimes of (proton,neutron)$\to$($\pi,K,\eta$) +(${\bar \nu},e^+,\mu^+$) decay modes. We point out the necessity of disentangling two form factors that contribute to the matrix element; previous calculations did not make the separation, which led to an underestimate of the physical matrix elements. With a correct separation, we find that the matrix elements have values 3-5 times larger than the smallest estimates employed in phenomenological analyses of the nucleon decays, which could give strong constraints on several GUT models. We also find that the values of the matrix elements are comparable with the tree-level predictions of chiral lagrangian.Comment: 53 pages, 18 eps figure

Red wine polyphenols prevent metabolic and cardiovascular alterations associated with obesity in Zucker fatty rats (Fa/Fa)

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