bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of infected grandmothers in transmission of Helicobacter pylori to children in a Japanese rural town
Authors: Urita Yoshihisa , Watanabe Toshiyasu , Kawagoe Naoyuki , Takemoto Ikutaka , Tanaka Hideki , Kijima Sho , Kido Hidenori , Maeda Tadashi , Sugasawa Yasuyuki , Miyazaki Taito , Honda Yoshiko , Nakanishi Kazushige , Shimada Nagato , Nakajima Hitoshi , Sugimoto Motonobu , Urita Chisako
Published: April 2013

Aim

Although the prevalence of Helicobacter pylori (H. pylori) increases with age and the main period of acquisition is childhood, the route of transmission of H. pylori infection remains unclear. This study aims to evaluate the relationship between prevalence of children and grandparents.

Methods

A total of 838 consecutive children who attended the Urita clinic and whose blood was taken for work up were enrolled in the present study. They were 449 boys and 389 girls, with a mean age of 12.4 years. H. pylori serology of their family members who were living together in one house was picked up to analyse intra‐familial clustering of H. pylori infection. The family members of these children consisted of 448 fathers, 597 mothers, 205 grandfathers, 361 grandmothers and 589 siblings.

Results

The seropositive rates of mothers, grandmother and siblings in seropositive children were significantly higher than those in seronegative children. H. pylori infection in mothers and grandmothers was a marked risk factor for infection in the index children. Larger family size was not a risk factor for H. pylori infection. In contrast, having an infected father or grandfather was not an independent predictor for children infection.

Conclusions

Our data demonstrate that not only mother‐to‐child transmission but also grandmother‐to‐child transmission is an important mechanism for the spread of H. pylori in a three‐generation household.
Uptake of iodide in the marine haptophyte Isochrysis sp. (T.ISO) driven by iodide oxidation
Authors: van Bergeijk Stef A. , Hernández Javier Laura , Heyland Andreas , Manchado Manuel , Pedro Cañavate José
Published: April 2013

Uptake of iodide was studied in the marine microalga Isochrysis sp. (isol. Haines, T.ISO) during short‐term incubations with radioactive iodide (125I−). Typical inhibitors of the sodium/iodide symporter (NIS) did not inhibit iodide uptake, suggesting that iodide is not taken up through this transport protein, as is the case in most vertebrate animals. Oxidation of iodide was found to be an essential step for its uptake by T.ISO and it seemed likely that hypoiodous acid (HOI) was the form of iodine taken up. Uptake of iodide was inhibited by the addition of thiourea and of other reducing agents, like L‐ascorbic acid, L‐glutathione and L‐cysteine and increased after the addition of oxidized forms of the transition metals Fe and Mn. The simultaneous addition of both hydrogen peroxide (H2O2) and a known iodide‐oxidizing myeloperoxidase (MPO) significantly increased iodine uptake, but the addition of H2O2 or MPO separately, had no effect on uptake. This confirms the observation that iodide is oxidized prior to uptake, but it puts into doubt the involvement of H2O2 excretion and membrane‐bound or extracellular haloperoxidase activity of T.ISO. The increase of iodide uptake by T.ISO upon Fe(III) addition suggests the nonenzymatic oxidation of iodide by Fe(III) in a redox reaction and subsequent influx of HOI. This is the first report on the mechanism of iodide uptake in a marine microalga.
The Cognition Hypothesis: A Synthesis and Meta‐Analysis of Research on Second Language Task Complexity
Authors: Jackson Daniel O. , Suethanapornkul Sakol
Published: April 2013

This study employed synthetic and meta‐analytic techniques to review the literature on the Cognition Hypothesis, which predicts that increasing task complexity influences the quality of second language production. Based on 8 inclusion criteria, 17 published studies were synthesized according to key features. A subset of these studies (k = 9) was also meta‐analyzed to investigate the overall effects of raising resource‐directing task demands on learner output during monologic tasks. The synthesis of 17 primary studies revealed an assortment of treatments and measures. Among the 9 comparable studies, the meta‐analysis uncovered small positive effects for accuracy and small negative effects for fluency. This lends support to the Cognition Hypothesis; however, the present study also disconfirms predictions regarding syntactic complexity. Implications for research and pedagogy are discussed.
Developing strategic readers: a multimodal analysis of a primary school teacher's use of speech, gesture and artefacts
Authors: Shanahan Lynn E. , Roof Lisa M.
Published: April 2013

Research on implementing reading strategy instruction has primarily focused on teachers' verbal communication with limited attention to other semiotic resources such as gesture and artefacts. In this paper, we construct a ‘telling case’ on the basis of how one primary teacher from the United States used speech, gesture and artefacts as a means of communication while instructing her students in reasons to predict when reading. Data sources for this case study consisted of field notes, artefacts and digital video. We analysed the teacher's use of gesture, speech and artefacts from a social semiotic multimodal perspective. Findings indicate that the teacher created meaning by interweaving multiple modes in the communicative contexts of strategy instruction using speech, deictic gestures, metaphoric gestures and artefacts. These findings are important to reading strategy instruction because much of the research and discussion of practice to date has centred on the instruction of reading strategies using teacher and student speech and not attending to the use of semiotic resources beyond speech.
Ries crater and suevite revisited—Observations and modeling Part I: Observations
Authors: Stöffler Dieter , Artemieva Natalia A. , Wünnemann Kai , Reimold W. Uwe , Jacob Juliane , Hansen Birgit K. , Summerson Iona A. T.
Published: April 2013

We report results of an interdisciplinary project devoted to the 26 km‐diameter Ries crater and to the genesis of suevite. Recent laboratory analyses of “crater suevite” occurring within the central crater basin and of “outer suevite” on top of the continuous ejecta blanket, as well as data accumulated during the past 50 years, are interpreted within the boundary conditions imposed by a comprehensive new effort to model the crater formation and its ejecta deposits by computer code calculations (Artemieva et al. 2013). The properties of suevite are considered on all scales from megascopic to submicroscopic in the context of its geological setting. In a new approach, we reconstruct the minimum/maximum volumes of all allochthonous impact formations (108/116 km3), of suevite (14/22 km3), and the total volume of impact melt (4.9/8.0 km3) produced by the Ries impact event prior to erosion. These volumes are reasonably compatible with corresponding values obtained by numerical modeling. Taking all data on modal composition, texture, chemistry, and shock metamorphism of suevite, and the results of modeling into account, we arrive at a new empirical model implying five main consecutive phases of crater formation and ejecta emplacement. Numerical modeling indicates that only a very small fraction of suevite can be derived from the “primary ejecta plume,” which is possibly represented by the fine‐grained basal layer of outer suevite. The main mass of suevite was deposited from a “secondary plume” induced by an explosive reaction (“fuel‐coolant interaction”) of impact melt with water and volatile‐rich sedimentary rocks within a clast‐laden temporary melt pool. Both melt pool and plume appear to be heterogeneous in space and time. Outer suevite appears to be derived from an early formed, melt‐rich and clast‐poor plume region rich in strongly shocked components (melt ≫ clasts) and originating from an upper, more marginal zone of the melt pool. Crater suevite is obviously deposited from later formed, clast‐rich and melt‐poor plumes dominated by unshocked and weakly shocked clasts and derived from a deeper, central zone of the melt pool. Genetically, we distinguish between “primary suevite” which includes dike suevite, the lower sublayer of crater suevite, and possibly a basal layer of outer suevite, and “secondary suevite” represented by the massive upper sublayer of crater suevite and the main mass of outer suevite.
Caterpillar cereal as a potential complementary feeding product for infants and young children: nutritional content and acceptability
Authors: Bauserman Melissa , Lokangaka Adrien , Kodondi Kule‐Koto , Gado Justin , Viera Anthony J. , Bentley Margaret E. , Engmann Cyril , Tshefu Antoinette , Bose Carl
Published: April 2013

Micronutrient deficiency is an important cause of growth stunting. To avoid micronutrient deficiency, the World Health Organization recommends complementary feeding with animal‐source foods. However, animal‐source foods are not readily available in many parts of the Democratic Republic of Congo (DRC). In such areas, caterpillars are a staple in adult diets and may be suitable for complementary feeding for infants and young children. We developed a cereal made from dried caterpillars and other locally available ingredients (ground corn, palm oil, sugar and salt), measured its macro‐ and micronutrient contents and evaluated for microbiologic contamination. Maternal and infant acceptability was evaluated among 20 mothers and their 8–10‐month‐old infants. Mothers were instructed in the preparation of the cereal and asked to evaluate the cereal in five domains using a Likert scale. Mothers fed their infants a 30‐g portion daily for 1 week. Infant acceptability was based on cereal consumption and the occurrence of adverse events. The caterpillar cereal contained 132 kcal, 6.9‐g protein, 3.8‐mg iron and 3.8‐mg zinc per 30 g and was free from microbiologic contamination. Mothers’ median ratings for cereal characteristics were (5 = like very much): overall impression = 4, taste = 5, smell = 4, texture = 4, colour = 5, and consistency = 4. All infants consumed more than 75% of the daily portions, with five infants consuming 100%. No serious adverse events were reported. We conclude that a cereal made from locally available caterpillars has appropriate macro‐ and micronutrient contents for complementary feeding, and is acceptable to mothers and infants in the DRC.
The devil in the detail of secretions
Authors: TYERMAN STEVE D.
Published: April 2013

This article comments on: Dynamic secretion changes in the salt glands of the mangrove tree species Avicennia officinalis in response to a changing saline environment
Effects of BRAF inhibitors on human melanoma tissue before treatment, early during treatment, and on progression
Authors: Long Georgina V. , Wilmott James S. , Haydu Lauren E. , Tembe Varsha , Sharma Raghwa , Rizos Helen , Thompson John F. , Howle Julie , Scolyer Richard A. , Kefford Richard F.
Published: April 2013

Selective BRAF inhibitors (BRAFi) are a standard of care for the treatment of BRAFV600‐mutant metastatic melanoma. We analyzed a unique set of serial triplicate human metastatic melanoma tumor biopsies to identify biomarkers of BRAFi response and resistance. Morphologic features and immunohistochemical biomarkers were analyzed in 37 metastatic melanoma biopsies at pretreatment (PRE), early during treatment (EDT), and on progression (PROG) from 15 patients treated with a BRAFi and correlated with response and outcome. At EDT, proliferative markers decreased regardless of response, whereas markers of cell death increased in responders. High expression of nuclear p27 at baseline was the strongest predictor of a poorer OS and predicted worse response. The results show that BRAFi are universally antiproliferative, regardless of clinical response, whereas markers of cell death increased only in responders. The addition of therapies targeting the cell cycle machinery may improve the response and duration of BRAFi, and investigation of the mechanisms of apoptosis may provide additional therapeutic targets.
Chk1 is essential for the development of murine epidermal melanocytes
Authors: Smith Joanne , Larue Lionel , Gillespie David A.
Published: April 2013

Embryonic deletion of mouse Chk1 is lethal; however, whether Chk1 is essential in all individual tissues is unknown. By breeding C57Bl/ 6 mice homozygous for a conditional allele of Chk1 (Chk1fl/fl) and bearing melanocyte‐specific Tyr::Cre and DCT:: LacZ transgenes, we investigated the consequences of Chk1 deletion in the melanocytic lineage. We show that adult Tyr::Cre; Chk1fl/fl mice lack coat pigmentation and epidermal melanocytes in the hair follicles, but retain eye pigmentation in the retinal pigmented epithelium (RPE). Melanoblasts formed normally during embryogenesis in Tyr::Cre; Chk1fl/fl mice at early times (embryonic day 10.5; E10.5) but were completely absent by stage E13.5, most probably as a consequence of spontaneous DNA damage and apoptosis. By contrast, melanoblast numbers were only slightly reduced in heterozygous Tyr::Cre; Chk1fl/ + embryos, and these mice exhibited normal coat pigmentation as adults. Thus, Chk1 is essential for the developmental formation of murine epidermal melanocytes but hemizygosity has little, if any, permanent developmental consequence in this cell type.
Successful Treatment of Congenital Erythropoietic Porphyria Using Matched Unrelated Hematopoietic Stem Cell Transplantation
Authors: Martinez Peinado Carmen , Díaz de Heredia Cristina , To‐Figueras Jordi , Arias‐Santiago Salvador , Nogueras Paloma , Elorza Izaskun , Olivé Teresa , Bádenas Célia , Moreno Mª José , Tercedor Jesús , Herrero Carmen
Published: April 2013

Congenital erythropoietic porphyria (CEP), or Günther's disease, is an inborn error of metabolism produced by a deficiency of uroporphyrinogen III synthase (UROS), the fourth enzyme of the heme biosynthesis pathway. This enzymatic defect induces the accumulation of isomer I porphyrins in erythrocytes, skin, and tissues, producing various clinical manifestations. Severe cases are characterized by extreme photosensitivity, causing scarring and mutilations, and by hemolytic anemia, reducing life expectancy. CEP is caused by mutations in the UROS gene, and one of the most severe forms of the disease is associated with a cysteine to arginine substitution at residue 73 of the protein (C73R). CEP has been successfully treated only by the transplantation of hematopoietic precursors. We report the case of a male infant with severe postdelivery symptoms diagnosed with CEP and found to be homozygous for the C73R mutation. He underwent successful allogeneic bone marrow transplantation from a matched unrelated donor at 7 months of age. The hemolytic anemia was corrected and the porphyrin overproduction was significantly reduced. The patient remained asymptomatic after 1 year. This new case confirms that patients with severe CEP can benefit from early postnatal hematopoietic stem cell transplantation.
Building from Within: Pastoral Insights into Community Resources and Assets
Authors: Ford Cassandra D.
Published: April 2013

Objectives

To explore perceptions of community pastors regarding the extent of community resources and assets in a rural, Southern, African American community.

Design and Sample

Utilizing a qualitative, descriptive design, interviews were conducted with six African American pastors.

Measures

Interviews were conducted using a semi‐structured interview guide based on an assets‐oriented approach.

Results

Pastors discussed various resources and assets, probable within the community that may be considered as support for program development. Key themes included: (1) community strengths, (2) community support, and (3) resources for a healthy lifestyle. The church was identified, throughout the interviews, as a primary source of strength and support for community members.

Conclusions

In this study of African American pastors, various perceptions of community resources were identified. Findings indicate that a sample, rural, Southern, African American community has a wealth of resources and assets, but additional resources related to health promotion are still necessary to produce optimal results. Specific programs to prevent chronic conditions such as cardiovascular disease can provide an effective means for addressing related health disparities. Programs implemented through churches can reach large numbers of individuals in the community and provide an important source of sustainable efforts to improve the health of African Americans.
Ability of leaf mesophyll to retain potassium correlates with salinity tolerance in wheat and barley
Authors: Wu Honghong , Shabala Lana , Barry Karen , Zhou Meixue , Shabala Sergey
Published: April 2013

This work investigated the importance of the ability of leaf mesophyll cells to control K+ flux across the plasma membrane as a trait conferring tissue tolerance mechanism in plants grown under saline conditions. Four wheat (Triticum aestivum and Triticum turgidum) and four barley (Hordeum vulgare) genotypes contrasting in their salinity tolerance were grown under glasshouse conditions. Seven to 10‐day‐old leaves were excised, and net K+ and H+ fluxes were measured from either epidermal or mesophyll cells upon acute 100 mM treatment (mimicking plant failure to restrict Na+ delivery to the shoot) using non‐invasive microelectrode ion flux estimation (the MIFE) system. To enable net ion flux measurements from leaf epidermal cells, removal of epicuticular waxes was trialed with organic solvents. A series of methodological experiments was conducted to test the efficiency of different methods of wax removal, and the impact of experimental procedures on cell viability, in order to optimize the method. A strong positive correlation was found between plants' ability to retain K+ in salt‐treated leaves and their salinity tolerance, in both wheat and especially barley. The observed effects were related to the ionic but not osmotic component of salt stress. Pharmacological experiments have suggested that voltage‐gated K+‐permeable channels mediate K+ retention in leaf mesophyll upon elevated NaCl levels in the apoplast. It is concluded that MIFE measurements of NaCl‐induced K+ fluxes from leaf mesophyll may be used as an efficient screening tool for breeding in cereals for salinity tissue tolerance.
Policy Perspectives on National Security and Foreign Policy Decision Making
Authors: Redd Steven B. , Mintz Alex
Published: April 2013

This article reviews major decision‐making models with an emphasis on basic theoretical perspectives as well as on how these models explain foreign policy decision making and national and international security decisions. Furthermore, we examine how these models have been utilized in explanations of various international crises. Specifically, for each model, we present examples drawn from the literature on applications of the respective model to foreign policy and national security decisions. The theories we have reviewed are as follows: rational choice, cybernetic model, prospect theory, poliheuristic theory, organizational and bureaucratic politics, groupthink and polythink, and analogical reasoning. We also review theAppliedDecisionAnalysis method, and the concept of biases in decision making.
Law and Public Policy
Authors: Kreis Anthony Michael , Christensen Robert K.
Published: April 2013

Law and public policy is a dynamic, interdisciplinary area of study that has broad appeal to scholars, policymakers, and stakeholders. Scholarship in the subfield is critical to our general understanding of existing public policies and calls for future and reformed policies. While some of the subfield's utility and commonalities are obscured by diverging methodological approaches and topical foci, this review highlights some common fibers that run through the scholarship streams from public policy, public law, and doctrinal disciplines. We focus on several substantive policy areas to illustrate some of the best studies in the subfield and how scholars might better embrace the strength of the subfield's diversity by coordinating with scholars with similar topical interests. In so doing, we attempt to articulate clearer boundaries that integrate discipline, method, and the distinction between law and public policy.
Disentangling the Poverty Effects of Sectoral Output, Prices, and Policies in India
Authors: Mallick Sushanta K.
Published: April 2013

This paper attempts to disentangle the poverty effects of key policy variables that directly affect the poor (namely the government‐led channel of development spending and financing) in both agricultural and non‐agricultural sectors after accounting for the effect of respective sectoral per capita income and prices, using data from India over five decades. The paper emphasizes the sectoral composition of income and prices as mechanisms influencing the level of poverty and establishes empirically that it is the rise in non‐agricultural per capita income that reduces rural poverty via the channel of internal migration, after having controlled for the variation in key components of fiscal spending and monetary/financial policy via the availability of credit. Uneven sectoral growth pattern explains why urban poverty becomes a spill‐over of persistent rural poverty when the agricultural sector shrinks. While checking for robustness, there is evidence that the rise in non‐agricultural income alone may not reduce rural poverty, when measured in terms of rural infant mortality rate as a non‐income indicator of well‐being.
Correlates of Suicide Stigma and Suicide Literacy in the Community
Authors: Batterham Philip J. , Calear Alison L. , Christensen Helen
Published: April 2013

Public knowledge and attitudes toward suicide may influence help‐seeking for suicidality. This study aimed to identify correlates of suicide attitudes and knowledge. Australian adults were invited to complete an online survey, with 1,286 responders. Less exposure to suicide, older age, male gender, less education, and culturally diverse backgrounds were associated with poorer knowledge; while younger age, male gender, and culturally diverse backgrounds were associated with more stigmatizing attitudes toward people who die by suicide. The results suggest suicide literacy and stigma reduction programs would benefit community members, particularly males and individuals from culturally diverse backgrounds.
What to Trust: Reconciling Mathematical Work Done by Hand with Conflicting Graphing Calculator Solutions
Authors: McCulloch Allison W. , Kenney Rachael H. , Keene Karen Allen
Published: April 2013

This paper reports on a mixed‐methods study of 111 Advanced Placement calculus students' self‐reports of their graphing calculator use, comfort, and rationale for trusting a solution produced with or without a graphing calculator when checking written work. It was found that there was no association between gender, teacher‐reported mathematical ability, or comfort with the graphing calculator and students' trust in either a graphing calculator‐produced solution or a solution produced without a graphing calculator. Furthermore, regardless of solution choice, the same four categories were evident in students' rationale for their solution choice: (a) an awareness of the possibility of careless errors, (b) the importance of checking over work, (c) a recognition of the limitations or affordances of the graphing calculator, and (d) a confidence (or lack thereof) in their own mathematical abilities. These results have implications for mathematics teaching as graphing calculators are used extensively in middle and high school mathematics classrooms and standardized tests in the United States.
Varied Meanings and Engagement in School Mathematics: Cross‐Case Analysis of Three High‐Achieving Young Adolescent Girls
Authors: Lim Jae Hoon , Chae Jeong‐Lim , Schinck‐Mikel Amélie G. , Watson Jimmy
Published: April 2013

This paper presents an in‐depth cross‐case analysis of three high‐achieving young adolescent girls who had contrasting mathematics learning experiences during the first year of middle school. In particular, this study examines the foundation for their motivation, as well as the dominant mode of learning and academic engagement in relation to three sociocultural factors, family background, the role of peers, and the level of teachers' understanding of the students and instructional support provided. Our data analysis revealed that the three girls possessed motivation structures and learning dispositions that are more or less prone to conceptual or procedural understanding in mathematics. This resulted in a significant variation in the mode of their academic engagement with the subject, and this provided a different set of challenges in each girl's pursuit of higher level of mathematics learning.
Teaching the Devout Student: Faith and Scholarship in the Classroom
Authors: Smith Brian H.
Published: April 2013

Increasing numbers of college students enrolling in religion courses in recent years are looking to develop their religious faith or spirituality, while professors of religion want students to use and appreciate scholarly tools to study religion from an academic perspective. Some scholars argue that it is not possible to satisfy both goals in the classroom, while authors in this journal have given suggestions on how to bridge the gap between faith and scholarship. I argue that such authors are correct and that, in my experience, historical‐critical methods can help devout students understand the original texts in their own religion better, comprehend why changes in interpretation have occurred over time, and appreciate the values in religions other than their own. Not all devout students are comfortable with an academic study of religion, but many can attain a more mature faith by such an approach.
The relationship between antenatal provider type and maternal care in rural Ghana: a cross‐sectional study
Authors: Atunah‐Jay S. J. , Pettingell S. , Ohene S.‐A. , Michael Oakes J. , Borowsky I. W.
Published: April 2013

Objectives

To investigate the influence of antenatal provider type on maternity care in rural Ghana.

Methods

An analysis of maternal care by antenatal provider type using the 2008 Ghana Demographic and Health Survey. Study population included rural Ghanaian women aged 15–49 years with report of a live birth between 2003 and 2008. Bivariate chi‐square analysis was performed to examine differences in maternal report of WHO Maternal Health Interventions. Multivariate linear and logistic regression were performed to assess differences in antenatal care (ANC) scales and maternal care packages.

Results

Thousand and three hundred and sixty‐seven rural women reported a live birth. Provider distribution was: doctor, 15.6%; midwife, 70%; community health officer (CHO), 9.1%; no provider, 5.3%. Women from lower socio‐demographic categories were more likely to report midwife or CHO. Report of CHO vs. no provider was positively associated with maternal services (P < 0.01). Report of doctor or midwife vs. CHO was significantly associated with maternal services (P < 0.01).

Conclusion

There is a positive association between antenatal provider length of training and maternal specialization and report of maternal services. Community‐based providers are associated with markedly increased report of maternal services compared with no provider. Structural factors appear to underlie some differences in service provision.
Accuracy of Individual Trabecula Segmentation Based Plate and Rod Finite Element Models in Idealized Trabecular Bone Microstructure
Authors: Wang Hong , Sherry Liu X. , Zhou Bin , Wang Ji , Ji Baohua , Huang Yonggang , Hwang Keh-Chih , Edward Guo X.
Published: April 2013

Currently, specimen-specific micro finite element (μFE) analysis based micro computed tomography (μCT) images have become a major computational tool for the assessment of the mechanical properties of human trabecular bone. Despite the fine characterization of the three-dimensional (3D) trabecular microstructure based on high-resolution μCT images, conventional μFE models with each voxel converted to an element are not efficient in predicting the nonlinear failure behavior of bone due to a prohibitive computational cost. Recently, a highly efficient individual trabecula segmentation (ITS)-based plate and rod (PR) modeling technique has been developed by substituting individual plates and rods with shell and beam elements, respectively. In this technical brief, the accuracy of novel PR μFE models was examined in idealized microstructure models over a broad range of trabecular thicknesses. The Young's modulus and yield strength predicted by simplified PR models strongly correlated with those of voxel models at various voxel sizes. The conversion from voxel models to PR models resulted in an ∼762-fold reduction in the largest model size and significantly accelerated the nonlinear FE analysis. The excellent predictive power of the PR μFE models, demonstrated in an idealized trabecular microstructure, provided a quantitative mechanical basis for this promising tool for an accurate and efficient assessment of trabecular bone mechanics and fracture risk.
Targeted Inhibition of Mutant IDH2 in Leukemia Cells Induces Cellular Differentiation
Authors: Wang Fang , Travins Jeremy , DeLaBarre Byron , Penard-Lacronique Virginie , Schalm Stefanie , Hansen Erica , Straley Kimberly , Kernytsky Andrew , Liu Wei , Gliser Camelia , Yang Hua , Gross Stefan , Artin Erin , Saada Veronique , Mylonas Elena , Quivoron Cyril , Popovici-Muller Janeta , Saunders Jeffrey O. , Salituro Francesco G. , Yan Shunqi , Murray Stuart , Wei Wentao , Gao Yi , Dang Lenny , Dorsch Marion , Agresta Sam , Schenkein David P. , Biller Scott A. , Su Shinsan M. , de Botton Stephane , Yen Katharine E.
Published: April 2013

IDHology

Among the most exciting drug targets to emerge from cancer genome sequencing projects are two related metabolic enzymes, isocitrate dehydrogenases 1 and 2 (IDH1, IDH2). Mutations in the
IDH1
and
IDH2
genes are common in certain types of human cancer. Whether inhibition of mutant IDH activity might offer therapeutic benefits is unclear (see the Perspective by

Kim and DeBerardinis

).

F. Wang
et al.

(p.
622
, published online 4 April) isolated a small molecule that selectively inhibits mutant IDH2, describe the structural details of its binding to the mutant enzyme, and show that this compound suppresses the growth of patient-derived leukemia cells harboring the
IDH2
mutation.

Rohle
et al.

(p.
626
, published online 4 April) show that a small molecule inhibitor of IDH1 selectively slows the growth of patient-derived brain tumor cells with the
IDH1
mutation.
Genome Sequencing of Bacillus subtilis Strain XF-1 with High Efficiency in the Suppression of
Plasmodiophora brassicae
Authors: Guo Shengye , Mao Zichao , Wu Yixin , Hao Kun , He Pengfei , He Yueqiu
Published: April 2013

The genome of the rhizobacterium
Bacillus subtilis
XF-1 is 4.06 Mb in size and harbors 3,853 coding sequences (CDS). Giant gene clusters were dedicated to the nonribosomal synthesis of antimicrobial lipopeptides and polyketides. Remarkably, XF-1 possesses a gene cluster involved in the synthesis of chitosanase that is related to the suppression of the pathogen
Plasmodiophora brassicae
.
Complete Genome Sequence of Wohlfahrtiimonas chitiniclastica Strain SH04, Isolated from
Chrysomya megacephala
Collected from Pudong International Airport in China
Authors: Cao Xiao-Mei , Chen Tuo , Xu Li-Zhi , Yao Li-Si , Qi Jun , Zhang Xiao-Long , Yan Qing-Li , Deng Yao-Hua , Guo Tian-Yu , Wang Jing , Hu Kong-Xin , Xu Bao-Liang
Published: April 2013

Wohlfahrtiimonas chitiniclastica
bacilli that live in the larvae of a parasitic fly were recently isolated and are speculated to be the cause of fulminant sepsis. Here we report and analyze the complete genome sequence of
Wohlfahrtiimonas chitiniclastica
strain SH04. No complete genome sequence of a
Wohlfahrtiimonas chitiniclastica
isolate has been documented previously.
Complete Genome Sequence of Serratia marcescens WW4
Authors: Chung Wan-Chia , Chen Ling-Ling , Lo Wen-Sui , Kuo Pei-An , Tu Jenn , Kuo Chih-Horng
Published: April 2013

Serratia marcescens
WW4 is a biofilm-forming bacterium isolated from paper machine aggregates. Under conditions of phosphate limitation, this bacterium exhibits intergeneric inhibition of
Pseudomonas aeruginosa
. Here, the complete genome sequence of
S. marcescens
WW4, which consists of one circular chromosome (5,241,455 bp) and one plasmid (pSmWW4; 3,248 bp), was determined.
Draft Genome Sequence of Rhodococcus ruber Strain BKS 20-38
Authors: Bala Monu , Kumar Shailesh , Raghava Gajendra Pal Singh , Mayilraj Shanmugam
Published: April 2013

We report the 6.1-Mb genome sequence of
Rhodococcus ruber
strain BKS 20-38, isolated from the palm tree rhizosphere soil of Bhitarkanika National Park, Odhisha, India. The draft genome sequence of strain BKS 20-38 consists of 6,126,900 bp, with a G+C content of 69.72%, 5,716 protein-coding genes, and 49 RNAs.
Socioeconomic characteristics of residential areas and risk of death: is variation in spatial units for analysis a source of heterogeneity in observed associations?
Authors: Halonen Jaana I , Vahtera Jussi , Oksanen Tuula , Pentti Jaana , Virtanen Marianna , Jokela Markus , Diez-Roux Ana V , Kivimäki Mika
Published: April 2013

Objectives

Evidence on the association between the adverse socioeconomic characteristics of residential area and mortality is mixed. We examined whether the choice of spatial unit is critical in detecting this association.

Design

Register-linkage study.

Setting

Data were from the Finnish Public Sector study's register cohort.

Participants

The place of residence of 146 600 cohort participants was linked to map grids and administrative areas, and they were followed up for mortality from 2000 to 2011. Residential area socioeconomic deprivation and household crowding were aggregated into five alternative areas based on map grids (250×250 m, 1×1 km and 10×10 km squares), and administrative borders (zip-code area and town).

Primary and secondary outcome measures

All-cause mortality.

Results

For the 250×250 m area, mortality risk increased with increasing socioeconomic deprivation (HR for top vs bottom quintile 1.36, 95% CI 1.21 to 1.52). This association was either weaker or missing when broader spatial units were used. For household crowding, excess mortality was observed across all spatial units, the HRs ranging from 1.14 (95% CI 1.03 to 1.25) for zip code, and 1.21 (95% CI 1.11 to 1.31) for 250×250 m areas to 1.28 (95% CI 1.10 to 1.50) for 10×10 km areas.

Conclusions

Variation in spatial units for analysis is a source of heterogeneity in observed associations between residential area characteristics and risk of death.
Executive functioning in children with unilateral cerebral palsy: protocol for a cross-sectional study
Authors: Bodimeade Harriet L , Whittingham Koa , Lloyd Owen , Boyd Roslyn N
Published: April 2013

Introduction

Early brain injury, as found in children with unilateral cerebral palsy (CP), may cause deficits in higher-order cognitive tasks known as executive functions (EF). EF has been conceptualised as comprised of four distinct yet inter-related components: (1) attentional control, (2) cognitive flexibility, (3) goal setting and (4) information processing. The aim of this study was to examine EF in children with unilateral CP and compare their performance with a typically developing reference group (TDC). The potential laterality effects of unilateral CP on EF will be explored, as will the relationship between the cognitive measures of EF, behavioural manifestations of EF, psychological functioning and clinical features of unilateral CP.

Methods and analysis

This cross-sectional study aims to recruit a total of 42 children with unilateral CP (21 right unilateral CP and 21 left unilateral CP) and 21 TDC aged between 8 and 16 years. Clinical severity will be described for gross motor function and manual ability. Outcomes for cognitive EF measureswill include subtests from the Wechsler Intelligence Scale for Children—Fourth Edition, Delis-Kaplan Executive Function System, Rey Complex Figure Test and the Test of Everyday Attention for Children. Behavioural manifestations of EF will be assessed using the Behaviour Rating Inventory of Executive Function, Parent and Teacher versions. Psychological functioning will be examined using the Strengths and Difficulties Questionnaire. Between-groups differences will be examined in a series of one-way analyses of covariance and followed up using linear comparisons. An overall composite of cognitive EF measures will be created. Bivariate correlations between the EF composite and psychological measures will be calculated.

Ethics and dissemination

This protocol describes a study that, to our knowledge, is the first to examine multiple components of EF using a cohort of children with unilateral CP. Exploration of potential laterality effects of EF among children with a congenital, unilateral brain injury is also novel. Possible relationships between EF and psychological functioning will also be investigated. Ethics have been obtained through the University of Queensland School of Psychology Ethics Committee and the Queensland Children's Health Services Human Research Ethics Committee. Results will be disseminated in peer reviewed publications and presentations at national and international conferences. This study is registered with the Australian New Zealand Clinical Trials Registry (ACTRN12611000263998).
Web-based general public opinion study of automated versus manual external chest compression
Authors: Lapostolle Frédéric , Bertrand Philippe , Agostinucci Jean-Marc , Pradeau Catherine , Tazarourte Karim , Grave Mélanie , Galinski Michel , Adnet Frédéric
Published: April 2013

Background

Only a few cardiac-arrest victims receive external chest compression (ECC) by a bystander.

Objective

To test the hypothesis that the general public might start ECC more often if they used an automated device rather than a manual massage.

Methods

Web-based public opinion survey based on two short videos, one showing manual ECC and the other automated ECC (Autopulse, Zoll, France). Advantages and disadvantages (perceived efficacy, reproducibility, hazard, apprehension and acceptability) of the two techniques were evaluated on a visual analogue scale (VAS). A VAS of 1–3 was considered to indicate preference for manual ECC, 8–10 for automated ECC and 4–7 for no clear preference. The final global score was the difference between advantage and disadvantage scores.

Results

Overall, 1769 persons answered the questionnaire. The median VAS score for each variable was as follows: 7 (25–75 percentiles, 5–9) for efficacy, 8 (3–10) for reproducibility, 5 (3–8) for hazard, 5 (2–8) for apprehension and 5 (2–8) for acceptability. The overall median score indicated that 1034 persons (58%) preferred use of the device, 618 (35%) preferred manual ECC and 117 (7%) had no preference. There was no significant difference in the preference according to gender, education and training in first aid. However, older persons (0) preferred the use of device.

Conclusions

The better ‘advantages over disadvantages’ score for the automated ECC device over manual ECC indicated that the general public might envisage use of the device. This could contribute to increase the frequency of resuscitation attempts by bystanders.
How emergency physicians use biomarkers: insights from a qualitative assessment of script concordance tests
Authors: Claessens Yann-Erick , Wannepain Sophie , Gestin Stéphanie , Magdelein Xavier , Ferretti Elsa , Guilly Marine , Charlin Bernard , Pelaccia Thierry
Published: April 2013

Objectives

Biomarkers have been developed in emergency medicine to improve decision at bedside using Bayesian approach. We intend to determine the cognitive process actually utilised by emergency physicians to incorporate biomarkers in clinical reasoning.

Design

We invited eight emergency physicians to answer eight script concordance tests. Interviews were tape-recorded and qualitatively analysed using predetermined categories until saturation.

Results

Emergency physicians mainly mobilised intuition and non-Bayesian reasoning to incorporate biomarkers for diagnosis or treatment strategies.

Conclusions

Although biomarkers have been developed to be used in a Bayesian approach, emergency physicians mainly use other analytical and non-analytical cognitive processes to introduce these tools in their clinical reasoning.
Strong expression of the neuronal transcription factor FOXP2 is linked to an increased risk of early PSA recurrence in ERG fusion-negative cancers
Authors: Stumm Laura , Burkhardt Lia , Steurer Stefan , Simon Ronald , Adam Meike , Becker Andreas , Sauter Guido , Minner Sarah , Schlomm Thorsten , Sirma Hüseyin , Michl Uwe
Published: April 2013

Background and aims

Transcription factors of the forkhead box P (FOXP1-4) family have been implicated in various human cancer types before. The relevance and role of neuronal transcription factor FOXP2 in prostate cancer is unknown.

Methods

A tissue microarray containing samples from more than 11 000 prostate cancers from radical prostatectomy specimens with clinical follow-up data was analysed for FOXP2 expression by immunohistochemistry. FOXP2 data were also compared with pre-existing ERG fusion (by fluorescence in situ hybridisation and immunohistochemistry) and cell proliferation (Ki67 labelling index) data.

Results

There was a moderate to strong FOXP2 protein expression in basal and secretory cells of normal prostatic glands. As compared with normal cells, FOXP2 expression was lost or reduced in 25% of cancers. Strong FOXP2 expression was linked to advanced tumour stage, high Gleason score, presence of lymph node metastases and early tumour recurrence (p<0.0001; each) in ERG fusion-negative, but not in ERG fusion-positive cancers. High FOXP2 expression was linked to high Ki67 labelling index (p<0.0001) in all cancers irrespective of ERG fusion status.

Conclusions

These data demonstrate that similar high FOXP2 protein levels as in normal prostate epithelium exert a ‘paradoxical’ oncogenic role in ‘non fusion-type’ prostate cancer. It may be speculated that interaction of FOXP2 with members of pathways that are specifically activated in ‘non fusion-type’ cancers may be responsible for this phenomenon.
Mitochondrial myopathy with autophagic vacuoles in patients with the m.8344A>G mutation
Authors: Yuan Jun-Hui , Sakiyama Yusuke , Higuchi Itsuro , Inamori Yukie , Higuchi Yujiro , Hashiguchi Akihiro , Higashi Keiko , Yoshimura Akiko , Takashima Hiroshi
Published: April 2013

Background and aims

In mitochondrial myopathy, autophagy is presumed to play an important role in mitochondrial dysfunction. Rimmed vacuoles (RVs), a sign of autophagy, can be seen as a secondary phenomenon in muscle ragged-red fibres (RRFs), whereas the uncommon presentation is that some fibres contain RVs, but without any mitochondrial abnormalities. To investigate the pathogenesis beneath this pathological phenomenon.

Methods

We reviewed 783 skeletal muscle specimens and selected five obtained from patients with suspected mitochondrial myopathy, characterised by clearly visible autophagic vacuoles in non-RRFs, besides the coexistence of RRFs and cytochrome oxidase-negative fibres. Immunohistochemical staining with LC-3, and electron microscopy studies were performed. Using resequencing microarray and a next-generation sequencing system, the mitochondrial DNA was screened for mutations and the heteroplasmic level was measured in skeletal muscle and blood.

Results

Muscle fibres with RVs and RRFs, as well as some morphologically normal fibres, stained strongly for LC-3. Electron microscopy disclosed significant abnormal mitochondrial proliferation and existence of autophagic vacuoles. After mutation screening, m.8344A>G in the tRNALysgene was detected in two patients. The heteroplasmy of mutated G was 45.1% in skeletal muscle and 17.8% in blood in patient 1; patient 2 exhibited 80.3% mutated G in skeletal muscle and 25.2% in blood.

Conclusions

These findings demonstrate a new pathological phenotype for the m.8344A>G mutation- related disease and also provide pathological evidence of a correlation between mitochondrial abnormalities and autophagy.
HOŘAVA–LIFSHITZ MODIFICATIONS OF THE CASIMIR EFFECT
Authors: FERRARI A. F. , GIROTTI H. O. , GOMES M. , PETROV A. YU. , DA SILVA A. J.
Published: April 2013

We study the modifications induced by spacetime anisotropy on the Casimir effect in the case of two parallel plates. Non-perturbative and perturbative regimes are analyzed. In the first case, the Casimir force either vanishes or it reverses its direction which, in any case, makes the proposal untenable. On the other hand, the perturbative model enables us to incorporate appropriately the effects of spacetime anisotropy.
UNCONVENTIONAL AND EXOTIC MAGNETISM IN CARBON-BASED STRUCTURES AND RELATED MATERIALS
Authors: KUZEMSKY A. L.
Published: April 2013

The detailed analysis of the problem of possible magnetic behavior of the carbon-based structures was fulfilled to elucidate and resolve (at least partially) some unclear issues. It was the purpose of the present paper to look more critically into some conjectures which have been made and to the peculiar and contradictory experimental results in this rather indistinct and disputable field. First the basic physics of magnetism was briefly addressed. Then a few basic questions were thoroughly analyzed and critically reconsidered to elucidate the possible relevant mechanism (if any) which may be responsible for observed peculiarities of the "magnetic" behavior in these systems. The arguments supporting the existence of the intrinsic magnetism in carbon-based materials, including pure graphene were analyzed critically. It was concluded that recently published works have shown that the results of the previous studies, where the "ferromagnetism" was detected in pure graphene, were incorrect. Rather, graphene is strongly diamagnetic, similar to graphite. Thus the possible traces of a quasi-magnetic behavior which some authors observed in their samples may be attributed rather to induced magnetism due to the impurities, defects, etc. On the basis of the present analysis the conclusion was made that the thorough and detailed experimental studies of these problems only may shed light on the very complicated problem of the magnetism of carbon-based materials. Lastly the peculiarities of the magnetic behavior of some related materials and the trends for future developments were mentioned.
ELECTRON OPTICS WITH DIRAC FERMIONS: ELECTRON TRANSPORT IN MONOLAYER AND BILAYER GRAPHENE THROUGH MAGNETIC BARRIER AND THEIR SUPERLATTICES
Authors: AGRAWAL (GARG) NEETU , GHOSH SANKALPA , SHARMA MANISH
Published: April 2013

In this review article we discuss the recent progress in studying ballistic transport for charge carriers in graphene through highly inhomogeneous magnetic field known as magnetic barrier in combination with gate voltage induced electrostatic potential. Starting with cases for a single or double magnetic barrier we also review the progress in understanding electron transport through the superlattices created out of such electromagnetic potential barriers and discuss the possibility of experimental realization of such systems. The emphasis is particularly on the analogy of such transport with propagation of light wave through medium with alternating dielectric constant. In that direction we discuss electron analogue of optical phenomena like Fabry–Perot resonances, negative refraction, Goos–Hänchen effect, beam collimation in such systems and explain how such analogy is going to be useful for device generation. The resulting modification of band structure of Dirac fermions, the emergence of additional Dirac points was also discussed accompanied by brief section on the interconvertibility of electric and magnetic field for relativistic Dirac fermions. We also discuss the effect of such electromagnetic potential barrier on bilayer graphene (BLG) in a similar framework.