bluuebunny/crossref_metadata_2025 huggingface dataset:
Incremental Bayesian learning for in‐service analysis of aeronautic composites
Authors: Cacciola Matteo , Megali Giuseppe , Lay‐Ekuakille Aimé
Published: August 2013

Incremental learning could be really useful for fault detection and anticipation in non‐destructive testing and evaluation. The real‐time monitoring could be proficiently exploited when an early warning system is required for the human safety. This is the case of aeronautic transportation of persons and goods. Here, an automated neural‐based system for defect detection in aeronautic composites is proposed. The entire system consists of a stand‐alone defect classifier based on a Bayesian neural network (BNN) combined with advantages of Very Large Scale Integration (VLSI)implementation. Exploiting a parallel implementation is worthwhile when high computational speed, special operating conditions, portability, limited physical size, low‐power dissipation and reliability are required. This study shows how hardware‐based neural network can increase processing speed and defect identification rate. Secondary random access memory‐based field programmable gate arrays represent a suitable platform to realise these models, since their re‐programmability can rapidly change the parameters of the network if a new training is needed. With the hardware‐based BNN, 100% of delamination bottom/top, inclusion bottom/middle/top, porosity and 99.6% of delamination middle were correctly identified. The achieved results highlight the efficient design of the hardware network, obtained also using a new circuit to compute the activation function of neurons.
Genetic parameters for calf mortality and correlated cow and calf traits in tropically adapted beef breeds managed in extensive Australian production systems
Authors: Bunter Kim L. , Johnston David J.
Published: August 2013

The genetic associations between cow teat and udder traits with maternal contributions to calf mortality were studied in Brahman (BRAH) and Tropical Composite (TCOMP) cattle managed in extensive production systems of northern Australia. Data from 9286 purebred and crossbred calves, progeny of 2076 cows and 149 sires, were recorded from 2003 to 2011. Calf weights at birth (BWT) and weaning (WWT) were routinely recorded. The event of calf death before weaning (DWEAN) was analysed as a repeated-measure of the cow. Cows were also scored at each calving for front- and back-teat size and udder size (US) on an ascending five-point scale. Heritabilities for front-teat size, back-teat size and US were 0.38 ± 0.05, 0.31 ± 0.05 and 0.49 ± 0.01, and estimates were the same for BRAH and TCOMP. The heritability of DWEAN was higher in BRAH (0.09 ± 0.02) than in TCOMP (0.02 ± 0.01). Variance ratios for maternal genetic effects contributing to variation in BWT and WWT were 0.13 ± 0.02 and 0.18 ± 0.05, and tended to be larger in TCOMP than in BRAH. Teat and udder scores were moderately correlated phenotypically (0.37 ± 0.01) and genetically (0.53 ± 0.04) with each other. Both traits were uncorrelated genetically with calf birthweight but positively correlated with WWT and DWEAN. The genetic correlation between average teat score at calving and DWEAN was larger (0.54 ± 0.05) than that between US and DWEAN (0.33 ± 0.06), whereas the genetic correlation between US and maternal effects for WWT was larger (0.60 ± 0.08) than the corresponding value for average teat score with maternal WWT (0.37 ± 0.13). Correlations between BWT and WWT were high for both direct (0.63 ± 0.07) and maternal (0.50 ± 0.09) genetic effects. Genetic correlations between maternal effects for BWT or WWT with DWEAN were both negative (–0.23 ± 0.10 and –0.21 ± 0.04), while the correlation between BWT and WWT for maternal effects was positive (0.54 ± 0.09), showing that larger calves at birth are less likely to die before weaning and have heavier weaning weights from maternal genetic contributions to these traits. Selection on maternal components of BWT and WWT should be accompanied by recording for teat and udder characteristics to assist in preventing any undesired correlated response in teat or udder size, which can have detrimental outcomes for calf survival, despite expectations of higher milk yield.
Genetics of early and lifetime annual reproductive performance in cows of two tropical beef genotypes in northern Australia
Authors: Johnston D. J. , Barwick S. A. , Fordyce G. , Holroyd R. G. , Williams P. J. , Corbet N. J. , Grant T.
Published: August 2013

Reproduction records from 2137 cows first mated at 2 years of age and recorded through to 8.5 years of age were used to study the genetics of early and lifetime reproductive performance from two genotypes (1020 Brahman and 1117 Tropical Composite) in tropical Australian production systems. Regular ultrasound scanning of the reproductive tract, coupled with full recording of mating, calving and weaning histories, allowed a comprehensive evaluation of a range of reproductive traits. Results showed components traits of early reproductive performance had moderate to high heritabilities, especially in Brahmans. The heritability of lactation anoestrous interval in 3-year-old cows was 0.51 ± 0.18 and 0.26 ± 0.11 for Brahman and Tropical Composite, respectively. Heritabilities of binary reproductive output traits (conception rate, pregnancy rate, calving rate and weaning rate) from first and second matings were generally moderate to high on the underlying scale. Estimates ranged from 0.15 to 0.69 in Brahman and 0.15 to 0.34 in Tropical Composite, but were considerably lower when expressed on the observed scale, particularly for those traits with high mean levels. Heritabilities of lifetime reproduction traits were low, with estimates of 0.11 ± 0.06 and 0.07 ± 0.06 for lifetime annual weaning rate in Brahman and Tropical Composite, respectively. Significant differences in mean reproductive performance were observed between the two genotypes, especially for traits associated with anoestrus in first-lactation cows. Genetic correlations between early-in-life reproductive measures and lifetime reproduction traits were moderate to high. Genetic correlations between lactation anoestrous interval and lifetime annual weaning rate were –0.62 ± 0.24 in Brahman and –0.87 ± 0.32 in Tropical Composite. The results emphasise the substantial opportunity that exists to genetically improve weaning rates in tropical beef cattle breeds by focusing recording and selection on early-in-life female reproduction traits, particularly in Brahman for traits associated with lactation anoestrus.
Calcium-mediated Hydrophosphorylation of Organic Isocyanates with Diphenylphosphane Oxide
Authors: Härling Stephan , Greiser Julia , Al-Shboul Tareq M. A. , Görls Helmar , Krieck Sven , Westerhausen Matthias
Published: August 2013

The calcium-mediated addition of diphenylphosphane oxide to organic isocyanates and isothiocyanates yields N-alkyl and N-aryl substituted diphenylphosphorylformamides (E = O, R = iPr, tBu, cHex, Ph, C6H4-4-Br, C6H2-2,4,6-Me3, and Naph) and -thioformamides (E = S, R = iPr, cHex, Ph, and C6H4-4-Me), respectively, of the type Ph2P(O)–C(E)–N(H)R. All derivatives were characterized by IR and NMR spectroscopy as well as X-ray diffraction experiments. The wavenumbers of the N–H stretching modes are smaller for the thio analogues and N-aryl substituents. In the solid state all formamides and thioformamides form dimers by N–H⋯O–P hydrogen bridges. The P–CCE bonds are significantly elongated compared with the P–CPh distances.
Synthesis and Characterisation of RuII Polypyridyl Complexes: DNA-Binding, Photocleavage, and Topoisomerase I and II Inhibitory Activity
Authors: He Xiaojun , Yang Guang , Sun Xiaonan , Xie Lingjun , Tan Lifeng
Published: August 2013

Two mixed-ligand ruthenium(ii) complexes [Ru(phen)2(cptcp)]2+ (Ru1; phen = 1,10-phenanthroline, cptcp = 2-(4-carbazol-9-yl-phenyl)-1H-1,3,7,8-tetraaza-cyclopenta-[l]-phenanthrene) and [Ru(phen)2(btcpc)]2+ (Ru2; btcpc = 9-butyl-6-(1H-1,3,7,8-tetraaza-cyclo-cyclopenta-[l]-phenanthren-2-yl)-9H-carbazole-3-carbaldehyde) have been synthesised and characterised. The DNA-binding behaviours of the two complexes have been investigated by using spectroscopic and viscosity measurements. Results suggest that the two complexes bind to DNA by intercalation. The photocleavage of plasmid pBR322 DNA indicates that Ru1 exhibits more effective DNA cleavage activity in comparison to that exhibited by Ru2 under the same conditions, and different cleavage mechanisms are determined. Topoisomerase inhibition and DNA strand passage assay confirm that Ru1 may act as an efficient dual inhibitor of topoisomerases I and II, whereas Ru2 may only act as a single inhibitor of topoisomerases II.
Biomarker assessment of spatial and temporal changes in the composition of flocculent material (floc) in the subtropical wetland of the Florida Coastal Everglades
Authors: Pisani Oliva , Louda J. William , Jaffé Rudolf
Published: August 2013

Environmental context
Flocculent material (floc) in freshwater and coastal areas of the Florida Everglades plays an important role in food web dynamics and nutrient cycling. Using biomarkers and pigment chemotaxonomy, we determined the organic matter composition of floc from different environments in the Everglades, and found that it is dominated by local biomass inputs and influenced by hydrological regimes. With the on-going restoration of the Florida Everglades, it is important to gain a better understanding of the biogeochemical dynamics of floc, including its sources, transformations and reactivity.

Abstract
Flocculent material (floc) is an important energy source in wetlands. In the Florida Everglades, floc is present in both freshwater marshes and coastal environments and plays a key role in food webs and nutrient cycling. However, not much is known about its environmental dynamics, in particular its biological sources and bio-reactivity. We analysed floc samples collected from different environments in the Florida Everglades and applied biomarkers and pigment chemotaxonomy to identify spatial and seasonal differences in organic matter sources. An attempt was made to link floc composition with algal and plant productivity. Spatial differences were observed between freshwater marsh and estuarine floc. Freshwater floc receives organic matter inputs from local periphyton mats, as indicated by microbial biomarkers and chlorophyll-a estimates. At the estuarine sites, the floc is dominated by mangrove as well as diatom inputs from the marine end-member. The hydroperiod (duration and depth of inundation) at the freshwater sites influences floc organic matter preservation, where the floc at the short-hydroperiod site is more oxidised likely due to periodic dry-down conditions. Seasonal differences in floc composition were not consistent and the few that were observed are likely linked to the primary productivity of the dominant biomass (periphyton in the freshwater marshes and mangroves in the estuarine zone). Molecular evidence for hydrological transport of floc material from the freshwater marshes to the coastal fringe was also observed. With the on-going restoration of the Florida Everglades, it is important to gain a better understanding of the biogeochemical dynamics of floc, including its sources, transformations and reactivity.
Improving access to electronic health records for people with intellectual disability: a qualitative study
Authors: van Dooren Kate , Lennox Nick , Stewart Madeline
Published: August 2013

People with intellectual disability represent ~2–3% of the Australian population and experience elevated rates of mortality and morbidity compared with the general population. People with intellectual disability, and their families and carers, must keep track of extensive medical information while also managing turnover of paid staff, general practitioners and other health professionals, making them beneficiaries of Australia’s new eHealth record system. Although they are key users, there is a lack of knowledge about the accessibility of the system for individuals with intellectual disability, or those responsible for managing their health information. This is a missed opportunity to improve the lives of an already overlooked group. This study aimed to identify the facilitators and barriers to registering for an eHealth record network for people with intellectual disability and those supporting them to manage their health information. We interviewed potential users of eHealth records, including four people with intellectual disability, three family members and two residential support workers. Our findings suggest that decision-makers involved in the roll-out of the eHealth record networks should incorporate ‘reasonable accommodations’ to improve accessibility for people with intellectual disability and those who support them to manage their health information. This includes identifying and eliminating the barriers to accessibility of eHealth records and taking appropriate measures to promote access to individuals with intellectual disability. People with intellectual disability and the people who support them are a diverse group with a range of abilities. The translation of their views into practice will help to improve the eHealth system for this and other vulnerable population groups.
Transgenic mouse model for the study of enterovirus 71 neuropathogenesis
Authors: Fujii Ken , Nagata Noriyo , Sato Yuko , Ong Kien Chai , Wong Kum Thong , Yamayoshi Seiya , Shimanuki Midori , Shitara Hiroshi , Taya Choji , Koike Satoshi
Published: August 2013

Significance

EV71 infection with severe neurological complications has become a serious public health concern. However, suitable small animal models to study human EV71 pathogenesis are not available. We have generated a Tg mouse model by expressing the human EV71 receptor, Scavenger receptor B2, and found it to be susceptible to EV71 infection. This Tg mouse model exhibits neurological disease and pathology very similar to that observed in humans. The results confirm that the Scavenger receptor B2 receptor is important for EV71 infection in vivo. Further development of this new small animal model should greatly contribute toward investigation of EV71 pathogenesis and development of vaccines and antiviral drugs.
Low levels of copper disrupt brain amyloid-β homeostasis by altering its production and clearance
Authors: Singh Itender , Sagare Abhay P. , Coma Mireia , Perlmutter David , Gelein Robert , Bell Robert D. , Deane Richard J. , Zhong Elaine , Parisi Margaret , Ciszewski Joseph , Kasper R. Tristan , Deane Rashid
Published: August 2013

Significance

The causes of the sporadic form of Alzheimer’s disease (AD) are unknown. In this study we show that copper (Cu) critically regulates low-density lipoprotein receptor-related protein 1–mediated Aβ clearance across the blood–brain barrier (BBB) in normal mice. Faulty Aβ clearance across the BBB due to increased Cu levels in the aging brain vessels may lead to accumulation of neurotoxic Aβ in brains. In a mouse model of AD low levels of Cu also influences Aβ production and neuroinflammation. Our study suggests that Cu may also increase the severity of AD.
Two distinct forms of functional lateralization in the human brain
Authors: Gotts Stephen J. , Jo Hang Joon , Wallace Gregory L. , Saad Ziad S. , Cox Robert W. , Martin Alex
Published: August 2013

Significance

This study alters our fundamental understanding of the functional interactions between the cerebral hemispheres of the human brain by establishing that the left and right hemispheres have qualitatively different biases in how they dynamically interact with one another. Left-hemisphere regions are biased to interact more strongly within the same hemisphere, whereas right-hemisphere regions interact more strongly with both hemispheres. These two different patterns of interaction are associated with left-lateralized functions, such as language and motor abilities, and right-lateralized functions, such as visuospatial attention. Importantly, the magnitude of lateralization measured for individual participants in these regions predicted the level of cognitive ability for the respective function, demonstrating that lateralization of function is associated with improved cognitive ability.
Salicylic acid 3-hydroxylase regulates
Arabidopsis
leaf longevity by mediating salicylic acid catabolism
Authors: Zhang Kewei , Halitschke Rayko , Yin Changxi , Liu Chang-Jun , Gan Su-Sheng
Published: August 2013

The plant hormone salicylic acid (SA) plays critical roles in plant defense, stress responses, and senescence. Although SA biosynthesis is well understood, the pathways by which SA is catabolized remain elusive. Here we report the identification and characterization of an SA 3-hydroxylase (S3H) involved in SA catabolism during leaf senescence.
S3H
is associated with senescence and is inducible by SA and is thus a key part of a negative feedback regulation system of SA levels during senescence. The enzyme converts SA (with a
K
m
of 58.29 µM) to both 2,3-dihydroxybenzoic acid (2,3-DHBA) and 2,5-DHBA in vitro but only 2,3-DHBA in vivo. The
s3h
knockout mutants fail to produce 2,3-DHBA sugar conjugates, accumulate very high levels of SA and its sugar conjugates, and exhibit a precocious senescence phenotype. Conversely, the gain-of-function lines contain high levels of 2,3-DHBA sugar conjugates and extremely low levels of SA and its sugar conjugates and display a significantly extended leaf longevity. This research reveals an elegant SA catabolic mechanism by which plants regulate SA levels by converting it to 2,3-DHBA to prevent SA overaccumulation. The research also provides strong molecular genetic evidence for an important role of SA in regulating the onset and rate of leaf senescence.
Chronic alcohol produces neuroadaptations to prime dorsal striatal learning
Authors: DePoy Lauren , Daut Rachel , Brigman Jonathan L. , MacPherson Kathryn , Crowley Nicole , Gunduz-Cinar Ozge , Pickens Charles L. , Cinar Resat , Saksida Lisa M. , Kunos George , Lovinger David M. , Bussey Timothy J. , Camp Marguerite C. , Holmes Andrew
Published: August 2013

Significance

Alcoholism is characterized by a progressive degradation of executive control and an increase in compulsive alcohol seeking that is hypothesized to involve a shift from prefrontal cortex to dorsal striatal (DLS) control over behavior. Here, we show that mice exposed to chronic intermittent alcohol exhibited expansion of dendritic material in DLS neurons, coupled with loss of endocannabinoid CB1 receptor signaling and CB1-mediated long-term depression in the DLS. Behaviorally, chronic alcohol exposure facilitated various forms of DLS-dependent learning and augmented in vivo DLS neuronal activity as correct learned choices were made. These findings support a model in which chronic ethanol causes DLS neuroadaptations that prime for greater striatal control over behavior, potentially contributing to the progression of alcoholism.
Glycosylated linkers in multimodular lignocellulose-degrading enzymes dynamically bind to cellulose
Authors: Payne Christina M. , Resch Michael G. , Chen Liqun , Crowley Michael F. , Himmel Michael E. , Taylor Larry E. , Sandgren Mats , Ståhlberg Jerry , Stals Ingeborg , Tan Zhongping , Beckham Gregg T.
Published: August 2013

Plant cell-wall polysaccharides represent a vast source of food in nature. To depolymerize polysaccharides to soluble sugars, many organisms use multifunctional enzyme mixtures consisting of glycoside hydrolases, lytic polysaccharide mono-oxygenases, polysaccharide lyases, and carbohydrate esterases, as well as accessory, redox-active enzymes for lignin depolymerization. Many of these enzymes that degrade lignocellulose are multimodular with carbohydrate-binding modules (CBMs) and catalytic domains connected by flexible, glycosylated linkers. These linkers have long been thought to simply serve as a tether between structured domains or to act in an inchworm-like fashion during catalytic action. To examine linker function, we performed molecular dynamics (MD) simulations of the
Trichoderma reesei
Family 6 and Family 7 cellobiohydrolases (
Tr
Cel6A and
Tr
Cel7A, respectively) bound to cellulose. During these simulations, the glycosylated linkers bind directly to cellulose, suggesting a previously unknown role in enzyme action. The prediction from the MD simulations was examined experimentally by measuring the binding affinity of the Cel7A CBM and the natively glycosylated Cel7A CBM-linker. On crystalline cellulose, the glycosylated linker enhances the binding affinity over the CBM alone by an order of magnitude. The MD simulations before and after binding of the linker also suggest that the bound linker may affect enzyme action due to significant damping in the enzyme fluctuations. Together, these results suggest that glycosylated linkers in carbohydrate-active enzymes, which are intrinsically disordered proteins in solution, aid in dynamic binding during the enzymatic deconstruction of plant cell walls.
Pulsed hydrogen–deuterium exchange mass spectrometry probes conformational changes in amyloid beta (Aβ) peptide aggregation
Authors: Zhang Ying , Rempel Don L. , Zhang Jun , Sharma Anuj K. , Mirica Liviu M. , Gross Michael L.
Published: August 2013

Probing the conformational changes of amyloid beta (Aβ) peptide aggregation is challenging owing to the vast heterogeneity of the resulting soluble aggregates. To investigate the formation of these aggregates in solution, we designed an MS-based biophysical approach and applied it to the formation of soluble aggregates of the Aβ
42
peptide, the proposed causative agent in Alzheimer’s disease. The approach incorporates pulsed hydrogen–deuterium exchange coupled with MS analysis. The combined approach provides evidence for a self-catalyzed aggregation with a lag phase, as observed previously by fluorescence methods. Unlike those approaches, pulsed hydrogen–deuterium exchange does not require modified Aβ
42
(e.g., labeling with a fluorophore). Furthermore, the approach reveals that the center region of Aβ
42
is first to aggregate, followed by the C and N termini. We also found that the lag phase in the aggregation of soluble species is affected by temperature and Cu
2+
ions. This MS approach has sufficient structural resolution to allow interrogation of Aβ aggregation in physiologically relevant environments. This platform should be generally useful for investigating the aggregation of other amyloid-forming proteins and neurotoxic soluble peptide aggregates.
Insights into Eph receptor tyrosine kinase activation from crystal structures of the EphA4 ectodomain and its complex with ephrin-A5
Authors: Xu Kai , Tzvetkova-Robev Dorothea , Xu Yan , Goldgur Yehuda , Chan Yee-Peng , Himanen Juha P. , Nikolov Dimitar B.
Published: August 2013

Significance

Our paper describes the high-resolution structures of the complete EphA4 receptor tyrosine kinase ectodomain and its complex with ephrin-A5. These structures reveal for the first time how ephrin binding promotes Eph conformational changes allowing for the formation of ordered signaling clusters at the sites of cell–cell contact. In addition, the structural data, combined with structure-based mutagenesis and cell-based assays, reveal a previously undescribed receptor–receptor interaction between the EphA4 ligand-binding and membrane-proximal fibronectin domains, which is functionally important for efficient Eph activation. Based on the data we suggest a mechanism for Eph preclustering and recruitment of unliganded Eph into existing Eph/ephrin signaling clusters.
Nationalization campaigns and teachers’ practices in Belgian–German and Polish–German border regions (1945–1956)
Authors: Venken Machteld
Published: August 2013

This contribution looks into nationalization and education in European borderlands in the early post-World War II period. Belonging to Belgium and Poland, respectively, in the interwar years, the Eupen–St. Vith–Malmedy and the East-Upper Silesia regions came under German rule during World War II. Returned to the Belgian and Polish nation-states once the war was over, the regions experienced a pronounced upheaval in the population profile as a result of population transfers and reorientations in education curricula. The aim of these measures was to guarantee the national reliability of borderland inhabitants, with a special role being designated for teachers, who were perceived as crucial in the raising of children as national citizens imbued with certain core values. This contribution compares the methods employed by the authorities in selecting educational personnel for their borderlands, the nationalizing role teachers were to play and the way teachers gave meaning to their professional practices.
Reproductive Biology of the Cuban Dogfish in the Northern Gulf of Mexico
Authors: Jones Lisa M. , Driggers William B. , Hoffmayer Eric R. , Hannan Kristin M. , Mathers Alyssa N.
Published: August 2013

Within the northern Gulf of Mexico, the Cuban Dogfish Squalus cubensis is the most frequently encountered squalid in continental shelf and slope waters. Despite the relatively high abundance of Cuban Dogfish in the region, there is a dearth of information regarding even the most basic aspects of the species’ biology. Furthermore, what has been reported is conflicting and of questionable utility. From 2005 to 2012, 139 male and 252 female Cuban Dogfish were collected opportunistically. The analyses indicated that male Cuban Dogfish reach 50% maturity at 379 mm stretch total length (STL) and are capable of reproducing throughout the year. Females reach 50% maturity at 466 mm STL and 50% maternity at 478 mm STL. Brood size ranges from one to four, and vitellogenesis and gestation are concurrent. Although samples were not collected during all months of the year, the presence of ova in the blastodisc stage of development during the summer and fall, coupled with the relatively high variability of embryo size within fall months, suggest that Cuban Dogfish reproduce asynchronously.

Received October 29, 2012; accepted January 9, 2013
Invariance entropy for topological semigroup actions
Authors: Colonius Fritz , Fukuoka Ryuichi , Santana Alexandre
Published: August 2013

Invariance entropy for the action of topological semigroups acting on metric spaces is introduced. It is shown that invariance entropy is invariant under conjugations and a lower bound and upper bounds of invariance entropy are obtained. The special case of control systems is discussed.
HippDB: a database of readily targeted helical protein–protein interactions
Authors: Bergey Christina M. , Watkins Andrew M. , Arora Paramjit S.
Published: August 2013

Summary: HippDB catalogs every protein–protein interaction whose structure is available in the Protein Data Bank and which exhibits one or more helices at the interface. The Web site accepts queries on variables such as helix length and sequence, and it provides computational alanine scanning and change in solvent-accessible surface area values for every interfacial residue. HippDB is intended to serve as a starting point for structure-based small molecule and peptidomimetic drug development.

Availability and implementation: HippDB is freely available on the web at http://www.nyu.edu/projects/arora/hippdb. The Web site is implemented in PHP, MySQL and Apache. Source code freely available for download at http://code.google.com/p/helidb, implemented in Perl and supported on Linux.

Contact: arora@nyu.edu
A fast Peptide Match service for UniProt Knowledgebase
Authors: Chen Chuming , Li Zhiwen , Huang Hongzhan , Suzek Baris E. , Wu Cathy H. ,   UniProt Consortium
Published: August 2013

Summary: We have developed a new web application for peptide matching using Apache Lucene-based search engine. The Peptide Match service is designed to quickly retrieve all occurrences of a given query peptide from UniProt Knowledgebase (UniProtKB) with isoforms. The matched proteins are shown in summary tables with rich annotations, including matched sequence region(s) and links to corresponding proteins in a number of proteomic/peptide spectral databases. The results are grouped by taxonomy and can be browsed by organism, taxonomic group or taxonomy tree. The service supports queries where isobaric leucine and isoleucine are treated equivalent, and an option for searching UniRef100 representative sequences, as well as dynamic queries to major proteomic databases. In addition to the web interface, we also provide RESTful web services. The underlying data are updated every 4 weeks in accordance with the UniProt releases.

Availability:  http://proteininformationresource.org/peptide.shtml

Contact:  chenc@udel.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Influence of Bran Particle Size on Bread‐Baking Quality of Whole Grain Wheat Flour and Starch Retrogradation
Authors: Cai Liming , Choi Induck , Hyun Jong‐Nae , Jeong Young‐Keun , Baik Byung‐Kee
Published: August 2013

The influence of bran particle size on bread‐baking quality of whole grain wheat flour (WWF) and starch retrogradation was studied. Higher water absorption of dough prepared from WWF with added gluten to attain 18% protein was observed for WWFs of fine bran than those of coarse bran, whereas no significant difference in dough mixing time was detected for WWFs of varying bran particle size. The effects of bran particle size on loaf volume of WWF bread and crumb firmness during storage were more evident in hard white wheat than in hard red wheat. A greater degree of starch retrogradation in bread crumb stored for seven days at 4°C was observed in WWFs of fine bran than those of coarse bran. The gels prepared from starch–fine bran blends were harder than those prepared from starch–unground bran blends when stored for one and seven days at 4°C. Furthermore, a greater degree of starch retrogradation was observed in gelatinized starch containing fine bran than that containing unground bran after storage for seven days at 4°C. It is probable that finely ground bran takes away more water from gelatinized starch than coarsely ground bran, increasing the extent of starch retrogradation in bread and gels during storage.
Stochastic description of delayed systems
Authors: Lafuerza L. F. , Toral R.
Published: August 2013

We study general stochastic birth and death processes including delay. We develop several approaches for the analytical treatment of these non-Markovian systems, valid, not only for constant delays, but also for stochastic delays with arbitrary probability distributions. The interplay between stochasticity and delay and, in particular, the effects of delay in the fluctuations and time correlations are discussed.
Chaos in networks with time-delayed couplings
Authors: Kinzel Wolfgang
Published: August 2013

Networks of nonlinear units coupled by time-delayed signals can show chaos. In the limit of long delay times, chaos appears in two ways: strong and weak, depending on how the maximal Lyapunov exponent scales with the delay time. Only for weak chaos, a network can synchronize completely, without time shift. The conditions for strong and weak chaos and synchronization in networks with multiple delay times are investigated.
Delayed feedback control in quantum transport
Authors: Emary Clive
Published: August 2013

Feedback control in quantum transport has been predicted to give rise to several interesting effects, among them quantum state stabilization and the realization of a mesoscopic Maxwell's daemon. These results were derived under the assumption that control operations on the system are affected instantaneously after the measurement of electronic jumps through it. In this contribution, I describe how to include a delay between detection and control operation in the master equation theory of feedback-controlled quantum transport. I investigate the consequences of delay for the state stabilization and Maxwell's daemon schemes. Furthermore, I describe how delay can be used as a tool to probe coherent oscillations of electrons within a transport system and how this formalism can be used to model finite detector bandwidth.
The dynamics of genetic control in the cell: the good and bad of being late
Authors: Tiana G. , Jensen M. H.
Published: August 2013

The expression of genes in the cell is controlled by a complex interaction network involving proteins, RNA and DNA. The molecular events associated with the nodes of such a network take place on a variety of time scales, and thus cannot be regarded as instantaneous. In many cases, the cell is robust with respect to the delay in gene expression control, behaving as if it were instantaneous. However, there are specific cases in which delay gives rise to temporal oscillations. This is the case, for example, of the expression of tumour-suppressor protein p53, of protein Hes1, involved in the differentiation of stem cells, of NFkB and Wnt, in which case delay arises implicitly from the structure of the associated network. By means of delay rate equations, we study the kinetics of small regulatory networks, emphasizing the role of delay in an evolutionary context. These models suggest that oscillations are a typical outcome of the dynamics of regulatory networks, and evolution has to work to avoid them when not required (and not vice versa).
Epigenomic enhancer annotation reveals a key role for NFIX in neural stem cell quiescence
Authors: Martynoga Ben , Mateo Juan L. , Zhou Bo , Andersen Jimena , Achimastou Angeliki , Urbán Noelia , van den Berg Debbie , Georgopoulou Dimitra , Hadjur Suzana , Wittbrodt Joachim , Ettwiller Laurence , Piper Michael , Gronostajski Richard M. , Guillemot François
Published: August 2013

The majority of neural stem cells (NSCs) in the adult brain are quiescent, and this fraction increases with aging. Although signaling pathways that promote NSC quiescence have been identified, the transcriptional mechanisms involved are mostly unknown, largely due to lack of a cell culture model. In this study, we first demonstrate that NSC cultures (NS cells) exposed to BMP4 acquire cellular and transcriptional characteristics of quiescent cells. We then use epigenomic profiling to identify enhancers associated with the quiescent NS cell state. Motif enrichment analysis of these enhancers predicts a major role for the nuclear factor one (NFI) family in the gene regulatory network controlling NS cell quiescence. Interestingly, we found that the family member NFIX is robustly induced when NS cells enter quiescence. Using genome-wide location analysis and overexpression and silencing experiments, we demonstrate that NFIX has a major role in the induction of quiescence in cultured NSCs. Transcript profiling of NS cells overexpressing or silenced for Nfix and the phenotypic analysis of the hippocampus of Nfix mutant mice suggest that NFIX controls the quiescent state by regulating the interactions of NSCs with their microenvironment.
Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence
Authors: Sadaie Mahito , Salama Rafik , Carroll Thomas , Tomimatsu Kosuke , Chandra Tamir , Young Andrew R.J. , Narita Masako , Pérez-Mancera Pedro A. , Bennett Dorothy C. , Chong Heung , Kimura Hiroshi , Narita Masashi
Published: August 2013

Senescence is a stress-responsive form of stable cell cycle exit. Senescent cells have a distinct gene expression profile, which is often accompanied by the spatial redistribution of heterochromatin into senescence-associated heterochromatic foci (SAHFs). Studying a key component of the nuclear lamina lamin B1 (LMNB1), we report dynamic alterations in its genomic profile and their implications for SAHF formation and gene regulation during senescence. Genome-wide mapping reveals that LMNB1 is depleted during senescence, preferentially from the central regions of lamina-associated domains (LADs), which are enriched for Lys9 trimethylation on histone H3 (H3K9me3). LMNB1 knockdown facilitates the spatial relocalization of perinuclear H3K9me3-positive heterochromatin, thus promoting SAHF formation, which could be inhibited by ectopic LMNB1 expression. Furthermore, despite the global reduction in LMNB1 protein levels, LMNB1 binding increases during senescence in a small subset of gene-rich regions where H3K27me3 also increases and gene expression becomes repressed. These results suggest that LMNB1 may contribute to senescence in at least two ways due to its uneven genome-wide redistribution: first, through the spatial reorganization of chromatin and, second, through gene repression.
A novel pentacoordinated cadmium compound:catena-poly[benzyltriethylammonium [[chloridocadmate(II)]-di-μ-chlorido]]
Authors: Sun Su-Wen , Jin Lei
Published: August 2013

The structure of the title one-dimensionalABX3-type organic–inorganic hybrid complex, {(C13H22N)[CdCl3]}n, consists of benzyltriethylammonium cations and one-dimensional anionic {[CdCl3]−}nchains, in which the CdIIcentres are in an unusual two-layer five-coordinated arrangement. The CdIIatom is pentacoordinated by four bridging and one terminal chloride ligand, forming a slightly distorted trigonal bipyramidal ClCd(μ-Cl)4arrangement. The trigonal bipyramid is linked by two opposite shared faces, giving rise to a zigzag linear anionic {[CdCl3]−}nchain. The benzyltriethylammonium cations are located in the inter-space of the inorganic network. There are C—H...Cl hydrogen bonds present and these play a crucial role in linking the organic cations and inorganic layers, and also help assemble the components into a three-dimensional network.
Human capital disclosures in developing countries: figureheads and value creators
Authors: Choo Huang Ching , Luther Robert , Tayles Michael , Haniffa Roszaini
Published: August 2013

Purpose

– The purpose of this paper is to explore if any disparity exists between human capital information desired by financial analysts and fund managers and actual disclosure of such information in company annual reports, in the context of developing countries.

Design/methodology/approach

– Financial analysts and fund managers were interviewed to obtain opinions on the importance attributed to human capital information and whether their desired information is disclosed in the annual reports. Content analysis was then used to assess the extent and nature of human capital information actually provided in the annual reports of 100 listed companies in Malaysia.

Findings

– Interviewees seek information on company management and key corporate decision makers who could provide a firm with competitive advantage. However, the human capital information provided is limited, and tends to focus on directors, many of whom may be figureheads with little impact on the way companies are run and in creating value for the firm. Accordingly, analysts rely on alternative sources to get their desired information – a costly process for private shareholders.

Originality/value

– The paper contributes to the literature on the demand for, and disclosure of, human capital information in the context of developing countries. It identifies the inadequacy of current human capital disclosure practices in company annual reports. The authors theorise that in developing countries, resource dependence, legitimacy-seeking and “culture” cause companies to pay relatively more attention to figureheads than value creators.
Corrosion behaviour of Mn‐Si‐Fe‐Cu‐Al alloy explosion suppression materials
Authors: Jing Yan , Zhang Chao , Ma Jun , Jia Yongzhong
Published: August 2013

Purpose

The purpose of this paper is to prepare the Mn‐Si‐Fe‐Cu‐Al alloy explosion suppression materials, and determine the corrosion behavior of aluminum alloy explosion suppression materials in HCl and NaOH solutions. The different mechanism of corrosion was discussed.

Design/methodology/approach

In this paper, Mn‐Si‐Fe‐Cu‐Al alloy explosion suppression materials were prepared, and the electrochemical behavior of the EAESM was studied. The corrosion parameters were calculated and the mechanism of the corrosion process was discussed. The corrosion behavior was characterized by immersion tests and SEM at room temperature.

Findings

Mn‐Si‐Fe‐Cu‐Al alloy explosion suppression materials have been prepared. SEM, the polarization curves showed that materials have corrosion resistance. The best content of Al alloy is Mn 0.880%, Si 0.135%, Fe 0.383% and Cu 0.0835%.

Originality/value

The results of this investigation show that adding alloying elements can form new strengthening phases that influence the corrosion resistance of alloys.
Research into sulfide resistant polymer latex cement for sour well applications
Authors: Ren Chengqiang , He Yi , Zeng Dezhi , Shi Taihe
Published: August 2013

Purpose

The long‐term durability of cement becomes an important challenge in oil and gas wells due to the aggressive acid gas. H2S has been found in more and more wells. The purpose of this research was to add polymer latex to the Class G cement in order to promote the H2S corrosion resistance of oilwell cement.

Design/methodology/approach

The water loss and thickening time of cement slurry and compressive strength and gas permeability of bond cement were investigated to determine the cement formulation. The corrosion resistance of the polymer cement was compared to base Class G cement in solution with 1.8 MPa H2S at 120°C.

Findings

The optimum concentration of polystyrene latex was determined as 5 percent. The permeability change, compressive strength loss and corrosion ratio of latex cement were all lower than for the base Class G cement. The electrochemical impedance spectroscopy results and microstructure details confirmed that the latex cement had stronger resistance to the aggressive medium. Thus, latex cement had excellent corrosion resistance to H2S.

Originality/value

The findings of this study can further improve the sulfide resistance of Class G cement. Two roles of the polystyrene latex were observed in the cement, including interstitial in‐filling of the pore structure and packing around hydration products, which are proposed to properly explain the results.
Optimization of the aircraft general overhaul process
Authors: Rašuo Boško , Đuknić Gradimir
Published: August 2013

Purpose

The purpose of this paper is to present the development results of the overhaul melioration plan for the following aircraft types: MiG‐21Bis, G‐4 Galeb and SA‐341 helicopter. This research has been conducted based on available knowledge and extensive experience gained by performing general maintenance of the Air Force of Serbia aircraft.

Design/methodology/approach

A general analysis was performed by processing data collected while performing maintenance and repair procedures. The magnitude of data is based on detecting the delays and errors that occurred while going through the operational and inter‐operational stages of aircraft overhaul. On the basis of the obtained research results, a proposal for the aircraft overhaul optimization is offered.

Findings

The proposed overhaul improvement plan points out the priority steps to be taken in order to optimize the most critical features that jeopardize the quality of the aircraft overhaul process relating to organization, technology and design. Moreover, existing technical logistics have been used for providing actions to achieve the objective in focus: the all‐encompassing optimization of the above selected aircraft overhaul.

Research limitations/implications

The method of the overhaul optimization has so far been applicable to the aircraft of the Army of Serbia. However, the particular methodology can be proved potentially useful and highly germane when applying to other aircraft types.

Originality/value

A plan to optimize the overhaul is based on a one‐year monitoring process of the aforementioned aircraft. It enables significant savings in performing overhauls within the financial realm as well as time‐wise.
Reusable boosted vehicle attitude controller design
Authors: Xu Jiangtao , Qi Hui , Chen Weidong , Wu Xiande
Published: August 2013

Purpose

The purpose of this paper is to develop an attitude control strategy for the reusable boosted vehicle with large angle of attack, and to remove the cross coupling among roll, pitch and yaw channels.

Design/methodology/approach

The coordinated gain scheduling control strategy consists mainly of two parts. First, initially ignoring dynamic coupling, single channel gain scheduling controller is designed based on linearized models, respectively. Second, with respect to main channel gain scheduling controller, coordinated scheduling controller is used to generate intentionally cross coupling to partly cancel inter‐channel cross coupling of reusable boosted vehicle.

Findings

A coordinated gain scheduling control strategy is presented, and no such analytical solution can be found for the reusable boosted vehicle.

Practical implications

The design idea of coordinated gain scheduling strategy is straightforward in physical concepts and has great value for engineering applications.

Originality/value

Coordinated gain scheduling control strategy is novel in that single channel gain scheduling design does not involve small perturbation linearization and coordinated channel is scheduled.
Optimization of flatback airfoils for wind turbine blades
Authors: Chen Xiaomin , Agarwal Ramesh
Published: August 2013

Purpose

In recent years, the airfoil sections with blunt trailing edge (called flatback airfoils) have been proposed for the inboard regions of large wind‐turbine blades because they provide several structural and aerodynamic performance advantages. The purpose of this paper is to optimize the shape of these airfoils for optimal performance using a multi‐objective genetic algorithm.

Design/methodology/approach

A multi‐objective genetic algorithm is employed for shape optimization of flatback airfoils to achieve two objectives, namely the generation of maximum lift as well as the maximum lift to drag ratio. The commercially available software FLUENT is employed for calculation of the flow field using the Reynolds‐Averaged Navier‐Stokes (RANS) equations in conjunction with a two‐equation Shear Stress Transport (SST) turbulence model and a three‐equation k‐kl‐ω turbulence model.

Findings

It is shown that the multi‐objective genetic algorithm based optimization can generate superior flatback airfoils compared to those obtained by using a single objective genetic algorithm.

Research limitations/implications

The method of employing genetic algorithms for shape optimization of flatback airfoils could be considered as an excellent example for the optimization of other types of wind turbine blades such as DU FX and S series airfoils.

Originality/value

This paper is the first to employ the multi‐objective genetic algorithm for shape optimization of flatback airfoils for wind‐turbine blades to achieve superior performance.
Turbofan multiobjective‐multipoint optimization for UAV/UCAV applications
Authors: Benini Ernesto , Chiereghin Nicola
Published: August 2013

Purpose

The purpose of this paper is to present a multi‐objective and multi‐point optimization method to support the preliminary design of an unmixed turbofan mounted on a sample UAV/UCAV aircraft.

Design/methodology/approach

An in‐house multi‐objective evolutionary algorithm, a flight simulator and a validated engine simulator are implemented and joined together using object‐oriented programming.

Findings

Optimal values are found of the pressure ratio and corrected mass flow of both the engine fan and compressor as they operate in on/off design conditions (multipoint approach), as well as the engine by‐pass ratio, that contextually minimize time and engine fuel consumption required to cover a fixed trajectory (mission profile). Furthermore, the optimal distribution of the thermodynamic quantities along the trajectory is determined.

Research limitations/implications

The research deals with a preliminary design of an engine, therefore no detailed engine geometry can be found.

Practical implications

The paper shows how a multiobjective and multipoint approach to the design of an engine can affect the choice of the engine architecture. In particular, major practical implications regard how the mission profile can affect the choice of the design point: in fact, there is no longer a definitive design point but the design of a UAV/UCAV should be addressed as a function of the mission profile.

Originality/value

The paper presents a multiobjective and multipoint approach to engine optimization as a function of the mission profile.