bluuebunny/crossref_metadata_2025 huggingface dataset:
Avoidance of roads and selection for recent cutovers by threatened caribou: fitness-rewarding or maladaptive behaviour?
Authors: Dussault Christian , Pinard Véronique , Ouellet Jean-Pierre , Courtois Réhaume , Fortin Daniel
Published: September 2012

The impact of anthropogenic disturbance on the fitness of prey should depend on the relative effect of human activities on different trophic levels. This verification remains rare, however, especially for large animals. We investigated the functional link between habitat selection of female caribou (
Rangifer tarandus
) and the survival of their calves, a fitness correlate. This top-down controlled population of the threatened forest-dwelling caribou inhabits a managed forest occupied by wolves (
Canis lupus
) and black bears (
Ursus americanus
). Sixty-one per cent of calves died from bear predation within two months following their birth. Variation in habitat selection tactics among mothers resulted in different mortality risks for their calves. When calves occupied areas with few deciduous trees, they were more likely to die from predation if the local road density was high. Although caribou are typically associated with pristine forests, females selected recent cutovers without negative impact on calf survival. This selection became detrimental, however, as regeneration took place in harvested stands owing to increased bear predation. We demonstrate that human disturbance has asymmetrical consequences on the trophic levels of a food web involving multiple large mammals, which resulted in habitat selection tactics with a greater short-term fitness payoff and, therefore, with higher evolutionary opportunity.
Discovery of hundreds of mirtrons in mouse and human small RNA data
Authors: Ladewig Erik , Okamura Katsutomo , Flynt Alex S. , Westholm Jakub O. , Lai Eric C.
Published: September 2012

Atypical miRNA substrates do not fit criteria often used to annotate canonical miRNAs, and can escape the notice of miRNA genefinders. Recent analyses expanded the catalogs of invertebrate splicing-derived miRNAs (“mirtrons”), but only a few tens of mammalian mirtrons have been recognized to date. We performed meta-analysis of 737 mouse and human small RNA data sets comprising 2.83 billion raw reads. Using strict and conservative criteria, we provide confident annotation for 237 mouse and 240 human splicing-derived miRNAs, the vast majority of which are novel genes. These comprise three classes of splicing-derived miRNAs in mammals: conventional mirtrons, 5′-tailed mirtrons, and 3′-tailed mirtrons. In addition, we segregated several hundred additional human and mouse loci with candidate (and often compelling) evidence. Most of these loci arose relatively recently in their respective lineages. Nevertheless, some members in each of the three mirtron classes are conserved, indicating their incorporation into beneficial regulatory networks. We also provide the first Northern validation for mammalian mirtrons, and demonstrate Dicer-dependent association of mature miRNAs from all three classes of mirtrons with Ago2. The recognition of hundreds of mammalian mirtrons provides a new foundation for understanding the scope and evolutionary dynamics of Dicer substrates in mammals.
Predicting cell-type–specific gene expression from regions of open chromatin
Authors: Natarajan Anirudh , Yardımcı Galip Gürkan , Sheffield Nathan C. , Crawford Gregory E. , Ohler Uwe
Published: September 2012

Complex patterns of cell-type–specific gene expression are thought to be achieved by combinatorial binding of transcription factors (TFs) to sequence elements in regulatory regions. Predicting cell-type–specific expression in mammals has been hindered by the oftentimes unknown location of distal regulatory regions. To alleviate this bottleneck, we used DNase-seq data from 19 diverse human cell types to identify proximal and distal regulatory elements at genome-wide scale. Matched expression data allowed us to separate genes into classes of cell-type–specific up-regulated, down-regulated, and constitutively expressed genes. CG dinucleotide content and DNA accessibility in the promoters of these three classes of genes displayed substantial differences, highlighting the importance of including these aspects in modeling gene expression. We associated DNase I hypersensitive sites (DHSs) with genes, and trained classifiers for different expression patterns. TF sequence motif matches in DHSs provided a strong performance improvement in predicting gene expression over the typical baseline approach of using proximal promoter sequences. In particular, we achieved competitive performance when discriminating up-regulated genes from different cell types or genes up- and down-regulated under the same conditions. We identified previously known and new candidate cell-type–specific regulators. The models generated testable predictions of activating or repressive functions of regulators. DNase I footprints for these regulators were indicative of their direct binding to DNA. In summary, we successfully used information of open chromatin obtained by a single assay, DNase-seq, to address the problem of predicting cell-type–specific gene expression in mammalian organisms directly from regulatory sequence.
Widespread plasticity in CTCF occupancy linked to DNA methylation
Authors: Wang Hao , Maurano Matthew T. , Qu Hongzhu , Varley Katherine E. , Gertz Jason , Pauli Florencia , Lee Kristen , Canfield Theresa , Weaver Molly , Sandstrom Richard , Thurman Robert E. , Kaul Rajinder , Myers Richard M. , Stamatoyannopoulos John A.
Published: September 2012

CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin structure. Because of its critical role in genome function, CTCF binding patterns have long been assumed to be largely invariant across different cellular environments. Here we analyze genome-wide occupancy patterns of CTCF by ChIP-seq in 19 diverse human cell types, including normal primary cells and immortal lines. We observed highly reproducible yet surprisingly plastic genomic binding landscapes, indicative of strong cell-selective regulation of CTCF occupancy. Comparison with massively parallel bisulfite sequencing data indicates that 41% of variable CTCF binding is linked to differential DNA methylation, concentrated at two critical positions within the CTCF recognition sequence. Unexpectedly, CTCF binding patterns were markedly different in normal versus immortal cells, with the latter showing widespread disruption of CTCF binding associated with increased methylation. Strikingly, this disruption is accompanied by up-regulation of CTCF expression, with the result that both normal and immortal cells maintain the same average number of CTCF occupancy sites genome-wide. These results reveal a tight linkage between DNA methylation and the global occupancy patterns of a major sequence-specific regulatory factor.
Understanding transcriptional regulation by integrative analysis of transcription factor binding data
Authors: Cheng Chao , Alexander Roger , Min Renqiang , Leng Jing , Yip Kevin Y. , Rozowsky Joel , Yan Koon-Kiu , Dong Xianjun , Djebali Sarah , Ruan Yijun , Davis Carrie A. , Carninci Piero , Lassman Timo , Gingeras Thomas R. , Guigó Roderic , Birney Ewan , Weng Zhiping , Snyder Michael , Gerstein Mark
Published: September 2012

Statistical models have been used to quantify the relationship between gene expression and transcription factor (TF) binding signals. Here we apply the models to the large-scale data generated by the ENCODE project to study transcriptional regulation by TFs. Our results reveal a notable difference in the prediction accuracy of expression levels of transcription start sites (TSSs) captured by different technologies and RNA extraction protocols. In general, the expression levels of TSSs with high CpG content are more predictable than those with low CpG content. For genes with alternative TSSs, the expression levels of downstream TSSs are more predictable than those of the upstream ones. Different TF categories and specific TFs vary substantially in their contributions to predicting expression. Between two cell lines, the differential expression of TSS can be precisely reflected by the difference of TF-binding signals in a quantitative manner, arguing against the conventional on-and-off model of TF binding. Finally, we explore the relationships between TF-binding signals and other chromatin features such as histone modifications and DNase hypersensitivity for determining expression. The models imply that these features regulate transcription in a highly coordinated manner.
What does our genome encode?
Authors: Stamatoyannopoulos John A.
Published: September 2012

In its first production phase, The ENCODE Project Consortium (ENCODE) has generated thousands of genome-scale data sets, resulting in a genomic “parts list” that encompasses transcripts, sites of transcription factor binding, and other functional features that now number in the millions of distinct elements. These data are reshaping many long-held beliefs concerning the information content of the human and other complex genomes, including the very definition of the gene. Here I discuss and place in context many of the leading findings of ENCODE, as well as trends that are shaping the generation and interpretation of ENCODE data. Finally, I consider prospects for the future, including maximizing the accuracy, completeness, and utility of ENCODE data for the community.
catena-Poly[[silver(I)-μ-[9,10-bis(1H-benzimidazol-1-ylmethyl)anthracene]-κ2N3:N3′] bis(nitrato-κO)silver(I)]
Authors: Du Jian-Long , Zhu Xiao-Long , Li Pei
Published: September 2012

Yellow needle-shaped crystals of the title compound, {[Ag(C30H22N4)][Ag(NO3)2]}n, were obtained by the reaction of AgNO3and 9,10-bis(benzimidazol-1-ylmethyl)anthracene (L) in a 2:1 ratio. The asymmetric unit consists of two AgIcations, one halfLligand and one nitrate anion. One AgIcation occupies a crystallographic inversion centre and links two N-atom donors of two distinctLligands to form an infinite one-dimensional coordination polymer. The second AgIcation lies on a crystallographic twofold axis and is coordinated by two O-atom donors of two nitrate anions to form an [Ag(NO3)2]−counter-ion. The polymeric chains are linked into a supramolecular frameworkviaweak Ag...O [3.124 (5) Å] and Ag...π (2.982 Å) interactions (π is the centroid of an outer anthracene benzene ring). The π interactions contain two short Ag...C contacts [2.727 (6) and 2.765 (6) Å], which can be considered to define Ag–η2-anthracene bonding interactions. In comparison with a previously reported binuclear AgIcomplex [Du, Hu, Zhang, Zeng & Bu (2008).CrystEngComm,10, 1866–1874], this new one-dimensional coordination polymer was obtained by changing the metal–ligand ratio during the synthesis.
The management of knowledge resources in SMEs: an Australian case study
Authors: Coyte Rodney , Ricceri Federica , Guthrie James
Published: September 2012

Purpose

The paper's aim is to examine processes used to control the management of knowledge resources in small and medium enterprises (SMEs) and to compare the findings with the underlying assumptions and prescriptions of intellectual capital guidelines designed for SMEs.

Design/methodology/approach

An in‐depth case study of a successful Australian SME is conducted to identify the means used to control strategizing and the management of knowledge resources.

Findings

It was found that informal, intensive dialogue based processes, structured by an overriding management philosophy, governed strategization and the management of knowledge resources. These governance processes were affected by a combination of formal and informal controls and serendipitous outcomes.

Research limitations/implications

The paper examines only one organization and the study can be extended to other SMEs to develop more detailed specific policy recommendations.

Practical implications

Intellectual capital management guidelines developed for SMEs may have little benefit due to assumptions of resource availability and the fundamental importance of formalization of strategy and control, ignoring possible scarcity of resources and the benefits of flexibility and responsiveness afforded by informal controls in SMEs. The research shows that knowledge harvesting is affected through the way knowledge is used rather than what is developed.

Originality/value

The paper empirically examines the management of knowledge resources in an Australian SME and outlines the way formal and informal controls were interwoven in organizational practices to manage knowledge harvesting. It provides a critique of intellectual capital guidelines in SMEs, highlighting a potential mis‐match between practice and key assumptions underlying the guidelines.
Well‐being through design: transferability of design concepts for healthcare environments to ordinary community settings
Authors: Boex Will , Boex Sam
Published: September 2012

Purpose

The paper aims to explore current interest in the concept of well‐being, and to trace, with examples, the growing use of design ideas in healthcare settings to reduce stress and maximise efficiency. Finally, it seeks to look at the relevance or transferability of such design principles and approaches to opportunities to enhance well‐being through design in community settings.

Design/methodology/approach

The potential in this approach is illustrated with some examples of design approaches applied in healthcare, teasing out the wider implications with ways to explore and arrange the patient journey, for example, or the “care pathway” for a vulnerable adult into a care or support service for maximum benefit.

Findings

Thinking on enhancing well‐being by design has been further advanced in applications in the health service, but a number of design concepts and approaches seem to promise similar benefits in community settings where issues in managing the health and well‐being of vulnerable individuals are equally relevant.

Originality/value

Design principles may be especially useful in current efforts towards creating dementia‐friendly homes and communities, or “psychologically informed environments” in services for marginalized and excluded individuals.
A new germline VHL gene mutation in three patients with apparently sporadic pheochromocytoma
Authors: D'Elia Angela V. , Grimaldi Franco , Pizzolitto Stefano , De Maglio Giovanna , Bregant Elisa , Passon Nadia , Franzoni Alessandra , Verrienti Antonella , Tamburrano Giulia , Durante Cosimo , Filetti Sebastiano , Fogolari Federico , Russo Diego , Damante Giuseppe
Published: September 2012

Context

Germline mutations in four genes (RET, VHL, SDHB and SDHD) are detected in about 17% of patients with apparently sporadic pheochromocytoma. Thus, genetic screening of all patients with this disease is suggested for a rational diagnostic approach and management.

Objective

To report the clinical, biochemical and genetic analysis of three unrelated patients affected by pheochromocytoma.

Design and patients

All the coding regions and exon–intron boundaries of RET, VHL, SDHB and SDHD genes were sequenced in three unrelated patients with intra‐adrenal pheochromocytoma: a 17‐year‐old girl, a 15‐year‐old boy and a 73‐year‐old man. The family history of all three cases was negative for von Hippel–Lindau lesions or other types of endocrine tumours. Structural modelling of the VHL protein was then performed.

Results

We identified a novel germline VHL gene point mutation, a G to A nucleotide substitution in exon 3, leading to an aspartate to asparagine amino acid change in codon 197 (D197N). No mutations were found in RET, SDHB and SDHD genes. Structural modelling of the VHL protein suggests that the D197N mutation could have a functional role.

Conclusions

Our study expands the number of VHL gene known mutations and indicates the usefulness of performing the genetic analysis in all patients with apparently sporadic pheochromocytoma.
Contrasting influence of flow regime on freshwater fishes displaying diadromous and nondiadromous life histories
Authors: Crow Shannan K. , Booker Doug J. , Snelder Ton H.
Published: September 2012

Flow variability structures freshwater fish community traits and life‐history patterns such as migration patterns between fresh and saltwater (diadromy). Few studies, however, have explored relationships between diadromy and flow regime while accounting for other abiotic covariables. The present paper used canonical ordinations to remove the shared variation between groups of explanatory variables that explain variation in fish communities and examine two objectives with New Zealand fishes: (i) to compare the unique contributions of Hydrological Regime, Climate, Habitat and Spatial‐Seasonal data sets to the variation of diadromous and nondiadromous fishes and (ii) to compare the relative contributions of a Hydrological Variability and Low‐Flow data set to community structure of both life‐history patterns. All explanatory variables explained a total of 20.15% and 29.58% of the variation in diadromous and nondiadromous fishes, respectively. Objective 1 analyses showed that the largest unique component of variation was explained by Hydrological Regime for nondiadromous fishes (12.17%), while Climate uniquely explained the most variation in diadromous fishes (4.3%), followed closely by Hydrological Regime (3.08%). Objective 2 analyses showed that Hydrological Variability uniquely explained five and 11 times more variation than the Low‐Flow data set in diadromous and nondiadromous fishes, respectively. Findings illustrate the importance of hydrological regime to New Zealand freshwater fishes. Specifically, aspects of hydrological variability uniquely account for more variation than aspects of low flow. Differing relative influences of hydrology between life‐history patterns suggest that diadromy may mediate the influence of flow regime. Results outline difficulties for environmental flow settings when biota display differing life histories.
The role of time preference in smoking cessation: a longitudinal analysis of data from the Household Income and Labour Dynamics of Australia survey, 2001–08
Authors: Brown Heather , Adams Jean
Published: September 2012

Aims

Time preference describes how consideration of future events may affect present‐day behavioural decisions. The aim was to establish whether time preference predicts smoking cessation in a longitudinal analysis.

Design

Secondary analysis of data from the Household Income and Labour Dynamics of Australia survey.

Setting

Australian community.

Participants

Members of the Household Income and Labour Dynamics of Australia survey panel, aged 15–64 years, who responded to at least four waves of data collection between 2001 and 2008, and reported any level of tobacco consumption at any wave.

Measurements

Smoking cessation was measured using a self‐report questionnaire. Time preference was measured using self‐reported time‐period for financial planning. A range of socio‐demographic and smoking‐related covariates were controlled for.

Findings

A total of 1817 individuals were included in the analysis, representing 7913 separate observations. After controlling for socio‐demographic and smoking‐related covariates, the hazard ratio of quitting in those with longer versus shorter‐term time preference (95% confidence intervals) = 1.28 (1.02–1.59).

Conclusions

Adult smokers with a longer‐term time preference, who are more likely to consider future events when making present‐day decisions, are more likely to quit smoking.
A comparison of intra‐operative blood loss and acid–base balance between vasopressor and inotrope strategy during living donor liver transplantation: a randomised, controlled study
Authors: Hong S. H. , Park C. S. , Jung H. S. , Choi H. , Lee S. R. , Lee J. , Choi J. H.
Published: September 2012

Administration of vasopressors or inotropes during liver transplant surgery is almost universal, as this procedure is often accompanied by massive haemorrhage, acid–base imbalance, and cardiovascular instability. However, the actual agents that should be used and the choice between a vasopressor and an inotrope strategy are not clear from existing published evidence. In this prospective, randomised, controlled and single‐blinded study, we compared the effects of a vasopressor strategy on intra‐operative blood loss and acid–base status with those of an inotrope strategy during living donor liver transplantation. Seventy‐six adult liver recipients with decompensated cirrhosis were randomly assigned to receive a continuous infusion of either phenylephrine at a dose of 0.3–0.4 μg.kg−1.min−1 or dopamine and/or dobutamine at 2–8 μg.kg−1.min−1 during surgery. Vascular resistance was higher over time in the phenylephrine group than in the dopamine/dobutamine group. Estimated blood loss was significantly lower in the phenylephrine group than in the dopamine/dobutamine group (mean (SD) 4.5 (1.8) l vs 6.1 (3.4) l, respectively, p = 0.011). Patients in the phenylephrine group had lower lactate levels in the late pre‐anhepatic and the early anhepatic phase and needed less bicarbonate administration than those in the dopamine/dobutamine group (median (IQR [range]) 40 (0–100 [0–160]) mEq vs 70 (40–163 [0–260]) mEq, respectively, p = 0.018). Postoperative clinical outcomes and laboratory‐measured hepatic and renal function did not differ between the groups. Increased vascular resistance and reduction of portal blood flow by intra‐operative phenylephrine infusion is assumed to decrease the amount of intra‐operative bleeding and thereby ameliorate the progression of lactic acidosis during liver transplant surgery.
Health supervision of young women during pregnancy and early motherhood: A Norwegian qualitative study
Authors: Fredriksen Anne Mari , Lyberg Anne , Severinsson Elisabeth
Published: September 2012

This study describes and interprets midwives' and public health nurses' perceptions of their experiences of caring for young women during pregnancy and early motherhood. A number of studies suggest that teenage pregnancy is associated with many adverse psychological, physical, social, and financial outcomes. Multistage focus group interviews were conducted with six professionals, and a qualitative content analysis was performed. The result of this descriptive and explorative study comprised one main theme, creating a trusting and committed relationship to support immature young women, characterized by two themes: searching for security and love in daily life and active involvement with “the children of their hearts”. In summary, in order to support the young women, the informants used modeling as a strategy to achieve self‐esteem, thus helping them to cope with daily life. Continuity of team supervision should be improved to enhance midwives' and public health nurses' professional roles.
Syntaxin 1 is required for DCC/Netrin‐1‐dependent chemoattraction of migrating neurons from the lower rhombic lip
Authors: Cotrufo Tiziana , Andrés Rosa María , Ros Oriol , Pérez‐Brangulí Francesc , Muhaisen Ashraf , Fuschini Giulia , Martínez Ramón , Pascual Marta , Comella Joan X. , Soriano Eduardo
Published: September 2012

Directed cell migration and axonal guidance are essential steps in neural development that share many molecular mechanisms. The guidance of developing axons and migrating neurons is likely to depend on the precise control of plasmalemma turnover in selected regions of leading edges and growth cones, respectively. Previous results provided evidence of a signaling mechanism that couples chemotropic deleted in colorectal cancer (DCC)/Netrin‐1 axonal guidance and exocytosis through Syntaxin1(Sytx1)/TI‐VAMP SNARE proteins. Here we studied whether Netrin‐1‐dependent neuronal migration relies on a similar SNARE mechanism. We show that migrating neurons in the lower rhombic lip (LRL) express several SNARE proteins, and that DCC co‐associates with Sytx1 and TI‐VAMP in these cells. We also demonstrate that cleavage of Sytx1 by botulinum toxin C1 (BoNT/C1) abolishes Netrin‐1‐dependent chemoattraction of migrating neurons, and that interference of Sytx1 functions with shRNAs or Sytx1‐dominant negatives disrupts Netrin‐1‐dependent chemoattraction of LRL neurons. These findings indicate that a Sytx1/DCC interaction is required for Netrin‐1 guidance of migrating neurons, thereby highlighting a relationship between guidance signaling and SNARE proteins that regulate membrane turnover.
INTERVIEW: DR ANWAR GARGASH
Authors: Scott Andrew
Published: September 2012

With its oil wealth and increasingly influential role in the world, the United Arab Emirates (UAE) is moving towards the economic centre stage. Dr Anwar Gargash, the UAE's Minister of Foreign Affairs, talks with Andrew Scott, Professor of Economics at London Business School.
THE TALENT FACTORY OF THE FUTURE
Authors: Gratton Lynda
Published: September 2012

India's economic rise has been dramatic. But as the growth slows, what does the future hold?Lynda Gratton offers a personal view.
ALTERNATIVE INSPIRATION: WHY CURRY SPICE AND OLD SPICE ARE THE NEW MANAGEMENT MODELS
Authors: Peters Georgina
Published: September 2012

Where should managers look for inspiration about best practice?Georgina Peters suggests they look further afield than the usual corporate suspects.
MY DAY: LYNDON FAULKNER
Authors: Crainer Stuart
Published: September 2012

Lyndon Faulkner is President and CEO of Pelican Products, the global leader in design and manufacture of high‐performance protective case solutions and advanced portable lighting systems, based in California. Faulkner has steered Pelican from $80 million worth of sales in 2006 to $350 million in sales today. Here is what his day looks like.
Monuments of memory: defensive mechanisms of the collective psyche and their manifestation in the memorialization process
Authors: Kalinowska Malgorzata
Published: September 2012

Abstract:  The paper searches for insight in the area of collective memory as a part of collective consciousness, a phenomenon understood as a stabilizing factor for a society's self‐image and identity. Collective memories are seen as originating from shared communications transmitting and creating the meaning of the past in the form of narrative, symbols and signs. As such, they contain the individual, embodied and lived side of our relations to the past. As well as the identity‐building and meaning‐making functions of collective memories, their defensive function is discussed with a focus on commemorative practices taking place in a transitional space between psychic and social life. Fears of a lack of collective identity and coherence have contributed to the way Polish commemorative practices have been shaped. This is considered in relation to the Smolensk catastrophe in 2010, viewed in the context of the Jungian concept of the collective psyche and the psychoanalytical understanding of defensive group mechanisms against trauma, especially those relating to loss and mourning. It leads to a consideration of how historical experiences and the experience of history can be accessed, as well as their meaning for individual and group development.
Analysis of measures for attention to diversity in Compulsory Secondary Education: the case of the Region of Murcia, Spain
Authors: Arnaiz Pilar , Martínez Rogelio , de Haro Remedios , Escarbajal Andrés
Published: September 2012

In this paper, we present an analysis of the implementation of measures of attention to diversity for students with special educational support needs studying Compulsory Secondary Education (12–16 years) in the Region of Murcia, Spain. Our aim is to learn about the organisational and curricular structures implemented in five secondary education schools with a total of 1967 students. These structures are used to deal with student diversity through common and specific measures of attention to diversity and are established by law. We intend to verify and assess whether these are properly and effectively implemented, providing a quality educational response in conformity with the discourse on inclusion and social cohesion. A review of existing legislation suggests that it may be advisable to apply common measures before specific ones in the event that a student has educational support needs and, if possible, in the usual context, that is, within the regular classroom.
Deoxidization of V2O5 Powder into VO2 Assisted by an Electrochemical Lithium Intercalation Technique
Authors: Chen Jikun , Liu Xinling , Chen Lidong , Chen Nuofu , Dai Lei , Gao Yanfeng
Published: September 2012

This article demonstrates a method to fabricate VO2 powder by annealing a precursor that was obtained by electrochemical intercalation of lithium into layered structured V2O5. The method includes three steps. First, Li+ was intercalated into interlayers of V2O5 through an electrochemical process with precisely controlled electrical discharging currents and intercalation amounts, and at the same time V5+ would be deoxidized into V4+. Secondly, the Li+‐intercalated powder was rinsed in an acid solution to achieve an ion exchanging process of replacing the Li+ in the V–O frame with H+. Thirdly, the powder was annealed at 800°C in N2 atmosphere for dehydration and VO2 crystallization. By DSC investigation, the as‐produced final product has a strong endothermic peak at around 68°C in a heating semicycle, which is indicative of the phase transition from VO2(M) to VO2(R). This approach can be extended to the fabrication of other sub‐valence oxides by lithium intercalation and deoxidization of its higher valence layer‐structured precursors.
Culture‐Based and Denaturing Gradient Gel Electrophoresis Analysis of the Bacterial Community from Chungkookjang, a Traditional Korean Fermented Soybean Food
Authors: Hong Sung Wook , Choi Jae Young , Chung Kun Sub
Published: September 2012

Abstract:  The bacterial community of Chungkookjang and raw rice‐straw collected from various areas in South Korea was investigated using both culture‐dependent and culture‐independent methods. Pure cultures were isolated from Chungkookjang and raw rice‐straw on tryptic soy agar plates with 72 to 121 colonies and identified by 16S rDNA gene sequence analysis, respectively. The traditional culture‐based method and denaturing gradient gel electrophoresis analysis of PCR‐amplified 16S rDNA confirmed that Pantoea agglomerans and B. subtilis were identified as predominant in the raw rice‐straw and Chungkookjang, respectively, from Iljuk district of Gyeonggi province, P. ananatis and B. licheniformis were identified as predominant in the raw rice‐straw and Chungkookjang from Wonju district of Gangwon province, and Microbacterium sp. and B. licheniformis were identified as predominant in the raw rice‐straw and Chungkookjang from Sunchang district of Jeolla province. Other strains, such as Bacillus, Enterococcus, Pseudomonas, Rhodococcus, and uncultured bacteria were also present in raw rice‐straw and Chungkookjang.

Practical Application:  A comprehensive analysis of these microorganisms would provide a more detailed understanding of the biologically active components of Chungkookjang and help improve its quality. Polymerase chain reaction‐denaturing gradient gel electrophoresis analysis can be successfully applied to a fermented food to detect unculturable or more species than the culture‐dependent method. This technique is an effective and convenient culture‐independent method for studying the bacterial community in Chungkookjang. In this study, the bacterial community of Chungkookjang collected from various areas in South Korea was investigated using both culture‐dependent and culture‐independent methods.
A Road Map for an Emerging Psychology of Social Class
Authors: Kraus Michael W. , Stephens Nicole M.
Published: September 2012

Though the scientific study of social class is over a century old, theories regarding how social class shapes psychological experience are in their infancy. In this review, we provide a road map for the empirical study of an emerging psychology of social class. Specifically, we outline key measurement issues in the study of social class – including the importance of both objective indicators and subjective perceptions of social class – as well as theoretical insights into the role of the social class context in influencing behavior. We then summarize why a psychology of social class is likely to be a fruitful area of research and propose that social class environments guide psychological experience because they shape fundamental aspects of the self and patterns of relating to others. Finally, we differentiate social class from other rank‐relevant states (e.g., power) and social categories (e.g., race/ethnicity), while also outlining potential avenues of future research.
Mindfulness: Towards A Critical Relational Perspective
Authors: Stanley Steven
Published: September 2012

Significant attention has been given to mindfulness and mindfulness meditation in Western culture – often allied with a concern to enhance ‘subjective wellbeing’ through interventions aiming to ameliorate stress, depression and anxiety. While much professional and scientific research has been conducted which studies the nature and effectiveness of mindfulness‐based interventions, few critical accounts exist. I seek to produce a social critique of current understandings of mindfulness in relation to contemporary psychology. I illustrate how mindfulness has become individualised as an object of contemporary psychological investigation. I then propose a relational approach which instead sees mindfulness as socially contingent and as a potential resource for individuals and communities to cultivate a critically distant stance towards society. This involves revisioning our basic understanding of mindfulness as not only an inner state of mind, but also as a public social practice.
Directive 2010/63/EU on animal welfare: a review on the existing scientific knowledge and implications in cephalopod aquaculture research
Authors: Sykes António V. , Baptista Filipa D. , Gonçalves Rui A. , Andrade José P.
Published: September 2012

This review intends to provide a reflection regarding Directive 2010/63/EU, on animal welfare, and its application concerning cephalopod breeding and experimentation in aquaculture research. To do so, we gathered different perspectives of our group members, involving two cephalopod aquaculture researchers, an aquaculture fish production technician and a veterinary professional, the latter with no background on cephalopod research. The inclusion of this class in the animal welfare legislation; the definition of live cephalopods, stress, pain and suffering are revised according to the latest scientific knowledge. Considering the 15 year background that the Centre of Marine Sciences holds on the cultivation of the European cuttlefish, an evaluation of existing production protocols, aquaculture technology related research, ethics and cephalopod welfare are discussed. The application of anaesthesia, analgesia and euthanasia is discussed, bearing in mind the different procedures applied on a daily basis in aquaculture breeding and experimentation and the requirements of the new Directive. Finally, an overview of the above and progress on 3Rs (replacement of animals, reduction in number of animals and refinement of procedures) application to cephalopod welfare is presented.
How Multi‐stakeholder is Global Policy?
Authors: Khanna Parag
Published: September 2012

The global financial crisis revealed not only the need for greater oversight of the private sector, but also the co‐dependence of governments and those firms. From national economic governance to transnational regulations such as the Basel III regulations, the continued strong influence of the private sector in negotiating, setting standards and implementing them through private bodies such as the US Financial Industry Regulatory Authority (FINRA) remains undeniable. The global financial crisis thus illustrates how even amidst valid claims that ‘the state is back’, global policy making is increasingly multi‐stakeholder in character. This article provides a snapshot of the increasing extensiveness of multi‐stakeholder processes through a conceptual overview and an empirical survey, highlighting instances in which various actor pillars (governments, intergovernmental organisations, civil society organisations, corporations, etc.) have begun to expand their membership and participation to include other stakeholders. It demonstrates that even as the main actor groups that serve as the foundation of global policy processes remain mostly unchanged, the extent to which each pursues multi‐stakeholder approaches has increased.
Impact of Cry1Ab toxin expression on the non‐target insects dwelling on maize plants
Authors: Habuštová O. , Doležal P. , Spitzer L. , Svobodová Z. , Hussein H. , Sehnal F.
Published: September 2012

The effect of transgenic maize MON810 (Bt maize) on the diversity and abundance of plant‐dwelling insects was tested under field conditions in southern Bohemia (coordinates 48°N, 14ºE, 384 m a.s.l.) for three successive years. The experiment was carried out on 10 0.5‐ha plots of which five were seeded with the Bt maize and five with the non–Bt parental cultivar. The content of Bt toxin (Cry1Ab) was measured in plant tissues with a commercial ELISA kit. Randomly chosen plants (10 per plot) were taken from the field during the vegetation period in about 2‐week intervals and thoroughly examined in the laboratory. Collected insects were identified and their counts were statistically analysed with CANOCO with respect to the Bt toxin, developmental stage of maize and the year of cultivation. No significant effect of Bt maize on the plant‐dwelling non‐target insects was detected. Correlation between the number of plants and detected insect diversity revealed that inspection of 20 plants (four per each of five plots) provided data reliable at 95% probability level; six plants per plot were sufficient for the analysis of aphids, thrips and Orius bugs.
Sigma factor‐mediated plastid retrograde signals control nuclear gene expression
Authors: Woodson Jesse D. , Perez‐Ruiz Juan M. , Schmitz Robert J. , Ecker Joseph R. , Chory Joanne
Published: September 2012

Retrograde signalling from plastids to the nucleus is necessary to regulate the organelle's proteome during the establishment of photoautotrophy and fluctuating environmental conditions. Studies that used inhibitors of chloroplast biogenesis have revealed that hundreds of nuclear genes are regulated by retrograde signals emitted from plastids. Plastid gene expression is the source of at least one of these signals, but the number of signals and their mechanisms used to regulate nuclear gene expression are unknown. To further examine the effects of plastid gene expression on nuclear gene expression, we analyzed Arabidopsis mutants that were defective in each of the six sigma factor (SIG) genes that encode proteins utilized by plastid‐encoded RNA polymerase to transcribe specific sets of plastid genes. We showed that SIG2 and SIG6 have partially redundant roles in plastid transcription and retrograde signalling to control nuclear gene expression. The loss of GUN1 (a plastid‐localized pentatricopeptide repeat protein) is able to restore nuclear (but not plastid) gene expression in both sig2 and sig6, whereas an increase in heme synthesis is able to restore nuclear gene expression in sig2 mutants only. These results demonstrate that sigma factor function is the source of at least two retrograde signals to the nucleus; one likely to involve the transcription of tRNAGlu. A microarray analysis showed that these two signals accounted for at least one subset of the nuclear genes that are regulated by the plastid biogenesis inhibitors norflurazon and lincomycin. Together these data suggest that such inhibitors can induce retrograde signalling by affecting transcription in the plastid.
The Draw-Bend Fracture Test and Its Application to Dual-Phase and Transformation Induced Plasticity Steels
Authors: Hyun Sung Ji , Hoon Kim Ji , Wagoner R. H.
Published: September 2012

Unpredicted sheet forming failures of dual-phase (DP) steels can occur in regions of high curvature and with little apparent necking. Such failures are often referred to as “shear fractures”. In order to reproduce such fractures in a laboratory setting, and to understand their origin and the inability to predict them, a novel draw-bend formability (DBF) test was devised using dual displacement rate control. DP steels from several suppliers, with tensile strengths ranging from 590 to 980 MPa, were tested over a range of rates and bend ratios (R/t) along with a TRIP (transformation induced plasticity) steel for comparison. The new test reliably reproduced three kinds of failures identified as types 1, 2, and 3, corresponding to tensile failure, transitional failure, and shear fracture, respectively. The type of failure depends on R/t and strain rate, and presumably on the initial specimen width, which was constant in this study. Two critical factors influencing the lack of accurate failure prediction were identified. The dominant one is deformation-induced heating, which is particularly significant for advanced high strength steels because of their high energy product. Temperature rises of up to 100 deg. C were observed. This factor reduces formability at higher strain rates, and promotes a transition from types 1 to 3. The second factor is related to microstructural features. It was significant in only one material in one test direction (of 11 tested) and only for this case was the local fracture strain different from that in a tensile failure. Alternate measures for assessing draw-bend formability were introduced and compared. They can be used to rank the formability of competing materials and to detect processing problems that lead to unsuitable microstructures.
Striation-based beamforming for active sonar with a horizontal line array
Authors: Zurk Lisa M. , Rouseff Daniel
Published: September 2012

A physics-based method for beamforming signals measured on a horizontal array is developed with an application to underwater active sonar systems. The proposed striation-based beamformer coherently combines the pressure from each element in the array at different frequencies, and these frequencies are selected based on a striation hypothesis. The linear frequency shift and corresponding phase term introduced in the array weight vector accounts for multipath-induced fading, producing beam output with increased signal gain. The method is demonstrated using data collected on an array towed in the North Atlantic. The combination of the striation-based beamformer with the waveguide invariant concept to improve tracker performance is discussed.
Immunocytochemistry for Vancomycin Using a Monoclonal Antibody That Reveals Accumulation of the Drug in Rat Kidney and Liver
Authors: Fujiwara Kunio , Yoshizaki Yohei , Shin Masashi , Miyazaki Tsubasa , Saita Tetsuya , Nagata Shuichi
Published: September 2012

We prepared monoclonal antibodies against
N
-(γ-maleimidobutyryloxy)succinimide-conjugated vancomycin (VM). The monoclonal antibody was specific for conjugated or free VM. The monoclonal antibody enabled us to develop an immunocytochemical method for detecting the uptake of VM in the rat kidney and liver. Three hours after a single intravenous (i.v.) injection of VM at the therapeutic dose, the immunocytochemistry revealed that VM accumulated in large amounts in both the S1 and S2 segments and in much smaller amounts in the S3 segment of the proximal tubules as well as in the distal tubules and collecting ducts. The drug was detected in the cytoplasm, cytoplasmic irregular granules, nuclei, and microvilli of the proximal tubule cells. The distal tubules and collecting ducts contained scattered swollen cells in which both the nuclei and cytoplasm were heavily immunostained. Twenty-four hours after injection, most of the swollen cells returned back to normal size and had somewhat decreased immunostaining. Also, significant amounts of VM remained accumulated for as long as 8 days postadministration. In the liver, similar drug accumulation was observed in the Kupffer cells and the endothelial cells of the hepatic sinusoids but not in the hepatocytes, suggesting that vancomycin cannot be eliminated via the liver. Immunoelectron microscopic studies demonstrated that in the collecting ducts, uptake of VM occurred exclusively in the lysosomes and cytoplasm of the principal cells and scarcely in the intercalated cells. Furthermore, double fluorescence staining using rats simultaneously administered with VM and gentamicin strongly suggests that both drugs colocalized in lysosomes in the proximal tubule cells of kidneys.
Genotypic and Phenotypic Evaluation of the Evolution of High-Level Daptomycin Nonsusceptibility in Vancomycin-Resistant Enterococcus faecium
Authors: Humphries Romney M. , Kelesidis Theodoros , Tewhey Ryan , Rose Warren E. , Schork Nicholas , Nizet Victor , Sakoulas George
Published: September 2012

Whole-genome sequencing and cell membrane studies of three clonal
Enterococcus faecium
strains with daptomycin MICs of 4, 32, and 192 μg/ml were performed, revealing nonsynonymous single nucleotide variants in eight open reading frames, including those predicted to encode a phosphoenolpyruvate-dependent, mannose-specific phosphotransferase system, cardiolipin synthetase, and EzrA. Membrane studies revealed a higher net surface charge among the daptomycin-nonsusceptible isolates and increased septum formation in the isolate with a daptomycin MIC of 192 μg/ml.
INTEGRATED SYSTEMS AND OUTSOURCING: PROCESS INNOVATION IN AEROSPACE PRODUCT DESIGN
Authors: TAIFI NOUHA , LAZOI MARIANGELA , CORALLO ANGELO , PASSIANTE GIUSEPPINA , LAZOI MARIANGELA
Published: September 2012

Organizations need to share and acquire new information to sustain competitive advantage in complex environment. They communicate through IT-based integrated systems to fasten communication and knowledge sharing for the creation of innovative products. Firms are, thus, extending their operations to integrate strategic knowledge from partners in the product development process. In this paper, we present a case study related to process innovation in an aerospace firm integrating its information systems with one of its partners to facilitate the design of the models of a complex product. We investigate on the strategy followed to integrate the information systems, the types of these latter, on their success factors and their impact on the product development. The case study provides important insights on the integration of information systems for product design outsourcing.
Composite Match Index with Application of Interior Deformation Field Measurement from Magnetic Resonance Volumetric Images of Human Tissues
Authors: Zhang Penglin , Zhang Xubing , Chen Jiangping
Published: September 2012

Whereas a variety of different feature-point matching approaches have been reported in computer vision, few feature-point matching approaches employed in images from nonrigid, nonuniform human tissues have been reported. The present work is concerned with interior deformation field measurement of complex human tissues from three-dimensional magnetic resonance (MR) volumetric images. To improve the reliability of matching results, this paper proposes composite match index (CMI) as the foundation of multimethod fusion methods to increase the reliability of these various methods. Thereinto, we discuss the definition, components, and weight determination of CMI. To test the validity of the proposed approach, it is applied to actual MR volumetric images obtained from a volunteer’s calf. The main result is consistent with the actual condition.