bluuebunny/crossref_metadata_2025 huggingface dataset:
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
Authors: MacLean Brendan , Tomazela Daniela M. , Shulman Nicholas , Chambers Matthew , Finney Gregory L. , Frewen Barbara , Kern Randall , Tabb David L. , Liebler Daniel C. , MacCoss Michael J.
Published: February 2010

Summary: Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM). Skyline supports using and creating MS/MS spectral libraries from a wide variety of sources to choose SRM filters and verify results based on previously observed ion trap data. Skyline exports transition lists to and imports the native output files from Agilent, Applied Biosystems, Thermo Fisher Scientific and Waters triple quadrupole instruments, seamlessly connecting mass spectrometer output back to the experimental design document. The fast and compact Skyline file format is easily shared, even for experiments requiring many sample injections. A rich array of graphs displays results and provides powerful tools for inspecting data integrity as data are acquired, helping instrument operators to identify problems early. The Skyline dynamic report designer exports tabular data from the Skyline document model for in-depth analysis with common statistical tools.

Availability: Single-click, self-updating web installation is available at http://proteome.gs.washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project.

Contact:  brendanx@u.washington.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Presentation and Management of Genital Herpes
Authors: Nicum Sonal , Mahida Nikunj
Published: February 2010

Genital herpes is a common condition which is caused by the herpes simplex virus (HSV). There are two viral types, HSV1 and HSV2, both of which contribute to oral and genital infections. HSV is readily inactivated at room temperature and by drying, so transmission is by close physical contact, either sexual or genital. Most people acquire HSV subclinically through an infected contact. After the primary infection, the virus lies dormant in local sensory ganglia and reactivates intermittently resulting in lesions or asymptomatic shedding of virus.
Marine no-take zone rapidly benefits endangered penguin
Authors: Pichegru L. , Grémillet D. , Crawford R. J. M. , Ryan P. G.
Published: February 2010

No-take zones may protect populations of targeted marine species and restore the integrity of marine ecosystems, but it is unclear whether they benefit top predators that rely on mobile pelagic fishes. In South Africa, foraging effort of breeding African penguins decreased by 30 per cent within three months of closing a 20 km zone to the competing purse-seine fisheries around their largest colony. After the fishing ban, most of the penguins from this island had shifted their feeding effort inside the closed area. Birds breeding at another colony situated 50 km away, whose fishing grounds remained open to fishing, increased their foraging effort during the same period. This demonstrates the immediate benefit of a relatively small no-take zone for a marine top predator relying on pelagic prey. Selecting such small protected areas may be an important first conservation step, minimizing stakeholder conflicts and easing compliance, while ensuring benefit for the ecosystems within these habitats.
Systems engineering medicine: engineering the inflammation response to infectious and traumatic challenges
Authors: Parker Robert S. , Clermont Gilles
Published: February 2010

The complexity of the systemic inflammatory response and the lack of a treatment breakthrough in the treatment of pathogenic infection demand that advanced tools be brought to bear in the treatment of severe sepsis and trauma.Systems medicine, the translational science counterpart to basic science'ssystems biology, is the interface at which these tools may be constructed. Rapid initial strides in improving sepsis treatment are possible through the use of phenomenological modelling and optimization tools for process understanding and device design. Higher impact, and more generalizable, treatment designs are based on mechanistic understanding developed through the use of physiologically based models, characterization of population variability, and the use of control-theoretic systems engineering concepts. In this review we introduce acute inflammation and sepsis as an example of just one area that is currently underserved by the systems medicine community, and, therefore, an area in which contributions of all types can be made.
Exploring and communicating knowledge of trees in the early Royal Society
Authors: Hartley Beryl
Published: February 2010

For nearly 150 years after its foundation, Fellows of the Royal Society collected information on trees, investigated their anatomy and physiology, promoted planting and improved planting practices, and introduced, naturalized and classified foreign species. Their discoveries and advice were widely disseminated and used. Historians have generally neglected this interest, although the Society's first publication was an influential work on trees. They have also overlooked the significance of Stephen Hales's remark in
Vegetable Staticks
—that he hoped his enquiries into the nature of plants would improve skills in agriculture and gardening—and his linking of sap movement to tree pruning. Fellows' experiments and field trials not only advanced knowledge of the structure, nutrition and growth of trees but also provided empirical evidence supporting instructions for cultivating them.
Spinning rough disc moving in a rarefied medium
Authors: Plakhov Alexander , Tchemisova Tatiana , Gouveia Paulo
Published: February 2010

We study the Magnus effect: deflection of the trajectory of a spinning body moving in a gas. It is well known that in rarefied gases, the
inverse
Magnus effect takes place, which means that the transversal component of the force acting on the body has opposite signs in sparse and relatively dense gases. The existing works derive the inverse effect from
non-elastic
interaction of gas particles with the body. We propose another (complementary) mechanism of creating the transversal force owing to
multiple
collisions of particles in cavities of the body surface. We limit ourselves to the two-dimensional case of a rough disc moving through a zero-temperature medium on the plane, where reflections of the particles from the body are elastic and mutual interaction of the particles is neglected. We represent the force acting on the disc and the moment of this force as functionals depending on ‘shape of the roughness’, and determine the set of all admissible forces. The disc trajectory is determined for several simple cases. The study is made by means of billiard theory, Monge–Kantorovich optimal mass transport and by numerical methods.
Visual pigment in the lens eyes of the box jellyfish
Chiropsella bronzie
Authors: O'Connor Megan , Garm Anders , Marshall Justin N. , Hart Nathan S. , Ekström Peter , Skogh Charlotta , Nilsson Dan-Eric
Published: February 2010

Box jellyfish (Cubomedusae) possess a unique visual system comprising 24 eyes of four morphological types. Moreover, box jellyfish display several visually guided behaviours, including obstacle avoidance and light-shaft attractance. It is largely unknown what kind of visual information box jellyfish use for carrying out these behaviours. Brightness contrast is almost certainly involved, but it is also possible that box jellyfish extract colour information from their surroundings. The possible presence of colour vision in box jellyfish has previously been investigated using behavioural, electrophysiological and immunohistochemical methods. However, the results from these studies are to some degree conflicting and inconclusive. Here, we present results from an investigation into the visual system of the box jellyfish
Chiropsella bronzie
, using microspectrophotometry and immunohistochemistry. Our results strongly indicate that only one type of visual pigment is present in the upper and lower lens eyes with a peak absorbance of approximately 510 nm. Additionally, the visual pigment appears to undergo bleaching, similar to that of vertebrate visual pigments.
The fine structure of honeybee head and body yaw movements in a homing task
Authors: Boeddeker Norbert , Dittmar Laura , Stürzl Wolfgang , Egelhaaf Martin
Published: February 2010

Honeybees turn their thorax and thus their flight motor to change direction or to fly sideways. If the bee's head were fixed to its thorax, such movements would have great impact on vision. Head movements independent of thorax orientation can stabilize gaze and thus play an important and active role in shaping the structure of the visual input the animal receives. Here, we investigate how gaze and flight control interact in a homing task. We use high-speed video equipment to record the head and body movements of honeybees approaching and departing from a food source that was located between three landmarks in an indoor flight arena. During these flights, the bees' trajectories consist of straight flight segments combined with rapid turns. These short and fast yaw turns (‘saccades’) are in most cases accompanied by even faster head yaw turns that start about 8 ms earlier than the body saccades. Between saccades, gaze stabilization leads to a behavioural elimination of rotational components from the optical flow pattern, which facilitates depth perception from motion parallax.
Crystal Structure and Functional Insights of Hemopexin Fold Protein from Grass Pea
Authors: Gaur Vineet , Qureshi Insaf A. , Singh Apekshita , Chanana Veenu , Salunke Dinakar M.
Published: February 2010

A regulatory protein from grass pea (Lathyrus sativus), LS-24, a close homolog of albumin 2 from garden pea (Pisum sativum) that is associated with polyamine biosynthesis, was characterized and the structure of a hemopexin-type fold among plant proteins illustrated. Crystal structure of LS-24 determined at 2.2 Å resolution by multiple isomorphous replacement phasing showed four-bladed β-propeller structure having a pseudo 4-fold molecular symmetry along a metal ion-binding central channel. The structure represents typical mammalian hemopexin fold with discernible features correlated with the possible functional variations. The protein was found to exist in the dimeric state. While LS-24 dimer binds to spermine in the crystal structure as well as in solution, binding of heme in solution resulted in the dissociation of the dimer into monomers with concomitant release of bound spermine. Interactions of heme and spermine with LS-24 bear physiological implications. While binding of spermine to LS-24 can be linked with polyamine biosynthesis that of heme correlates with oxidative stress. Mutually exclusive binding of heme and spermine in different oligomeric states suggest a role for LS-24 in sensing oxidative stress through a ligand-regulated monomer-dimer transition switch.
Mathematical Modeling-Guided Evaluation of Biochemical, Developmental, Environmental, and Genotypic Determinants of Essential Oil Composition and Yield in Peppermint Leaves
Authors: Rios-Estepa Rigoberto , Lange Iris , Lee James M. , Lange B. Markus
Published: February 2010

We have previously reported the use of a combination of computational simulations and targeted experiments to build a first generation mathematical model of peppermint (Mentha × piperita) essential oil biosynthesis. Here, we report on the expansion of this approach to identify the key factors controlling monoterpenoid essential oil biosynthesis under adverse environmental conditions. We also investigated determinants of essential oil biosynthesis in transgenic peppermint lines with modulated essential oil profiles. A computational perturbation analysis, which was implemented to identify the variables that exert prominent control over the outputs of the model, indicated that the essential oil composition should be highly dependent on certain biosynthetic enzyme concentrations [(+)-pulegone reductase and (+)-menthofuran synthase], whereas oil yield should be particularly sensitive to the density and/or distribution of leaf glandular trichomes, the specialized anatomical structures responsible for the synthesis and storage of essential oils. A microscopic evaluation of leaf surfaces demonstrated that the final mature size of glandular trichomes was the same across all experiments. However, as predicted by the perturbation analysis, differences in the size distribution and the total number of glandular trichomes strongly correlated with differences in monoterpenoid essential oil yield. Building on various experimental data sets, appropriate mathematical functions were selected to approximate the dynamics of glandular trichome distribution/density and enzyme concentrations in our kinetic model. Based on a χ  2 statistical analysis, simulated and measured essential oil profiles were in very good agreement, indicating that modeling is a valuable tool for guiding metabolic engineering efforts aimed at improving essential oil quality and quantity.
The cross-correlation function: main properties and first applications
Authors: Carrozzini Benedetta , Cascarano Giovanni Luca , Giacovazzo Carmelo
Published: February 2010

When a model structure, and more generally a model electron density ρM(r), is available, its cross-correlation functionC(u) with the unknown true structure ρ(r) cannot be exactly calculated. A useful approximation ofC(u) is obtained by replacing exp[i(φh − φMh)] by its expected value. In this caseC′(u), a potentially useful approximation of the functionC(u), is obtained. In this paper the main crystallographic properties of the functionsC(u) andC′(u) are established. It is also shown that such functions may be useful for the success of the phasing process.
Crystal structure of cobalt-substituted calcium hydroxyapatite nanopowders prepared by hydrothermal processing
Authors: Veselinović Ljiljana , Karanović Ljiljana , Stojanović Zoran , Bračko Ines , Marković Smilja , Ignjatović Nenad , Uskoković Dragan
Published: February 2010

A series of cobalt-exchanged hydroxyapatite (CoHAp) powders with different Ca/Co ratios and nominal unit-cell contents Ca10−xCox(PO4)6(OH)2,x= 0, 0.5, 1.0, 1.5 and 2.0, were synthesized by hydrothermal treatment of a precipitate at 473 K for 8 h. Based on ICP (inductively coupled plasma) emission spectroscopy analysis, it was established that the maximum amount of cobalt incorporation saturated at ∼12 at.% under these conditions. The effects of cobalt content on the CoHAp powders were investigated using ICP emission spectroscopy, particle size analysis, transmission electron microscopy (TEM) and high-resolution transmission electron microscopy (HRTEM) analyses as well as X-ray powder diffraction (XRPD) including Rietveld analysis. According to XRPD, all the materials are single-phase HAp and CoHAp of low crystallinity. Rietveld analysis shows that Co enrichment causes theccell parameter to decrease at a faster rate than theacell parameter. A microstructural analysis showed anisotropic X-ray line broadening due to crystallite size reduction. In CoHAp there is significant crystal elongation in [001], and the average size decreases with increasing cobalt content. The crystallite morphology transforms from rod-like for the pure HAp to lamellae at the highest degree of Co substitution. The results of Rietveld refinement (symmetry, size and morphology of the crystallites) were confirmed by TEM and HRTEM analysis.
WebCSD: the online portal to the Cambridge Structural Database
Authors: Thomas Ian R. , Bruno Ian J. , Cole Jason C. , Macrae Clare F. , Pidcock Elna , Wood Peter A.
Published: February 2010

WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer.
AMINONET– a tool to construct and visualize amino acid networks, and to calculate topological parameters
Authors: Aftabuddin Md. , Kundu Sudip
Published: February 2010

AMINONETis a Java-based software tool to construct different protein contact networks (unweighted and weighted; long range, short range and any range; hydrophobic, hydrophilic, charged or all-amino-acid networks). The networks thus constructed can be visualized. The software will also help in the calculation of the values of the different topological parameters of the constructed networks. The user can either provide a PDB ID or upload a structure file in PDB format as input. If necessary, the user can also do the same for a large number of proteins, uploading a batch file as input (details described in the document available online).
Calibration of a silicon crystal for absolute nuclear spectroscopy
Authors: Massa Enrico , Mana Giovanni , Kuetgens Ulrich , Ferroglio Luca
Published: February 2010

To tie the wavelengths of γ-rays to a visible standard is a key element of accurate determinations of the Planck constant and of tests of the Einstein mass–energy equivalence. This link is achievedviasmall diffraction angle measurements and perfect single crystals, the lattice parameter of which is determined by combined X-ray and optical interferometry. The present paper concerns the lattice parameter measurement of an Si crystal, of a natural isotopic composition, designed to be used both as the analyser crystal of an X-ray interferometer and the reference grating of a γ-ray spectrometer.
Simulation of modulated reflections
Authors: Lovelace Jeffrey J. , Winn Martyn D. , Borgstahl Gloria E. O.
Published: February 2010

In a modulated crystal, the repeating unit is not periodic but contains a disorder of the molecules that can sometimes be described with a mathematical function. In the diffraction pattern from such a modulated crystal the standard periodic main reflections are flanked by satellite reflections. Generally, incommensurately modulated crystal diffraction cannot be simply described using integers along the reciprocal-lattice directions. However, in the special commensurate case where the satellite spacing is rational relative to the main reflections, a supercell can be used to describe the modulation. Using a supercell allows structural processing to proceed in a `normal' fashion but with the downside of dealing with many more atoms. Not much is known about the relationship between a highly modulated macromolecular crystal and the resulting satellite intensities so in this study a modulated protein crystal was simulated using a supercell approach. The protein superstructure was modulated to varying degrees and the resultant diffraction patterns and electron-density maps were studied to understand better how a modulation may manifest itself in real protein data. In the case that was evaluated, relatively small structural modulation resulted in significant satellite intensities. Interesting cases were observed where extinguished main reflections had strong satellites.
Accommodation of structural rearrangements in the huntingtin-interacting protein 1 coiled-coil domain
Authors: Wilbur Jeremy D. , Hwang Peter K. , Brodsky Frances M. , Fletterick Robert J.
Published: February 2010

Huntingtin-interacting protein 1 (HIP1) is an important link between the actin cytoskeleton and clathrin-mediated endocytosis machinery. HIP1 has also been implicated in the pathogenesis of Huntington's disease. The binding of HIP1 to actin is regulated through an interaction with clathrin light chain. Clathrin light chain binds to a flexible coiled-coil domain in HIP1 and induces a compact state that is refractory to actin binding. To understand the mechanism of this conformational regulation, a high-resolution crystal structure of a stable fragment from the HIP1 coiled-coil domain was determined. The flexibility of the HIP1 coiled-coil region was evident from its variation from a previously determined structure of a similar region. A hydrogen-bond network and changes in coiled-coil monomer interaction suggest that the HIP1 coiled-coil domain is uniquely suited to allow conformational flexibility.
Introduction of a leucine half-zipper engenders multiple high-quality crystals of a recalcitrant tRNA synthetase
Authors: Guo Min , Shapiro Ryan , Schimmel Paul , Yang Xiang-Lei
Published: February 2010

AlthoughEscherichia colialanyl-tRNA synthetase was among the first tRNA synthetases to be sequenced and extensively studied by functional analysis, it has proved to be recalcitrant to crystallization. This challenge remained even for crystallization of the catalytic fragment. By mutationally introducing three stacked leucines onto the solvent-exposed side of an α-helix, an engineered catalytic fragment of the synthetase was obtained that yielded multiple high-quality crystals and cocrystals with different ligands. The engineered α-helix did not form a leucine zipper that interlocked with the same α-helix from another molecule. Instead, using the created hydrophobic spine, it interacted with other surfaces of the protein as a leucine half-zipper (LHZ) to enhance the crystal lattice interactions. The LHZ made crystal lattice contacts in all crystals of different space groups. These results illustrate the power of introducing an LHZ into helices to facilitate crystallization. The authors propose that the method can be unified with surface-entropy reduction and can be broadly used for protein-surface optimization in crystallization.
Deleting two C-terminal α-helices is effective to crystallize the bacterial ABC transporterEscherichia coliMsbA complexed with AMP-PNP
Authors: Terakado Kanako , Kodan Atsushi , Nakano Hiroaki , Kimura Yasuhisa , Ueda Kazumitsu , Nakatsu Toru , Kato Hiroaki
Published: February 2010

An MsbA deletion mutant ΔC21 that lacks the two C-terminal α-helices was expressed inEscherichia colistrain C41 and purified by metal-affinity and gel-filtration chromatography. Purified ΔC21 retained 26% of the activity of the wild-type ATPase and had a similar binding affinity to fluorescent nucleotide derivatives. Although crystals of wild-type MsbA complexed with adenosine 5′-(β,γ-imido)triphosphate could not be obtained, crystals of ΔC21 that diffracted to 4.5 Å resolution were obtained. The preliminary ΔC21 structure had the outward-facing conformation, in contrast to the previously reportedE. coliMsbA structure. This result suggests that deletion of the C-terminal α-helices may play a role in facilitating the outward-facing nucleotide-bound crystal structure of EcMsbA.
pH-dependent structural changes in haemoglobin component V from the midge larvaPropsilocerus akamusi(Orthocladiinae, Diptera)
Authors: Kuwada Takao , Hasegawa Tomokazu , Takagi Takashi , Sato Isamu , Shishikura Fumio
Published: February 2010

Haemoglobin component V (Hb V) from the midge larvaPropsilocerus akamusiexhibits oxygen affinity despite the replacement of HisE7 and a pH-dependence of its functional properties. In order to understand the contribution of the distal residue to the ligand-binding properties and the pH-dependent structural changes in this insect Hb, the crystal structure of Hb V was determined under five different pH conditions. Structural comparisons of these Hb structures indicated that at neutral pH ArgE10 contributes to the stabilization of the haem-bound ligand molecule as a functional substitute for the nonpolar E7 residue. However, ArgE10 does not contribute to stabilization at acidic and alkaline pH because of the swinging movement of the Arg side chain under these conditions. This pH-dependent behaviour of Arg results in significant differences in the hydrogen-bond network on the distal side of the haem in the Hb V structures at different pH values. Furthermore, the change in pH results in a partial movement of the F helix, considering that coupled movements of ArgE10 and the F helix determine the haem location at each pH. These results suggested that Hb V retains its functional properties by adapting to the structural changes caused by amino-acid replacements.
Rapid model building of β-sheets in electron-density maps
Authors: Terwilliger Thomas C.
Published: February 2010

A method for rapidly building β-sheets into electron-density maps is presented. β-Strands are identified as tubes of high density adjacent to and nearly parallel to other tubes of density. The alignment and direction of each strand are identified from the pattern of high density corresponding to carbonyl and Cβatoms along the strand averaged over all repeats present in the strand. The β-strands obtained are then assembled into a single atomic model of the β-sheet regions. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 Å. The β-sheet regions were nearly completely built in all but two cases, the exceptions being one structure at 2.5 Å resolution in which a third of the residues in β-sheets were built and a structure at 3.8 Å in which under 10% were built. The overall average r.m.s.d. of main-chain atoms in the residues built using this method compared with refined models of the structures was 1.5 Å.
DJ‐1: A novel independent prognostic marker for survival in glottic squamous cell carcinoma
Authors: Zhu Xiao‐Lin , Wang Zhang‐Feng , Lei Wen‐Bin , Zhuang Hui‐Wen , Jiang Hong‐Yan , Wen Wei‐Ping
Published: February 2010

DJ‐1 is frequently overexpressed in a large variety of solid tumors, but the DJ‐1 expression in laryngeal squamous cell cancer and its clinical/prognostic significance is unclear. We aimed to evaluate DJ‐1 protein expression in glottic squamous cell carcinoma (GSCC) and to correlate this with clinicopathological data including patient survival. The expression of DJ‐1 in GSCCs (60) and adjacent normal tissue (44) was assessed by immunohistochemistry and western blot analysis. In addition, the role of DJ‐1 was investigated in tumorigenesis by transfecting DJ1‐specific siRNA into laryngeal squamous cell carcinoma (LSCC) Hep‐2 cells. Our data showed that positive expression of DJ‐1 was found in 85% of GSCCs. In univariate survival analysis of the GSCC cohorts, a highly significant association between DJ‐1 expression with shortened patient overall survival (5‐year survival rate 92.9%vs 66.6%; P = 0.001; log rank test) was demonstrated. In multivariate analyses, DJ‐1, tumor grading, and pT status were significant prognostic parameters for shortened patient overall survival. Furthermore, siRNA targeting DJ‐1 can effectively inhibit DJ‐1 expression, resulting in enhanced apoptosis and less proliferation of Hep‐2 cells. We concluded that DJ‐1 overexpression might be a novel independent molecular marker for poor prognosis (shortened overall survival) of patients with GSCC.

(Cancer Sci 2010; 101: 1320–1325)
Association between nitrous oxide and the incidence of postoperative nausea and vomiting in adults: a systematic review and meta‐analysis
Authors: Fernández‐Guisasola J. , Gómez‐Arnau J. I. , Cabrera Y. , del Valle S. García
Published: February 2010

Some, but not all studies have suggested intra‐operative use of nitrous oxide is correlated with postoperative nausea and vomiting. We performed a meta‐analysis of randomised controlled trials to compare the incidence of nausea and vomiting in adults following general anaesthesia with or without nitrous oxide. We retrieved 30 studies (incorporating 33 separate trials) that investigated a ‘nitrous oxide group’ (total 2297 patients) vs a ‘no‐nitrous oxide group’ (2301 patients). Omitting nitrous oxide significantly reduced postoperative nausea and vomiting (pooled relative risk 0.80, 95% CI 0.71–0.90, p = 0.0003). However, the absolute incidence of nausea and vomiting was high in both the nitrous oxide and no‐nitrous oxide groups (33% vs 27%, respectively). In subgroup analysis, the maximal risk reduction was obtained in female patients (pooled relative risk 0.76, 95% CI 0.60–0.96). When nitrous oxide was used in combination with propofol, the antiemetic effect of the latter appeared to compensate the emetogenic effect of nitrous oxide (pooled relative risk 0.94, 95% CI 0.77–1.15). We conclude that avoiding nitrous oxide does reduce the risk of postoperative nausea and vomiting, especially in women, but the overall impact is modest.
Developing a scale for teacher integration of information and communication technology in grades 1–9
Authors: Hsu S.
Published: February 2010

There is no unified view about how teachers' integration of information and communication technology (ICT) should be measured. While many instruments have focused on the technological aspects, recent studies have suggested teachers' pedagogical considerations, professional development, and emerging ethical and safety issues should be included when assessing teachers' ICT literacy. Using the performance standards created by the International Society for Technology in Education, a group of Taiwanese teachers developed equivalent items. After consulting expert panels and interviewing teachers, a scale was constructed. Using this instrument, 3729 teachers from grades 1 through 9 in Taiwan were sampled. Half of the data was analysed by exploratory factor analysis to find the underpinning structure, and the second half was analysed by confirmatory factor analysis to verify the subscales. The results confirmed six subscales for teachers' ICT integration: (1) information collection and preparation; (2) material production and troubleshooting; (3) communication and sharing; (4) planning, teaching and evaluation; (5) professional development and self‐study; and (6) ethical, health and safety issues. Using two teacher attributes, school levels and course or degree obtained, the scale was further verified for its feasibility. The established scale examines the existing concerns for technology, pedagogy and professional development at once with a new addition of ethical and safety issues, which demand growing attention in teachers of future generation.
Viral haemorrhagic septicaemia virus IVb experimental infection of rainbow trout, Oncorhynchus mykiss (Walbaum), and fathead minnow, Pimphales promelas (Rafinesque)
Authors: Al‐Hussinee L , Huber P , Russell S , LePage V , Reid A , Young K M , Nagy E , Stevenson R M W , Lumsden J S
Published: February 2010

Viral haemorrhagic septicaemia virus (VHSV) in the Great Lakes has had a dramatic impact on fish husbandry because of the implications of the presence of a reportable disease. Experimental infections with VHSV IVb were conducted in rainbow trout, Oncorhynchus mykiss (Walbaum), and fathead minnows, Pimphales promelas (Rafinesque), to examine their susceptibility and the clinical impact of infection. Triplicate groups of rainbow trout (n = 40) were injected intraperitoneally (i.p.) with 100 μL 106.550% tissue culture infective doses (TCID50) or waterborne exposed to graded doses (104.5, 106.5, and 108.5 TCID50 mL−1) of VHSV IVb. Duplicate groups of fathead minnows (n = 15) were i.p. injected with (106.5 TCID50 100 μL) or waterborne exposed (106.5 TCID50 mL−1). All experiments were performed with single‐pass well water maintained at 12 °C. Following either i.p. or waterborne exposure, VHSV RNA was detectable in both rainbow trout and fathead minnows by nested reverse transcription polymerase chain reaction (nRT‐PCR) as early as 4–7 days post‐infection (p.i.). Infected fathead minnow and rainbow trout exhibited lesions characteristic of VHS at 9 and 15 days p.i., respectively. Route of exposure had little effect on the onset of clinical signs. Cumulative mean mortality in rainbow trout was 4.4%, 2.6%, 2.6% and less than 1% in the i.p., high, medium and low dose waterborne exposures, respectively. Cumulative average mortality of 50% and 13% occurred in i.p. and waterborne‐exposed fathead minnows, respectively. VHSV was detected from pooled rainbow trout tissue by RT‐PCR and virus isolation at 38 days p.i., but not at 74 days p.i., regardless of the exposure route. Immunohistochemistry (IHC) with a rabbit antibody to VHSV IVb revealed the viral tissue tropisms following infection, with the identification of viral antigen in myocardium and necrotic branchial epithelium of both species and in gonadal tissue of fathead minnows. Rainbow trout, but not fathead minnows, are relatively refractory to experimental infection with VHSV IVb.
Impact of yellow head virus outbreaks in the whiteleg shrimp, Penaeus vannamei (Boone), in Thailand
Authors: Senapin S , Thaowbut Y , Gangnonngiw W , Chuchird N , Sriurairatana S , Flegel T W
Published: February 2010

Yellow head virus (YHV) is known as a major pathogen in the black tiger shrimp, Penaeus (Penaeus) monodon. It can also cause serious mortality in farmed whiteleg shrimp, Penaeus (Litopenaeus) vannamei. However, there is no published information on the economic and/or production impact of the disease in P. vannamei. Shrimp with gross signs of YHV disease (faded body colour and 60–70% mortality) were observed in 20 study farms rearing P. vannamei in the central part of Thailand from the end of 2007 through early 2008. The estimated economic loss for these farms according to the Thai Animal Aquaculture Association was approximately US$3 million. Detailed sequence analysis of RT‐PCR amplicons from shrimp in all the study ponds revealed the presence of YHV Type 1b (YHV‐1b) alone (characterized by a 162‐bp deletion in the ORF3 region encoding the structural gene for gp116) and the absence of YHV Type 1a (YHV‐1a), the original YHV type reported from Thailand. Despite the large 162‐bp deletion (= 54 deduced amino acids) in the gp116 structural gene, histopathology of YHV‐1b infections was identical to that of YHV‐1a infections, and electron microscopy revealed that YHV‐1b virions were morphologically indistinguishable from those previously reported for YHV‐1a. In addition, an existing commercial RT‐PCR detection kit and an immunochromatographic test strip for the detection of YHV were proven to have been valid tests for both YHV‐1b and YHV‐1a. The source of the virus for these outbreaks was unlikely to have been the post‐larvae used to stock the ponds, as they were derived from domesticated specific pathogen‐free stocks free of YHV. Thus, it is possible that they originated from an unknown, natural reservoir.
Phenotype determining alleles in GM1 gangliosidosis patients bearing novel GLB1 mutations
Authors: Hofer D , Paul K , Fantur K , Beck M , Roubergue A , Vellodi A , Poorthuis BJ , Michelakakis H , Plecko B , Paschke E
Published: February 2010

Hofer D, Paul K, Fantur K, Beck M, Roubergue A, Vellodi A, Poorthuis BJ, Michelakakis H, Plecko B, Paschke E. Phenotype determining alleles in GM1 gangliosidosis patients bearing novel GLB1 mutations.

GM1 gangliosidosis manifests with progressive psychomotor deterioration and dysostosis of infantile, juvenile, or adult onset, caused by alterations in the structural gene coding for lysosomal acid ß‐galactosidase (GLB1). In addition, allelic variants of this gene can result in Morquio B disease (MBD), a phenotype with dysostosis multiplex and entire lack of neurologic involvement. More than 100 sequence alterations in the GLB1 gene have been identified so far, but only few could be proven to be predictive for one of the GM1 gangliosidosis subtypes or MBD. We performed genotype analyses in 16 GM1 gangliosidosis patients of all phenotypes and detected 28 different genetic lesions. Among these, p.I55FfsX16, p.W65X, p.F107L, p.H112P, p.C127Y, p.W161X, p.I181K, p.C230R, p.W273X, p.R299VfsX5, p.A301V, p.F357L, p.K359KfsX23, p.L389P, p.D448V, p.D448GfsX8, and the intronic mutation IVS6‐8A>G have not been published so far. Due to their occurrence in homozygous patients, four mutations could be correlated to a distinct GM1 gangliosidosis phenotype. Furthermore, the missense mutations from heteroallelic patients and three artificial nonsense mutations were characterized by overexpression in COS‐1 cells, and the subcellular localization of the mutant proteins in fibroblasts was assessed. The phenotype specificity of 10 alleles can be proposed on the basis of our results and previous data.
Two percent of patients suspected of having Angelman syndrome have TCF4 mutations
Authors: Takano K , Lyons M , Moyes C , Jones J , Schwartz CE
Published: February 2010

Takano K, Lyons M, Moyes C, Jones J, Schwartz CE. Two percent of patients suspected of having Angelman syndrome have TCF4 mutations.

The TCF4 gene encodes a basic helix–loop–helix (bHLH) transcription factor which belongs to the family of E‐proteins. E‐proteins form homo‐ and heterodimers with other members of the HLH family and bind to the common DNA sequence called E‐box. Haploinsufficiency of the TCF4 gene has been found to be associated with the Pitt–Hopkins syndrome (PTHS). PTHS is characterized by severe mental retardation, a wide mouth plus other distinctive facial features (fleshy lips, beaked nose, broad nasal bridge) and breathing abnormalities. Because of some phenotypical overlap with Angelman syndrome (AS), it has been suggested that PTHS be considered in its differential diagnosis. To explore this possibility, we screened 86 patients who were suspected of having AS. All the patients were negative for UBE3A testing, and 53 were known to be negative for methylation analysis. We identified two TCF4 mutations in this cohort. The p.S384Tfsx7 mutation lacks the bHLH domain. The p.R582P mutation lies within the bHLH domain in which seven other missense mutations have been reported. Both mutations most likely affect the critical function of the bHLH domain of the TCF4 protein. In summary, we found two TCF4 mutations in 86 patients (2%) suspected to have AS. Screening for mutations in this gene should be considered in patients who present with findings of AS but who have been negative for methylation and UBE3A testing.
Congenital central hypoventilation syndrome: genotype–phenotype correlation in parents of affected children carrying a PHOX2B expansion mutation
Authors: Parodi S , Vollono C , Baglietto MP , Balestri M , Di Duca M , Landri PA , Ceccherini I , Ottonello G , Cilio MR
Published: February 2010

Parodi S, Vollono C, Baglietto MP, Balestri M, Di Duca M, Landri PA, Ceccherini I, Ottonello G, Cilio MR. Congenital central hypoventilation syndrome: genotype–phenotype correlation in parents of affected children carrying a PHOX2B expansion mutation.

Congenital Central Hypoventilation Syndrome (CCHS) is a rare genetic disorder. Although most CCHS associated PHOX2B mutations occur de novo, about 10% of the cases are inherited from apparently asymptomatic parents, thus confirming variable expressivity and incomplete penetrance of PHOX2B mutations. Three asymptomatic parents of children affected with CCHS, and found to carry the same PHOX2B expansion mutations as their siblings, were studied by overnight polysomnography and somatic mosaicism analysis. In one case, significant sleep breathing control anomalies were detected, while the other two resulted in normal. In tissue‐specific allele studies, mosaicism with a comparatively low mutant allele proportion was showed in the two unaffected adult carriers. Accurate polysomnography and assessment of the degree of somatic mosaicism should be conducted in asymptomatic carriers of PHOX2B mutations, as they may unmask subclinical but significant anomalies
A homozygous FKRP start codon mutation is associated with Walker–Warburg syndrome, the severe end of the clinical spectrum
Authors: Van Reeuwijk J , Olderode‐Berends MJW , Van Den Elzen C , Brouwer OF , Roscioli T , Van Pampus MG , Scheffer H , Brunner HG , Van Bokhoven H , Hol FA
Published: February 2010

van Reeuwijk J, Olderode‐Berends MJW, van den Elzen C, Brouwer OF, Roscioli T, van Pampus MG, Scheffer H, Brunner HG, van Bokhoven H, Hol FA. A homozygous FKRP start codon mutation is associated with Walker–Warburg syndrome, the severe end of the clinical spectrum.

Dystroglycanopathies are a heterogeneous group of disorders caused by defects in the glycosylation pathway of α‐dystroglycan. The clinical spectrum ranges from severe congenital muscular dystrophy with structural brain and eye involvement to a relatively mild adult onset limb‐girdle muscular dystrophy without brain abnormalities and normal intelligence. Mutations have been identified in one of six putative or demonstrated glycosyltransferases. Many different FKRP mutations have been identified, which cover the complete clinical spectrum of dystroglycanopathies. In contrast to the other known genes involved in these disorders, genotype–phenotype correlations are not obvious for FKRP mutations. To date, no homozygous or compound heterozygous null mutations have been identified in FKRP, suggesting that null mutations in FKRP could result in embryonic lethality. We report a family with two siblings carrying a homozygous mutation in the start codon of FKRP that is likely to result in a loss of functional FKRP protein. The clinical phenotype of the patients was consistent with Walker–Warburg syndrome, the most severe disorder in the disease spectrum of dystroglycanopathies.
Molecular characterization of five patients with homocystinuria due to severe methylenetetrahydrofolate reductase deficiency
Authors: Urreizti R , Moya‐García AA , Pino‐Ángeles A , Cozar M , Langkilde A , Fanhoe U , Esteves C , Arribas J , Vilaseca MA , Pérez‐Dueñas B , Pineda M , González V , Artuch R , Baldellou A , Vilarinho L , Fowler B , Ribes A , Sánchez‐Jiménez F , Grinberg D , Balcells S
Published: February 2010

Urreizti R, Moya‐García AA, Pino‐ Ángeles A, Cozar M, Langkilde A, Fanhoe U, Esteves C, Arribas J, Vilaseca MA, Pérez‐Dueñas B, Pineda M, González V, Artuch R, Baldellou, A, Vilarinho L, Fowler B, Ribes A, Sánchez‐Jiménez F, Grinberg D, Balcells S. Molecular characterization of five patients with homocystinuria due to severe MTHFR deficiency.

Methylenetetrahydrofolate reductase (MTHFR) plays a major role in folate metabolism. Disturbed function of the enzyme results in hyperhomocysteinemia and causes severe vascular and neurological disorders and developmental delay. Five patients suspected of having non‐classical homocystinuria due to MTHFR deficiency were examined with respect to their symptoms, MTHFR enzyme activity and genotypes of the MTHFR gene. All patients presented symptoms of severe central nervous system disease. Two patients died, at the ages of 15 months and 14 years. One patient is currently 32 years old, and is being treated with betaine and folinic acid. The other two patients, with an early diagnosis and a severe course of the disease, are currently improving under treatment. MTHFR enzyme activity in the fibroblasts of four of the patients was practically undetectable. We found four novel mutations, three of which were missense changes c.664G> T (p.V218L), c.1316T> C (p.F435S) and c.1733T> G (p.V574G), and the fourth was the 1‐bp deletion c.1780delC (p.L590CfsX72). We also found the previously reported nonsense mutation c.1420G> T (p.E470X). All the patients were homozygous. Molecular modelling of the double mutant allele (p.V218L; p.A222V) revealed that affinity for FAD was not affected in this mutant. For the p.E470X mutation, the evidence pointed to nonsense‐mediated mRNA decay. In general, genotype–phenotype analysis predicts milder outcomes for patients with missense changes than for those in which mutations led to severe alterations of the MTHFR protein.
A case report of systemic capillary leak syndrome (Clarkson's disease)
Authors: HOLLENBERG J. , FRYKMAN J. , LUNDBERG L.‐G. , FORSBERG S.
Published: February 2010

Systemic capillary leak syndrome (SCLS) is a very rare disorder also known as Clarkson's disease. The condition is characterized by recurrent episodes of severe capillary hyperpermeability resulting in severe hemoconcentration, hypoalbuminemia, hypovolemia and shock. We describe a 41‐year‐old previously healthy man who was admitted to hospital on several occasions with rapidly developing hypovolemic shock accompanied by extreme hemoconcentration and hypoalbuminemia. Our case is similar to other reports describing patients with SCLS where the initial suspicions have been pointing towards septic shock. He received a combination of prophylactic treatment with theophylline, β‐agonists, immunoglobulins and statins but eventually died after a severe episode of SCLS that ended with recurrent cardiac arrest. Clinical autopsy revealed pulmonary edema and acute and chronical organic fluid overload. SCLS should be kept in mind when treating patients suffering from attacks of severe idiopathic edema and mimics recurrent septic shock where no pathogen is found. The pathogenesis is unknown and the attacks may be lethal.
Multi‐trait BLUP in half‐sib selection of annual crops
Authors: Viana J. M. S. , Sobreira F. M. , De Resende M. D. V. , Faria V. R.
Published: February 2010

With 2 tables

The Best Linear Unbiased Prediction (BLUP) methodology, which is widely used in animal and forestry genetic evaluation, can also be applied to annual crop breeding. The objective of this study was to compare the accuracy and efficiency of among‐ and within‐half‐sib family selection through the use of single‐ and multi‐trait BLUP, and BLUE/anova methods. Expansion volume and yield data from two recurrent selection cycles of a popcorn population were analyzed. Progeny tests were designed as a lattice. To maximize accuracy of the prediction of breeding values, the BLUP analyses included phenotypic values of the two cycles. All BLUP analyses were performed using the ASReml software. The multi‐trait BLUP method demonstrated greater accuracy and efficiency in family selection. In the case of within‐family selection, both accuracy and efficiency of multi‐ and single‐trait BLUP methods were equivalent. The selection efficiency of the multi‐trait BLUP was dependent on the estimated genetic parameters, particularly the difference between the genetic and environmental correlations of the traits.
Neutrophil gelatinase‐associated lipocalin levels in chronic haemodialysis patients
Authors: BOLIGNANO DAVIDE , COPPOLINO GIUSEPPE , ROMEO ADOLFO , LACQUANITI ANTONIO , BUEMI MICHELE
Published: February 2010

Neutrophil gelatinase‐associated lipocalin (NGAL), a small 25 kDa protein strongly induced in injured renal tubular cells, represents an interesting emerging biomarker in the field of clinical nephrology. The aim of the present pilot study was to analyze circulating NGAL levels in a small cohort of 30 patients on chronic haemodialysis (HD), in order to assess any relationships with different laboratory and clinical parameters. Pre‐ and post‐HD levels were higher in patients than in healthy subjects (485.2 ± 49.7 vs 51.2 ± 4.6 ng/mL; P < 0.001; and 167.4 ± 48.0 vs 51.2 ± 4.6 ng/mL; P = 0.01). Furthermore, a single HD session decreased NGAL levels by approximately fourfold (485.2 ± 49.7 vs 167.4 ± 48.0 ng/mL; p:0.01), with a reduction ratio of 73 ± 14%. At baseline, direct and independent correlations were found between NGAL and, respectively, high‐sensitivity C‐reactive protein (β = 0.34; P = 0.03) and spKt/V (β = 0.35; P = 0.02). The findings showed that HD patients have chronically increased levels of circulating NGAL. However, with a single HD session, a marked reduction was achieved in circulating NGAL values, probably as a result of an important dialytic removal, similar to that observed for other cytokines. Finally, the direct independent correlation found between NGAL and spKt/V raises the question of whether, in the future, NGAL may also become a useful tool in predicting the adequacy of dialysis and in guiding the management of dialysis prescriptions.