bluuebunny/crossref_metadata_2025 huggingface dataset:
Feedback-controlled laser fabrication of micromirror substrates
Authors: Petrak Benjamin , Konthasinghe Kumarasiri , Perez Sonia , Muller Andreas
Published: December 2011

Short (40–200 μs) single focused CO2 laser pulses of energy ≳100 μJ were used to fabricate high quality concave micromirror templates on silica and fluoride glass. The ablated features have diameters of ≈20–100 μm and average root-mean-square (RMS) surface microroughness near their center of less than 0.2 nm. Temporally monitoring the fabrication process revealed that it proceeds on a time scale shorter than the laser pulse duration. We implement a fast feedback control loop (≈20 kHz bandwidth) based on the light emitted by the sample that ensures an RMS size dispersion of less than 5% in arrays on chips or in individually fabricated features on an optical fiber tip, a significant improvement over previous approaches using longer pulses and open loop operation.
Negative capacitor paves the way to ultra-broadband metamaterials
Authors: Hrabar Silvio , Krois Igor , Bonic Ivan , Kiricenko Aleksandar
Published: December 2011

Experimental demonstration of the overcoming of basic dispersion-energy constraints in metamaterials with the help of active non-Foster negative capacitors is reported. The experimental metamaterial operates in RF regime, and it is based on air transmission line loaded with negative capacitors. Measurement results clearly show almost dispersionless Epsilon-Near-Zero behavior, accompanied with superluminal both phase and group velocities, over a bandwidth of more than four octaves (2 MHz-40 MHz). The principle of periodic loading of transmission line with negative capacitors may find applications in ultra-broadband active metamaterials for antennas and cloaking technology.
Ultraviolet assisted processing: A unique approach to mitigate oxygen vacancies and attain low loss highly tunable Ba0.60Sr0.40TiO3 thin films
Authors: Cole M. W. , Toonen R. C. , Ivill M. , Hirsch S. G. , Ngo E. , Hubbard C.
Published: December 2011

Isothermal (700 °C) ultraviolet annealing (UVA) processing of crystallized Ba0.60Sr0.40TiO3 (BST) thin films for exposure times up to 225 min films has been studied. The BST films, grown on PtSi wafers via the metalorganic solution deposition (MOSD) technique, were crystallized via conventional furnace annealing (CFA) prior to UVA treatment, and the effects of UV annealing time on the structural, dielectric, and insulation properties were evaluated. The experimental results demonstrated significantly improved structural, dielectric, and insulation properties for the UVA films. Specifically, lattice parameter contraction (toward that of bulk BST60/40) and a 20% reduction in loss were observed for the UVA treated films with respect to the CFA/control film. Leakage current characteristics were found to be the most sensitive characterization technique to access material property modification as a result of UVA exposure time. Specifically, the 225 min UVA exposure time resulted in a three-order of magnitude reduction in leakage current density compared to the CFA film, and the lowest value observed was 1.06 × 10−7 A/cm2 at E = 300 kV/cm. The useable tunability (tunability value at the maximum acceptable leakage current, 500 pA) was found to be elevated by a factor of two with respect to that of the CFA/control BST film (52.31%/UVA film vs. 18.5%/control film). It is suggested that the improved material properties are due to the mitigation of unwanted oxygen vacancies within the film after UV-annealing. A mechanistic model is presented and discussed.
A review of the effects of different marking and tagging techniques on marine mammals
Authors: Walker Kristen A. , Trites Andrew W. , Haulena Martin , Weary Daniel M.
Published: December 2011

Wildlife research often requires marking and tagging animals to collect data on survival, reproduction, movement, behaviour and physiology. Identification of individual marine mammals can be carried out using tags, brands, paint, dye, photogrammetry, telemetry and other techniques. An analysis of peer-reviewed articles published from January 1980 to April 2011 addressing the effects of marking revealed a preponderance of studies focussed on short-term effects such as injuries and behavioural changes. Some marking techniques were reported to cause pain and to change swimming and haul-out behaviour, maternal attendance, and duration of foraging trips. However, marking has typically not been found to affect survival. No published research has addressed other possible long-term effects of marking related to injuries or pain responses. Studies of the more immediate effects of marking (mostly related to externally attached devices such as radio-transmitters) have shown a variety of different types and magnitudes of responses. It is important to note that studies failing to find treament differences are less likely to be published, meaning that the present and any other reviews based on published literature may be a biased sample of all research conducted on the topic. Publishing results that found no or low impacts (i.e. best practices) as well as those that found significant impacts on animals should both be encouraged. Future research under more controlled conditions is required to document acute effects of marking, including injury and pain, and to better understand longer-term effects on health, reproduction and survival. We recommend that studies using marked animals standardise their reports, with added detail on methodology, monitoring and sampling design, and address practices used to minimise the impact of marking on marine mammals.
Skeletogenic phenotype of human Marfan embryonic stem cells faithfully phenocopied by patient-specific induced-pluripotent stem cells
Authors: Quarto Natalina , Leonard Brian , Li Shuli , Marchand Melanie , Anderson Erica , Behr Barry , Francke Uta , Reijo-Pera Renee , Chiao Eric , Longaker Michael T.
Published: December 2011

Marfan syndrome (MFS) is a heritable connective tissue disorder caused by mutations in the gene coding for FIBRILLIN-1 (FBN1), an extracellular matrix protein. MFS is inherited as an autosomal dominant trait and displays major manifestations in the ocular, skeletal, and cardiovascular systems. Here we report molecular and phenotypic profiles of skeletogenesis in tissues differentiated from human embryonic stem cells and induced pluripotent stem cells that carry a heritable mutation inFBN1. We demonstrate that, as a biological consequence of the activation of TGF-β signaling, osteogenic differentiation of embryonic stem cells with aFBN1mutation is inhibited; osteogenesis is rescued by inhibition of TGF-β signaling. In contrast, chondrogenesis is not perturbated and occurs in a TGF-β cell-autonomous fashion. Importantly, skeletal phenotypes observed in human embryonic stem cells carrying the monogenicFBN1mutation (MFS cells) are faithfully phenocopied by cells differentiated from induced pluripotent-stem cells derived independently from MFS patient fibroblasts. Results indicate a unique phenotype uncovered by examination of mutant pluripotent stem cells and further demonstrate the faithful alignment of phenotypes in differentiated cells obtained from both human embryonic stem cells and induced pluripotent-stem cells, providing complementary and powerful tools to gain further insights into human molecular pathogenesis, especially of MFS.
Structural basis of coactivation of liver receptor homolog-1 by β-catenin
Authors: Yumoto Fumiaki , Nguyen Phuong , Sablin Elena P. , Baxter John D. , Webb Paul , Fletterick Robert J.
Published: December 2011

We report the three-dimensional structure of a β-catenin armadillo repeat in complex with the liver receptor homolog-1 (LRH-1) ligand binding domain at 2.8 Å resolution as the first structure of β-catenin in complex with any nuclear receptor. The surface of β-catenin that binds LRH-1 partly overlaps defined contact sites for peptide segments of β-catenin partners, including T-cell factor-4. The surface of LRH-1 that engages β-catenin is comprised of helices 1, 9, and 10 and is distinct from known interaction surfaces of LRH-1, including corepressor and coactivator binding sites. Targeted mutagenesis of amino acids forming both sides of the LRH-1/β-catenin interface reveals that they are essential for stable interactions between these proteins in solution. The LRH-1 binding site in β-catenin is also required for association with androgen receptor, providing evidence that the observed LRH-1/β-catenin interaction may be prototypic.
Communication and understanding
Authors: Janicki Karol
Published: December 2011

This article consists of two sections: in the first one, I discuss one of the most prevalent lay myths in the Western world with respect to communication and understanding, namely, the view that meaning resides in words and that it is transmitted from one language user to another in a conduit, as it were. In the second section, I refer to my own research illustrating the prevalence of the myth in question in a variety of domains, for instance, in politics and academia. I also refer briefly to my own empirical studies on the role that communicational and understanding problems play, in the opinion of the lay language user, in a variety of social contexts.
First language acquisition and teaching
Authors: Cruz-Ferreira Madalena
Published: December 2011

“First language acquisition” commonly means the acquisition of a single language in childhood, regardless of the number of languages in a child’s natural environment. Language acquisition is variously viewed as predetermined, wondrous, a source of concern, and as developing through formal processes. “First language teaching” concerns schooling in the language that is intended to become the child’s first (or “main”) one. Mainstream teaching practices similarly take languages as formal objects, focusing on literacy skills, so-called phonological awareness, and other teaching about the language. This article gives a first overview of folk beliefs associated with language acquisition and teaching, highlighting whether and how they can guide applied linguists’ concerns about child language development and early pedagogical practices.
That which We Call a Rose by any Other Name Would Sound as Sweet
Authors: McKenzie Robert M. , Osthus Dietmar
Published: December 2011

Folk perceptions of language diversity often differ from the criteria laid out by linguists and have particular implications for applied/sociolinguists since the collective identification of language diversity largely determines the ways in which individuals regard the categorisation of their own (and others) linguistic uses as belonging to a specific social and/or regional variety. Folk perceptions can thus help define speech communities as well as explain sociolinguistic other phenomena. This paper provides a critical analysis of the existing folk linguistic research into language variation in a number of different contexts: the UK, the USA, France and Japan. It is hoped that the information gained will help build up a more detailed sociolinguistic picture of the complex and often contradictory nature of lay individuals’ attitudes towards linguistic variation. In the final sections of the paper the authors argue for a greater deal of recognition within modern linguistics of the value of examining folk perceptions of language diversity.
Cultural mediation through translingual narrative
Authors: Wilson Rita
Published: December 2011

Translingual writers, in attempting to navigate between languages and the associated social contexts, bring both linguistic and cultural translation into play as processes fostering encounter and transformation. This paper considers the thematic function of translation within recent translingual narrative, where it appears both as a literarytoposand as an ideological subtext. It attempts to illustrate how, contrary to postcolonial writers whose narratives self-consciously engage with their own linguistic or cultural hybridity by thematizing the power relationships between different linguistic strands, the narratives of transnational/ translingual writers explore new identities by constructing new dialogic spaces in which language choice is located outside the oppositional model set up by the traditional binaries of postcolonial theorizing. Through a reading of the work of Amara Lakhous, a contemporary Italian writer, born and educated in Algiers and writing in both Arabic and Italian, it is argued that translingual works suggest an understanding of translation as not only something that happens after the story ends, but is a crucial part of the narrative itself; one that generates plot and meaning, and is indispensable to an understanding of the concrete processes of cultural translation that shape relationships, identities, and interactions globally.
Flow in translation
Authors: Mirlohi Mehdi , Egbert Joy , Ghonsooly Behzad
Published: December 2011

The study reported here examined the amount and quality of flow experienced by trainee translators while translating different text genres. Flow (Csikszentmihalyi 1975) is an optimal experience, characterized by intense focus, control, interest and skills-challenge balance that leads to enhanced performance on a task. Although investigated in areas such as professional sports, surgery, and music, Flow Theory has not yet been tested in the area of translation. This study aimed at identifying which discourse genre would induce most flow in trainee translators while translating. Fifty-six Iranian English Translation majors studying at the University of Kashan translated three 180-word texts of narrative, expository, and descriptive genres. After each translation, they responded to a Flow Perceptions Questionnaire (Egbert, 2003) in the Likert format to report their perceptions of flow. Using repeated measures ANOVA, the researchers investigated flow differences among genres. The results indicated that flow existed in the translation classroom and that there were significant differences in the flow scores engendered by different genres. To support the findings drawn from the numerical analysis, four participants, selected from the population of subjects from the first phase, were interviewed, and the analysis of the interviews generally corroborated the statistical findings.
Novel search method for the discovery of functional relationships
Authors: Ramírez Fidel , Lawyer Glenn , Albrecht Mario
Published: December 2011

Motivation: Numerous annotations are available that functionally characterize genes and proteins with regard to molecular process, cellular localization, tissue expression, protein domain composition, protein interaction, disease association and other properties. Searching this steadily growing amount of information can lead to the discovery of new biological relationships between genes and proteins. To facilitate the searches, methods are required that measure the annotation similarity of genes and proteins. However, most current similarity methods are focused only on annotations from the Gene Ontology (GO) and do not take other annotation sources into account.

Results: We introduce the new method BioSim that incorporates multiple sources of annotations to quantify the functional similarity of genes and proteins. We compared the performance of our method with four other well-known methods adapted to use multiple annotation sources. We evaluated the methods by searching for known functional relationships using annotations based only on GO or on our large data warehouse BioMyn. This warehouse integrates many diverse annotation sources of human genes and proteins. We observed that the search performance improved substantially for almost all methods when multiple annotation sources were included. In particular, our method outperformed the other methods in terms of recall and average precision.

Contact:  mario.albrecht@mpi-inf.mpg.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Selenium‐ and zinc‐deficient cardiomyopathy in human intestinal malabsorption: preliminary results of selenium/zinc infusion
Authors: Frustaci Andrea , Sabbioni Enrico , Fortaner Salvador , Farina Massimo , del Torchio Riccardo , Tafani Marco , Morgante Emanuela , Ciriolo Maria Rosa , Russo Matteo A. , Chimenti Cristina
Published: December 2011

Aims

Patients with intestinal malabsorption may develop cardiac dysfunction the origin of which is often unclear. We sought to investigate the pathogenesis of dilated cardiomyopathy in human malabsorption.

Methods and results

Eighteen patients with intestinal bypass as treatment for severe obesity and cardiomyopathy underwent endomyocardial biopsy. Biopsies were processed by histology, electron microscopy, polymerase chain reaction (PCR) for cardiotropic viruses, instrumental neutron activation analysis (INAA) of 33 myocardial trace elements, and assessment of glutathione peroxidase (GPX) activity and LC3‐II expression. Histology and electron microscopy showed hypertrophy/degeneration of cardiomyocytes with pronounced cell autophagy and high expression of LC3‐II. PCR was negative for viral genomes. INAA showed severe myocardial selenium (Se) and zinc (Zn) deficiency and reduced GPX activity vs. both patients with idiopathic dilated cardiomyopathy and normal controls. Se and Zn were added to antifailing heart therapy in 10 patients (group A1) agreeing to a control biopsy, and the response was compared with that of 8 patients (group A2) on supportive therapy alone. After 6 months, myocardial normalization of Se, Zn, LC3‐II, and GPX in group A1 was associated with recovery of cardiomyocyte degeneration and autophagy, and significant improvement in cardiac dimension and function, that remained unchanged in group A2.

Conclusion

A reversible Se‐ and Zn‐deficient cardiomyopathy may occur in patients with intestinal malabsorption. It is characterized by decline of myocardial antioxidant reserve, oxidative damage of cell membranes, and enhanced cell autophagy.
Variation in the Practice of Preoperative Medical Consultation for Major Elective Noncardiac Surgery
Authors: Wijeysundera Duminda N. , Austin Peter C. , Beattie W. Scott , Hux Janet E. , Laupacis Andreas
Published: December 2011

Background

Patients scheduled for major elective noncardiac surgery frequently undergo preoperative medical consultations. However, the factors that determine whether individuals undergo consultation and the extent of interhospital variation remain unclear.

Methods

The authors used population-based administrative databases to conduct a cohort study of patients, aged 40 yr or older, who underwent major elective noncardiac surgery in Ontario, Canada, between April 2004 and February 2009. Multilevel logistic regression models were used to identify patient- and hospital-level predictors of consultation.

Results

Within the cohort of 204,819 patients who underwent surgery at 79 hospitals, 38% (n = 77,965) underwent preoperative medical consultation. Although patient- and surgery-level factors did predict consultation use, they explained only 5.9% of variation in consultation rates. Differences in rates across hospitals were large (range, 10-897 per 1,000 procedures), were not explained by surgical procedure volume or hospital teaching status, and persisted after adjustment for patient- and surgery-level factors. The median odds of undergoing consultation were 3.51 times higher if the same patient had surgery at one randomly selected hospital as opposed to another.

Conclusions

One-third of surgical patients undergo preoperative medical consultation. Although patient- and surgery-level factors are weak predictors of consultation use, the individual hospital is the major determinant of whether patients undergo consultation. Additional research is needed to better understand the basis for this substantial interhospital variation and to determine which patients benefit most from preoperative consultation.
Deadly diving? Physiological and behavioural management of decompression stress in diving mammals
Authors: Hooker S. K. , Fahlman A. , Moore M. J. , Aguilar de Soto N. , Bernaldo de Quirós Y. , Brubakk A. O. , Costa D. P. , Costidis A. M. , Dennison S. , Falke K. J. , Fernandez A. , Ferrigno M. , Fitz-Clarke J. R. , Garner M. M. , Houser D. S. , Jepson P. D. , Ketten D. R. , Kvadsheim P. H. , Madsen P. T. , Pollock N. W. , Rotstein D. S. , Rowles T. K. , Simmons S. E. , Van Bonn W. , Weathersby P. K. , Weise M. J. , Williams T. M. , Tyack P. L.
Published: December 2011

Decompression sickness (DCS; ‘the bends’) is a disease associated with gas uptake at pressure. The basic pathology and cause are relatively well known to human divers. Breath-hold diving marine mammals were thought to be relatively immune to DCS owing to multiple anatomical, physiological and behavioural adaptations that reduce nitrogen gas (N2) loading during dives. However, recent observations have shown that gas bubbles may form and tissue injury may occur in marine mammals under certain circumstances. Gas kinetic models based on measured time-depth profiles further suggest the potential occurrence of high blood and tissue N2tensions. We review evidence for gas-bubble incidence in marine mammal tissues and discuss the theory behind gas loading and bubble formation. We suggest that diving mammals vary their physiological responses according to multiple stressors, and that the perspective on marine mammal diving physiology should change from simplyminimizing N2loadingtomanagement of the N2load. This suggests several avenues for further study, ranging from the effects of gas bubbles at molecular, cellular and organ function levels, to comparative studies relating the presence/absence of gas bubbles to diving behaviour. Technological advances in imaging and remote instrumentation are likely to advance this field in coming years.
Macellibacteroides fermentans gen. nov., sp. nov., a member of the family

Porphyromonadaceae

isolated from an upflow anaerobic filter treating abattoir wastewaters
Authors: Jabari Linda , Gannoun Hana , Cayol Jean-Luc , Hedi Abdeljabbar , Sakamoto Mitsuo , Falsen Enevold , Ohkuma Moriya , Hamdi Moktar , Fauque Guy , Ollivier Bernard , Fardeau Marie-Laure
Published: December 2011

A novel obligately anaerobic, non-spore-forming, rod-shaped mesophilic bacterium, which stained Gram-positive but showed the typical cell wall structure of Gram-negative bacteria, was isolated from an upflow anaerobic filter treating abattoir wastewaters in Tunisia. The strain, designated LIND7HT, grew at 20–45 °C (optimum 35–40 °C) and at pH 5.0–8.5 (optimum pH 6.5–7.5). It did not require NaCl for growth, but was able to grow in the presence of up to 2 % NaCl. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Strain LIND7HT used cellobiose, glucose, lactose, mannose, maltose, peptone, rhamnose, raffinose, sucrose and xylose as electron donors. The main fermentation products from glucose metabolism were lactate, acetate, butyrate and isobutyrate. The predominant cellular fatty acids were anteiso-C15 : 0, C15 : 0, C17 : 0 2-OH and a summed feature consisting of C18 : 2ω6,9c and/or anteiso-C18 : 0, and the major menaquinones were MK-9, MK-9(H2) and MK-10. The G+C content of the genomic DNA was 41.4 mol%. Although the closest phylogenetic relatives of strain LIND7HT were

Parabacteroides merdae

,

Parabacteroides goldsteinii

and

Parabacteroides gordonii

, analysis of the hsp60 gene sequence showed that strain LIND7HT was not a member of the genus

Parabacteroides

. On the basis of phylogenetic inference and phenotypic properties, strain LIND7HT ( = CCUG 60892T = DSM 23697T = JCM 16313T) is proposed as the type strain of a novel species in a new genus within the family

Porphyromonadaceae

, Macellibacteroides fermentans gen. nov., sp. nov.
Rhodovulum bhavnagarense sp. nov., a phototrophic alphaproteobacterium isolated from a pink pond
Authors: Srinivas A. , Rahul K. , Ramaprasad E. V. V. , Sasikala Ch. , Ramana Ch. V.
Published: December 2011

An oval to rod-shaped, Gram-stain-negative, phototrophic bacterium, strain JA738T, was isolated from a sediment sample collected from a pink pond. Strain JA738T was non-motile and had vesicular-type intracellular photosynthetic membranes. Bacteriochlorophyll a and carotenoids of the spheroidene series were present as the major photosynthetic pigments. Strain JA738T required thiamine and pantothenate for growth. The major cellular fatty acids were C18 : 1ω7c, C18 : 1ω5c, C18 : 0 and C18 : 1ω7c11-methyl; minor amounts of C10 : 0 3-OH and C16 : 0 were also present. The major quinone was Q-10 and major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and two unidentified sulfolipids (SL1–2). Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA738T clustered with species of the genus

Rhodovulum

in the class

Alphaproteobacteria

. Strain JA738T was most closely related to

Rhodovulum adriaticum

DSM 2781T (96.4 % 16S rRNA gene sequence similarity) and other members of the genus

Rhodovulum

(<96.1 %). On the basis of phenotypic and molecular genetic evidence, it is proposed that strain JA738T should be classified as a novel species of the genus

Rhodovulum

for which the name Rhodovulum bhavnagarense sp. nov. is proposed. The type strain is JA738T ( = DSM 24766T = KCTC 15110T).
The transcriptional coactivator TAZ regulates mesenchymal differentiation in malignant glioma
Authors: Bhat Krishna P.L. , Salazar Katrina L. , Balasubramaniyan Veerakumar , Wani Khalida , Heathcock Lindsey , Hollingsworth Faith , James Johanna D. , Gumin Joy , Diefes Kristin L. , Kim Se Hoon , Turski Alice , Azodi Yasaman , Yang Yuhui , Doucette Tiffany , Colman Howard , Sulman Erik P. , Lang Frederick F. , Rao Ganesh , Copray Sjef , Vaillant Brian D. , Aldape Kenneth D.
Published: December 2011

Recent molecular classification of glioblastoma (GBM) has shown that patients with a mesenchymal (MES) gene expression signature exhibit poor overall survival and treatment resistance. Using regulatory network analysis of available expression microarray data sets of GBM, including The Cancer Genome Atlas (TCGA), we identified thetranscriptional coactivator with PDZ-binding motif(TAZ), to be highly associated with the MES network.TAZexpression was lower in proneural (PN) GBMs and lower-grade gliomas, which correlated with CpG island hypermethylation of theTAZpromoter compared with MES GBMs. Silencing of TAZ in MES glioma stem cells (GSCs) decreased expression of MES markers, invasion, self-renewal, and tumor formation. Conversely, overexpression of TAZ in PN GSCs as well as murine neural stem cells (NSCs) induced MES marker expression and aberrant osteoblastic and chondrocytic differentiation in a TEAD-dependent fashion. Using chromatin immunoprecipitation (ChIP), we show that TAZ is directly recruited to a majority of MES gene promoters in a complex with TEAD2. The coexpression of TAZ, but not a mutated form of TAZ that lacks TEAD binding, with platelet-derived growth factor-B (PDGF-B) resulted in high-grade tumors with MES features in a murine model of glioma. Our studies uncover a direct role for TAZ and TEAD in driving the MES differentiation of malignant glioma.
A new ‘Linc’ between noncoding RNAs and blood development: Figure 1.
Authors: Paralkar Vikram R. , Weiss Mitchell J.
Published: December 2011

Long noncoding RNAs (lncRNAs) are a large and diverse class of functional RNAs that regulate important biological processes, including cell division, survival, and differentiation. In this issue of Genes & Development, Hu and colleagues (2573–2578) report the discovery of LincRNA erythroid prosurvival (LincRNA-EPS), a murine lncRNA that facilitates red blood cell formation (erythropoiesis) by suppressing apoptosis. This finding expands the repertoire of lncRNA functions and illustrates a novel genetic pathway that potentially can be exploited for treating anemias.
Cooperation between Polycomb and androgen receptor during oncogenic transformation
Authors: Zhao Jonathan C. , Yu Jianjun , Runkle Christine , Wu Longtao , Hu Ming , Wu Dayong , Liu Jun S. , Wang Qianben , Qin Zhaohui S. , Yu Jindan
Published: December 2011

Androgen receptor (AR) is a hormone-activated transcription factor that plays important roles in prostate development and function, as well as malignant transformation. The downstream pathways of AR, however, are incompletely understood. AR has been primarily known as a transcriptional activator inducing prostate-specific gene expression. Through integrative analysis of genome-wide AR occupancy and androgen-regulated gene expression, here we report AR as a globally acting transcriptional repressor. This repression is mediated by androgen-responsive elements (ARE) and dictated by Polycomb group protein EZH2 and repressive chromatin remodeling. In embryonic stem cells, AR-repressed genes are occupied by EZH2 and harbor bivalent H3K4me3 and H3K27me3 modifications that are characteristic of differentiation regulators, the silencing of which maintains the undifferentiated state. Concordantly, these genes are silenced in castration-resistant prostate cancer rendering a stem cell–like lack of differentiation and tumor progression. Collectively, our data reveal an unexpected role of AR as a transcriptional repressor inhibiting non-prostatic differentiation and, upon excessive signaling, resulting in cancerous dedifferentiation.
Copper Chaperone-Dependent and -Independent Activation of Three Copper-Zinc Superoxide Dismutase Homologs Localized in Different Cellular Compartments in Arabidopsis
Authors: Huang Chien-Hsun , Kuo Wen-Yu , Weiss Celeste , Jinn Tsung-Luo
Published: December 2011

Superoxide dismutases (SODs) are important antioxidant enzymes that catalyze the disproportionation of superoxide anion to oxygen and hydrogen peroxide to guard cells against superoxide toxicity. The major pathway for activation of copper/zinc SOD (CSD) involves a copper chaperone for SOD (CCS) and an additional minor CCS-independent pathway reported in mammals. We characterized the CCS-dependent and -independent activation pathways for three CSDs localized in different cellular compartments in Arabidopsis (Arabidopsis thaliana). The main activation pathway for CSD1 in the cytoplasm involved a CCS-dependent and -independent pathway, which was similar to that for human CSD. Activation of CSD2 in chloroplasts depended totally on CCS, similar to yeast (Saccharomyces cerevisiae) CSD. Peroxisome-localized CSD3 via a CCS-independent pathway was similar to nematode (Caenorhabditis elegans) CSD in retaining activity in the absence of CCS. In Arabidopsis, glutathione played a role in CCS-independent activation, as was reported in humans, but an additional factor was required. These findings reveal a highly specific and sophisticated regulation of CSD activation pathways in planta relative to other known CCS-independent activation.
The RootChip: An Integrated Microfluidic Chip for Plant Science
Authors: Grossmann Guido , Guo Woei-Jiun , Ehrhardt David W. , Frommer Wolf B. , Sit Rene V. , Quake Stephen R. , Meier Matthias
Published: December 2011

Studying development and physiology of growing roots is challenging due to limitations regarding cellular and subcellular analysis under controlled environmental conditions. We describe a microfluidic chip platform, called RootChip, that integrates live-cell imaging of growth and metabolism of Arabidopsis thaliana roots with rapid modulation of environmental conditions. The RootChip has separate chambers for individual regulation of the microenvironment of multiple roots from multiple seedlings in parallel. We demonstrate the utility of The RootChip by monitoring time-resolved growth and cytosolic sugar levels at subcellular resolution in plants by a genetically encoded fluorescence sensor for glucose and galactose. The RootChip can be modified for use with roots from other plant species by adapting the chamber geometry and facilitates the systematic analysis of root growth and metabolism from multiple seedlings, paving the way for large-scale phenotyping of root metabolism and signaling.
Different Gene Families inArabidopsis thalianaTransposed in Different Epochs and at Different Frequencies throughout the Rosids
Authors: Woodhouse Margaret R. , Tang Haibao , Freeling Michael
Published: December 2011

Certain types of gene families, such as those encoding most families of transcription factors, maintain their chromosomal syntenic positions throughout angiosperm evolutionary time. Other nonsyntenic gene families are prone to deletion, tandem duplication, and transposition. Here, we describe the chromosomal positional history of all genes in Arabidopsis thaliana throughout the rosid superorder. We introduce a public database where researchers can look up the positional history of their favorite A. thaliana gene or gene family. Finally, we show that specific gene families transposed at specific points in evolutionary time, particularly after whole-genome duplication events in the Brassicales, and suggest that genes in mobile gene families are under different selection pressure than syntenic genes.
A manual low-cost protein-crystallization plate jig forin situdiffraction in the home laboratory
Authors: Hargreaves David
Published: December 2011

A prototype jig to attach a protein crystallization plate to a standard X-ray goniometer has been designed and constructed in partnership with an engineering firm. This allows a low-cost implementation ofin situdiffraction using the available home-laboratory X-ray source.
Convergence acceleration in the polarization method for nonlinear periodic fields
Authors: Ciric Ioan R. , Hantila Florea I. , Maricaru Mihai
Published: December 2011

Purpose

The purpose of this paper is to present three novel techniques aimed at increasing the efficiency of the polarization fixed point method for the solution of nonlinear periodic field problems.

Design/methodology/approach

Firstly, the characteristic B‐M resulting from the constitutive relation B‐H is replaced by a relation between the components of the harmonics of the vectors B and M. Secondly, a dynamic overrelaxation method is implemented for the convergence acceleration of the iterative process involved. Thirdly, a modified dynamic overrelaxation method is proposed, where only the relation B‐M between the magnitudes of the field vectors is used.

Findings

By approximating the actual characteristic B‐M by the relation between the components of the harmonics of the vectors B and M, the amount of computation required for the field analysis is substantially reduced. The rate of convergence of the iterative process is increased by implementing the proposed dynamic overrelaxation technique, with the convergence being further accelerated by applying the modified dynamic overrelaxation presented. The memory space is also well reduced with respect to existent methods and accurate results for nonlinear fields in a real world structure are obtained utilizing a normal size processor notebook in a time of about one‐half of one minute when no induced currents are considered and of about one minute when eddy currents induced in solid ferromagnetic parts are also fully analyzed.

Originality/value

The originality of the novel techniques presented in the paper consists in the drastic approximations proposed for the material characteristics of the nonlinear ferromagnetic media in the analysis of periodic electromagnetic fields. These techniques are highly efficient and yield accurate numerical results.
Decomposition and regularization of nonlinear anisotropic curl‐curl DAEs
Authors: Clemens Markus , Scho¨ps Sebastian , De Gersem Herbert , Bartel Andreas
Published: December 2011

Purpose

The space discretization of eddy‐current problems in the magnetic vector potential formulation leads to a system of differential‐algebraic equations. They are typically time discretized by an implicit method. This requires the solution of large linear systems in the Newton iterations. The authors seek to speed up this procedure. In most relevant applications, several materials are non‐conducting and behave linearly, e.g. air and insulation materials. The corresponding matrix system parts remain constant but are repeatedly solved during Newton iterations and time‐stepping routines. The paper aims to exploit invariant matrix parts to accelerate the system solution.

Design/methodology/approach

Following the principle “reduce, reuse, recycle”, the paper proposes a Schur complement method to precompute a factorization of the linear parts. In 3D models this decomposition requires a regularization in non‐conductive regions. Therefore, the grad‐div regularization is revisited and tailored such that it takes anisotropies into account.

Findings

The reduced problem exhibits a decreased effective condition number. Thus, fewer preconditioned conjugate gradient iterations are necessary. Numerical examples show a decrease of the overall simulation time, if the step size is small enough. 3D simulations with large time step sizes might not benefit from this approach, because the better condition does not compensate for the computational costs of the direct solvers used for the Schur complement. The combination of the Schur approach with other more sophisticated preconditioners or multigrid solvers is subject to current research.

Originality/value

The Schur complement method is adapted for the eddy‐current problem. Therefore, a new partitioning approach into linear/non‐linear and static/dynamic domains is proposed. Furthermore, a new variant of the grad‐div gauging is introduced that allows for anisotropies and enables the Schur complement method in 3D.
Multi‐domain topology optimization with ant colony systems
Authors: Batista Lucas S. , Campelo Felipe , Guimarães Frederico G. , Ramírez Jaime A.
Published: December 2011

Purpose

The purpose of this paper is to present a graph representation of the design space that is suitable for the ant colony optimization (ACO) method in topology optimization (TO) problems.

Design/methodology/approach

The ACO is employed to obtain optimal routes in an equivalent graph representation of the discretized design space, with each route corresponding to a given distribution of material.

Findings

The problem associated with the maximization of the torque of a c‐core magnetic actuator is investigated, in which part of the yoke is discretized into a 16×8 grid and can assume three different materials: air, pure iron and a magnetic material.

Research limitations/implications

The results of the c‐core magnetic actuator problem, which are in agreement with literature available, show the adequacy of the proposed approach to TO of electromagnetic devices.

Practical implications

The graph representation of the design space permits the solution of topological design problems with an arbitrary number of materials.

Originality/value

The results illustrate the potential of the methodology in dealing with multi‐domain TO problems, and the possibility to extend the application to 3D problems.
Accelerated Markov chain Monte Carlo sampling in electrical capacitance tomography
Authors: Watzenig Daniel , Neumayer Markus , Fox Colin
Published: December 2011

Purpose

The purpose of this paper is to establish a cheap but accurate approximation of the forward map in electrical capacitance tomography in order to approach robust real‐time inversion in the framework of Bayesian statistics based on Markov chain Monte Carlo (MCMC) sampling.

Design/methodology/approach

Existing formulations and methods to reduce the order of the forward model with focus on electrical tomography are reviewed and compared. In this work, the problem of fast and robust estimation of shape and position of non‐conducting inclusions in an otherwise uniform background is considered. The boundary of the inclusion is represented implicitly using an appropriate interpolation strategy based on radial basis functions. The inverse problem is formulated as Bayesian inference, with MCMC sampling used to efficiently explore the posterior distribution. An affine approximation to the forward map built over the state space is introduced to significantly reduce the reconstruction time, while maintaining spatial accuracy. It is shown that the proposed approximation is unbiased and the variance of the introduced additional model error is even smaller than the measurement error of the tomography instrumentation. Numerical examples are presented, avoiding all inverse crimes.

Findings

Provides a consistent formulation of the affine approximation with application to imaging of binary mixtures in electrical tomography using MCMC sampling with Metropolis‐Hastings‐Green dynamics.

Practical implications

The proposed cheap approximation indicates that accurate real‐time inversion of capacitance data using statistical inversion is possible.

Originality/value

The proposed approach demonstrates that a tolerably small increase in posterior uncertainty of relevant parameters, e.g. inclusion area and contour shape, is traded for a huge reduction in computing time without introducing bias in estimates. Furthermore, the proposed framework – approximated forward map combined with statistical inversion – can be applied to all kinds of soft‐field tomography problems.
Adaptive strategies for fast frequency sweeps
Authors: Konkel Yves , Farle Ortwin , Köhler Andreas , Schultschik Alwin , Dyczij‐Edlinger Romanus
Published: December 2011

Purpose

The purpose of this paper is to compare competing adaptive strategies for fast frequency sweeps for driven and waveguide‐mode problems and give recommendations for practical implementations.

Design/methodology/approach

The paper first summarizes the theory of adaptive strategies for multi‐point (MP) sweeps and then evaluates the efficiency of such methods by means of numerical examples.

Findings

The authors' numerical tests give clear evidence for exponential convergence. In the driven case, highly resonant structures lead to pronounced pre‐asymptotic regions, followed by almost immediate convergence. Bisection and greedy point‐placement methods behave similarly. Incremental indicators are trivial to implement and perform similarly well as residual‐based methods.

Research limitations/implications

While the underlying reduction methods can be extended to any kind of affine parameter‐dependence, the numerical tests of this paper are for polynomial parameter‐dependence only.

Practical implications

The present paper describes self‐adaptive point‐placement methods and termination criteria to make MP frequency sweeps more efficient and fully automatic.

Originality/value

The paper provides a self‐adaptive strategy that is efficient and easy to implement. Moreover, it demonstrates that exponential convergence rates can be reached in practice.
Finite element analysis of electrical machines and transformers
Authors: Schmidt Erich
Published: December 2011

Purpose

The purpose of this paper is to discuss the state of the art of finite element analysis of electrical machines and transformers. Electrical machines and transformers are prime examples of multi‐physical systems involving electromagnetics, thermal issues, fluid dynamics, structural mechanics as well as acoustic phenomena. An accurate operational performance with different electrical and mechanical load situations is more and more evaluated using various numerical analysis methods including the couplings between the various physical domains. Therefore, numerical analysis methods are increasingly utilized not only for the verification of contractual values of existing machines, but also for the initial design process and for the design optimization of new machines.

Design/methodology/approach

The finite element method is the most powerful numerical analysis method for such multi‐physical devices. Since optimizations with respect to the overall performance and also the total manufacturing costs will become more important, the utilization of coupled multi‐physical analyses is of growing interest. For the fast and powerful application of this numerical analysis method, special attention should be given to the requirements of these electromagnetic devices.

Findings

Various methods of coupling the different physical domains of multi‐field finite element analyses are described. Thereby, weakly coupled cascade algorithms can be used with most problems in the field of electrical machines and transformers. On the other hand, a prime objective is to derive comprehensive, multi‐physical simulation models which are easily incorporated into design tools used by engineering professionals.

Research limitations/implications

The development of robust and reliable computer‐aided tools for an optimal design of multi‐physical devices such electrical machines and transformers has to argue about the best possible coupling of various simulation methods. Special consideration shall be paid more and more to a treatment of uncertainties and tolerances by means of statistical and probabilistic approaches.

Originality/value

The paper discusses state of the art of finite element analyses of the mentioned devices. Various optimized methods of modelling and analysis concerning the repetitive structure of electrical machines for electromagnetic analyses are compared with their advantages and drawbacks. Further, various methods of coupling the different domains of multi‐field analyses in case of electrical machines and transformers are described.
Stress zone imaging in steel plates of electrical machines
Authors: Neumayer Markus , Watzenig Daniel , Brandstätter Bernhard
Published: December 2011

Purpose

The purpose of this paper is to demonstrate an inverse problem approach for the determination of stress zones in steel plates of electrical machines. Steel plates of electrical machines suffer large mechanical stress by processes like cutting or punching during the fabrication. The mechanical stress has effects on the electrical properties of the steel, and thus on the losses of the machine.

Design/methodology/approach

In this paper, the authors present a sensor arrangement and an appropriate algorithm for determining the spatial permeability distribution in steel plates. The forward problem for stress zone imaging is explained and an appropriate numerical solution technique is proposed. Then an inverse problem formulation is introduced and the nature of the problem is analyzed.

Findings

Based on sensitivity analysis, different measurement procedures are compared and a measurement setup is suggested. Further the ill‐posed nature of the inverse problem is analyzed by the Picard condition.

Practical implications

Because of the increased losses due to stress zones, the quantification of stress effects is of interest to adjust the production process. Stress zone imaging is a first approach for the application of an imaging system to quantify these material defects.

Originality/value

This paper presents a simulation study about the applicability of an inverse problem for stress zone imaging and presents first reconstruction results. Further, the paper discusses several issues about stress zone imaging for the ongoing research.
I have seen the future and it sucks: reactionary reflections on reading, writing and research
Authors: Brown Stephen
Published: December 2011

Purpose

Reading and writing are crucial components of the research process and academic life as a whole. The purpose of this paper is to ask if conventional reading and writing practices are fit for marketing purpose.

Design/methodology/approach

The paper consists of an extended autobiographical essay, which reflects on the relevance of academic research output. The concerns of marketing thought leaders are also incorporated as required.

Findings

Academic articles are unreadable and unread. This is due to extant writing practices which result in characterless papers with little reader appeal.

Research limitations/implications

The best way forward is to look back at the approaches that prevailed prior to marketing's mid‐'60s “scientific revolution”. If adopted, they'll make learned research papers and monographs much more readable than they are at present.

Practical implications

If marketing academics embrace this paper's recommendations, their writings are more likely to be read and acted upon by practitioners, policy makers and other important stakeholders.

Originality/value

The style of the article is in keeping with the content. It demonstrates as well as describes.