bluuebunny/crossref_metadata_2025 huggingface dataset:
West Nile Virus in North‐Eastern Italy, 2011: Entomological and Equine IgM‐Based Surveillance to Detect Active Virus Circulation
Authors: Mulatti Paolo , Bonfanti Lebana , Capelli Gioia , Capello Katia , Lorenzetto Monica , Terregino Calogero , Monaco Federica , Ferri Gaetana , Marangon Stefano
Published: September 2012

Since 2008, West Nile Virus (WNV) has expanded its range in several Italian regions, and its yearly recurrence suggests the virus may have become endemic in some areas. In 2011, a new plan based also on the detection of IgM antibodies was implemented in the north‐eastern Italian regions of Veneto and Friuli Venezia Giulia, aiming to early detect WNV infections in areas where the virus had already circulated during the previous summers, and in adjacent zones. From July to November 2011, 1880 sera from 521 equine premises were screened by a commercial IgM capture ELISA. Mosquitoes were captured by CDC‐CO2 traps at 61 locations in the two regions. Collected mosquitoes were identified, pooled by species/date/location and examined by real‐time RT‐PCR and sequencing. Passive surveillance was carried out on clinically affected horses and non‐migratory wild birds found dead. IgM sero‐positive equines were detected in 19 holdings, five in the area with WNV circulation (AWC) and 14 in the surveillance area (SA); 10 more horse premises tested positive to further serological controls within 4 km of the positive holdings. A total of 85 398 mosquitoes of 15 species were collected and 2732 pools examined. Five Culex pipiens pools tested positive for the presence of WNV. Passive surveillance on non‐migratory wild birds allowed detection of the virus only in one found dead collared dove (Streptopelia decaocto), of 82 birds sampled. The WNV belonged to the lineage 2, which had been isolated for the first time in Italy earlier in 2011. By the first week of October, nine human cases had been confirmed in the same area. The implementation of a protocol combining IgM screening of horses with surveillance on mosquito vectors proved to be valuable for early detecting WNV circulation.
Estimation of State Transition Probabilities in Asynchronous Vector Markov Processes
Authors: Farahat Waleed A. , Asada H. Harry
Published: September 2012

Vector Markov processes (also known as population Markov processes) are an important class of stochastic processes that have been used to model a wide range of technological, biological, and socioeconomic systems. The dynamics of vector Markov processes are fully characterized, in a stochastic sense, by the state transition probability matrix P. In most applications, P has to be estimated based on either incomplete or aggregated process observations. Here, in contrast to established methods for estimation given aggregate data, we develop Bayesian formulations for estimating P from asynchronous aggregate (longitudinal) observations of the population dynamics. Such observations are common, for example, in the study of aggregate biological cell population dynamics via flow cytometry. We derive the Bayesian formulation, and show that computing estimates via exact marginalization are, generally, computationally expensive. Consequently, we rely on Monte Carlo Markov chain sampling approaches to estimate the posterior distributions efficiently. By explicitly integrating problem constraints in these sampling schemes, significant efficiencies are attained. We illustrate the algorithm via simulation examples and show that the Bayesian estimation schemes can attain significant advantages over point estimates schemes such as maximum likelihood.
Design, Modeling, and Validation of a High-Speed Rotary Pulse-Width-Modulation On/Off Hydraulic Valve
Authors: Tu Haink C. , Rannow Michael B. , Wang Meng , Li Perry Y. , Chase Thomas R. , Van de Ven James D.
Published: September 2012

Efficient high-speed on/off valves are an enabling technology for applying digital control techniques such as pulse-width-modulation (PWM) to hydraulic systems. Virtually variable displacement pumps (VVDPs) are one application where variable displacement functionality is attained using a fixed-displacement pump paired with an on/off valve and an accumulator. High-speed valves increase system bandwidth and reduce output pressure ripple by enabling higher switching frequencies. In addition to fast switching, on/off valves should also have small pressure drop and low actuation power to be effective in these applications. In this paper, a new unidirectional rotary valve designed for PWM is proposed. The valve is unique in utilizing the hydraulic fluid flowing through it as a power source for rotation. An unoptimized prototype capable of high flow rate (40 lpm), high speed (2.8 ms transition time at 100 Hz PWM frequency), and low pressure drop (0.62 MPa), while consuming little actuation power (<0.5% full power or 30 W, scavenged from fluid stream), has been constructed and experimentally validated. This paper describes the valve design, analyzes its performance and losses, and develops mathematical models that can be used for design and simulation. The models are validated using experimental data from a proof-of-concept prototype. The valve efficiency is quantified and suggestions for improving the efficiency in future valves are provided.
Motion mitigation in intensity modulated particle therapy by internal target volumes covering range changes
Authors: Graeff Christian , Durante Marco , Bert Christoph
Published: September 2012

Purpose:

Particle therapy offers benefits over conventional photon therapy but also introduces sensitivity to changes in the water‐equivalent path length (WEPL) in case of target motion, e.g., breathing. Target motion can be addressed by the internal target volume (ITV) approach, defined as the CTV plus target movement. In photon therapy, the ITV can be constructed as the geometric union of CTVs in all motion states (GEO‐ITV) of a 4D‐CT, but this does not account for WEPL‐changes. An ITV including WEPL‐changes can be defined as the union of all CTVs transformed to a WEPL‐equivalent axis along beamˈs eye view. The resulting WEPL‐ITV is field‐specific and thus unsuitable for intensity modulated particle therapy (IMPT). The purpose of this study was an IMPT‐compatible ITV by splitting geometrical motion and field‐specific WEPL changes, following ICRU 78 recommendations.

Methods:

For all fields, the GEO‐ITV was used as a common target. This identical geometry for all fields was mapped to an enlarged WEPL extent with a field‐specific transformation. As the dose distribution is determined by the WEPL, this is sufficient to achieve equivalent dose coverage as for a geometrically enlarged target volume. The WEPL enlargement is only visible to the specific field and therefore does not increase the target volume of other fields. This avoids unnecessary lateral field extensions, reducing the dose to normal tissue. Homogeneous dose coverage in IMPT is achieved only if the inhomogeneous doses from the individual fields match up during delivery. As the course of the WEPL within each motion phase differs, this cannot be guaranteed by optimizing the fields only in the reference phase. The WEPL‐ITV for the reference phase can be amended by CTVs from a subset of motion phases (4D‐WEPL‐ITV). Here, end‐exhale as the reference phase was combined with end‐inhale to cover the whole motion range. The GEO‐ITV, WEPL‐ITV, and 4D‐WEPL‐ITV were applied in an IMPT simulation of a lung cancer patient case using a four‐field geometry and the heart as an OAR. A static plan of the CTV in end‐exhale was computed for reference. The CTV was moving approximately 20 mm in SI and was partly overlapping the heart. For a single fraction a target dose of 17.7 GyE was prescribed, with a 50% maximum dose for the heart.

Results:

With 21 rescans to counter interplay, the homogeneity (D5‐D95) was 17.0%, 9.0%, 6.0%, and 3.5% for the GEO‐ITV, WEPL‐ITV, 4D‐WEPL‐ITV, and a 3D CTV plan computed for reference, respectively. Due to the overlap, the 50% maximum dose was violated by all plans, with V50 of 3.8%, 3.5%, 3.7%, and 2.0% for the four plans.

Conclusions:

A 4D‐WEPL‐ITV method was developed that is suitable for IMPT, covers range changes, and drastically improves dose homogeneity in the target without increasing the OAR dose.
Dynamics of DNA Supercoils
Authors: van Loenhout M. T. J. , de Grunt M. V. , Dekker C.
Published: September 2012

Watching Supercoiled DNA

The DNA double helix can undergo additional twisting, or supercoiling, that plays a role in transciption and protein binding, in part by bringing distant DNA locations together. The process forms intertwined loops, called plectonemes, and van

Loenhout
et al.

(p.
94
, published online 13 September; see the Perspective by

Sheinin and Wang

) visualized plectoneme dynamics of fluorescently labeled, 21-kilobase tethered DNA molecules using magnetic tweezers to apply twisting forces. Plectonemes could diffuse along the DNA, but move more rapidly if they “hopped”—nucleating a plectoneme at a new position.
Modeling the Growth of Listeria monocytogenes in Soft Blue-White Cheese
Authors: Rosshaug Per Sand , Detmer Ann , Ingmer Hanne , Larsen Marianne Halberg
Published: September 2012

The aim of this study was to develop a predictive model simulating growth over time of the pathogenic bacterium
Listeria monocytogenes
in a soft blue-white cheese. The physicochemical properties in a matrix such as cheese are essential controlling factors influencing the growth of
L. monocytogenes
. We developed a predictive tertiary model of the bacterial growth of
L. monocytogenes
as a function of temperature, pH, NaCl, and lactic acid. We measured the variations over time of the physicochemical properties in the cheese. Our predictive model was developed based on broth data produced in previous studies. New growth data sets were produced to independently calibrate and validate the developed model. A characteristic of this tertiary model is that it handles dynamic growth conditions described in time series of temperature, pH, NaCl, and lactic acid. Supplying the model with realistic production and retail conditions showed that the number of
L. monocytogenes
cells increases 3 to 3.5 log within the shelf life of the cheese.
Annotation of the Modular Polyketide Synthase and Nonribosomal Peptide Synthetase Gene Clusters in the Genome of Streptomyces tsukubaensis NRRL18488
Authors: Blažič Marko , Starcevic Antonio , Lisfi Mohamed , Baranasic Damir , Goranovič Dušan , Fujs Štefan , Kuščer Enej , Kosec Gregor , Petković Hrvoje , Cullum John , Hranueli Daslav , Zucko Jurica
Published: September 2012

The high G+C content and large genome size make the sequencing and assembly of
Streptomyces
genomes more difficult than for other bacteria. Many pharmaceutically important natural products are synthesized by modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). The analysis of such gene clusters is difficult if the genome sequence is not of the highest quality, because clusters can be distributed over several contigs, and sequencing errors can introduce apparent frameshifts into the large PKS and NRPS proteins. An additional problem is that the modular nature of the clusters results in the presence of imperfect repeats, which may cause assembly errors. The genome sequence of
Streptomyces tsukubaensis
NRRL18488 was scanned for potential PKS and NRPS modular clusters. A phylogenetic approach was used to identify multiple contigs belonging to the same cluster. Four PKS clusters and six NRPS clusters were identified. Contigs containing cluster sequences were analyzed in detail by using the ClustScan program, which suggested the order and orientation of the contigs. The sequencing of the appropriate PCR products confirmed the ordering and allowed the correction of apparent frameshifts resulting from sequencing errors. The product chemistry of such correctly assembled clusters could also be predicted. The analysis of one PKS cluster showed that it should produce a bafilomycin-like compound, and reverse transcription (RT)-PCR was used to show that the cluster was transcribed.
HIV-1-Specific Enzyme-Linked Immunosorbent Spot Assay Responses in HIV-1-Exposed Uninfected Partners in Discordant Relationships Compared to Those in Low-Risk Controls
Authors: Guthrie Brandon L. , Lohman-Payne Barbara , Liu Amy Y. , Bosire Rose , Nuvor Samuel Victor , Choi Robert Y. , Mackelprang Romel D. , Kiarie James N. , De Rosa Stephen C. , Richardson Barbra A. , John-Stewart Grace C. , Farquhar Carey
Published: September 2012

A number of studies of highly exposed HIV-1-seronegative individuals (HESN) have found HIV-1-specific cellular responses. However, there is limited evidence that responses prevent infection or are linked to HIV-1 exposure. Peripheral blood mononuclear cells (PBMC) were isolated from HESN in HIV-1-discordant relationships and low-risk controls in Nairobi, Kenya. HIV-1-specific responses were detected using gamma interferon (IFN-γ) enzyme-linked immunosorbent spot (ELISpot) assays stimulated by peptide pools spanning the subtype A HIV-1 genome. The HIV-1 incidence in this HESN cohort was 1.5 per 100 person years. Positive ELISpot responses were found in 34 (10%) of 331 HESN and 14 (13%) of 107 low-risk controls (odds ratio [OR] = 0.76;P= 0.476). The median immunodominant response was 18.9 spot-forming units (SFU)/106peripheral blood mononuclear cells (PBMC). Among HESN, increasing age (OR = 1.24 per 5 years;P= 0.026) and longer cohabitation with the HIV-1-infected partner (OR = 5.88 per 5 years;P= 0.003) were associated with responses. These factors were not associated with responses in controls. Other exposure indicators, including the partner's HIV-1 load (OR = 0.99 per log10copy/ml;P= 0.974) and CD4 count (OR = 1.09 per 100 cells/μl;P= 0.238), were not associated with responses in HESN. HIV-1-specific cellular responses may be less relevant to resistance to infection among HESN who are using risk reduction strategies that decrease their direct viral exposure.
Differential Control of the Rate of 5′-End-Dependent mRNA Degradation in Escherichia coli
Authors: Luciano Daniel J. , Hui Monica P. , Deana Atilio , Foley Patricia L. , Belasco Kevin J. , Belasco Joel G.
Published: September 2012

Many
Escherichia coli
mRNAs are degraded by a 5′-end-dependent mechanism in which RppH-catalyzed conversion of the 5′-terminal triphosphate to a monophosphate triggers rapid endonucleolytic cleavage by RNase E. However, little is understood about what governs the decay rates of these transcripts. We investigated the decay of three such messages—
rpsT
P1,
yfcZ
, and
ydfG—
to characterize the rate-determining step in their degradation. The steady-state ratio of monophosphorylated to triphosphorylated
rpsT
P1 and
yfcZ
mRNA indicates that their decay rate is limited by cleavage of the monophosphorylated intermediate, making RNase E critical for their rapid turnover. Conversely, the decay rate of
ydfG
is limited by generation of the monophosphorylated intermediate; therefore, either RNase E or its less abundant paralog RNase G is sufficient for rapid
ydfG
degradation. Although all three transcripts are stabilized when RppH is absent, overproducing RppH does not accelerate their decay, nor does RppH overproduction appear to influence the longevity of most other messages that it targets. The failure of excess RppH to hasten
rpsT
P1 and
yfcZ
degradation despite increasing the percentage of each that is monophosphorylated is consistent with the observation that pyrophosphate removal is not the rate-limiting step in their decay. In contrast, neither the
ydfG
decay rate nor the fraction of
ydfG
transcripts that are monophosphorylated increases when the cellular concentration of RppH is raised, suggesting that, for some RppH targets, the rate of formation of the monophosphorylated intermediate is limited by an ancillary factor or by a step that precedes pyrophosphate removal.
Crystal Structures of Complexes of the Branched-Chain Aminotransferase from Deinococcus radiodurans with α-Ketoisocaproate and
l-
Glutamate Suggest the Radiation Resistance of This Enzyme for Catalysis
Authors: Chen Chung-De , Lin Chih-Hao , Chuankhayan Phimonphan , Huang Yen-Chieh , Hsieh Yin-Cheng , Huang Tien-Feng , Guan Hong-Hsiang , Liu Ming-Yih , Chang Wen-Chang , Chen Chun-Jung
Published: September 2012

Branched-chain aminotransferases (BCAT), which utilize pyridoxal 5′-phosphate (PLP) as a cofactor, reversibly catalyze the transfer of the α-amino groups of three of the most hydrophobic branched-chain amino acids (BCAA), leucine, isoleucine, and valine, to α-ketoglutarate to form the respective branched-chain α-keto acids and glutamate. The BCAT from
Deinococcus radiodurans
(
Dr
BCAT), an extremophile, was cloned and expressed in
Escherichia coli
for structure and functional studies. The crystal structures of the native
Dr
BCAT with PLP and its complexes with
l
-glutamate and α-ketoisocaproate (KIC), respectively, have been determined. The
Dr
BCAT monomer, comprising 358 amino acids, contains large and small domains connected with an interdomain loop. The cofactor PLP is located at the bottom of the active site pocket between two domains and near the dimer interface. The substrate (
l
-glutamate or KIC) is bound with key residues through interactions of the hydrogen bond and the salt bridge near PLP inside the active site pocket. Mutations of some interaction residues, such as Tyr71, Arg145, and Lys202, result in loss of the specific activity of the enzymes. In the interdomain loop, a dynamic loop (Gly173 to Gly179) clearly exhibits open and close conformations in structures of
Dr
BCAT without and with substrates, respectively.
Dr
BCAT shows the highest specific activity both in nature and under ionizing radiation, but with lower thermal stability above 60°C, than either BCAT from
Escherichia coli
(
e
BCAT) or from
Thermus thermophilus
(HB8BCAT). The dimeric molecular packing and the distribution of cysteine residues at the active site and the molecular surface might explain the resistance to radiation but small thermal stability of
Dr
BCAT.
Epidemiology and Genotypic Characteristics of Methicillin-Resistant Staphylococcus aureus Strains of Porcine Origin
Authors: Molla Bayleyegn , Byrne Megan , Abley Melanie , Mathews Jennifer , Jackson Charlene R. , Fedorka-Cray Paula , Sreevatsan Srinand , Wang Ping , Gebreyes Wondwossen A.
Published: September 2012

The main goal of this study was to determine the prevalence of methicillin-resistant
Staphylococcus aureus
(MRSA), particularly livestock-associated MRSA (LA-MRSA) in pigs and pork. The genotypic relatedness of isolates on the farm, at slaughter, and at the retail level was assessed. Paired nasal and perianal swab samples were collected from 10 cohorts of market-age pigs (24 pigs per cohort) and carcasses at slaughterhouse, and pork samples were collected at retail. Staphylococci were isolated using selective enrichment method. Isolates were tested for antimicrobial resistance by broth microdilution. Duplex PCR was used to confirm MRSA using species-specific (
nuc
) and methicillin resistance (
mecA
) genes. The clonal relatedness of isolates was determined using pulsed-field gel electrophoresis (PFGE),
Staphylococcus
protein A (
spa
) typing, multilocus sequence typing (MLST), and staphylococcal cassette chromosome
mec
element (SCC
mec
) typing. MRSA was detected in 5 of the 10 cohorts (50%), with the prevalence ranging from 0% to 12.5% per cohort. Of all the pigs sampled on the farm before they went to market, 3% (7/240) were MRSA positive. A higher prevalence of MRSA was detected at holding pens at the slaughterhouse (11% [27/240]). MRSA was also detected in 2% (4/235) of the carcasses and 4% (5/135) of the retail pork. While the isolates appear predominantly to be highly clonal, PFGE had a relatively higher discriminatory power (discriminatory index [DI] = 0.624). Four genotypic clusters were identified by PFGE; of the four clusters, clonal type B was predominant across the farm-to-retail continuum. MLST findings revealed that sequence type 5 (ST5) was the most predominant subtype (32/50). The livestock-associated MRSA (clonal complex 398 [CC398] or sequence type 398 [ST398]) was the second common type (12/50) and was detected at all stages from farm to retail. Nine of the 50 (18%) MRSA isolates belonged to
spa
type 539/t034 that were of ST398 based on MLST. The results of this study confirm that MRSA, including LA-MRSA, is common in herds of swine in Ohio and hereby shown to persist in the farm to processing and retail continuum.
Production of 2-Aminophenoxazin-3-one by Staphylococcus aureus Causes False-Positive Results in β-Galactosidase Assays
Authors: Tse Herman , Chan Elaine , Lam Ching-Wan , Leung Ka-Fai , Chow Pat , Lee Kim-Chung , Sze Kong-Hung , Cheung Stanley K. K. , Tse Man-Kit , Ho Pak-Leung , Leung Sze-Pui , Lau Susanna K. P. , Woo Patrick C. Y. , Yuen Kwok-Yung
Published: September 2012

Staphylococcus aureuscan be distinguished from similar coagulase-positive staphylococci by its absence of β-galactosidase activity. This is commonly tested usingo-nitrophenyl-β-d-galactopyranoside (ONPG) as the substrate. Unexpectedly, 111 and 58 of 123 isolates displayed apparent β-galactosidase activity in the ONPG assay and on the Vitek 2 system, respectively. Compositional analysis showed that the yellow coloration of the positive ONPG assay resulted from production of 2-aminophenoxazin-3-one. Alternative β-galactosidase substrates like X-Gal (5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside) should be used for testing staphylococci.
Rapid Transepithelial Transport of Prions following Inhalation
Authors: Kincaid Anthony E. , Hudson Kathryn F. , Richey Matthew W. , Bartz Jason C.
Published: September 2012

Prion infection and pathogenesis are dependent on the agent crossing an epithelial barrier to gain access to the recipient nervous system. Several routes of infection have been identified, but the mechanism(s) and timing of
in vivo
prion transport across an epithelium have not been determined. The hamster model of nasal cavity infection was used to determine the temporal and spatial parameters of prion-infected brain homogenate uptake following inhalation and to test the hypothesis that prions cross the nasal mucosa via M cells. A small drop of infected or uninfected brain homogenate was placed below each nostril, where it was immediately inhaled into the nasal cavity. Regularly spaced tissue sections through the entire extent of the nasal cavity were processed immunohistochemically to identify brain homogenate and the disease-associated isoform of the prion protein (PrP
d
). Infected or uninfected brain homogenate was identified adhering to M cells, passing between cells of the nasal mucosa, and within lymphatic vessels of the nasal cavity at all time points examined. PrP
d
was identified within a limited number of M cells 15 to 180 min following inoculation, but not in the adjacent nasal mucosa-associated lymphoid tissue (NALT). While these results support M cell transport of prions, larger amounts of infected brain homogenate were transported paracellularly across the respiratory, olfactory, and follicle-associated epithelia of the nasal cavity. These results indicate that prions can immediately cross the nasal mucosa via multiple routes and quickly enter lymphatics, where they can spread systemically via lymph draining the nasal cavity.
A clinical audit of changes in suicide ideas with internet treatment for depression
Authors: Watts Sarah , Newby Jill M , Mewton Louise , Andrews Gavin
Published: September 2012

Objectives

To examine reductions in suicidal ideation among a sample of patients who were prescribed an internet cognitive behavior therapy (iCBT) course for depression.

Design

Effectiveness study within a quality assurance framework.

Setting

Primary care.

Participants

299 patients who were prescribed an iCBT course for depression by primary care clinicians.

Intervention

Six lesson, fully automated cognitive behaviour therapy course delivered over the internet. Primary outcome: suicidal ideation as measured by question 9 on the Patient Health Questionnaire (PHQ-9).

Results

Suicidal ideation was common (54%) among primary care patients prescribed iCBT treatment for depression but dropped to 30% post-treatment despite minimal clinician contact and the absence of an intervention focused on suicidal ideation. This reduction in suicidal ideation was evident regardless of sex and age.

Conclusions

The findings do not support the exclusion of patients with significant suicidal ideation.
Evaluation of a predevelopment service delivery intervention: an application to improve clinical handovers
Authors: Yao Guiqing Lily , Novielli Nicola , Manaseki-Holland Semira , Chen Yen-Fu , van der Klink Marcel , Barach Paul , Chilton Peter J , Lilford Richard J
Published: September 2012

Background

We developed a method to estimate the expected cost-effectiveness of a service intervention at the design stage and ‘road-tested’ the method on an intervention to improve patient handover of care between hospital and community.

Method

The development of a nine-step evaluation framework:

1. Identification of multiple endpoints and arranging them into manageable groups;

2. Estimation of baseline overall andpreventablerisk;

3. Bayesian elicitation of expected effectiveness of the planned intervention;

4. Assigning utilities to groups of endpoints;

5. Costing the intervention;

6. Estimating health service costs associated with preventable adverse events;

7. Calculating health benefits;

8. Cost-effectiveness calculation;

9. Sensitivity and headroom analysis.

Results

    Literature review suggested that adverse events follow 19% of patient discharges, and that one-third are preventable by improved handover (ie, 6.3% of all discharges). The intervention to improve handover would reduce the incidence of adverse events by 21% (ie, from 6.3% to 4.7%) according to the elicitation exercise. Potentially preventable adverse events were classified by severity and duration. Utilities were assigned to each category of adverse event. The costs associated with each category of event were obtained from the literature. The unit cost of the intervention was €16.6, which would yield a Quality Adjusted Life Year (QALY) gain per discharge of 0.010. The resulting cost saving was €14.3 per discharge. The intervention is cost-effective at approximately €214 per QALY under the base case, and remains cost-effective while the effectiveness is greater than 1.6%.

Conclusions

We offer a usable framework to assist in ex ante health economic evaluations of health service interventions.
MODE SUMMATION APPROACH TO CASIMIR EFFECT BETWEEN TWO OBJECTS
Authors: TEO L. P.
Published: September 2012

In the last few years, several approaches have been developed to compute the exact Casimir interaction energy between two nonplanar objects, all lead to the same functional form, which is called the TGTG formula. In this paper, we explore the TGTG formula from the perspective of mode summation approach. Both scalar fields and electromagnetic fields are considered. In this approach, one has to first solve the equation of motion to find a wave basis for each object. The two T's in the TGTG formula are [Formula: see text]-matrices representing the Lippmann–Schwinger T-operators, one for each of the objects. Each [Formula: see text]-matrix can be found by matching the boundary conditions imposed on the object, and it is independent of the other object. However, it depends on whether the object is interacting with an object outside it, or an object inside it. The two G's in the TGTG formula are the translation matrices, relating the wave basis of an object to the wave basis of the other object. These translation matrices only depend on the wave basis chosen for each object, and they are independent of the boundary conditions on the objects. After discussing the general theory, we apply the prescription to derive the explicit formulas for the Casimir energies for the sphere–sphere, sphere–plane, cylinder–cylinder and cylinder–plane interactions. First the [Formula: see text]-matrices for a plane, a sphere and a cylinder are derived for the following cases: the object is imposed with Dirichlet, Neumann or general Robin boundary conditions; the object is semitransparent; and the object is a magnetodielectric object immersed in a magnetodielectric media. Then the operator approach developed by R. C. Wittman [IEEE Trans. Antennas Propag.36, 1078 (1988)] is used to derive the translation matrices. From these, the explicit TGTG formula for each of the scenarios can be written down. On the one hand, we have summarized all the TGTG formulas that have been derived so far for the sphere–sphere, cylinder–cylinder, sphere–plane and cylinder–plane configurations. On the other hand, we provide the TGTG formulas for some scenarios that have not been considered before.
ON SL(2, ℝ) AND AdS GRAVITY
Authors: HU SEN , HU ZHI , ZHANG RUORAN
Published: September 2012

In this paper, we first view the three-dimensional gravity as the fixed points of generalized Ricci flow. Next we discuss the linear AdS3 gravity, and show some interesting topological properties in the Bañados, Teitelboim and Zanelli (BTZ) construction by manipulation of the group-theoretic properties of SL(2, ℝ). Finally we embed SL(2, ℝ) into OSp(1|2, ℝ) and consider the corresponding super-Chern–Simons action.
A GENERALIZATION OF A THEOREM OF KLEITMAN AND KRIEGER
Authors: ZERNISCH JAN B.
Published: September 2012

In this paper, we prove that any finite or infinite family of squares with total area at most 1 can be packed into the rectangle with dimensions [Formula: see text] and that this rectangle is unique with this property and minimum area. Furthermore, we show that for a finite unit family of n squares which are given sorted by their side lengths, a packing into the [Formula: see text] rectangle can be found in linear time, which yields an O(n log n) time algorithm for the general case. With a restriction to finite unit families, the former statement has been published by D. J. Kleitman and M. Krieger, who – as they state themselves – only provide "a general discussion of the methods used [throughout the proof] and an outline of the major cases". Although they refer their proof to as "being constructive", it is not clear from their presentation how a packing algorithm would look like. Regarding the fact that there are some other results that rely on this statement – some of which even make use of a corresponding packing algorithm – it is important to have an complete and preferably constructive published proof for it. The proof that is presented here is constructive and uses an interesting technique based on quadratic programming which could be applicable to other packing problems as well.
THE INFLUENCE OF MINIMAL SUBGROUPS ON THE STRUCTURE OF FINITE GROUPS
Authors: LU JIAKUAN , GUO XIUYUN , LI XUAN
Published: September 2012

A subgroup H of a finite group G is called ss-supplemented in G if there exists a subgroup K of G such that G = HK and H ∩ K is s-quasinormal in K. In this paper, we investigate the influence of ss-supplemented minimal subgroups on the structure of finite groups and obtain some interesting results.
EXT ALGEBRA OF NICHOLS ALGEBRAS OF CARTAN TYPE A2
Authors: YU XIAOLAN , ZHANG YINHUO
Published: September 2012

We give the full structure of the Ext algebra of any Nichols algebra of Cartan type A2by using the Hochschild–Serre spectral sequence. As an application, we show that the pointed Hopf algebras [Formula: see text] with Dynkin diagrams of type A, D, or E, except for A1and A1× A1with the order NJ> 2 for at least one component J, are wild.
GLOBALIZATION OF PARTIAL ACTIONS ON SEMIPRIME RINGS
Authors: BEMM LAERTE , FERRERO MIGUEL
Published: September 2012

In this paper we consider partial actions of groups on semiprime rings. Our purpose is to study when such a partial action has a globalization.
ON THE RELATIONSHIPS BETWEEN VARIOUS LATTICE-VALUED TOPOLOGICAL GROUPS AND THEIR UNIFORMITIES
Authors: AL-MUFARRIJ J. , AHSANULLAH T. M. G.
Published: September 2012

The purpose of this article is to investigate the relationships between some of the lattice-valued topological groups, and the lattice-valued uniformities that they inherit. In so doing, we look at the relationship between (a) crisp sets of lattice-valued neighborhood groups and lattice-valued neighborhood topological groups, and their uniformities; (b) lattice-valued topological groups of ordinary subsets and fuzzy neighborhood groups, and their uniformities. We also investigate the connection between stratified lattice-valued neighborhood topological group and its level spaces.
USING FRINGES FOR MINIMAL CONCEPTUAL DECOMPOSITION OF BINARY CONTEXTS
Authors: JAOUA ALI , SALAH MOHAMED , YAHIA SADOK BEN , AL-JA'AM JIHAD M.
Published: September 2012

Extracting knowledge from huge data in a reasonable time is still a challenging problem. Most real data (structured or not) can be mapped to an equivalent binary context, with or without using a scaling method, as for extracting associations between words in a text, or in machine learning systems. In this paper, our objective is to find a minimal coverage of a relation [Formula: see text] with formal concepts. The problem is known to be NP-complete.1 In this paper, we exploit a particular difunctional relation embedded in any binary relation [Formula: see text], the fringe of [Formula: see text], to find an approximate conceptual coverage of [Formula: see text]. We use formal properties of fringes to find better algorithms calculating the minimal rectangular coverage of binary relation. Here, a formal context is considered as a binary relation. By exploiting some background on relational algebra in the present work, we merge some results of Belohlavek and Vichodyl,2 using formal concept analysis with previous results obtained by Kcherif et al.3 using relational algebra. We finally propose decomposition algorithms based on the relational formalization and fringe relations.
The Oligotrophic Ocean Is Autotrophic
Authors: Williams Peter J. le B. , Quay Paul D. , Westberry Toby K. , Behrenfeld Michael J.
Published: September 2012

In vitro observations of net community production (NCP) imply that the oligotrophic subtropical gyres of the open ocean are net heterotrophic; in situ observations, in contrast, consistently imply that they are net autotrophic. At least one approach must be returning an incorrect answer. We find that (a) no bias in in situ oxygen-based production estimates would give false-positive (net autotrophy) rates, (b) observed 13C enrichment of surface water dissolved inorganic carbon (DIC) can be explained only by positive NCP (net autotrophy), (c) lateral and vertical inputs of organic carbon are insufficient to sustain net heterotrophy, and (d) atmospheric input of organic material is too small to support in vitro rates of net heterotrophy and would yield δ13C depletion of surface DIC, quite the opposite of what is observed in the subtropical gyres. We conclude that the in vitro observations, implying net heterotrophy, must contain a bias that is due to an underestimate of photosynthetic rate and/or an overestimate of respiration rate.
Consistent activation of the β-catenin pathway by Salmonella type-three secretion effector protein AvrA in chronically infected intestine
Authors: Lu Rong , Liu Xingyin , Wu Shaoping , Xia Yinglin , Zhang Yong-guo , Petrof Elaine O. , Claud Erika C. , Sun Jun
Published: September 2012

Salmonella infection is a common public health problem that can become chronic and increase the risk of cancer. Live, mutated Salmonella is used to target cancer cells. However, few studies have addressed chronic Salmonella infection in vivo. AvrA is a Salmonella type-three secretion effector that is multifunctional, inhibiting intestinal inflammation and enhancing proliferation. β-catenin is a key player in intestinal renewal, inflammation, and tumorigenesis. We hypothesize that in Salmonella -infected intestine, AvrA chronically activates the β-catenin pathway and increases cell proliferation, thus deregulating the intestinal responses to bacterial infection. We followed mice with Salmonella infection for 27 wk and investigated the physiological effects and role of AvrA on β-catenin in chronically infected intestine. We found that AvrA persistently regulated β-catenin posttranslational modifications, including phosphorylation and acetylation. Moreover, the upstream regulator Akt, transcription factors, T cell factors, nuclear β-catenin, and β-catenin target genes were enhanced in mice infected with Salmonella -expressing AvrA. AvrA has a chronic functional role in promoting intestinal renewal. In summary, we have uncovered an essential role of Salmonella AvrA in chronically activating β-catenin and impacting intestinal renewal in small intestine and colon. Our study emphasizes the importance of AvrA in chronic bacterial infection.
Sex differences in mesenteric endothelial function of streptozotocin-induced diabetic rats: a shift in the relative importance of EDRFs
Authors: Zhang Rui , Thor Der , Han Xiaoyuan , Anderson Leigh , Rahimian Roshanak
Published: September 2012

Several studies suggest that diabetes affects male and female vascular beds differently. However, the mechanisms underlying the interaction of sex and diabetes remain to be investigated. This study investigates whether there are 1) sex differences in the development of abnormal vascular responses and 2) changes in the relative contributions of endothelium-derived relaxing factors in modulating vascular reactivity of mesenteric arteries taken from streptozotocin (STZ)-induced diabetic rats at early and intermediate stages of the disease (1 and 8 wk, respectively). We also investigated the mesenteric expression of the mRNAs for endothelial nitric oxide (NO) synthase (eNOS) and NADPH oxidase (Nox) in STZ-induced diabetes in both sexes. Vascular responses to acetylcholine (ACh) in mesenteric arterial rings precontracted with phenylephrine were measured before and after pretreatment with indomethacin (cyclooxygenase inhibitor), Nω-nitro-l-arginine methyl ester (NOS inhibitor), or barium chloride (Kirblocker) plus ouabain (Na+-K+-ATPase inhibitor). We demonstrated that ACh-induced relaxations were significantly impaired in mesenteric arteries from both male and female diabetic rats at 1 and 8 wk. However, at 8 wk the extent of impairment was significantly greater in diabetic females than diabetic males. Our data also showed that in females, the levels of eNOS, Nox2, and Nox4 mRNA expression and the relative importance of NO to the regulation of vascular reactivity were substantially enhanced, whereas the importance of endothelium-derived hyperpolarizing factor (EDHF) was significantly reduced at both 1 and 8 wk after the induction of diabetes. This study reveals the predisposition of female rat mesenteric arteries to vascular injury after the induction of diabetes may be due to a shift away from a putative EDHF, initially the major vasodilatory factor, toward a greater reliance on NO.
Preconditioning protects the heart in a prolonged uremic condition
Authors: Kocsis Gabriella F. , Sárközy Márta , Bencsik Péter , Pipicz Márton , Varga Zoltán V. , Pálóczi János , Csonka Csaba , Ferdinandy Péter , Csont Tamás
Published: September 2012

Metabolic diseases such as hyperlipidemia and diabetes attenuate the cardioprotective effect of ischemic preconditioning. In the present study, we examined whether another metabolic disease, prolonged uremia, affects ischemia/reperfusion injury and cardioprotection by ischemic preconditioning. Uremia was induced by partial nephrectomy in male Wistar rats. The development of uremia was verified 29 wk after surgery. Transthoracic echocardiography was performed to monitor cardiac function. At week 30, hearts of nephrectomized and sham-operated rats were isolated and subjected to a 30-min coronary occlusion followed by 120 min reperfusion with or without preceding preconditioning induced by three intermittent cycles of brief ischemia and reperfusion. In nephrectomized rats, plasma uric acid, carbamide, and creatinine as well as urine protein levels were increased as compared with sham-operated controls. Systolic anterior and septal wall thicknesses were increased in nephrectomized rats, suggesting the development of a minimal cardiac hypertrophy. Ejection fraction was decreased and isovolumic relaxation time was shortened in nephrectomized rats demonstrating a mild systolic and diastolic dysfunction. Infarct size was not affected significantly by nephrectomy itself. Ischemic preconditioning significantly decreased infarct size from 24.8 ± 5.2% to 6.6 ± 1.3% in the sham-operated group and also in the uremic group from 35.4 ± 9.5% to 11.9 ± 3.1% of the area at risk. Plasma ANG II and nitrotyrosine were significantly increased in the uremic rats. We conclude that although prolonged experimental uremia leads to severe metabolic changes and the development of a mild myocardial dysfunction, the cardioprotective effect of ischemic preconditioning is still preserved.
Temporal organization of activity in the brown bear (Ursus arctos): roles of circadian rhythms, light, and food entrainment
Authors: Ware Jasmine V. , Nelson O. Lynne , Robbins Charles T. , Jansen Heiko T.
Published: September 2012

Seasonal cycles of reproduction, migration, and hibernation are often synchronized to changes in daylength (photoperiod). Ecological and evolutionary pressures have resulted in physiological specializations enabling animals to occupy a particular temporal niche within the diel cycle leading to characteristic activity patterns. In this study, we characterized the annual locomotor activity of captive brown bears (Ursus arctos). Locomotor activity was observed in 18 bears of varying ages and sexes during the active (Mar-Oct) and hibernating (Nov-Feb) seasons. All bears exhibited either crepuscular or diurnal activity patterns. Estimates of activity duration (α) and synchronization to the daily light:dark cycle (phase angles) indirectly measured photoresponsiveness. α increased as daylength increased but diverged near the autumnal equinox. Phase angles varied widely between active and hibernating seasons and exhibited a clear annual rhythm. To directly test the role of photoperiod, bears were exposed to controlled photoperiod alterations. Bears failed to alter their daily activity patterns (entrain) to experimental photoperiods during the active season. In contrast, photic entrainment was evident during hibernation when the daily photocycle was shifted and when bears were exposed to a skeleton (11:1:11:1) photoperiod. To test whether entrainment to nonphotic cues superseded photic entrainment during the active season, bears were exposed to a reversed feeding regimen (dark-fed) under a natural photocycle. Activity shifted entirely to a nocturnal pattern. Thus daily activity in brown bears is highly modifiable by photoperiod and food availability in a stereotypic seasonal fashion.
Cardiovascular responses to lower body negative pressure before and after 4 h of head-down bed rest and seated control in men and women
Authors: Edgell H. , Grinberg A. , Gagné N. , Beavers K. R. , Hughson R. L.
Published: September 2012

Cardiovascular deconditioning after a 4-h head-down bed rest (HDBR) might be a consequence of the time of day relative to pre-HDBR testing, or simply 4 h of confinement and inactivity rather than the posture change. Ten men and 11 women were studied during lower body negative pressure (LBNP) before and after 4-h HDBR and 4-h seated posture (SEAT) as a control for time of day and physical inactivity effects to test the hypotheses that cardiovascular deconditioning was a consequence of the HDBR posture, and that women would have a greater deconditioning response. Following HDBR, men and women had lower blood volume, higher heart rate with a greater increase during LBNP, a greater decrease of stroke volume during LBNP, lower central venous pressure, smaller inferior vena cava diameter, higher portal vein resistance index with a greater increase during LBNP, but lower forearm vascular resistance, lower norepinephrine, and lower renin. Women had lower vasopressin and men had higher vasopressin after HDBR, and women had lower pelvic impedance and men higher pelvic impedance. Following SEAT, brachial vascular resistance was reduced, thoracic impedance was elevated, the reduction of central venous pressure during LBNP was changed, women had higher angiotensin II whereas men had lower levels, and pelvic impedance increased in women and decreased in men. Cardiovascular deconditioning was greater after 4-h HDBR than after SEAT. Women and men had similar responses for most cardiovascular variables in the present study that tested the responses to LBNP after short-duration HDBR compared with a control condition.
Changes in wrist muscle activity with forearm posture: implications for the study of sensorimotor transformations
Authors: de Rugy Aymar , Davoodi Rahman , Carroll Timothy J.
Published: September 2012

The primate wrist is an ideal model system for studying the reference frames in which movements are coded within the central nervous system, as a simple rotation of the forearm allows dissociation between extrinsic and body-referenced coordinates. Important information regarding coordinate frame transformations has been obtained using this system, particularly from studies involving extracellular cortical and spinal recordings from monkeys. Because preferred directions of muscle use were reported to rotate by less than half of the joint rotation, the system was considered to dissociate three reference frames: extrinsic (direction of movement in space), muscle (activity of muscles), and joint (angle of the wrist joint). However, given the relatively minor changes in reported muscle biomechanics with human forearm rotation, the reported distinction between joint space and muscle space is surprisingly large. Here, we reassessed patterns of wrist muscle activity with changes in forearm posture in humans, during an isometric force-aiming task with a device that enabled stringent control of the musculoskeletal configuration. Results show that the preferred directions for wrist muscle activation closely follow forearm orientation (i.e., by 88%). Control experiments confirmed this, whether the hand was clamped passively by a device or grasped a handle. Furthermore, the remaining 12% discrepancy between intended changes in wrist orientation and muscle use also occurred for muscle-pulling directions obtained by intramuscular electrical stimulation. The findings prompt reconsideration of data based on the previously reported dissociation between joint space and muscle space and have critical implications for future investigations of sensorimotor transformations and their adaptation using the wrist.