bluuebunny/crossref_metadata_2025 huggingface dataset:
OSMOTIC DEHYDRATION OF POMEGRANATE SEEDS (PUNICA GRANATUM L.): EFFECT OF FREEZING PRE‐TREATMENT
Authors: BCHIR BRAHIM , BESBES SOUHAIL , ATTIA HAMADI , BLECKER CHRISTOPHE
Published: March 2011

The osmotic dehydration of pomegranate seeds was compared using fresh and frozen seeds. The process was carried out at 50C in a 55°Brix solution of sucrose. Freezing pomegranate seeds before osmotic dehydration involved an increase of effective diffusivity and a reduction in dehydration time. The most significant changes of water loss (WL) (46 g/100 g of fresh seeds [FS]) and solids gain (SG) (7 g/100 g of FS) took place during the first 20 min for frozen seeds. After this period, seeds WL and SG ranged on average close to 43 and 8 g/100 g of FS, respectively. Osmotic dehydration was slower starting from fresh fruits but led to a higher rate of WL (62 g/100 g of FS) at the end of the process. Both scanning electron microscopy and texture analysis showed a destruction of cell structure and seed texture during the pretreatment (freezing). The same techniques also revealed a texture/structure modification induced by the osmotic dehydration process.

PRACTICAL APPLICATIONS

In Tunisia, the research of addition value to pomegranate seeds is very limited and presents a traditional feature such as jam preparation or direct consummation of fruit during the crop season (between September and December). However, other perspectives of transformation and exploitation of the pomegranate seeds should be undertaken to give an added value to this typical fruit. Osmotic dehydration can be an alternative process to increase the conservation time of fruit and to give a new osmodehydrated fruit that can be included in some food formulation such as ice cream, cereals, dairy, confectionery and bakery products.
POLYPHENOLOXIDASE DEACTIVATION IN JUICE FROM “CAMPBELL EARLY” GRAPES BY HEATING UNDER VACUUM PRESSURE
Authors: GHAFOOR KASHIF , CHOI YONG HEE
Published: March 2011

The juice of “Campbell Early” grapes was analyzed to assess the effect of heating under low vacuum pressure on the inhibition of polyphenoloxidase (PPO), the enzyme that catalyzes browning reactions in grape juice. Treatment of grapes by heating under low vacuum pressure of 200–600 mmHg significantly inhibited the activity of PPO. Up to 82.15% reduction in the enzyme activity was observed in the grape juice by heating “Campbell Early” grapes at 65C for 20 min under 600 mmHg vacuum pressure. The vacuum heating of grapes also resulted in a significant increase in total phenols and total sugars in the grape juice, which also had improved sensory properties.

PRACTICAL APPLICATIONS

Vacuum heating enables us to attain the desired quality attributes during processing of fruits and vegetables at reduced temperature. Our study revealed that it not only deactivated polyphenoloxidase in grape juice but also increased other functional and sensory characteristics. Vacuum heating can be effectively applied in the fruits and vegetables processing industry for prevention of enzymatic browning as an alternate to the use of chemical preservatives and more costly enzyme inactivation techniques such as pulse electric fields.
Long-Term Outcome following Attendance at a Transient Ischemic Attack Clinic
Authors: Cameron Alan C. , Dawson Jesse , Quinn Terence J. , Walters M.R. , McInnes Gordon T. , Morrison David , Sloan William , Lees Kennedy R.
Published: March 2011

Background and purpose

Many patients who attend transient ischemic attack clinics have a noncerebrovascular diagnosis. The long-term outcomes in this group are not well described. We evaluated these in a cohort referred to a transient ischemic attack clinic with a suspected transient ischemic attack.

Methods

Patients were clinically classified as having stroke or a transient ischemic attack or a noncerebrovascular diagnosis (nontransient ischemic attack). Follow-up was via electronic record linkage. The primary endpoint was cardiovascular death or a major cardiovascular event. Secondary outcomes included incident neurological disease (excluding stroke or transient ischemic attack) and the need for permanent pacemaker insertion. Outcomes in the transient ischemic attack and nontransient ischemic attack cohorts were compared using Cox's proportional hazards models. Mortality outcomes were further compared with those in a contemporary control group of individuals with hypertension.

Results

Of the 3533 patients who attended the transient ischemic attack clinic, 53·5% had a transient ischemic attack. Of these, 769 (40·7%) suffered a cardiovascular endpoint, compared with 458 (27·9%) with a nontransient ischemic attack (hazard ratio 1·53, 95% confidence interval 1·36–1·72). The risk remained higher but was attenuated following adjustment (hazard ratio 1·21, 95% confidence interval 1·05–1·41). Cardiovascular mortality in both groups was higher than that in hypertensive controls. The risk of a subsequent nonstroke neurological event was higher in those without a transient ischemic attack.

Conclusions

Patients without a transient ischemic attack referred to a transient ischemic attack clinic have a high risk of future vascular events that exceeds risk in a cohort with hypertension. All patients attending transient ischemic attack clinics should undergo assessment of their cardiovascular risk and the use of methods to reduce this risk should be explored.
Life history of the Indo‐Pacific humpback dolphin in the Pearl River Estuary, southern China
Authors: Jefferson Thomas A. , Hung Samuel K. , Robertson Kelly M. , Archer Frederick I.
Published: March 2011

Abstract

We studied life history characteristics of the Hong Kong/Pearl River Estuary population of Indo‐Pacific humpback dolphins (Sousa chinensis), based on data from 120 specimens stranded between 1995 and 2009, 40 individuals biopsied at sea, and a long‐term (14+ yr) photo‐identification study. Ages were determined for 112 specimens by thin‐sectioning teeth and counting growth layer groups. Estimated length at birth was 101 cm. Longevity was at least 38 yr, and there was little difference in growth patterns of males and females. Growth was described by a Bayesian two‐phase Gompertz model; asymptotic length was reached at 249 cm. The tooth pulp cavity filled at an average of 18.5 yr of age. Physical maturity was reached at between 14 and 17 yr of age, apparently a few years after attainment of sexual maturity. Maximum lengths and weights of about 268 cm and 240 kg were attained. Females appear to lose all their spots by 30 yr, although males may retain some spotting throughout life. Calving occurred throughout the year, with a broad peak from March to June. Of 60 females monitored at sea for >14 yr of the study, none were documented to have more than three calves, suggestive of low reproductive output or low calf survival.
Functional benefit of the bone‐anchored hearing aid with different auditory profiles: objective and subjective measures
Authors: van Wieringen A. , De Voecht K. , Bosman A.J. , Wouters J.
Published: March 2011

Clin. Otolaryngol. 2011, 36, 114–120

Objectives:  To examine sentence recognition and self‐report outcomes in hearing‐impaired persons with different auditory profiles and who were fitted unilaterally with a bone‐anchored hearing aid.

Study‐design:  Prospective cohort study.

Setting:  Tertiary referral unit.

Patients:  Data were collected of six patients with single‐sided deafness (SSD), seven with a mild to severe hearing loss at the bone‐anchored hearing aid side and (near‐)normal hearing at the other side and six with a severe bilateral hearing loss.

Main outcome measurements:  Sound field thresholds, and sentence recognition in noise (presented from different angles) with bone‐anchored hearing aid, without bone‐anchored hearing aid and with bone‐anchored hearing aid and other ear occluded. In addition, the Speech, Spatial and Qualities of hearing scale and the Abbreviated Profile of Hearing Aid Benefit questionnaire were administered as self‐report measures.

Results:  Patients with single‐sided deafness listened mainly with their non‐bone‐anchored hearing aid ear, although the bone‐anchored hearing aid lifted the head shadow effect. Patients with mild to severe hearing loss at the bone‐anchored hearing aid side and (near‐)normal hearing at the other side performed significantly differently in aided and unaided conditions and even regained limited binaural sensitivity with the device. The latter was also true for the patients with severe bilateral hearing loss. However, their hearing loss at the non‐bone‐anchored hearing aid side was too great to contribute to hearing and they listened predominantly with their bone‐anchored hearing aid. Self‐report outcomes provided useful information on hearing disability, although this information was not significantly differently for the 3 groups of patients.

Conclusions:  The bone‐anchored hearing aid enhanced performance in different hearing configurations, albeit to different extents.
Melanoma cell invasiveness is regulated by miR‐211 suppression of the BRN2 transcription factor
Authors: Boyle Glen M. , Woods Susan L. , Bonazzi Vanessa F. , Stark Mitchell S. , Hacker Elke , Aoude Lauren G. , Dutton‐Regester Ken , Cook Anthony L. , Sturm Richard A. , Hayward Nicholas K.
Published: March 2011

To identify microRNAs potentially involved in melanomagenesis, we compared microRNA expression profiles between melanoma cell lines and cultured melanocytes. The most differentially expressed microRNA between the normal and tumor cell lines was miR‐211. We focused on this pigment‐cell‐enriched miRNA as it is derived from the microphthalmia‐associated transcription factor (MITF)‐regulated gene, TRPM1 (melastatin). We find that miR‐211 expression is greatly decreased in melanoma cells and melanoblasts compared to melanocytes. Bioinformatic analysis identified a large number of potential targets of miR‐211, including POU3F2 (BRN2). Inhibition of miR‐211 in normal melanocytes resulted in increased BRN2 protein, indicating that endogenous miR‐211 represses BRN2 in differentiated cells. Over‐expression of miR‐211 in melanoma cell lines changed the invasive potential of the cells in vitro through directly targeting BRN2 translation. We propose a model for the apparent non‐overlapping expression levels of BRN2 and MITF in melanoma, mediated by miR‐211 expression.
Balancing Competing Demands: Position Taking and Election Proximity in the European Parliament
Authors: LINDSTÄDT RENÉ , SLAPIN JONATHAN B. , VANDER WIELEN RYAN J.
Published: March 2011

Parties value unity, yet members of parliament have incentives to deviate from the party line. This article examines how members of the European Parliament (EP) respond to competing demands from national parties and European party groups. We examine ideological shifts within a single parliamentary term to assess how election proximity affects party group cohesion. Our formal model of legislative behavior suggests that when EP elections are proximate, national party delegations shift toward national party positions, thus weakening EP party group cohesion. Our Bayesian item‐response analysis of roll calls in the 5th EP supports our theoretical predictions.
Reexamining the Institutional Effects of Term Limits in U.S. State Legislatures
Authors: MILLER SUSAN M. , NICHOLSON‐CROTTY JILL , NICHOLSON‐CROTTY SEAN
Published: March 2011

Research on term limits suggests that they have substantial consequences for the power of legislatures vis‐à‐vis the executive and interest groups and for the relationship between leaders and rank‐and‐file members within a chamber. Existing work, however, has not accounted for the actual power of relevant state actors. We contribute to this research by examining the effect of term limits on the influence of institutional actors conditional on the existing political power structure in a state. The inclusion of controls for the direct and moderating effect of actual institutional power suggests some significant extensions of previous findings regarding the institutional effects of term limits.
Impact cratering in H2O‐bearing targets on Mars: Thermal field under craters as starting conditions for hydrothermal activity
Authors: IVANOV Boris A. , PIERAZZO Elisabetta
Published: March 2011

Abstract– We present a case modeling study of impact crater formation in H2O‐bearing targets. The main goal of this work was to investigate the postimpact thermal state of the rock layers modified in the formation of hypervelocity impact craters. We present model results for a target consisting of a mixture of H2O‐ice and rock, assuming an ice/water content variable with depth. Our model results, combined with results from previous work using dry targets, indicate that for craters larger than about 30 km in diameter, the onset of postimpact hydrothermal circulation is characterized by two stages: first, the formation of a mostly dry, hot central uplift followed by water beginning to flow in and circulate through the initially dry and hot uplifted crustal rocks. The postimpact thermal field in the periphery of the crater is dependent on crater size: in midsize craters, 30–50 km in diameter, crater walls are not strongly heated in the impact event, and even though ice present in the rock may initially be heated enough to melt, overall temperatures in the rock remain below melting, undermining the development of a crater‐wide hydrothermal circulation. In large craters (with diameters more than 100 km or so), the region underneath the crater floor and walls is heated well above the melting point of ice, thus facilitating the onset of an extended hydrothermal circulation. These results provide preliminary constraints in characterizing the many water‐related features, both morphologic and spectroscopic, that high‐resolution images of Mars are now detecting within many Martian craters.
Aeroelastic Analysis of Membrane Microair Vehicles—Part II: Computational Study of a Plunging Membrane Airfoil
Authors: Attar Peter J. , Gordnier Raymond E. , Johnston Jordan W. , Romberg William A. , Parthasarathy Ramkumar N.
Published: March 2011

In the second paper of the two part study of membrane microair vehicles, computations are performed for a plunging membrane airfoil. The computational model uses a sixth-order finite difference solution of the Navier–Stokes equations coupled to a finite element solution of a set of nonlinear string equations. The effect, on the structural and fluid response, of plunging Strouhal number, reduced frequency, and static angle of attack is examined. Qualitatively, the flow field is found to be very complex with interactions of vortices shed from various locations along the chord of the airfoil. At a low angle of attack and a low Strouhal number, increasing reduced frequency results in a decrease and an increase in the mean sectional lift and drag coefficients, respectively. Also, at a low angle of attack, increasing the Strouhal number has minimal effect at high and low values of reduced frequencies, but a significant effect is found at an intermediate value of reduced frequency. When the effect of angle of attack is studied for fixed values of Strouhal number and reduced frequency, it is found that the act of plunging gives improved mean sectional lift when compared with the case of a fixed flexible airfoil. The improvement does not increase monotonically with the angle of attack but instead is maximum at an intermediate value. Finally, increasing the value of the membrane prestrain, which stiffens the airfoil, results in a reduced value of the sectional lift coefficient for a given Strouhal number, reduced frequency, and angle of attack.
Numerical Solution of the Boltzmann Based Lubrication Equation for the Air-Bearing Interface Between a Skewed Slider and a Disk With Discrete Data Tracks
Authors: White James
Published: March 2011

Discrete track recording (DTR) is a method for increasing the recording density of a data storage disk by use of a pattern arrangement of discrete tracks. The DTR track structure consists of a pattern of very narrow concentric raised areas and recessed areas underneath a magnetic recording layer. In order to design the air-bearing slider platform that houses the magnetic transducer for DTR application at very low fly heights, the influence of the disk surface topography as a surface roughness effect must be taken into account. This paper is focused on the numerical solution of the roughness averaged lubrication equation reported recently in the work of White (2010, “A Gas Lubrication Equation for High Knudsen Number Flows and Striated Rough Surfaces,” ASME J. Tribol., 132, p. 021701) and is specialized for the influence of discrete disk data tracks on the recording head slider-disk air-bearing interface subject to a nonzero skew angle formed between the slider longitudinal axis and the direction of disk motion. The generalized lubrication equation for a smooth surface bearing and appropriate for high Knudsen number analysis is quite nonlinear. And including the averaging process required for treatment of a nonsmooth disk surface, as well as the rotational transformation required to allow for a nonzero skew angle, increases further the nonlinearity and general complexity of the lubrication equation. Emphasis is placed on development of a numerical algorithm that is fast, accurate, and robust for air-bearing analysis of complex slider surfaces. The numerical solution procedure developed utilizes a time integration of the lubrication equation for both steady-state and dynamic analyses. The factored-implicit scheme, a form of the more general alternating-direction-implicit numerical approach, was chosen to deal with the two-dimensional and highly nonlinear aspects of the problem. Factoring produces tightly banded coefficient matrices and results in an algorithm that is second-order accurate in time while requiring only the solution of tridiagonal systems of linear equations in advancing the computation from one time level to the next. Numerical solutions are presented that demonstrate the performance of the computational scheme and illustrate the influence of some discrete track parameters on skewed air-bearing performance as compared with a flat surface data storage disk.
A Brief Social-Belonging Intervention Improves Academic and Health Outcomes of Minority Students
Authors: Walton Gregory M. , Cohen Geoffrey L.
Published: March 2011

Reducing feelings of social exclusion yields lasting improvements in academic performance and health in college students.
An Emerging Role of Zoos to Conserve Biodiversity
Authors: Conde D. A. , Flesness N. , Colchero F. , Jones O. R. , Scheuerlein A.
Published: March 2011

Roughly one in seven threatened terrestrial vertebrate species are held in captivity, a resource for ex situ conservation efforts.
Heat and Light Switch a Chiral Catalyst and Its Products
Authors: Ooi Takashi
Published: March 2011

A rotary molecular motor acts as a chiral catalyst and can produce products of either handedness after external stimuli change its structure.
Differences in Antibody Responses of Individuals with Natural Infection and Those Vaccinated against Pandemic H1N1 2009 Influenza
Authors: Chan Kwok-Hung , To Kelvin K. W. , Hung Ivan F. N. , Zhang Anna J. X. , Chan Jasper F. W. , Cheng Vincent C. C. , Tse Herman , Che Xiao-Yan , Chen Honglin , Yuen Kwok-Yung
Published: March 2011

The differential antibody response measured by the commonly used hemagglutination inhibition (HI) and microneutralization (MN) assays in patients with natural infection and vaccination has not been fully assessed. HI and conventional MN (CMN) assays were performed on sera from 651 patients with natural infection by pandemic H1N1 2009 influenza virus and on sera from 567 recipients of the corresponding vaccine. Surprisingly, the overall seroprotection rates determined by CMN and HI assays in vaccine recipients were only 44.8 and 35.1%, respectively. Antibody titers measured by the CMN assay was significantly higher than that obtained by HI assay in vaccine recipients aged ≥50 years, but these titers were not significantly different among younger vaccine recipients. In contrast, the HI titer was greater than the CMN titer for the age group from 16 to 29 years but was not significantly different in other age groups for natural infection. Lower antibody levels were found in both naturally infected patients and immunized recipients in the older than in the younger age groups, but naturally infected patients exhibited higher HI and CMN titers than did the corresponding vaccine recipients. In addition, we developed a rapid fluorescent focus microneutralization (FFMN) assay to test sera from naturally infected patients. The FFMN assay has a better correlation with CMN than with HI (ρ = 0.810 versus 0.684), which is expected of neutralizing antibody mainly targeted toward the inhibition of viral entry into cells. The higher antibody level elicited by natural infection than by vaccination may be related to differences between antigen presentation by the intramuscular route of vaccination and mucosal viral replication in mucosal cells of the respiratory tract.
Activity of TDT 067 (Terbinafine in Transfersome) against Agents of Onychomycosis, as Determined by Minimum Inhibitory and Fungicidal Concentrations
Authors: Ghannoum Mahmoud , Isham Nancy , Herbert Jacqueline , Henry William , Yurdakul Sam
Published: March 2011

TDT 067 is a novel carrier-based dosage form (liquid spray) of 15 mg/ml of terbinafine in Transfersome that has been developed to deliver terbinafine to the nail bed to treat onychomycosis. In this study, we report the
in vitro
activities of TDT 067 against dermatophytes, compared with those of the Transfersome vehicle, naked terbinafine, and commercially available terbinafine (1%) spray. The MICs of TDT 067 and comparators against 25 clinical strains each of
Trichophyton rubrum
,
T. mentagrophytes
, and
Epidermophyton floccosum
were determined according to the CLSI M38–A2 susceptibility method (2008). Minimum fungicidal concentrations (MFCs) were determined by subculturing visibly clear wells from the MIC microtiter plates. TDT 067 demonstrated potent activity against the dermatophyte strains tested, with an MIC range of 0.00003 to 0.015 μg/ml. Overall, TDT 067 MIC
50
values (defined as the lowest concentrations to inhibit 50% of the strains tested) were 8-fold and 60-fold lower than those of naked terbinafine and terbinafine spray, respectively. The Transfersome vehicle showed minimal inhibitory activity. TDT 067 demonstrated lower MFC values for
T. rubrum
and
E. floccosum
than naked terbinafine and terbinafine spray. TDT 067 has more potent antifungal activity against dermatophytes that cause nail infection than conventional terbinafine preparations. The Transfersome vehicle appears to potentiate the antifungal activity of terbinafine. Clinical investigation of TDT 067 for the topical treatment of onychomycosis is warranted.
Transfer of KPC-2 Carbapenemase from Klebsiella pneumoniae to Escherichia coli in a Patient: First Case in Europe
Authors: Richter Sara N. , Frasson Ilaria , Bergo Cristina , Parisi Saverio , Cavallaro Antonietta , Palù Giorgio
Published: March 2011

The first case in Europe of
Klebsiella pneumoniae
carbapenemase (KPC) 2 transfer from
K. pneumoniae
to
Escherichia coli
in the same patient is described. KPC-positive plasmids from the two species were identical, indicating horizontal plasmid transfer. Selection of the KPC-producing
E. coli
strain was triggered by therapy with meropenem.
Use of a Novel Real-Time PCR Assay To Detect Oral Polio Vaccine Shedding and Reversion in Stool and Sewage Samples after a Mexican National Immunization Day
Authors: Troy Stephanie B. , Ferreyra-Reyes Leticia , Huang ChunHong , Mahmud Nadim , Lee Yu-Jin , Canizales-Quintero Sergio , Flaster Harry , Báez-Saldaña Renata , García-García Lourdes , Maldonado Yvonne
Published: March 2011

During replication, oral polio vaccine (OPV) can revert to neurovirulence and cause paralytic poliomyelitis. In individual vaccinees, it can acquire specific revertant point mutations, leading to vaccine-associated paralytic poliomyelitis (VAPP). With longer replication, OPV can mutate into vaccine-derived poliovirus (VDPV), which causes poliomyelitis outbreaks similar to those caused by wild poliovirus. After wild poliovirus eradication, safely phasing out vaccination will likely require global use of inactivated polio vaccine (IPV) until cessation of OPV circulation. Mexico, where children receive routine IPV but where OPV is given biannually during national immunization days (NIDs), provides a natural setting to study the duration of OPV circulation in a population primarily vaccinated with IPV. We developed a real-time PCR assay to detect and distinguish revertant and nonrevertant OPV serotype 1 (OPV-1), OPV-2, and OPV-3 from RNA extracted directly from stool and sewage. Stool samples from 124 children and 8 1-liter sewage samples from Orizaba, Veracruz, Mexico, collected 6 to 13 weeks after a NID were analyzed. Revertant OPV-1 was found in stool at 7 and 9 weeks, and nonrevertant OPV-2 and OPV-3 were found in stool from two children 10 weeks after the NID. Revertant OPV-1 and nonrevertant OPV-2 and -3 were detected in sewage at 6 and 13 weeks after the NID. Our real-time PCR assay was able to detect small amounts of OPV in both stool and sewage and to distinguish nonrevertant and revertant serotypes and demonstrated that OPV continues to circulate at least 13 weeks after a NID in a Mexican population routinely immunized with IPV.
First Reported Isolation of Neisseria canis from a Deep Facial Wound Infection in a Dog
Authors: Cantas Hasan , Pekarkova Marta , Kippenes Hege S. , Brudal Espen , Sorum Henning
Published: March 2011

Neisseria caniswas isolated in pure culture from a mandibular abscess in a dog. Ultrasound-guided fine-needle aspiration was used to obtain a sample from the abscess. Conventional bacteriological examination techniques followed by 16S rRNA gene sequencing from pure subculture and construction of a phylogenetic tree verified the isolate asN. canis. 16S rRNA sequence analysis revealed that a broader phylogenetic platform is needed in the part of the phylogenetic tree where the canine pathogenicN. canisisolate is located. The canine pathogenic isolate was found to be resistant to cephalexin and trimethoprim.
Residues of the UL25 Protein of Herpes Simplex Virus That Are Required for Its Stable Interaction with Capsids
Authors: Cockrell Shelley K. , Huffman Jamie B. , Toropova Katerina , Conway James F. , Homa Fred L.
Published: March 2011

The herpes simplex virus 1 (HSV-1) UL25 gene product is a minor capsid component that is required for encapsidation, but not cleavage, of replicated viral DNA. UL25 is located on the capsid surface in a proposed heterodimer with UL17, where five copies of the heterodimer are found at each of the capsid vertices. Previously, we demonstrated that amino acids 1 to 50 of UL25 are essential for its stable interaction with capsids. To further define the UL25 capsid binding domain, we generated recombinant viruses with either small truncations or amino acid substitutions in the UL25 N terminus. Studies of these mutants demonstrated that there are two important regions within the capsid binding domain. The first 27 amino acids are essential for capsid binding of UL25, while residues 26 to 39, which are highly conserved in the UL25 homologues of other alphaherpesviruses, were found to be critical for stable capsid binding. Cryo-electron microscopy reconstructions of capsids containing either a small tag on the N terminus of UL25 or the green fluorescent protein (GFP) fused between amino acids 50 and 51 of UL25 demonstrate that residues 1 to 27 of UL25 contact the hexon adjacent to the penton. A second region, most likely centered on amino acids 26 to 39, contacts the triplex that is one removed from the penton. Importantly, both of these UL25 capsid binding regions are essential for the stable packaging of full-length viral genomes.
Cardiomyopathy Syndrome of Atlantic Salmon (Salmo salar L.) Is Caused by a Double-Stranded RNA Virus of the Totiviridae Family
Authors: Haugland Øyvind , Mikalsen Aase B. , Nilsen Pål , Lindmo Karine , Thu Beate J. , Eliassen Trygve M. , Roos Norbert , Rode Marit , Evensen Øystein
Published: March 2011

Cardiomyopathy syndrome (CMS) of farmed and wild Atlantic salmon (
Salmo salar
L.) is a disease of yet unknown etiology characterized by a necrotizing myocarditis involving the atrium and the spongious part of the heart ventricle. Here, we report the identification of a double-stranded RNA virus likely belonging to the family
Totiviridae
as the causative agent of the disease. The proposed name of the virus is piscine myocarditis virus (PMCV). On the basis of the RNA-dependent RNA polymerase (RdRp) sequence, PMCV grouped with
Giardia lamblia
virus and infectious myonecrosis virus of penaeid shrimp. The genome size of PMCV is 6,688 bp, with three open reading frames (ORFs). ORF1 likely encodes the major capsid protein, while ORF2 encodes the RdRp, possibly expressed as a fusion protein with the ORF1 product. ORF3 seems to be translated as a separate protein not described for any previous members of the family
Totiviridae
. Following experimental challenge with cell culture-grown virus, histopathological changes are observed in heart tissue by 6 weeks postchallenge (p.c.), with peak severity by 9 weeks p.c. Viral genome levels detected by real-time reverse transcription (RT)-PCR peak earlier at 6 to 7 weeks p.c. The virus genome is detected by
in situ
hybridization in degenerate cardiomyocytes from clinical cases of CMS. Virus genome levels in the hearts from clinical field cases correlate well with the severity of histopathological changes in heart tissue. The identification of the causative agent for CMS is important for improved disease surveillance and disease control and will serve as a basis for vaccine development against the disease.
A New Ebola Virus Nonstructural Glycoprotein Expressed through RNA Editing
Authors: Mehedi Masfique , Falzarano Darryl , Seebach Jochen , Hu Xiaojie , Carpenter Michael S. , Schnittler Hans-Joachim , Feldmann Heinz
Published: March 2011

Ebola virus (EBOV), an enveloped, single-stranded, negative-sense RNA virus, causes severe hemorrhagic fever in humans and nonhuman primates. The EBOV glycoprotein (GP) gene encodes the nonstructural soluble glycoprotein (sGP) but also produces the transmembrane glycoprotein (GP
1,2
) through transcriptional editing. A third GP gene product, a small soluble glycoprotein (ssGP), has long been postulated to be produced also as a result of transcriptional editing. To identify and characterize the expression of this new EBOV protein, we first analyzed the relative ratio of GP gene-derived transcripts produced during infection
in vitro
(in Vero E6 cells or Huh7 cells) and
in vivo
(in mice). The average percentages of transcripts encoding sGP, GP
1,2
, and ssGP were approximately 70, 25, and 5%, respectively, indicating that ssGP transcripts are indeed produced via transcriptional editing. N-terminal sequence similarity with sGP, the absence of distinguishing antibodies, and the abundance of sGP made it difficult to identify ssGP through conventional methodology. Optimized 2-dimensional (2D) gel electrophoresis analyses finally verified the expression and secretion of ssGP in tissue culture during EBOV infection. Biochemical analysis of recombinant ssGP characterized this protein as a disulfide-linked homodimer that was exclusively N glycosylated. In conclusion, we have identified and characterized a new EBOV nonstructural glycoprotein, which is expressed as a result of transcriptional editing of the GP gene. While ssGP appears to share similar structural properties with sGP, it does not appear to have the same anti-inflammatory function on endothelial cells as sGP.
The Breadth and Potency of Passively Acquired Human Immunodeficiency Virus Type 1-Specific Neutralizing Antibodies Do Not Correlate with the Risk of Infant Infection
Authors: Lynch John B. , Nduati Ruth , Blish Catherine A. , Richardson Barbra A. , Mabuka Jennifer M. , Jalalian-Lechak Zahra , John-Stewart Grace , Overbaugh Julie
Published: March 2011

Although a major goal of human immunodeficiency virus type 1 (HIV-1) vaccine efforts is to elicit broad and potent neutralizing antibodies (NAbs), there are no data that directly demonstrate a role for such NAbs in protection from HIV-1 infection in exposed humans. The setting of mother-to-child transmission provides an opportunity to examine whether NAbs provide protection from HIV-1 infection because infants acquire passive antibodies from their mothers prior to exposure to HIV-1 through breastfeeding. We evaluated the characteristics of HIV-1-specific NAbs in 100 breast-fed infants of HIV-1-positive mothers who were HIV-1 negative at birth and monitored them until age 2. A panel of eight viruses that included variants representative of those in the study region as well as more diverse strains was used to determine the breadth of the infant NAbs. From their mothers, infants acquired broad and potent NAbs that were capable of recognizing heterologous circulating HIV-1 variants of diverse subtypes, but the presence of NAbs of broad HIV-1 specificity was not associated with transmission risk. There was also no correlation between responses to any particular virus tested, which included a range of diverse variants that demonstrated different neutralization profiles, including recognition by specific antibodies with known epitope targets. The eight viruses tested exhibited neutralization profiles to a variety of monoclonal antibodies (2F5, PG9, and VRC01) similar to those of viruses present in pregnant women in the cohort. These results suggest that the breadth and potency of the heterologous antibody response in exposed infants, measured against a virus panel comprised of variants typical of those circulating in the population, does not predict protection.
Valproic Acid Antagonizes the Capacity of Other Histone Deacetylase Inhibitors To Activate the Epstein-Barr Virus Lytic Cycle
Authors: Daigle Derek , Gradoville Lyn , Tuck David , Schulz Vince , Wang'ondu Ruth , Ye Jianjiang , Gorres Kelly , Miller George
Published: March 2011

Diverse stimuli reactivate the Epstein-Barr virus (EBV) lytic cycle in Burkitt lymphoma (BL) cells. In HH514-16 BL cells, two histone deacetylase (HDAC) inhibitors, sodium butyrate (NaB) and trichostatin A (TSA), and the DNA methyltransferase inhibitor azacytidine (AzaCdR) promote lytic reactivation. Valproic acid (VPA), which, like NaB, belongs to the short-chain fatty acid class of HDAC inhibitors, fails to induce the EBV lytic cycle in these cells. Nonetheless, VPA behaves as an HDAC inhibitor; it causes hyperacetylation of histone H3 (J. K. Countryman, L. Gradoville, and G. Miller, J. Virol.82:4706–4719, 2008). Here we show that VPA blocked the induction of EBV early lytic proteins ZEBRA and EA-D in response to NaB, TSA, or AzaCdR. The block in lytic activation occurred prior to the accumulation of BZLF1 transcripts. Reactivation of EBV in Akata cells, in response to anti-IgG, and in Raji cells, in response to tetradecanoyl phorbol acetate (TPA), was also inhibited by VPA. MS-275 and apicidin, representing two additional classes of HDAC inhibitors, and suberoylanilide hydroxamic acid (SAHA) reactivated EBV in HH514-16 cells; this activity was also inhibited by VPA. Although VPA potently blocked the expression of viral lytic-cycle transcripts, it did not generally block the transcription of cellular genes and was not toxic. The levels and kinetics of specific cellular transcripts, such as Stat3, Frmd6, Mad1, Sepp1, c-fos, c-jun, andegr1, which were activated by NaB and TSA, were similar in HH514-16 cells treated with VPA. When combined with NaB or TSA, VPA did not inhibit the activation of these cellular genes. Changes in cellular gene expression in response to VPA, NaB, or TSA were globally similar as assessed by human genome arrays; however, VPA selectively stimulated the expression of some cellular genes, such as MEF2D, YY1, and ZEB1, that could repress the EBV lytic cycle. We describe a novel example of functional antagonism between HDAC inhibitors.
Electron transfer dissociation of a melectin peptide: correlating the precursor ion structure with peptide backbone dissociations
Authors: Moss Christopher L. , Chung Thomas W. , Čeřovský Václav , Tureček František
Published: March 2011

Electron transfer dissociation (ETD) of doubly and triply charged ions from the amphipathic N-terminal decapeptide GFLSILKKVL-NH2 segment of melectin gave different distributions of fragment ions. The triply charged ions generated extensive series of fragment ions of c and z type that covered the entire sequence from both the N and C termini. In contrast, electron transfer to the doubly charged ions caused backbone cleavages that occurred at residues close to the N and C termini. Attachment of a free low-energy electron to the doubly charged ions caused primary dissociations close to the N and C termini that were followed by consecutive dissociations of z ions. The structure of gaseous doubly charged ions from the melectin peptide was elucidated by a combination of exhaustive conformational search by force-field molecular dynamics, large-scale gradient optimization using the semiempirical PM6 method, and density functional theory single-point energy and gradient optimization calculations. The most stable doubly charged ions were found to be protonated at the lysine ε-amino groups and have globular conformations. The backbone cleavages in ETD correlated with the electronic structure of cation-radicals produced by electron attachment to the most stable conformers. The charged lysine ammonium groups direct the incoming electron to the π* orbitals at the proximate amide groups at Phe, Leu, Lys and Val residues that show the highest spin densities. Electron attachment at these amide groups weakens the N–Cα bonds between the Phe-Leu, Leu-Ser, Lys-Lys and Lys-Val residues and causes backbone dissociations.
PREPARATION AND SURFACE PLASMON RESONANCE OF COPPER NANOCAP ARRAYS
Authors: XIAO GUI-NA , MAN SHI-QING , ZHANG HUA-LI , FENG YAN-XIAO
Published: March 2011

Copper nanocap arrays, consisting of a SiO 2 core with a Cu cap, were prepared by chemical synthesis combined with physical evaporation technique. The obtained samples were characterized by scanning electron microscopy, atomic force microscopy, X-ray diffraction, and ultraviolet-visible-near-infrared spectrophotometer. The copper nanocap arrays were found to exhibit tunable surface plasmon resonance (SPR) absorption peaks that were red-shifted as the ratio of the SiO 2 core diameter to the Cu cap thickness increased. While the cap thickness varied between 20 nm and 50 nm, the SPR peak shifted from 1650 nm to 1230 nm. While the core diameter varied between 140 nm and 400 nm, the longitudinal SPR peak shifted from 1243 nm to 1830 nm.
CONTINUOUS TRANSITION OF DEFECT CONFIGURATION IN A DEFORMED LIQUID CRYSTAL FILM
Authors: HASEGAWA ISAKU , SHIMA HIROYUKI
Published: March 2011

We investigate energetically favorable configurations of point disclinations in nematic films having a bump geometry. Gradual expansion in the bump width Δ gives rise to a sudden shift in the stable position of the disclinations from the top to the skirt of the bump. The positional shift observed across a threshold Δ th obeys a power law function of |Δ - Δ th |, indicating a new class of continuous phase transition that governs the defect configuration in curved nematic films.
Evaluation of EPR monitoring of singlet oxygen production using the photosensitizer chloroboron subphthalocyanine
Authors: Berliner Lawrence J. , Görner Helmut , Schuchmann Heinz-Peter
Published: March 2011

Singlet molecular oxygen produced in the presence of 2,2,6,6-tetramethyl-4-piperidone (TMPD) in 1,4-dioxan, by boron subphthalocyanine chloride as the sensitizer, was monitored by Electron Paramagnetic Resonance (EPR) via the oxidation of TMPD to the corresponding aminoxyl radical. This radical product is formed in low yields along the singlet oxygen pathway. A kinetic analysis of the process allows one to understand the reasons behind this, while affording more accurate quantitative insights into the mechanistic details. A crucial aspect of this reaction system, which explains the low aminoxyl radical yields along the singlet oxygen pathway, is the disappearance of the sensitizer triplet state in a reaction with TMPD, which has a rate constant of 1 × 109M-1.s-1.
Logical time
Authors: Mallet Frédéric , André Charles , de Simone Robert
Published: March 2011

MARTE/CCSL specifications express chronological and causal relations on UML models. In a previous work, we proposed a mechanism to verify Esterel implementations against MARTE/CCSL specifications. The mechanism was thought to be general enough to be extended to other languages. However, preserving the polychronous semantics of CCSL was pretty easy with a synchronous language but is much harder when the target language does not directly support coincidence/simultaneity. We show here how coincidence can be encoded. The process is illustrated using VHDL
Fault tree synthesis from UML models for reliability analysis at early design stages
Authors: Lauer Christoph , German Reinhard , Pollmer Jens
Published: March 2011

System reliability analysis is often neglected at early design stages when design decisions change the system architecture rigorously. This is because appropriate methods are time consuming and require an in-depth knowledge about the applied method. We propose a modeling approach that focuses on reusability and automatic fault tree synthesis of the models. We use UML to model application dependent and application independent views on the system and allocate steps of the application definition to architecture elements. In doing so various different system concepts can be investigated with minimal re-modeling effort. We identify capturing fault propagation and fault containment information as a major challenge in automatic fault tree synthesis and offer an application dependent and an application independent approach to modeling this kind of information. Then we introduce an algorithm that transforms the UML model into a fault tree representation of the respective system and validate our approach using an example from the automotive domain. The results from the validation highlight the validity of the generated trees, the efficiency with which different system concepts may be evaluated, and the degree to which the analysis results can be generalized
Querying XML data sources that export very large sets of views
Authors: Cautis Bogdan , Deutsch Alin , Onose Nicola , Vassalos Vasilis
Published: March 2011

We study the problem of querying XML data sources that accept only a limited set of queries, such as sources accessible by Web services which can implement very large (potentially infinite) families of XPath queries. To compactly specify such families of queries we adopt the Query Set Specifications, a formalism close to context-free grammars.

We say that query
Q
is
expressible
by the specification P if it is equivalent to some expansion of P.
Q
is
supported
by P if it has an equivalent rewriting using some finite set of P's expansions. We study the complexity of expressibility and support and identify large classes of XPath queries for which there are efficient (PTIME) algorithms. Our study considers both the case in which the XML nodes in the results of the queries lose their original identity and the one in which the source exposes persistent node ids.
Path-tree
Authors: Jin Ruoming , Ruan Ning , Xiang Yang , Wang Haixun
Published: March 2011

Reachability query is one of the fundamental queries in graph database. The main idea behind answering reachability queries is to assign vertices with certain labels such that the reachability between any two vertices can be determined by the labeling information. Though several approaches have been proposed for building these reachability labels, it remains open issues on how to handle increasingly large number of vertices in real-world graphs, and how to find the best tradeoff among the labeling size, the query answering time, and the construction time. In this article, we introduce a novel graph structure, referred to as
path-tree
, to help labeling very large graphs. The path-tree cover is a spanning subgraph of
G
in a tree shape. We show path-tree can be generalized to chain-tree which theoretically can has smaller labeling cost. On top of path-tree and chain-tree index, we also introduce a new compression scheme which groups vertices with similar labels together to further reduce the labeling size. In addition, we also propose an efficient incremental update algorithm for dynamic index maintenance. Finally, we demonstrate both analytically and empirically the effectiveness and efficiency of our new approaches.
Removal of Anodic Aluminum Oxide Barrier Layer on Silicon Substrate by using Cl2/BCl3 Neutral Beam Etching
Authors: Yeon J. K. , Lim W. S. , Park J. B. , Kwon N. Y. , Kim S. I. , Min K. S. , Chung I. S. , Kim Y. W. , Yeom G. Y.
Published: March 2011

The barrier layer of anodic aluminum oxide (AAO) formed on the silicon substrate was etched with Cl2/BCl3 gas mixtures by a neutral beam and the results were compared with the AAO etched by an ion beam. The etch rate of AAO itself was increased with the increase of BCl3 in Cl2/BCl3 up to 60% in the gas mixture. And, the etching of AAO itself was related to the Cl radical density in the plasma and the formation of volatile BOxCly on the AAO surface for both the neutral beam etching and the ion beam etching. The AAO itself could be etched by both the neutral beam and the ion beam in all Cl2/BCl3 gas mixtures. However, the barrier layer of the AAO located near the bottom of the AAO pore could not be etched using the ion beam etching due to the charging of the nanometer size AAO pore similar to the case of conventional reactive ion etching. Using the neutral beam etching, the barrier layer of AAO pore could be successfully etched with BCl3-rich BCl3/Cl2 gas mixtures by removing the barrier layer without charging the AAO pore and by the forming volatile BOxCly.
VIP-dependent increase in F508del-CFTR membrane localization is mediated by PKCε
Authors: Alcolado Nicole , Conrad Dustin J. , Rafferty Sara , Chappe Frédéric G. , Chappe Valérie M.
Published: March 2011

The most common cystic fibrosis causing mutation F508del induces early degradation and reduced trafficking of cystic fibrosis transmembrane conductance regulator (CFTR) chloride channels to the apical membrane of epithelial cells. In the human nasal epithelial cells JME/CF15, we previously reported that vasoactive intestinal peptide (VIP) exposure corrects trafficking and membrane insertion of functional F508del-CFTR channels at 37°C. Correction of trafficking was PKA dependent, whereas enhanced membrane localization involved PKC. In the present study, we have identified PKCε as the isoform involved in VIP-dependent F508del-CFTR membrane insertion. Iodide effluxes were used to monitor the presence of VIP-rescued functional F508del-CFTR channels at the surface of JME/CF15 cells maintained at 37°C. Iodide efflux peaks measured in response to stimulation with forskolin were insensitive to PKC α, β, γ, δ, ζ inhibitors. In contrast, efflux peaks were completely inhibited by pretreatment with the PKCε inhibitor peptide EAVSLKPT with an IC50 of 4.9 μM or by PKCε small interfering RNA (siRNA). Immunostaining and confocal microscopy confirmed that membrane localization of F508del-CFTR induced by VIP was abolished in the presence of EAVSLKPT but not with other isoform inhibitors. In recombinant baby hamster kidney cells, endogenously expressing PKCε but no VIP receptor, wild-type, and F508del-CFTR sensitivity to cpt-cAMP stimulation was increased by PMA treatment. Biotinylation assays and immunoblots confirmed that PMA (0.5–2 h) induced a greater than threefold increase in membrane CFTR, whereas forskolin had no effect. The PMA effect was abolished by specifically inhibiting PKCε (EAVSLKPT IC50 = 5.7 μM) but not other PKC isoforms. Taken together, these results indicate that stimulating PKCε by VIP or PMA increases membrane insertion and activity of WT- and F508del-CFTR.