Protein fold recognition without Boltzmann statistics or explicit physical basis

We present a fast method for finding optimal parameters for a low-resolution (threading) force field intended to distinguish correct from incorrect folds for a given protein sequence. In contrast to other methods, the parameterization uses information from >10(7) misfolded structures as well as a set of native sequence-structure pairs. In addition to testing the resulting force field's performance on the protein sequence threading problem, results are shown that characterize the number of parameters necessary for effective structure recognition.

Assessing the competitiveness of loss allocation methods in a deregulated electricity market

This paper critically assesses several loss allocation methods based on the type of competition each method promotes. This understanding assists in determining which method will promote more efficient network operations when implemented in deregulated electricity industries. The methods addressed in this paper include the pro rata [1], proportional sharing [2], loss formula [3], incremental [4], and a new method proposed by the authors of this paper, which is loop-based [5]. These methods are tested on a modified Nordic 32-bus network, where different case studies of different operating points are investigated. The varying results obtained for each allocation method at different operating points make it possible to distinguish methods that promote unhealthy competition from those that encourage better system operation.

A hybrid probabilistic criterion for market-based transmission expansion planning

Market-based transmission expansion planning gives information to investors on where is the most cost efficient place to invest and brings benefits to those who invest in this grid. However, both market issue and power system adequacy problems are system planers’ concern. In this paper, a hybrid probabilistic criterion of Expected Economical Loss (EEL) is proposed as an index to evaluate the systems’ overall expected economical losses during system operation in a competitive market. It stands on both investors’ and planner’s point of view and will further improves the traditional reliability cost. By applying EEL, it is possible for system planners to obtain a clear idea regarding the transmission network’s bottleneck and the amount of losses arises from this weak point. Sequentially, it enables planners to assess the worth of providing reliable services. Also, the EEL will contain valuable information for moneymen to undertake their investment. This index could truly reflect the random behaviors of power systems and uncertainties from electricity market. The performance of the EEL index is enhanced by applying Normalized Coefficient of Probability (NCP), so it can be utilized in large real power systems. A numerical example is carried out on IEEE Reliability Test System (RTS), which will show how the EEL can predict the current system bottleneck under future operational conditions and how to use EEL as one of planning objectives to determine future optimal plans. A well-known simulation method, Monte Carlo simulation, is employed to achieve the probabilistic characteristic of electricity market and Genetic Algorithms (GAs) is used as a multi-objective optimization tool.

Investigations into effective methods for assessing the condition of insulation in aged power transformers

This paper investigates the effective diagnostic technique(s) for assessing the condition of insulation in aged power transformers. A number of electrical, mechanical and chemical techniques were investigated. Many of these techniques are already used by the utility engineers and two comparatively new techniques are proposed in this paper. Results showing the effectiveness of these diagnostics are presented and correlation between the techniques are also presented. Finally, merits and suitability of different techniques are discussed in this paper.

Protein fold recognition score functions: Unusual construction strategies

We describe two ways of optimizing score functions for protein sequence to structure threading. The first method adjusts parameters to improve sequence to structure alignment. The second adjusts parameters so as to improve a score function's ability to rank alignments calculated in the first score function. Unlike those functions known as knowledge-based force fields, the resulting parameter sets do not rely on Boltzmann statistics, have no claim to representing free energies and are purely constructions for recognizing protein folds. The methods give a small improvement, but suggest that functions can be profitably optimized for very specific aspects of protein fold recognition, Proteins 1999;36:454-461. (C) 1999 Wiley-Liss, Inc.

Comparison of coherent and weakly incoherent transport models for the interlayer magnetoresistance of layered Fermi liquids

The interlayer magnetoresistance of layered metals in a tilted magnetic field is calculated for two distinct models for the interlayer transport. The first model involves coherent interlayer transport, and makes use of results of semiclassical or Bloch-Boltzmann transport theory. The second model involves weakly incoherent interlayer transport where the electron is scattered many times within a layer before tunneling into the next layer. The results are relevant to the interpretation of experiments on angular-dependent magnetoresistance oscillations (AMRO) in quasi-one- and quasi-two-dimensional organic metals. We find that the dependence of the magnetoresistance on the direction of the magnetic field is identical for both models except when the field is almost parallel to the layers. An important implication of this result is that a three-dimensional Fermi surface is not necessary for the observation of the Yamaji and Danner oscillations seen in quasi-two- and quasi-one-dimensional metals, respectively. A universal expression is given for the dependence of the resistance at AMRO maxima and minima on the magnetic field and scattering time (and thus the temperature). We point out three distinctive features of coherent interlayer transport: (i) a beat frequency in the magnetic oscillations of quasi-two-dimensional systems, (ii) a peak in the angular-dependent magnetoresistance when the field is sufficiently large and parallel to the layers, and (iii) a crossover from a linear to a quadratic field dependence for the magnetoresistance when the field is parallel to the layers. Properties (i) and (ii) are compared with published experimental data for a range of quasi-two-dimensional organic metals. [S0163-1829(99)02236-5].

Sausage: protein threading with flexible force fields

Sausage is a protein sequence threading program, but with remarkable run-time flexibility. Using different scripts, it can calculate protein sequence-structure alignments, search structure libraries, swap force fields, create models form alignments, convert file formats and analyse results. There are several different force fields which might be classed as knowledge-based, although they do not rely on Boltzmann statistics. Different force fields are used for alignment calculations and subsequent ranking of calculated models.

The co-segregation of psychosis and selected physical disorders within families of patients with psychosis versus well controls

While it has been reported that individuals with psychosis are at increased or decreased risk of various physical disorders such as cancer and rheumatoid arthritis, there has been less research on the co-segregation of physical disorders within the first-degree relatives of those with psychosis compared to relatives of well controls. The aim of this study was to examine these issues in an epidemiologically informed catchment-area based case-control study. Patients with psychosis were drawn from a prevalence study undertaken as part of the Australian National Mental Health Survey. In addition, we recruited well controls who resided in the same catchment area. For each subject, we drew pedigrees and used a structured checklist to assess the presence of selected psychiatric disorders, and selected disorders such as multiple sclerosis, epilepsy, spina bifida, thyroid disorders, diabetes, asthma and eczema. Data based on pedigrees from 293 individuals with psychosis and 292 well controls was available. As expected, the odds of havingschizophrenia and affective disorders were significantly increased in the families of cases versus controls. The odds of havingeczema were significantly reduced in the relatives of those with psychosis. All other disorders occurred with equal frequency in cases versus control pedigrees. Current theories of eczema suggest that an absence of early life exposure to antigens and infectious agents may fail to prime the na¨ıve immune system, and leave the person at increased risk of eczema. The results of this study suggest that genetic andror environmental factors that facilitate psychosis may protect against eczema. The Stanley Foundation supported this project.

Decreased perinatal sunshine duration is associated with increased non-affective but not affective psychosis birth rates

We have previously found an association between variations in schizophrenia birth rates and varyinglevels of perinatal sunshine duration. This study examines whether such an association can also be found for Ža. affective psychosis, and Žb. broadly defined nonaffective psychoses. Data for individuals born between 1931 and 1970 in Australia with ICD9 Other PsychosisŽ295–299.were obtained from the Queensland Mental Health Statistical System. ‘Affective psychosis’ included affective psychosis, schizo-affective psychosis, and depressive and excitative non-organic psychoses. ‘Non-affective psychosis’ included chizophrenia, paranoid disorders and other non-organic psychoses. Those receiving both affective and non-affective psychotic diagnoses were excluded. Rates per 10,000 live monthly general population births were calculated. For each month, we assessed the agreementŽusing the kappa statistic. between trends in Ža. birth rates and Žb. long-term trends in seasonally adjusted perinatal sunshine duration. The analyses were performed separately for males and females. There were 6265 with non-affective psychosis ŽMs3964 rate 66r10,000; Fs2299 44r10,000. and 2858 with affective psychosisŽMs1392 24r10,000; Fs1466 28r10,000.. There were no significant associations between Ža. affective psychosis birth rates for either males or females and Žb. sunshine duration. There was a significant association between nonaffective psychosis birth rates for males only and Žb. sunshine duration Žkappas0.15 p-0.001.. This suggests that, as a risk factor, the effect of reduced perinatal sunshine is specifically associated with males who develop non-affective psychosis. The Stanley Foundation supported this project.

No association between the deficit syndrome in psychosis and summer birth in the Southern Hemisphere

Recent studies have shown that individuals with schizophrenia who are born in summer have an increased odds of have deficit syndrome versus nondeficit syndrome. This study extends this work to examiningthis issue in patients from the Southern Hemisphere. Data which included OPCRITrSCAN items and demographic information was obtained for Australian-born cases from the Australian National Mental Health Survey. Followingpreviously published methods, cases were assigned to the deficit group Žns153.or non-deficit groupŽns228.. A logistic regression analysis was used to ascertain whether beingborn in summer ŽDecember, January, February.in the Southern Hemisphere altered the odds of havingdeficit syndrome. There was no association between summer birth and odds of havingdeficit versus non-deficit schizophrenia ŽOdds Ratios0.75, 95% CI 0.49–1.16.. Based on our previous work showingthat the size of the winterrspringbirth excess in schizophrenia is reduced in the Southern Hemisphere, we speculate that factors that influence the association between summer birth and non-deficit syndrome may also vary across geography andror latitude. The Stanley Foundation supported this project.