bluuebunny/crossref_metadata_2025 huggingface dataset:
A universal state-selective approach to multireference coupled-cluster non-iterative corrections
Authors: Kowalski Karol
Published: May 2011

A new form of the asymmetric energy functional for multireference coupled cluster (MRCC) theories is discussed from the point of view of an energy expansion in a quasidegenerate situation. The resulting expansion for the exact electronic energy can be used to define the non-iterative corrections to approximate MRCC approaches. In particular, we show that in the proposed framework the essential part of dynamic correlation can be encapsulated in the so-called correlation Hamiltonian, which in analogy to the effective Hamiltonian, is defined in the model space (\documentclass[12pt]{minimal}\begin{document}${\cal M}_0$\end{document}M0). The proper parametrization of the exact/trial wavefunctions leads to the cancellation of the overlap-type numerators and to a connected form of the correlation Hamiltonian and size-extensive energies. Within this parametrization, when the trial wavefunctions are determined without invoking a specific form of the MRCC sufficiency conditions, the ensuing correction can be universally applied to any type of the approximate MRCC method. The analogies with other MRCC triples corrections to MRCC theories with singles and doubles (MRCCSD) are outlined. In particular, we discuss the approach, which in analogy to the Λ-Mk-MRCCSD(T) method [F. A. Evangelista, E. Prochnow, J. Gauss, H. F. Schaefer III, J. Chem. Phys. 132, 074107 (2010)], introduces an approximate form of the triply-excited clusters into the effective and correlation Hamiltonians. Since the discussed corrections can be calculated as a sum of independent reference-related contributions, possible parallel algorithms are also outlined.
Complete solution of the problem of one-dimensional non-covalent non-cooperative self-assembly in two-component systems
Authors: Evstigneev V. P. , Mosunov A. A. , Buchelnikov A. S. , Hernandez Santiago A. A. , Evstigneev M. P.
Published: May 2011

Equations for the mass conservation law and the molecular parameters observed in spectroscopic experiments have been derived for non-covalent, non-cooperative, one-dimensional self-assembly in systems containing two types of interacting molecules (hetero-association), taking into account “reflected” complexes and “edge effects.”
Far-infrared study of substrate-effect on large scale graphene
Authors: Kim Joo Youn , Lee Chul , Bae Sukang , Kim Keun Soo , Hong Byung Hee , Choi E. J.
Published: May 2011

From far-IR Drude absorption measurement we determine carrier density (N) and carrier scattering rate (Γ) of graphene deposited on buffer-layer/SiO2 composite substrate. Two types of buffer-layers, (1) polar dielectric oxide ZnO and SrTiO3 (2) organic thin film hexamethyldisilazane and polymethyl methacrylate (PMMA) were studied. N varies widely over 0.12–11.8(×1012 cm−2) range depending on the buffer-layer. In contrast Γ remains almost constant, ∼100 cm−1, irrespective of the buffer-layers. This indicates that carrier mobility (μ) of graphene depends on substrate through N, but not by Γ as commonly believed.
Real-space mapping of dynamic phenomena during hysteresis loop measurements: Dynamic switching spectroscopy piezoresponse force microscopy
Authors: Kumar A. , Ovchinnikov O. S. , Funakubo H. , Jesse S. , Kalinin S. V.
Published: May 2011

Dynamic switching spectroscopy piezoresponse force microscopy is developed to separate thermodynamic and kinetic effects in local bias-induced phase transitions. The approaches for visualization and analysis of five-dimensional data are discussed. The spatial and voltage variability of relaxation behavior of the a-c domain lead zirconate-titanate surface suggest the interpretation in terms of surface charge dynamics. This approach is applicable to local studies of dynamic behavior in any system with reversible bias-induced phase transitions ranging from ferroelectrics and multiferroics to ionic systems such as batteries, fuel cells, and electroresistive materials.
The role of activation energy and reduced viscosity on the enhancement of water flow through carbon nanotubes
Authors: Babu Jeetu S. , Sathian Sarith P.
Published: May 2011

Molecular dynamics simulations are carried out to study the pressure driven fluid flow of water through single walled carbon nanotubes. A method for the calculation of viscosity of the confined fluid based on the Eyring theory of reaction rates is proposed. The method involves the calculation of the activation energy directly from the molecular dynamics trajectory information. Computations are performed using this method to study the effect of surface curvature on the confined fluid viscosity. The results indicate that the viscosity varies nonlinearly with the carbon nanotube diameter. It is concluded that the reason behind the observed enhancement in the rate of fluid flow through carbon nanotubes could be the nonlinear variation of viscosity.
Strong room-temperature optical and spin polarization in InAs/GaAs quantum dot structures
Authors: Beyer J. , Buyanova I. A. , Suraprapapich S. , Tu C. W. , Chen W. M.
Published: May 2011

Room-temperature optical and spin polarization up to 35% is reported in InAs/GaAs quantum dots in zero magnetic field under optical spin injection using continuous-wave optical orientation spectroscopy. The observed strong spin polarization is suggested to be facilitated by a shortened trion lifetime, which constrains electron spin relaxation. Our finding provides experimental demonstration of the highly anticipated capability of semiconductor quantum dots as highly polarized spin/light sources and efficient spin detectors, with efficiency greater than 35% in the studied quantum dots.
Influence of secondary phase CuxSe on the optoelectronic quality of chalcopyrite thin films
Authors: Larsen Jes K. , Gütay Levent , Siebentritt Susanne
Published: May 2011

The effect of secondary phase CuxSe on the absorber quality of epitaxial CuGaSe2 films is studied by spatially resolved photoluminescence combined with scanning electron microscopy. We show that the presence of CuxSe crystals on the absorber during growth under Cu excess results in a locally increased crystal quality in the vicinity of the CuxSe crystallites, affecting the defect structure of the absorber. This effect remains after removal of CuxSe and induces a local reduction in the recombination centers, resulting in locally higher excess carrier concentrations and larger splitting of quasi-Fermi levels.
Liquid-core low-refractive-index-contrast Bragg fiber sensor
Authors: Qu Hang , Skorobogatiy Maksim
Published: May 2011

We propose and experimentally demonstrate a low-refractive-index-contrast hollow-core Bragg fiber sensor for liquid analyte refractive index detection. The sensor operates using a resonant sensing principle—when the refractive index of a liquid analyte in the fiber core changes, the resonant confinement of the fiber guided mode will also change, leading to both the spectral shifts and intensity changes in fiber transmission. As a demonstration, we characterize the Bragg fiber sensor using a set of NaCl solutions with different concentrations. Strong spectral shifts are obtained with the sensor experimental sensitivity found to be ∼1400 nm/refractive index unit, which is comparable to that of a surface plasmon resonance sensor. Besides using theoretical modeling we show that low-refractive-index-contrast Bragg fibers are more suitable for liquid-analyte sensing applications than their high-refractive-index-contrast counterparts.
Holocaust remembrance in Ukraine: memorialization of the Jewish tragedy at Babi Yar
Authors: Burakovskiy Aleksandr
Published: May 2011

At the core of the debate in Ukraine about Babi Yar lies the Holocaust. Between 1941 and 1943 1.5 million Jews perished in Ukraine, yet a full understanding of that tragedy has been suppressed consistently by ideologies and interpretations of history that minimize or ignore this tragedy. For Soviet ideologues, admitting to the existence of the Holocaust would have been against the tenet of a “Soviet people” and the aggressive strategy of eliminating national and religious identities. A similar logic of oneness is being applied now in the ideological formation of an independent Ukraine. However, rather than one Soviet people, now there is one Ukrainian people under which numerous historical tragedies are being subsumed, and the unique national tragedies of other peoples on the territory of Ukraine, such as the massive destruction of Jews, is again being suppressed. According to this political idea assiduously advocated most recently during the Yushchenko presidency, the twentieth century in Ukraine was a battle for liberation. Within this new, exclusive history, the Holocaust, again, has found no real place. The author reviews the complicated history regarding the memorialization of the Jewish tragedy in Babi Yar through three broad chronological periods: 1943-1960, 1961-1991, and 1992-2009.
Market meets nationalism: making entrepreneurial state subjects in post-Soviet Russia
Authors: Müller Martin
Published: May 2011

This paper argues that nationalism and neoliberalism should not be considered as conflicting ideologies, but can enter into a productive association. This association creates an entrepreneurial nationalism that people can actively embrace as self-governing subjects in pursuit of a good life and successful career, rather than as subjects governed through state-mandated projects from above. The paper illustrates this argument with material from nine months of fieldwork at a Russian elite university. While students at that university strive to develop their potential and increase their market value to be successful in the competition for the best jobs, they also emphasize that developing themselves is not antithetical to serving Russia and being true to one's country. On the contrary, advancing Russia and advancing one's own career are articulated as two sides of the same coin. At the same time, the Russian nationalist project is reframed in entrepreneurial terms: making the Russian nation strong is about developing its potential and raising its competitiveness in the global marketplace.
Discriminating between the Effects of Valence and Salience in the Implicit Association Test
Authors: Chang Betty P. I. , Mitchell Chris J.
Published: May 2011

The Implicit Association Test (IAT) is the most widely used indirect measure of attitudes in social psychology. It has been suggested that artefacts such as salience asymmetries and familiarity can influence performance on the IAT. Chang and Mitchell (2009) proposed that the ease with which IAT stimuli are classified (classification fluency) is the common mechanism underlying both of these factors. In the current study, we investigated the effect of classification fluency on the IAT and trialled a measure—the split IAT—for dissociating between the effects of valence and salience in the IAT. Across six experiments, we examined the relationship between target classification fluency and salience asymmetries in the IAT. In the standard IAT, the more fluently classified target category was, all else being equal, compatible with pleasant attributes over unpleasant attributes. Furthermore, the more fluently classified target category was more easily classified with the more salient attribute category in the split IAT, independent of evaluative associations. This suggests that the more fluently classified category is also the more salient target category.
Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy
Authors: Hou Tingjun , Li Youyong , Wang Wei
Published: May 2011

Motivation: Favorable interaction between the regulatory subunit of the cAMP-dependent protein kinase (PKA) and a peptide in A-kinase anchoring proteins (AKAPs) is critical for translocating PKA to the subcellular sites where the enzyme phosphorylates its substrates. It is very hard to identify AKAPs peptides binding to PKA due to the high sequence diversity of AKAPs.

Results: We propose a hierarchical and efficient approach, which combines molecular dynamics (MD) simulations, free energy calculations, virtual mutagenesis (VM) and bioinformatics analyses, to predict peptides binding to the PKA RIIα regulatory subunit in the human proteome systematically. Our approach successfully retrieved 15 out of 18 documented RIIα-binding peptides. Literature curation supported that many newly predicted peptides might be true AKAPs. Here, we present the first systematic search for AKAP peptides in the human proteome, which is useful to further experimental identification of AKAPs and functional analysis of their biological roles.

Contact:  tingjunhou@hotmail.com; tjhou@suda.edu.cn; wei-wang@ucsd.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Sensitive and fast mapping of di-base encoded reads
Authors: Hormozdiari Farhad , Hach Faraz , Sahinalp S. Cenk , Eichler Evan E. , Alkan Can
Published: May 2011

Motivation: Discovering variation among high-throughput sequenced genomes relies on efficient and effective mapping of sequence reads. The speed, sensitivity and accuracy of read mapping are crucial to determining the full spectrum of single nucleotide variants (SNVs) as well as structural variants (SVs) in the donor genomes analyzed.

Results: We present drFAST, a read mapper designed for di-base encoded ‘color-space’ sequences generated with the AB SOLiD platform. drFAST is specially designed for better delineation of structural variants, including segmental duplications, and is able to return all possible map locations and underlying sequence variation of short reads within a user-specified distance threshold. We show that drFAST is more sensitive in comparison to all commonly used aligners such as Bowtie, BFAST and SHRiMP. drFAST is also faster than both BFAST and SHRiMP and achieves a mapping speed comparable to Bowtie.

Availability: The source code for drFAST is available at http://drfast.sourceforge.net

Contact:  calkan@u.washington.edu
Transmission and dose–response experiments for social animals: a reappraisal of the colonization biology of
Campylobacter jejuni
in chickens
Authors: Conlan Andrew J. K. , Line John E. , Hiett Kelli , Coward Chris , Van Diemen Pauline M. , Stevens Mark P. , Jones Michael A. , Gog Julia R. , Maskell Duncan J.
Published: May 2011

Dose–response experiments characterize the relationship between infectious agents and their hosts. These experiments are routinely used to estimate the minimum effective infectious dose for an infectious agent, which is most commonly characterized by the dose at which 50 per cent of challenged hosts become infected—the ID
50
. In turn, the ID
50
is often used to compare between different agents and quantify the effect of treatment regimes. The statistical analysis of dose–response data typically makes the assumption that hosts within a given dose group are independent. For social animals, in particular avian species, hosts are routinely housed together in groups during experimental studies. For experiments with non-infectious agents, this poses no practical or theoretical problems. However, transmission of infectious agents between co-housed animals will modify the observed dose–response relationship with implications for the estimation of the ID
50
and the comparison between different agents and treatments. We derive a simple correction to the likelihood for standard dose–response models that allows us to estimate dose–response and transmission parameters simultaneously. We use this model to show that: transmission between co-housed animals reduces the apparent value of the ID
50
and increases the variability between replicates leading to a distinctive all-or-nothing response; in terms of the total number of animals used, individual housing is always the most efficient experimental design for ascertaining dose–response relationships; estimates of transmission from previously published experimental data for
Campylobacter
spp. in chickens suggest that considerable transmission occurred, greatly increasing the uncertainty in the estimates of dose–response parameters reported in the literature. Furthermore, we demonstrate that accounting for transmission in the analysis of dose–response data for
Campylobacter
spp. challenges our current understanding of the differing response of chickens with respect to host-age and
in vivo
passage of bacteria. Our findings suggest that the age-dependence of transmissibility between hosts—rather than their susceptibility to colonization—is the mechanism behind the ‘lag-phase’ reported in commercial flocks, which are typically found to be
Campylobacter
free for the first 14–21 days of life.
Methaemalbumin formation in sickle cell disease: effect on oxidative protein modification and HO‐1 induction
Authors: Hanson Madelyn S. , Piknova Barbora , Keszler Agnes , Diers Anne R. , Wang Xunde , Gladwin Mark T. , Hillery Cheryl A. , Hogg Neil
Published: May 2011

Normally, cell free haemoglobin is bound by haptoglobin and efficiently cleared. However, the chronic haemolysis in sickle cell disease (SCD) overwhelms haptoglobin binding capacity and protein turnover, resulting in elevated cell free haemoglobin. Cell free haemoglobin acts as both a scavenger of vasoactive nitric oxide and a pro‐oxidant. In addition, methaemoglobin (metHb) releases the haem moiety, which can bind to albumin to form methaemalbumin (metHSA). This study used electron paramagnetic resonance to detect metHSA in SCD plasma and demonstrated that haptoglobin prevents haem transfer from metHb to HSA. MetHSA may either provide a second line of defence against haemoglobin/haem‐mediated oxidation or contribute to the pro‐oxidant environment of SCD plasma. We demonstrated that HSA inhibited oxidative protein modification induced by metHb. Additionally, we showed that while metHb induced haem oxygenase 1 (HO‐1), an indicator of oxidative stress, HSA attenuated metHb induction of this enzyme, thereby limiting the potential benefits of HO‐1. Furthermore, HO‐1 induction by metHSA was less than HO‐1 induction by equimolar metHb not bound to albumin. Our findings confirm the presence of metHSA in SCD and suggest that haem transfer from metHb to HSA reduces the oxidative effects of free haemoglobin/haem on endothelium with both beneficial (reduced protein oxidation) and potentially harmful (reduced HO‐1 induction) outcomes.
C‐type lectins on macrophages participate in the immunomodulatory response to Fasciola hepatica products
Authors: Guasconi Lorena , Serradell Marianela C. , Garro Ana P. , Iacobelli Luciana , Masih Diana T.
Published: May 2011

Fasciola hepatica releases excretory–secretory products (FhESP), and immunomodulatory properties have been described for the carbohydrates present in these parasite products. The interaction of FhESP with the innate immune cells, such as macrophages, is crucial in the early stage of infection. In this work we observed that peritoneal macrophages from naive BALB/c mice stimulated in vitro with FhESP presented: an increased arginase activity as well as Arginase I expression, and high levels of transforming growth factor‐β and interleukin‐10. A similar macrophage population was also observed in the peritoneum of infected mice. A partial inhibition of the immunomodulatory effects described above was observed when macrophages were pre‐incubated with Mannan, anti‐mannose receptor, Laminarin or anti‐Dectin‐1, and then stimulated with FhESP. In addition, we observed a partial inhibition of these effects in macrophages obtained from mice that were intraperitoneally injected with Mannan or Laminarin before being infected. Taken together, these results suggest the participation of at least two C‐type lectin receptors, mannose receptor and Dectin‐1, in the interaction of FhESP with macrophages, which allows this parasite to induce immunoregulatory effects on these important innate immune cells and may constitute a crucial event for extending its survival in the host.
Production of pure protein and antibodies and development of immunoassays to detect Ara h 3 levels in peanut varieties
Authors: Hurlburt Barry K. , Schmitt David , Isleib Thomas G. , Cheng Hsiaopo , Garvey Cathryn , Koenig Robbin L. , Maleki Soheila J.
Published: May 2011

Peanuts are one of the most allergenic foods and are widespread in western food products. Therefore, there has been intense research into the allergic nature of the proteins involved. Ara h 3 is one of three immunodominant allergenic proteins. It is a 60‐kDa protein, which forms following cleavage of the preprotein and association of the resultant 40‐ and 20‐kDa subunits. The large subunit has been shown to harbour most of the reactive epitopes and has the protein fold likely responsible for its trypsin inhibitor activity. In this work, we have developed a method for the high‐level expression and purification of recombinant Ara h 3 40‐kDa subunit. Specific antibodies have been produced and applied to the secondary and tertiary screens of hundreds of peanut cultivars. Several of these cultivars were identified that have significantly reduced accumulation of Ara h 3.
Evaluation of the fouling phenomenon in the membrane clarification of black mulberry juice
Authors: Hojjatpanah Ghazaleh , Emam‐Djomeh Zahra , Ashtari Ahmad Kalbasi , Mirsaeedghazi Hossein , Omid Mahmoud
Published: May 2011

Mixed cellulose ester (MCE) flat membranes were used to clarify black mulberry juice, the yield of which was limited by fouling. The effects of membrane pore size (0.025, 0.1 and 0.22 μm), transmembrane pressure (0.5, 1, 1.5 and 200 kPa), and cross‐flow velocity (0.1, 0.2, 0.3 and 0.4 m s−1) on membrane fouling were evaluated; the results showed that fouling increased with increased pore size and pressure, and decreased with increased velocity. Analysis of different resistances showed that both reversible and irreversible fouling resistances have an important role in fouling‐resistance changes. There is no cake resistance in all processes. Microstructure analysis of membrane using scanning electron microscopy confirmed the theory that intermediate blocking was the dominant fouling mechanism in MCE 0.025 μm, and standard blocking was the dominant mechanism in MCE 0.1 and 0.22 μm.
Preparation and characteristics of yak casein hydrolysate–iron complex
Authors: Wang Xu , Li Ming , Li Min , Mao Xueying , Zhou Jie , Ren Fazheng
Published: May 2011

The effect of mass ratio between yak casein hydrolysate and FeSO4, reaction temperature, pH and holding time on ferrous‐binding capacity of yak casein hydrolysate was investigated. Iron‐releasing percentage and structural characteristics of the formed yak casein hydrolysate–iron complex were also examined. Results showed that casein hydrolysates with different hydrolysis degrees (DH) possessed different ferrous‐binding capacities with the highest of 7‐h hydrolysate. The optimal binding conditions between yak casein hydrolysate and iron are mass ratio of casein hydrolysate to FeSO4 of 15:1 for 20 min at 40 °C and pH 6.0. The principal binding site for Fe2+ in yak casein hydrolysate consists of the carboxylate groups and amide groups. Compared with ferrous sulphate, yak casein hydrolysate–iron complex has higher iron‐releasing percentage at basic conditions, such as pH 7.0, 7.5 and 8.0. Ferrous‐iron enriched casein hydrolysate, i.e. yak casein hydrolysate–iron complex, may have great potential as an effective delivery vehicle of bioavailable iron.
‘Your good days and your bad days’ An exploration and consideration of how lay people conceptualize depression
Authors: HOGG C.
Published: May 2011

Accessible summary

This paper presents findings from one part of a research study exploring lay people's beliefs and attitudes to mental disorder.

Twenty‐two ‘lay people’ (i.e. people who did not have professional qualifications in mental health care), were interviewed.

The interviews used open‐ended questions and a vignette describing a woman experiencing depression.

The findings of the study show that:

The people interviewed had a good understanding of depression. They were able to identify the symptoms of depression in the case study.

They were able to discuss depression at length, using either their own experiences of depression or through people they knew with the disorder.

Many people saw depression as ‘part of life’ and as a social condition as opposed to an illness.

The paper argues that lay people in this research study had a clear understanding of depression and that it was not a taboo or stigmatizing issue as is suggested in the prevailing literature.

Depression remains a significant public health issue globally; 121 million people are affected by depression health education campaigns. Regardless of the prevalence of depression and recent health education campaigns to reduce the burden of depression, many people are still stigmatized and sometimes excluded from the society in which they live. Using qualitative research, the aim of this study was to explore lay people's perceptions and attitudes of mental disorder and in particular depression. A purposive sample of 22 lay people were each asked to read a case scenario which was then followed up by the researcher using open‐ended questions to explore their knowledge and attitudes and beliefs relating to depression. The data was analysed using Braun & Clarke's strategy of thematic analysis. The results revealed that many of the participants were familiar with the concept of depression, either through their own experiences of the disorder or through knowing people with depression. The participants also drew from psychosocial explanations of depression and located depression as part of the human condition. The paper suggests that lay people's concepts of depression offer rich complex and diverse perspectives that enhance professional views and may lead to a greater understanding of uptake and acceptance of care for depression.
Childhood internalizing behaviour: analysis and implications
Authors: LIU J. , CHEN X. , LEWIS G.
Published: May 2011

Accessible summary

Important internalizing conditions include depressive disorders, anxiety disorders, somatic complaints and teenage suicide.

Genetic, environmental and social factors have been implicated as potential causes. Data on the prevalence of these disorders varies.

Although cognitive‐behavioural and pharmacological approaches therapies have been effective in managing symptoms, prevention programmes aimed at reducing exposure to drugs, environmental chemicals and violence/abuse are also important given the large role that environmental and social factors play.

Apart from the significant impact internalizing behaviour can have by itself, it is also associated with other negative outcomes including other psychological disorders.

Therefore, implementing early treatment and prevention programmes for internalizing disorders needs to be a priority in order to pre‐empt these serious consequences.

The concept of ‘internalizing behaviour’ reflects a child's emotional or psychological state and typically includes depressive disorders, anxiety disorders, somatic complaints and teenage suicide. Genetic and environmental causes have been largely implicated, although research continues to explore social etiological factors. Some research suggests females may be especially vulnerable to internalizing disorders, while data across ethnicities are somewhat variable. Regarding treatment, cognitive‐behavioural therapies and use of pharmacological approaches (i.e. selective serotonin reuptake inhibitors) have both shown great promise in reducing symptoms of internalizing disorders. However, given the role of the social environment, prevention programmes aimed at reducing exposure to drugs, violence/abuse and environmental toxins are highly important. Internalizing disorders are associated with a host of deleterious outcomes (e.g. school drop‐out, substance use and potentially suicide) as well as psychopathological outcomes (e.g. co‐morbid anxiety or depression, externalizing disorders – including suicide). Children with mental health problems suffer educationally and are more likely to become entangled in the justice and welfare systems. Clearly, early treatment and prevention programmes for internalizing disorders need to be a priority from a public health perspective as well as from a family and community perspective.
Arginase‐1‐expressing macrophages are dispensable for resistance to infection with the gastrointestinal helminth Trichuris muris
Authors: BOWCUTT R. , BELL L. V. , LITTLE M. , WILSON J. , BOOTH C. , MURRAY P. J. , ELSE K. J. , CRUICKSHANK S. M.
Published: May 2011

Alternatively activated macrophages (AAMs) have key roles in the immune response to a variety of gastrointestinal helminths such as Heligmosomoides bakeri and Nippostrongylus brasiliensis. In addition, AAMs have been implicated in the resolution of infection‐induced pathology in Schistosoma mansoni infection. AAMs exert their activity in part via the enzyme arginase‐1 (Arg1), which hydrolyses l‐arginine into urea and ornithine, and can supply precursor substrate for proline and polyamine production. Trichuris muris is a worm that resides in the large intestine with resistance being characterized by a Th2 T‐cell response, which drives alternatively activated macrophage production in the local environment of the infection. To investigate the role of AAMs in T. muris infection, we used independent genetic and pharmacologic models of arginase deficiency. In acute infection and Th2‐dominated immunity, arginase‐deficient models expelled worms normally. Macrophage‐Arg1‐deficient mice showed cytokine and antibody levels comparable to wild‐type animals in acute and chronic infection. We also found no role for AAMs and Arg1 in infection‐induced pathology in the response to T. muris in either chronic (Th1 dominated) or acute (Th2 dominated) infections. Our data demonstrate that, unlike other gastrointestinal helminths, Arg1 expression in AAMs is not essential for resistance to T. muris in effective resolution of helminth‐induced inflammation.
A boy with an unusual scalp birthmark
Authors: Sikorski Deanna , Parker Jana , Shwayder Tor
Published: May 2011

What is your diagnosis?
Colonization with community‐acquired methicillin‐resistant Staphylococcus aureus in children with atopic dermatitis: a cross‐sectional study
Authors: Balma‐Mena Alexandra , Lara‐Corrales Irene , Zeller Jeanne , Richardson Susan , McGavin Martin J. , Weinstein Miriam , Pope Elena
Published: May 2011

Background  Bacterial infection with Staphylococcus aureus is a common complication of atopic dermatitis (AD). The incidence of community‐acquired methicillin‐resistant S. aureus infection (MRSA) in the AD population is unknown.

Objectives  This study aimed to assess the prevalence of S. aureus and MRSA in pediatric patients with AD, to compare disease severity, and to characterize the clonal diversity of the isolates.

Methods  We carried out a prospective, cross‐sectional study of 200 patients with AD. The severity of AD was defined as mild, moderate, or severe depending on a composite AD severity score. A swab was taken from the nares of each patient and another from affected skin or folds. Genotyping of all S. aureus isolates was conducted by polymerase chain reaction (PCR) amplification of the S. aureus protein A (spa) gene.

Results  According to the severity score, 66.5% of subjects were ranked as having mild AD, 29.5% as having moderate and 4% as having severe AD. Staphylococcus aureus colonization was seen in 61.5% of all patients, represented by 43.7% of skin swabs and 48% of nares swabs. Only one of the isolations represented MRSA. Older age and higher AD severity scores were associated with S. aureus colonization (P = 0.03 and P < 0.001, respectively). No significant associations were noted for attendance at day care, family members with frequent skin infections, or family members working in healthcare. Isolates from spa CC015 were cultured in 19.2% of patient samples. The single MRSA culture showed a new spa type that belonged to CC127.

Conclusions  The results of this study confirm a high rate of S. aureus colonization of pediatric patients with AD. The low rate of MRSA requires further proof from larger prospective studies.
Prematurity: is it a risk factor for striae distensae?
Authors: Kelekci Kiymet Handan , Kelekci Sefa , Destegul Emre , Aksoy Ayhan , Sut Necdet , Yilmaz Bulent
Published: May 2011

Background  Although the causes of striae distensae (SD) remain to be elucidated, the condition is known to relate to changes in the structures that provide the skin with its tensile strength and elasticity.

Objective  This study was conducted to evaluate whether premature birth is a risk factor for SD.

Methods  A total of 15,475 parous women ranging in age from 18‐45 years were interviewed between January 2007 and June 2009. After exclusion criteria were applied, a total of 1336 women were included in the study. Group 1 consisted of 1231 women of reproductive age who had been born at term. Group 2 included 105 women of reproductive age who had been born prematurely. The main outcome measure was the prevalence of SD.

Results  The overall prevalence of SD was 34.6% (462/1336). Mild SD was significantly more common (P < 0.01) in women who had been born prematurely (49.5%) than in women who had been born at term (31.8%). A multivariate analysis using backward stepwise logistic regression analysis identified that height, weight, gravidity, parity and abortion were found to be significantly associated with SD.

Conclusions  Striae distensae was significantly more common in women who had been born prematurely than in women who had been born at term.
Long‐term results of the percutaneous transhepatic venoplasty of portal vein stenoses after pediatric liver transplantation
Authors: Carnevale Francisco Cesar , de Tarso Machado Alexandre , Moreira Airton Mota , dos Santos Aline Christine Barbosa , da Motta‐Leal‐Filho Joaquim Mauricio , Suzuki Lisa , Cerri Giovanni Guido , Tannuri Uenis
Published: May 2011

Carnevale FC, de Tarso Machado A, Moreira AM, dos Santos ACB, da Motta‐Leal‐Filho JM, Suzuki L, Cerri GG, Tannuri U. Long‐term results of the percutaneous transhepatic venoplasty of portal vein stenoses after pediatric liver transplantation.  Pediatr Transplantation 2011: 15: 476–481. © 2011 John Wiley & Sons A/S.

Abstract:  This paper has the objective to evaluate retrospectively the long‐term results of transhepatic treatment of PV stenoses after pediatric LT. During an eight‐yr period, 15 children with PV stenoses underwent PTA with balloon dilation or stent placement in case of PTA failure after LT. Patients’ body weights ranged from 9.3 to 46 kg (mean, 15.5 kg). PV patency was evaluated in the balloon dilation and in the stent placement groups. Technical and clinical successes were achieved in all cases with no complication. Eleven patients (11/15; 73.3%) were successfully treated by single balloon dilation. Four patients (4/15; 26.7%) needed stent placement. One patient was submitted to stent placement during the same procedure because of PTA failure. The other three developed clinical signs of portal hypertension because of PV restenoses two, eight, and twenty‐eight months after the first PTA. They had to be submitted to a new procedure with stent placement. The follow‐up time ranged from 3 to 8.1 yr (mean, 6.3 yr). In conclusion, transhepatic treatment of PV stenoses after pediatric LT with balloon dilation or stent placement demonstrated to be a safe and effective treatment that results in long‐term patency.
Cell‐cycle checkpoint for transition from cell division to differentiation
Authors: Maeda Yasuo
Published: May 2011

In general, growth and differentiation are mutually exclusive, but they are cooperatively regulated during the course of development. Thus, the process of a cell’s transition from growth to differentiation is of general importance for the development of organisms, and terminally differentiated cells such as nerve cells never divide. Meanwhile, the growth rate speeds up when cells turn malignant. The cellular slime mold Dictyostelium discoideum grows and multiplies as long as nutrients are supplied, and its differentiation is triggered by starvation. A critical checkpoint (growth/differentiation transition or GDT point), from which cells start differentiating in response to starvation, has been precisely specified in the cell cycle of D. discoideum Ax‐2 cells. Accordingly, integration of GDT point‐specific events with starvation‐induced events is needed to understand the mechanism regulating GDTs. A variety of intercellular and intracellular signals are involved positively or negatively in the initiation of differentiation, making a series of cross‐talks. As was expected from the presence of the GDT point, the cell’s positioning in cell masses and subsequent cell‐type choices occur depending on the cell’s phase in the cell cycle at the onset of starvation. Since novel and multiple functions of mitochondria in various respects of development including the initiation of differentiation have been directly realized in Dictyostelium cells, they are also reviewed in this article.
Control of prestalk‐cell differentiation by transcription factors
Authors: Fukuzawa Masashi
Published: May 2011

Transcriptional control of developmental genes is important for cell differentiation and pattern formation. Developing Dictyostelium discoideum cells form a multicellular structure in which individual cells differentiate into either stalk cells or spores. This simplicity makes the organism an attractive model for studying fundamental problems in developmental biology. However, the morphogenetic process of forming a stalked fruiting body conceals a certain degree of complexity. This is reflected in the presence of multiple prestalk subtypes that have individual roles to generate the fruiting body. This review describes recent advances in understanding the molecular mechanisms, mediated by transcription factors that generate prestalk‐cell heterogeneity.
Human dendritic cells transfected with amplified MUC1 mRNA stimulate cytotoxic T lymphocyte responses against pancreatic cancer in vitro
Authors: Chen Jiang , Li Hong‐Yu , Wang Di , Zhao Jia‐Jun , Guo Xiao‐Zhong
Published: May 2011

Background and Aim:  Mucin (MUC) 1 is an epithelial cell glycoprotein that is aberrantly overexpressed in many adenocarcinomas, including pancreatic cancer (PC), providing an ideal tumor‐associated antigen and target for immunotherapy. In this study, we investigated whether the cytotoxic T lymphocytes (CTLs) induced by dendritic cells (DCs) transfected with amplified MUC1 mRNA could respond against PC in vitro.

Methods:  Amplified mRNA encoding MUC1 were transfected into DCs using electroporation with an optimized setting and the MUC1 expression were evaluated by quantitative real‐time polymerase chain reaction and Western blot. The MUC1 specific CTL responses were measured using the standard chromium 51 (51Cr)‐release assays and the interferon‐γ release assay.

Results:  Dendritic cells could be transfected with amplified MUC1 mRNA efficiently. The transfected DCs were remarkably effective in stimulating MUC1‐specific CTL responses in vitro. The function of MUC1 specific CTLs, induced by MUC1 mRNA‐transfected DCs, was restricted by major histocompatibility complex (MHC) class I antigen presentation.

Conclusion:  The CTL responses stimulated by DCs transfected with MUC1 mRNA could only recognize and lyse HLA‐A2+/MUC1+ PC and other target cells under restriction by MHC class I‐specific antigen presentation, providing a preclinical rationale for using MUC1 as a target structure for immunotherapeutic strategies against PC.
Prevalence of two homologous genes encoding glycosyltransferases of Helicobacter pylori in the United States and Japan
Authors: Matsuda Miyuki , Shiota Seiji , Matsunari Osamu , Watada Masahide , Murakami Kazunari , Fujioka Toshio , Yamaoka Yoshio
Published: May 2011

Background and Aim:  jhp0562 and β‐(1,3)galT (jhp0563) of Helicobacter pylori have been suggested as novel virulent factors; however, the clinical associations and functions of these genes remain unclear. We examined the prevalence of jhp0562, β‐(1,3)galT, and cagA in the United States (US) and Japanese populations.

Methods:  A total of 308 strains (171 from the US and 137 from Japan) were examined for the status of jhp0562, β‐(1,3)galT, and cagA by polymerase chain reaction.

Results:  There were significant differences in the status of jhp0562, β‐(1,3)galT and cagA between the US and Japanese populations (P < 0.001). In the US, the prevalence of β‐(1,3)galT was significantly lower in strains isolated from patients with duodenal ulcer (DU) or gastric ulcer (GU) than those with gastritis (47.8% and 32.1% vs 72.0%, P < 0.01), and the absence of β‐(1,3)galT was an independent factor discriminating DU and GU from gastritis (adjusted odds ratios, 4.21 and 8.52; 95% confidence intervals, 1.75 to 10.12 and 2.76 to 26.33, respectively). In the US, the prevalence of the jhp0562‐positive/β‐(1,3)galT‐negative genotype was significantly higher in strains from DU and GU patients than in those from gastritis patients (50.0%, 67.9%, and 24.4%, P < 0.01) and the cagA status was significantly correlated with that of jhp0562 and inversely correlated with that of β‐(1,3)galT. In contrast, the prevalence of these three genes was not significantly different in Japan.

Conclusions:  jhp0562 or β‐(1,3)galT can be used to discriminate peptic ulcers from gastritis in the US, but not in Japan.
Th17 cells are increased with severity of liver inflammation in patients with chronic hepatitis C
Authors: Chang Qing , Wang Yan‐Kun , Zhao Qing , Wang Chang‐Zheng , Hu Ya‐Zhuo , Wu Ben‐Yan
Published: May 2011

Background and Aim:  As a newly identified subset of T helper cells, T‐helper 17 cells (Th17) are major mediators of inflammation‐associated disease. Some reports have revealed significantly increased Th17 cells in hepatitis B virus‐infected patients, and a recent study has demonstrated that hepatitis C virus (HCV)‐specific Th17 cells can be induced in vitro and regulated by transforming growth factor‐β. This study attempted to characterize the role of Th17 cells in the disease progression of chronic hepatitis C (CHC).

Methods:  The current study enrolled 53 patients with CHC and 23 healthy controls, in which the circulating and liver‐infiltrating Th17 cells were monitored.

Results:  We found that CHC patients had increased proportions of both circulating and liver‐infiltrating Th17 cells compared to healthy individuals, and both measures of Th17 cells were correlated with severity of liver inflammation. We further demonstrated that the HCV‐specific Th17 cells were correlated with liver damage but not HCV viral replication.

Conclusions:  Such a correlation between the severity of liver damage of CHC and Th17 cells illustrated in this study sheds some light on the understanding of the pathogenesis of CHC.
Internet‐based approach to population screening for common hemoglobinopathies in United Arab Emirates
Authors: Matar Maryam , Naveed Mohammed , Salim Sajala , Hareb Nevin , Alba Emayla , Hino Minako , Nitta Takenori , Adhiyanto Chris , Yamashiro Yasuhiro , Hattori Yukio
Published: May 2011

This article reports on efforts to overcome common hurdles that were faced during population‐based screening for common hemoglobinopathies in the United Arab Emirates. An Internet‐based approach was designed and implemented to increase the acceptance of the screening program. The process involved: an awareness campaign, a simple bilingual (Arabic/English) online consent form and registration process, the use of a barcode for sample labeling, an equipment upgrade, electronic communication of a successful registration process, test results, and a counseling process. Before the implementation of the Internet‐based system, great concern was noted among the clients in terms of the availability of accurate and timely test results, the need for pretest and post‐test counseling, and the way that their personal health information was handled. Lapses in information exchange between the clients who participated in the screening program for the carrier state of inherited disorders and the screening laboratory posed significant challenges. The emphasis on confidentiality and the ease of access to services was instrumental in increasing the level of acceptance of these services in our community. Based on an analysis of > 10,000 samples, we conclude that Internet–based reporting holds much promise for improving the quality of care that clients receive.
The papal anatomist: Eustachius in renaissance Rome
Authors: Simpson Donald
Published: May 2011

Bartholomeo Eustachi, usually latinized as Eustachius, was an important anatomist in the 16th century, arguably second only to his contemporary and rival Andreas Vesalius. He was the first to identify several important anatomical structures, including the suprarenal glands, though he was probably not the first to describe the Eustachian tube. However, it has been hard to evaluate his achievements, because during his lifetime he published only some short monographs, and his career as a teacher in Rome is not well documented. He and his assistant P.M. Pini were the first to use copper plate engravings to illustrate human and animal anatomy, but most of their engravings were not published in their time, and the original plates were lost for some 140 years after the death of Eustachius. Early in the 18th century, these plates were rediscovered by the anatomist and papal physician G.M. Lancisi; he published the engravings in a book which aroused much interest and many reprintings. In 1744, Bernhard Siegfried Albinus of Leiden University published a version of these engravings, with commentaries by himself.

The engraved illustrations prepared by Eustachius and Pini are clear and largely accurate. They idealize the findings of actual dissections, and have a diagrammatic quality that facilitates understanding and memory. They are the ancestors of later anatomical atlases, which have helped generations of surgeons in teaching and in planning operations.
Predictors for clinically relevant Gleason score upgrade in patients undergoing radical prostatectomy
Authors: Thomas Christian , Pfirrmann Karin , Pieles Frauke , Bogumil Alexander , Gillitzer Rolf , Wiesner Christoph , Thüroff Joachim W. , Melchior Sebastian W.
Published: May 2011

Study Type – Diagnostic (exploratory cohort)

Level of Evidence 2b

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

Clinically relevant GSU in the prostatectomy specimen is a common phenomenon.

Clinically relevant GSU occurs in one of three patients with clinically ‘very’ low‐risk PCa, and a low number of biopsy cores is the key negative predictor.

OBJECTIVE

• To evaluate clinical predictors for Gleason score upgrade (GSU) in radical prostatectomy (RP) specimen, especially in patients with ‘very’ low risk PCA (T1c and biopsy Gleason score ≤6 and PSA <10 ng/ml and ≤2 positive biopsy cores and PSA density <0.15).

Patients and Methods

• 402 consecutive patients undergoing RP between 2004 and 2006, including a subgroup of 62 patients with ‘very’ low risk PCA, were examined.

• Patients were categorized for clinically relevant GSU (defined as upgrade into a higher PCA risk category).

• Parameters including number of biopsy cores obtained, positive biopsy cores, prostate weight, PSA, DRE and pathology department were evaluated for their role as predictors.

• Furthermore, GSU in RP specimen was analyzed for its impact on pT‐stage.

RESULTS

• Clinically relevant GSU occurred in 38.1% in the whole cohort and in 32.3% in the ‘very’ low risk PCA subgroup. Gleason score downgrade (GSD) occurred in 4.7%.

• Number of biopsy cores obtained and prostate weight were independent negative predictors of GSU in all 402 patients (P = 0.02 and P = 0.03, respectively).

• In the ‘very’ low risk group, only number of biopsy cores obtained revealed as an independent negative predictor of GSU (P = 0.02).

• PSA, DRE, number of positive cores or pathology department were not associated to GSU.

• In the ‘very’ low risk group, GSU was related with extracapsular tumor extension (P = 0.05).

Conclusions

• Clinically relevant GSU in RP specimen is still a challenging problem.

• Increasing the number of biopsy cores lower this risk significantly. GSD is rare and thus of minor importance for treatment decisions.