bluuebunny/crossref_metadata_2025 huggingface dataset:
Formation of coupled three-dimensional GeSi quantum dot crystals
Authors: Ma Y. J. , Zhong Z. , Lv Q. , Zhou T. , Yang X. J. , Fan Y. L. , Wu Y. Q. , Zou J. , Jiang Z. M.
Published: April 2012

Coupled three-dimensional GeSi quantum dot crystals (QDCs) are realized by multilayer growth of quantum dots (QDs) on patterned SOI (001) substrates. Photoluminescence spectra of these QDCs show non-phonon (NP) recombination and its transverse-optical (TO) phonon replica of excitons in QDs. With increasing excitation power, peak energies of both the NP and TO peaks remain nearly constant and the width of the TO peak decreases. These anomalous features of the PL peaks are attributed to miniband formation due to strong coupling of the holes and the emergence of quasioptical phonon modes due to periodic scatters in ordered GeSi QDs.
Conditional expectation and Bayes’ rule for quantum random variables and positive operator valued measures
Authors: Farenick Douglas , Kozdron Michael J.
Published: April 2012

A quantum probability measure ν is a function on a σ-algebra of subsets of a (locally compact and Hausdorff) sample space that satisfies the formal requirements for a measure, but where the values of ν are positive operators acting on a complex Hilbert space, and a quantum random variable is a measurable operator valued function. Although quantum probability measures and random variables are used extensively in quantum mechanics, some of the fundamental probabilistic features of these structures remain to be determined. In this paper, we take a step toward a better mathematical understanding of quantum random variables and quantum probability measures by introducing a quantum analogue for the expected value \documentclass[12pt]{minimal}\begin{document}$\mathbb E_\nu [\psi ]$\end{document}Eν[ψ] of a quantum random variable ψ relative to a quantum probability measure ν. In so doing we are led to theorems for a change of quantum measure and a change of quantum variables. We also introduce a quantum conditional expectation which results in quantum versions of some standard identities for Radon-Nikodým derivatives. This allows us to formulate and prove a quantum analogue of Bayes’ rule.
Coherent acoustic wave oscillations and melting on Ag(111) surface by time resolved x-ray diffraction
Authors: Oguz Er Ali , Chen Jie , Tang Jau , Rentzepis Peter M.
Published: April 2012

The transient structural disorder on the Ag(111) crystal after excitation with fs pulses was studied by means of time resolved x-ray diffraction. The lattice disorder after UV irradiation is detected by changes in the XRD rocking curve including peak shift, broadening, and total diffraction intensity. We have observed blast and pressure wave formation and melting and mosaic crystal formation during re-crystallization. A blast force was formed within 2 ps after fs UV irradiation of the crystal, followed lattice contraction, melting phase transition, and mosaic crystal formation as the temperature decreases below melting. The experimental data are also supported by theoretical simulations.
Analysis of dielectric loaded surface plasmon waveguide structures: Transfer matrix method for plasmonic devices
Authors: He Xiao Yong , Wang Qi Jie , Yu Siu Fung
Published: April 2012

The propagation properties of dielectric loaded surface plasmon polariton (DLSPP) waveguide structures have been investigated by using the transfer matrix method (TMM), which is simple and has a fast calculation speed. The results obtained from the TMM agree well with those from the finite element method. As a demonstration, we investigate the waveguide properties of DLSPP structures in the terahertz and near-infrared regimes. The TMM is potentially a powerful and effective tool for studying various plasmonic waveguide structures, which may find important applications in integrated photonic devices and sensors.
The anharmonic vibration of Li in lithium amide
Authors: Paik B. , Hasegawa T. , Ishii I. , Michigoe A. , Suzuki T. , Udagawa M. , Ogita N. , Ichikawa T. , Kojima Y.
Published: April 2012

A large amplitude rattling-type anharmonic vibration of Li is possible without guest-host type structure, as we report here for tetragonal LiNH2 crystal. The low temperature (0.4–300 K) specific heat capacity and Raman spectroscopy support the phonon model of site-specific Li activities governed by the symmetry of the potential energy distribution around the Li atoms in LiNH2, which yields the anharmonic Li3 vibration (optical) in one direction (either X or Y axis of the crystal), while the Li1 and Li2 atoms remain silent. Our finding may help to correlate ionic conductivity, thermal, and hydrogenation properties of LiNH2.
Coordination variation of hydrated Cu2+/Br1− ions traversing the interfacial water in mesopores
Authors: Wang Q. , Huang X. F. , Li C. X. , Pan L. Q. , Wu Z. H. , Hu T. D. , Jiang Z. , Huang Y. Y. , Cao Z. X. , Sun G. , Lu K. Q.
Published: April 2012

Resolution of the atomistic and electronic details about the coordination structure variation of hydrated ions in the interfacial water is still a tough challenge, which is, however, essentially important for the understanding of ion adsorption, permeation and other similar processes in aqueous solutions. Here we report the tracing of coordination structure variation for hydrated Cu2+/Br1- ions traversing the interfacial water in Vycor mesopores (ϕ = 7.6 nm) by employing both X-ray absorption near edge structure and extended X-ray absorption fine structure spectroscopies. By controlled desorption/adsorption of water, the filling fraction of the mesopores, thus the water layer thickness, can be adjusted, which in turn effects the variation of coordination structure of the ions therein. It is found that both Cu2+ and Br1- ions prefer staying exclusively in the core water, and in this circumstance no ion pairs have been detected in the solution of concentrations up to 1.0 M. Following capillary decondensation occurring at a filling fraction of ∼35% which corresponds to a water layer of about three monolayers, Br1- ions begin immediately to reconstruct their first coordination shell, characterized by ionic dehydration, shrinkage of ion-water bond length, and formation of ion pairs. In contrast, Cu2+ ions can retain a bulk-like coordination structure till being driven to bond directly to the pore surface when the filling fraction is below 20%. At the final stage of dehydration via thermal vacuum treatment at 110°C, Cu2+ ions can be completely reduced to the Cu1+ state, and recover at room temperature only when the filling fraction is above 14%. These results may be inspirable for the investigation of similar problems concerning hydrated ions in water solution under different confining conditions.
Soft matrix and fixed point of Lennard-Jones potentials for different hard-clusters in size at glass transition
Authors: Wu Jia Lin
Published: April 2012

The existence of fixed point in self-similar Lennard-Jones (L-J) potentials has been proved based on the mosaic geometric structure theory of glass transition (GT) [J. L. Wu, Soft Nanoscience letters, 1, 3–86 (2011)]. A geometric local-global mode-coupling recursive equation, different from the current Mode-Coupling Theories, has been introduced to find out the non-integrable induced potential structure of boson peak at GT. The recursively defined variable in reduced recursive equation is the potential fluctuation of reduced L-J potentials associated with reduced geometric phase potentials. A series of results have been deduced directly at GT. (i) There are only 8 orders of molecule-clusters. (ii) Two orthogonally fast-slow reduced phase potentials, 3/8 and 5/8, are accompanied with density fluctuation and clusters hop-delocalization along 8 geodesics. (iii) The stability condition of potential fluctuation is the Lindemann ratio. (iv) A new reduced attractive potential of –17/16, lower than reduced potential well energy –1, occurs.
The Biomimetic Inspiration for Renewable Hydrogen Fuel Production from Water Oxidation within Artificial Photosynthesis
Authors: Pace Ron J. , Stranger Rob
Published: April 2012

The thermodynamic constraints for the operation of the water oxidizing Mn4/Ca cluster within Photosystem II (PS II) are discussed. These are then examined in the light of the known redox chemistry of hydrated Mn-oxo systems and relevant model compounds. It is shown that the latest high resolution crystal structure of cyanobacterial PS II suggests an organization of the mono Ca tetranuclear Mn cluster that naturally accommodates the stringent requirements for successive redox potential constancy, with increasing total oxidation state, which the enzyme function imposes. This involves one region of the Mn4/Ca cluster being dominantly involved with substrate water binding, while a separate, single Mn is principally responsible for the redox accumulation function. Recent high level computational chemical investigations by the authors’ strongly support this, with a computed pattern of Mn oxidation states throughout the catalytic cycle being completely consistent with this interpretation. Strategies to design synthetic, biomimetic constructs utilizing this approach for efficient electrolytic generation of hydrogen fuel within artificial photosynthesis are briefly discussed.
New Synthesis of Dibenzofulvenes by Palladium-Catalyzed Double Cross-Coupling Reactions
Authors: Shimizu Masaki , Nagao Ikuhiro , Kiyomoto Shin-ichi , Hiyama Tamejiro
Published: April 2012

Palladium-catalyzed double cross-coupling reactions of 1,1-bis(pinacolato)borylalk-1-enes with 2,2′-dibromobiaryls and of 9-stannafluorenes with 1,1-dibromoalk-1-enes have been demonstrated to serve as new synthetic methods for dibenzofulvenes.
Short-term effects of a wildfire on the water quality and macroinvertebrate community of a saline stream
Authors: Corbin Tracy A.
Published: April 2012

The effects of a wildfire on the water quality and macroinvertebrate community of a saline stream in a semiarid, predominantly cleared catchment were investigated. Samples collected for 12 months following the fire were compared with pre-fire conditions. Small increases in filterable reactive phosphorus, total Kjeldahl nitrogen, total phosphorus, colour and turbidity and decreases in dissolved oxygen were recorded the day after the fire; however, most concentrations returned to pre-fire conditions within 2–3 months. Increases in nutrients were likely due to the deposition of ash, smoke and debris. Total phosphorus and total Kjeldahl nitrogen in the lower part of the catchment remained significantly higher for the year after the fire. No fire-related changes in the macroinvertebrate community structure were apparent. Reduced rainfall following the fire, the predominantly cleared catchment and the presence of a saline-tolerant macroinvertebrate assemblage all contributed to the reduced effects from the fire.
Seasonal variation in surface fuel moisture between unthinned and thinned mixed conifer forest, northern California, USA
Authors: Estes Becky L. , Knapp Eric E. , Skinner Carl N. , Uzoh Fabian C. C.
Published: April 2012

Reducing stand density is often used as a tool for mitigating the risk of high-intensity crown fires. However, concern has been expressed that opening stands might lead to greater drying of surface fuels, contributing to increased fire risk. The objective of this study was to determine whether woody fuel moisture differed between unthinned and thinned mixed-conifer stands. Sections of logs representing the 1000- and 10 000-h fuel sizes were placed at 72 stations within treatment units in the fall (autumn) of 2007. Following snow-melt in 2008, 10-h fuel sticks were added and all fuels were weighed every 1–2 weeks from May until October. Moisture of the 1000- and 10 000-h fuels peaked at the end of May, and then decreased steadily through the season. Moisture of the 10- and 1000-h fuels did not differ between unthinned and thinned stands at any measurement time. The 10 000-h fuel moisture was significantly less in thinned than unthinned stands only in early to mid-May. Overall, even when fuel moisture varied between treatments, differences were small. The long nearly precipitation-free summers in northern California appear to have a much larger effect on fuel moisture than the amount of canopy cover. Fuel moisture differences resulting from stand thinning would therefore not be expected to substantially influence fire behaviour and effects during times of highest fire danger in this environment.
Framing the Ultimatum Game: Gender differences and autonomic responses
Authors: Sarlo Michela , Lotto Lorella , Palomba Daniela , Scozzari Simona , Rumiati Rino
Published: April 2012

The present study aimed at investigating whether the way offers are framed in the Ultimatum Game (UG) affects behavioral and autonomic responses in men and women. The “I give you” and “I take” expressions were used as gain and loss frames, respectively. Skin conductance and heart rate were recorded as indices of autonomic activation in response to unfair, mid‐value, and fair offers. Acceptance rates were higher in men than in women under the gain frame. Moreover, men showed higher acceptance rates under the gain than under the loss frame with mid‐value offers, whereas women's choices were not affected by frame. On the physiological level, men produced differential autonomic response patterns during decision‐making when offers were presented under gain and loss framing. The “I take” frame, by acting as a loss frame, elicited in men the characteristic defensive response pattern that is evoked by aversive stimulation, in which increases in skin conductance are coupled with increases in heart rate. On the other hand, the “I give you” frame, by acting as a gain frame, elicited in men increases in skin conductance associated with prevailing heart rate deceleratory responses, reflecting a state of enhanced attention and orienting. In contrast, women's autonomic reactivity was not affected by frame, consistent with behavioral results. Phasic changes in heart rate were crucial in revealing differential functional significance of skin conductance responses under different frames in men, thus questioning the assumption that this autonomic measure can be used as an index of negative emotional arousal in the UG.
Egg Disinfection to Improve Conservation Aquaculture of Leatherside Chub
Authors: Wagner Eric J , Bartley Matthew S , Oplinger Randall W
Published: April 2012

Leatherside chub Lepidomeda copei eggs were obtained as part of separate spawning and life history experiments. This paper summarizes several egg disinfection tests conducted between 2007 and 2010 to develop protocols for controlling fungus and improving hatching success. Several disinfection strategies that have worked for other species did not result in improved hatch rates, namely, formalin (1,000–2,000 mg/L for 15 min), ultraviolet light (10,200 mW/cm2), or sodium sulfite (1.5% for 5 min). However, petri dish incubation after treatment with copper sulfate (CuSO4) or hydrogen peroxide (H2O2) provided high hatch rates. Eggs treated with 40 or 60 mg/L CuSO4 for 2 min had significantly higher hatch rates than untreated controls. Daily or repeated (2-d) treatments using H2O2 or CuSO4 did not significantly improve survival to hatch relative to treating only once, but fungal growth was better controlled in the daily H2O2 treatments. The highest percentage of hatching (100%) was observed in petri dishes in which eggs were treated daily with either 1,000 or 2,000 mg/L H2O2 for 2 min. Disinfection of eggs left on the rock substrate was also successful with 60 mg/L CuSO4 when treated on days 1 and 3 postcollection. These data provide information that will help eliminate fungal infection of eggs and remove an obstacle to the conservation aquaculture of this increasingly rare cyprinid.
A theoretical and experimental study of ac electrothermal flows
Authors: Loire S , Kauffmann P , Mezić I , Meinhart C D
Published: April 2012

Electrokinetic flows lead to promising utilization for mixing, concentration, pumping and have applications from basic studies of convective flows to fully integrated lab on chip developments. Despite these wide applications, electrothermal flow models have been scarcely studied. We find that the model widely used by the microfluidic community does not fit correctly the measured ac electrothermal fluid flows at higher voltages (10 V
pp and above). We thus analyse both theoretically and experimentally the importance of electrothermal coupling and the buoyancy effect. Numerical simulations are compared with micro-particle image velocimetry measurements of the vortices. Our enhanced model successfully matches our measurements over a wide range of conductivities and voltages.
TFIIIC localizes budding yeastETCsites to the nuclear periphery
Authors: Hiraga Shin-ichiro , Botsios Sotirios , Donze David , Donaldson Anne D.
Published: April 2012

Chromatin function requires specific three-dimensional architectures of chromosomes. We investigated whether Saccharomyces cerevisiae extra TFIIIC (ETC) sites, which bind the TFIIIC transcription factor but do not recruit RNA polymerase III, show specific intranuclear positioning. We show that six of the eight known S. cerevisiae ETC sites localize predominantly at the nuclear periphery, and that ETC sites retain their tethering function when moved to a new chromosomal location. Several lines of evidence indicate that TFIIIC is central to the ETC peripheral localization mechanism. Mutating or deleting the TFIIIC-binding consensus ablated ETC -site peripheral positioning, and inducing degradation of the TFIIIC subunit Tfc3 led to rapid release of an ETC site from the nuclear periphery. We find, moreover, that anchoring one TFIIIC subunit at an ectopic chromosomal site causes recruitment of others and drives peripheral tethering. Localization of ETC sites at the nuclear periphery also requires Mps3, a Sad1-UNC-84–domain protein that spans the inner nuclear membrane. Surprisingly, we find that the chromatin barrier and insulator functions of an ETC site do not depend on correct peripheral localization. In summary, TFIIIC and Mps3 together direct the intranuclear positioning of a new class of S. cerevisiae genomic loci positioned at the nuclear periphery.
Lamin B1 loss is a senescence-associated biomarker
Authors: Freund Adam , Laberge Remi-Martin , Demaria Marco , Campisi Judith
Published: April 2012

Cellular senescence is a potent tumor-suppressive mechanism that arrests cell proliferation and has been linked to aging. However, studies of senescence have been impeded by the lack of simple, exclusive biomarkers of the senescent state. Senescent cells develop characteristic morphological changes, which include enlarged and often irregular nuclei and chromatin reorganization. Because alterations to the nuclear lamina can affect both nuclear morphology and gene expression, we examined the nuclear lamina of senescent cells. We show here than lamin B1 is lost from primary human and murine cell strains when they are induced to senesce by DNA damage, replicative exhaustion, or oncogene expression. Lamin B1 loss did not depend on the p38 mitogen-activated protein kinase, nuclear factor-κB, ataxia telangiectasia–mutated kinase, or reactive oxygen species signaling pathways, which are positive regulators of senescent phenotypes. However, activation of either the p53 or pRB tumor suppressor pathway was sufficient to induce lamin B1 loss. Lamin B1 declined at the mRNA level via a decrease in mRNA stability rather than by the caspase-mediated degradation seen during apoptosis. Last, lamin B1 protein and mRNA declined in mouse tissue after senescence was induced by irradiation. Our findings suggest that lamin B1 loss can serve as biomarker of senescence both in culture and in vivo.
Vitamin K epoxide reductase contributes to protein disulfide formation and redox homeostasis within the endoplasmic reticulum
Authors: Rutkevich Lori A. , Williams David B.
Published: April 2012

The transfer of oxidizing equivalents from the endoplasmic reticulum (ER) oxidoreductin (Ero1) oxidase to protein disulfide isomerase is an important pathway leading to disulfide formation in nascent proteins within the ER. However, Ero1-deficient mouse cells still support oxidative protein folding, which led to the discovery that peroxiredoxin IV (PRDX4) catalyzes a parallel oxidation pathway. To identify additional pathways, we used RNA interference in human hepatoma cells and evaluated the relative contributions to oxidative protein folding and ER redox homeostasis of Ero1, PRDX4, and the candidate oxidants quiescin-sulfhydryl oxidase 1 (QSOX1) and vitamin K epoxide reductase (VKOR). We show that Ero1 is primarily responsible for maintaining cell growth, protein secretion, and recovery from a reductive challenge. We further show by combined depletion with Ero1 that PRDX4 and, for the first time, VKOR contribute to ER oxidation and that depletion of all three activities results in cell death. Of importance, Ero1, PRDX4, or VKOR was individually capable of supporting cell viability, secretion, and recovery after reductive challenge in the near absence of the other two activities. In contrast, no involvement of QSOX1 in ER oxidative processes could be detected. These findings establish VKOR as a significant contributor to disulfide bond formation within the ER.
Fast and accurate inference of local ancestry in Latino populations
Authors: Baran Yael , Pasaniuc Bogdan , Sankararaman Sriram , Torgerson Dara G. , Gignoux Christopher , Eng Celeste , Rodriguez-Cintron William , Chapela Rocio , Ford Jean G. , Avila Pedro C. , Rodriguez-Santana Jose , Burchard Esteban Gonzàlez , Halperin Eran
Published: April 2012

Motivation: It is becoming increasingly evident that the analysis of genotype data from recently admixed populations is providing important insights into medical genetics and population history. Such analyses have been used to identify novel disease loci, to understand recombination rate variation and to detect recent selection events. The utility of such studies crucially depends on accurate and unbiased estimation of the ancestry at every genomic locus in recently admixed populations. Although various methods have been proposed and shown to be extremely accurate in two-way admixtures (e.g. African Americans), only a few approaches have been proposed and thoroughly benchmarked on multi-way admixtures (e.g. Latino populations of the Americas).

Results: To address these challenges we introduce here methods for local ancestry inference which leverage the structure of linkage disequilibrium in the ancestral population (LAMP-LD), and incorporate the constraint of Mendelian segregation when inferring local ancestry in nuclear family trios (LAMP-HAP). Our algorithms uniquely combine hidden Markov models (HMMs) of haplotype diversity within a novel window-based framework to achieve superior accuracy as compared with published methods. Further, unlike previous methods, the structure of our HMM does not depend on the number of reference haplotypes but on a fixed constant, and it is thereby capable of utilizing large datasets while remaining highly efficient and robust to over-fitting. Through simulations and analysis of real data from 489 nuclear trio families from the mainland US, Puerto Rico and Mexico, we demonstrate that our methods achieve superior accuracy compared with published methods for local ancestry inference in Latinos.

Availability:  http://lamp.icsi.berkeley.edu/lamp/lampld/

Contact:  bpasaniu@hsph.harvard.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human
Authors: Qin Bo , Zhou Meng , Ge Ying , Taing Len , Liu Tao , Wang Qian , Wang Su , Chen Junsheng , Shen Lingling , Duan Xikun , Hu Sheng'en , Li Wei , Long Henry , Zhang Yong , Liu X. Shirley
Published: April 2012

Summary: Transcription and chromatin regulators, and histone modifications play essential roles in gene expression regulation. We have created CistromeMap as a web server to provide a comprehensive knowledgebase of all of the publicly available ChIP-Seq and DNase-Seq data in mouse and human. We have also manually curated metadata to ensure annotation consistency, and developed a user-friendly display matrix for quick navigation and retrieval of data for specific factors, cells and papers. Finally, we provide users with summary statistics of ChIP-Seq and DNase-Seq studies.

Availability: Freely available on the web at http://cistrome.dfci.harvard.edu/pc/

Contact:  yzhang@tongji.edu.cn; xsliu@jimmy.harvard.edu
ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R
Authors: Popescu Andrei-Alin , Huber Katharina T. , Paradis Emmanuel
Published: April 2012

Summary: Reflecting its continuously increasing versatility and functionality, the popularity of the ape (analysis of phylogenetics and evolution) software package has grown steadily over the years. Among its features, it has a strong distance-based component allowing the user to compute distances from aligned DNA sequences based on most methods from the literature and also build phylogenetic trees from them. However, even data generated with modern genomic approaches can fail to give rise to sufficiently reliable distance estimates. One way to overcome this problem is to exclude such estimates from data analysis giving rise to an incomplete distance data set (as opposed to a complete one). So far their analysis has been out of reach for ape. To remedy this, we have incorporated into ape several methods from the literature for phylogenetic inference from incomplete distance matrices. In addition, we have also extended ape's repertoire for phylogenetic inference from complete distances, added a new object class to efficiently encode sets of splits of taxa, and extended the functionality of some of its existing functions.

Availability: ape is distributed through the Comprehensive R Archive Network: http://cran.r-project.org/web/packages/ape/index.html Further information may be found at http://ape.mpl.ird.fr/pegas/

Contact:  Katharina.Huber@cmp.uea.ac.uk, Emmanuel.Paradis@ird.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Identification and characterization of bocaviruses in cats and dogs reveals a novel feline bocavirus and a novel genetic group of canine bocavirus
Authors: Lau Susanna K. P. , Woo Patrick C. Y. , Yeung Hazel C. , Teng Jade L. L. , Wu Ying , Bai Ru , Fan Rachel Y. Y. , Chan Kwok-Hung , Yuen Kwok-Yung
Published: April 2012

We report the identification and genome characterization of a novel bocavirus, feline bocavirus (FBoV), and novel bocaviruses closely related to canine bocavirus (CBoV) strain Con-161 in stray cats and dogs in Hong Kong, respectively. FBoV was detected by PCR in 7.2, 0.3, 1.6, 2.0 and 0.8 % of faecal, nasal, urine, kidney and blood samples, respectively, from 364 cats, while CBoV was detected in 4.6, 5.1, 6.3 and 0.3 % of faecal, nasal, urine and blood samples, respectively, from 351 dogs. Three FBoV genomes sequenced revealed the presence of three ORFs characteristic of bocaviruses. Phylogenetic analysis showed that FBoVs were related only distantly to other bocaviruses, forming a distinct cluster within the genus, with ≤59.7 % nucleotide identities to the genome of minute virus of canines. The four CBoV genomes sequenced shared 87.4–89.2 % nucleotide identities with that of CBoV strain Con-161. In addition to the three bocavirus ORFs, they encoded an additional ORF, ORF4, immediately downstream of the ORF for non-structural protein 1 (NS1), which was not found in other bocaviruses including CBoV strain Con-161. They also possessed a putative second exon encoding the C-terminal region of NS1 and conserved RNA-splicing signals, previously described in human bocaviruses. Partial VP1/VP2 sequence analysis of 23 FBoV and 25 CBoV strains demonstrated inter-host genetic diversity, with two potential genetic groups of FBoV and a novel CBoV group, CBoV-HK, distinct from the three groups, CBoV-A to -C, found in the USA. Although the pathogenicity of FBoV and CBoV remains to be determined, their presence in different host tissues suggested wide tissue tropism.
Targeting nuclear factor‐κB suppresses the negative effect of Toll‐like receptor 4 signaling on antimetastasis therapy based on targeting αvβ3
Authors: Zhu Jian‐Hua , Yuan Ye , Li Dong , Liao Sheng‐Jun , Zhou Yuan‐Hong , Wang Qi , Shu Yu , Yan Bin , Wei Jing‐Jing , Sun Rui , Zhang Gui‐Mei , Feng Zuo‐Hua
Published: April 2012

The targeting of αvβ3 is a promising therapeutic strategy for suppressing tumor metastasis. However, it is unclear whether the therapeutic efficacy could be influenced by metastasis‐promoting factor(s) in vivo. Here we report that Toll‐like receptor 4 (TLR4) ligand released from damaged tumor cells or bacteria had a negative effect on the therapeutic effect of a recombinant CBD‐HepII polypeptide of fibronectin (CH50) that suppresses tumor metastasis by targeting αvβ3. The TLR4 ligand could antagonize the inhibitory effect of CH50 on tumor cell adhesion and invasion by promoting the expression and activity of αvβ3 in tumor cells. The TLR4 ligand also reduced the antimetastasis effect of CH50 by promoting tumor cell survival in circulation. Moreover, TLR4 ligands released by tumor cells in circulation could increase the survival and proliferation capacity of tumor cells after extravasation, resulting in the formation of more metastatic nodules. The effect of TLR4 signaling was mainly mediated by nuclear factor‐κB (NF‐κB). Inhibiting NF‐κB could abrogate the negative effect of TLR4 ligand, and augment the inhibitory effect of CH50 on tumor metastasis. Consistently, the combination of NF‐κB inhibitor and CH50 significantly inhibited metastasis of tumor cells in vivo and prolonged the survival of mice. The findings in this study suggest that the combination of NF‐κB inhibitor and αvβ3 antagonist would be a novel therapeutic option for the prevention of tumor metastasis. (Cancer Sci 2012; 103: 1319–1326)
Application of flow cytometric in situ hybridization assay to Epstein–Barr virus‐associated T/natural killer cell lymphoproliferative diseases
Authors: Kawabe Shinji , Ito Yoshinori , Gotoh Kensei , Kojima Seiji , Matsumoto Kimikazu , Kinoshita Tomohiro , Iwata Seiko , Nishiyama Yukihiro , Kimura Hiroshi
Published: April 2012

Epstein–Barr virus (EBV) infects various types of lymphocytes and is associated with not only B cell‐origin lymphoma, but also T or natural killer cell lymphoproliferative diseases (T/NK LPD). Recently, we established a novel assay to identify EBV‐infected cells using FISH. Using this assay, dual staining with antibodies to both surface antigens and an EBV‐encoded small RNA (EBER) probe can be performed. In the present study, we applied this recently developed FISH assay to EBV‐associated T/NK LPD to confirm its diagnostic utility. Using FISH, we prospectively analyzed peripheral blood from patients with suspected EBV‐associated T/NK LPD. The results were compared with those obtained using immunobead sorting followed by quantitative PCR. In all, 26 patients were included study. Using FISH, 0.15–67.0% of peripheral blood lymphocytes were found to be positive for EBER. Dual staining was used to determine EBER‐positive cell phenotypes in 23 of 26 subjects (88.5%). In five of seven patients with hydroa vacciniforme‐like lymphoma (an EBV‐positive cutaneous T cell lymphoma), EBER‐positive cells were identified as CD3+CD4−CD8− TCRγδ+ T cells. Furthermore, in a 25‐year‐old male patient with systemic EBV‐positive T cell LPD, two lymphocyte lineages were positive for EBER: CD4+CD8− and CD4−CD8+T cells. Thus, we confirmed that our newly developed assay is useful for quantifying and characterizing EBV‐infected lymphocytes in EBV‐associated T/NK LPD and that it can be used not only to complement the pathological diagnosis, but also to clarify the pathogenesis and to expand the spectrum of EBV‐associated diseases. (Cancer Sci, doi: 10.1111/j.1349‐7006.2012.02305.x, 2012)
Review of invasive cervical cancers and uptake of disclosure of results: an audit of procedures and response
Authors: Prabakar I. , Moss E. L. , Douce G. , Parkes J. , Redman C. W. E.
Published: April 2012

I. Prabakar, E. L. Moss, G. Douce, J. Parkes and C. W. E. Redman

Review of invasive cervical cancers and uptake of disclosure of results: an audit of procedures and response

Objective:  To audit the process and outcome of case reviews performed for invasive cervical cancers diagnosed between 2003 and 2007, and the timely disclosure of results to the respective patients.

Methods:  Invasive cervical cancer reviews were performed on all cases of cervical cancer diagnosed between 2003 and 2007. Following the review, women were classified into two categories: a group who developed invasive cancer despite adherence to the screening programme or in whom a management or diagnostic decision was determined to have been a principal factor in the development of their disease (Group A), and a second group who either had never undergone a cervical smear or had been established defaulters from the screening programme (Group B).

Results:  Ninety‐seven of the 98 cases of invasive cervical cancer diagnosed in the 4‐year study period were reviewed. Sixty of the 61 women in Group A were sent an invitation to discuss the results of their case review. Thirty‐six (37%) were classified as Group B, and it was deemed neither appropriate nor possible to invite the patients for a review consultation. Of the women sent an invitation, only 24 (40%) chose to attend.

Conclusion:  A policy of selective invitation for the disclosure of invasive review results is feasible. Less than one‐half of patients diagnosed with cervical cancer appear to want to know how they developed cervical cancer despite previously participating in a screening programme.
VEGF is indirectly associated with NO production and acutely increases in response to hyperglycaemia1
Authors: Siervo Mario , Tomatis Virginia , Stephan Blossom C. M. , Feelisch Martin , Bluck Les J. C.
Published: April 2012

Eur J Clin Invest 2012; 42 (9): 967–973

Background  Increased levels of vascular endothelial growth factor (VEGF) have been observed in patients with metabolic syndrome (MetS). Nitric oxide (NO) formation is reduced in MetS, but its relationship to VEGF production remains poorly defined. We evaluated the association between VEGF/NO synthesis and insulin sensitivity in obese subjects and investigated the secretory response of VEGF to an acute elevation of glucose.

Materials and methods  Seven healthy normal‐weight subjects, seven obese subjects without MetS and seven obese subjects with MetS were recruited. Anthropometry, body composition and cardiometabolic functions (blood pressure, glucose, insulin, triglycerides, total cholesterol, HDL‐C and VEGF) were measured, and a novel stable isotope method was used to assess in vivo rates of NO production. A frequent sampling intravenous glucose tolerance test was performed to study the dynamics of VEGF release.

Results  Fasting VEGF levels were significantly higher in the two obese groups compared to the control group (P for trend = 0·02), but the difference was not significant after adjustment for age. Vascular endothelial growth factor levels were associated with systolic blood pressure (ρ = 0·54; P = 0·01) and NO production (ρ = −0·44; P = 0·04). Vascular endothelial growth factor levels increased in response to acute hyperglycaemia in normal‐weight and obese subjects (P < 0·001).

Conclusions  Vascular endothelial growth factor levels rapidly increase during hyperglycaemia and are inversely related to NO production at steady state. The potential link between the acute secretion of VEGF and atherosclerotic risk in subjects with poorly controlled glycaemia as well as the potential of lowering elevated VEGF levels by increasing NO production and/or availability warrants further investigation.
Self‐care after traumatic injury and the use of the therapeutic self care scale in trauma populations
Authors: Chaboyer Wendy , Ringdal Mona , Aitken Leanne , Kendall Elizabeth
Published: April 2012

chaboyer w., ringdal m., aitken l. & kendall e. (2012) Self‐care after traumatic injury and the use of the therapeutic self‐care scale in trauma populations. Journal of Advanced Nursing69(2), 286–294 doi: 10.1111/j.1365‐2648.2012.06005.x.

Aims.  To report a correlational study of the relationship between gender, age, severity of injury, length of hospital stay and self‐care behaviour in patients with traumatic injuries.

Background.  This study may provide a foundation for targeted nursing intervention and education programmes to help patients better recover from their injury, which is a fundamental aspect of nursing.

Design.  A longitudinal cohort study.

Method.  This study of patients hospitalized for traumatic injury was conducted from May 2006–November 2007. The Therapeutic Self Care Scale along with demographic and clinical data, were completed at 3 and 6 months after hospital discharge. Using data from the 3‐month survey, the validity and reliability of the scale was calculated. Multiple regression was used to identify predictors of self‐care at 3 and 6 months.

Finding.  Participants (n = 125) completed the questionnaire at 3 months and 103 participants completed it at 6 months. Self‐care was high on both occasions and high self‐care at 3 months was related to high self‐care at 6 months. Older participants reported higher self‐care at 3 months compared with younger patients. Factor analysis of the scale revealed three clear components; taking medication, recognition and managing symptoms and managing changes in health conditions, which explained a total of 59·8% of the variance. The 10‐item revised scale was reliable.

Conclusion.  The findings indicate that self‐care remains fairly high and stable in the first 6 months after trauma. The revised Therapeutic Self Care Scale was valid and reliable in the trauma population.
Administrative stressors and nursing job outcomes in Australian public and non‐profit health care organisations
Authors: Teo Stephen TT , Yeung Melissa , Chang Esther
Published: April 2012

Aims and objectives.  The main aim of this study is to develop a path model to examine the effect of administrative stressors on nursing work outcomes in a sample of Australian public and non‐profit nurses.

Background.  The implementation of managerial reform initiatives has negative consequences on work outcomes. However, less is known about the effects of these stressors in public and non‐profit health care organisations.

Design.  An online, self‐completion questionnaire was sent to a random sample of nurses, employed in nursing‐related occupations.

Participants.  Useable surveys were received from 251 nurses.

Methods.  The path model was analysed using SmartPLS software (SmartPLS, Hamburg, Germany).

Results.  Public and non‐profit nurses experienced time and resource administrative‐related stressors (such as resource shortage and pay not as good as other people doing similar work). They relied on work‐related social support to reduce the negative consequences. Resource stressors led to job dissatisfaction while time stressors led to psychological strain. Nursing staff who reported better psychological health reported higher job satisfaction and higher level of commitment towards their organisations.

Conclusions.  Context‐specific administrative stressors have a negative impact on the work outcomes of public and non‐profit nurses. Work‐related social support mechanisms were found to mediate the negative consequences of administrative resourcing stressors on nursing job satisfaction.

Relevance to clinical practice.  Nursing managers have to be sympathetic and care for the negative experiences of nursing staff, especially when there is an increasing level of administrative expectations during organisational change. Senior management should take note of the stressors caused by the lack of resources such as information, staffing and resources, as these were found to lead to an increase in nurses seeking work‐related social support from their peers and supervisors. Effective implementation of these strategies would lead to a nursing workforce, which has higher level of psychological health, job satisfaction and organisational commitment.
Fine‐scale changes in connectivity affect the metapopulation dynamics of a bryophyte confined to ephemeral patches
Authors: Zartman Charles E. , Nascimento Henrique E. M. , Cangani Katia G. , Alvarenga Lisi D. P. , Snäll Tord
Published: April 2012

1. We test how fine‐scale (≤ 400 m2) connectivity to conspecifics influences metapopulation dynamics using a field experiment in central Amazonia with the epiphyllous (i.e. leaf‐inhabiting) bryophyteRadula flaccidaGott. (Radulaceae). This is a natural model system with spatially structured ephemeral patches at the leaf and phorophyte scale.

2. The aim was to test how the rates of leaf colonization, local abundance, growth and extinction of bryophytes from both leaves and host phorophytes were affected by experimentally manipulated variation in connectivity to conspecifics. We also investigated the relative importance of local stochastic extinctions and deterministic extinctions at both spatial scales.

3. Approximately 3500 leaves on 70 phorophytes were censused six times over a 15‐month period by utilizing a repeated block design with control, positive control and three pulse‐style reduction treatments, which varied in connectivity to surrounding conspecifics.

4. An increase in stochastic extinction events was only accompanied by a reduction in colonization in the treatment in which focal and neighbouring phorophytes within the 400 m2plots were experimentally denuded of their natural populations, suggesting that epiphyllous cryptogams are subject to fine‐scale (withinphorophyte) rescue effects. Negative density‐dependent growth was also detected in within‐leaf population dynamics, suggesting that resource limitation or intraspecific competition influences local population growth. Finally, stochastic extinctions from viable leaves occurred with nearly the same frequency as deterministic events (e.g. leaf fall), whereas at the phorophyte scale only stochastic extinctions were observed.

5. Synthesis.The experiment demonstrates that rescue effects occur at fine scales even for vagile plant taxa, such as cryptogams, which may inhabit spatially isolated substrates characterized by turnover rates as fast as their own population dynamics. Furthermore, the results highlight the importance of quantifying both stochastic and deterministic extinction modes, as underestimating either of these parameters leads to over optimistic projections of future metapopulation size.
Chance in plant communities: a new approach to its measurement using the nugget from spatial autocorrelation
Authors: Brownstein Gretchen , Steel John B. , Porter Stefan , Gray Abraham , Wilson Craig , Wilson Padarn G. , Bastow Wilson J.
Published: April 2012

1. The unpredictable component of community structure – chance/randomness/stochasticity – is increasingly discussed, recently in terms of Neutral Theory, but is never directly measured. We show that a direct estimate of chance can be made from spatial autocorrelation, and demonstrate this usage.

2. The dissimilarity between two patches of vegetation was plotted against the distance between the patches, and a curve fitted. We argue that the y‐intercept of the curve, i.e. the ‘nugget’, represents the amount of chance variation in species composition, because when distance is zero all dispersal limitation and spatially correlated environmental differences are excluded, and only chance remains.

3. The method estimated that in 16 sites around the South Island of New Zealand, 0–71% of the variation in plant community composition was due to chance, with a mean of 34%.

4. Synthesis. The new analysis method provides information on the amount of randomness in community species composition and could be applied to the many dissimilarity/distance studies in the literature. The amount of randomness in the 16 study sites was not related to the type of plant community or to the species richness per quadrat. However, randomness was positively correlated with whole‐community species richness, supporting previous suggestions of a relationship between chance, the size of the species pool and redundancy.
Surface plasmon microscopy: resolution, sensitivity and crosstalk
Authors: PECHPRASARN S. , SOMEKH M.G.
Published: April 2012

This paper develops the theoretical framework to understand the capability of the interferometric surface plasmon microscope to quantify sample properties in a confined region. We use rigorous diffraction theory to quantify the ability of the system to measure local properties and eliminate crosstalk from adjacent regions. We argue that the interferometric system in the defocused condition defines the measured point of excitation and reradiation of the surface plasmons; which greatly improves localisation. We also present results for the noninterferometric microscope, which confirm that the interferometric based system can perform quantitative measurements over smaller regions.
Brood mixing and reduced polyandry in a maternally mouthbrooding cichlid with elevated among‐breeder relatedness
Authors: SEFC KRISTINA M. , HERMANN CAROLINE M. , TABORSKY BARBARA , KOBLMÜLLER STEPHAN
Published: April 2012

Uniparental maternal brood care often coincides with multiple paternity and single maternity of broods, possibly reflecting benefits of polyandry and costs of uniparental care. Genetic data from the maternally mouthbrooding cichlid fishSimochromis pleurospilusrevealed the opposite pattern – low polyandry and allomaternal care. More than 70% of the investigated females had mated with a single male, and 14% of the females had unrelated fry in their broods. Broods with foreign fry were in the late stage of brood care, in which females guard free‐swimming fry and recall the broods into their mouths for protection. With one exception, fostering females were related to their adopted fry at the level of first cousins (RQG > 0.12), but relatedness between fosters and adopted fry was not significantly higher than between fosters and fry tended by other females. Relatedness among breeders extended to the level of first‐order relatives. Mean relatedness among contemporaneously breeding dams (RQG = 0.08) was significantly higher than among dams breeding in different seasons (RQG = −0.04), which suggests a temporal or spatial concentration of mouthbrooding relatives. Indeed, females sometimes brood in small groups. This behaviour may reduce brood predation but will increase the risk of brood mixing, which is possibly mitigated by low costs of brood care and indirect benefits accrued by relatedness among the breeders in the group. Remarkably, the apparent inbreeding potential did not give rise to bet‐hedging polyandry or active avoidance of relatives, as half of the mated individuals were related atRQG > 0.13 and polyandry did not coincide with high within‐pair relatedness.