bluuebunny/crossref_metadata_2025 huggingface dataset:
Synchronization of a renewable energy inverter with the grid
Authors: Anani Nader , Al-Kharji AlAli Omar , Al-Qutayri Mahmoud , AL-Araji Saleh
Published: July 2012

The design, mathematical analysis, and testing results of the architecture of a new all-digital phase-locked loop system for synchronizing a voltage source DC-AC single-phase inverter with the low voltage utility grid are presented. The system which is based on the time-delay digital tanlock loop was simulated using matlab/simulink and was tested by subjecting the grid voltage to various perturbations similar to those which can occur in a real power system, such as voltage sags and nonlinear distortion of the grid voltage waveform. Results indicate that even in the presence of such perturbations the system achieved and/or re-gained synchronization within 100 ms. The proposed system is all-digital and can be readily implemented using a field programmable gate array and easily embedded into a power inverter.
Enhanced magnetoelectric effect in self-stressed multi-push-pull mode Metglas/Pb(Zr,Ti)O3/Metglas laminates
Authors: Li Menghui , Wang Yaojin , Gao Junqi , Li Jiefang , Viehland D.
Published: July 2012

Two methods to effectively induce self-stress on Metglas/Pb(Zr,Ti)O3/Metglas laminate are presented: (i) applying a dc magnetic field to the Metglas layers or (ii) applying a dc electric field to the core piezoelectric composites. An optimum self-stress enhances the magnetoelectric (ME) effect in the laminates. With a 20 Oe dc magnetic bias, the value of αME for the self-stressed laminate was enhanced to 31.4 V/cm · Oe, which was by a factor of 1.24× compared to the laminate without self-stress. Furthermore, the equivalent magnetic noise floor was reduced by the self-stress at low frequencies.
Silver nanoclusters decked diamond thin film as a substrate for surface-enhanced Raman scattering
Authors: Ojha Harish , Gangadharani Upender , Ravulapalli Satyavathi , Kuntumalla Mohan Kumar , Srikanth Vadali Venkata Satya Siva , Desai Narayana Rao , Bansal Chandrahas
Published: July 2012

Modified diamondthin filmsurfaces are proven candidates for bio-sensoric applications. A typical polycrystalline diamond thin film surface decked with silver (Ag) nanoclusters is found to be suitable for surface-enhanced Raman scattering (SERS). Simple and time effective procedures are used to fabricate Ag nanoclusters/diamond/silicon structure. Standard Rhodamine 6G probe molecules are used to access the SERS activity of the test surface. The observed SERS activity is explained in terms of predominant electromagnetic enhancement mechanism. This work is expected to benefit SERS based bio-sensing with diamond as the core sensing material.
Inelastic electron and light scattering from the elementary electronic excitations in quantum wells: Zero magnetic field
Authors: Kushwaha Manvir S.
Published: July 2012

The most fundamental approach to an understanding of electronic, optical, and transport phenomena which the condensed matter physics (of conventional as well as nonconventional systems) offers is generally founded on two experiments: the inelastic electron scattering and the inelastic light scattering. This work embarks on providing a systematic framework for the theory of inelastic electron scattering and of inelastic light scattering from the electronic excitations in GaAs/Ga1−xAlxAs quantum wells. To this end, we start with the Kubo's correlation function to derive the generalized nonlocal, dynamic dielectric function, and the inverse dielectric function within the framework of Bohm-Pines’ random-phase approximation. This is followed by a thorough development of the theory of inelastic electron scattering and of inelastic light scattering. The methodological part is then subjected to the analytical diagnoses which allow us to sense the subtlety of the analytical results and the importance of their applications. The general analytical results, which know no bounds regarding, e.g., the subband occupancy, are then specified so as to make them applicable to practicality. After trying and testing the eigenfunctions, we compute the density of states, the Fermi energy, the full excitation spectrum made up of intrasubband and intersubband – single-particle and collective (plasmon) – excitations, the loss functions for all the principal geometries envisioned for the inelastic electron scattering, and the Raman intensity, which provides a measure of the real transitions induced by the (laser) probe, for the inelastic light scattering. It is found that the dominant contribution to both the loss peaks and the Raman peaks comes from the collective (plasmon) excitations. As to the single-particle peaks, the analysis indicates a long-lasting lack of quantitative comparison between theory and experiments. It is inferred that the inelastic electron scattering can be a potential alternative of the inelastic light scattering for investigating elementary electronic excitations in quantum wells.
Spontaneous symmetry breaking in active droplets provides a generic route to motility
Authors: Tjhung Elsen , Marenduzzo Davide , Cates Michael E.
Published: July 2012

We explore a generic mechanism whereby a droplet of active matter acquires motility by the spontaneous breakdown of a discrete symmetry. The model we study offers a simple representation of a “cell extract” comprising, e.g., a droplet of actomyosin solution. (Such extracts are used experimentally to model the cytoskeleton). Actomyosin is an active gel whose polarity describes the mean sense of alignment of actin fibres. In the absence of polymerization and depolymerization processes (‘treadmilling’), the gel’s dynamics arises solely from the contractile motion of myosin motors; this should be unchanged when polarity is inverted. Our results suggest that motility can arise in the absence of treadmilling, by spontaneous symmetry breaking (SSB) of polarity inversion symmetry. Adapting our model to wall-bound cells in two dimensions, we find that as wall friction is reduced, treadmilling-induced motility falls but SSB-mediated motility rises. The latter might therefore be crucial in three dimensions where frictional forces are likely to be modest. At a supracellular level, the same generic mechanism can impart motility to aggregates of nonmotile but active bacteria; we show that SSB in this (extensile) case leads generically to rotational as well as translational motion.
Fibrillation precursor of superoxide dismutase 1 revealed by gradual tuning of the protein-folding equilibrium
Authors: Lang Lisa , Kurnik Martin , Danielsson Jens , Oliveberg Mikael
Published: July 2012

Although superoxide dismutase 1 (SOD1) stands out as a relatively soluble protein in vitro, it can be made to fibrillate by mechanical agitation. The mechanism of this fibrillation process is yet poorly understood, but attains considerable interest due to SOD1’s involvement in the neurodegenerative disease amyotrophic lateral sclerosis (ALS). In this study, we map out the apoSOD1 fibrillation process from how it competes with the global folding events at increasing concentrations of urea: We determine how the fibrillation lag time (τ
lag
) and maximum growth rate (ν
max
) depend on gradual titration of the folding equilibrium, from the native to the unfolded state. The results show that the agitation-induced fibrillation of apoSOD1 uses globally unfolded precursors and relies on fragmentation-assisted growth. Mutational screening and fibrillation
m
-values (∂ log τ
lag
/∂[urea] and ∂ log ν
max
/∂[urea]) indicate moreover that the fibrillation pathway proceeds via a diffusely bound transient complex that responds to the global physiochemical properties of the SOD1 sequence. Fibrillation of apoSOD1, as it bifurcates from the denatured ensemble, seems thus mechanistically analogous to that of disordered peptides, save the competing folding transition to the native state. Finally, we examine by comparison with in vivo data to what extent this mode of fibrillation, originating from selective amplification of mechanically brittle aggregates by sample agitation, captures the mechanism of pathological SOD1 aggregation in ALS.
A public resource facilitating clinical use of genomes
Authors: Ball Madeleine P. , Thakuria Joseph V. , Zaranek Alexander Wait , Clegg Tom , Rosenbaum Abraham M. , Wu Xiaodi , Angrist Misha , Bhak Jong , Bobe Jason , Callow Matthew J. , Cano Carlos , Chou Michael F. , Chung Wendy K. , Douglas Shawn M. , Estep Preston W. , Gore Athurva , Hulick Peter , Labarga Alberto , Lee Je-Hyuk , Lunshof Jeantine E. , Kim Byung Chul , Kim Jong-Il , Li Zhe , Murray Michael F. , Nilsen Geoffrey B. , Peters Brock A. , Raman Anugraha M. , Rienhoff Hugh Y. , Robasky Kimberly , Wheeler Matthew T. , Vandewege Ward , Vorhaus Daniel B. , Yang Joyce L. , Yang Luhan , Aach John , Ashley Euan A. , Drmanac Radoje , Kim Seong-Jin , Li Jin Billy , Peshkin Leonid , Seidman Christine E. , Seo Jeong-Sun , Zhang Kun , Rehm Heidi L. , Church George M.
Published: July 2012

Rapid advances in DNA sequencing promise to enable new diagnostics and individualized therapies. Achieving personalized medicine, however, will require extensive research on highly reidentifiable, integrated datasets of genomic and health information. To assist with this, participants in the Personal Genome Project choose to forgo privacy via our institutional review board- approved “open consent” process. The contribution of public data and samples facilitates both scientific discovery and standardization of methods. We present our findings after enrollment of more than 1,800 participants, including whole-genome sequencing of 10 pilot participant genomes (the PGP-10). We introduce the Genome-Environment-Trait Evidence (GET-Evidence) system. This tool automatically processes genomes and prioritizes both published and novel variants for interpretation. In the process of reviewing the presumed healthy PGP-10 genomes, we find numerous literature references implying serious disease. Although it is sometimes impossible to rule out a late-onset effect, stringent evidence requirements can address the high rate of incidental findings. To that end we develop a peer production system for recording and organizing variant evaluations according to standard evidence guidelines, creating a public forum for reaching consensus on interpretation of clinically relevant variants. Genome analysis becomes a two-step process: using a prioritized list to record variant evaluations, then automatically sorting reviewed variants using these annotations. Genome data, health and trait information, participant samples, and variant interpretations are all shared in the public domain—we invite others to review our results using our participant samples and contribute to our interpretations. We offer our public resource and methods to further personalized medical research.
Regulatory element copy number differences shape primate expression profiles
Authors: Iskow Rebecca C. , Gokcumen Omer , Abyzov Alexej , Malukiewicz Joanna , Zhu Qihui , Sukumar Ann T. , Pai Athma A. , Mills Ryan E. , Habegger Lukas , Cusanovich Darren A. , Rubel Meagan A. , Perry George H. , Gerstein Mark , Stone Anne C. , Gilad Yoav , Lee Charles
Published: July 2012

Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across three primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs that were processed pseudogenes and some of which were expressed. Furthermore, there were copy number-different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA.
Mechanical elasticity as a physical signature of conformational dynamics in a virus particle
Authors: Castellanos Milagros , Pérez Rebeca , Carrasco Carolina , Hernando-Pérez Mercedes , Gómez-Herrero Julio , de Pablo Pedro J. , Mateu Mauricio G.
Published: July 2012

In this study we test the hypothesis that mechanically elastic regions in a virus particle (or large biomolecular complex) must coincide with conformationally dynamic regions, because both properties are intrinsically correlated. Hypothesis-derived predictions were subjected to verification by using 19 variants of the minute virus of mice capsid. The structural modifications in these variants reduced, preserved, or restored the conformational dynamism of regions surrounding capsid pores that are involved in molecular translocation events required for virus infectivity. The mechanical elasticity of the modified capsids was analyzed by atomic force microscopy, and the results corroborated every prediction tested: Any mutation (or chemical cross-linking) that impaired a conformational rearrangement of the pore regions increased their mechanical stiffness. On the contrary, any mutation that preserved the dynamics of the pore regions also preserved their elasticity. Moreover, any pseudo-reversion that restored the dynamics of the pore regions (lost through previous mutation) also restored their elasticity. Finally, no correlation was observed between dynamics of the pore regions and mechanical elasticity of other capsid regions. This study (
i
) corroborates the hypothesis that local mechanical elasticity and conformational dynamics in a viral particle are intrinsically correlated; (
ii
) proposes that determination by atomic force microscopy of local mechanical elasticity, combined with mutational analysis, may be used to identify and study conformationally dynamic regions in virus particles and large biomolecular complexes; (
iii
) supports a connection between mechanical properties and biological function in a virus; (
iv
) shows that viral capsids can be greatly stiffened by protein engineering for nanotechnological applications.
Modelling invasion probability of giant hogweed (
Heracleum mantegazzianum
) with logistic GLMM.
Authors: Thiele J. , Markussen B.
Published: July 2012

In this worked example of the application of
generalized linear mixed models
, we model the invasion probability of an invasive plant species, giant hogweed (
Heracleum mantegazzianum
), based on field surveys of 20 study areas of 1 km2 which were situated in areas of Germany most invaded by this species This forms Supplement B to Thiele J, Markussen B. Potential of GLMM in modelling invasive spread.
Age and Population Size Estimates of Overwintering Shortnose Sturgeon in the Saint John River, New Brunswick, Canada
Authors: Usvyatsov Sima , Watmough James , Litvak Matthew K.
Published: July 2012

The densities and overall abundances of overwintering shortnose sturgeon Acipenser brevirostrum were estimated using underwater video at the Kennebecasis River overwintering site in 2009 and 2011. In 2009, underwater cameras coupled with lasers provided image‐based estimates of fish lengths (and therefore ages). The precision and accuracy of laser‐based measurements were estimated by laboratory experiments. In total, 362 and 222 overwintering shortnose sturgeon were counted in the 0.02‐km2 area during 2009 and 2011, respectively. The fork lengths of 83 overwintering shortnose sturgeon measured in 2009 ranged from 54 to 119 cm, corresponding to ages of 11–57 years (20.3 ± 7.9 years [mean ± SD]). Length measurement accuracy was highest (±10% fork length) when fish were positioned at 0 ± 30° or 180 ± 30° to the camera's lens. Three different models of spatial fish density estimated a total of 3,852–5,222 shortnose sturgeon in 2009 and 2011, similar to the 2005 local population estimate of 4,836 shortnose sturgeon. The consistent, high‐density aggregation of subadults and adults at this small site between 2005 and 2011 suggests that the site is important for protection of shortnose sturgeon in the Saint John River system.
The Use of Fluorescent Randomly Amplified Polymorphic DNA Markers to Identify Hybrids: A Case Study Evaluating the Origins of Saugeye following the Cessation of Stocking in an Ohio Reservoir
Authors: Sovic Michael G. , Denlinger Jonathan C. , Fuerst Paul A.
Published: July 2012

Hybridization and introgression continue to gain recognition as important issues in the management and conservation of native fishes. It is often necessary to identify hybrids in natural populations and to distinguish among individuals of various hybrid categories. Molecular methods are important for these purposes, and it is valuable if researchers have a range of molecular methods to apply, since each method has unique advantages and disadvantages. The determination of the best class of marker for a particular study depends on various factors, including the goals of the study, the resolution required, and the genomic and marker information already available for the taxa of interest. We modified a protocol to generate fluorescent randomly amplified polymorphic DNA (FRAPD) markers for hybridization studies. To our knowledge, this type of marker has not previously been used for hybrid identification. To demonstrate the utility of the modified methods, FRAPD markers were used to evaluate potential reproduction by saugeye (female walleye Sander vitreus × male sauger Sander canadensis) in a central Ohio reservoir. Our approach successfully generated a battery of diagnostic genetic markers that were used to test the hypothesis that young-of-year saugeye were later-generation offspring of saugeye cohorts previously stocked into the reservoir. Alternatively, the fish may have been immigrant first-generation saugeye from other sources. Data obtained from the FRAPD markers provided strong support favoring the alternative hypothesis. These methods provide a very useful tool for distinguishing between pure parentals and various classes of hybrid individuals, both in Sander spp. and in other taxa, offering a powerful and easily developed alternative to other molecular methods of generating informative genetic markers for hybridization studies.

Received September 20, 2011; accepted April 5, 2012
Use of Night Video to Enumerate Adult Pacific Lamprey Passage at Hydroelectric Dams: Challenges and Opportunities to Improve Escapement Estimates
Authors: Clabough Tami S. , Keefer Matthew L. , Caudill Christopher C. , Johnson Eric L. , Peery Christopher A.
Published: July 2012

Reliable estimates of adult Pacific lamprey Entosphenus tridentatus escapement are critically needed to improve management of this declining and ecologically important species. The longest time series of Pacific lamprey counts are from count stations at Columbia River basin dams designed to enumerate adult salmonids during the day, but many Pacific lamprey pass at night. To estimate their total escapement, we used video to monitor nighttime lamprey passage in combination with daytime counts at two count stations at Bonneville Dam and two at The Dalles Dam in 2007–2008. We examined relationships among day and night counts and evaluated the potential for using expansion factors to estimate total escapement from past and future daytime count data. As expected, daytime counts systematically underestimated total lamprey passage, and day and night counts were positively correlated in most comparisons. Unexpectedly, ratios of night: day counts varied widely among sites and years because patterns of upstream and downstream movements past count stations varied. We highlight challenges associated with enumerating cryptic and nocturnal species, such as Pacific lamprey, the potential impact of species-specific behaviors on enumeration efforts, and the importance of appropriate count station location and structure for video monitoring of fish passage.

Received August 9, 2011; accepted April 27, 2012
Prebiotics Have Limited Effects on Nutrient Digestibility of a Diet Based on Fish Meal and Soybean Meal in Goldfish
Authors: Raggi Thiago , Gatlin Delbert M
Published: July 2012

This study evaluated four prebiotics: GroBiotic-A (a mixture of partially autolyzed brewers yeast, dairy ingredient components and dried fermentation products), mannanoligosaccharide (MOS), galactooligosaccharide (GOS), and the fructooligosaccharide (FOS) inulin on digestibility of diets based on fish meal and soybean meal by goldfish Carassius auratus. A basal diet was formulated with 50% of the protein provided by dehulled, solvent-extracted, soybean meal and the other 50% by menhaden Brevoortia sp. fish meal. Each prebiotic was supplemented to the basal diet at 1% by weight. A diet containing all of its protein from menhaden fish meal also was prepared as a control diet. Chromic oxide was added to the diets at 1% by weight. Each diet was fed to adult goldfish in duplicate 110-L aquaria for 8 weeks. The dried fecal material from each aquarium was pooled over time and analyzed for protein, lipid, organic matter, and chromium in order to compute coefficients of apparent digestibility. Genomic DNA of luminal gut microbiota also was isolated from the fecal samples of goldfish fed the various diets and was subjected to PCR using bacteria-specific PCR primers. Then, denaturing gradient gel electrophoresis (DGGE) of the resulting amplicons was conducted as a means of assessing diversity of microbiota in the gastrointestinal (GI) tract. Results revealed that none of the prebiotics affected apparent digestibility coefficients of the diet based on fish meal and soybean meal compared with the basal diet, although the diet supplemented with MOS consistently yielded the lowest values. In addition, goldfish digested the fish-meal–soybean-meal-based diets as well as the control diet. No differences in microbiota of goldfish fed the various prebiotics were revealed by DGGE. These results are in contrast to those obtained with carnivorous fish species such as the red drum Sciaenops ocellatus in which the prebiotics increased digestibility coefficients of diets based on fish meal and soybean meal and altered GI tract microbiota.
Pilot Field Trial to Evaluate SLICE (0.2% Emamectin Benzoate)–Medicated Feed to Reduce a Natural Infestation of Salmincola californiensis in Freshwater-Reared Rainbow Trout
Authors: Gunn Carolyn , Carty Daniel , Walker Peter G , Colburn Patricia A , Bowker James D
Published: July 2012

Salmincola spp. infestations can adversely affect freshwater-reared salmonids. Control methods tested to date have had limited success; consequently, we conducted a pilot field trial to evaluate SLICE (0.2% emamectin benzoate [EB])–medicated feed to reduce a natural infestation of S. californiensis in freshwater-reared rainbow trout Oncorhynchus mykiss. Before the trial started, 96 of 1,500 rainbow trout broodstock held in a flow-through raceway were impartially captured, sedated, uniquely tagged, and returned to the raceway. Pretreatment S. californiensis infestation prevalence and intensity were 97% and 10.4 ± 7.6 (mean ± SD) adult female parasites per fish, respectively. Treatment was administered at 50 μg EB·kg fish−1·d−1 for 7 d. By the end of the trial (43 d posttreatment), infestation prevalence and intensity had decreased to 32% and 1.6 ± 1.1 adult female parasites per fish, respectively. These results suggest that SLICE-medicated feed can be used to reduce natural infestations of S. californiensis in freshwater-reared rainbow trout.
How Economic Contractions and Expansions Affect Expenditure Patterns
Authors: Kamakura Wagner A. , Yuxing Du Rex
Published: July 2012

In this study, we attempt to understand how household budget allocations across various expenditure categories change when the economy is in recession or expansion. The common assumption is that a household’s tastes would not change as a function of economic conditions and therefore any adjustments in expenditure patterns during economic contractions/expansions would simply be due to changes in the consumption budget. Standard economic models translate these budgetary effects into lateral movements along a set of fixed Engel curves, which relate category expenditure shares to total expenditures. We propose and test a conceptual framework based on the notion of relative consumption, which prescribes that, for any given total consumption budget, expenditure shares for positional goods/services will decrease during a recession, while shares for nonpositional goods/services will increase (i.e., shifting the entire Engel curve upward or downward, depending on the nature of the expenditure category and the economic conditions).
Plate Size and Color Suggestibility: The Delboeuf Illusion’s Bias on Serving and Eating Behavior
Authors: Van Ittersum Koert , Wansink Brian
Published: July 2012

Despite the challenged contention that consumers serve more onto larger dinnerware, it remains unclear what would cause this and who might be most at risk. The results of five studies suggest that the neglected Delboeuf illusion may explain how the size of dinnerware creates two opposing biases that lead people to overserve on larger plates and bowls and underserve on smaller ones. A countercyclical sinus-shaped relationship is shown to exist between these serving biases and the relative gap between the edge of the food and the edge of the dinnerware. Although these serving biases are difficult to eliminate with attention and education, changing the color of one’s dinnerware or tablecloth may help attenuate them. By showing that the Delboeuf illusion offers a mechanistic explanation for how dinnerware size can bias serving and intake, we open new theoretical opportunities for linking illusions to eating behavior and suggest how simple changes in design can improve consumer welfare.
How Happiness Affects Choice
Authors: Mogilner Cassie , Aaker Jennifer , Kamvar Sepandar D.
Published: July 2012

Consumers want to be happy, and marketers are increasingly trying to appeal to consumers’ pursuit of happiness. However, the results of six studies reveal that what happiness means varies, and consumers’ choices reflect those differences. In some cases, happiness is defined as feeling excited, and in other cases, happiness is defined as feeling calm. The type of happiness pursued is determined by one’s temporal focus, such that individuals tend to choose more exciting options when focused on the future, and more calming options when focused on the present moment. These results suggest that the definition of happiness, and consumers’ resulting choices, are dynamic and malleable.
Consumer Response to Versioning: How Brands’ Production Methods Affect Perceptions of Unfairness
Authors: Gershoff Andrew D. , Kivetz Ran , Keinan Anat
Published: July 2012

Marketers often extend product lines by offering limited-capability models that are created by removing or degrading features in existing models. This production method, called versioning, has been lauded because of its ability to increase both consumer and firm welfare. According to rational utility models, consumers weigh benefits relative to their costs in evaluating a product. So the production method should not be relevant. Anecdotal evidence suggests otherwise. Six studies show how the production method of versioning may be perceived as unfair and unethical and lead to decreased purchase intentions for the brand. Building on prior work in fairness, the studies show that this effect is driven by violations of norms and the perceived similarity between the inferior, degraded version of a product and the full-featured model offered by the brand.
A dichotomy for expansions of the real field
Authors: Fornasiero Antongiulio , Hieronymi Philipp , Miller Chris
Published: July 2012

A dichotomy for expansions of the real field is established: Either

Z

\mathbb Z

is definable or every nonempty bounded nowhere dense definable subset of

R

\mathbb R

has Minkowski dimension zero.
Paving the future: finding suitable ISMB venues
Authors: Rost Burkhard , Gaasterland Terry , Lengauer Thomas , Linial Michal , Markel Scott , Morrison McKay B.J. , Schneider Reinhard , Horton Paul , Kelso Janet
Published: July 2012

The International Society for Computational Biology, ISCB, organizes the largest event in the field of computational biology and bioinformatics, namely the annual international conference on Intelligent Systems for Molecular Biology, the ISMB. This year at ISMB 2012 in Long Beach, ISCB celebrated the 20th anniversary of its flagship meeting. ISCB is a young, lean and efficient society that aspires to make a significant impact with only limited resources. Many constraints make the choice of venues for ISMB a tough challenge. Here, we describe those challenges and invite the contribution of ideas for solutions.

Contact:  assistant@rostlab.org
RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps
Authors: Pandurangan Arun Prasad , Topf Maya
Published: July 2012

Motivation: To better analyze low-resolution cryo electron microscopy maps of macromolecular assemblies, component atomic structures frequently have to be flexibly fitted into them. Reaching an optimal fit and preventing the fitting process from getting trapped in local minima can be significantly improved by identifying appropriate rigid bodies (RBs) in the fitted component.

Results: Here we present the RIBFIND server, a tool for identifying RBs in protein structures. The server identifies RBs in proteins by calculating spatial proximity between their secondary structural elements.

Availability: The RIBFIND web server and its standalone program are available at http://ribfind.ismb.lon.ac.uk.

Contact:  a.pandurangan@mail.cryst.bbk.ac.uk

Supplementary Information: Supplementary data are available at Bioinformatics online.
A regression model for estimating DNA copy number applied to capture sequencing data
Authors: Rigaill Guillem J. , Cadot Sidney , Kluin Roelof J.C. , Xue Zheng , Bernards Rene , Majewski Ian J. , Wessels Lodewyk F.A.
Published: July 2012

Motivation: Target enrichment, also referred to as DNA capture, provides an effective way to focus sequencing efforts on a genomic region of interest. Capture data are typically used to detect single-nucleotide variants. It can also be used to detect copy number alterations, which is particularly useful in the context of cancer, where such changes occur frequently. In copy number analysis, it is a common practice to determine log-ratios between test and control samples, but this approach results in a loss of information as it disregards the total coverage or intensity at a locus.

Results: We modeled the coverage or intensity of the test sample as a linear function of the control sample. This regression approach is able to deal with regions that are completely deleted, which are problematic for methods that use log-ratios. To demonstrate the utility of our approach, we used capture data to determine copy number for a set of 600 genes in a panel of nine breast cancer cell lines. We found high concordance between our results and those generated using a single-nucleotide polymorphsim genotyping platform. When we compared our results with other log-ratio-based methods, including ExomeCNV, we found that our approach produced better overall correlation with SNP data.

Availability: The algorithm is implemented in C and R and the code can be downloaded from http://bioinformatics.nki.nl/ocs/

Contact:  l.wessels@nki.nl

Supplementary information: Supplementary data are available at Bioinformatics online.
Is juvenile anchovy a feeding resource for the demersal community in the Bay of Biscay? On the availability of pelagic prey to demersal predators
Authors: López-López Lucía , Preciado Izaskun , Villamor Begoña , Velasco Francisco , Iglesias Magdalena , Nogueira Enrique , Gutierrez-Zabala Jose Luis , Olaso Ignacio
Published: July 2012

López-López, L., Preciado, I., Villamor, B., Velasco, F., Iglesias, M., Nogueira, E. Gutierrez-Zabala, J. L., and Olaso, I. 2012. Is juvenile anchovy a feeding resource for the demersal community in the Bay of Biscay? On the availability of pelagic prey to demersal predators. – ICES Journal of Marine Science, 69: . The role that juvenile anchovy (Engraulis encrasicolus) play as a food resource for the demersal community in the southern Bay of Biscay is assessed using 21 years of anchovy abundance data and demersal predator diets. During the study period, a total of 26 fish and elasmobranch species preyed on anchovy either frequently or occasionally. Predators with a crustacean-based diet targeted the smaller anchovy individuals. The size range of anchovy juveniles (centred at 7.5–8.9 cm) was comparable to that of the largest nektonic–benthic crustaceans, but generally smaller than other demersal and pelagic fish prey. Hake (Merluccius merluccius) and megrim (Lepidorhombus whiffiagonis) were the predators that consumed the highest number of anchovy, one of the main prey items driving the variability of their diets. Anchovy consumption conformed only partially to the abundance of anchovy in the southern Bay of Biscay, suggesting that factors other than abundance might condition its availability to demersal predators. Prey size could be one of them, as the size of the anchovy preyed on proved to be significantly smaller than the individuals collected with bottom trawls. However, other factors, such as the vertical position of the shoals of anchovy juveniles, could also constrain anchovy availability to demersal predators.
Home Noninvasive Ventilation
Authors: Brown Karen A. , Bertolizio Gianluca , Leone Marisa , Dain Steven L. , Warner David S.
Published: July 2012

Treatment of chronic respiratory failure with noninvasive ventilation (NIV) is standard pediatric practice, and NIV systems are commonly used in the home setting. Although practice guidelines on the perioperative management of children supported with home NIV systems have yet to be published, increasingly these patients are referred for consultation regarding perioperative management. Just as knowledge of pharmacology underlies the safe prescription of medication, so too knowledge of biomedical design is necessary for the safe prescription of NIV therapy. The medical device design requirements developed by the Organization for International Standardization provide a framework to rationalize the safe prescription of NIV for hospitalized patients supported at home with NIV systems. This review article provides an overview of the indications for home NIV therapy, an overview of the medical devices currently available to deliver it, and a specific discussion of the management conundrums confronting anesthesiologists.
Are Anesthesia and Surgery during Infancy Associated with Altered Academic Performance during Childhood?
Authors: Block Robert I. , Thomas Joss J. , Bayman Emine O. , Choi James Y. , Kimble Karolie K. , Todd Michael M.
Published: July 2012

Background

Although studies in neonatal animals show that anesthetics have neurotoxic effects, relevant human evidence is limited. We examined whether children who had surgery during infancy showed deficits in academic achievement.

Methods

We attempted to contact parents of 577 children who, during infancy, had one of three operations typically performed in otherwise healthy children. We compared scores on academic achievement tests with population norms.

Results

Composite scores were available for 287 patients. The mean normal curve equivalent score was 43.0±22.4 (mean±SD), lower than the expected normative value of 50, P<0.0001 by one-sample Student t test; and 35 (12%) had scores below the 5th percentile, more than expected, P<0.00001 by binomial test. Of 133 patients who consented to participate so that their scores could be examined in relation to their medical records, the mean score was 45.9±22.9, P=0.0411; and 15 (11%) scored below the 5th percentile, P=0.0039. Of 58 patients whose medical records showed no central nervous system problems/potential risk factors during infancy, 8 (14%) scored below the 5th percentile, P=0.008; however, the mean score, 47.6±23.4, was not significantly lower than expected, P=0.441. Duration of anesthesia and surgery correlated negatively with scores (r=-0.34, N=58, P=0.0101).

Conclusions

Although the findings are consistent with possible adverse effects of anesthesia and surgery during infancy on subsequent academic achievement, other explanations are possible and further investigations are needed.
Formation of Complex Extrachromosomal T-DNA Structures in Agrobacterium tumefaciens-Infected Plants
Authors: Singer Kamy , Shiboleth Yoel M. , Li Jianming , Tzfira Tzvi
Published: July 2012

Agrobacterium tumefaciens is a unique plant pathogenic bacterium renowned for its ability to transform plants. The integration of transferred DNA (T-DNA) and the formation of complex insertions in the genome of transgenic plants during A. tumefaciens-mediated transformation are still poorly understood. Here, we show that complex extrachromosomal T-DNA structures form in A. tumefaciens-infected plants immediately after infection. Furthermore, these extrachromosomal complex DNA molecules can circularize in planta. We recovered circular T-DNA molecules (T-circles) using a novel plasmid-rescue method. Sequencing analysis of the T-circles revealed patterns similar to the insertion patterns commonly found in transgenic plants. The patterns include illegitimate DNA end joining, T-DNA truncations, T-DNA repeats, binary vector sequences, and other unknown “filler” sequences. Our data suggest that prior to T-DNA integration, a transferred single-stranded T-DNA is converted into a double-stranded form. We propose that termini of linear double-stranded T-DNAs are recognized and repaired by the plant’s DNA double-strand break-repair machinery. This can lead to circularization, integration, or the formation of extrachromosomal complex T-DNA structures that subsequently may integrate.
Library automation in sub Saharan Africa: case study of the University of Botswana
Authors: Mudogo Mutula Stephen
Published: July 2012

Purpose

This article aims to present experiences and the lessons learned from the University of Botswana (UB) library automation project. The implications of the project for similar libraries planning automation in sub Saharan Africa and beyond are adduced.

Design/methodology/approach

The article is a case study of library automation at the University of Botswana.

Findings

The successful implementation of the library automation project was attributed to a number of factors, among them ensuring strategic management buy‐in, extensive consultations with key stakeholders, alignment of library automation with goals of the university, capacity building of librarians and assuring librarians that their jobs were safe. The impact of the automation project included increased access to diversity of electronic resources, enhanced image of librarians, introduction of new services, freeing of library physical space, transformation of the library into a social learning environment, access to local content made possible through digitisation, new skills acquisitions, access to library electronic resources from remote sites, and increased roles and responsibilities for librarians. Challenges faced included staff anxiety about the prospect of losing jobs, learning of new skills, added responsibilities for librarians, raised expectations of users, high costs of subscription to full text journals, and bandwidth bottlenecks among others.

Research limitations and implications

This article is based on a case study of library automation at the University of Botswana. The results may not therefore be widely replicated. Besides, the article did not delve deep into technology acceptance and diffusion of innovation issues that could illuminate further the case study.

Practical implications

Most university libraries in sub Saharan Africa are yet to successfully and fully automate their information services. Consequently the lessons learned from the University of Botswana case could help inform the planning and implementation of automations projects in similar libraries.

Social implications

The automation of the University of Botswana library resulted in enhanced quality of information services, re‐skilling of librarians, enhanced image of librarians, user satisfaction and transformation of the university into a learning and research hub.

Originality/value

This article is based on practical experiences of library automation at the University of Botswana and its impact on services, and human and physical resources. Previous studies on this subject at the university only covered migration from one system to another and the technical perspectives of the process of library automation. This study is broad in scope covering both technical and managerial processes of managing change in the context of library automation at the University of Botswana.
Of private sector fear and prejudice
Authors: Al‐Waqfi Mohammed A. , Forstenlechner Ingo
Published: July 2012

Purpose

The uncompromising preference of citizens for public sector employment throughout the Middle East is not new. However, with the recent saturation of the public sector job market and demographic pressures, it has grown to become a problem of unpredictable economic and social consequences. This paper aims to explore the factors determining career choice behaviour and the underlying career expectations and perceptions of young citizens in one Middle Eastern country, the United Arab Emirates (UAE), where the preference for public sector employment is not only very strong, but is also perceived as increasingly problematic.

Design/methodology/approach

Semi‐structured interviews were conducted with a total of 60 UAE citizens in the age group of 18‐23.

Findings

The authors explore and discuss cognitive, social, and institutional factors that influence the job‐seeking behaviour of young Emiratis and lead to negative attitudes towards the private sector. They further suggest potential causes of the very low private sector employment levels among UAE citizens and discuss their implications for policy makers. The authors argue for two main approaches: first, a focus on training and orientation of young citizens to enable them to confidently pursue job opportunities in the private sector. This may also include ways for providing young UAE citizens with private sector exposure, as 98 per cent of the national workforce is currently working in the public sector and a lot of what young UAE citizens think they know about the private sector is not founded in reality. Second, interventions to address structural and institutional challenges hindering employment of citizens including gaps in employment conditions and remuneration levels for citizens between the public and private employment sectors.

Originality/value

While much previous research in this field has focused on the perceptions of employers, this is the first paper to actually explore the perceptions of those at the centre of the discussion – young UAE citizens themselves.
Examining the exclusion of employees with Asperger syndrome from the workplace
Authors: Richards James
Published: July 2012

Purpose

The purpose of this paper is to critically examine reasons for disproportionately high levels of exclusion from the workplace of adults with Asperger syndrome.

Design/methodology/approach

The methodology adopted involves empirical analysis of secondary, qualitative datasets. The twin datasets applied are examined using labour process analysis.

Findings

The main findings highlight the role of new and subtle forms of management control, a deficient yet necessary conflict dynamic in the employment relationship, and a reluctance of employers to involve third parties, in the exclusion process.

Research limitations/implications

The study is limited because of the use of secondary datasets. Further research should be based on primary data collection and analysis, particularly in terms of seeking the views of other important parties to the exclusion process.

Practical implications

The problem of exclusion is unlikely to be improved without considering strategies to address the challenging customary social relations between employer and employee.

Social implications

Improving employment inclusion is likely to reduce mental health problems for adults with Asperger syndrome and reduce the burden on those who play a broader supporting role.

Originality/value

The topic of Asperger syndrome and employment has yet to permeate the academic literature on human resource management, employment relations and organisation studies.
Do “hard” diversity policies increase ethnic minority representation?
Authors: Verbeek Stijn , Groeneveld Sandra
Published: July 2012

Purpose

This study aims to examine the effectiveness of three types of diversity policies in improving the numerical representation of ethnic minorities in organizations: the assignment of responsibility for the policy within the organization, tiebreak preferential treatment, i.e. selecting the ethnic minority candidate if the best applicants are equally qualified, and the formulation of target figures.

Design/methodology/approach

The dataset consists of 8,283 official reports of Dutch work organizations filed in 2001 and 2002 to comply with the Act Stimulation Labor Participation Minorities (Wet SAMEN). The research is embedded in the broader literature on the underlying motivations for diversity policies and on their potential “symbolic” character.

Findings

The analysis suggests that the three diversity policies and ethnic minority representation are correlated. However, the policies do not impact ethnic minority participation rates in the short run.

Research limitations/implications

Future research should also include long‐term effects, actual implementation processes, and the effectiveness of these three policies in combination with other policies and in specific contexts.

Practical implications

Policymakers and strategic HRM practitioners should adopt a long time frame in trying to increase ethnic minority representation. In line with previous research, the study evaluates assigning responsibility within organizations most positively.

Originality/value

These “hard” policies are central to the debate on equal opportunities, employment equity, and ethnic diversity, but few large N effectiveness studies are available.
Reasons to expatriate and work outcomes of self‐initiated expatriates
Authors: Selmer Jan , Lauring Jakob
Published: July 2012

Purpose

Through a large‐scale quantitative study, this paper aims to test and extend the qualitative findings of Richardson and McKenna and of Osland on reasons to expatriate and relate them to work outcomes.

Design/methodology/approach

Examining how reasons to expatriate may affect work outcomes, quantitative data was collected from self‐initiated expatriate academics from 60 countries employed in 35 universities in five northern European countries.

Findings

Results mostly indicated support for the proposed hypotheses. The most striking finding was the apparently uniformly destructive influence of behaviour associated with escape from one's previous life as a reason to expatriate on all of the studied work outcomes.

Research limitations/implications

The self‐developed scales measuring reasons for self‐initiated expatriates to expatriate may have been inadequate to capture all relevant aspects of their behavioural intentions and the data from the retrospective type of questioning regarding the original reasons to expatriate may have been biased by memory effects.

Practical implications

Any organization recruiting self‐initiated expatriates may want to inquire about the reasons for them to expatriate. Although there may be a plethora of other requirements on job applicants, the findings of this study may be used as contributing to additional hiring criteria.

Originality/value

Most of the fast growing literature on business expatriates has focused on organizational expatriates who have been assigned by their parent companies to the foreign location. However, there is much less research on self‐initiated expatriates, who themselves have decided to expatriate to work abroad.