bluuebunny/crossref_metadata_2025 huggingface dataset:
Classifying spaces and Dirac operators coupled to instantons
Authors: Sanders Marc
Published: June 2012

LetM(k,SU(l))M(k,SU(l))denote the moduli space of based gauge equivalence classes ofSU(l)SU(l)instantons on principal bundles overS4{S^4}with second Chern class equal tokk. In this paper we use Dirac operators coupled to such connections to study the topology of these moduli spaces asllincreases relative tokk. This "coupling" procedure produces maps∂u:M(k,SU(l))→BU(k){\partial _u}:M(k,SU(l)) \to BU(k), and we prove that in the limit overllsuch maps recover Kirwan’s[K][\text {K}]homotopy equivalenceM(k,SU)≃BU(k)M(k,SU) \simeq BU(k). We also compute, for anykkandll, the image of the homology map<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="left-parenthesis partial-differential Subscript u Baseline right-parenthesis Subscript asterisk Baseline colon upper H Subscript asterisk Baseline left-parenthesis upper M left-parenthesis k comma upper S upper U left-parenthesis l right-parenthesis right-parenthesis semicolon upper Z right-parenthesis right-arrow upper H Subscript asterisk Baseline left-parenthesis upper B upper U left-parenthesis k right-parenthesis semicolon upper Z right-parenthesis">(∂u)∗:H∗(M(k,SU(l));Z)→H∗(BU(k);Z){({\partial _u})_ * }:{H_ * }(M(k,SU(l));Z) \to {H_ * }(BU(k);Z). Finally, we prove all the analogous results forSp(l)Sp(l)instantons.
On minimal sets of scalar parabolic equations with skew-product structures
Authors: Shen Wen Xian , Yi Yingfei
Published: June 2012

Skew-product semi-flow

Π
t

:
X
×
Y
→
X
×
Y

{\Pi _t}:X \times Y \to X \times Y

which is generated by
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="StartLayout Enlarged left-brace 1st Row u Subscript t Baseline equals u Subscript x x Baseline plus f left-parenthesis y dot t comma x comma u comma u Subscript x Baseline right-parenthesis comma t greater-than 0 comma 0 greater-than x greater-than 1 comma y element-of upper Y comma 2nd Row upper D or upper N boundary conditions EndLayout">

{

u
t

=

u

x
x

+
f
(
y
⋅

t
,
x
,
u
,

u
x

)
,

t
>
0
,

0
>
x
>
1
,

y
∈
Y
,

D

or 

N

boundary conditions

\left \{ \begin {gathered} {u_t} = {u_{xx}} + f(y \cdot \,t,x,u,{u_x}),\qquad t > 0,\;0 > x > 1,\;y \in Y, \hfill \\ D\;{\text {or }}N\;{\text {boundary conditions}} \hfill \\ \end {gathered} \right .

\]
is considered, where

X
X

is an appropriate subspace of

H
2

(
0
,
1
)
,

(
Y
,

R

)

{H^2}(0,1),\;(Y,\,\mathbb {R})

is a minimal flow with compact phase space. It is shown that a minimal set

E
⊂
X
×
Y

E \subset X \times Y

of

Π
t

{\Pi _t}

is an almost

1

 - 

1

1{\text { - }}1

extension of

Y
Y

, that is, set

Y
0

=
{
y
∈
Y

|

card
⁡
(
E
⊂

P

−
1

(
y
)
)
=
1
}

{Y_0} = \{ y \in Y|\operatorname {card} (E \subset {P^{ - 1}}(y)) = 1\}

is a residual subset of

Y
Y

, where

P
:
X
×
Y
→
Y

P:X \times Y \to Y

is the natural projection. Consequently, if

(
Y
,

R

)

(Y,\mathbb {R})

is almost periodic minimal, then any minimal set

E
⊂
X
×
Y

E \subset X \times Y

of

Π
t

{\Pi _t}

is an almost automorphic minimal set. It is also proved that dynamics of

Π
t

{\Pi _t}

is closed in the category of almost automorphy, that is, a minimal set

E
⊂
X
×
Y

E \subset X \times Y

of

Π
t

{\Pi _t}

is almost automorphic minimal if and only if

(
Y
,

R

)

(Y,\mathbb {R})

is almost automorphic minimal. Asymptotically almost periodic parabolic equations and certain coupled parabolic systems are discussed. Examples of nonalmost periodic almost automorphic minimal sets are provided.
Automorphisms of spaces with finite fundamental group
Authors: Triantafillou Georgia
Published: June 2012

Let

X
X

be a finite CW-complex with finite fundamental group. We show that the group

aut

(
X
)

{\text {aut}}(X)

of homotopy classes of self-homotopy equivalences of

X
X

is commensurable to an arithmetic group. If in addition

X
X

is an oriented manifold then the subgroup

au

t

t

(
X
)

{\text {au}}{{\text {t}}_t}(X)

of homotopy classes of tangential homotopy equivalences is commensurable to an arithmetic group. Moreover if

X
X

is a smooth manifold of dimension

⩾
5

\geqslant 5

then the subgroup

diff

(
X
)

{\text {diff}}(X)

of

aut

(
X
)

{\text {aut}}(X)

the elements of which are represented by diffeomorphisms is also commensurable to an arithmetic group.
Periods for transversal maps via Lefschetz numbers for periodic points
Authors: Guillamon A. , Jarque X. , Llibre J. , Ortega J. , Torregrosa J.
Published: June 2012

Let

f
:
M
→
M

f:M \to M

be a

C
1

{C^1}

map on a

C
1

{C^1}

differentiable manifold. The map

f
f

is called transversal if for all

m
∈

N

m \in \mathbb {N}

the graph of

f
m

{f^m}

intersects transversally the diagonal of

M
×
M

M \times M

at each point

(
x
,
x
)

(x,x)

such that

x
x

is a fixed point of

f
m

{f^m}

. We study the set of periods of

f
f

by using the Lefschetz numbers for periodic points. We focus our study on transversal maps defined on compact manifolds such that their rational homology is

H
0

≈

Q

{H_0} \approx \mathbb {Q}

,

H
1

≈

Q

⊕

Q

{H_1} \approx \mathbb {Q} \oplus \mathbb {Q}

and

H
k

≈
{
0
}

{H_k} \approx \{ 0\}

for

k
≠
0
,
1

k \ne 0,1

.
NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species
Authors: Kreimer Anat , Doron-Faigenboim Adi , Borenstein Elhanan , Freilich Shiri
Published: June 2012

Summary: NetCmpt is a tool for calculating the competitive potential between pairs of bacterial species. The score describes the effective metabolic overlap (EMO) between two species, derived from analyzing the topology of the corresponding metabolic models. NetCmpt is based on the EMO algorithm, developed and validated in previous studies. It takes as input lists of species-specific enzymatic reactions (EC numbers) and generates a matrix of the potential competition scores between all pairwise combinations.

Availability and implementation: NetCmpt is provided as both a web tool and a software package, designed for the use of non-computational biologists. The NetCmpt web tool, software, examples, and documentation are freely available online at http://app.agri.gov.il/shiri/NetComp.php.

Contact:  anat.kreimer@gmail.com; shiri.freilich@gmail.com

Supplementary Information: Supplementary data are available at Bioinformatics online.
SYNCSA—R tool for analysis of metacommunities based on functional traits and phylogeny of the community components
Authors: Debastiani Vanderlei J. , Pillar Valério D.
Published: June 2012

Summary: SYNCSA is an R package for the analysis of metacommunities based on functional traits and phylogeny of the community components. It offers tools to calculate several matrix correlations that express trait-convergence assembly patterns, trait-divergence assembly patterns and phylogenetic signal in functional traits at the species pool level and at the metacommunity level.

Availability and implementation: SYNCSA is a package for the R environment, under a GPL-2 open-source license and freely available on CRAN official web server for R (http://cran.r-project.org).

Contact:  vanderleidebastiani@yahoo.com.br
Arabinogalactan Proteins Occur in the Free-Living Cyanobacterium Genus Nostoc and in Plant–Nostoc Symbioses
Authors: Jackson Owen , Taylor Oliver , Adams David G. , Knox J. Paul
Published: June 2012

Arabinogalactan proteins (AGP) are a diverse family of proteoglycans associated with the cell surfaces of plants. AGP have been implicated in a wide variety of plant cell processes, including signaling in symbioses. This study investigates the existence of putative AGP in free-living cyanobacterial cultures of the nitrogen-fixing, filamentous cyanobacteria Nostoc punctiforme and Nostoc sp. strain LBG1 and at the symbiotic interface in the symbioses between Nostoc spp. and two host plants, the angiosperm Gunnera manicata (in which the cyanobacterium is intracellular) and the liverwort Blasia pusilla (in which the cyanobacterium is extracellular). Enzyme-linked immunosorbent assay, immunoblotting, and immunofluorescence analyses demonstrated that three AGP glycan epitopes (recognized by monoclonal antibodies LM14, MAC207, and LM2) are present in free-living Nostoc cyanobacterial species. The same three AGP glycan epitopes are present at the Gunnera–Nostoc symbiotic interface and the LM2 epitope is detected during the establishment of the Blasia–Nostoc symbiosis. Bioinformatic analysis of the N. punctiforme genome identified five putative AGP core proteins that are representative of AGP classes found in plants. These results suggest a possible involvement of AGP in cyanobacterial–plant symbioses and are also suggestive of a cyanobacterial origin of AGP.
Host Specificity of Sporisorium reilianum Is Tightly Linked to Generation of the Phytoalexin Luteolinidin by Sorghum bicolor
Authors: Zuther Katja , Kahnt Jörg , Utermark Jan , Imkampe Julia , Uhse Simon , Schirawski Jan
Published: June 2012

The smut fungus Sporisorium reilianum occurs in two varieties (S. reilianum f. sp. reilianum and S. reilianum f. sp. zeae) that cause head smut disease on sorghum and maize, respectively. Prior to plant infection, compatible haploid sporidia of S. reilianum fuse to form infectious dikaryotic hyphae that penetrate the leaf surface, spread throughout the plant, and reach the inflorescences, in which spore formation occurs. To elucidate the basis of host specificity of the two S. reilianum varieties, we compared disease etiology of S. reilianum f. sp. reilianum and S. reilianum f. sp. zeae on sorghum and maize. Both varieties could penetrate and multiply in both hosts. However, red spots appeared on inoculated leaves after sorghum infection with S. reilianum f. sp. zeae. Using matrix-assisted laser desorption-ionization time of flight analysis of leaf extracts, we show that sorghum reacts with the production of the red and orange phytoalexins luteolinidin and apigeninidin upon colonization by S. reilianum f. sp. zeae but not by S. reilianum f. sp. reilianum. Using in vitro growth assays, we demonstrate that luteolinidin but not apigeninidin slows vegetative growth of both S. reilianum f. sp. zeae and S. reilianum f. sp. reilianum. However, the phytoalexin biosynthesis gene SbDFR3 is only induced in sorghum after infection with S. reilianum f. sp. zeae, as shown by quantitative real-time polymerase chain reaction. This suggests that regulation of luteolinidin biosynthesis determines infection success of S. reilianum on sorghum.
First Report of Zonate Leaf Spot of Cinnamomum kanehirae Caused by Hinomyces moricola in Taiwan
Authors: Fu C. H. , Lin F. Y.
Published: June 2012

Cinnamomum kanehirae, a native tree of Taiwan, is an important tree that hosts popular medicinal fungi. In the winter of 2011, zonate leaf spots were observed at a nursery garden in Wu-Lai, Taiwan. Initial symptoms included small brown lesions on leaves that became larger leaf spots after expanding or fusing together, causing a leaf blight and eventually defoliation. Sporophores on the host were generally hypophyllous but sometimes amphigenous, solitary, erect, easily detachable. The upper portion of the sporophore was considered an individual conidium and consisted of a pyramidal head that was fusiform to ventricose, 320 to 580 μm long and 100 to 130 μm wide at the broadest point. Branches within the pyramidal head were short and compact, and dichotomously or trichotomously branched. The sporophore initials were hyaline, broad, septate, tapering toward an acute apex, and sometimes constricted at the basal septum. Sclerotia were observed in older lesions, grey or black, spherical, and 1 to 2.5 mm in diameter. The fungus was isolated from infected tissue and sporophores, maintained on potato dextrose agar (PDA) at 20°C in darkness. Sclerotia were produced on PDA after 4 to 5 weeks and were irregular or spherical, but sporophores didn't develop on agar medium. The fungus was identified as Hinomyces moricola on the basis of morphological characteristics (1). Koch's postulates were performed by inoculating four 1-year-old, asymptomatic, potted C. kanehirae plants; every plant was inoculated with sporophores from infected leaves on each of five leaves. Four noninoculated plants were kept in separate pots and served as controls. All plants were covered with transparent plastic bags individually and incubated in a growth chamber at 18 to 20°C. Symptoms were observed after 2 to 4 days on every inoculated plant but not on uninoculated plants. The leaf spots were similar to those originally observed. The pathogen was reisolated from spots of inoculated plants. The pathogenicity test was repeated once. H. moricola is known to cause severe defoliation on woody and annual plants, including at least 73 host species and 36 families distributed in the eastern United States and Japan (2).

References: (1) N.-S. Tomoko et al. Mycoscience. 47:351, 2006. (2) J. C. Trolinger et al. Plant Dis. Reptr. 62:710, 1978.
Deceptive vibratory communication: pupae of a beetle exploit the freeze response of larvae to protect themselves
Authors: Kojima Wataru , Ishikawa Yukio , Takanashi Takuma
Published: June 2012

It is argued that animal signals may have evolved so as to manipulate the response of receivers in a way that increases the fitness of the signallers. In deceptive communication, receivers incur costs by responding to false signals. Recently, we reported that pupae of the soil-inhabiting Japanese rhinoceros beetle
Trypoxylus dichotoma
produce vibratory signals to deter burrowing larvae, thereby protecting themselves. In the present study, monitoring of vibrations associated with larval movement revealed that
T. dichotoma
larvae remained motionless for
ca
10 min when pupal vibratory signals were played back transiently (freeze response). Furthermore, pupal signals of
T. dichotoma
elicited a freeze response in three other scarabaeid species, whose pupae do not produce vibratory signals. This indicates that the freeze response to certain types of vibration evolved before the divergence of these species and has been evolutionarily conserved, presumably because of the fitness advantage in avoiding predators. Pupae of
T. dichotoma
have probably exploited pre-existing anti-predator responses of conspecific larvae to protect themselves by emitting deceptive vibratory signals.
Nanoscale characterization of the biomechanical hardening of bovine zona pellucida
Authors: Boccaccio Antonio , Frassanito Maria Cristina , Lamberti Luciano , Brunelli Roberto , Maulucci Giuseppe , Monaci Maurizio , Papi Massimiliano , Pappalettere Carmine , Parasassi Tiziana , Sylla Lakamy , Ursini Fulvio , De Spirito Marco
Published: June 2012

The zona pellucida (ZP) is an extracellular membrane surrounding mammalian oocytes. The so-called zona hardening plays a key role in fertilization process, as it blocks polyspermy, which may also be caused by an increase in the mechanical stiffness of the ZP membrane. However, structural reorganization mechanisms leading to ZP's biomechanical hardening are not fully understood yet. Furthermore, a correct estimate of the elastic properties of the ZP is still lacking. Therefore, the aim of the present study was to investigate the biomechanical behaviour of ZP membranes extracted from mature and fertilized bovine oocytes to better understand the mechanisms involved in the structural reorganization of the ZP that may lead to the biomechanical hardening of the ZP. For that purpose, a hybrid procedure is developed by combining atomic force microscopy nanoindentation measurements, nonlinear finite element analysis and nonlinear optimization. The proposed approach allows us to determine the biomechanical properties of the ZP more realistically than the classical analysis based on Hertz's contact theory, as it accounts for the nonlinearity of finite indentation process, hyperelastic behaviour and material heterogeneity. Experimental results show the presence of significant biomechanical hardening induced by the fertilization process. By comparing various hyperelastic constitutive models, it is found that the Arruda–Boyce eight-chain model best describes the biomechanical response of the ZP. Fertilization leads to an increase in the degree of heterogeneity of membrane elastic properties. The Young modulus changes sharply within a superficial layer whose thickness is related to the characteristic distance between cross-links in the ZP filamentous network. These findings support the hypothesis that biomechanical hardening of bovine ZP is caused by an increase in the number of inter-filaments cross-links whose density should be higher in the ZP inner side.
Modelling cell motility and chemotaxis with evolving surface finite elements
Authors: Elliott Charles M. , Stinner Björn , Venkataraman Chandrasekhar
Published: June 2012

We present a mathematical and a computational framework for the modelling of cell motility. The cell membrane is represented by an evolving surface, with the movement of the cell determined by the interaction of various forces that act normal to the surface. We consider external forces such as those that may arise owing to inhomogeneities in the medium and a pressure that constrains the enclosed volume, as well as internal forces that arise from the reaction of the cells' surface to stretching and bending. We also consider a protrusive force associated with a reaction–diffusion system (RDS) posed on the cell membrane, with cell polarization modelled by this surface RDS. The computational method is based on an evolving surface finite-element method. The general method can account for the large deformations that arise in cell motility and allows the simulation of cell migration in three dimensions. We illustrate applications of the proposed modelling framework and numerical method by reporting on numerical simulations of a model for eukaryotic chemotaxis and a model for the persistent movement of keratocytes in two and three space dimensions. Movies of the simulated cells can be obtained fromhttp://homepages.warwick.ac.uk/∼maskae/CV_Warwick/Chemotaxis.html.
Transmission, attenuation and reflection of shear waves in the human brain
Authors: Clayton Erik H. , Genin Guy M. , Bayly Philip V.
Published: June 2012

Traumatic brain injuries (TBIs) are caused by acceleration of the skull or exposure to explosive blast, but the processes by which mechanical loads lead to neurological injury remain poorly understood. We adapted motion-sensitive magnetic resonance imaging methods to measure the motion of the human brain
in vivo
as the skull was exposed to harmonic pressure excitation (45, 60 and 80 Hz). We analysed displacement fields to quantify the transmission, attenuation and reflection of distortional (shear) waves as well as viscoelastic material properties. Results suggest that internal membranes, such as the falx cerebri and the tentorium cerebelli, play a key role in reflecting and focusing shear waves within the brain. The skull acts as a low-pass filter over the range of frequencies studied. Transmissibility of pressure waves through the skull decreases and shear wave attenuation increases with increasing frequency. The skull and brain function mechanically as an integral structure that insulates internal anatomic features; these results are valuable for building and validating mathematical models of this complex and important structural system.
Location, location, location: finding a suitable home among the noise
Authors: Stanley Jenni A. , Radford Craig A. , Jeffs Andrew G.
Published: June 2012

While sound is a useful cue for guiding the onshore orientation of larvae because it travels long distances underwater, it also has the potential to convey valuable information about the quality and type of the habitat at the source. Here, we provide, to our knowledge, the first evidence that settlement-stage coastal crab species can interpret and show a strong settlement and metamorphosis response to habitat-related differences in natural underwater sound. Laboratory- and field-based experiments demonstrated that time to metamorphosis in the settlement-stage larvae of common coastal crab species varied in response to different underwater sound signatures produced by different habitat types. The megalopae of five species of both temperate and tropical crabs showed a significant decrease in time to metamorphosis, when exposed to sound from their optimal settlement habitat type compared with other habitat types. These results indicate that sounds emanating from specific underwater habitats may play a major role in determining spatial patterns of recruitment in coastal crab species.
An information-theoretic approach to evaluating the size and temperature dependence of metabolic rate
Authors: White Craig R. , Frappell Peter B. , Chown Steven L.
Published: June 2012

The effects of body mass and temperature on metabolic rate (MR) are among the most widely examined physiological relationships. Recently, these relationships have been incorporated into the metabolic theory of ecology (MTE) that links the ecology of populations, communities and ecosystems to the MR of individual organisms. The fundamental equation of MTE derives the relation between mass and MR using first principles and predicts the temperature dependence of MR based on biochemical kinetics. It is a deliberately simple, zeroth-order approximation that represents a baseline against which variation in real biological systems can be examined. In the present study, we evaluate the fundamental equation of MTE against other more parameter-rich models for MR using an information-theoretic approach to penalize the inclusion of additional parameters. Using a comparative database of MR measurements for 1359 species, from 11 groups ranging from prokaryotes to mammals, and spanning 16 orders of magnitude in mass and a 59°C range in body temperature, we show that differences between taxa in the mass and temperature dependence of MR are sufficiently large as to be retained in the best model for MR despite the requirement for estimation of 22 more parameters than the fundamental equation of MTE.
Embryonic Cell Ablation in Drosophila Using Lasers
Authors: Sweeney Sean T. , Hidalgo Alicia , de Belle J. Steven , Keshishian Haig
Published: June 2012

Cell ablation is a powerful tool in the study of eukaryotic developmental biology. The selective removal of cells by ablation may provide much information about their origin, fate, or function in the developing organism. Laser-based techniques have an advantage over genetic or chemical ablation methods in that the operations can be performed in essentially any cell pattern and at any time in development. This protocol describes the methods needed to target and ablate specific cells of interest in Drosophila embryos with lasers.
Imaging Neocortical Neurons through a Chronic Cranial Window
Authors: Holtmaat Anthony , de Paola Vincenzo , Wilbrecht Linda , Trachtenberg Josh T. , Svoboda Karel , Portera-Cailliau Carlos
Published: June 2012

The rich structural dynamics of axonal arbors and neuronal circuitry can only be revealed through direct and repeated observations of the same neuron(s) over time, preferably in vivo. This protocol describes a long-term, high-resolution method for imaging neocortical neurons in vivo, using a combination of two-photon laser scanning microscopy (2PLSM) and a surgically implanted chronic cranial window. The window is used because the skull of most mammals is too opaque to allow high-resolution imaging of cortical neurons. Using this method, it is feasible to image the smallest neuronal structures in the superficial layers of the neocortex, such as dendritic spines and axonal boutons. Because the surface area of the craniotomy is relatively large, this technique is even suitable for use when labeled neurons are relatively uncommon. The surgery and imaging procedures are illustrated with examples from our studies of structural plasticity in the developing or adult mouse brain. The protocol is optimized for adult mice; we have used mice up to postnatal day 511 (P511). With minor modifications, it is possible to image neurons in rats and mice from P2. Most of our studies have used the Thy1 promoter to drive expression of fluorophores in subsets of cortical neurons.
The effect of temperature on sperm motility and enzymatic activity in brown trout Salmo trutta, burbot Lota lota and grayling Thymallus thymallus
Authors: Lahnsteiner F. , Mansour N.
Published: June 2012

The effect of temperature on sperm motility was investigated in brown trout Salmo trutta, burbot Lota lota and grayling Thymallus thymallus using water and sperm motility prolonging saline solution (SMPS) for motility activation. The effect of temperature (4–20° C) on spermatozoal enzymes for energy supply [malate dehydrogenase (MDH), pyruvate kinase (PK), adenylate kinase (AK)], flagellar movement [Mg2+adenosine triposphatase (ATPase)] and oxidative defence [peroxidase (POX)] were measured in S. trutta and L. lota. Temperatures yielding the highest initial sperm motility rates and swimming velocities were 4–6° C for S. trutta [investigated range (IR) = 4–12° C] and L. lota (IR = 2–8° C) and 8–16° C (IR = 4–16° C) for T. thymallus. Motility variables were re‐measured after 30 s in S. trutta, after 45 s in T. thymallus and after 60 s in L. lota in water and after 2 min in all investigated species in SMPS. Motility variables were increased by low temperatures and the results differed between water and SMPS. In S. trutta and L. lota, the temperature resulting in highest activities of MDH, PK, AK and ATPase was 4° C. POX had a very narrow temperature optimum at 20° C in both species. This may indicate that the temperature optimum of enzymes of energy supply and flagellar movement are closely related to motility. The present data show that the variables are affected by temperatures in an ecologically relevant range. Too low, as well as too high temperatures affected sperm motility, and the winter spawners (S. trutta and L. lota) have a narrower temperature optimum than the spring spawner T. thymallus.
Review article: biofilm formation by Helicobacter pylori as a target for eradication of resistant infection
Authors: Cammarota G. , Sanguinetti M. , Gallo A. , Posteraro B.
Published: June 2012

Background

Helicobacter pylori is one of the most common causes of bacterial infection in humans. Resistance of this infection to conventional therapies has suggested the role of a biofilm‐growing bacterium, which is recalcitrant to many antimicrobial agents.

Aim

To review the current knowledge on biofilm formation by H. pylori and to discuss the implications of this behaviour in the context of human infections and their treatment.

Results

Scanning electron microscopy analysis of gastric biopsies of infected patients demonstrated that H. pylori forms biofilm on the gastric mucosa epithelium. Adaptation to the biofilm environment may produce many persister cells, namely dormant cells, which are highly tolerant to antimicrobials that could account for the recalcitrance of H. pylori infections in vivo. Resistant H. pylori infection has become increasingly common with triple or quadruple therapy, even in the presence of H. pylori strains susceptible to all antibiotics. The mucolytic and thiol‐containing antioxidant N‐acetylcysteine, associated with antibiotics, was successfully used in clinic for therapy of patients with chronic respiratory tract infections. Consistently, N‐acetylcysteine treatment prior to starting antibiotic therapy allowed the disappearance of gastric biofilm in all patients in whom H. pylori was eradicated.

Conclusion

Effective strategies targeting H. pylori biofilm infections are possible, through the use of substances degrading components of the biofilm.
Understanding looked‐after childhoods
Authors: Goodyer Annabel
Published: June 2012

The absence of a sociological discourse about children in the past meant that child and family social work has largely relied on psychological interpretations of children and their behaviour. However, since the 1990s, the sociology of childhood has been developed in the UK. The aim of this paper is to explore the relevance of the sociology of childhood in understanding looked‐after childhoods and in informing contemporary social work practice with looked‐after children and young people. The central argument of this paper is that, in order to fulfil professional responsibilities and to implement current and forthcoming UK social policies for looked‐after children, social work needs to employ broad understandings of children, young people and looked‐after childhoods. The paper goes on to discuss the ways in which a social work approach drawing on the sociology of childhood can offer such a conceptualization.
Balancing platform control and external contribution in third‐party development: the boundary resources model
Authors: Ghazawneh Ahmad , Henfridsson Ola
Published: June 2012

Prior research documents the significance of using platform boundary resources (e.g. application programming interfaces) for cultivating platform ecosystems through third‐party development. However, there are few, if any, theoretical accounts of this relationship. To this end, this paper proposes a theoretical model that centres on two drivers behind boundary resources design and use – resourcing and securing – and how these drivers interact in third‐party development. We apply the model to a detailed case study of Apple's iPhone platform. Our application of the model not only serves as an illustration of its plausibility but also generates insights about the conflicting goals of third‐party development: the maintenance of platform control and the transfer of design capability to third‐party developers. We generate four specialised constructs for understanding the actions taken by stakeholders in third‐party development: self‐resourcing, regulation‐based securing, diversity resourcing and sovereignty securing. Our research extends and complements existing platform literature and contributes new knowledge about an alternative form of system development.
Morphogenetic and developmental functions of the Aspergillus nidulans homologues of the yeast bud site selection proteins Bud4 and Axl2
Authors: Si Haoyu , Rittenour William R. , Xu Kaimei , Nicksarlian Mark , Calvo Ana M. , Harris Steven D.
Published: June 2012

The yeast bud site selection system represents a paradigm for understanding how fungal cells regulate the formation of a polarity axis. In Saccharomyces cerevisiae, Bud4 and Axl2 are components of the axial bud site marker. To address the possibility that these proteins regulate cellular morphogenesis in filamentous fungi, we have characterized homologues of Bud4 and Axl2 in Aspergillus nidulans. Our results show that Bud4 is involved in septum formation in both hyphae and developing conidiophores. Whereas Axl2 appears to have no obvious role in hyphal growth, it is required for the regulation of phialide morphogenesis during conidiation. In particular, Axl2 localizes to the phialide–spore junction, where it appears to promote the recruitment of septins. Furthermore, the developmental regulators BrlA and AbaA control the expression of Axl2. Additional studies indicate that Axl2 is also involved in the regulation of sexual development, not only in A. nidulans, but also in the phylogenetically unrelated fungus Fusarium graminearum. Our results suggest that Axl2 plays a key role in phialide morphogenesis and/or function during conidiation in the aspergilli.
The connector SafA interacts with the multi‐sensing domain of PhoQ in Escherichia coli
Authors: Eguchi Yoko , Ishii Eiji , Yamane Masatake , Utsumi Ryutaro
Published: June 2012

Sensor histidine kinases of two‐component signal transduction systems (TCSs) respond to various environmental signals and transduce the external stimuli across the cell membrane to their cognate response regulators. Recently, membrane proteins that modulate sensory systems have been discovered. Among such proteins is SafA, which activates the PhoQ/PhoP TCS by direct interaction with the sensor PhoQ. SafA is directly induced by the EvgS/EvgA TCS, thus connecting the two TCSs, EvgS/EvgA and PhoQ/PhoP. We investigated how SafA interacted with PhoQ. Bacterial two‐hybrid and reporter assays revealed that the C‐terminal region (41–65 aa) of SafA activated PhoQ at the periplasm. Adding synthetic SafA(41–65) peptide to the cell culture also activated PhoQ/PhoP. Furthermore, direct interaction between SafA(41–65) and the sensor domain of PhoQ was observed by means of surface plasmon resonance. NMR spectroscopy of 15N‐labelled PhoQ sensor domain confirmed that SafA and Mg2+ provoked a different conformational change of PhoQ. Site‐directed mutagenesis studies revealed that R53, within SafA(41–65), was important for the activation of PhoQ, and D179 of the PhoQ sensor domain was required for its activation by SafA. SafA activated PhoQ by a different mechanism from cationic antimicrobial peptides and acidic pH, and independent of divalent cations and MgrB.
Identification of a novel HLA‐DQB1*03:38 allele by polymerase chain reaction sequence‐based typing in a Chinese bone marrow donor
Authors: Tao S‐D. , He Y‐M. , He J. , Zhu F‐M. , Lv H‐J.
Published: June 2012

HLA‐DQB1*03:38 differs from HLA‐DQB1*03:03:02:01 at nucleotide position 184 T>C in exon 2.
Role of mannose‐binding lectin‐2 polymorphism in the development of acute cellular rejection after transplantation for hepatitis C virus‐induced liver disease
Authors: Eurich D. , Boas‐Knoop S. , Yahyazadeh A. , Neuhaus R. , Somasundaram R. , Ruehl M. , Puhl G. , Neuhaus P. , Neumann U.P. , Bahra M.
Published: June 2012

The development of liver and graft disease is suspected to be affected by genetic diversity. Mannose‐binding lectin‐2 (MBL‐2) is an important immunomodulatory factor that is involved in complement activation. The aim of our study was to elucidate the role of MBL‐2 genotypes after liver transplantation (LT) for hepatitis C virus (HCV)‐induced liver disease regarding the incidence of acute cellular rejection (ACR), graft inflammation, fibrosis development, and antiviral treatment response.

Methods

A group of 149 patients who underwent LT for HCV‐induced liver disease were genotyped for MBL‐2 (rs7096206; G/C) by TaqMan genotyping assay. We evaluated 518 post‐LT protocol biopsies and at least 98 urgent liver biopsies regarding graft fibrosis stages, inflammation grades, and evidence for rejection within MBL‐2 genotype groups.

Result

No association of MBL‐2 polymorphisms was observed regarding inflammation, fibrosis, and antiviral treatment outcome. However, the C allele of the MBL‐2 gene (P = 0.001) and gender compatibility (P = 0.012) were factors significantly associated with the incidence of ACR.

Conclusion

MBL‐2 polymorphisms and gender are involved in the development of ACR after LT. CC genotype and gender match may be regarded as risk factors for ACR in HCV‐positive graft recipients. Further studies are needed to confirm and verify this observation in non‐HCV groups as well.
Pre‐transplant myeloid dendritic cell deficiency associated with cytomegalovirus infection and death after kidney transplantation
Authors: Sun Q. , Hall E.C. , Huang Y. , Chen P. , Dibadj K. , Murawski M. , Shraybman R. , Van Kirk K. , Tang V. , Peng R. , Patton P.R. , Clare‐Salzler M.J. , Kaplan B. , Segev D.L. , Womer K.L.
Published: June 2012

Background

Dendritic cells (DCs) are potent antigen‐presenting cells critical for immunity. We previously demonstrated a significant association between pre‐transplant blood myeloid dendritic cell (mDC) and plasmacytoid dendritic cell (pDC) deficiency and post‐transplant BK viremia in renal transplant recipients. In the current post‐hoc analysis, we studied the association of these same pre‐transplant DC levels with other post‐transplant outcomes.

Methods

Pre‐transplant peripheral blood mDC and pDC levels were quantified using flow cytometry in 78 patients undergoing kidney transplantation. Post‐transplant outcomes were analyzed, including infection, rejection, and patient death, with a median follow‐up of 5.3 years. Associations between DC levels and outcomes were assessed using logistic regression analysis and Cox proportional hazards models.

Results

An independent association of mDC levels with post‐transplant cytomegalovirus infection (adjusted odds ratio 7.0, P = 0.01) and patient death (adjusted hazard ratio 13.0, P = 0.015) was found. No associations were demonstrated between levels of either DC subtype and bacterial infections or rejection.

Conclusions

Pre‐transplant mDC deficiency is significantly associated with CMV infection and death after kidney transplantation.
Efficacy of a penile variable tension loop for improving climacturia after radical prostatectomy
Authors: Mehta Akanksha , Deveci Serkan , Mulhall John P.
Published: June 2012

What's known on the subject? and What does the study add?

Climacturia is present in ∼20–40% of men after radical prostatectomy, and adversely affects sexual satisfaction. Although several strategies have been proposed for the treatment of climacturia, none have been systematically studied to date.

This observational study shows that use of a penile variable tension loop can significantly reduce the degree and frequency of orgasm‐associated incontinence, and the associated distress experienced by patients and partners. Climacturia resolves completely in half the patients, and occurs occasionally or rarely in the remainder.

Objective

To define the impact of the use of a penile variable tension loop on climacturia and on the distress level experienced by patients and their partners as a result of climacturia.

Patients and Methods

All patients presenting for sexual function assessment after radical prostatectomy (RP) were questioned regarding climacturia.

The study population consisted of men who had undergone RP < 6 months before initial evaluation, had reported having climacturia on ≥25% attempts where orgasm was achieved, had agreed to use the variable tension loop consistently, and continued to have climacturia when not using the loop at follow‐up.

Patients were interviewed regarding the frequency and degree of climacturia, and their own and their partner's distress levels secondary to climacturia, both with and without the use of the variable tension loop.

Results

The study population comprised 124 men.

At baseline, the degree of climacturia was small, moderate, and large in 16%, 72%, 12% of patients, respectively, and 28%, 26% and 0%, respectively, at follow‐up (all P < 0.01).

Climacturia occurred rarely, occasionally, most of the time, or always in 15%, 48%, 16% and 21% of cases, respectively, at baseline, and 48% of patients experienced no climacturia with use of the variable tension loop.

Distress was experienced by 14% and 61% of patients and partners at baseline, and 2% and 11% of patients and partners at follow up (P < 0.01).

Severity of distress was significantly lower at follow‐up for both partners and patients (P < 0.01).

Conclusions

Climacturia is a common complication of radical prostatectomy.

Application of the variable tension loop can result in a significant decrease in the frequency and volume of climacturia.

Use of the variable tension loop is a simple and non‐invasive strategy for relieving the distress associated with climacturia in patients who have undergone RP and their partners.
Saying something interesting about responsibility for health
Authors: Snelling Paul C.
Published: June 2012

The concept of responsibility for health is a significant feature of health discourse and public health policy, but application of the concept is poorly understood. This paper offers an analysis of the concept in two ways. Following an examination of the use of the word ‘responsibility’ in the nursing and wider health literature using three examples, the concept of ‘responsibility for health’ as fulfilling a social function is discussed with reference to policy documents from the UK. The philosophical literature on moral responsibility is introduced, and in considering two versions, reactive attitudes and accountability, it is argued that in application both can be regarded, though with different emphasis, as being constituted in three parts: (i) a responsible agent; (ii) having obligations (responsibilities); and (iii) being susceptible to being held responsible (that is blamed) if he fails to meet them. The three‐stage model is consistent with the examples of the word responsibility in use, but application to the social function model causes a number of problems for healthcare practice, especially for the reactive attitudes account. Apart from considerable problems in stating what exactly the obligations are and how they can be justified; and how blame might justly be apportioned and by whom, the very ideas of obligation and blame are in conflict within healthcare systems and professional nursing practice which have foundations deeply embedded in the notion of the supremacy of personal autonomy. It is concluded that current application of the concept of responsibility for health is conceptually incoherent, and if it is to retain its place in health policy and discourse, urgent remedy is required.
TILLING in extremis
Authors: Wang Trevor L. , Uauy Cristobal , Robson Fran , Till Brad
Published: June 2012

Targeting induced local lesions in genomes (TILLING), initially a functional genomics tool in model plants, has been extended to many plant species and become of paramount importance to reverse genetics in crops species. Because it is readily applicable to most plants, it remains a dominant non‐transgenic method for obtaining mutations in known genes. The process has seen many technological changes over the last 10 years; a major recent change has been the application of next‐generation sequencing (NGS) to the process, which permits multiplexing of gene targets and genomes. NGS will ultimately lead to TILLING becoming an in silico procedure. We review here the history and technology in brief, but focus more importantly on recent developments in polyploids, vegetatively propagated crops and the future of TILLING for plant breeding.
Corporate Responsibility and Compliance with the Law: A Case Study of Land, Dispossession, and Aftermath at Newmont's Ahafo Project in Ghana1
Authors: MARES RADU
Published: June 2012

An important part of responsible business practices is compliance with the law. This article details what actually happens when the laws of the host country fail to ensure adequate protection. The focus here is on land dispossession and loss of livelihood in relation to a gold mine project in central Ghana. How is it that a well‐known international company—Newmont—with its own corporate social responsibility (CSR) statements sets up a project in the year 2003 that displaces subsistence farmers from their land without compensating in cash or with replacement land? The analysis identifies the factors that lead the company to not compensate farmers for their lost land: cost‐cutting, strict adherence to the law, CSR commitment that was new and not internalized, complexities of the Ghanaian land tenure system, peer pressure to preserve the status quo, selection of an “old‐school” CSR manager, and the inadequacy of Ghanaian mining law to account for relatively novel, “open‐pit” mining techniques. However, the specter of famine raised by civil society activism, the involvement of the International Financial Corporation, and a better qualified CSR team constitute another set of factors that lead to a comprehensive package of livelihood improvement measures. There is a contrast between the complexity, long‐term, and advanced type of assistance Newmont currently envisages and the backward, short‐term, formalism, and brutality of denying compensation for land back in 2003. This research is based on the extensive documentation Newmont makes available on its web site, interviews conducted in Ghana, and literature research.
Health‐care Nonprofits: Enhancing Governance and Public Trust
Authors: BLODGETT MARK S. , MELCONIAN LINDA
Published: June 2012

Nonprofits are a major part of the U.S. economy and they are not immune from corporate malfeasance controversies. Even Congress has expressed concern about the crisis in nonprofit governance. The nonprofit response to Congress has been a historic initiative recognizing critical challenges to nonprofit governance. In contrast to their for‐profit counterparts, nonprofits are committed to missions serving the public benefit and not to shareholder profits. Accordingly, their missions and financial resources are intrinsic to their very existence, which is built upon the public trust. That trust is rooted in fiduciary responsibility and reflected in best practices. This article traces the history of the nonprofit public trust and fiduciary standards and examines principles of Sarbanes–Oxley and other best practices as they apply to nonprofits. The authors sampled 80 health‐care nonprofit corporation web sites from eight asset classes to determine compliance with Sarbanes–Oxley and identification of fiduciary duty, ethical values, and other best practices. Among the very largest health‐care nonprofits, many comply with Sarbanes–Oxley and identify fiduciary duty, ethical values, and other best practices. However, there are substantial deficiencies in such compliance and identification among all remaining seven asset classes ranging from 99.9 million to less than 100,000. The results appear to corroborate the urgent necessity for reform articulated by the Congress and the nonprofit sector. Nonprofit governance has entered a new era where best practices must be implemented to sustain the public trust.
Demonstrating the Need for Effective Business Ethics: An Alternative Approach
Authors: CHILDS JASON
Published: June 2012

Since the financial crisis, the malfeasance of business leaders has been a recurring theme in the news, along with calls for increased regulation and oversight. This focus on the ethics of the business community raises a concern about the ethics of those in business or going into business. The ethics of business people and business students has been explored by a number of researchers using survey techniques. We propose and report the results of an alternative method for investigating unethical behavior by students. In a motivated economic experiment with introductory level students, we find that business students were almost twice as likely to lie for a monetary reward as students in other disciplines, demonstrating the need for effective business ethics.
State v. Danila Kuz′mich: Soviet Desertion Laws and Industrial Child Labor during World War II
Authors: KUCHERENKO OLGA
Published: June 2012

During the Second World War, teenage labor was an economic necessity in the Soviet Union. Though the Stalinist government attempted to protect teenagers’ rights, the coercive labor policies it enacted and the general systemic deficiencies indirectly resulted in the abuse and exploitation of young workers. Although life was hard for all Soviet workers during the war, factory apprentices usually led a far more precarious existence than their adult colleagues. The inability of the state to realize its welfare objectives and to live up to its promises bred low morale and work inefficiency among many teenage workers. Instilled with a sense of entitlement and self‐efficacy, they resisted by leaving their trade schools and factories. The regime proclaimed such actions unpatriotic and criminal, at the same time refusing to take responsibility for widespread abuse. This essay looks at the institutional interaction and the actual experience of teenage workers on the factory floor and within the penal system. It argues that Soviet wartime labor policies were a failure; Stalinist humanitarian pretensions—a sham; and the regime's claims of being in full control of its labor force—at best optimistic.