bluuebunny/crossref_metadata_2025 huggingface dataset:
Knockout of Eva1a leads to rapid development of heart failure by impairing autophagy
Authors: Zhang Shu , Lin Xin , Li Ge , Shen Xue , Niu Di , Lu Guang , Fu Xin , Chen Yingyu , Cui Ming , Bai Yun
Published: February 2017

EVA1A (Eva-1 homologue A) is a novel lysosome and endoplasmic reticulum-associated protein that can regulate cell autophagy and apoptosis. Eva1a is expressed in the myocardium, but its function in myocytes has not yet been investigated. Therefore, we generated inducible, cardiomyocyte-specific Eva1a knockout mice with an aim to determine the role of Eva1a in cardiac remodelling in the adult heart. Data from experiments showed that loss of Eva1a in the adult heart increased cardiac fibrosis, promoted cardiac hypertrophy, and led to cardiomyopathy and death. Further investigation suggested that this effect was associated with impaired autophagy and increased apoptosis in Eva1a knockout hearts. Moreover, knockout of Eva1a activated Mtor signalling and the subsequent inhibition of autophagy. In addition, Eva1a knockout hearts showed disorganized sarcomere structure and mitochondrial misalignment and aggregation, leading to the lack of ATP generation. Collectively, these data demonstrated that Eva1a improves cardiac function and inhibits cardiac hypertrophy and fibrosis by increasing autophagy. In conclusion, our results demonstrated that Eva1a may have an important role in maintaining cardiac homeostasis.
Effect of tiotropium and olodaterol on symptoms and
patient-reported outcomes in patients with COPD: results from four randomised, double-blind studies
Authors: Ferguson Gary T. , Karpel Jill , Bennett Nathan , Clerisme-Beaty Emmanuelle , Grönke Lars , Voß Florian , Buhl Roland
Published: February 2017

Chronic obstructive pulmonary disease is associated with significant morbidity and mortality. Trials of maintenance chronic obstructive pulmonary disease treatments focus on improvement in lung function and reductions in exacerbations, while patients are much more concerned about symptoms and health status. Our aim was to investigate the effects of tiotropium + olodaterol on patient-reported health outcomes, breathlessness and night-time rescue medication use in patients with chronic obstructive pulmonary disease, compared to placebo, tiotropium or olodaterol monotherapy. Two pairs of replicate, phase III studies of 12 (OTEMTO 1 + 2) and 52 weeks’ (TONADO 1 + 2) duration were evaluated, in which patients received either tiotropium + olodaterol 2.5/5 or 5/5 μg, tiotropium 2.5 or 5 μg, olodaterol 5 μg or placebo, all delivered once daily via Respimat inhaler. Patient-reported outcomes included breathlessness assessed by transition dyspnoea index focal score, health status assessed by St George’s Respiratory Questionnaire total score and night-time rescue medication use at 12 or 24 weeks. Outcomes from the pooled study data are reported. Overall, 1621 and 5162 patients were treated in the OTEMTO and TONADO trials, respectively. Significantly larger improvements in St George’s Respiratory Questionnaire and transition dyspnoea index focal scores were observed and a greater proportion of patients were responders to therapy (based on minimum clinically important differences in St George’s Respiratory Questionnaire and transition dyspnoea index) with tiotropium + olodaterol compared to either monotherapy or to placebo. Tiotropium + olodaterol 5/5 µg significantly reduced night-time rescue medication usage.
A novel semiconductor-based, fully incoherent amplified spontaneous emission light source for ghost imaging
Authors: Hartmann Sébastien , Elsäßer Wolfgang
Published: February 2017

Initially, ghost imaging (GI) was demonstrated with entangled light from parametric down conversion. Later, classical light sources were introduced with the development of thermal light GI concepts. State-of-the-art classical GI light sources rely either on complex combinations of coherent light with spatially randomizing optical elements or on incoherent lamps with monochromating optics, however suffering strong losses of efficiency and directionality. Here, a broad-area superluminescent diode is proposed as a new light source for classical ghost imaging. The coherence behavior of this spectrally broadband emitting opto-electronic light source is investigated in detail. An interferometric two-photon detection technique is exploited in order to resolve the ultra-short correlation timescales. We thereby quantify the coherence time, the photon statistics as well as the number of spatial modes unveiling a complete incoherent light behavior. With a one-dimensional proof-of-principle GI experiment, we introduce these compact emitters to the field which could be beneficial for high-speed GI systems as well as for long range GI sensing in future applications.
Rapid cell separation with minimal manipulation for autologous cell therapies
Authors: Smith Alban J. , O’Rorke Richard D. , Kale Akshay , Rimsa Roberts , Tomlinson Matthew J. , Kirkham Jennifer , Davies A. Giles , Wälti Christoph , Wood Christopher D.
Published: February 2017

The ability to isolate specific, viable cell populations from mixed ensembles with minimal manipulation and within intra-operative time would provide significant advantages for autologous, cell-based therapies in regenerative medicine. Current cell-enrichment technologies are either slow, lack specificity and/or require labelling. Thus a rapid, label-free separation technology that does not affect cell functionality, viability or phenotype is highly desirable. Here, we demonstrate separation of viable from non-viable human stromal cells using remote dielectrophoresis, in which an electric field is coupled into a microfluidic channel using shear-horizontal surface acoustic waves, producing an array of virtual electrodes within the channel. This allows high-throughput dielectrophoretic cell separation in high conductivity, physiological-like fluids, overcoming the limitations of conventional dielectrophoresis. We demonstrate viable/non-viable separation efficacy of >98% in pre-purified mesenchymal stromal cells, extracted from human dental pulp, with no adverse effects on cell viability, or on their subsequent osteogenic capabilities.
From seleno-mediated radical polymerization to seleno-containing branched polymers and dynamic hydrogel
Authors: Lu Weihong , An Xiaowei , Zhu Jian , Zhou Nianchen , Zhang Zhengbiao , Pan Xiangqiang , Zhu Xiulin
Published: February 2017

A protocol of introducing redox responsive Se–Se bond into well-defined hydrogel backbone.
Unravelling the energy transfer mechanism in bismuth co-activation of LaInO3:Sm3+/Ho3+ nanophosphor for color-tunable luminescence
Authors: Kamal Ch. Satya , Visweswara Rao T. K. , Reddy P. V. S. S. S. N. , Sujatha K. , Ajayi Babajide Patrick , Jasinski Jacek B. , Rao K. Ramachandra
Published: February 2017

A series of single-phased and color tunable LaInO3:Bi3+,Ho3+/Sm3+ nano phosphors were synthesized via a cost effective and low temperature chemical route.
Surfactant-exfoliated 2D hexagonal boron nitride (2D-hBN): role of surfactant upon the electrochemical reduction of oxygen and capacitance applications
Authors: Khan Aamar F. , Down Michael P. , Smith Graham C. , Foster Christopher W. , Banks Craig E.
Published: February 2017

Surfactant-exfoliated 2D hexagonal boron nitride (2D-hBN) nanosheets are fabricated using the surfactant sodium cholate in aqueous media and are explored towards the electrochemical reduction of oxygen.
Incorporation of graphene nanodots and oxygen defects triggers robust coupling between solar energy and reactive oxygen
Authors: Hao Yuchen , Dong Xiaoli , Wang Xiuying , Ma Hongchao , Zhang Xiufang
Published: February 2017

Efficient coupling between solar energy and active oxygen-related radicals plays a very important role in promoting photocatalytic oxidation processes; however, the poor solar energy harvesting, serious carrier recombination and especially sluggish interfacial reaction kinetics always make this process very inefficient.
Compact graphene/MoS2composite films for highly flexible and stretchable all-solid-state supercapacitors
Authors: Li Ning , Lv Tian , Yao Yao , Li Huili , Liu Kai , Chen Tao
Published: February 2017

Highly flexible and stretchable electrodes and all-solid-state supercapacitors have been developed by using graphene-based films with a compact structure.
Molybdenum disulfide and Au ultrasmall nanohybrids as highly active electrocatalysts for hydrogen evolution reaction
Authors: Zhang Jinxuan , Wang Tanyuan , Liu Lu , Du Kuangzhou , Liu Wanglian , Zhu Zhiwei , Li Meixian
Published: February 2017

MoS2–Au nanohybrids prepared from MoS2 nanoparticles with gold nanoclusters by a solvothermal method showed outstanding electrocatalytic activity toward HER.
Hydrophilic graphene oxide/bismuth selenide nanocomposites for CT imaging, photoacoustic imaging, and photothermal therapy
Authors: Zhang Yixue , Zhang Hao , Wang Yanke , Wu Huixia , Zeng Bo , Zhang Yingjian , Tian Qiwei , Yang Shiping
Published: February 2017

GO/Bi2Se3/PVP nanocomposites fabricated by a one-pot solvothermal method show good performance in CT/photoacoustic imaging and photothermal therapy.
Quantitative Anterior and Posterior Clinoidectomy Analysis and Mobilization of the Oculomotor Nerve during Surgical Exposure of the Basilar Apex Using Frameless Stereotaxis
Authors: Cetas Justin , Anderson Gregory , Rekito Andy , Delashaw Johnny , Dogan Aclan
Published: February 2017

Background Anterior and posterior clinoidectomies have been proposed to augment exposure of the basilar apex. A sequential quantitative benefit analysis offered by these maneuvers has not been reported.

Methods Fourteen datasets from eight cadaveric specimens were analyzed. A modified orbitozygomatic frontotemporal craniotomy was performed. The extent of proximal control of the basilar artery was determined through the exposed opticocarotid and carotidoculomotor triangles before and after clinoidectomies and mobilization of the third nerve at the porous oculomotarius.

Results Removal of the anterior and posterior clinoids significantly improved proximal basilar artery access (p < 0.012) and increased the opticocarotid triangle and carotidoculomotor triangle areas (p < 0.017). Surgical freedom increased inferosuperiorally in the opticocarotid triangle following anterior clinoidectomy (p < 0.047) and in carotidoculomotor triangle following posterior clinoidectomy (p < 0.047). Mobilization of the third nerve increased surgical freedom in the mediolateral projection of the carotidoculomotor triangle (p < 0.047).

Conclusion Anterior and posterior clinoidectomies significantly improved the area of exposure of the opticocarotid triangle, carotidoculomotor triangle, and the exposed length of the basilar artery available for proximal control. This improvement is extremely important for large or giant aneurysms of the upper basilar artery or aneurysms hidden by the posterior clinoid.
Head and Neck Lymphomas in HIV Patients: a Clinical Perspective
Authors: Oishi Natsuki , Bagán José , Javier Karla , Zapater Enrique
Published: February 2017

Introduction Because of the many HIV-related malignancies, the diagnosis and treatment of lymphoma in patients infected with human immunodeficiency virus are challenging.

Objective Here, we review current knowledge of the pathogenesis, epidemiology, symptomatology, diagnosis, and treatment of head and neck lymphomas in HIV patients from a clinical perspective.

Data Synthesis Although Hodgkin's lymphoma is not an AIDS-defining neoplasm, its prevalence is ten times higher in HIV patients than in the general population. NHL is the second most common malignancy in HIV patients, after Kaposi's sarcoma. In this group of patients, NHL is characterized by rapid progression, frequent extranodal involvement, and a poor outcome. HIV-related salivary gland disease is a benign condition that shares some features with lymphomas and is considered in their differential diagnosis.

Conclusion The otolaryngologist may be the first clinician to diagnose head and neck lymphomas. The increasing survival of HIV patients implies clinical and epidemiological changes in the behavior of this disease. Early diagnosis is important to improve the prognosis and avoid the propagation of HIV infection.
Levitation dynamics of a collection of charged droplets in an electrodynamic balance
Authors: Singh Mohit , Mayya Y. S. , Gaware Jitendra , Thaokar Rochish M.
Published: February 2017

The study explores the stable levitation and self-organization of charged multi-drop assemblies in a large sized quadrupole trap both experimentally and through numerical simulations. The trap is benchmarked by comparing single drop levitation experiments with numerical simulations. Important observation and findings of the study are: (i) long time stabilization and formation of patterns of droplet collections over a range of operating parameters (ii) Numerical prediction of polygonal patterns for few drop (2 to 8) systems and lattice structures for many drop (>10) systems, (iii) Numerical prediction of Non-dependence of the inter-drop spacing on droplet charge for similarly charged drops, consistent with earlier analytical formulations [Aardahl et al., J. Aerosol Sci. 28, 1491–1505 (1997)], (iv) numerical observation of two drops oscillations with a secular frequency distinctly higher than the single drop Dehmelt frequency (v) Simulations of a systematic transition from disordered to coulombic crystals with mean size increasing with the number of levitated drops (N) as ∼N0.29. The experimental observations on different patterns and lattice spacings are closely reproduced by simulations.
Single-residue molecular switch for high-temperature dependence of vanilloid receptor TRPV3
Authors: Liu Beiying , Qin Feng
Published: February 2017

Significance

Thermal TRP channels are principal molecular entities of transducing thermal and noxious stimuli. The mechanisms by which they detect temperature remain elusive, however. Our and others’ recent studies show that thermal channels, such as the vanilloid receptor transient receptor potential 3 (TRPV3), are strongly use-dependent. Here, by exploring this distinct feature using fast temperature jumps, we have identified a molecular basis for temperature-dependent gating of ion channels.
An intramolecular interaction within the lipid kinase Fab1 regulates cellular phosphatidylinositol 3,5-bisphosphate lipid levels
Authors: Lang Michael J. , Strunk Bethany S. , Azad Nadia , Petersen Jason L. , Weisman Lois S.
Published: February 2017

Phosphorylated phosphoinositide lipids (PPIs) are low-abundance signaling molecules that control signal transduction pathways and are necessary for cellular homeostasis. The PPI phosphatidylinositol (3,5)-bisphosphate (PI(3,5)P2) is essential in multiple organ systems. PI(3,5)P2is generated from PI3P by the conserved lipid kinase Fab1/PIKfyve. Defects in the dynamic regulation of PI(3,5)P2are linked to human diseases. However, few mechanisms that regulate PI(3,5)P2have been identified. Here we report an intramolecular interaction between the yeast Fab1 kinase region and an upstream conserved cysteine-rich (CCR) domain. We identify mutations in the kinase domain that lead to elevated levels of PI(3,5)P2and impair the interaction between the kinase and CCR domain. We also identify mutations in the CCR domain that lead to elevated levels of PI(3,5)P2. Together these findings reveal a regulatory mechanism that involves the CCR domain of Fab1 and contributes to dynamic control of cellular PI(3,5)P2synthesis.
HOPS catalyzes the interdependent assembly of each vacuolar SNARE into a SNARE complex
Authors: Orr Amy , Song Hongki , Rusin Scott F. , Kettenbach Arminja N. , Wickner William
Published: February 2017

Rab GTPases, their effectors, SNAREs of the R, Qa, Qb, and Qc families, and SM SNARE-binding proteins catalyze intracellular membrane fusion. At the vacuole/lysosome, they are integrated by the homotypic fusion and vacuole protein sorting (HOPS) complex. Two HOPS subunits bind vacuolar Rabs for tethering, another binds the Qc SNARE, and a fourth HOPS subunit, an SM protein, has conserved grooves that bind R- and Qa-SNARE domains. Spontaneous quaternary SNARE complex assembly is very slow. We report an assay of SNARE complex assembly that does not rely on fusion and for which tethering does not coenrich the four SNAREs. HOPS is required in this assay for rapid SNARE complex assembly. Optimal assembly needs HOPS, lipid membranes to which the R- or Qa-SNARE and Ypt7:GTP are integrally bound, and each of the other three SNAREs. Each SNARE assembles into this complex relying on the others, suggesting four-SNARE complex assembly rather than direct binding of each to HOPS. SNAREs can be disassociated by Sec 17/Sec 18/ATP, completing a catalyzed cycle of SNARE assembly and disassembly.
In situ measurements of orange roughy (Hoplostethus atlanticus) target strength
Authors: Coombs Roger F. , Barr Richard
Published: February 2017

Coombs, R. F., and Barr, R. 2007. In situ measurements of orange roughy (Hoplostethus atlanticus) target strength. – ICES Journal of Marine Science, 64: 1220–1234. Orange roughy (Hoplostethus atlanticus) support one of New Zealand's most valuable commercial fisheries, and its assessment poses many problems. Acoustic estimation using echo integration has become one of the main sources of biomass information, and for this an estimate of orange roughy target strength (TS) is needed. Its schooling characteristics together with patterns in the rate of change of phase vs. TS plots are used to identify ensembles of orange roughy targets from in situ TS data collected from a wide range of fishing areas off eastern New Zealand. The results suggest a TS of −49.3 dB for an orange roughy of 35 cm standard length.
Fluctuations and forecasts in the fishery for queen scallops (Aequipecten opercularis) around the Isle of Man
Authors: Vause B. J. , Beukers-Stewart B. D. , Brand A. R.
Published: February 2017

Vause, B. J., Beukers-Stewart, B. D., and Brand, A. R. 2007. Fluctuations and forecasts in the fishery for queen scallops (Aequipecten opercularis) around the Isle of Man. – ICES Journal of Marine Science, 64: 1124–1135. The annual success of the queen scallop fishery around the Isle of Man in the northern Irish Sea is dependent on the strength of recruitment. We examined data from surveys and commercial logbooks on the annual density of spat, juvenile, and adult queen scallops in the fishery between 1982 and 2002. These were used to examine past population and fishery trends and the potential for formulating a predictive model for the fishery. The results were highly variable on both temporal and spatial scales, but there were some general trends. Density appeared to have been relatively stable during the 1980s, declined sharply from the early to mid-1990s, then recovered to produce relatively good catch rates thereafter. There was no relationship between spat settlement and the subsequent density of juveniles or adults in stock surveys or with commercial catch rates. However, within the stock surveys, there were three different significant relationships between cohort densities over time. Additionally, there was a significant relationship between the density of 1-year-olds caught on the surveys and commercial catch rates the following year. Monitoring juvenile queen scallop density would therefore allow prediction of recruitment and fisheries variations at least 1 year in advance, allowing perhaps for more effective management, including reducing the fluctuations in the fishery and helping to ensure long-term sustainability.
Gonad maturation in Octopus vulgaris during ongrowing, under different conditions of sex ratio
Authors: Estefanell Juan , Socorro Juan , Roo Francisco J. , Guirao Rafael , Fernández-Palacios Hipólito , Izquierdo Marisol
Published: February 2017

Estefanell, J., Socorro, J., Roo, F. J., Fernández-Palacios, H., and Izquierdo, M. 2010. Gonad maturation in Octopus vulgaris during ongrowing, under different conditions of sex ratio. – ICES Journal of Marine Science, 67: 1487–1493. Octopus vulgaris is a suitable candidate for aquaculture, but there are problems with breeding in captivity, such as aggressive behaviour among males and the frequent death of females after the eggs hatch. To avoid these problems and further understand the sexual maturation of common octopus in captivity, males and females were reared together and separately under similar culture conditions. In all trials, the initial rearing density was 10 kg m−3. Females (n = 15, sex ratio 0:1) and males (n = 11, sex ratio 1:0) were kept in circular tanks, and a mixed group (n = 209, sex ratio 4:1) in floating cages. Trials started in November 2008 and octopuses from each treatment were examined macroscopically and histologically in December and January to assess sexual maturation. All the males matured, regardless of the sex ratio during rearing, as did all females in the mixed group. In contrast, a large proportion of the females kept isolated from males was still immature in December and January. Although maturation was successful in floating cages, there was 76% mortality there, in contrast to the zero mortality in tanks. Moreover, most of the dead octopuses from the cages were in post-reproductive condition, with a low digestive gland index, suggesting that this was natural post-reproductive mortality. Therefore, sex segregation is deemed advantageous to avoiding early mortality.
Changes in cell wall architecture during cell elongation
Authors: McCann Maureen C. , Roberts Keith
Published: February 2017

A model of the plant cell wall of dicotyledons and non-graminaceous monocotyledons contains two principal structural polysaccharide networks: a stretch-resistant load-bearing cellulose/xyloglucan network, and a compression-resistant pectic polysaccharide network. Structural modifications to either polysaccharide network are likely to have profound consequences for cell wall properties, including tensile strength and extensibility.

We have described dynamic changes in the pattern of esterification of pectic polysaccharides that correlate with cell growth in both carrot and tobacco suspension cells. During elongation, cellulose microfibrils become oriented transversely with respect to the long axis of the cell. Other matrix polymers such as pectin and protein also acquire a net orientation, but in a tissue-specific manner. Preliminary results from Zinnia mesophyll cells suggest that some wall modifications such as the removal of fucose from xyloglucan may be developmentally regulated, but are not required for elongation per se. Our observations lead us to propose a tentative model for the molecular rearrangements that occur within these walls during cell elongation. Our use of methodologies which are suitable for analysis at the single cell wall level has demonstrated that the apoplastic continuum is a mosaic of different architectures, with major architectural differences between species, between tissues, and between domains within a single wall, and we discuss the implications of this heterogeneity for our model.
The Galactic chemical evolution of oxygen inferred from 3D non-LTE spectral-line-formation calculations
Authors: Amarsi A. M. , Asplund M. , Collet R. , Leenaarts J.
Published: February 2017

We revisit the Galactic chemical evolution of oxygen, addressing the systematic errors inherent in classical determinations of the oxygen abundance that arise from the use of one-dimensional (1D) hydrostatic model atmospheres and from the assumption of local thermodynamic equilibrium (LTE). We perform detailed 3D non-LTE radiative-transfer calculations for atomic oxygen lines across a grid of 3D hydrodynamic stagger model atmospheres for dwarfs and subgiants. We apply our grid of predicted line strengths of the [O i] 630 nm and O i 777 nm lines using accurate stellar parameters from the literature. We infer a steep decay in [O/Fe] for [Fe/H] ≳ −1.0, a plateau [O/Fe] ≈ 0.5 down to [Fe/H] ≈ −2.5, and an increasing trend for [Fe/H] ≲ −2.5. Our 3D non-LTE calculations yield overall concordant results from the two oxygen abundance diagnostics.
Non-cosmological FRBs from young supernova remnant pulsars
Authors: Connor Liam , Sievers Jonathan , Pen Ue-Li
Published: February 2017

We propose a new extra but non-cosmological explanation for fast radio bursts (FRBs) based on very young pulsars in supernova remnants. Within a few hundred years of a core-collapse supernova, the ejecta is confined within ∼1 pc, providing a high enough column density of free electrons for the observed 375–1600 pc cm−3 of dispersion measure (DM). By extrapolating a Crab-like pulsar to its infancy in an environment like that of SN 1987A, we hypothesize such an object could emit supergiant pulses sporadically which would be bright enough to be seen at a few hundred megaparsecs. We hypothesize that such supergiant pulses would preferentially occur early in the pulsar's life when the free electron density is still high, which is why we do not see large numbers of moderate DM FRBs (≲300 pc cm−3). In this scenario, Faraday rotation at the source gives rotation measures (RMs) much larger than the expected cosmological contribution. If the emission were pulsar-like, then the polarization vector could swing over the duration of the burst, which is not expected from non-rotating objects. In this model, the scattering, large DM, and commensurate RM all come from one place which is not the case for the cosmological interpretation. The model also provides testable predictions of the flux distribution and repeat rate of FRBs, and could be furthermore verified by spatial coincidence with optical supernovae of the past several decades and cross-correlation with nearby galaxy maps.
The Influence of TL Glow Curve Evaluation Algorithms on the Reproducibility of Dosemeter Readings
Authors: Drazic G. , Miklavzic U. , Mihelic M.
Published: February 2017

Using a microcomputer-controlled TL analyser, which permits automatic application of several different dose-evaluating programs on each measured glow curve, the influence of different evaluation algorithms on the reproducibility and sensitivity of dose determination was studied. Peak height as well as glow curve areas between different floating and fixed limits were used as dose evaluating quantities. Measurements were performed with CaF2:Mn sintered TL dosemeters from our own production and with LiF TLD-100 dosemeters from Harshaw. Experimental results were compared with distributions of theoretically calculated dose responses obtained by random variation of glow curve kinetic parameters. For both types of TLDs the floating integration limits set at certain fractions of the peak height showed the optimum reproducibility, while the peak height proved to be less influenced by fading.
propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis
Authors: Quinn Thomas , Richardson Mark F. , Lovell David , Crowley Tamsyn
Published: February 2017

In the life sciences, many assays measure only the relative abundances of components for each sample. These data, called compositional data, require special handling in order to avoid misleading conclusions. For example, in the case of correlation, treating relative data like absolute data can lead to the discovery of falsely positive associations. Recently, researchers have proposed proportionality as a valid alternative to correlation for calculating pairwise association in relative data. Although the question of how to best measure proportionality remains open, we present here a computationally efficient R package that implements two proposed measures of proportionality. In an effort to advance the understanding and application of proportionality analysis, we review the mathematics behind proportionality, demonstrate its application to genomic data, and discuss some ongoing challenges in the analysis of relative abundance data.
SvABA: Genome-wide detection of structural variants and indels by local assembly
Authors: Wala Jeremiah , Bandopadhayay Pratiti , Greenwald Noah , O’Rourke Ryan , Sharpe Ted , Stewart Chip , Schumacher Steve , Li Yilong , Weischenfeldt Joachim , Yao Xiaotong , Nusbaum Chad , Campbell Peter , Meyerson Matthew , Zhang Cheng-Zhong , Imielinski Marcin , Beroukhim Rameen
Published: February 2017

Structural variants (SVs), including small insertion and deletion variants (indels), are challenging to detect through standard alignment-based variant calling methods. Sequence assembly offers a powerful approach to identifying SVs, but is difficult to apply at-scale genome-wide for SV detection due to its computational complexity and the difficulty of extracting SVs from assembly contigs. We describe SvABA, an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements. We evaluated SvABA’s performance on the NA12878 human genome and in simulated and real cancer genomes. SvABA demonstrates superior sensitivity and specificity across a large spectrum of SVs, and substantially improved detection performance for variants in the 20-300 bp range, compared with existing methods. SvABA also identifies complex somatic rearrangements with chains of short (< 1,000 bp) templated-sequence insertions copied from distant genomic regions. We applied SvABA to 344 cancer genomes from 11 cancer types, and found that templated-sequence insertions occur in ~4% of all somatic rearrangements. Finally, we demonstrate that SvABA can identify sites of viral integration and cancer driver alterations containing medium-sized SVs.
Effects of Historical Coinfection on Host Shift Abilities of Exploitative and Competitive Viruses
Authors: Singhal Sonia , Turner Paul E.
Published: February 2017

Rapid evolution contributes to frequent emergence of RNA viral pathogens on novel hosts. However, accurately predicting which viral genotypes will emerge has been elusive. Prior work with lytic RNA bacteriophage f6 (family Cystoviridae) suggested that evolution under low multiplicity of infection (MOI; proportion of viruses to susceptible cells) selected for greater host exploitation, while evolution under high MOI selected for better intracellular competition against co-infecting viruses. We predicted that phage genotypes that experienced 300 generations of low MOI ecological history would be relatively advantaged in growth on two novel hosts. We inferred viral growth through changes in host population density, specifically by analyzing five attributes of growth curves of infected bacteria. Despite equivalent growth of evolved viruses on the original host, low MOI evolved clones were generally advantaged relative to high MOI clones in exploiting novel hosts. We also observed genotype-specific differences in clone infectivity: High fitness genotypes on the original host also performed better on novel hosts. Our results indicated that traits allowing greater exploitation of the original host correlated positively with performance on novel hosts. Based on infectivity differences of viruses from high versus low MOI histories, we suggest that prior MOI selection can later affect emergence potential.
Alcatel-Lucent falls, Huawei ascends: new product development makes the difference
Authors: Yan Jie , Wang Le , Xiong Jie
Published: February 2017

Purpose

This study aims to use the new product development (NPD) perspective to understand why traditional leading telecom equipment companies, such as Alcatel-Lucent (ALu), have stagnated but the newcomer Huawei has achieved steady growth.

Design/methodology/approach

This paper takes the form of a comparative case study.

Findings

Three significant differences in NPD process between the companies were discovered: first, although both companies claim that they are market-oriented, Huawei’s NPD projects are customer-driven, and ALu projects are joint considerations of customer demand and technology leadership; second, Huawei uses a design-to-value strategy, and ALu applies a design-for-quality-premium strategy; third, resources are allocated and shared at the corporate level in Huawei and at the business division level in ALu.

Practical implications

This study offers several implications for NPD managers. First, holding a market leader position is more important than being a technology leader. Companies must fundamentally change their mind-sets, restructure NPD models and prioritize and empower marketing and sales departments in the decision-making and management of NPD projects. Second, to maximize customer value, managers must balance cost and quality and avoid overengineering. A quality premium no longer necessarily leads to product competitiveness. Third, to improve the efficiency of NPD performance, companies must build up a mechanism to enable across-boundary resources.

Originality/value

This study highlights a number of key NPD strategy issues. It was conducted in the telecom equipment industry, but NPD managers of other industries will also gain useful insights from the discussion.
Tax havens: conduits for corporate tax malfeasance
Authors: Jalan Akanksha , Vaidyanathan R.
Published: February 2017

Purpose

This paper is an effort to demystify tax havens – what they mean, what they offer and why they are harmful. It offers a detailed analysis of abusive tax planning by multinational corporations, involving the use of tax havens, shedding light on how corporations use “egregious” tax-sheltering techniques right from their incorporation to avoid payment of income taxes. The paper also discusses global efforts against the phenomenon and policy recommendations.

Design/methodology/approach

The paper brings together definitions from various sources to accurately define and identify tax haven economies. The key contribution of the paper is to diagrammatically explain the use of tax havens by MNCs right from the time they are incorporated. It explains how every big and small corporate decision is motivated by the desire to save taxes and how tax havens come in handy for such corporations.

Findings

This paper finds that base erosion and profit shifting (BEPS) is a pervasive phenomenon, largely due to the suppliers of tax haven operations. Here, corporate decisions are divided into strategic and operational and further subdivided into investing, operating and financing activities, and provide real-life corporate examples of how tax havens fit into almost every corporate decision. This is the key contribution of the paper.

Research limitations/implications

This is a review paper that sums up knowledge about tax havens and their use by MNCs. It does not, however, use empirical data to corroborate its findings. It would be interesting to see empirically whether MNCs with greater tax haven operations actually have lower effective tax rates.

Practical implications

The paper can provide a framework for designing tax policies in a manner that geographical arbitrage can be minimized. It can enable formulation of the necessary incentive structures in the form of penalties, rewards and the like for both the users and providers of tax haven services to curb massive base and profit shifting out of high-tax countries.

Social implications

The paper is one small step in the direction of bringing about equality in tax payments, i.e. to align real tax systems with the canon of equality that Adam Smith once dreamt of. Taxes should be progressive in nature, implying that the amount of taxes paid should increase with one’s income. However, with the advent of offshore financial centres and egregious tax planning techniques, only the smaller corporations and middle-class individuals end up paying taxes, while the rich and bigger corporations get away easily.

Originality/value

The paper explores in detail the manner in which MNCs use, rather exploit, regulatory loopholes in tax systems of different countries to save on tax payments. By shifting their tax base from one country to another, MNCs not only hamper Treasury collections but also breed disrespect for the global tax system. The paper can help in designing tax laws in tune with such corporate motives.
Prospects of an online dispute resolution framework for Islamic Banks in Malaysia
Authors: Oseni Umar A. , Omoola Sodiq O.
Published: February 2017

Purpose

This study aims to examine the prospects of using an online dispute resolution (ODR) platform for resolving relevant Islamic banking disputes in the usual banker–customer relationship in Malaysia. It is argued that through proper regulation, such innovative dispute management mechanism would not only address some legal risks associated with banking disputes but could also prevent reputational risks in the Islamic financial services industry.

Design/methodology/approach

Based on an internet survey, responses were obtained from about 109 respondents in Malaysia. The data obtained were subjected to multivariate statistical analyses considering factors such as access to justice, attitude of stakeholders, resolving disputes, practical issues and understanding of ODR.

Findings

The results obtained showed that “access to justice”, “attitude of stakeholders” and “resolving disputes” are the most influencing factors affecting the intention to use ODR among stakeholders, particularly customers and bankers in the Islamic financial services industry in Malaysia.

Practical implications

This study provides a way in which the recently introduced Islamic Financial Services (Financial Ombudsman Scheme) Regulations 2015 can be better enhanced to cater for internet banking disputes which might require an ODR framework.

Originality/value

Though there have been numerous studies on the dispute resolution framework in the Islamic banking industry in Malaysia generally, the current study focuses on a less explored framework – ODR– a new framework for handling banking disputes.
Correlation of colour, antioxidant capacity and phytochemical diversity of imported saffron by principal components analysis
Authors: Anuar Nordiyanah , Taha R.M. , Mahmad Noraini , Mohajer Sadegh , Che Musa Siti Aisha Na’illa , Zainal Abidin Zul Hazrin
Published: February 2017

Purpose

The aim of the present study is to gain correlation between saffron colours, their antioxidant capacity and the constituents of the secondary metabolites of three different saffron samples commonly available in the Malaysian market.

Design/methodology/approach

In this study, saffron samples imported from Iran, Spain and Kashmir were extracted using methanol and the total antioxidant capacity were analysed using 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical-scavenging assay. Ultra-high performance liquid chromatography (UHPLC) and electrospray ionization coupled with mass spectrometry (ESI-MS/MS) were then used to identify secondary metabolites present in the saffron crude extracts. The colour variation of the saffron extract was expressed by the CIELAB colorimeter in terms of lightness (L*), greenness (a*), yellowness (b*), chroma (C) and hue angle (H°). Principle component analysis (PCA) was carried out to analyse the similarities and correlation between variables.

Findings

This study reveals that antioxidant has a positive correlation with flavanols, especially quercetin and kaempferol. In addition, colour appearance is not necessarily an indicator for the antioxidant level.

Research limitations/implications

The major classes of polyphenolics identified in saffron methanolic crude extract are flavonoids and phenolic acids. Further improvements in the extraction and identification methods may find other compounds that could attribute to the visual factors and antioxidant capacity as a complement for this preliminary study.

Practical implications

This analysis provides comparison basis and valuable information for saffron consumers in Malaysia depending on the consumers’ purpose of whether to have a certain desired colour or health benefits.

Originality/value

A comparative study about saffron product available in Malaysian market is original. To the best of the authors’ knowledge, this is the first attempt of evaluation on a saffron product that has been carried out in Malaysia.
Influence of acid hydrolysis on properties of maize starch adhesive
Authors: Qiao Zhibang , Lv Shanshan , Gu Jiyou , Tan Haiyan , Shi Junyou , Zhang Yanhua
Published: February 2017

Purpose

The purpose of this paper is to obtain high-solids-content and low-viscosity starch adhesive, and improve bonding strength of the pure starch adhesive.

Design/methodology/approach

Maize starch was treated by hydrochloric acid solution with different concentrations, and acid-thinned starch adhesive was prepared. Polyisocyanate as a crosslinking agent was added to improve water resistance of the pure starch adhesive.

Findings

The physical and chemical properties of the acid-thinned starch adhesive were characterised. Acid hydrolysis did not change structure of starch granules, but increased its crystallinity. After acid modification, starch granules became less smooth and some fragments appeared. Acid treatment had little influence on thermal stability of starch, when acid hydrolysis was not strong. High concentration of HCl solution led to starch granules being destroyed, resulting in decrease in bonding strength. The optimal HCl concentration was 0.5 mol/L. Polyisocyanate addition was beneficial to improve the bonding strength of the acid-thinned starch adhesive.

Research limitations/implications

Acid hydrolysis changed the properties of the starch adhesive.

Practical implications

Acid hydrolysis decreased viscosity of the starch adhesive and improved its solids content, which had a positive effect on the application of the starch adhesive.

Social implications

It was helpful to develop an environment-friendly, natural polymer-based wood adhesive.

Originality/value

The properties of acid-thinned starch and acid-thinned starch adhesive were studied.
A study on mechanical, thermal and flame retardant properties of epoxy/expandable graphite composites
Authors: Mamani Arezoo , Ebrahimi Morteza , Ataeefard Maryam
Published: February 2017

Purpose

The purpose of this paper is to investigate the effect of expandable graphite (EG) plates’ incorporation on the mechanical, thermal and fire-retardant properties of an epoxy–aliphatic amine system. In addition, the optimum amount of EG in epoxy/EG composites is determined to achieve the best thermal and mechanical properties at the same time.

Design/methodology/approach

The epoxy/EG composites were prepared by using (1-4) phr of EG. The morphological structure of epoxy/EG composites was studied by using scanning electron microscopy. The thermal, flame-retardant and mechanical properties of epoxy/EG composites were evaluated by using thermogravimetric analysis (TGA), oxygen index test and dynamic mechanical analysis and tensile and impact test, respectively.

Findings

TGA results showed that the incorporation of EG to the epoxy resin increased the initial decomposition temperature and residue weight of the composites. It was found that, with increasing EG concentration up to 4 phr, the oxygen index, glass transition temperature and Young’s modulus of epoxy/EG composites increased up to 60 per cent, 4.1°C and 50 per cent, respectively. On the other hand, the sample with 2 phr EG provided the maximum values of tensile strength, storage modulus, cross-linking density, ultimate tensile strain and impact strength.

Practical implications

Prepared epoxy/EG composites can be used as halogen-free flame-retardant composites. The proposed process for the preparation of the composites is simple and can easily be implicated in the industry.

Originality/value

To the best of the authors’ knowledge, there is no other publication that considers mechanical, thermal and fire-retardant properties of epoxy/EG composites in one paper. In this work, the optimum concentration of EG in epoxy/EG composites was determined, considering all these properties.
Elevated transglutaminase‐2 expression in the epidermis of psoriatic skin and its role in the skin lesion development
Authors: Su Ching‐Chyuan , Su Tzu‐Rong , Lai Ji‐Ching , Tsay Gregory‐J , Lin Hung‐Ke
Published: February 2017

Psoriasis, an inflammatory skin disease triggered by the immune system, presents keratinocyte hyperproliferation, differentiation and angiogenesis. The role of transglutaminase‐2 (TG2) in psoriasis has not been fully established yet. In this retrospective, non‐randomized and non‐blinded study, skin biopsies were collected from 37 psoriatic patients and immunohistochemical staining was performed. TG2 staining was positive in all 37 samples, among which 32 were strong and five weak. The localization of TG2 staining was present in the epidermis and spreading from basal layer to stratum granulosum in decreasing staining intensity. However, TG2 was also expressed in the basal layer in the non‐lesional site of psoriasis and the skin of healthy people. The presence of TG2 was not associated with disease duration, stage of disease and subtype of psoriasis. Overexpression of TG2 seems to be an important role in psoriatic development.
Identification of second arginine‐glycine‐aspartic acid motif of ovine vitronectin as the complement C9 binding site and its implication in bacterial infection
Authors: Prasada Rao T. , Lakshmi Prasanth T. , Parvathy R. , Murugavel S. , Karuna Devi , Paritosh Joshi
Published: February 2017

Vitronectin (Vn), a multifunctional protein of blood and extracellular matrix, interacts with complement C9. This interaction may modulate innate immunity. Details of Vn–C9 interactions are limited. Vn–C9 interactions were assessed by employing a goat homologous system and observing Vn binding to C9 in three different assays. Using recombinant fragments, C9 binding was mapped to the N‐terminus of Vn. Site directed mutagenesis was performed to alter the second arginine glycine aspartic acid (RGD) sequence (RGD‐2) of Vn. Changing R to G or D to A in RGD‐2 caused significant decrease in Vn binding to C9 whereas changing of R to G in the first RGD motif (RGD‐1) had no effect on Vn binding to C9. These results imply that the RGD‐2 of goat Vn is involved in C9 binding. In a competitive binding assay, the presence of soluble RGD peptide inhibited Vn binding to C9 whereas heparin had no effect. Vn binding to C9 was also evaluated in terms of bacterial pathogenesis. Serum dependent inhibition ofEscherichia coligrowth was significantly reverted when Vn or its N‐fragment were included in the assay. The C‐fragment, which did not support C9 binding, also partly nullified serum‐dependent inhibition of bacterial growth, probably through other serum component(s).
HEURISTICS AND BIASES, RATIONAL CHOICE, AND SANCTION PERCEPTIONS*
Authors: POGARSKY GREG , ROCHE SEAN PATRICK , PICKETT JUSTIN T.
Published: February 2017

The relevance of several cognitive heuristics and related biases for rational choice perspectives on crime, and for perceptions of sanction risk, were investigated. We present findings from a series of randomized experiments, embedded in two nationwide surveys of American adults (18 and older) in 2015 (N = 1,004 and 623). The results reveal that offender estimates of detection risk are less probabilistically precise and more situationally variable than under prevailing criminological perspectives, most notably, rational choice and Bayesian learning theories. This, in turn, allows various decision‐making heuristics—such as anchoring and availability—to influence and potentially bias the perceptual updating process.