Effect of surface roughness on diffusion-limited charge transfer

A theory is developed for diffusion-limited charge transfer on a non-fractally rough electrode. The perturbation expressions are obtained for concentration, current density and measured diffusion-limited current for arbitrary one- and two-dimensional surface profiles. The random surface model is employed for a rough electrode\electrolyte interface. In this model the gross geometrical property of an electrochemically active rough surface - the surface structure factor-is related to the average electrode current, current density and concentration. Under short and long time regimes, various morphological features of the rough electrodes, i.e. excess area (related to roughness slope), curvature, correlation length, etc. are related to the (average) current transients. A two-point Pade approximant is used to develop an all time average current expression in terms of partial morphological features of the rough surface. The inverse problem of predicting the surface structure factor from the observed transients is also described. Finally, the effect of surface roughness is studied for specific surface statistics, namely a Gaussian correlation function. It is shown how the surface roughness enhances the overall diffusion-limited charge transfer current.

Using Correlated Parameters for Improved Ranking of Protein-Protein Docking Decoys

A successful protein-protein docking study culminates in identification of decoys at top ranks with near-native quaternary structures. However, this task remains enigmatic because no generalized scoring functions exist that effectively infer decoys according to the similarity to near-native quaternary structures. Difficulties arise because of the highly irregular nature of the protein surface and the significant variation of the nonbonding and solvation energies based on the chemical composition of the protein-protein interface. In this work, we describe a novel method combining an interface-size filter, a regression model for geometric compatibility (based on two correlated surface and packing parameters), and normalized interaction energy (calculated from correlated nonbonded and solvation energies), to effectively rank decoys from a set of 10,000 decoys. Tests on 30 unbound binary protein-protein complexes show that in 16 cases we can identify at least one decoy in top three ranks having <= 10 angstrom backbone root mean square deviation from true binding geometry. Comparisons with other state-of-art methods confirm the improved ranking power of our method without the use of any experiment-guided restraints, evolutionary information, statistical propensities, or modified interaction energy equations. Tests on 118 less-difficult bound binary protein-protein complexes with <= 35% sequence redundancy at the interface showed that in 77% cases, at least 1 in 10,000 decoys were identified with <= 5 angstrom backbone root mean square deviation from true geometry at first rank. The work will promote the use of new concepts where correlations among parameters provide more robust scoring models. It will facilitate studies involving molecular interactions, including modeling of large macromolecular assemblies and protein structure prediction. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 32: 787-796, 2011.

PRUNE and PROBE-two modular web services for protein-protein docking

The protein-protein docking programs typically perform four major tasks: (i) generation of docking poses, (ii) selecting a subset of poses, (iii) their structural refinement and (iv) scoring, ranking for the final assessment of the true quaternary structure. Although the tasks can be integrated or performed in a serial order, they are by nature modular, allowing an opportunity to substitute one algorithm with another. We have implemented two modular web services, (i) PRUNE: to select a subset of docking poses generated during sampling search (http://pallab.serc.iisc.ernet.in/prune) and (ii) PROBE: to refine, score and rank them (http://pallab.serc.iisc.ernet.in/probe). The former uses a new interface area based edge-scoring function to eliminate > 95% of the poses generated during docking search. In contrast to other multi-parameter-based screening functions, this single parameter based elimination reduces the computational time significantly, in addition to increasing the chances of selecting native-like models in the top rank list. The PROBE server performs ranking of pruned poses, after structure refinement and scoring using a regression model for geometric compatibility, and normalized interaction energy. While web-service similar to PROBE is infrequent, no web-service akin to PRUNE has been described before. Both the servers are publicly accessible and free for use.

On the Limits of Spatial Reuse and Cooperative Communication for Dense Wireless Networks

We consider a dense ad hoc wireless network comprising n nodes confined to a given two dimensional region of fixed area. For the Gupta-Kumar random traffic model and a realistic interference and path loss model (i.e., the channel power gains are bounded above, and are bounded below by a strictly positive number), we study the scaling of the aggregate end-to-end throughput with respect to the network average power constraint, P macr, and the number of nodes, n. The network power constraint P macr is related to the per node power constraint, P macr, as P macr = np. For large P, we show that the throughput saturates as Theta(log(P macr)), irrespective of the number of nodes in the network. For moderate P, which can accommodate spatial reuse to improve end-to-end throughput, we observe that the amount of spatial reuse feasible in the network is limited by the diameter of the network. In fact, we observe that the end-to-end path loss in the network and the amount of spatial reuse feasible in the network are inversely proportional. This puts a restriction on the gains achievable using the cooperative communication techniques studied in and, as these rely on direct long distance communication over the network.

Improving query focused summarization using look-ahead strategy

Query focused summarization is the task of producing a compressed text of original set of documents based on a query. Documents can be viewed as graph with sentences as nodes and edges can be added based on sentence similarity. Graph based ranking algorithms which use 'Biased random surfer model' like topic-sensitive LexRank have been successfully applied to query focused summarization. In these algorithms, random walk will be biased towards the sentences which contain query relevant words. Specifically, it is assumed that random surfer knows the query relevance score of the sentence to where he jumps. However, neighbourhood information of the sentence to where he jumps is completely ignored. In this paper, we propose look-ahead version of topic-sensitive LexRank. We assume that random surfer not only knows the query relevance of the sentence to where he jumps but he can also look N-step ahead from that sentence to find query relevance scores of future set of sentences. Using this look ahead information, we figure out the sentences which are indirectly related to the query by looking at number of hops to reach a sentence which has query relevant words. Then we make the random walk biased towards even to the indirect query relevant sentences along with the sentences which have query relevant words. Experimental results show 20.2% increase in ROUGE-2 score compared to topic-sensitive LexRank on DUC 2007 data set. Further, our system outperforms best systems in DUC 2006 and results are comparable to state of the art systems.

Information content of molecular graph and prediction of gas phase thermal entropy of organic compounds

Entropy is a fundamental thermodynamic property that has attracted a wide attention across domains, including chemistry. Inference of entropy of chemical compounds using various approaches has been a widely studied topic. However, many aspects of entropy in chemical compounds remain unexplained. In the present work, we propose two new information-theoretical molecular descriptors for the prediction of gas phase thermal entropy of organic compounds. The descriptors reflect the bulk and size of the compounds as well as the gross topological symmetry in their structures, all of which are believed to determine entropy. A high correlation () between the entropy values and our information-theoretical indices have been found and the predicted entropy values, obtained from the corresponding statistically significant regression model, have been found to be within acceptable approximation. We provide additional mathematical result in the form of a theorem and proof that might further help in assessing changes in gas phase thermal entropy values with the changes in molecular structures. The proposed information-theoretical molecular descriptors, regression model and the mathematical result are expected to augment predictions of gas phase thermal entropy for a large number of chemical compounds.

Baryon squishing in synthetic dimensions by effective SU(M) gauge fields

The ``synthetic dimension'' proposal A. Celi et al., Phys. Rev. Lett. 112, 043001 (2014)] uses atoms with M internal states (''flavors'') in a one-dimensional (1D) optical lattice, to realize a hopping Hamiltonian equivalent to the Hofstadter model (tight-binding model with a given magnetic flux per plaquette) on an M-sites-wide square lattice strip. We investigate the physics of SU(M) symmetric interactions in the synthetic dimension system. We show that this system is equivalent to particles with SU(M) symmetric interactions] experiencing an SU(M) Zeeman field at each lattice site and a non-Abelian SU(M) gauge potential that affects their hopping. This equivalence brings out the possibility of generating nonlocal interactions between particles at different sites of the optical lattice. In addition, the gauge field induces a flavor-orbital coupling, which mitigates the ``baryon breaking'' effect of the Zeeman field. For M particles, concomitantly, the SU(M) singlet baryon which is site localized in the usual 1D optical lattice, is deformed to a nonlocal object (''squished baryon''). We conclusively demonstrate this effect by analytical arguments and exact (numerical) diagonalization studies. Our study promises a rich many-body phase diagram for this system. It also uncovers the possibility of using the synthetic dimension system to laboratory realize condensed-matter models such as the SU(M) random flux model, inconceivable in conventional experimental systems.

Number of prior episodes and the presence of depressive symptoms are associated with longer length of stay for patients with acute manic episodes

Background: Few studies have analyzed predictors of length of stay (LOS) in patients admitted due to acute bipolar manic episodes. The purpose of the present study was to estimate LOS and to determine the potential sociodemographic and clinical risk factors associated with a longer hospitalization. Such information could be useful to identify those patients at high risk for long LOS and to allocate them to special treatments, with the aim of optimizing their hospital management. Methods: This was a cross-sectional study recruiting adult patients with a diagnosis of bipolar disorder (Diagnostic and Statistical Manual of Mental Disorders, 4th edition, text revision (DSM-IV-TR) criteria) who had been hospitalized due to an acute manic episode with a Young Mania Rating Scale total score greater than 20. Bivariate correlational and multiple linear regression analyses were performed to identify independent predictors of LOS. Results: A total of 235 patients from 44 centers were included in the study. The only factors that were significantly associated to LOS in the regression model were the number of previous episodes and the Montgomery-Åsberg Depression Rating Scale (MADRS) total score at admission (P < 0.05). Conclusions: Patients with a high number of previous episodes and those with depressive symptoms during mania are more likely to stay longer in hospital. Patients with severe depressive symptoms may have a more severe or treatment-resistant course of the acute bipolar manic episode.

Contribution of Resource-Based View and Entrepreneurial Orientation on Small Firm Growth

[EN] This research provides a useful framework for identifying a small firms’ propensity to engage in entrepreneurial orientation. We examine the impact of the Entrepreneurial Orientation (EO) as a main resource and capability on small firm’ growth. The growth seems to come out as an important demonstration of the entrepreneurial orientation of small firms (Davidsson, 1989; Green and Brown, 1997; Janney and Gregory, 2006). Thus, this research builds on prior conceptual research that suggests a positive integration between entrepreneurial orientation and resource-based view. In the first instance, the research will focus on reviewing literature in the emerging area of entrepreneurial orientation as it applies to growth oriented small firms and resource-based view of the firm. Secondly, an empirical study was developed based on a stratified sample of small firms of manufacturing industry. Data were submitted to a multivariate statistical analysis and a linear regression model was performed in order to predict the influence of the resources and capabilities on small firms’ growth. In this sense, we consider the construct growth as a dependent variable and the ones relates with resources and capabilities (entrepreneur resources, firm resources, networks and EO) as independent variables. The research results suggest a set of resources and capabilities that promote the growth of the small firms. Also, the EO seems to have a predictive value on growth. Explaining variables related with resources and capabilities and EO were identified as essential in growth oriented small firms. It was still possible to conclude that the entrepreneurial firms which grew seem to have resources and develop more capabilities and take advantage in the search for those competences. This attitude reflects on the EO of the firm. This study has important implication for both researchers and practitioners. It highlights the necessity of firms to develop superior EO of all their members and also to invest on better resources and consequently superior capabilities as a way of reaching higher levels of growth. While previous authors have attempted to analyse certain aspects of this process (linkage between entrepreneurial orientation and growth), this research developed a framework that combines these and others factors (resource-based view) pertinent to growth oriented small firms. The results support the necessity to identify explicative variables of multiple levels to explain the growth of small firms. The adoption of an entrepreneurial orientation as an indispensable variable to the growth oriented small firms seems pertinent.

Spawning, egg development, and early life history dynamics of arrowtooth flounder (Atheresthes stomias) in the Gulf of Alaska

Arrowtooth flounder (Atheresthes stomias) has the highest biomass of any groundfish species in the Gulf of Alaska, is a voracious predator of age 1 walleye pollock (Theragra chalcogramma), and is a major component in the diet of Steller sea lions (Eumetopias jubatus). Owing to its ecological importance in the Gulf of Alaska and the limited information available on its reproduction, interest has intensified in describing its spawning and early life history. A study was undertaken in late January–February 2001–2003 in the Gulf of Alaska to obtain information on adult spawning location, depth distribution, and sexual maturity, and to obtain fertilized eggs for laboratory studies. Adults were found 200–600 m deep east of Kodiak Island over the outer continental shelf and upper slope, and southwest along the shelf break to the Shumagin Islands. Most ripe females (oocytes extruded with light pressure) were found at 400 m and most ripe males (milt extruded with light pressure) were found at depths ≥450 m. Eggs were fertilized and incubated in the laboratory at 3.0°, 4.5°, and 6.0°C. Eggs were reared to hatching, but larvae did not survive long enough to complete yolk absorption and develop pigment. Eggs were staged according to morphological hallmarks and incubation data were used to produce a stage duration table and a regression model to estimate egg age based on water temperature and developmental stage. Arrowtooth flounder eggs (1.58–1.98 mm in diameter) were collected in ichthyoplankton surveys along the continental shelf edge, primarily at depths ≥400 m. Early-stage eggs were found in tows that sampled to depths of ≥450 m. Larvae, which hatch between 3.9 and 4.8 mm standard length, increased in abundance with depth. Observations on arrowtooth flounder eggs and early-stage larvae were used to complete the description of the published partial developmental series.(PDF file contains 34 pages.)

Strategic Votes and Sincere Counterfactuals

The Random Utility Model (RUM) of voting behavior can account for strategic voting by making use of proxy indicators that measure voter incentives to vote strategically. The contribution of this paper is to propose a new method to estimate the RUM in the presence of strategic voters, without having to construct proxy measures of strategic voting incentives. Our method can be used to infer the counterfactual sincere vote of those who vote strategically and provides an estimate of the size of strategic voting. We illustrate the procedure using post-electoral survey data from Spain. Our calculations indicate that strategic voting in Spain is about 2.19 per cent

Identification and estimation of size from the beaks of 18 species of cephalopods from the Pacific Ocean

A method of identifying the beaks and estimating body weight and mantle length of 18 species of cephalopods from the Pacific Ocean is presented. Twenty specimens were selected from each of the following cephalopod species: Symplectoteuthis oualaniensis, Dosidicus gigas, Ommastrephes bartramii, S. luminosa, Todarodes pacificus, Nototodarus hawaiiensis, Ornithoteuthis volalilis, Hyaloteuthis pelagica, Onychoteuthis banksii, Pterygioteuthis giardi, Abraliopsis affinis, A. felis, Liocranchia reinhardti, Leachia danae, Histioteuthis heteropsis, H. dofleini, Gonalus onyx, and Loligo opalescens. Dimensions measured on the upper and lower beak are converted to ratios and compared individually among the species using an analysis of variance procedure with Tukey's omega and Duncan's multiple range tests. Significant differences (P =0.05) observed among the species' beak ratio means and structural characteristics are used to construct artificial keys for the upper and lower beaks of the 18 species. Upper and lower beak dimensions are used as independent variables in a linear regression model with mantle length and body weight (log transformed). (PDF file contains 56 pages.)

Use of generalised additive models to categorise continuous variables in clinical prediction

13 P.

Catch rates as indices of abundance of yellowfin tuna, Thunnus albacares, in the Eastern Pacific Ocean

ENGLISH: Catch and effort data from logbooks of tuna seiners were used to make estimates of catch per hour of searching for 1970-1980. The estimates were standardized using a regression model to make annual estimates of abundance adjusted for fishing mode, speed, capacity, use of aerial assistance, net dimensions, and sea-surface temperature. Inside the CYRA the standardized estimates for tuna schools associated with dolphins and those for schools not associated with dolphins showed a similar overall pattern of decline. The 1980 catch rates were about 300/0 of the 1970 rates, the decline being greater for the schools not associated with dolphins. Dolphin-associated schools outside the CYRA declined to about 60% of the 1970 levels. SPANISH: Se emplearon los datos de la captura y el esfuerzo de los cuadernos de bitácora de las embarcaciones cerqueras para hacer las estimaciones de la captura por hora de búsqueda correspondientes a 1970-1980. Se normalizaron estas estimaciones usando un modelo de regresión con el fin' de hacer las estimaciones anuales de la abundancia, ajustadas según la moda de pesca, velocidad, capacidad, uso de ayuda aérea, dimensiones de la red y temperatura de la superficie del mar. En el ARCAA las estimaciones normalizadas de los cardúmenes de atún asociados con delfines y aquellas de los cardúmenes no asociados con delfines, indicaron una pauta general similar de reducción. Las proporciones de captura de 1980, fueron cerca del 300/0 de las de 1970, encontrándose la mayor reducción en los cardúmenes no asociados con delfines. Los cardúmenes asociados con delfines, fuera del ARCAA, se redujeron en un 60% con respecto a los niveles de 1970. (PDF contains 79 pages.)

A geometric analysis of convex demixing

Demixing is the task of identifying multiple signals given only their sum and prior information about their structures. Examples of demixing problems include (i) separating a signal that is sparse with respect to one basis from a signal that is sparse with respect to a second basis; (ii) decomposing an observed matrix into low-rank and sparse components; and (iii) identifying a binary codeword with impulsive corruptions. This thesis describes and analyzes a convex optimization framework for solving an array of demixing problems.

Our framework includes a random orientation model for the constituent signals that ensures the structures are incoherent. This work introduces a summary parameter, the statistical dimension, that reflects the intrinsic complexity of a signal. The main result indicates that the difficulty of demixing under this random model depends only on the total complexity of the constituent signals involved: demixing succeeds with high probability when the sum of the complexities is less than the ambient dimension; otherwise, it fails with high probability.

The fact that a phase transition between success and failure occurs in demixing is a consequence of a new inequality in conic integral geometry. Roughly speaking, this inequality asserts that a convex cone behaves like a subspace whose dimension is equal to the statistical dimension of the cone. When combined with a geometric optimality condition for demixing, this inequality provides precise quantitative information about the phase transition, including the location and width of the transition region.