bluuebunny/crossref_metadata_2025 huggingface dataset:
Perturbation of cytosolic calcium by 2‐aminoethoxydiphenyl borate and caffeine affects zebrafish myofibril alignment
Authors: Wu Hsin‐Ju , Fong Tsorng‐Harn , Chen Shen‐Liang , Wei Jen‐Cheng , Wang I‐Jong , Wen Chi‐Chung , Chang Chao‐Yuan , Chen Xing‐Guang , Chen Wei‐Yu , Chen Hui‐Min , Horng Juin‐Lin , Wang Yun‐Hsin , Chen Yau‐Hung
Published: September 2014

The objective of the current study was to investigate the effects of Ca2+ levels on myofibril alignment during zebrafish embryogenesis. To investigate how altered cytoplasmic Ca2+ levels affect myofibril alignment, we exposed zebrafish embryos to 2‐aminothoxyldiphenyl borate (2‐APB; an inositol 1,4,5‐trisphosphate receptor inhibitor that reduces cytosolic Ca2+ levels) and caffeine (a ryanodine receptor activator that enhances cytosolic Ca2+ levels). The results demonstrated that the most evident changes in zebrafish embryos treated with 2‐APB were shorter body length, curved trunk and malformed somite boundary. In contrast, such malformed phenotypes were evident neither in untreated controls nor in caffeine‐treated embryos. Subtle morphological changes, including changes in muscle fibers, F‐actin and ultrastructures were easily observed by staining with specific monoclonal antibodies (F59 and α‐laminin), fluorescent probes (phalloidin) and by transmission electron microscopy. Our data suggested that: (1) the exposure to 2‐APB and/or caffeine led to myofibril misalignment; (2) 2‐APB‐treated embryos displayed split and short myofibril phenotypes, whereas muscle fibers from caffeine‐treated embryos were twisted and wavy; and (3) zebrafish embryos co‐exposed to 2‐APB and caffeine resulted in normal myofibril alignment. In conclusion, we proposed that cytosolic Ca2+ is important for myogenesis, particularly for myofibril alignment. Copyright © 2014 John Wiley & Sons, Ltd.
Pin1 Plays a Critical Role as a Molecular Switch in Canonical BMP Signaling
Authors: Yoon Won‐Joon , Islam Rabia , Cho Young‐Dan , Ryu Kyung‐Min , Shin Hye‐Rim , Woo Kyung‐Mi , Baek Jeong‐Hwa , Ryoo Hyun‐Mo
Published: September 2014

Pin1 is a peptidyl prolyl cis‐trans isomerase that specifically binds to the phosphoserine–proline or phosphothreonine–proline motifs of numerous proteins. Previously, we reported that Pin1 deficiency resulted in defects in osteoblast differentiation during early bone development. In this study, we found that adult Pin1‐deficient mice developed osteoporotic phenotypes compared to age‐matched controls. Since BMP2 stored in the bone matrix plays a critical role in adult bone maintenance, we suspected that BMP R‐Smads (Smad1 and Smad5) could be critical targets for Pin1 action. Pin1 specifically binds to the phosphorylated linker region of Smad1, which leads to structural modification and stabilization of the Smad1 protein. In this process, Pin1‐mediated conformational modification of Smad1 directly suppresses the Smurf1 interaction with Smad1, thereby promoting sustained activation of the Smad1 molecule. Our data demonstrate that post‐phosphorylational prolyl isomerization of Smad1 is a converging signal to stabilize the Smad1 molecule against the ubiquitination process mediated by Smurf1. Therefore, Pin1 is a critical molecular switch in the determination of Smad1 fate, opposing the death signal transmitted to the Smad1 linker region by phosphorylation cascades after its nuclear localization and transcriptional activation. Thus, Pin1 could be developed as a major therapeutic target in many skeletal diseases. J. Cell. Physiol. 230: 640–647, 2015. © 2014 Wiley Periodicals, Inc., A Wiley Company
The Cooperation of CREB and NFAT Is Required for PTHrP‐Induced RANKL Expression in Mouse Osteoblastic Cells
Authors: Park Hyun‐Jung , Baek Kyunghwa , Baek Jeong‐Hwa , Kim Hyung‐Ryong
Published: September 2014

Parathyroid hormone‐related protein (PTHrP) is known to induce the expression of receptor activator of NF‐κB ligand (RANKL) in stromal cells/osteoblasts. However, the signaling pathways involved remain controversial. In the present study, we investigated the role of cAMP/protein kinase A (PKA) and calcineurin/NFAT pathways in PTHrP‐induced RANKL expression in C2C12 and primary cultured mouse calvarial cells. PTHrP‐mediated induction of RANKL expression was significantly inhibited by H89 and FK506, an inhibitor of PKA and calcineurin, respectively. PTHrP upregulated CREB phosphorylation and the transcriptional activity of NFAT. Knockdown of CREB or NFATc1 blocked PTHrP‐induced RANKL expression. PTHrP increased the activity of the RANKL promoter reporter that contains approximately 2 kb mouse RANKL promoter DNA sequences. Insertions of mutations in CRE‐like element or in NFAT‐binding element abrogated PTHrP‐induced RANKL promoter activity. Chromatin immunoprecipitation assays showed that PTHrP increased the binding of CREB and NFATc1/NFATc3 to their cognate binding elements in the RANKL promoter. Inhibition of cAMP/PKA and its downstream ERK activity suppressed PTHrP‐induced expression and transcriptional activity of NFATc1. CREB knockdown prevented PTHrP induction of NFATc1 expression. Furthermore, NFATc1 and CREB were co‐immunoprecipitated. Mutations in CRE‐like element completely blocked NFATc1‐induced transactivation of the RANKL promoter reporter; however, mutations in NFAT‐binding element partially suppressed CREB‐induced RANKL promoter activity. Overexpression of CREB increased NFATc1 binding to the RANKL promoter and vice versa. These results suggest that PTHrP‐induced RANKL expression depends on the activation of both cAMP/PKA and calcineurin/NFAT pathways, and subsequently, CREB and NFAT cooperate to transactivate the mouse RANKL gene. J. Cell. Physiol. 230: 667–679, 2015. © 2014 Wiley Periodicals, Inc., A Wiley Company
A comparison of fruit quality parameters of wild bilberry (Vaccinium myrtillus L.) growing at different locations
Authors: Mikulic‐Petkovsek Maja , Schmitzer Valentina , Slatnar Ana , Stampar Franci , Veberic Robert
Published: September 2014

BACKGROUND

As a part of the ongoing interest in nutritional and nutraceutical properties of locally produced fruits, the aim of the article was to determine sugars, organic acids, polyphenols and antioxidant capacity of wild bilberries grown in Slovenia. Primary and secondary metabolite composition of bilberry fruit was compared among six phyto‐climatic conditions, differing in photosynthetic active radiation and light intensity.

RESULTS

Three sugars were quantified in bilberry fruit, the predominant being fructose and glucose, along with five organic acids. Bilberry fruit contained high levels of anthocyanins (cyanidin, delphinidin, malvidin, petunidin and peonidin glycosides), hydroxycinnamic acid derivatives and low levels of flavonol glycosides (mainly quercetin and myricetin glycosides), flavan‐3‐ols, proanthocyanidins and iridoids. The results of the study indicate that bilberries growing in sites with high photosynthetic active radiation (PAR) contained higher levels of total sugars, anthocyanins, flavonols and hydroxycinnamic acids and lower levels of organic acids compared with bilberry fruit from low‐light locations. Consequently, total phenolic content and antioxidative capacity of the fruit from high‐PAR locations were significantly increased.

CONCLUSION

Bilberries from different natural habitats differ significantly in the quantity of sugars, organic acids and phenolic compounds. Our results contribute to a fuller understanding of the relationships between environmental factors and accumulation of primary and secondary metabolites in bilberry fruits. © 2014 Society of Chemical Industry
Active hexose correlated compound exerts therapeutic effects in lymphocyte driven colitis
Authors: Mascaraque Cristina , Suárez María Dolores , Zarzuelo Antonio , de Medina Fermín Sánchez , Martínez‐Augustin Olga
Published: September 2014

Active hexose correlated compound (AHCC) is a commercial extract of Basidiomycetes fungi enriched in oligosaccharides that is used as a human nutritional supplement for various purposes in humans. Our aim was to study the anti‐inflammatory effect of AHCC in the CD4+ CD62L+ T cell transfer model of colitis, considered one of the closest to the human disease. Colitis was induced by transfer of CD4+ CD62L+ T cells to recombination activating gene 1−/− mice. AHCC (75 mg/d) was administered by gavage as a post‐treatment. Three groups were established: noncolitic, colitic (CD4+ CD62L+ transferred mice treated with vehicle), and AHCC (colitic treated with AHCC). AHCC improved colitis, as evidenced by a 24% lower colonic myeloperoxidase and a 21% lower alkaline phosphatase activity. In addition, a decreased secretion of proinflammatory genes assessed by RT‐qPCR was observed, particularly TNF‐α and IL‐1β. Ex vivo mesenteric lymph node cells obtained from AHCC treated mice exhibited a fully normalized production of IL‐6, IL‐17, and IL‐10 (p < 0.05). Also, AHCC treated mice exhibited decreased STAT4 and IκB‐α phosphorylation in splenic CD4+ cells. Our data provide validation of AHCC colonic anti‐inflammatory activity in a chronic, T cell driven model of inflammatory bowel disease.
Numerical computations of rock dissolution and geomechanical effects for CO2 geological storage
Authors: Wojtacki K. , Lewandowska J. , Gouze Ph. , Lipkowski A.
Published: September 2014

The paper is motivated by the long‐term safety analysis of the CO2 geological storage. We present a methodology for the assessment of the geomechanical impact of progressive rock dissolution. The method is based on the use of X‐ray tomography and the numerical dissolution technique. The influence of evolution of the microstructure on the macroscopic properties of the rock is analysed by using periodic homogenization method. The numerical computations show progressive degradation of all components of the stiffness (orthotropic) tensor. Moreover, the evolution of associated mass transfer properties (as tortuosity and conductivity tensors), by using the periodic homogenization method, is also calculated. The correlation between the mechanical parameters and the transfer properties during the dissolution process is presented. The results show that the highest increase of the hydraulic conductivity (in direction Y) is not associated with the highest decrease of Young modulus in this direction. Moreover, the highest decrease of Young modulus (in the direction X) is not associated with percolation in this direction. Finally, an incremental law to calculate settlement, in case of a rock with evolving microstructure, is proposed. The solution of the macroscopic settlement problem under constant stress and drained conditions showed that the geomechanical effects of the rock dissolution are rather limited. Copyright © 2014 John Wiley & Sons, Ltd.
Epstein–Barr virus‐encoded EBNA1 and ZEBRA: targets for therapeutic strategies against EBV‐carrying cancers
Authors: Daskalogianni Chrysoula , Pyndiah Slovénie , Apcher Sébastien , Mazars Anne , Manoury Bénédicte , Ammari Nisrine , Nylander Karin , Voisset Cécile , Blondel Marc , Fåhraeus Robin
Published: September 2014

The EBV‐encoded EBNA1 was first discovered 40 years ago, approximately 10 years after the presence of EBV had been demonstrated in Burkitt's lymphoma cells. It took another 10 years before the functions of EBNA1 in maintaining the viral genome were revealed, and it has since been shown to be an essential viral factor expressed in all EBV‐carrying cells. Apart from serving to maintain the viral episome and to control viral replication and gene expression, EBNA1 also harbours a cis‐acting mechanism that allows virus‐carrying host cells to evade the immune system. This relates to a particular glycine–alanine repeat (GAr) within EBNA1 that has the capacity to suppress antigen presentation to the major histocompatibility complex (MHC) class I pathway. We discuss the role of the GAr sequence at the level of mRNA translation initiation, rather than at the protein level, as at least part of the mechanism to avoid MHC presentation. Interfering with this mechanism has become the focus of the development of immune‐based therapies against EBV‐carrying cancers, and some lead compounds that affect translation of GAr‐carrying mRNAs have been identified. In addition, we describe the EBV‐encoded ZEBRA factor and the switch from the latent to the lytic cycle as an alternative virus‐specific target for treating EBV‐carrying cancers. Understanding the molecular mechanisms of how EBNA1 and ZEBRA interfere with cellular pathways not only opens new therapeutic approaches but continues to reveal new cell‐biological insights on the interplay between host and virus. This review is a tale of discoveries relating to how EBNA1 and ZEBRA have emerged as targets for specific cancer therapies against EBV‐carrying diseases, and serves as an illustration of how mRNA translation can play roles in future immune‐based strategies to target viral disease. Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Mycobacterium tuberculosis dysregulates MMP/TIMP balance to drive rapid cavitation and unrestrained bacterial proliferation
Authors: Kübler André , Luna Brian , Larsson Christer , Ammerman Nicole C , Andrade Bruno B , Orandle Marlene , Bock Kevin W , Xu Ziyue , Bagci Ulas , Mollura Daniel J , Marshall John , Burns Jay , Winglee Kathryn , Ahidjo Bintou Ahmadou , Cheung Laurene S , Klunk Mariah , Jain Sanjay K , Kumar Nathella Pavan , Babu Subash , Sher Alan , Friedland Jon S , Elkington Paul TG , Bishai William R
Published: September 2014

Active tuberculosis (TB) often presents with advanced pulmonary disease, including irreversible lung damage and cavities. Cavitary pathology contributes to antibiotic failure, transmission, morbidity and mortality. Matrix metalloproteinases (MMPs), in particular MMP‐1, are implicated in TB pathogenesis. We explored the mechanisms relating MMP/TIMP imbalance to cavity formation in a modified rabbit model of cavitary TB. Our model resulted in consistent progression of consolidation to human‐like cavities (100% by day 28), with resultant bacillary burdens (>107 CFU/g) far greater than those found in matched granulomatous tissue (105 CFU/g). Using a novel, breath‐hold computed tomography (CT) scanning and image analysis protocol, we showed that cavities developed rapidly from areas of densely consolidated tissue. Radiological change correlated with a decrease in functional lung tissue, as estimated by changes in lung density during controlled pulmonary expansion (R2 = 0.6356, p < 0.0001). We demonstrated that the expression of interstitial collagenase (MMP‐1) was specifically greater in cavitary compared to granulomatous lesions (p < 0.01), and that TIMP‐3 significantly decreased at the cavity surface. Our findings demonstrated that an MMP‐1/TIMP imbalance is associated with the progression of consolidated regions to cavities containing very high bacterial burdens. Our model provided mechanistic insight, correlating with human disease at the pathological, microbiological and molecular levels. It also provided a strategy to investigate therapeutics in the context of complex TB pathology. We used these findings to predict a MMP/TIMP balance in active TB and confirmed this in human plasma, revealing the potential of MMP/TIMP levels as key components of a diagnostic matrix aimed at distinguishing active from latent TB (PPV = 92.9%, 95% CI 66.1–99.8%, NPV = 85.6%; 95% CI 77.0–91.9%). Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd
Aryl hydrocarbon receptor knock‐out exacerbates choroidal neovascularization via multiple pathogenic pathways
Authors: Choudhary Mayur , Kazmin Dmitri , Hu Peng , Thomas Russell S , McDonnell Donald P , Malek Goldis
Published: September 2014

The aryl hydrocarbon receptor (AhR) is a heterodimeric transcriptional regulator with pleiotropic functions in xenobiotic metabolism and detoxification, vascular development and cancer. Herein, we report a previously undescribed role for the AhR signalling pathway in the pathogenesis of the wet, neovascular subtype of age‐related macular degeneration (AMD), the leading cause of vision loss in the elderly in the Western world. Comparative analysis of gene expression profiles of aged AhR−/− and wild‐type (wt) mice, using high‐throughput RNA sequencing, revealed differential modulation of genes belonging to several AMD‐related pathogenic pathways, including inflammation, angiogenesis and extracellular matrix regulation. To investigate AhR regulation of these pathways in wet AMD, we experimentally induced choroidal neovascular lesions in AhR−/− mice and found that they measured significantly larger in area and volume compared to age‐matched wt mice. Furthermore, these lesions displayed a higher number of ionized calcium‐binding adaptor molecule 1‐positive (Iba1+) microglial cells and a greater amount of collagen type IV deposition, events also seen in human wet AMD pathology specimens. Consistent with our in vivo observations, AhR knock‐down was sufficient to increase choroidal endothelial cell migration and tube formation in vitro. Moreover, AhR knock‐down caused an increase in collagen type IV production and secretion in both retinal pigment epithelial (RPE) and choroidal endothelial cell cultures, increased expression of angiogenic and inflammatory molecules, including vascular endothelial growth factor A (VEGFA) and chemokine (C–C motif) ligand 2 (CCL2) in RPE cells, and increased expression of secreted phosphoprotein 1 (SPP1) and transforming growth factor‐β1 (TGFβ1) in choroidal endothelial cells. Collectively, our findings identify AhR as a regulator of multiple pathogenic pathways in experimentally induced choroidal neovascularization, findings that are consistent with a possible role of AhR in wet AMD. The data discussed in this paper have been deposited in NCBI's Gene Expression Omnibus; GEO Submission No. GSE56983, NCBI Tracking System No. 17021116. © 2014 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Linking cancer genome to proteome: NCI's investment into proteogenomics
Authors: Rivers Robert C. , Kinsinger Christopher , Boja Emily S. , Hiltke Tara , Mesri Mehdi , Rodriguez Henry
Published: September 2014

Advances in both targeted and unbiased MS‐based proteomics are now at a mature stage for comprehensively and reproducibly characterizing a large part of the cancer proteome. These developments combined with the extensive genomic characterization of several cancer types by large‐scale initiatives such as the International Cancer Genome Consortium and Cancer Genome Atlas Project have paved the way for proteogenomic analysis of omics datasets and integration methods. The advances serve as the basis for the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium and this article highlights its current work and future steps in the area of proteogenomics.
Biomarker discovery in asthma and COPD by proteomic approaches
Authors: Rossi Rossana , De Palma Antonella , Benazzi Louise , Riccio Anna Maria , Canonica Giorgio Walter , Mauri Pierluigi
Published: September 2014

Asthma and chronic obstructive pulmonary disease (COPD) are multifactorial respiratory diseases, characterized by reversible and irreversible airway obstruction, respectively. Even if the primary causes of these diseases remain unknown, inflammation is a central feature that leads to progressive and permanent pulmonary tissue damage (airway remodeling) up to the total loss of lung function. Therefore, the elucidation of the inflammation mechanisms and the characterization of the biological pathways, involved in asthma and COPD pathogenesis, are relevant in finding new possible diagnostic/prognostic biomarkers and for the validation of new drug targets. In this context, current advances in proteomic approaches, especially those based on MS, provide new tools to facilitate the discovery‐driven studies of new biomarkers in respiratory diseases and improve the clinical reliability of the next generation of biomarkers for these diseases consisting of multiple phenotypes. This review will report an overview of the current proteomic methods applied to the discovery of candidate biomarkers for asthma and COPD, giving a special emphasis to emerging MS‐based techniques.
Multiple structural forms of a vacancy in silicon as evidenced by vacancy profiles produced by rapid thermal annealing
Authors: Voronkov Vladimir , Falster Robert
Published: September 2014

Vacancy depth profiles installed by rapid thermal annealing can be monitored either by Pt diffusion or through vacancy‐assisted oxygen precipitation. The features of these profiles clearly show that the vacancy species manifested in these experiments is a “slow vacancy”, Vs. The evolution of Vs depth profiles is controlled by an exchange with another (mobile) kind of vacancy that is likely to be a “Watkins vacancy”, Vw, first observed at cryogenic temperatures. At low T the conversion of Vs into Vw is slow and practically irreversible. At higher T the two species coexist in an equilibrium ratio and diffuse as one entity with an averaged diffusivity. This model provides a good fit to the RTA‐installed depth profiles of Vs. The total vacancy community includes, beside Vs and Vw, also a fast vacancy Vf that is responsible for the vacancy contribution into self‐diffusion at high T. In RTA experiments, the Vf species seems to be completely annihilated by self‐interstitials which leaves only two other vacancy species, Vs and Vw.
Synoptic‐scale precursors of the East Asia/Pacific teleconnection pattern responsible for persistent extreme precipitation in the Yangtze River Valley
Authors: Chen Yang , Zhai Panmao
Published: September 2014

Synoptic‐scale precursors of the typical East Asia/Pacific (EAP) teleconnection pattern responsible for persistent extreme precipitation events (PEPEs) in the Yangtze River Valley (YRV) are investigated, based on a composite analysis. The results reveal that, about one week prior to PEPEs, a blocking high develops near the Sea of Okhotsk owing to an eastward energy dispersion and further strengthens markedly due to poleward energy dispersion from low latitudes. Subsequently, a meridional tripole structure of the typical EAP pattern becomes well established by this blocking, along with a westward‐migrated strong negative anomaly at midlatitudes/positive anomaly at lower latitudes. In the lower troposphere, a westward‐progressive anomalous anticyclone–cyclone pair can be identified up to about a week prior to PEPEs, contributing to greatly enhanced moisture transport towards the YRV with a magnitude anomaly over three standard deviations above normal. A midlatitude anomalous cyclone associated with the EAP pattern evolution and the eastward‐extended South Asia High combine to provide favourable upper‐level divergence. Correspondingly, strong ascent of low‐level warm/moist air along a quasi‐stationary front leads to PEPEs in the YRV. A contrastive analysis between evolution of typical wet and dry EAP regimes indicates that EAP‐induced PEPEs are more likely to occur in the YRV, with the ridge of the western Pacific subtropical high typically staying around the northeastern quadrant of the South China Sea. This contrasting analysis also highlights the importance of the upstream pre‐existing ridge to early strengthening of the Okhotsk blocking.
On the connection between tropical circulation, convective mixing, and climate sensitivity
Authors: Tomassini L. , Voigt A. , Stevens B.
Published: September 2014

The connection between the large‐scale tropical circulation of the atmosphere, convective mixing, and climate sensitivity is explored in a wide range of climates through a perturbed‐parameter ensemble of a comprehensive Earth System Model. Four parameters related to the representation of atmospheric moist convection are found to dominate the response of the model. Their values govern the strength of the tropical circulation, the surface temperature, atmospheric humidity, and the strength of the tropical overturning circulation, largely through their influence on the atmospheric stability. The same convective parameters, albeit in different combinations, also have a strong influence on the equilibrium climate sensitivity of the model, which ranges from a little over 3 °C to more than 10 °C. The importance of the most poorly represented processes in determining important aspects of the behaviour of the model argues for the need to move beyond statistical approaches to estimating climate sensitivity and to focus on the development of a better understanding and representation of convective mixing, particularly in the Tropics.
Angiogenesis is inhibitory for mammalian digit regeneration
Authors: Yu Ling , Yan Mingquan , Simkin Jennifer , Ketcham Paulina D. , Leininger Eric , Han Manjong , Muneoka Ken
Published: September 2014

The regenerating mouse digit tip is a unique model for investigating blastema formation and epimorphic regeneration in mammals. The blastema is characteristically avascular and we previously reported that blastema expression of a known anti‐angiogenic factor gene, Pedf, correlated with a successful regenerative response (Yu, L., Han, M., Yan, M., Lee, E. C., Lee, J. & Muneoka, K. (2010). BMP signaling induces digit regeneration in neonatal mice. Development, 137, 551–559). Here we show that during regeneration Vegfa transcripts are not detected in the blastema but are expressed at the onset of differentiation. Treating the amputation wound with vascular endothelial growth factor enhances angiogenesis but inhibits regeneration. We next tested bone morphogenetic protein 9 (BMP9), another known mediator of angiogenesis, and found that BMP9 is also a potent inhibitor of digit tip regeneration. BMP9 induces Vegfa expression in the digit stump suggesting that regenerative failure is mediated by enhanced angiogenesis. Finally, we show that BMP9 inhibition of regeneration is completely rescued by treatment with pigment epithelium‐derived factor. These studies show that precocious angiogenesis is inhibitory for regeneration, and provide compelling evidence that the regulation of angiogenesis is a critical factor in designing therapies aimed at stimulating mammalian regeneration.
A non‐parametric statistical test to compare clusters with applications in functional magnetic resonance imaging data
Authors: Fujita André , Takahashi Daniel Y. , Patriota Alexandre G. , Sato João R.
Published: September 2014

Statistical inference of functional magnetic resonance imaging (fMRI) data is an important tool in neuroscience investigation. One major hypothesis in neuroscience is that the presence or not of a psychiatric disorder can be explained by the differences in how neurons cluster in the brain. Therefore, it is of interest to verify whether the properties of the clusters change between groups of patients and controls. The usual method to show group differences in brain imaging is to carry out a voxel‐wise univariate analysis for a difference between the mean group responses using an appropriate test and to assemble the resulting ‘significantly different voxels’ into clusters, testing again at cluster level. In this approach, of course, the primary voxel‐level test is blind to any cluster structure. Direct assessments of differences between groups at the cluster level seem to be missing in brain imaging. For this reason, we introduce a novel non‐parametric statistical test called analysis of cluster structure variability (ANOCVA), which statistically tests whether two or more populations are equally clustered. The proposed method allows us to compare the clustering structure of multiple groups simultaneously and also to identify features that contribute to the differential clustering. We illustrate the performance of ANOCVA through simulations and an application to an fMRI dataset composed of children with attention deficit hyperactivity disorder (ADHD) and controls. Results show that there are several differences in the clustering structure of the brain between them. Furthermore, we identify some brain regions previously not described to be involved in the ADHD pathophysiology, generating new hypotheses to be tested. The proposed method is general enough to be applied to other types of datasets, not limited to fMRI, where comparison of clustering structures is of interest. Copyright © 2014 John Wiley & Sons, Ltd.
A case study of normalization, missing data and variable selection methods in lipidomics
Authors: Kujala M. , Nevalainen J.
Published: September 2014

Lipidomics is an emerging field of science that holds the potential to provide a readout of biomarkers for an early detection of a disease. Our objective was to identify an efficient statistical methodology for lipidomics—especially in finding interpretable and predictive biomarkers useful for clinical practice. In two case studies, we address the need for data preprocessing for regression modeling of a binary response. These are based on a normalization step, in order to remove experimental variability, and on a multiple imputation step, to make the full use of the incompletely observed data with potentially informative missingness. Finally, by cross‐validation, we compare stepwise variable selection to penalized regression models on stacked multiple imputed data sets and propose the use of a permutation test as a global test of association. Our results show that, depending on the design of the study, these data preprocessing methods modestly improve the precision of classification, and no clear winner among the variable selection methods is found. Lipidomics profiles are found to be highly important predictors in both of the two case studies. Copyright © 2014 John Wiley & Sons, Ltd.
On the use of European and American building codes with low‐strength mortars
Authors: Duplan François , Abou‐Chakra Ariane , Turatsinze Anaclet , Escadeillas Gilles , Brûlé Stéphane , Javelaud Emmanuel , Massé Frédéric
Published: September 2014

The standard European building specifications, grouped in a nine‐volume Eurocode, describe different approaches for determining the properties of commonly used building materials such as steel, aluminium, concrete, etc.

The American Concrete Institute (ACI) also offers different reports concerning concrete structures (ACI 318R), lightweight concrete (ACI 213R) and the long‐term mechanical behaviour (ACI 209R) of concrete. Those reports, used as building codes, are applicable when the properties and composition of the material respect various criteria.

All those materials that do not meet the scope criteria of Eurocode 2 or ACI reports because of their composition, property values or application cannot be used in the design of structures with those building codes. Regarding cement‐based materials, concretes and mortars whose compressive strength is lower than the minima might not be useful for structures; however, they present an interesting potential for applications such as infrastructure materials, slabs‐on‐ground, etc. When designing structures and infrastructures in those materials, the accuracy of any formula offered by those building codes should be checked before being used.

This article compares experimental measurements and predictive formulas for the engineering properties (compressive and tensile strengths, modulus of elasticity). The results show that the addition of specific aggregates with low stiffness and strength modifies the relation between those engineering properties, thus reducing the accuracy of some of the predictive formulas suggested in ACI reports or Eurocodes.
Thin‐walled shell structures made of textile‐reinforced concrete
Authors: Scholzen Alexander , Chudoba Rostislav , Hegger Josef
Published: September 2014

The present paper describes a design approach for textile‐reinforced concrete (TRC) shells which reflects the interaction between normal forces and bending moments based on the cross‐sectional strength characteristics of the material determined experimentally. The influence of oblique loading on the composite strength of TRC elements with flexible reinforcement is included in a normalized interaction diagram for combined loading. As an example, the design approach is applied to the ultimate limit state assessment of a TRC shell in double curvature. Furthermore, the general applicability of the design approach is discussed in the light of the non‐linear loadbearing behaviour of TRC. Due to its strain‐hardening tensile response, stress redistributions within the shell result in loadbearing reserves. Details of the structural design and production solutions developed and applied during the realization of the TRC shell structure are described in the companion paper (Part I).
Minimum reinforcement for crack width control in restrained concrete members considering the deformation compatibility
Authors: Schlicke Dirk , Tue Nguyen Viet
Published: September 2014

The current design code EC2 [1] regulates the minimum reinforcement for crack width control in restrained concrete members by taking up the cracking force of the cross section. Although this concept gives straightforward results, its consistent application can lead to high reinforcement amounts with increasing member thickness. The reason is the simplifying assumption of an infinite member length neglecting the deformation compatibility.

The cracking force approach was therefore empirically modified to reflect practical experience, see [2]. However, the main modification of a limited tensile strength seems particularly dubious, as the primarily affected thick members have already a strong developed tensile strength before any risk of cracking occurs at all.

Finally, this circumstance leaves the structural designer with the dilemma of being either uneconomic or having no mechanical proof in a possible case of damage.

However, the mechanically consistent estimation of the minimum reinforcement for crack width control can be achieved by considering the deformation compatibility of the restrained member, see [3]. With the introduction of [4], this deformation‐based design concept became state of the art for mass concrete members of hydraulic structures.

This contribution presents the general application of the deformation‐based design concept due the findings of [5]. The reliability and the practicability of this approach will then be illustrated by the deformation‐based minimum reinforcement design of a trough structure.
Characterization and site-directed mutation of a novel aldo–keto reductase from Lodderomyces elongisporus NRRL YB-4239 with high production rate of ethyl (R)-4-chloro-3-hydroxybutanoate
Authors: Wang Qiuyan , Ye Tingting , Ma Zhuanzhuan , Chen Rong , Xie Tian , Yin Xiaopu
Published: September 2014

A novel aldo–keto reductase (LEK) from Lodderomyces elongisporus NRRL YB-4239 (ATCC 11503) was discovered by genome database mining for carbonyl reduction. LEK was overexpressed in Escherichia coli BL21 (DE3), purified to homogeneity and the catalytic properties were studied. Among the substrates, ethyl 4-chloro-3-oxobutanoate was converted to ethyl (R)-4-chloro-3- hydroxybutanoate ((R)-CHBE), an important pharmaceutical intermediate, with an excellent enantiomeric excess (e.e.) (>99 %). The mutants W28A and S209G obtained by site-directed mutation were identified with much higher molar conversion yields and lower Km values. Further, the constructed coenzyme regeneration system with glucose as co-substrate resulted in a yield of 100 %, an enantioselectivity of >99 %, and the calculated production rate of 56.51 mmol/L/H. These results indicated the potential of LEK for the industrial production of (R)-CHBE and other valuable chiral alcohols.
Glycosylation and subsequent malonylation of isoflavonoids in E. coli: strain development, production and insights into future metabolic perspectives
Authors: Koirala Niranjan , Pandey Ramesh Prasad , Van Thang Duong , Jung Hye Jin , Sohng Jae Kyung
Published: September 2014

Genistin and daidzein exhibit a protective effect on DNA damage and inhibit cell proliferation. Glycosylation and malonylation of the compounds increase water solubility and stability. Constructed pET15b-GmIF7GT and pET28a-GmIF7MAT were used for the transformation of Escherichia coli and bioconversion of genistein and daidzein. To increase the availability of malonyl-CoA, a critical precursor of GmIF7MAT, genes for the acyl-CoA carboxylase α and β subunits (nfa9890 and nfa9940), biotin ligase (nfa9950), and acetyl-CoA synthetase (nfa3550) from Nocardia farcinia were also introduced. Thus, the isoflavonoids were glycosylated at position 7 by 7-O-glycosyltranferase and were further malonylated at position 6″ of glucose by malonyl-CoA: isoflavone 7-O-glucoside-6″-O-malonyltransferase both from Glycine max. Engineered E. coli produced 175.7 µM (75.90 mg/L) of genistin and 14.2 µM (7.37 mg/L) genistin 6″-O-malonate. Similar conditions produced 162.2 µM (67.65 mg/L) daidzin and 12.4 µM (6.23 mg/L) daidzin 6″-O-malonate when 200 µM of each substrate was supplemented in the culture. Based on our findings, we speculate that isoflavonoids and their glycosides may prove useful as anticancer drugs with added advantage of increased solubility, stability and bioavailability.
The effect of polyhexamethylene guanidine hydrochloride (PHMG) derivatives introduced into polylactide (PLA) on the activity of bacterial enzymes
Authors: Walczak Maciej , Richert Agnieszka , Burkowska-But Aleksandra
Published: September 2014

The present study was aimed at investigating bactericidal properties of polylactide (PLA) films containing three different polyhexamethylene guanidine hydrochloride (PHMG) derivatives and effect of the derivatives on extracellular hydrolytic enzymes and intracellular dehydrogenases. All PHMG derivatives had a slightly stronger bactericidal effect on Staphylococcus aureus than on E. coli but only PHMG granular polyethylene wax (at the concentration of at least 0.6 %) has a bactericidal effect. PHMG derivatives introduced into PLA affected the activity of microbial hydrolases to a small extent. This means that the introduction of PHMG derivatives into PLA will not reduce its enzymatic biodegradation significantly. On the other hand, PHMG derivatives introduced into PLA strongly affected dehydrogenases activity in S. aureus than in E. coli.
Dietary Hyodeoxycholic Acid Exerts Hypolipidemic Effects by Reducing Farnesoid X Receptor Antagonist Bile Acids in Mouse Enterohepatic Tissues
Authors: Watanabe Shiro , Fujita Kyosuke
Published: September 2014

Mice were fed a control diet or a diet supplemented with hyodeoxycholic acid, the most abundant bile acid contained in pig bile, for 4 weeks, after which their serum and livers were collected. The contents of total fatty acids of serum and liver cholesteryl esters, and of liver triglycerides, were reduced following the administration of the hyodeoxycholic acid‐supplemented diet, which was mainly due to the reductions in the contents of monounsaturated fatty acids. Free cholesterol contents in the serum and liver were not changed by hyodeoxycholic acid administration. Hyodeoxycholic acid administration reduced the gene expression levels of sterol regulatory element binding protein 1c, acetyl‐CoA carboxylase, fatty acid synthase, and stearoyl‐CoA desaturase‐1. Hyodeoxycholic acid administration markedly changes the ratio of FXR‐antagonist/FXR‐agonist bile acids in the enterohepatic tissues of the mice (1.13 and 7.60 in hyodeoxycholic acid and control diet groups, respectively). Our findings demonstrate that hyodeoxycholic acid administration exerts the hypolipidemic effect in mice, in which downregulations of de novo lipogenesis and desaturation of saturated fatty acids are suggested to play important roles. In addition, regulation of FXR activation through the selective modification of the enterohepatic bile acid pool may be involved in the hypolipidemic effect of hyodeoxycholic acid administration.
A note on interpreting damn expressives: transferring the blame
Authors: FRAZIER LYN , DILLON BRIAN , CLIFTON CHARLES
Published: September 2014

abstract

Expressives like damn convey a negative attitude toward an entity or toward a situation. What is particularly interesting about such expressions is the looseness of the relation between their syntax, which is the syntax of normal attribute adjectives, and their interpretation (Potts 2005, 2007). An experiment on various negative expressives manipulated the placement of the expressive as a prior utterance, or inside the subject or inside an object of the verb or preposition. Experimental participants were asked what the speaker was most likely to have a negative attitude towards − the subject, the object, or the entire situation. The test items were of two types, ‘non-causal’ and ‘causal’, exemplified by The holiday is on the damn weekend and The dog is on the damn couch. In the non-causal items, the subject (holiday) cannot plausibly be taken as being responsible for the state of affairs described. However, in the causal items, the subject might be responsible for the state of affairs described. The same range of interpretations was observed for all placements of damn. The prior utterance condition (Damn. The dog is on the couch.) yielded more entire situation interpretations than the sentence-internal damn items. Overall, subject damn items yielded more subject interpretations than object damn items. However, as predicted by the hypothesis that blame would devolve on a potentially responsible agent (the culprit hypothesis), there were more subject interpretations in the causal items than in the non-causal items. The results suggest that considerable pragmatic inferencing is involved in the interpretation of expressives, consistent with a proposal that an expressive constitutes a separate speech act.
Effects of supplementation with two sources and two levels of copper on meat lipid oxidation, meat colour and superoxide dismutase and glutathione peroxidase enzyme activities in Nellore beef cattle
Authors: Correa Lísia Bertonha , Zanetti Marcus Antonio , Del Claro Gustavo Ribeiro , de Paiva Fernanda Alves , da Luz e Silva Saulo , Netto Arlindo Saran
Published: September 2014

In the present study, thirty-five Nellore bulls were used to determine the effects of two levels and two sources (organic and inorganic) of Cu supplementation on the oxidative stability of lipids, measured by the thiobarbituric acid-reactive substance (TBARS) test, meat colour and superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) enzyme activities. The following treatments were used: (1) control (C) – basal diet without supplementation of Cu (7 mg Cu/kg DM); (2) I10 – basal diet supplemented with 10 mg Cu/kg DM in the form of copper sulphate (inorganic form); (3) I40 – basal diet supplemented with 40 mg Cu/kg DM in the form of copper sulphate; (4) O10 – basal diet supplemented with 10 mg Cu/kg DM in the form of copper proteinate (organic form); (5) O40 – basal diet supplemented with 40 mg Cu/kg DM in the form of copper proteinate. Lipid oxidation was determined in meat samples exposed to display, modified atmosphere (MA) and vacuum packaging (VC) conditions and in liver samples using the TBARS test. These samples were also evaluated for meat discolouration after exposure to air. The activities of SOD and GSH-Px enzymes were determined in liver samples. In display, MA and VC conditions, the TBARS values of samples from animals supplemented with 40 mg Cu/kg DM were lower than those of samples from control animals. There was no effect of treatment on the colour variables (L*,a*,b*). There was also no significant effect of treatment on hepatic TBARS concentrations and GSH-Px activity. Supplementation with Cu at 40 mg/kg, regardless of the source, induced higher hepatic SOD activity compared with the control treatment. In conclusion, Cu supplementation improved the oxidative stability of lipids in samples exposed to display, MA and VC conditions, demonstrating the antioxidant effect of this mineral.
Effects of dietary fructo-oligosaccharide supplementation on the growth performance, haemato-immunological parameters, gut microbiota and stress resistance of common carp (Cyprinus carpio) fry
Authors: Hoseinifar Seyed Hossein , Soleimani Narges , Ringø Einar
Published: September 2014

The present study was conducted to investigate the effects of dietary fructo-oligosaccharide (FOS) (0, 1, 2 and 3 %) supplementation on the growth performance, haemato-immunological parameters, cultivable autochthonous (non-adherent) intestinal microbiota and stress resistance of common carp (Cyprinus carpio) fry (3·23 (sem 0·14) g). These parameters were measured after feeding the carp fry with the experimental diets for 7 weeks. Dietary FOS supplementation had no significant effects on the growth performance and food intake of carp fry compared with the control treatment. It also had no significant effects on the following haematological parameters: erythrocyte count; leucocyte counts (WBC); haematocrit; Hb; mean corpuscular volume; mean corpuscular Hb content; mean corpuscular Hb concentration. However, WBC and respiratory burst activity were significantly affected by dietary FOS supplementation. Evaluation of the cultivable autochthonous intestinal microbiota revealed a significant increase in the levels of total viable heterotrophic aerobic bacteria and lactic acid bacteria in fish fed diets supplemented with 2 and 3 % FOS. Furthermore, dietary FOS supplementation significantly increased the survival rate and stress resistance of carp fry compared with the control treatment. These results encourage conducting further research on the administration of FOS and other prebiotics in carp fry studies.
Comparison of two exploratory dietary patterns in association with the metabolic syndrome in a Northern German population
Authors: Barbaresko Janett , Siegert Sabine , Koch Manja , Aits Imke , Lieb Wolfgang , Nikolaus Susanna , Laudes Matthias , Jacobs Gunnar , Nöthlings Ute
Published: September 2014

Diet is related to many chronic disease conditions such as the metabolic syndrome (MetS). We set out to compare behaviour-related with disease-related patterns and their association with the MetS in a German cross-sectional study. A total of 905 participants of a Northern German cohort (aged 25–82 years) completed a FFQ, underwent anthropometric assessments and provided a blood sample. Dietary patterns were derived by principal component analysis (PCA) and reduced-rank regression (RRR) from forty-two food groups. Components of the MetS were used as response variables for the RRR analysis. Simplified patterns comprising ten food groups were generated. Logistic regression analysis was performed to evaluate the likelihood of having the MetS across the quartiles of simplified pattern scores. We identified two similar dietary patterns derived by PCA and RRR characterised by high intakes of potatoes, various vegetables, red and processed meat, fats, sauce and bouillon. Comparing simplified patterns, an increased RRR pattern score was associated with a higher OR (2·18, 95 % CI 1·25, 3·81) of having the MetS than an increased PCA pattern score (OR 1·92, 95 % CI 1·21, 3·03). Comparing concordant food groups by both dietary pattern methods, a diet high in legumes, beef, processed meat and bouillon was also positively associated with the prevalence of the MetS after adjustment for potential confounders (OR 1·71, 95 % CI 1·04, 2·79). We identified a behaviour-related pattern that was positively associated with the MetS. The application of both dietary pattern methods may be advantageous to obtain information for designing and realising dietary guidelines. Prospective studies are needed to confirm the results.