bluuebunny/crossref_metadata_2025 huggingface dataset:
On the septimic character of 2 and 3
Authors: Alderson Helen Popova
Published: November 2008

Let e be an integer greater than 1 and let pbe a prime such that p ≡ 1 (mod e). Criteria for 2 to be a residue of degree e modulo p have been obtained in various forms for e = 2, 3, 4 and 5. Thus, Euler and Lagrange proved that 2 is a quadratic residue mod p if and only if p ≡ ± 1 (mod 8). Gauss showed that 2 is a cubic residue mod p if and only if p is representable as p = l2 + 27m2 with integers l and m, and that 2 is a quartic residue mod p if and only if p is representable as p = 12 + 64m2. Lehmer (5) and Alderson (1) have found similar but more complicated conditions for 2 to be a quintic residue mod p. There are analogous results about 3. For example, it follows from quadratic reciprocity that 3 is a quadratic residue mod p if and only if p ≡ ± 1 (mod 12), and Jacobi(4) showed that 3 is a cubic residue mod p if and only if 4p is representable as l2 + 35m2.
The Radioactivity Produced by the Bombardment of Lithium with Deuterons
Authors: Bower J. C. , Petrie D. P. R.
Published: November 2008

In an investigation of the disintegration ofby protons, resulting in the emission of three α-particles, Dee and Gilbert* found that the observed distributions of ranges and angles of these particles could be explained by assuming that one α-particle is first ejected, leaving a short-lived, excitednucleus which then decomposes into two more α-particles. The half-life of this excited beryllium nucleus was estimated to be about 10–21sec.
Efficient self-interpretation in lambda calculus
Authors: Mogensen Torben Æ.
Published: November 2008

We start by giving a compact representation schema for λ-terms, and show how this leads to an exceedingly small and elegant self-interpreter. We then define the notion of aself-reducer, and show how this too can be written as a small λ-term. Both the self-interpreter and the self-reducer are proved correct. We finally give a constructive proof for the second fixed point theorem for the representation schema. All the constructions have been implemented on a computer, and experiments verify their correctness. Timings show that the self-interpreter and self-reducer are quite efficient, being about 35 and 50 times slower than direct execution using a call-by-need reductions strategy
Dynamic typing in polymorphic languages
Authors: Abadi M. , Cardelli L. , Pierce B. , Rémy D.
Published: November 2008

There are situations in programming where some dynamic typing is needed, even in the presence of advanced static type systems. We investigate the interplay of dynamic types with other advanced type constructions, discussing their integration into languages with explicit polymorphism (in the style of system F), implicit polymorphism (in the style of ML), abstract data types, and subtyping.
Semantics directed program execution monitoring
Authors: Kishon Amir , Hudak Paul
Published: November 2008

Monitoring semanticsis a formal model of program execution which captures ‘monitoring activity’ as found in profilers, tracers, debuggers, etc. Beyond its theoretical interest, this formalism provides a new methodology for implementing a large family of source-level monitoring activities for sequential deterministic programming languages. In this article we explore the use of monitoring semantics in the specification and implementation of a variety of monitors: profilers, tracers, collecting interpreters, and, most importantly, interactive source-level debuggers. Although we consider such monitors only for (both strict and non-strict) functional languages, the methodology extends easily to imperative languages, since it begins with a continuation semantics specification.

In addition, using standard partial evaluation techniques as an optimization strategy, we show that the methodology forms a practical basis for building real monitors. Our system can be optimized at two levels of specialization: specializing the interpreter with respect to a monitor specification automatically yields an instrumented interpreter; further specializing this instrumented interpreter with respect to a source program yields an instrumented program, i.e. one in which the extra code to perform monitoring has been automatically embedded into the program.
VEGETATION COMPOSITION, STRUCTURE AND PATTERNS OF DIVERSITY: A CASE STUDY FROM THE TROPICAL WET EVERGREEN FORESTS OF THE WESTERN GHATS, INDIA
Authors: Giriraj A. , Murthy M. S. R. , Ramesh B. R.
Published: October 2008

The composition, abundance, population structure and distribution patterns of the woody species having a girth at breast height of ≥ 10 cm were investigated in the tropical wet evergreen forests of the Kalakad-Mundanthurai Tiger Reserve in the southern Western Ghats, India. A 3 ha plot was established with an altitudinal range of 1170 to 1306 m. In the study plot 5624 individuals (mean density 1875 ha−1) covering 68 woody species belonging to 52 genera and 27 families were enumerated. The mean basal area was 47.01 m2 ha–1 and the Shannon and Simpson diversity indices were 4.89 and 0.95, respectively. Of these woody species nearly 51% are endemic to the Western Ghats. The four dominant species, Cullenia exarillata, Palaquium ellipticum, Aglaia bourdillonii and Myristica dactyloides, account for 34% of the trees and 67% of the basal area, and therefore constitute the main structure of the forest. Within this forest type, five species assemblages corresponding to altitudinal gradient were identified using correspondence analysis. Management of such mid elevation evergreen forests necessarily depends on knowledge of recognisable community types and their environmental variables. The present study provides essential background for formulating strategies for sustainable conservation of forest communities at the local level.
NOVITATES GABONENSES 68. THE GENUS CASSIPOUREA (RHIZOPHORACEAE) IN CONTINENTAL TROPICAL AFRICA WITH EMPHASIS ON GABON: SUBGENERIC DIVISION, IDENTIFICATION KEYS, AND DESCRIPTION OF TWO NEW SPECIES
Authors: Breteler F. J.
Published: October 2008

Cassipourea (Rhizophoraceae) is represented in Gabon by 11 species, of which C. nana Breteler and C. ndambiana Breteler are described as new and C. carringtoniana Mendes, C. gummiflua Tul. and C. ruwensorensis (Engl.) Alston are reported from this country for the first time. The subgeneric classification is discussed. An adapted key to the subgenera and a key to the Gabonese species is presented. A synopsis of the subgenera and of the Gabonese species is also given. The new species and Cassipourea carringtoniana are fully illustrated. A few illustrations of some other species to elucidate characters of the subgenera are provided.
BEGONIA VARIPELTATA (BEGONIACEAE): A NEW PELTATE SPECIES FROM SULAWESI, INDONESIA
Authors: Thomas D. C. , Hughes M.
Published: October 2008

A new species of Begonia (Begoniaceae), B. varipeltata D.C.Thomas, is described from the Indonesian island of Sulawesi. It exhibits peltate leaves, which are rare in Begonia section Petermannia, to which it belongs.
LKB1: cancer, polarity, metabolism, and now fertility
Authors: Shaw Reuben J.
Published: October 2008

The LKB1 serine/threonine kinase is a tumour suppressor responsible for the inherited familial cancer disorder Peutz-Jeghers syndrome and is inactivated in a large percentage of human lung cancers. LKB1 acts a master kinase, directly phosphorylating and activating a family of 14 AMPK (AMP-activated protein kinase)-related kinases which control cell metabolism, cell growth and cell polarity. In this issue of the Biochemical Journal, Hardie and colleagues discover an alternative splice form of LKB1 that alters the C-terminus of the protein containing a few known sites of post-translational regulation. Although widely expressed, the short isoform (LKB1s) is the sole splice isoform expressed in testes, and its expression peaks at the time of spermatid maturation. Male mice lacking the LKB1s isoform have dramatic defects in spermatozoa, resulting in sterility.
The Communicative Effectiveness Survey: Preliminary Evidence of Construct Validity
Authors: Donovan Neila J. , Kendall Diane L. , Young Mary Ellen , Rosenbek John C.
Published: October 2008

Purpose

To provide preliminary evidence of the construct validity of the Communicative Effectiveness Survey (CES) for individuals with dysarthria and idiopathic Parkinson’s disease (PD).

Method

In a prospective, quasi-experimental design, 25 participants each were assigned to 3 groups (N= 75): PD and dysarthria, non-PD and no dysarthria, and PD significant others (SOs). Mean CES ratings were used to test for significant differences between the PD and non-PD group, and PD and SO rating of PD’s communicative effectiveness. Multiple linear regression tested for significant predictors of CES ratings for PD group only using sentence intelligibility and spontaneous speech intelligibility scores as predictor variables.

Results

The PD group rated their CES significantly lower than did the non-PD group. The PD group rated their CES significantly higher than their SOs rated them. Neither speech intelligibility score was a significant predictor of CES ratings. In follow-up analysis, the Hoehn and Yahr PD staging accounted for 47% of the variability in CES ratings for the PD group participants.

Conclusions

This study provides preliminary evidence of the CES’s construct validity. Clinicians and researchers who assess and treat individuals with PD may consider adding an additional assessment to the traditional clinical measures (i.e., speech intelligibility) by obtaining a measure of communicative effectiveness.
Update on a Clinical Measure for the Assessment of Problem Solving
Authors: Marshall Robert C. , Karow Colleen M.
Published: October 2008

Purpose

The Rapid Assessment of Problem Solving test (RAPS) is a clinical measure of problem solving based on the 20 Questions Test. This article updates clinicians on the RAPS, addresses questions raised about the test in an earlier article (R. C. Marshall, C. M. Karow, C. Morelli, K. Iden, & J. Dixon, 2003a), and discusses the clinical utility of the RAPS.

Method

The RAPS was administered to 373 normal adults. Tests were analyzed to assess the impact of demographic, psychometric, and other factors on performance on the RAPS. To determine the effects of strategy selection on test scores, participants were assigned to novel, category-focused, or mixed strategy groups based on the types of first questions asked.

Results

Normal participants exhibited a range of performance levels on the RAPS. Participants in the novel strategy group performed significantly better than the participants in 2 other strategy groups.

Conclusions

The RAPS is a clinically useful tool to examine problem solving that is easy to administer and to score. Findings suggest clinicians can use the RAPS with greater confidence than was the case 4 years ago. The RAPS is now part of the public domain and may be used by clinicians to assess clients' problem-solving deficits.
Aromaticity in spin-polarized systems: Can rings be simultaneously alpha aromatic and beta antiaromatic?
Authors: Mandado Marcos , Graña Ana M. , Pérez-Juste Ignacio
Published: October 2008

The partition of the multicenter electron delocalization indices and the nucleus independent chemical shift indices into alpha and beta contributions in open-shell systems has been performed. In general it is shown that a full understanding of aromaticity in these systems cannot be achieved by restricting the calculations to the global properties but by dissecting these properties into α and β terms. The 4n+2- and 4n-aromaticity rules for singlet and triplet annulenes, respectively, reduce to a general aromaticity rule when the α and β terms are studied separately. This new rule allows us to extend the concept of conflicting aromaticities to radical systems that are simultaneously α-aromatic and β-antiaromatic or vice versa. The existence of such systems is demonstrated here by means of multicenter electron delocalization indices and nucleus independent chemical shifts. Finally, the global aromatic/antiaromatic character of these radical systems is estimated by means of aromatic stabilization energy, which is shown to be either slightly positive or slightly negative, thus reflecting the small aromatic/antiaromatic character of these radicals and reinforcing the conclusions obtained with aromaticity indices.
Low-energy ordered structures of Li2Mg(NH)2
Authors: Ma Zhu , Chou M. Y.
Published: October 2008

The Li–Mg–N–H system has been identified as a promising hydrogen storage material due to its moderate operation conditions as well as the high capacity and reversibility. Recently Rijssenbeek et al. [J. Alloys Compd. 454, 233 (2008)] reported that Li2Mg(NH)2 has disordered cation and vacancy arrangements at room temperature and above. We present our first-principles calculations to investigate a series of ordered low-energy configurations for this compound. Specific local orderings are found in the cation-vacancy arrangement, shedding light on the experimental disordered structure models. A possible ordered phase at low temperature is proposed based on these local orderings. Reaction energetics and phase stability are further discussed.
Structural and electronic properties of [0001] AlN nanowires: A first-principles study
Authors: Wu Yelong , Chen Guangde , Ye Honggang , Zhu Youzhang , Wei Su-Huai
Published: October 2008

Using first-principles methods, we investigated the atomic relaxations, electronic structure, and formation energies of nonpassivated AlN nanowires along [0001] directions. We find that all the nanowires prefer to have (101¯0) lateral facets and all the wires with (101¯0) lateral facets are semiconductors with a direct band gap. However, surface states that arise from the facet atoms exist inside the bulklike band gap, which can have a large effect on the optoelectronic properties of the nanowires. Our calculated formation energies of the nanowires show that there is a sublinear relationship between the formation energy and surface-to-volume ratio, indicating that the surface effect is localized and becomes more important for small nanowires.
In-plane c-axis oriented barium ferrite films with self-bias and low microwave loss
Authors: Song Young-Yeal , Das Jaydip , Wang Zihui , Tong Wei , Patton Carl E.
Published: October 2008

Hybrid pulse laser deposition and liquid phase epitaxy methods have been used to produce in-plane c-axis (IPCA) oriented barium ferrite (BaM) films on a-plane (112¯0) sapphire substrates with low microwave loss and a high remanence. Total thicknesses were from 5to20μm. A reasonable compromise for low loss and high remanence was reached at a thickness of 7μm, with a remanence ratio of 0.84 and a 59GHz peak-to-peak derivative linewidth of 250Oe. The 20μm thick film had a linewidth of 110Oe, one of the smallest values ever obtained for IPCA BaM films.
Energy transfer between silicon–oxygen-related defects and Yb3+ in transparent glass ceramics containing Ba2TiSi2O8 nanocrystals
Authors: Ye Song , Zhu Bin , Luo Jin , Teng Yu , Chen Jingxin , Lakshminarayana G. , Qian Guodong , Qiu Jianrong
Published: November 2008

We report on the conversion of near-ultraviolet radiation of 250–350 nm into near-infrared emission of 970–1100 nm in Yb3+-doped transparent glass ceramics containing Ba2TiSi2O8 nanocrystals due to the energy transfer from the silicon–oxygen-related defects to Yb3+ ions. Efficient Yb3+ emission (F25/2→F27/2) was detected under the excitation of defects absorption at 314 nm. The occurrence of energy transfer is proven by both steady state and time-resolved emission spectra, respectively, at 15 K. The Yb2O3 concentration dependent energy transfer efficiency has also been evaluated, and the maximum value is 65% for 8 mol % Yb2O3 doped glass ceramic. These materials are promising for the enhancement of photovoltaic conversion efficiency of silicon solar cells via spectra modification.
The Application of Visual Environmental Economics in the Study of Public Preference and Urban Greenspace
Authors: Laing Richard , Davies Anne-Marie , Miller David , Conniff Anna , Scott Stephen , Morrice Jane
Published: October 2008

Urban greenspace has consistently been argued to be of great importance to the wellbeing, health, and daily lives of residents and users. This paper reports results from a study that combined the visualisation of public results from a study that combined the visualisation of public greenspace with environmental economics, and that aimed to develop a method by which realistic computer models of sites could be used within preference studies. As part of a methodology that employed contingent rating to establish the values placed on specific greenspace sites, three-dimensional computer models were used to produce visualisations of particular environmental conditions. Of particular importance to the study was the influence of variables including lighting, season, time of day, and weather on the perception of respondents. This study followed previous work that established a suitable approach to the modelling and testing of entirely moveable physical variables within the built environment. As such, the study has established firmly that computer-generated visualisations are appropriate for use within environmental economic surveys, and that there is potential for a holistic range of attributes to be included in such studies.
Diurnal and monthly vertical profiles of benthic microalgae within intertidal sediments from two temperate localities
Authors: Jordan Leonie , McMinn Andrew , Wotherspoon Simon
Published: October 2008

Intertidal areas supporting microphytobenthos (MPB) are dynamic with changes in light intensity over short (tidal) and long (seasonal) time scales. The ability of MPB to migrate away from or towards the sediment surface to optimise sunlight is one reason they are so successful in intertidal areas. Over 12 months, we investigated the effects of time of day on the migration of benthic diatoms at two sites near Hobart, Tasmania, using a pulse amplitude modulation fluorometer to measure chlorophyll fluorescence. Chlorophyll a content and maximum quantum yield (FV/FM) were used to examine profiles of microalgal biomass within sediment cores. There was a seasonal pattern of chlorophyll a biofilm development, peaking in summer at the sandy site, Pipe Clay Lagoon, and in spring at the muddier Browns River. The muddier site had an overall greater MPB biomass than the sandy site. The FV/FM values demonstrated that cells were more ‘stressed’ at midday when sunlight was highest. However, significant seasonal variation was only observed at Browns River. Vertical migration through the sediment was not evident. It seems that the MPB at these two sites are using photoadaptive strategies along with small-scale vertical migration below the detection limit of the methods used in the present study.
Spatial variation in burrow morphology of the mud shore crab Helograpsus haswellianus (Brachyura, Grapsidae) in South Australian saltmarshes
Authors: Katrak G. , Dittmann S. , Seuront L.
Published: October 2008

Burrowing by crabs is an important component of their functional role in mangrove and saltmarsh habitats. The grapsid crab Helograpsus haswellianus (Whitelegge, 1889) is one of the more conspicuous burrowing organisms in the saltmarshes of southern Australia. To evaluate intraspecific differences in burrowing behaviour among saltmarshes on a regional scale, we compared vegetation cover, sediment composition and burrow morphology at four sites using resin casts. Six burrow morphology characters were measured (burrow depth, number, lengths and diameter of the shafts, ratio of the shafts, number and diameter of the burrow openings), and the overall 3D burrow complexity was described using a single parameter, the fractal dimension D. Apart from the number of shafts, all morphological characters of the burrows differed significantly among sites. Analyses of the fractal dimensions lead to the identification of three groups of burrows based on D: a group of highly complex burrows (one site), a group of burrows of intermediate complexity (two sites) and a group of less complex burrows (one site). Burrow morphology variation was correlated with non-dominant vegetation, plant matter in the soil and very coarse sand in the sediment. Site-specific differences in burrows caution against generalising the functional role of crabs across sites.
Diversity and distribution of large branchiopods in Kiskunság (Hungary) in relation to local habitat and spatial factors: implications for their conservation
Authors: Boven Liesbet , Vanschoenwinkel Bram , De Roeck Els R. , Hulsmans Ann , Brendonck Luc
Published: October 2008

Large branchiopods are threatened worldwide by the loss and degradation of their temporary aquatic habitats owing to drainage and intensive agriculture. Sound ecological knowledge of their diversity and distribution is a prerequisite to formulate effective conservation measures. In the present study, large branchiopods were collected from 82 temporary freshwater pools belonging to five habitat types in Kiskunság (Hungary). Dormant propagule bank analysis complemented the field survey. Eleven species were found, with large branchiopods occurring in more than half of the study systems. The high regional species richness and occurrence frequency of large branchiopods make Kiskunság a true ‘hot spot’ of large branchiopod diversity. The local environment was more important than spatial factors (isolation) in explaining the presence of the most common species. Dispersal was most likely not limiting for the large branchiopods in the study area and colonisation success of different species was differentially affected by local conditions, possibly invertebrate predation risk and hydroperiod. Meadow pools and wheel tracks contributed most to regional species richness through the presence of rare and exclusive species. To conserve branchiopod diversity, we stress the importance of high habitat diversity in the landscape and the need to conserve neglected habitats such as wheel tracks.
High-precision radiocarbon dating and historical biblical archaeology in southern Jordan
Authors: Levy Thomas E. , Higham Thomas , Bronk Ramsey Christopher , Smith Neil G. , Ben-Yosef Erez , Robinson Mark , Münger Stefan , Knabb Kyle , Schulze Jürgen P. , Najjar Mohammad , Tauxe Lisa
Published: October 2008

Recent excavations and high-precision radiocarbon dating from the largest Iron Age (IA,ca.1200–500 BCE) copper production center in the southern Levant demonstrate major smelting activities in the region of biblical Edom (southern Jordan) during the 10th and 9th centuries BCE. Stratified radiocarbon samples and artifacts were recorded with precise digital surveying tools linked to a geographic information system developed to control on-site spatial analyses of archaeological finds and model data with innovative visualization tools. The new radiocarbon dates push back by 2 centuries the accepted IA chronology of Edom. Data from Khirbat en-Nahas, and the nearby site of Rujm Hamra Ifdan, demonstrate the centrality of industrial-scale metal production during those centuries traditionally linked closely to political events in Edom's 10th century BCE neighbor ancient Israel. Consequently, the rise of IA Edom is linked to the power vacuum created by the collapse of Late Bronze Age (LB,ca.1300 BCE) civilizations and the disintegration of the LB Cypriot copper monopoly that dominated the eastern Mediterranean. The methodologies applied to the historical IA archaeology of the Levant have implications for other parts of the world where sacred and historical texts interface with the material record.
The filled skutterudite CeOs
4
As
12
: A hybridization gap semiconductor
Authors: Baumbach R. E. , Ho P. C. , Sayles T. A. , Maple M. B. , Wawryk R. , Cichorek T. , Pietraszko A. , Henkie Z.
Published: November 2008

X-ray diffraction, electrical resistivity, magnetization, specific heat, and thermoelectric power measurements are presented for single crystals of the new filled skutterudite compound CeOs
4
As
12
, which reveal phenomena that are associated with f-electron-conduction electron hybridization. Valence fluctuations or Kondo behavior dominates the physics down to
T
∼ 135 K. The correlated electron behavior is manifested at low temperatures as a hybridization gap-insulating state. The small energy gap Δ
1
/k
B
∼ 73 K, taken from fits to electrical resistivity data, correlates with the evolution of a weakly magnetic or nonmagnetic ground state, which is evident in the magnetization data below a coherence temperature
T
coh
∼ 45 K. Additionally, the low-temperature electronic specific heat coefficient is small, γ ∼ 19 mJ/mol K
2
. Some results for the nonmagnetic analogue compound LaOs
4
As
12
are also presented for comparison purposes.
Impact of an Education Program on the Incidence of Central Line-Associated Bloodstream Infection in 2 Medical-Surgical Intensive Care Units in Brazil
Authors: Santana Solange L. , Furtado Guilherme H. C. , Wey Sérgio Barsanti , Medeiros Eduardo A. S.
Published: October 2008

An intervention study was undertaken to evaluate the impact of an education program on the incidence of central line–associated bloodstream infection (CLABSI) in 2 intensive care units. There was a nonsignificant reduction in the incidence of CLABSI (odds ratio, 0.46 [95% confidence interval, 0.21–1.02]; P = .04) despite a significant increase in knowledge of CLABSI prevention by the staff of both intensive care units after the education program.
Induction for secant varieties of Segre varieties
Authors: Abo Hirotachi , Ottaviani Giorgio , Peterson Chris
Published: October 2008

This paper studies the dimension of secant varieties to Segre varieties. The problem is cast both in the setting of tensor algebra and in the setting of algebraic geometry. An inductive procedure is built around the ideas of successive specializations of points and projections. This reduces the calculation of the dimension of the secant variety in a high dimensional case to a sequence of calculations of partial secant varieties in low dimensional cases. As applications of the technique: We give a complete classification of defective

p
p

-secant varieties to Segre varieties for

p
≤
6

p\leq 6

. We generalize a theorem of Catalisano-Geramita-Gimigliano on non-defectivity of tensor powers of

P

n

\mathbb {P}{n}

. We determine the set of

p
p

for which unbalanced Segre varieties have defective

p
p

-secant varieties. In addition, we completely describe the dimensions of the secant varieties to the deficient Segre varieties

P

1

×

P

1

×

P

n

×

P

n

\mathbb {P}{1}\times \mathbb {P}{1} \times \mathbb {P}{n} \times \mathbb {P}{n}

and

P

2

×

P

3

×

P

3

\mathbb {P}{2}\times \mathbb {P}{3} \times \mathbb {P}{3}

. In the final section we propose a series of conjectures about defective Segre varieties.
Poisson approximation for significance in genome-wide ChIP-chip tiling arrays
Authors: Zhang Yu
Published: October 2008

Motivation: A genome-wide ChIP-chip tiling array study requires millions of simultaneous comparisons of hybridization for significance. Controlling the false positive rate in genome-wide tiling array studies is very important, because the number of computationally identified regions can easily go beyond the capability of experimental verification. No accurate and efficient method exists for evaluating statistical significance in tiling arrays. The Bonferroni method is overly conservative and the permutation test is time consuming for genome-wide studies.

Result: Motivated by the Poisson clumping heuristic, we propose an accurate and efficient method for evaluating statistical significance in genome-wide ChIP-chip tiling arrays. The method works accurately for any large number of multiple comparisons, and the computational cost for evaluating P-values does not increase with the total number of tests. Based on a moving window approach, we demonstrate how to combine results using various window sizes to increase the detection power while maintaining a specified type I error rate. We further introduce a new false discovery rate control that is more appropriate in measuring the false proportion of binding intervals in tiling array analysis. Our method is general and can be applied to many large-scale genomic and genetic studies.

Availability:  http://www.stat.psu.edu/~yuzhang/pass.tar

Contact:  yuzhang@stat.psu.edu
Modularity of cellular networks shows general center-periphery polarization
Authors: Vinogradov Alexander E.
Published: October 2008

The modular biology is supposed to be a bridge from the molecular to the systems biology. Using a new approach, it is shown here that the protein interaction networks of yeast Saccharomyces cerevisiae and bacteria Escherichia coli consist of two large-scale modularity layers, central and peripheral, separated by a zone of depressed modularity. This finding based on the analysis of network topology is further supported by the discovery that there are many more Gene Ontology categories (terms) and KEGG biochemical pathways that are overrepresented in the central and peripheral layers than in the intermediate zone. The categories of the central layer are mostly related to nuclear information processing, regulation and cell cycle, whereas the peripheral layer is dealing with various metabolic and energetic processes, transport and cell communication. A similar center-periphery polarization of modularity is found in the protein domain networks (‘built-in interactome’) and in a powergrid (as a non-biological example). These data suggest a ‘polarized modularity’ model of cellular networks where the central layer seems to be regulatory and to use information storage of the nucleus, whereas the peripheral layer seems devoted to more specialized tasks and environmental interactions, with a complex ‘bus’ between the layers.

Contact:  aevin@mail.cytspb.rssi.ru

Supplementary information:  Supplementary data are available at Bioinformatics online.
AUGIST: inferring species trees while accommodating gene tree uncertainty
Authors: Oliver Jeffrey C.
Published: October 2008

Summary: AUGIST (accomodating uncertainty in genealogies while inferring species tress) is a new software package for inferring species trees while accommodating uncertainty in gene genealogies. It is written for the Mesquite software system and provides sampling procedures to incorporate uncertainty in gene tree reconstruction while providing confidence estimates for inferred species trees.

Availability:  http://www.lycaenid.org/augist/

Contact:  jeffrey.oliver@yale.edu
BASH: a tool for managing BeadArray spatial artefacts
Authors: Cairns J. M. , Dunning M. J. , Ritchie M. E. , Russell R. , Lynch A. G.
Published: October 2008

Summary: With their many replicates and their random layouts, Illumina BeadArrays provide greater scope fordetecting spatial artefacts than do other microarray technologies. They are also robust to artefact exclusion, yet there is a lack of tools that can perform these tasks for Illumina. We present BASH, a tool for this purpose. BASH adopts the concepts of Harshlight, but implements them in a manner that utilizes the unique characteristics of the Illumina technology. Using bead-level data, spatial artefacts of various kinds can thus be identified and excluded from further analyses.

Availability: The beadarray Bioconductor package (version 1.10 onwards), www.bioconductor.org

Contact:  andy.lynch@cancer.org.uk

Supplementary information: Additional information and a vignette are included in the beadarray package.
Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol
Authors: Gallien Sébastien , Perrodou Emmanuel , Carapito Christine , Deshayes Caroline , Reyrat Jean-Marc , Van Dorsselaer Alain , Poch Olivier , Schaeffer Christine , Lecompte Odile
Published: October 2008

The progress in sequencing technologies irrigates biology with an ever-increasing number of genome sequences. In most cases, the gene repertoire is predicted in silico and conceptually translated into proteins. As recently highlighted, the predicted genes exhibit frequent errors, particularly in start codons, with a serious impact on subsequent biological studies. A new “ortho-proteogenomic” approach is presented here for the annotation refinement of multiple genomes at once. It combines comparative genomics with an original proteomic protocol that allows the characterization of both N-terminal and internal peptides in a single experiment. This strategy was applied to the Mycobacterium genus with Mycobacterium smegmatis as the reference, and identified 946 distinct proteins, including 443 characterized N termini. These experimental data allowed the correction of 19% of the characterized start codons, the identification of 29 proteins missed during the annotation process, and the curation, thanks to comparative genomics, of 4328 sequences of 16 other Mycobacterium proteomes.
ON THE STRUCTURE OF PREDICATE NP1
Authors: Holmberg Anders
Published: November 2008

Abstract. The central hypothesis in this paper is that a predicate NP is a maximal projection which is an open expression, meaning that it has an A‐trace in its highest spec‐position functioning as a predicate variable, while an argument NP is a closed expression, meaning that it has the head of an A‐chain, usually pro in its highest spec‐position. The distribution of articles, definite as well as indefinite, in combination with various attributes is explained largely as a consequence of licensing conditions on the highest spec‐position and the categories it hosts. In addition some hitherto unnoticed facts concerning possessors in predicate NPs are discussed.
THE EFFECT OF SALTS ON THERMAL AND HYDRIC DILATATION OF POROUS BUILDING STONE*
Authors: AL‐NADDAF M.
Published: November 2008

Fifteen desalinated sandstone drill core samples from Umm Ishrin Sandstone Formation in Petra (Cambrian age) were used for this study. The samples were mineralogically analysed using X‐ray diffraction and their physical properties were also determined. Samples with similar physical properties and mineralogical composition were taken for further experimental work. After desalination, thermal and hydric dilatation coefficients were measured, then three types of salts (NaCl, KCl and Na2SO4·10H2O), which have high solubility and consequently are the most dangerous to building stone (and are also detected in the sandstone monuments in Petra), were introduced into the samples and their contents were calculated. The results show that salt crystallization in the pores of building stones can increase their thermal dilatation and decrease their hydric dilatation to varying extents, depending on the nature of the salt. The average increase in the thermal dilatation coefficient per unit mass of salt is the lowest for the Na2SO4·10H2O‐salted samples with a value of 5.3%, while the NaCl‐salted samples have the highest value with 7.8% per salt mass. The average percentage of the decrease of the hydric dilatation coefficient is 1061% for Na2SO4·10H2O‐salted samples per mass of salt content; the NaCl‐salted samples have a value of 1510% per mass of salt content, and the KCl‐salted samples almost the same value. For the salt‐free samples, it was found that in climatic conditions with a high temperature range, the deterioration of sandstone due to temperature fluctuation is more effective than that caused by change in the moisture content, while samples with high salt content suffer more from hydric dilatation.
Comparison of the Dispersed Phase Coalescence Mechanisms in Different Tablespreads
Authors: Rousseau D. , Ghosh S. , Park H.
Published: November 2008

ABSTRACT:  Temperature‐induced destabilization of the dispersed phase in butter and margarine was compared by following changes in droplet size (d3,3), solid fat content (SFC), and fat crystal spatial organization in the 28–34 °C range. At 28 °C, both butter and margarine were stable, with similar d3,3 values (approximately 6 μm) and droplet size distributions. As the storage temperature was raised above 30 °C, notable droplet coalescence was observed (for example, at 32 °C d3,3 values of approximately 10 μm for butter and approximately 12 μm for margarine were obtained). Dispersed phase coalescence in butter was dominated by coagulation, with the fat crystal network‐limiting droplet–droplet contact until a minimum SFC was reached (approximately 2.5%). In margarine, the rate‐limiting step for coalescence was the melting of Pickering crystals present around the dispersed aqueous droplets. Unlike butter, there was no sharp change in stability at a particular temperature or critical SFC. With these differences, coalescence in butter could be modeled as a 2nd‐order process and as a 1st‐order process in margarine. Overall, these results demonstrated that the kinetic stability of the dispersed aqueous phase in butter and margarine depends on SFC and the spatial distribution of fat crystals within the spreads.
Neuromuscular blockade of slow twitch muscle fibres elevates muscle oxygen uptake and energy turnover during submaximal exercise in humans
Authors: Krustrup Peter , Secher Niels H. , Relu Mihai U. , Hellsten Ylva , Söderlund Karin , Bangsbo Jens
Published: October 2008

We tested the hypothesis that a greater activation of fast‐twitch (FT) fibres during dynamic exercise leads to a higher muscle oxygen uptake () and energy turnover as well as a slower muscle on‐kinetics. Subjects performed one‐legged knee‐extensor exercise for 10 min at an intensity of 30 W without (CON) and with (CUR) arterial injections of the non‐depolarizing neuromuscular blocking agent cisatracurium. In CUR, creatine phosphate (CP) was unaltered in slow twitch (ST) fibres and decreased (P < 0.05) by 28% in FT fibres, whereas in CON, CP decreased (P < 0.05) by 33% and 23% in ST and FT fibres, respectively. From 127 s of exercise, muscle was higher (P < 0.05) in CUR compared to CON (425 ± 25 (±s.e.m.) versus 332 ± 30 ml min−1) and remained higher (P < 0.05) throughout exercise. Using monoexponential fitting, the time constant of the exercise‐induced muscle response was slower (P < 0.05) in CUR than in CON (55 ± 6 versus 33 ± 5 s). During CUR and CON, muscle homogenate CP was lowered (P < 0.05) by 32 and 35%, respectively, and also muscle lactate production was similar in CUR and CON (37.8 ± 4.1 versus 35.2 ± 6.2 mmol). Estimated total muscle ATP turnover was 19% higher (P < 0.05) in CUR than in CON (1196 ± 90 versus 1011 ± 59 mmol) and true mechanical efficiency was lower (P < 0.05) in CUR than in CON (26.2 ± 2.0 versus 30.9 ± 1.5%). In conclusion, the present findings provide evidence that FT fibres are less efficient than ST fibres in vivo at a contraction frequency of 1 Hz, and that the muscle kinetics is slowed by FT fibre activation.
Performance Considerations in Replacement of Low-Pressure Turbine Rotors for Nuclear Power Plants: A Case Study
Authors: Sunder Raj Komandur S.
Published: October 2008

In recent years, the nuclear power industry has witnessed profound changes in terms of renewal of operating licenses and power uprates. Renewal of operating licenses for an additional 20 years beyond the original licensed period of 40 years entails several considerations relating to aging management, performance, reliability, availability, and maintainability. Power uprates range from a low of up to 2% due to improved techniques in feedwater flow measurement to a high of up to 20% for extended power uprates. Since the limitations of power uprates are generally encountered in design of the turbine cycle, the impact upon the performance, reliability, availability and maintainability of the equipment and components in the turbine cycle may vary from low or moderate to significant. Several nuclear power plant owners have already replaced the low-pressure turbine rotors of their nuclear units with improved designs to mitigate blade failures and forced outages due to stress corrosion cracking, to reduce inspection intervals and maintenance, achieve higher output due to improved efficiency, etc. Others are either embarking upon or planning similar initiatives to confront aging, performance, availability, reliability and maintainability concerns stemming from renewal of operating licenses as well as the need to accommodate higher pressures and flows accompanying the proposed power uprates. Typically, the original low-pressure turbine designs utilizing built-up rotors with shrunk-on disks are being replaced with monoblock rotors with fully integral disks, couplings, blading and shrouds. The last stage blading is also longer resulting in a larger annulus area. Since these replacement programs involve significant expenditures, several factors need to be considered in order to ensure that the objectives of the rotor replacement programs are met. Using a case study, this paper examines the various considerations involved in replacing the low-pressure turbine rotors for a nuclear power plant. Design, performance and test considerations that need to be addressed before and after the low-pressure turbine rotors are replaced are discussed. The use of performance modeling tools in evaluating performance gains from low-pressure turbine rotor replacements is reviewed. Finally, the paper provides recommendations for ensuring that the objectives of a low-pressure turbine rotor replacement program are met.
Protecting Intellectual Property in Power
Authors: Kaplan Kathleen M. , Kaplan John J.
Published: October 2008

Power Engineers sometimes lack an important area of the engineering profession: Intellectual Property Education. Intellectual Property (IP) encompasses the intangible “stuff” which is what power engineering is all about — original thought, invention, and progress. The three traditional areas of IP are copyrights, trademarks, and patents. A power engineer cannot protect his or her interest and truly benefit society, whether it be an invention, expression of idea, or some other non-tangible property, without understanding these three IP areas. Power engineers are not to be blamed; IP has not been incorporated into the engineering discipline. Unfortunately, with the lack of IP instruction, power engineers may be ignorant as to the protection of their creations. This impacts their futures as they will be entering the creative field of power engineering without IP knowledge and may miss precious opportunities to benefit from their creations. Of course, this lack of IP knowledge does not help the power engineer or the progression of power engineering. This paper, written by a patent agent and patent attorney, both holding doctorate degrees in computer science and electrical engineering, respectively, will introduce the concepts of intellectual property in an easy-to-understand format. The authors will cover all three traditional areas of IP: copyrights, trademarks, and patents. Within each, specific examples will be given with respect to power engineering. With the knowledge presented, the power engineer should be able to identify the type of intellectual property needed to protect his or her works.
Modeling and Simulation of Synchronous-Self-Shifting Clutch
Authors: Tian Ying , Sun Yufeng , Lu Qingchun
Published: October 2008

This paper is based on the improved combined diesel or gas turbine power plant experiment rig. Considering the effect of many frictions which have been ignored of each part in the synchronous-self-shifting clutch, a new model of the synchronous-self-shifting clutch is set up and made for the dynamic real time simulation by Matlab/Simulink, which provides the theory for studying the dynamic characteristics of the synchronous-self-shifting clutch on the main engine changeover, and it can be used for further study of the flexibility of the CODOG power plant.
Design of a Provisory Axle for Substitution of a 69MW Generator’s Rotor
Authors: Pinto Junior Salustiano Martins , De Pinho Carvalho Hernani
Published: October 2008

The paper presents results of a modal analysis for developing a project of a provisory axle of a 69 MW generator’s rotor. The uniqueness of this project, using the modal analysis technique, is that a whole generator set was temporarily (about 90 days) replaced by a sole axle projected, designed, and manufactured by the user. The specific aim of this provisory axle is to provide net 39 MW at 3600 rpm to the blower of the CST’s #1 Blast Furnace during maintenance period of the extracted rotor and without additional risks of interrupting normal operations of steel production. The theoretical modal analysis of the provisory axle was developed with the aid of ANSYS 5.6 with SOLID type elements. The project was based on the geometry of the rotor to be temporarily replaced and main field boundaries conditions were also taken in account as, for example, the clamps in the flanges and the supports in the bearings. After balancing, and under over speed conditions, experimental tests were accomplished successfully, by means of a test “shooting” tunnel, as to check the theoretical critical resonances data and to verify the structural integrity conditions after testing. The results of the theoretical model were also proved successful after the installation, start up, and operation in the field.
Analysis of Turbo-Generator Circulating Current Between Stator Winding Parallel-Connected Branches Under Fault Conditions
Authors: Wan Shuting , Li Heming , Li Yonggang , Meng Fanchao
Published: October 2008

Firstly analyzes the generator parameters of air-gap magnetomotive force, magnetic permeability, magnetic flux density, the stator winding parallel-connected branches electromotive force distribution, and gets voltage difference and circulating current expressions between stator winding parallel-connected branches. Secondly, through analyzing the parameters changing on normal operation and fault condition, the circulating current characteristics are given based on the expressions, which are that hasn’t the circulating current when generator operates normally, and second harmonic circulating current will increase when the rotor winding inter-turn short circuit fault has happened, and fundamental circulating current will increase when stator winding inter-turn short circuit or air-gap eccentricity fault has happened. Considering that different fault has different circulating current characteristic, the generator fault diagnosis method based on circulating current was developed. Finally practically acquires SDF-9 generator data on the fault, the results of verification show that analysis is correct.
Modern Reaction HP/IP Turbine Technology Advances and Experiences
Authors: Hurd Paul , Truckenmueller Frank , Thamm Norbert , Pollak Helmut , Neef Matthias , Deckers Mathias
Published: October 2008

Modern steam turbines of the author’s company are based on advanced technology such as high efficiency seals, 3D blading, single inner cylinders, and advanced materials. These technologies result in a compact opposed-flow HP/IP combined cylinder design with high long-term efficiency, reliability, and availability. This paper will illustrate the features, benefits, and operational experience of large steam turbines with advanced technologies using an opposed-flow HP/IP cylinder. The paper will also address the relative performance of this type of steam turbine against its predecessors. Specific examples will be examined: 350 MW fossil units in the Asian market, a typical 250 MW combined cycle steam turbine in the American market, a 700 MW three-cylinder class design for conventional steam plants developed for the global coal market, and a 600 MW steam turbine upgrade.
A Review of Seasonal Dispatch Modeling Methods
Authors: Milton J. W.
Published: October 2008

Rankine cycle power plants efficiency varies across the seasons due to changes in ambient air and cooling water temperatures. The size of this variation is influenced by the unit design. Test data collected on units to develop economic dispatch (input output) models produces an “as found” result. This result includes current imposed season influence and mechanical condition of the unit. With additional steps, these models can be adjusted to account for and quantify the seasonal efficiency changes. This paper will review the various methods used to account for these changes and evaluate the pros and cons of each method.