bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling disease progression using dynamics of pathway connectivity
Authors: Ma Xiaoke , Gao Long , Tan Kai
Published: April 2014

Motivation: Disease progression is driven by dynamic changes in both the activity and connectivity of molecular pathways. Understanding these dynamic events is critical for disease prognosis and effective treatment. Compared with activity dynamics, connectivity dynamics is poorly explored.

Results: We describe the M-module algorithm to identify gene modules with common members but varied connectivity across multiple gene co-expression networks (aka M-modules). We introduce a novel metric to capture the connectivity dynamics of an entire M-module. We find that M-modules with dynamic connectivity have distinct topological and biochemical properties compared with static M-modules and hub genes. We demonstrate that incorporation of module connectivity dynamics significantly improves disease stage prediction. We identify different sets of M-modules that are important for specific disease stage transitions and offer new insights into the molecular events underlying disease progression. Besides modeling disease progression, the algorithm and metric introduced here are broadly applicable to modeling dynamics of molecular pathways.

Availability and implementation:  M-module is implemented in R. The source code is freely available at http://www.healthcare.uiowa.edu/labs/tan/M-module.zip.

Contact:  kai-tan@uiowa.edu

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Residues of Intertwining Operators for U(3,3) and Base Change
Authors: Cai Li , Xu Bin
Published: April 2014

Let F be a p-adic local field with characteristic 0 and E/F a quadratic extension. Let σ=πG⊗πH be a supercuspidal representation of GL2(E)×UE/F(1,1) with πG conjugate self-dual. In this paper, we use a local approach developed by Shahidi to study the residue of the standard intertwining operator on the parabolic induced representation from σ to the quasi-split unitary group UE/F(3,3) at s=0, and show that if πG is a standard base change from UE/F(1,1), then the residue at s=0 is nonzero if and only if πG is the standard base change of πH.
Vega's hot dust from icy planetesimals scattered inwards by an outward-migrating planetary system
Authors: Raymond Sean N. , Bonsor Amy
Published: April 2014

Vega has been shown to host multiple dust populations, including both hot exozodiacal dust at sub-au radii and a cold debris disc extending beyond 100 au. We use dynamical simulations to show how Vega's hot dust can be created by long-range gravitational scattering of planetesimals from its cold outer regions. Planetesimals are scattered progressively inwards by a system of 5–7 planets from 30 to 60 au to very close-in. In successful simulations, the outermost planets are typically Neptune mass. The back-reaction of planetesimal scattering causes these planets to migrate outwards and continually interact with fresh planetesimals, replenishing the source of scattered bodies. The most favourable cases for producing Vega's exozodi have negative radial mass gradients, with sub-Saturn- to Jupiter-mass inner planets at 5–10 au and outer planets of 2.5 − 20 M⊕ . The mechanism fails if a Jupiter-sized planet exists beyond ∼15 au because the planet preferentially ejects planetesimals before they can reach the inner system. Direct-imaging planet searches can therefore directly test this mechanism.
Identification of non-coding RNAs with a new composite feature in the Hybrid Random Forest Ensemble algorithm
Authors: Lertampaiporn Supatcha , Thammarongtham Chinae , Nukoolkit Chakarida , Kaewkamnerdpong Boonserm , Ruengjitchatchawalya Marasri
Published: April 2014

To identify non-coding RNA (ncRNA) signals within genomic regions, a classification tool was developed based on a hybrid random forest (RF) with a logistic regression model to efficiently discriminate short ncRNA sequences as well as long complex ncRNA sequences. This RF-based classifier was trained on a well-balanced dataset with a discriminative set of features and achieved an accuracy, sensitivity and specificity of 92.11%, 90.7% and 93.5%, respectively. The selected feature set includes a new proposed feature, SCORE. This feature is generated based on a logistic regression function that combines five significant features—structure, sequence, modularity, structural robustness and coding potential—to enable improved characterization of long ncRNA (lncRNA) elements. The use of SCORE improved the performance of the RF-based classifier in the identification of Rfam lncRNA families. A genome-wide ncRNA classification framework was applied to a wide variety of organisms, with an emphasis on those of economic, social, public health, environmental and agricultural significance, such as various bacteria genomes, the Arthrospira (Spirulina) genome, and rice and human genomic regions. Our framework was able to identify known ncRNAs with sensitivities of greater than 90% and 77.7% for prokaryotic and eukaryotic sequences, respectively. Our classifier is available at http://ncrna-pred.com/HLRF.htm.
Regulation of the biosynthesis of thiopeptide antibiotic cyclothiazomycin by the transcriptional regulator SHJG8833 in Streptomyces hygroscopicus 5008
Authors: Zhang Peipei , Wu Hang , Chen Xiu-Lan , Deng Zixin , Bai Linquan , Pang Xiuhua
Published: April 2014

Cyclothiazomycin is a member of the thiopeptide antibiotics, which are usually complicated derivatives of ribosomally synthesized peptides. A gene cluster containing 12 ORFs identical to thecltcluster encoding cyclothiazomycin fromStreptomyces hygroscopicus10-22 was revealed by genome sequencing inS. hygroscopicus5008. GenesSHJG8833andSHJG8837of the cluster and flanking geneSHJG8838were predicted to encode regulatory proteins from different families. In this study, we showed that the newly identified cluster is functional and we investigated the roles of these regulatory genes in the regulation of cyclothiazomycin biosynthesis. We determined thatSHJG8833, but notSHJG8837orSHJG8838, is critical for cyclothiazomycin biosynthesis. The transcriptional start point ofSHJG8833was located to a thymidine 54 nt upstream of the start codon. Inactivation ofSHJG8833abrogated the production of cyclothiazomycin, and synthesis could be restored by reintroducingSHJG8833into the mutant strain. Gene expression analyses indicated that SHJG8833 regulates a consecutive set of seven genes fromSHJG8826toSHJG8832, whose products are predicted to be involved in different steps in the construction of the main framework of cyclothiazomycin. Transcriptional analysis indicated that these seven genes may form two operons,SHJG8826–27andSHJG8828–32. Gel-shift analysis demonstrated that the DNA-binding domain of SHJG8833 binds the promoters ofSHJG8826andSHJG8828and sequences internal toSHJG8826andSHJG8829, and a conserved binding sequence was deduced. These results indicate that SHJG8833 is a positive regulator that controls cyclothiazomycin biosynthesis by activating structural genes in thecltcluster.
Complex proteinopathy with accumulations of prion protein, hyperphosphorylated tau, α-synuclein and ubiquitin in experimental bovine spongiform encephalopathy of monkeys
Authors: Piccardo Pedro , Cervenak Juraj , Bu Ming , Miller Lindsay , Asher David M.
Published: April 2014

Proteins aggregate in several slowly progressive neurodegenerative diseases called ‘proteinopathies’. Studies with cell cultures and transgenic mice overexpressing mutated proteins suggested that aggregates of one protein induced misfolding and aggregation of other proteins as well – a possible common mechanism for some neurodegenerative diseases. However, most proteinopathies are ‘sporadic’, without gene mutation or overexpression. Thus, proteinopathies in WT animals genetically close to humans might be informative. Squirrel monkeys infected with the classical bovine spongiform encephalopathy agent developed an encephalopathy resembling variant Creutzfeldt–Jakob disease with accumulations not only of abnormal prion protein (PrPTSE), but also three other proteins: hyperphosphorylated tau (p-tau), α-synuclein and ubiquitin; β-amyloid protein (Aβ) did not accumulate. Severity of brain lesions correlated with spongiform degeneration. No amyloid was detected. These results suggested that PrPTSEenhanced formation of p-tau and aggregation of α-synuclein and ubiquitin, but not Aβ, providing a new experimental model for neurodegenerative diseases associated with complex proteinopathies.
MOHCA-seq: RNA 3D models from single multiplexed proximity-mapping experiments
Authors: Cheng Clarence , Chou Fang-Chieh , Kladwang Wipapat , Tian Siqi , Cordero Pablo , Das Rhiju
Published: April 2014

Large RNAs control myriad biological processes but challenge tertiary structure determination. We report that integrating Multiplexed OH Cleavage Analysis with tabletop deep sequencing (MOHCA-seq) gives nucleotide-resolution proximity maps of RNA structure from single straightforward experiments. After achieving 1-nm resolution models for RNAs of known structure, MOHCA-seq reveals previously unattainable 3D information for ligand-induced conformational changes in a double glycine riboswitch and the sixth community-wide RNA puzzle, an adenosylcobalamin riboswitch.
A Receptor-Like Kinase Mediates Ammonium Homeostasis and Is Important for the Polar Growth of Root Hairs inArabidopsis
Authors: Bai Ling , Ma Xiaonan , Zhang Guozeng , Song Shufei , Zhou Yun , Gao Lijie , Miao Yuchen , Song Chun-Peng
Published: April 2014

Ammonium (NH4  +) is both a necessary nutrient and an important signal in plants, but can be toxic in excess. Ammonium sensing and regulatory mechanisms in plant cells have not been fully elucidated. To decipher the complex network of NH4  + signaling, we analyzed [Ca2+]cyt-associated protein kinase (CAP) genes, which encode signaling components that undergo marked changes in transcription levels in response to various stressors. We demonstrated that CAP1, a tonoplast-localized receptor-like kinase, regulates root hair tip growth by maintaining cytoplasmic Ca2+ gradients. A CAP1 knockout mutant (cap1-1) produced elevated levels of cytoplasmic NH4  +. Furthermore, root hair growth of cap1-1 was inhibited on Murashige and Skoog medium, but NH4  + depletion reestablished the Ca2+ gradient necessary for normal growth. The lower net NH4  + influx across the vacuolar membrane and relatively alkaline cytosolic pH of cap1-1 root hairs implied that mutation of CAP1 increased NH4  + accumulation in the cytoplasm. Furthermore, CAP1 functionally complemented the npr1 (nitrogen permease reactivator protein) kinase yeast mutant, which is defective in high-affinity NH4  + uptake via MEP2 (methylammonium permease 2), distinguishing CAP1 as a cytosolic modulator of NH4  + levels that participates in NH4  + homeostasis-regulated root hair growth by modulating tip-focused cytoplasmic Ca2+ gradients.
Methylcrotonyl-CoA Carboxylase Regulates Triacylglycerol Accumulation in the Model Diatom Phaeodactylum tricornutum
Authors: Ge Feng , Huang Weichao , Chen Zhuo , Zhang Chunye , Xiong Qian , Bowler Chris , Yang Juan , Xu Jin , Hu Hanhua
Published: April 2014

The model marine diatom Phaeodactylum tricornutum can accumulate high levels of triacylglycerols (TAGs) under nitrogen depletion and has attracted increasing attention as a potential system for biofuel production. However, the molecular mechanisms involved in TAG accumulation in diatoms are largely unknown. Here, we employed a label-free quantitative proteomics approach to estimate differences in protein abundance before and after TAG accumulation. We identified a total of 1193 proteins, 258 of which were significantly altered during TAG accumulation. Data analysis revealed major changes in proteins involved in branched-chain amino acid (BCAA) catabolic processes, glycolysis, and lipid metabolic processes. Subsequent quantitative RT-PCR and protein gel blot analysis confirmed that four genes associated with BCAA degradation were significantly upregulated at both the mRNA and protein levels during TAG accumulation. The most significantly upregulated gene, encoding the β-subunit of methylcrotonyl-CoA carboxylase (MCC2), was selected for further functional studies. Inhibition of MCC2 expression by RNA interference disturbed the flux of carbon (mainly in the form of leucine) toward BCAA degradation, resulting in decreased TAG accumulation. MCC2 inhibition also gave rise to incomplete utilization of nitrogen, thus lowering biomass during the stationary growth phase. These findings help elucidate the molecular and metabolic mechanisms leading to increased lipid production in diatoms.
Multiple vs single lending relationships in the agricultural sector
Authors: E. Brewer Brady , A. Wilson Christine , M. Featherstone Allen , R. Langemeier Michael
Published: April 2014

Purpose

– The purpose of this paper is to examine the use of single vs multiple lenders by Kansas farms. Previous studies suggest that as the risk level of the firm changes, borrowers desire to enhance the probability of obtaining credit at the lowest possible cost may cause them to use multiple lenders.

Design/methodology/approach

– A model is adopted from the banking literature to describe farm behavior in obtaining credit from a single vs multiple lenders. Using farm-level data from the Kansas Farm Management Association, an empirical model analyzes how farm characteristics affect the number of lending relationships. A model is developed to analyze the number of lending relationships effect on the profitability of the farm.

Findings

– It is found that highly leveraged farms seek additional lending relationships supporting the theoretical model and that additional lending relationships correlate to a decrease in profitability. Roughly, 50 percent of Kansas farmers that borrow use a single lender. Roughly 48 percent use from two to four lenders, with the remaining 2 percent using more than four lenders.

Originality/value

– Provides empirical results to support developed theoretical framework on the number of lending institutions. This study helps understand factors correlated to a farmer's decision to use multiple lenders. Analyzing the number of lending relationships helps understand how farmers manage their debt to maintain access to credit when needed at the lowest possible cost.
Estimation of transient boundary flux for a developing flow in a parallel plate channel
Authors: Kumar Parwani Ajit , Talukdar Prabal , Subbarao P.M.V.
Published: April 2014

Purpose

– The purpose of this paper is to develop a numerical model for estimating the unknown boundary heat flux in a parallel plate channel for the case of a hydrodynamically and thermally developing laminar flow.

Design/methodology/approach

– The conjugate gradient method (CGM) is used to solve the inverse problem. The momentum equations are solved using an in-house computational fluid dynamics (CFD) source code. The energy equations along with the adjoint and sensitivity equations are solved using the finite volume method.

Findings

– The effects of number of measurements, distribution of measurements and functional form of unknown flux on the accuracy of estimations are investigated in this work. The prediction of boundary flux by the present algorithm is found to be quite reasonable.

Originality/value

– It is noticed from the literature review that study of inverse problem with hydrodynamically developing flow has not received sufficient attention despite its practical importance. In the present work, a hydrodynamically and thermally developing flow between two parallel plates is considered and unknown transient boundary heat flux at the upper plate of a parallel plate channel is estimated using CGM.
Computational fluid dynamics for thermal performance of a water-cooled minichannel heat sink with different chip arrangements
Authors: Xie Gongnan , Li Shian , Sunden Bengt , Zhang Weihong
Published: April 2014

Purpose

– With the development of electronic devices, including the desires of integration, miniaturization, high performance and the output power, cooling requirement of chips have been increased gradually. Water-cooled minichannel is an effective cooling technology for cooling of heat sinks. The minichannel flow geometry offers large surface area for heat transfer and a high convective heat transfer coefficient with only a moderate pressure loss. The purpose of this paper is to analyze a minichannel heat sink having the bottom size of 35 mm×35 mm numerically. Two kinds of chip arrangement are investigated: diagonal arrangement and parallel arrangement.

Design/methodology/approach

– Computational fluid dynamics (CFD) technique is used to investigate the flow and thermal fields in forced convection in a three-dimensional minichannels heat sink with different chip arrangements. The standard k-e turbulence model is applied for the turbulence simulations on the minichannel heat sink.

Findings

– The results show that the bottom surface of the heat sink with various chip arrangements will have different temperature distribution and thermal resistance. A suitable chip arrangement will achieve a good cooling performance for electronic devices.

Research limitations/implications

– The fluid is incompressible and the thermophysical properties are constant.

Practical implications

– New and additional data will be helpful as guidelines in the design of heat sinks to achieve a good thermal performance and a long lifetime in operation.

Originality/value

– In real engineering situations, chips are always placed in various manners according to design conditions and constraints. In this case the assumption of uniform heat flux is acceptable for the surfaces of the chips rather than for the entire bottom surface of the heat sink.
Unconditionally stable numerical scheme for natural convection problems
Authors: Górecki Bartosz , Szumbarski Jacek
Published: April 2014

Purpose

– Both the importance of the natural convection in science and engineering and the shortage of publications in the field of numerical features of time-stepping schemes for the simulation of coupled heat and fluid flow problems motivate the present work. The paper aims to discuss these issues.

Design/methodology/approach

– The paper presents the unconditionally stable time-stepping scheme for simulation of coupled problems of mass and heat transport. The paper is divided into two parts. The first part concerns the mathematical formulation of the scheme and discusses its implementation. The second part focuses on the numerical simulation and its results. A detailed investigation of the temporal order of the scheme with respect to the L2-norms of the errors of the pressure, velocity, temperature and divergence of velocity fields has also been given.

Findings

– The work shows that it is possible to formulate a numerical scheme which is unconditionally stable with respect to the time step size. Moreover, application of the spectral element method for the spatial discretization results in a high order of approximation in space and very good overall accuracy. Furthermore, the investigation of the numerical features of the scheme showed that the formal temporal order of the scheme (formally second order) has been deferred very slightly and the order of 1.8-1.9 is achieved for all unknown fields.

Originality/value

– The paper presents a new unconditionally stable scheme for simulation of unsteady flows with bidirectional coupling of heat transfer and the fluid flow. It also carefully investigates the numerical behaviour of the method.
Simulations of the PC boiler equipped with complex swirling burners
Authors: P. Adamczyk Wojciech , Kozolub Pawel , Węcel Gabriel , Ryfa Arkadiusz
Published: April 2014

Purpose

– The purpose of this paper is to show possible approaches which can be used for modeling complex flow phenomena caused by swirl burners combined with simulating coal combustion process using air- and oxy-combustion technologies. Additionally, the response of exist boiler working parameter on changing the oxidizer composition from air to a mixture of the oxygen and recirculated flue gases is investigated. Moreover, the heat transfer in the superheaters section of the boiler was taken into account by modeling of the heat exchange process between continuum phase and three stages of the steam superheaters.

Design/methodology/approach

– An accurate solution of the flow field is required in order to predict combustion phenomena correctly for numerical simulations of the industrial pulverized coal (PC) boilers. Nevertheless, it is a very demanding task due to the complicated swirl burner construction and complex character of the flow. The presented simulations were performed using the discrete phase model for tracking particles and combustion phenomena in a dispersed phase, whereas the Eulerian approach was applied for the volatile combustion process modeling in a gaseous phase.

Findings

– Applying the air- to oxy-combustion technology the temperature in the combustion chamber, decreased for investigated oxidizer compositions. This was caused by the higher heat capacity of flue gases which also influences on the level of the heat flux at the boiler walls. Simulations shows that increasing the O2 concentration to 30 percent of volume base in the oxidizer mixture provided the similar combustion conditions as those for the conventional air firing. Moreover, the evaluated results give a good overview of differences between approaches used for complex swirl burners simulations.

Practical implications

– Nowadays, the numerical techniques such as computational fluid dynamic (CFD) can be seen as an useful engineering tool for design and processes optimization purposes. The application of the CFD gives a possibility to predict the combustion phenomena in a large industrial PC boiler and investigate the impact of changing the combustion technology from a conventional air firing to oxy-fuel combustion.

Originality/value

– This paper gives good overview on existing technique, approaches used for modeling PC boiler equipped with complex swirl burners. Additionally, the novelty of this work is application of the heat exchanger model for predicting heat loses in convective section of the boiler. This usually is not taken into account during simulations. The reader can also find basic concept of oxy-combustion technology, and their impact on boiler working conditions.
Absorption line black body distribution function evaluated with proper orthogonal decomposition for mixture of CO2 and H2O
Authors: Węcel Gabriel , Ostrowski Ziemowit , Kozołub Pawel
Published: April 2014

Purpose

– The purpose of this paper is to present a new approach of evaluation of the absorption line black body distribution function (ALBDF) for a mixture of gases. Currently published correlations, which are used to reproduce the ALBDF, treat only single gases.

Design/methodology/approach

– A discrete form of the ALBDF is generated using line by line (LBL) calculations. The latest spectroscopic database HITEMP 2010 is used for the generation of the absorption coefficient histogram, which is cumulated later in order to produce a tabulated form of the ALBDF. The proper orthogonal decomposition (POD) statistical method is employed for the reproduction of the ALBDF. Interpolation property of the POD allows to reproduce the ALBDF for arbitrary gas mixture parameters.

Findings

– POD proved to possess optimal interpolation properties. Results obtained by using POD are in very good agreement with LBL integration.

Research limitations/implications

– One have to be aware that the model generated with the POD method can be used only within the range of parameters used to build the model. The POD does not perform any property extrapolation. The model is limited to a mixture of two gases, namely CO2 and H2O. Expanding the number of gases used in the mixture may lead to a relatively large matrix system, which is difficult to process with the POD approach.

Practical implications

– The presented approach can be used to produce absorption coefficients values and their weights, which can be applied in the gas radiative properties description using the weighted sum of gray gas (WSGG) concept. The proposed model can be used with any radiative transfer equation solver which employs the WSGG approach.

Originality/value

– For the first time, radiative properties of gas mixtures are reproduced using the POD approach.
Heat and mass transfer by natural convection flow about a truncated cone in porous media with Soret and Dufour effects
Authors: Rashad A. , Chamkha A.
Published: April 2014

Purpose

– The purpose of this paper is to study the effects of chemical reaction, thermal radiation and Soret and Dufour effects of heat and mass transfer by natural convection flow about a truncated cone in porous media.

Design/methodology/approach

– The problem is formulated and solved numerically by an accurate implicit finite-difference method.

Findings

– It is found that the Soret and Dufour effects as well as the thermal radiation and chemical reaction cause significant effects on the heat and mass transfer charateristics.

Originality/value

– The problem is relatively original as it considers Soret and Dufour as well as chemical reaction and porous media effects on this type of problem.
Melting heat transfer in the stagnation-point flow of Maxwell fluid with double-diffusive convection
Authors: Hayat Tasawar , Farooq Muhammad , Alsaedi Ahmad
Published: April 2014

Purpose

– The purpose of this paper is to analyze the melting heat transfer in the stagnation-point flow with double-diffusive convection.

Design/methodology/approach

– Series solutions for velocity, temperature and concentration are constructed via homotopy analysis method.

Findings

– The authors observed that the behaviors of N, ?2 and M on the velocity and boundary layer thickness are qualitatively similar. Further, for A<1 the velocity profile and boundary layer thickness increase with the increase of A. However, when A>1 then the velocity profile increases but the boundary layer thickness decreases when A is increased.

Originality/value

– This analysis has not been discussed in the literature previously.
Effects of green brand on green purchase intention
Authors: Huang Yi-Chun , Yang Minli , Wang Yu-Chun
Published: April 2014

Purpose

– The purpose of this paper is to build a comprehensive model and examine the relationship among green brand positioning (GBP), green brand knowledge (GBK), attitude toward green brand (AGB), and green purchase intention (GPI).

Design/methodology/approach

– A questionnaire survey was deployed to collect data from the members of Taiwan's Lifestyles of Health and Sustainability (LOHAS) Club, obtaining 425 valid samples which were analyzed with structural equation modeling.

Findings

– GBP and GBK influence green brand attitudes separately. GBK affects green brand attitudes. Meanwhile, green brand attitudes influence GPIs. Another finding indicates that the mediating effects exist.

Research limitations/implications

– By applying the environmental knowledge-attitude-intention paradigm to green brand research, it was empirically supported the existence of a GBK-attitude-intention hierarchy in the context of GPIs.

Practical implications

– GBP can be used as brand marketing strategy to improve consumers’ GBK and form positive green brand attitudes as well as enhance GPIs.

Originality/value

– Proposing two novel concepts, i.e. GBK and green brand attitude to develop and test the framework of this study.
Saving–investment Association and Regional Capital Mobility in China: A Nonparametric Panel Approach
Authors: Jiang Mingming
Published: April 2014

Using a nonparametric panel data model, this paper estimates the degree of time‐varying and province‐specific capital mobility in China during 1970–2006. We estimate the savings–investment association, that is, the savings retention rate à la Feldstein and Horioka, as a measure of capital mobility. We also split the total savings (investment) into private and government savings (investment) to explore the role of government in improving capital mobility. Over time, we find an improvement in capital mobility after the mid‐1990s. Across provinces, we observe higher capital mobility in eastern/coastal regions. From the 1990s, the government is found to play a less important role in promoting capital mobility. Across provinces, the government is found to be more important in either the municipalities (Shanghai and Beijing) or the less developed inland provinces.
China's Profits and Losses from Currency Intervention, 1994–2011
Authors: Jin Hailong , Choi E. Kwan
Published: April 2014

China's currency policy has been criticized for its apparent pursuit of mercantile advantage by artificially stimulating exports, with potential adverse effects on other economies. While China's currency policy may have positive output effects, there may be additional profits or losses. This paper computes the annual and cumulative accounting profits from currency intervention since 1994 when China began its currency intervention. It is shown that profits initially were positive but since 2007 China has lost a massive amount from the currency market.
Exchange Rate Exposure of Sectoral Returns and Volatilities: Further Evidence From Japanese Industrial Sectors
Authors: Jayasinghe Prabhath , Tsui Albert K. , Zhang Zhaoyong
Published: April 2014

In this paper we argue that the commonly employed exposure coefficient/beta is inadequate for capturing the entire impact of exchange rate changes on firms' future operating cash flows. Instead, we employ the bivariate Glosten–Jagannathan–Runkle generalized autoregressive conditional heteroskedasticity mean model to investigate four aspects of exchange rate exposure, including sensitivity of stock returns to exchange rate changes, sensitivity of stock returns to the volatility of exchange rate changes, sensitivity of conditional variance of returns to exchange rate volatility, and the dynamic conditional correlation between returns and exchange rate changes, respectively, using data from 10 industrial sectors in Japan. We find significant evidence of such exchange rate exposure which is not captured by the conventional measure. The diagnostic statistics confirm the adequacy of our model, and, hence, the robustness of the results.
Social theory and current affairs: a framework for intellectual engagement
Authors: Stones Rob
Published: April 2014

The paper aims to facilitate more adequate critical engagement with current affairs events by journalists, and with current affairs texts by audiences. It draws on social theory to provide the intellectual resources to enable this. The academic ambition is for the framework to be adopted and developed by social thinkers in producing exemplary critical readings of news and current affairs texts. To this end it is offered as a research paradigm. The paper situates its argument in relation to the wider literature in media and cultural studies, acknowledging the subtle skills required to appreciate the relative autonomy of texts. However, it draws attention to the lack of an adequate perspective with which to assess the frames, representations, and judgments within news and current affairs texts. To address this lacuna it proposes the conception of a social‐theoretical frame, based on a number of meta‐theoretical approaches, designed to provide audiences with a systematic means of addressing the status and adequacy of individual texts. Social theoretical frames can reveal the shortcomings of media framing of the contextual fields within which news and current affairs events take place. Two illustrative case studies are used to indicate the value and potential of the approach: the analysis of a short newspaper report of the return of protesters to Cairo's Tahrir Square in 2011, and a critique of four current affairs reports from various genres on the political turmoil in Thailand leading up to the clashes of May 2010.
Adults face increased asthma risk after infant RSV bronchiolitis and reduced respiratory health‐related quality of life after RSV pneumonia
Authors: Backman Katri , Piippo‐Savolainen Eija , Ollikainen Hertta , Koskela Heikki , Korppi Matti
Published: April 2014

Aim

To evaluate the association between hospitalisation for respiratory syncytial virus lower respiratory tract infection (RSV LRTI) in infancy and asthma, respiratory health‐related quality of life and lung function at 28–31 years of age.

Methods

In 2010, we carried out a 30‐year follow‐up on 43 adults admitted to Kuopio University Hospital, Finland, for RSV LRTI, 27 for bronchiolitis and 16 for pneumonia, between 1981 and 1982. Together with 86 population‐based controls, they completed the Saint George's Respiratory Questionnaire and underwent prebronchodilator (pre‐BD) and post‐BD spirometry tests to measure percentage of predicted forced vital capacity (FVC%), percentage of predicted forced expiratory volume in 1 sec (FEV1%) and percentage of predicted FEV1/FVC (FEV1/FVC%).

Results

Both the pre‐BD and post‐BD FEV1% and FEV1/FVC% were significantly lower in former RSV LRTI patients than in the controls. The bronchiolitis patients had more asthma in adulthood than the controls and pneumonia in infancy was associated with lower St George's Respiratory Questionnaire (SGRQ) scores.

Conclusion

Respiratory tract infection LRTI hospitalisation in infancy was associated with an increased risk of permanent obstructive lung function reduction in adulthood. The asthma risk was higher after hospitalisation for bronchiolitis, than in the controls, and respiratory health‐related quality of life was lower after hospitalisation for pneumonia.
Are baby hammocks safe for sleeping babies? A randomised controlled trial
Authors: Chiu Karen , Tonkin Shirley L. , Gunn Alistair J. , McIntosh Christine C.
Published: April 2014

Aim

Two reports of infants found dead after sleeping in baby hammocks have raised international concern about the safety of infant hammocks. We therefore tested whether hammock sleep affected oxygenation in infants, when they were at an age of high risk of sudden, unexpected infant death.

Methods

Healthy, full‐term 4‐ to 8‐week‐old infants were randomised to sleep either in a commercially available hammock (n = 14) or a standard bassinet (n = 9), and sleep state, oxygen desaturation (a fall in peripheral haemoglobin oxygen saturation (SpO2) ≥ 4%, for ≥ 4 sec from baseline to nadir), apnoea and hypopnoea, and mean SpO2 were analysed.

Results

There was no significant difference in mean SpO2 (both 98.5%) or rate of oxygen desaturation events between the hammock and the bassinet cot (mean ± SD, 24 ± 20 vs. 28 ± 23 events per hour), but infants slept less in the hammock (59 ± 31 vs. 81 ± 34 min, p < 0.02).

Conclusion

When correctly used, the hammock sleep position did not compromise the upper airway of sleeping infants. The significance of shorter duration of sleep in the hammocks is unclear. These findings should not be applied to all baby hammocks, nor to older babies, particularly once the infant can roll. Given that it is not possible to predict when an infant will be able to roll, we strongly recommend that hammocks should not be used for unsupervised sleep.
Is there income mobility in the Philippines?
Authors: Martinez Arturo , Western Mark , Haynes Michele , Tomaszewski Wojtek
Published: April 2014

Despite a more robust economic performance over the past decade compared with the 1980s and 1990s, growth in average household income is still far below what might be expected given the pace of economic expansion in the Philippines. Inequality of household income has also remained high, which leads to the question: is there income mobility in the Philippines? Using longitudinal data from three years of the redesigned Philippine Family Income and Expenditure Survey (2003, 2006, and 2009) and a variety of analytical tools, we examine the mobility of Filipino household income and show that it is less stagnant than is conventionally perceived. Empirical evidence suggests that significant positive and negative mobility exists; albeit, the two tend to offset each other, contributing to slow household income growth at the aggregate level. In addition, there is some evidence that transitory fluctuations contribute significantly to the observed level of income mobility. Overall, the findings are robust across different analytical tools used in measuring income mobility.
Carbonate apatite nephrolithiasis associated withCorynebacterium urealyticumurinary tract infection in a dog
Authors: Fleischhacker SN , Horstmann C , Hartmann K , Schubert S , Dorsch R
Published: April 2014

Background

Urinary tract infections caused byCorynebacterium urealyticumare uncommon in veterinary medicine. Encrusted cystitis, encrusted pyelitis and uroliths have been described as complications in humans, but only encrusted cystitis and cystoliths have been reported in dogs so far. BecauseC. urealyticumis usually resistant to all standard antibacterial drugs, antimicrobial treatment and elimination of this microorganism are challenging.

Case report

An 11‐month‐old female spayed mixed‐breed dog was evaluated because of aC. urealyticumurinary tract infection, mineralisation within both renal pelvises and failure of antimicrobial treatment. Physical examination, haematology and biochemistry were unremarkable. Radiographic and ultrasonographic examinations confirmed bilateral nephrolithiasis. Voided uroliths were composed of 100% carbonate apatite. Urinalysis was indicative of bacterial infection. Aerobic culture of the urine and 16SrRNAsequencing identified significant growth ofC. urealyticumand susceptibility testing revealed sensitivity to only vancomycin and linezolid.

Conclusion

Treatment with the oxazolidinone antibacterial, linezolid, in combination with a urine‐acidifying diet resulted in elimination of this multiresistant microorganism and complete resolution of nephrolithiasis.
PI3K‐dependent multiple myeloma cell survival is mediated by the PIK3CA isoform
Authors: Hofmann Claudia , Stühmer Thorsten , Schmiedl Nadine , Wetzker Reinhard , Mottok Anja , Rosenwald Andreas , Langer Christian , Zovko Josip , Chatterjee Manik , Einsele Hermann , Bargou Ralf C. , Steinbrunn Torsten
Published: April 2014

Constitutive phosphatidylinositide 3‐kinase (PI3K) signalling has been implicated in multiple myeloma (MM) pathophysiology and is regarded as an actionable target for pharmacological intervention. Isoform‐specific PI3K inhibition may offer the most focused treatment approach and could result in greater clinical efficacy and reduced side effects. We therefore performed isoform‐specific knockdown of PIK3CA, PIK3CB, PIK3CD, and PIK3CG to analyse their individual contributions to MM cell survival and downstream signalling. In addition, we tested the effectivity of the novel PI3K isoform‐specific inhibitors BYL‐719 (PIK3CA), TGX‐221 (PIK3CB), CAL‐101 (PIK3CD), and CAY10505 (PIK3CG). We found the PIK3CA isoform to be of paramount importance for constitutive Akt activity in MM cells, and – in contrast to inhibition of other class I isoforms – only the blockade of PIK3CA was sufficient to induce cell death in a sizeable subgroup of MM samples. Furthermore, pharmacological PIK3CA inhibition in combination treatments of BYL‐719 and established anti‐myeloma agents resulted in strongly enhanced MM cell death. Our data thus clearly indicate therapeutic potential of PIK3CA inhibitors and support their clinical evaluation in multiple myeloma.
Behavioral and Social Structure Effects on Seed Dispersal Curves of a Forest‐Interior Bulbul (Pycnonotidae) in a Tropical Evergreen Forest
Authors: Khamcha Daphawan , Savini Tommaso , Westcott David A. , McKeown Adam , Brockelman Warren Y. , Chimchome Vijak , Gale George A.
Published: April 2014

Movement patterns of animals can vary dramatically as a function of their reproductive cycle or social structure; however, little is known about how changes in the social structure of dispersers affect patterns of seed dispersal. We examined the movement patterns of the forest‐dwelling and cooperatively breeding Puff‐throated Bulbul (Alophoixus pallidus) in relation to different stages of their reproductive cycle, time of day, and group size, to determine potential impacts on the shape and scale of dispersal curves generated using a combination of gut passage time and displacement distance data. There were significant differences in dispersal distances depending on group size, season (breeding, non‐breeding), incubation (vs. other times of the year), and time of the day. The estimated median seed dispersal distance was 28 m. The median dispersal distances produced by birds in larger groups were longer than those of smaller groups (29 m vs. 25 m). During the breeding season, median dispersal distances were longer than during the non‐breeding season (31 m vs. 25 m), but the median dispersal distances were significantly shorter during incubation than during outside incubation (24 m vs. 28 m). The median dispersal distance produced in the early morning (30 m) was also longer than that of other times of the day (23 m late morning, 28 m early afternoon, and 26 m late afternoon). This study suggests that various aspects of an animal's behavior are likely to have significant effects on seed shadows and that this may vary significantly even among individuals of the same species.
Stratification in French Guiana: Cerambycid Beetles Go Up When Rains Come Down
Authors: Lee Christina J. , Baxt Alec , Castillo Suzette , Berkov Amy
Published: April 2014

When tropical rain forest insect species are associated with a particular season or forest stratum, it can imply tolerance for heat and drought—or moisture dependence; attributes that may predict their responses to global climate change. In French Guiana (1995–1996), wood‐boring cerambycid beetles made a seasonal shift in stratum. During the dry season, ground stratum bait branches were densely colonized, but during the rainy season almost all cerambycids emerged from canopy stratum branches. Because the same substrate was available at both levels, abiotic factors probably influenced branch selection. In this study, cerambycids were reared at the same site (2007–2008) to determine if the seasonal shift recurred. Microclimate data (temperature, relative humidity, and wind speed) were collected with portable weather meters to test the hypothesis that microclimate would be similar at ground stratum during the dry season, and at canopy stratum during the rainy season. The seasonal shift in stratum did recur; many cerambycid individuals (56%) belonged to species classified as ‘seasonal shifters’. Temperatures in the preferred microhabitats were intermediate, but relative humidity remained high during the rainy season (regardless of stratum) and it was windier in the canopy (regardless of season). The shifters preferentially colonized branches at moderate mean temperatures (23.0–24.3°C) and high mean relative humidities (91.3–100%). Shifters were considered season and stratum generalists because they were reared at both strata and were present in both seasons, but they may actually track a narrow microclimate window. Should the regional climate become warmer and drier, it would probably favor species currently restricted to the dry season or canopy stratum.
Phyllostomid Bat Assemblage Structure in Amazonian Flooded and Unflooded Forests
Authors: Bobrowiec Paulo Estefano D. , Rosa Leonardo dos Santos , Gazarini Janaina , Haugaasen Torbjørn
Published: April 2014

In Amazonia, the assemblages of several taxa differ significantly between upland terra firme and white‐water flooded várzea forests, but little is known about the diversity and distribution of bats in these two forest types. We compare the spatio‐temporal patterns of bat assemblage composition and structure in adjacent terra firme and várzea forests in the lower Purus River region of central Brazilian Amazonia. Bats were sampled using mist nets at five sites in each forest type during 40 nights (2400 net‐hours). We captured 1069 bats representing 42 species and Phyllostomidae bats comprised 99.3 percent of all captures. The bat assemblages in várzea and terra firme forests were significantly different, mainly due to a marked dissimilarity in species composition and in the number of captures during high‐water season. In addition, bat assemblages within forest types differed significantly between seasons for both terra firme and várzea. Frugivores dominated the bat assemblages in both forest types. Overall guild structure did not change between várzea and terra firme or between seasons, but frugivore and animalivore abundance increased significantly in várzea forest during the inundation. The difference in assemblage structure observed in the high‐water season is probably caused by the annual várzea flooding, which provides an effective barrier to the persistence of many understory bats. We also hypothesize that some bat species may undertake seasonal movements between forest types in response to fruit abundance, and our results further underline the importance of floodplain habitats for the conservation of species in the Amazon.
Induction of p53‐mediated transcription and apoptosis by exportin‐1 (XPO1) inhibition in mantle cell lymphoma
Authors: Yoshimura Mariko , Ishizawa Jo , Ruvolo Vivian , Dilip Archana , Quintás‐Cardama Alfonso , McDonnell Timothy J. , Neelapu Sattva S. , Kwak Larry W. , Shacham Sharon , Kauffman Michael , Tabe Yoko , Yokoo Masako , Kimura Shinya , Andreeff Michael , Kojima Kensuke
Published: April 2014

The nuclear transporter exportin‐1 (XPO1) is highly expressed in mantle cell lymphoma (MCL) cells, and is believed to be associated with the pathogenesis of this disease. XPO1‐selective inhibitors of nuclear export (SINE) compounds have been shown to induce apoptosis in MCL cells. Given that p53 is a cargo protein of XPO1, we sought to determine the significance of p53 activation through XPO1 inhibition in SINE‐induced apoptosis of MCL cells. We investigated the prognostic impact of XPO1 expression in MCL cells using Oncomine analysis. The significance of p53 mutational/functional status on sensitivity to XPO1 inhibition in cell models and primary MCL samples, and the functional role of p53‐mediated apoptosis signaling, were also examined. Increased XPO1 expression was associated with poor prognosis in MCL patients. The XPO1 inhibitor KPT‐185 induced apoptosis in MCL cells through p53‐dependent and ‐independent mechanisms, and p53 status was a critical determinant of its apoptosis induction. The KPT‐185‐induced, p53‐mediated apoptosis in the MCL cells occurred in a transcription‐dependent manner. Exportin‐1 appears to influence patient survival in MCL, and the SINE XPO1 antagonist KPT‐185 effectively activates p53‐mediated transcription and apoptosis, which would provide a novel strategy for the therapy of MCL.