bluuebunny/crossref_metadata_2025 huggingface dataset:
Phylogeography and evolutionary history of hepatitis B virus genotype F in Brazil
Authors: Mello Francisco CA , Araujo Oscar C , Lago Barbara V , Motta-Castro Ana Rita C , Moraes Marcia Terezinha B , Gomes Selma A , Bello Gonzalo , Araujo Natalia M
Published: July 2013

Background

Hepatitis B virus (HBV) genotype F (HBV/F) is considered to be indigenous to the Americas, but its emergence and spread in the continent remain unknown. Previously, only two HBV/F complete genome sequences from Brazil were available, limiting the contribution of Brazilian isolates to the phylogenetic studies of HBV/F. The present study was carried out to assess the proportion and geographic distributions of HBV/F subgenotypes in Brazil, to determine the full-length genomic sequences of HBV/F isolates from different Brazilian geographic regions, and to investigate the detailed evolutionary history and phylogeography of HBV/F in Brazil.

Methods

Complete HBV/F genomes isolated from 12 Brazilian patients, representing the HBV/F subgenotypes circulating in Brazil, were sequenced and analyzed together with sequences retrieved from GenBank, using the Bayesian coalescent and phylogeographic framework.

Results

Phylogenetic analysis using all Brazilian HBV/F S-gene sequences available in GenBank showed that HBV/F2a is found at higher frequencies countrywide and corresponds to all sequences isolated in the Brazilian Amazon Basin. In addition, the evolutionary analysis using complete genome sequences estimated an older median ancestral age for the Brazilian HBV/F2a compared to the Brazilian HBV/F1b and HBV/F4 subgenotypes, suggesting that HBV/F2a represents the original native HBV of Brazil. The phylogeographic patterns suggested a north-to-south flow of HBV/F2a from Venezuela to Brazil, whereas HBV/F1b and HBV/F4 strains appeared to have spread from Argentina to Brazil.

Conclusions

This study suggests a plausible route of introduction of HBV/F subgenotypes in Brazil and demonstrates the usefulness of recently developed computational tools for investigating the evolutionary history of HBV.
Characterization of recombinant human and bovine thyroid-stimulating hormone preparations by mass spectrometry and determination of their endotoxin content
Authors: Schaefer Sandra , Hassa Paul O , Sieber-Ruckstuhl Nadja S , Piechotta Marion , Reusch Claudia E , Roschitzki Bernd , Boretti Felicitas S
Published: July 2013

Background

The TSH stimulation test to confirm canine hypothyroidism is commonly performed using a recombinant human TSH (rhTSH), as up to date, canine TSH is not yet commercially available. Limiting factors for the use of rhTSH are its high costs and occasional difficulties in product availability. Less expensive bovine TSH preparations (bTSH) purified from bovine pituitary glands are readily commercially available. The aim of this study was to evaluate two different bTSH products as alternative to rhTSH using mass spectrometry.

Results

More than 50 proteins, including other pituitary hormones, bovine albumin, hemoglobin, and tissue proteins were identified in the bTSH preparations. In contrast, rhTSH proved to be a highly pure product. Significantly higher endotoxin levels could be detected in all bTSH products compared to the rhTSH.

Conclusions

Both bTSH products are crude mixtures and therefore not an acceptable alternative to rhTSH. Their use should be discouraged to prevent unintended side effects.
Reaction of 2,6-dichloroquinone-4-chloroimide (Gibbs reagent) with permethrin – an optical sensor for rapid detection of permethrin in treated wood
Authors: Arip Mohamad Nasir Mat , Heng Lee Yook , Ahmad Musa , Hasbullah Siti Aishah
Published: July 2013

Background

A novel optical sensor for the rapid and direct determination of permethrin preservatives in treated wood was designed. The optical sensor was fabricated from the immobilisation of 2,6-dichloro-p-benzoquinone-4-chloroimide (Gibbs reagent) in nafion/sol–gel hybrid film and the mode of detection was based on absorption spectrophotometry. Physical entrapment was employed as a method of immobilisation.

Results

The sensor gave a linear response range of permethrin between 2.56–383.00 μM with detection limit of 2.5 μM and demonstrated good repeatability with relative standard deviation (RSD) for 10 μM at 5.3%, 100 μM at 2.7%, and 200 μM at 1.8%. The response time of the sensor was 40 s with an optimum response at pH 11.

Conclusions

The sensor was useful for rapid screening of wood or treated wood products before detailed analysis using tedious procedure is performed. The validation study of the optical sensor against standard method HPLC successfully showed that the permethrin sensor tended to overestimate the permethrin concentration determined.
Effect of continuous compression and 30:2 cardiopulmonary resuscitation on cerebral microcirculation in a porcine model of cardiac arrest
Authors: Yang Lin , Wang Shuo , Li Chun-Sheng
Published: July 2013

Background

The effect of rescue breathing on neurologic prognosis after cardiopulmonary resuscitation (CPR) is controversial. Therefore, we investigated the cerebral microcirculatory and oxygen metabolism during continuous compression (CC) and 30:2 CPR (VC) in a porcine model of cardiac arrest to determine which is better for neurologic prognosis after CPR.

Methods

After 4 min of ventricular fibrillation, 20 pigs were randomised into two groups (n=10/group) receiving CC-CPR or VC-CPR. Cerebral oxygen metabolism and blood flow were measured continuously using laser Doppler flowmetry. Haemodynamic data were recorded at baseline and 5 min, 30 min, 2 h and 4 h after restoration of spontaneous circulation (ROSC).

Results

Compared with the VC group, the mean cortical cerebral blood flow was significantly higher at 5 min ROSC in the CC group (P<0.05), but the difference disappeared after that time point. Brain percutaneous oxygen partial pressures were higher, and brain percutaneous carbon dioxide partial pressures were lower, in the VC group from 30 min to 4 h after ROSC; significant differences were found between the two groups (P<0.05). However, no significant difference of the cerebral oxygen extraction fraction existed between the two groups.

Conclusions

Inconsistency of systemic circulation and cerebral microcirculation with regard to blood perfusion and oxygen metabolism is common after CPR. No significant differences in cortical blood flow and oxygen metabolism were found between the CC-CPR and VC-CPR groups after ROSC.
Metastatic MTLn3 and non-metastatic MTC adenocarcinoma cells can be differentiated by Pseudomonas aeruginosa
Authors: Novotny Matthew J. , Bridge Dacie R. , Martin Karen H. , Weed Scott A. , Wysolmerski Robert B. , Olson Joan C.
Published: July 2013

Cancer patients are known to be highly susceptible to Pseudomonas aeruginosa (Pa) infection, but it remains unknown whether alterations at the tumor cell level can contribute to infection. This study explored how cellular changes associated with tumor metastasis influence Pa infection using highly metastatic MTLn3 cells and non-metastatic MTC cells as cell culture models. MTLn3 cells were found to be more sensitive to Pa infection than MTC cells based on increased translocation of the type III secretion effector, ExoS, into MTLn3 cells. Subsequent studies found that higher levels of ExoS translocation into MTLn3 cells related to Pa entry and secretion of ExoS within MTLn3 cells, rather than conventional ExoS translocation by external Pa. ExoS includes both Rho GTPase activating protein (GAP) and ADP-ribosyltransferase (ADPRT) enzyme activities, and differences in MTLn3 and MTC cell responsiveness to ExoS were found to relate to the targeting of ExoS-GAP activity to Rho GTPases. MTLn3 cell migration is mediated by RhoA activation at the leading edge, and inhibition of RhoA activity decreased ExoS translocation into MTLn3 cells to levels similar to those of MTC cells. The ability of Pa to be internalized and transfer ExoS more efficiently in association with Rho activation during tumor metastasis confirms that alterations in cell migration that occur in conjunction with tumor metastasis contribute to Pa infection in cancer patients. This study also raises the possibility that Pa might serve as a biological tool for dissecting or detecting cellular alterations associated with tumor metastasis.
Wnt/β-catenin signalling regulates Sox17 expression and is essential for organizer and endoderm formation in the mouse
Authors: Engert Silvia , Burtscher Ingo , Liao W. Perry , Dulev Stanimir , Schotta Gunnar , Lickert Heiko
Published: July 2013

Several signalling cascades are implicated in the formation and patterning of the three principal germ layers, but their precise temporal-spatial mode of action in progenitor populations remains undefined. We have used conditional gene deletion of mouse β-catenin in Sox17-positive embryonic and extra-embryonic endoderm as well as vascular endothelial progenitors to address the function of canonical Wnt signalling in cell lineage formation and patterning. Conditional mutants fail to form anterior brain structures and exhibit posterior body axis truncations, whereas initial blood vessel formation appears normal. Tetraploid rescue experiments reveal that lack of β-catenin in the anterior visceral endoderm results in defects in head organizer formation. Sox17 lineage tracing in the definitive endoderm (DE) shows a cell-autonomous requirement for β-catenin in midgut and hindgut formation. Surprisingly, wild-type posterior visceral endoderm (PVE) in midgut- and hindgut-deficient tetraploid chimera rescues the posterior body axis truncation, indicating that the PVE is important for tail organizer formation. Upon loss of β-catenin in the visceral endoderm and DE lineages, but not in the vascular endothelial lineage, Sox17 expression is not maintained, suggesting downstream regulation by canonical Wnt signalling. Strikingly, Tcf4/β-catenin transactivation complexes accumulated on Sox17 cis-regulatory elements specifically upon endoderm induction in an embryonic stem cell differentiation system. Together, these results indicate that the Wnt/β-catenin signalling pathway regulates Sox17 expression for visceral endoderm pattering and DE formation and provide the first functional evidence that the PVE is necessary for gastrula organizer gene induction and posterior axis development.
Cdks, cyclins and CKIs: roles beyond cell cycle regulation
Authors: Lim Shuhui , Kaldis Philipp
Published: July 2013

Cyclin-dependent kinases (Cdks) are serine/threonine kinases and their catalytic activities are modulated by interactions with cyclins and Cdk inhibitors (CKIs). Close cooperation between this trio is necessary for ensuring orderly progression through the cell cycle. In addition to their well-established function in cell cycle control, it is becoming increasingly apparent that mammalian Cdks, cyclins and CKIs play indispensable roles in processes such as transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions and spermatogenesis. Even more remarkably, they can accomplish some of these tasks individually, without the need for Cdk/cyclin complex formation or kinase activity. In this Review, we discuss the latest revelations about Cdks, cyclins and CKIs with the goal of showcasing their functional diversity beyond cell cycle regulation and their impact on development and disease in mammals.
RhoA and Cdc42 are required in pre-migratory progenitors of the medial ganglionic eminence ventricular zone for proper cortical interneuron migration
Authors: Katayama Kei-ichi , Imai Fumiyasu , Campbell Kenneth , Lang Richard A. , Zheng Yi , Yoshida Yutaka
Published: July 2013

Cortical interneurons arise from the ganglionic eminences in the ventral telencephalon and migrate tangentially to the cortex. Although RhoA and Cdc42, members of the Rho family of small GTPases, have been implicated in regulating neuronal migration, their respective roles in the tangential migration of cortical interneurons remain unknown. Here we show that loss of RhoA and Cdc42 in the ventricular zone (VZ) of the medial ganglionic eminence (MGE) using Olig2-Cre mice causes moderate or severe defects in the migration of cortical interneurons, respectively. Furthermore, RhoA- or Cdc42-deleted MGE cells exhibit impaired migration in vitro. To determine whether RhoA and Cdc42 directly regulate the motility of cortical interneurons during migration, we deleted RhoA and Cdc42 in the subventricular zone (SVZ), where more fate-restricted progenitors are located within the ganglionic eminences, using Dlx5/6-Cre-ires-EGFP (Dlx5/6-CIE) mice. Deletion of either gene within the SVZ does not cause any obvious defects in cortical interneuron migration, indicating that cell motility is not dependent upon RhoA or Cdc42. These findings provide genetic evidence that RhoA and Cdc42 are required in progenitors of the MGE in the VZ, but not the SVZ, for proper cortical interneuron migration.
Netrin 1 contributes to vascular remodeling in the subventricular zone and promotes progenitor emigration after demyelination
Authors: Cayre Myriam , Courtès Sandrine , Martineau Fanny , Giordano Marilyn , Arnaud Karen , Zamaron Amandine , Durbec Pascale
Published: July 2013

Neural stem cells are maintained in the adult brain, sustaining structural and functional plasticity and to some extent participating in brain repair. A thorough understanding of the mechanisms and factors involved in endogenous stem/progenitor cell mobilization is a major challenge in the promotion of spontaneous brain repair. The main neural stem cell niche in the adult brain is the subventricular zone (SVZ). Following demyelination insults, SVZ-derived progenitors act in concert with oligodendrocyte precursors to repopulate the lesion and replace lost oligodendrocytes. Here, we showed robust vascular reactivity within the SVZ after focal demyelination of the corpus callosum in adult mice, together with a remarkable physical association between these vessels and neural progenitors exiting from their niche. Endogenous progenitor cell recruitment towards the lesion was significantly reduced by inhibiting post-lesional angiogenesis in the SVZ using anti-VEGF blocking antibody injections, suggesting a facilitating role of blood vessels for progenitor cell migration towards the lesion. We identified netrin 1 (NTN1) as a key factor upregulated within the SVZ after demyelination and involved in local angiogenesis and progenitor cell migration. Blocking NTN1 expression using a neutralizing antibody inhibited both lesion-induced vascular reactivity and progenitor cell recruitment at the lesion site. We propose a model in which SVZ progenitors respond to a demyelination lesion by NTN1 secretion that both directly promotes cell emigration and contributes to local angiogenesis, which in turn indirectly facilitates progenitor cell emigration from the niche.
Phagocytic receptor signaling regulates clathrin and epsin-mediated cytoskeletal remodeling during apoptotic cell engulfment inC. elegans
Authors: Shen Qian , He Bin , Lu Nan , Conradt Barbara , Grant Barth D. , Zhou Zheng
Published: July 2013

The engulfment and subsequent degradation of apoptotic cells by phagocytes is an evolutionarily conserved process that efficiently removes dying cells from animal bodies during development. Here, we report that clathrin heavy chain (CHC-1), a membrane coat protein well known for its role in receptor-mediated endocytosis, and its adaptor epsin (EPN-1) play crucial roles in removing apoptotic cells in Caenorhabditis elegans. Inactivating epn-1 or chc-1 disrupts engulfment by impairing actin polymerization. This defect is partially suppressed by inactivating UNC-60, a cofilin ortholog and actin server/depolymerization protein, further indicating that EPN-1 and CHC-1 regulate actin assembly during pseudopod extension. CHC-1 is enriched on extending pseudopods together with EPN-1, in an EPN-1-dependent manner. Epistasis analysis places epn-1 and chc-1 in the same cell-corpse engulfment pathway as ced-1, ced-6 and dyn-1. CED-1 signaling is necessary for the pseudopod enrichment of EPN-1 and CHC-1. CED-1, CED-6 and DYN-1, like EPN-1 and CHC-1, are essential for the assembly and stability of F-actin underneath pseudopods. We propose that in response to CED-1 signaling, CHC-1 is recruited to the phagocytic cup through EPN-1 and acts as a scaffold protein to organize actin remodeling. Our work reveals novel roles of clathrin and epsin in apoptotic-cell internalization, suggests a Hip1/R-independent mechanism linking clathrin to actin assembly, and ties the CED-1 pathway to cytoskeleton remodeling.
Jeb/Alk signalling regulates the Lame duck GLI family transcription factor in theDrosophilavisceral mesoderm
Authors: Popichenko Dmitry , Hugosson Fredrik , Sjögren Camilla , Dogru Murat , Yamazaki Yasuo , Wolfstetter Georg , Schönherr Christina , Fallah Mahsa , Hallberg Bengt , Nguyen Hanh , Palmer Ruth H.
Published: July 2013

The Jelly belly (Jeb)/Anaplastic Lymphoma Kinase (Alk) signalling pathway regulates myoblast fusion in the circular visceral mesoderm (VM) of Drosophila embryos via specification of founder cells. However, only a limited number of target molecules for this pathway are described. We have investigated the role of the Lame Duck (Lmd) transcription factor in VM development in relationship to Jeb/Alk signal transduction. We show that Alk signalling negatively regulates Lmd activity post-transcriptionally through the MEK/MAPK (ERK) cascade resulting in a relocalisation of Lmd protein from the nucleus to cytoplasm. It has previously been shown that downregulation of Lmd protein is necessary for the correct specification of founder cells. In the visceral mesoderm of lmd mutant embryos, fusion-competent myoblasts seem to be converted to ‘founder-like’ cells that are still able to build a gut musculature even in the absence of fusion. The ability of Alk signalling to downregulate Lmd protein requires the N-terminal 140 amino acids, as a Lmd141-866 mutant remains nuclear in the presence of active ALK and is able to drive robust expression of the Lmd downstream target Vrp1 in the developing VM. Our results suggest that Lmd is a target of Jeb/Alk signalling in the VM of Drosophila embryos.
Pdgfra protects against ethanol-induced craniofacial defects in a zebrafish model of FASD
Authors: McCarthy Neil , Wetherill Leah , Lovely C. Ben , Swartz Mary E. , Foroud Tatiana M. , Eberhart Johann K.
Published: July 2013

Human birth defects are highly variable and this phenotypic variability can be influenced by both the environment and genetics. However, the synergistic interactions between these two variables are not well understood. Fetal alcohol spectrum disorders (FASD) is the umbrella term used to describe the wide range of deleterious outcomes following prenatal alcohol exposure. Although FASD are caused by prenatal ethanol exposure, FASD are thought to be genetically modulated, although the genes regulating sensitivity to ethanol teratogenesis are largely unknown. To identify potential ethanol-sensitive genes, we tested five known craniofacial mutants for ethanol sensitivity: cyp26b1, gata3, pdgfra, smad5 and smoothened. We found that only platelet-derived growth factor receptor alpha (pdgfra) interacted with ethanol during zebrafish craniofacial development. Analysis of the PDGF family in a human FASD genome-wide dataset links PDGFRA to craniofacial phenotypes in FASD, prompting a mechanistic understanding of this interaction. In zebrafish, untreated pdgfra mutants have cleft palate due to defective neural crest cell migration, whereas pdgfra heterozygotes develop normally. Ethanol-exposed pdgfra mutants have profound craniofacial defects that include the loss of the palatal skeleton and hypoplasia of the pharyngeal skeleton. Furthermore, ethanol treatment revealed latent haploinsufficiency, causing palatal defects in ∼62% of pdgfra heterozygotes. Neural crest apoptosis partially underlies these ethanol-induced defects in pdgfra mutants, demonstrating a protective role for Pdgfra. This protective role is mediated by the PI3K/mTOR pathway. Collectively, our results suggest a model where combined genetic and environmental inhibition of PI3K/mTOR signaling leads to variability within FASD.
Boronic Acid-containing Ionic Liquid: Synthesis, Thermal Properties, and Conductivity
Authors: Yoshizawa-Fujita Masahiro , Kinoshita Tomoko , Ono Yuta , Takeoka Yuko , Rikukawa Masahiro
Published: July 2013

A new ionic liquid was prepared by introducing a boronic acid group to an imidazolium cation with a hydrophobic anion. The boronic acid-containing ionic liquid showed the best ionic conductivity of 6.5 × 10−4 S cm−1 at 50 °C, with a high lithium ion transference number of over 0.5, owing to the anion-trapping effect of the boronic acid group.
Effect of Surface Oxides and Steric Hindrance on the Adsorption of Dimethoxon from Chloroform on Activated Carbons
Authors: Yong-Ke Zhong , Ze-Li Yuan , Qing Wu , Xiao-Qiang Wan
Published: July 2013

Little information is available on the interaction between an adsorbate and the surface oxides of coal-based activated carbon (AC) in non-aqueous solutions. In this study, we investigated the effects of the type of surface oxide of ACs on the adsorption of dimethoxon, a model molecule with multiple groups, from chloroform. The surface oxides and the pores and/or carbon surface of ACs were found to adsorb dimethoxon in accordance with the Langmuir isotherm, with a linear correlation between the surface oxides and adsorbed dimethoxon (R2 ≈ 0.95). The interaction between ACs and dimethoxon was further investigated by replacing the adsorbed dimethoxon with compounds containing different substituent groups. At the same amount of the compound added, the amount of dimethoxon is replaced in the following order: butanoic acid > butanol > butanone > ethyl acetate. This finding indicates that both the type of oxide and steric hindrance are important for an AC to adsorb an adsorbate or for a compound itself to replace the dimethoxon adsorbed onto ACs. The results also showed that dimethoxon adsorbed on the surface oxides may be displaced, whereas those adsorbed in the pores, carbon surface of ACs or both cannot be displaced by those compounds.
Shape-Selective Adsorption of Substituted Aniline Pollutants from Wastewater
Authors: Albayati Talib M. , Doyle Aidan M.
Published: July 2013

ZSM-5 zeolite was used to treat wastewater containing aniline, 2-nitroaniline (2-NA), 3-nitroaniline (3-NA) and 4-nitroaniline (4-NA). Each molecule was removed from aqueous solution by Type I Langmuir adsorption onto ZSM-5. The quantities adsorbed varied greatly due to their shape-selective adsorption within the pores of ZSM-5. Aniline and 4-NA had maximum adsorption amounts of 161 and 265 mg g−1, respectively, while the maximum amounts of 3-NA and 2-NA were 94.3 and 37.2 mg g−1, corresponding to reductions of 64% and 86%, respectively, relative to 4-NA. This outcome was caused by the increase in the effective diameter for adsorption when the nitro group was located at the 2- and 3- positions of the molecule. This significantly reduced their ability to enter into, and diffuse through, the pores of ZSM-5. These findings underpin the importance of choosing the correct substrate when using such materials for water purification.
A Dynamic, Coupled Thermal Reservoir Approach to Atmospheric Energy Transfer Part I: Concepts
Authors: Clark Roy
Published: July 2013

A dynamic, coupled thermal reservoir description of the Earth's atmospheric energy transfer processes is presented. Solar heat is stored and released by four coupled reservoirs, the land, the oceans and the upper and lower troposphere. In addition to the temperature, there are three other important parameters need to be considered. The first is the thermal gradient, the second is the interaction length and the third is the time delay or phase shift between the incident flux and reservoir thermal response. The Earth's climate is stabilized by the heat stored in these thermal reservoirs, particularly the oceans and the lower troposphere up to 2 km. Almost all of the downward long wave infrared (LWIR) flux reaching the surface originates in the lower troposphere. The dominant energy transfer process within the troposphere is moist convection. At night, the lower troposphere acts as a thermal blanket that slows the surface cooling. The upper troposphere cools continuously by LWIR emission to space. A change in temperature requires a change in the heat stored in the reservoir that has to be calculated using the heat capacity and the time dependent flux balance. The LWIR flux cannot be separated and used to define a change in ‘average surface temperature’ using blackbody theory.
Exploring Urban Space
Authors: Leidi Michele , Schlüter Arno
Published: July 2013

This paper proposes a set of new analytic and visualization methods for conceptual design in the urban context. The methodology is based on the discretization of the urban site into a volumetric grid of points. For each of these points, different physical properties such as solar radiation, airflow, and visibility are computed. Subsequently interactive visualization techniques allow the observation of the site at a volumetric, directional and dynamic level, making visible information that is typically invisible. Several case-studies demonstrate how this allows to generate suggestions, for example, for the definition of the form of a building or for the rationalization of its surfaces. This approach aims at developing a conceptual design process that allows the fusion of active technologies, passive methods, and expressive aspects, in cohesive concepts able to embrace and exploit the diversities of an urban site.
Prototyping of an Adaptive Structure based on Physical Conditions
Authors: Kontovourkis Odysseas , Phocas Marios C. , Tryfonos George
Published: July 2013

Latest advances in digital architectural design enable applications of computation and fabrication strategies for the development of adaptive mechanisms. Adaptive design processes, influenced by environmental and human related conditions, are only developed partially with regard to the design, fabrication, and multi-objective performance based context. The current paper proposes an adaptive design process that investigates the design of a kinetic structure emphasizing material behaviour, embedded technology and computation. In parallel, it allows design proposals to adapt or transform with regard to geometrical configuration and structural behaviour according to external and internal influences. An adaptive hybrid structure is developed at digital and physical prototype level, where its behaviour is examined in real time under the influence of physical conditions. The development is based on a holistic design approach driven by environmental and human activity related conditions, while focusing on the application of elastic materials and embedded technology.
Transformative Solar Panels: A Multidisciplinary Approach
Authors: Sharif Shani , Gentry T. Russell , Yen Jeannette , Goodman Joseph N.
Published: July 2013

This paper focuses on the applications of geometrically transformable and expandable structures with deployed “energy production” mode and retracted “wind shedding” mode to replace the fixed photovoltaic (PV) panels and racking systems currently used in buildings rooftop installations. The significance of this expandable geometric system relies on its embedded motion grammar, i.e. rotation and translation transformations, in the system. The research draws inspiration from reconfiguration of compound tree leaves in nature, and addresses issues of redesign and modeling challenges that led to digital fabrication of the prototype. Finally, the research studies the development of a multidisciplinary research from the distributed cognition point of view, and emphasizes on the role of an iterative creation, sharing and reflection method for the development of a common ground for a successful collaboration.
Integrating Physical and Digital Assemblies
Authors: Zarzycki Andrzej
Published: July 2013

Computer-based tools have changed the focus and modes of design thinking in architecture. While often criticized for its overemphasis on formal expressions and its pursuit of the spectacular, digital creativity has begun to take into account a multiplicity of design factors that define architecture. These factors relate to performance simulation and analysis, constructability, and building information modeling (BIM). This paper discusses the use of physical and digital mock-ups in the context of building technology courses. It uses these mock-ups as an important vehicle that provides students with a feedback mechanism regarding often digitally idealized creative thinking.
Nanotechnology and medical devices: Risk, regulation and ‘meta’ registration
Authors: Grange Simon , Chettiar Kris , Arestu Mateen , Pilarski Patrick , Smitham Peter , Loizidou Marilena , Jell Gavin
Published: July 2013

A new approach to risk assessment for nanotechnology in healthcare includes the mapping of particles to risk profiles and the potential channels for the collection of relevant information. This relates assay type to processes probed and the recognition of the relevance of this to particle pathways. It is only by ensuring the sound regulation of this throughout the ‘life cycle’ of translational research and development, which we can ensure the true provenance of materials that we intend to use in the clinical environment.
Illumination intensity changes of side emitting optical fibers
Authors: Křemenáková Dana , Meryová Barbora , Militký Jiří , Lédl Vít
Published: July 2013

The main aim of this work is evaluation of side emitting plastic optical fibers (POF) illumination intensity changes in dependence on the distance from light source. Illumination intensity is measured along straight and bent fibers. The special devices for these measurements realization are described. The dependence of light intensity on the distance from light source for straight optical fibers is expressed by the exponential type model with two parameters, i.e. illumination intensity at the input into fiber and fiber attenuation factor. Preliminary results of measurement of light intensity in bent state are discussed. Influence of ratio between fiber diameter and bending cylinder diameter on the illumination intensity changes is presented.
Energy efficient optimization of wireless embedded sensor networks
Authors: Assaf Mansour , Khan Salema , Das Sunil , Biswas Satyendra
Published: July 2013

The energy optimization techniques developed for conventional ad hoc networks do not appropriately address the unique features of the wireless embedded sensor networks (WESNs). In the WESN environment, only reducing the overall energy consumption is not considered enough to maximize the life span of the entire network, but maintaining full network connectivity for a sufficiently long period of time is also an important design goal due to the energy constraints of each node. The wireless radio is a major energy user and is often the focus of energy conservation mechanisms, since the nodes communicate in a shared medium (air interface). The medium access control (MAC) layer of the communication protocol stack arbitrates access to the communications link by manipulating the sleep, listen, transmit, and receive states of the radio transceivers. The bursty traffic networks experience long periods of inactivity interrupted by unplanned and often short lived periods of high traffic loads. Currently available MAC protocols cannot meet application fidelity requirements of the bursty traffic networks since they are designed either for networks with periodic traffic or are not sufficiently traffic-adaptive, thereby introducing large multi-hop latency delays to realize network connectivity, overprovision during light traffic conditions, and slow ramp up at the initiation of a high traffic episode. This paper presents enhancements made to the energy efficient MAC protocol which is especially designed for the bursty traffic networks and in the process targets some available communication techniques used in the WESNs for discussion and comparison.
Adaptability of the nociceptive withdrawal reflex
Authors: Eckert Nathan , Riley Zachary A
Published: July 2013

The nociceptive withdrawal reflex is a protective mechanism to mediate interactions within a potentially dangerous environment. The reflex is formed by action-based sensory encoding during the early post-natal developmental period, and it is unknown if the protective motor function of the nociceptive withdrawal reflex in the human upper-limb is adaptable based on the configuration of the arm or if it can be modified by short-term practice of a similar or opposing motor action. In the present study, nociceptive withdrawal reflexes were evoked by a brief train of electrical stimuli applied to digit II, 1) in five different static arm positions and, 2) before and after motor practice that was opposite (EXT) or similar (FLEX) to the stereotyped withdrawal response, in 10 individuals. Withdrawal responses were quantified by the electromyography (EMG) reflex response in several upper limb muscles, and by the forces and moments recorded at the wrist. EMG onset latencies and response amplitudes were not significantly different across the arm positions or between the EXT and FLEX practice conditions, and the general direction of the withdrawal response was similar across arm positions. In addition, the force vectors were not different after practice in either the practice condition or between EXT and FLEX conditions. We conclude the withdrawal response is insensitive to changes in elbow or shoulder joint angles as well as remaining resistant to short-term adaptations from the practice of motor actions, resulting in a generalized limb withdrawal in each case. It is further hypothesized that the multisensory feedback is weighted differently in each arm position, but integrated to achieve a similar withdrawal response to safeguard against erroneous motor responses that could cause further harm. The results remain consistent with the concept that nociceptive withdrawal reflexes are shaped through long-term and not short-term action based sensory encoding.
News values, cultural proximity and cross-cultural media framing: How western and Muslim media covered Darfur
Authors: Galander Mahmoud M.
Published: July 2013

This article is an academic investigation of the burgeoning trend of cross-cultural transfer of images within the current global communication scene, in which a dominant technology is transcending political borders and geographical barriers, and threatening to create a global audience with a unified public opinion. News values, sensationalism and cross-cultural framing of news are three constructs pertinent to the investigation of the Darfur coverage in the international and Muslim media.

The article compares western media coverage and frames of the Darfur crisis with the coverage and frames present in two newspapers from the Muslim world. It tests the hypothesis that, in the absence of Islamic proximity as a news value, sensationalism-driven western news sources continue to dominate the news scene and, as a result, pass the negative characterization of Islam and Muslims to the Muslim world through a process of cross-cultural framing.
Decoding the Darfur conflict: Media framing of a complex humanitarian crisis
Authors: Taha Mustafa
Published: July 2013

This study uses frame analysis to examine how the New York Times framed the conflict in the Sudanese region of Darfur. A qualitative content analysis of the New York Times editorials (52 editorials) between 2003 and 2008 reveals a simplistic and reductionist framing of the conflict. Most of the New York Times’ depictions framed the conflict as an ethnic strife between ‘Arab’ invaders and ‘African’ victims. The New York Times blamed ‘the Arab-dominated’ Sudanese government for backing the Janjaweed (local Arab militia), called for more sanctions against the Sudanese government and demanded the bringing of war criminals to the International Criminal Court (ICC). To its credit, the New York Times highlighted vital humanitarian aspects of the conflict, yet failed to recognize its local intricacies and root causes. The author argues that the only viable solution to the conflict in Darfur will be a fair and equitable negotiated peace settlement between the Sudanese parties to the conflict.
Solidarity – rasa/autobiography – abhinaya: South Asian tactics for performing queerness
Authors: Chatterjee Sandra , Lee Cynthia Ling
Published: July 2013

This article examines the work of D’Lo, a Sri Lankan-transgender-hip hop performance artist, and the Post Natyam Collective, a transnational coalition that develops critical and creative approaches to South Asian dance. The works utilize two strategies for performing queerness in relation to South Asian cultural practices: (1) autobiographic performance art rooted in identity politics and (2) the South Asian technique of abhinaya. These strategies use different modes of identification and audience–performer relationships. Autobiographical solo performance creates solidarity through shared identity or alliances between performer and audience. Abhinaya evokes pleasure and sensuality in multiple, ambiguous ways towards the goal of evoking rasa, ideally the audience’s experience of emotional–spiritual transcendence. We investigate tactical crossovers between the strategies of autobiography and abhinaya in D’Lo’s and Post Natyam’s work: how do they interact, where might they exclude each other, and what kind of performance of queerness emerges through their interplay?
Dancing Krishna in the suburbs: Kinaesthetics in the South Asian American diaspora
Authors: Devarajan Arthi
Published: July 2013

This article explores kinaesthesia as a central aspect of religious pedagogy in a transnational Hindu community, through ethnographic observation of American practitioners of Bharatanatyam (classical Indian dance).1 The Natyanjali School of Dance (Andover, Massachusetts, United States) is a small, multigenerational community, comprised of dance teacher Jeyanthi Ghatraju, a group of South Indian first-generation immigrant IT professionals, and their American-born children. Through Bharatanatyam, pedagogical practices of physical training, repetition and constructions of body comportment, students learn South Asian languages, culture and Hindu religious narratives. Additionally, they absorb practices of social organization and moral knowledge through interactions with their teacher, elders and peers. Although studies of kinaesthesia attend to the physical body and its faculties of movement, sense, socialization and cognitive knowledge, the processes by which kinaesthetics inform the construction of religious experience, value, belief and identity remain relatively unexplored. This article examines the construction of Hindu and Indian identity, personal religiosity and morality, through the kinaesthetic pedagogies of basic step (adavu) repetition, the embodied and discursive pedagogies of dramatic gestural narration of sacred stories (natya), and the interpretive and devotional conjuring of expression (abhinaya) inherent in Bharatanatyam.
Imagining O encountering India: Recounting an embodied experience
Authors: Mitchell Roanna , Pakula Pablo
Published: July 2013

In February 2012, Richard Schechner’s performance-installation Imagining O travelled from its original place of creation in Canterbury (UK) to the International Theatre Festival of Kerala in Thrissur (India). Imagining O is an immersive and participatory experience that brings together voices of Shakespeare’s women and Pauline Reage’s classic French erotic novel The Story of O. This performance report explores the encounter of a primarily European company with the bodies/gazes of an Indian audience, and their role as spectators in shaping the living organism of the performance. Taking a dialogic structure, it exists in the space between two authors’ voices and experiences — Roanna Mitchell as movement director, Dr Pablo Pakula as performer – mirroring the production’s decentred nature and its refusal of an objective standpoint.
Performing agency: Body learning, Forum theatre and interactivity as democratic strategy
Authors: Yarrow Ralph
Published: July 2013

This article looks at how applications of Forum theatre process and related approaches in India may operate in terms of activation of particular modes of learning centred in the body. It discusses the body: as context (individual and collective, embedded in social, political, physical and emotional practices); with reference to process (activation, multiplication of kinds of knowing through theatre work); as extended beyond everyday operation and beyond the individual/egoic towards collective experience and action, including co-creativity and ‘rational collective action’. The article explores the operation of forms of embodied learning in Forum practice, with particular reference to the work of Jana Sanskriti, in India.
Book Review
Authors: Padden Mary
Published: July 2013

A History of the Jana Natya Manch: Plays for the People, Arjun Ghosh (2012) London and New Delhi: SAGE Publications, xx+293 pp., Hardback, Rs 695.00
The evolution of the local role(s) of the university in a low-tech region
Authors: Ortega-Colomer Francisco Javier
Published: July 2013

The present case study addresses the case of a geographical area neglected by most of the literature about the changing role of Higher Education Institutions (HEIs): the low-tech contexts. This literature has traditionally exhibited two primary aspects. First, a focus on success stories such as entrepreneurial universities located in high-tech regions (e.g. Silicon Valley). Second, it reveals an inclination towards an evolution from ivory towers to entrepreneurial universities. The article argues that this oversimplification does not apply exactly to some environments where the HEIs have maintained links with industry since their inception. The purpose is to demonstrate HEIs’ relevance in low-tech contexts with a pre-eminence of small and medium enterprises by taking a historical and qualitative perspective.
Supercuspidal part of the mod l cohomology of
GU(1,n - 1)-Shimura varieties
Authors: Shin Sug Woo
Published: July 2013

Let l be a prime. In this paper we are concerned with GU(1,n - 1)-type Shimura varieties with arbitrary level structure at l and investigate the part of the cohomology on which G(ℚ
p
) acts through mod l supercuspidal representations, where
p ≠ l is any prime such that G(ℚ
p
) is a general linear group.
The main theorem establishes the mod l analogue of the local-global compatibility. Our theorem also encodes a global
mod l Jacquet–Langlands correspondence in that the cohomology is described in terms of
mod l automorphic forms on some compact inner form of G.
Prediction of spontaneous preterm labour in at-risk pregnant women
Authors: Liong Stella , Di Quinzio Megan K W , Fleming Gabrielle , Permezel Michael , Rice Gregory E , Georgiou Harry M
Published: July 2013

The ability to recognise women who are at-risk of preterm labour (PTL) is often difficult. Over 50% of women who are identified with factors associated with an increased risk of preterm birth will ultimately deliver at term. The cervicovaginal fluid (CVF) comprises a range of proteins secreted by gestational tissues, making it an ideal candidate for the screening of differentially expressed proteins associated with PTL. CVF samples were collected from at-risk asymptomatic women. Two-dimensional gel electrophoresis techniques were used to examine the CVF proteome of women who spontaneously delivered preterm 11–22 days later compared with gestation-matched women who delivered at term. Five candidate biomarkers were selected for further validation in a larger independent cohort of asymptomatic women. Thioredoxin (TXN) and interleukin 1 receptor antagonist (IL1RN) concentrations in the CVF were found to be significantly reduced up to 90 days prior to spontaneous PTL compared with women who subsequently delivered at term. TXN was able to predict spontaneous PTL within 28 days after sampling with a high positive predictive value (PPV) and negative predictive value (NPV) of 75.0% and 96.4% respectively. IL1RN also showed comparable PPV and NPV of 72.7% and 95.7% respectively. The discovery of these differentially expressed proteins may assist in the development of a new predictive bedside test in identifying asymptomatic women who have an increased risk of spontaneous PTL.
Correlation Between Mutation Rate and Genome Size in Riboviruses: Mutation Rate of Bacteriophage Qβ
Authors: Bradwell Katie , Combe Marine , Domingo-Calap Pilar , Sanjuán Rafael
Published: July 2013

Genome sizes and mutation rates covary across all domains of life. In unicellular organisms and DNA viruses, they show an inverse relationship known as Drake’s rule. However, it is still unclear whether a similar relationship exists between genome sizes and mutation rates in RNA genomes. Coronaviruses, the RNA viruses with the largest genomes (∼30 kb), encode a proofreading 3′ exonuclease that allows them to increase replication fidelity. However, it is unknown whether, conversely, the RNA viruses with the smallest genomes tend to show particularly high mutation rates. To test this, we measured the mutation rate of bacteriophage Qβ, a 4.2-kb levivirus. Amber reversion-based Luria–Delbrück fluctuation tests combined with mutant sequencing gave an estimate of 1.4 × 10−4 substitutions per nucleotide per round of copying, the highest mutation rate reported for any virus using this method. This estimate was confirmed using a direct plaque sequencing approach and after reanalysis of previously published estimates for this phage. Comparison with other riboviruses (all RNA viruses except retroviruses) provided statistical support for a negative correlation between mutation rates and genome sizes. We suggest that the mutation rates of RNA viruses might be optimized for maximal adaptability and that the value of this optimum may in turn depend inversely on genome size.
Estimating Overweight Risk in Childhood From Predictors During Infancy
Authors: Weng Stephen F. , Redsell Sarah A. , Nathan Dilip , Swift Judy A. , Yang Min , Glazebrook Cris
Published: July 2013

OBJECTIVE:

The aim of this study was to develop and validate a risk score algorithm for childhood overweight based on a prediction model in infants.

METHODS:

Analysis was conducted by using the UK Millennium Cohort Study. The cohort was divided randomly by using 80% of the sample for derivation of the risk algorithm and 20% of the sample for validation. Stepwise logistic regression determined a prediction model for childhood overweight at 3 years defined by the International Obesity Task Force criteria. Predictive metrics R2, area under the receiver operating curve (AUROC), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated.

RESULTS:

Seven predictors were found to be significantly associated with overweight at 3 years in a mutually adjusted predictor model: gender, birth weight, weight gain, maternal prepregnancy BMI, paternal BMI, maternal smoking in pregnancy, and breastfeeding status. Risk scores ranged from 0 to 59 corresponding to a predicted risk from 4.1% to 73.8%. The model revealed moderately good predictive ability in both the derivation cohort (R2 = 0.92, AUROC = 0.721, sensitivity = 0.699, specificity = 0.679, PPV = 38%, NPV = 87%) and validation cohort (R2 = 0.84, AUROC = 0.755, sensitivity = 0.769, specificity = 0.665, PPV = 37%, NPV = 89%).

CONCLUSIONS:

Using a prediction algorithm to identify at-risk infants could reduce levels of child overweight and obesity by enabling health professionals to target prevention more effectively. Further research needs to evaluate the clinical validity, feasibility, and acceptability of communicating this risk.