bluuebunny/crossref_metadata_2025 huggingface dataset:
Shedding light on black boxes in protein identification
Authors: Vaudel Marc , Venne A. Saskia , Berven Frode S. , Zahedi René P. , Martens Lennart , Barsnes Harald
Published: February 2014

Performing a well thought‐out proteomics data analysis can be a daunting task, especially for newcomers to the field. Even researchers experienced in the proteomics field can find it challenging to follow existing publication guidelines for MS‐based protein identification and characterization in detail. One of the primary goals of bioinformatics is to enable any researcher to interpret the vast amounts of data generated in modern biology, by providing user‐friendly and robust end‐user applications, clear documentation, and corresponding teaching materials. In that spirit, we here present an extensive tutorial for peptide and protein identification, available at http://compomics.com/bioinformatics‐for‐proteomics. The material is completely based on freely available and open‐source tools, and has already been used and refined at numerous international courses over the past 3 years. During this time, it has demonstrated its ability to allow even complete beginners to intuitively conduct advanced bioinformatics workflows, interpret the results, and understand their context. This tutorial is thus aimed at fully empowering users, by removing black boxes in the proteomics informatics pipeline.
Cathepsin B: Multiple roles in cancer
Authors: Aggarwal Neha , Sloane Bonnie F.
Published: February 2014

Proteases, including intracellular proteases, play roles at many different stages of malignant progression. Our focus here is cathepsin B, a lysosomal cysteine cathepsin. High levels of cathepsin B are found in a wide variety of human cancers, levels that often induce secretion and association of cathepsin B with the tumor cell membrane. In experimental models, such as transgenic models of murine pancreatic and mammary carcinomas, causal roles for cathepsin B have been demonstrated in initiation, growth/tumor cell proliferation, angiogenesis, invasion, and metastasis. Tumor growth in transgenic models is promoted by cathepsin B in tumor‐associated cells, for example, tumor‐associated macrophages, as well as in tumor cells. In transgenic models, the absence of cathepsin B has been associated with enhanced apoptosis, yet cathepsin B also has been shown to contribute to apoptosis. Cathepsin B is part of a proteolytic pathway identified in xenograft models of human glioma; targeting only cathepsin B in these tumors is less effective than targeting cathepsin B in combination with other proteases or protease receptors. Understanding the mechanisms responsible for increased expression of cathepsin B in tumors and association of cathepsin B with tumor cell membranes is needed to determine whether targeting cathepsin B could be of therapeutic benefit.
Structure and function of LGR5: An enigmatic G‐protein coupled receptor marking stem cells
Authors: Kumar Kaavya Krishna , Burgess Antony W. , Gulbis Jacqueline M.
Published: February 2014

G‐protein coupled receptors (GPCRs) are an important class of membrane protein that transmit extracellular signals invoked by sensing molecules such as hormones and neurotransmitters. GPCR dysfunction is implicated in many diseases and hence these proteins are of great interest to academia and the pharmaceutical industry. Leucine‐rich repeat‐containing GPCRs contain a characteristic extracellular domain that is an important modulator of intracellular signaling. One member of this class is the leucine‐rich repeat‐containing G‐protein‐coupled receptor 5 (LGR5), a stem cell marker in intestinal crypts, and mammary glands. LGR5 modulates Wnt signaling in the presence of the ligand R‐spondin (RSPO). The mechanism of activation of LGR5 by RSPO is not understood, nor is the intracellular signaling mechanism known. Recently reported structures of the extracellular domain of LGR5 bound to RSPO reveal a horseshoe‐shaped architecture made up of consecutive leucine‐rich repeats, with RSPO bound on the concave surface. This review discusses the discovery of LGR5 and the impact it is having on our understanding of stem cell and cancer biology of the colon. In addition, it covers functional relationships suggested by sequence homology and structural analyses, as well as some intriguing conundrums with respect to the involvement of LGR5 in Wnt signaling.
Coherent electronic conductance of a nanowire in the presence of electron–phonon interaction
Authors: Mardaani Mohammad , Rabani Hassan
Published: February 2014

We study the effect of electron–phonon (e–ph) interaction on the coherent electronic conductance of a one‐dimensional extended nanowire within the nearest‐neighbour tight‐binding and harmonic approximations. We suppose that the electrodes at the end of the wire are rigid and the e–ph interaction exists only in the centre of the wire. Therefore, we can use closed boundary conditions to diagonalize the phononic part of the centre wire Hamiltonian. After separating the phononic modes, we employ the Green's function technique for the electronic tight‐binding Hamiltonian. Then, we calculate the electron transmission coefficient in the adiabatic regime at zero bias. The model is applied to a uniform chain and wires, which have alternating on‐site or hopping energies. The results show that in all of these systems, the e–ph interaction has more effect on the conductance at the edges of the energy band. Additionally, in the systems including an internal gap, the effect of the e–ph interaction is negligible in the gap region, especially for long lengths of the centre wire.
Effect of phonon focusing on the temperature dependence of thermal conductivity of silicon
Authors: Kuleyev I. I. , Kuleyev I. G. , Bakharev S. M. , Inyushkin A. V.
Published: February 2014

The effect of phonon focusing on the temperature dependence of thermal conductivity of single crystalline silicon is studied at temperatures from 3 to 40 K in the frame of generalized Callaway theory. Thermal conductivity has been calculated for silicon samples in the form of finite length rectangular rods with different orientations of long axis and side faces. To evaluate the phonon scattering rate due to diffuse boundary scattering, the analytical expressions derived recently by us were utilized. Theoretical results representing the dependence of on temperature and sample orientation are in agreement with experimental data. Contributions of different phonon polarizations to the thermal conductivity have been analyzed. The transverse phonon branches are most important as expected, the slow transverse mode being the most prominent in the formation of conductivity anisotropy. The phonon dispersion was found to have a weak effect on the calculated at these temperatures.
Semiconductor Nanostructures towards Electronic and Optoelectronic Device Applications
Authors: André Pascal , Reece Peter , Tomm Jens W. , Ribierre Jean‐Charles , Moreels Iwan
Published: February 2014

Semiconductor nanostructures are part of an emergent class of materials that provide unprecedented levels of functionality in building devices for electronics and optoelectronics applications. Associated nanoscale devices may be used to study new physics in low‐dimensional systems and enables a route for the development of new technologies in key areas, such as communications and information processing, sensing and renewable energy as well as biomedicine.

This symposium was the fourth instalment of a highly successful biennial series that began in 2007. Bringing together researchers working in academia and industry, it presented the latest research in semiconductor nanostructures and their applications to electronic, optoelectronic and photonic devices. Blending experimental with numerical and theoretical approaches, it covered all aspects from fundamental growth and material development, to interfaces, device integration and testing.
Functional Nanowires: Synthesis, Characterization and Applications
Authors: Méndez Bianchi , Lorenz Katharina , Fraboni Beatrice , Ambacher Oliver
Published: February 2014

This special issue contains papers presented at E‐MRS Spring Meeting – Symposium P “Functional Nanowires: Synthesis, Characterization and Applications”, which took place in Strasbourg, France, May 27–31, 2013.

The aim of the symposium was to gather researchers involved in studying relevant physical properties and applications of functional nanowires. The promising novel or improved properties of nanowires have been demonstrated in several families of functional materials, and we had organized the sessions accordingly. They were distributed on the following oral sessions: III–V semiconductors, Oxides, Group IV semiconductors, Doping features and Organic nanowires, Sensing and self‐assembly. Additionally, two poster sessions were held. There were more than 110 contributions, including invited speakers, oral and poster presentations, coming from 30 different countries, spanning five continents. It is worth mentioning the remarkable participation of Asia, with 32 contributions.

The organizing committee would like to thank all the participants for trusting on our symposium, contribute to create an enjoyable atmosphere during the sessions and enrich them with their latest nanowires research. It has been our pleasure to introduce this special issue with some papers presented at the symposium. We would also like to thank the E‐MRS Chairpersons and the company FEI for their support and for making the organization features easier.
The Long Road to Prosperity in CEE
Authors: Snip Eelco
Published: February 2014

Worries over economic outlook, but investment from China may boost region.
How Does Your Cappuccino Feel?
Authors: Pawle John , Delfaud Dominique
Published: February 2014

Using synaesthesia to measure emotional responses to different flavours.
ToF‐SIMS depth profiling of insulating samples, interlaced mode or non‐interlaced mode?
Authors: Wang Zhaoying , Jin Ke , Zhang Yanwen , Wang Fuyi , Zhu Zihua
Published: February 2014

Dual‐beam depth profiling strategy has been widely adopted in time‐of‐flight secondary ion mass spectrometry depth profiling, in which two basic operation modes, interlaced mode and non‐interlaced mode, are commonly used. Generally, interlaced mode is recommended for conductive or semi‐conductive samples, whereas non‐interlaced mode is recommended for insulating samples, where charge compensation can be an issue. Recent publications, however, show that the interlaced mode can be used effectively for glass depth profiling, despite the fact that glass is an insulator. In this study, we provide a simple guide for choosing between interlaced mode and non‐interlaced mode for insulator depth profiling. Two representative cases are presented: (i) depth profiling of a leached glass sample and (ii) depth profiling of a single‐crystal MgO sample. In summary, the interlaced mode should be attempted first, because (i) it may provide data with reasonable quality, (ii) it is time‐saving for most cases, and (iii) it introduces low H/C/O background. If data quality is the top priority and measurement time is flexible, non‐interlaced mode is recommended because interlaced mode may suffer from low signal intensity and poor mass resolution. A big challenge is tracking trace H/C/O in a highly insulating sample (e.g., MgO), because non‐interlaced mode may introduce strong H/C/O background, but interlaced mode may suffer from low signal intensity. Meanwhile, a C or Au coating is found to be very effective to improve the signal intensity. Surprisingly, the best analyzing location is not on the C or Au coating but at the edge (outside) of the coating. Copyright © 2014 John Wiley & Sons, Ltd.
Reconceptualizing competitive dynamics: A multidimensional framework
Authors: Chen Ming‐Jer , Miller Danny
Published: February 2014

Competitive dynamics research, despite progress, lacks a conceptual framework that can extend the field's reach to address today's environment. Increasing stakeholder power and globalization are but two of the organizational and economic forces compelling a broader conceptualization of competition. Our framework expands competitive dynamics along five dimensions—aims of competition, mode of competing, roster of actors, action toolkit, and time horizon of interaction—that prove useful for contrasting the rivalrous and competitive‐cooperative modes and a new approach we call relational competition. We draw conjectures about the moderators, such as industry and culture, that determine the appropriateness of these forms of interaction, and conclude by relating our method to three discrete perspectives: the configurational, transaction cost, and stakeholder views. Copyright © 2014 John Wiley & Sons, Ltd.
N‐Doped Graphene Field‐Effect Transistors with Enhanced Electron Mobility and Air‐Stability
Authors: Xu Wentao , Lim Tae‐Seok , Seo Hong‐Kyu , Min Sung‐Yong , Cho Himchan , Park Min‐Ho , Kim Young‐Hoon , Lee Tae‐Woo
Published: February 2014

Although graphene can be easily p‐doped by various adsorbates, developing stable n‐doped graphene that is very useful for practical device applications is a difficult challenge. We investigated the doping effect of solution‐processed (4‐(1,3‐dimethyl‐2,3‐dihydro‐1H‐benzoimidazol‐2‐yl)phenyl)dimethylamine (N‐DMBI) on chemical‐vapor‐deposited (CVD) graphene. Strong n‐type doping is confirmed by Raman spectroscopy and the electrical transport characteristics of graphene field‐effect transistors. The strong n‐type doping effect shifts the Dirac point to around ‐140 V. Appropriate annealing at a low temperature of 80 ºC enables an enhanced electron mobility of 1150 cm2 V−1 s−1. The work function and its uniformity on a large scale (1.2 mm × 1.2 mm) of the doped surface are evaluated using ultraviolet photoelectron spectroscopy and Kelvin probe mapping. Stable electrical properties are observed in a device aged in air for more than one month.
Profiling left and right ventricular proportional output during fetal life with a novel systolic index in the aortic isthmus
Authors: Chabaneix J. , Fouron J. C. , Sosa‐Olavarria A. , Gendron R. , Dahdah N. , Berger A. , Brisebois S.
Published: February 2014

Objective

Left ventricular ejection causes forward flow in the fetal aortic isthmus while the right ventricle has a retrograde influence. The aim of this study was to create reference values for an isthmic systolic index (ISI) reflecting the changing influence of right and left ventricular performance on Doppler flow velocity waveforms of the aortic isthmus throughout normal pregnancy.

Methods

Doppler recordings of 260 normal fetuses with a gestational age of 18–37 weeks were reviewed. Peak systolic velocity (PSV) and end‐systolic velocity (or systolic nadir; Ns) were measured on all aortic isthmus waveforms. An ISI was derived from the ratio Ns/PSV. Left and right ventricular outputs were also calculated.

Results

Up to 22–23 weeks' gestation, the mean ISI is stable at around 0.2. At about 28 weeks, a brief end‐systolic deceleration wave is observed on the aortic isthmus waveforms, progressing steadily with gestation and causing a fall of ISI towards a mean value of zero between 30 and 31 weeks. This trend continues thereafter and a mean value of –0.4 was observed at the end of pregnancy. An inverse correlation was found between right ventricular output and Ns (r = –0.334, P = 0.001). Simultaneous recordings of the isthmus and the ductus arteriosus Doppler waveforms demonstrated that the primary cause of the end‐systolic deceleration and ultimate reversal of flow at the isthmus is the increasingly dominant flow from the right ventricle.

Conclusion

The transitional changes of the respective right and left ventricular outputs throughout pregnancy are well profiled by the ISI. This index highlights the physiological increase in fetal right ventricle flow preponderance as pregnancy progresses. Alteration of the ISI profile could be expected in clinical conditions associated with unbalanced alteration of the fetal ventricular outputs. Copyright © 2014 ISUOG. Published by John Wiley & Sons Ltd
Real traffic logs creation for testing intrusion detection systems
Authors: El‒Hajj Wassim , Al‒Tamimi Mustafa , Aloul Fadi
Published: February 2014

Port scanning is one of the most popular reconnaissance techniques that many attackers use to profile running services on a potential target before launching an attack. Many port scanning detection mechanisms have been suggested in literature. To test the proposed detection approaches, researchers use data sets that are available online or simulate their own. However, the available data sets do not provide complete logs and are usually outdated. Furthermore, the simulated data sets provide logs that do not resemble real‒life scenarios. These deficiencies in the available data sets highly affect the performance of testing the intrusion detection systems (IDSs) and result in poor evaluations. Meanwhile, very little work has been done on generating port scanning benchmarks that researchers can use to test their detection methods. In this work, we suggest a simulation framework using OMNeT++ to generate benchmarks that resemble real‒life traffic. We approach the problem by dividing it into three modules: (1) topology creation; (2) good traffic generation; and (3) bad traffic generation, each of which are made realistic, similar to deployed and usable networks. The benchmark is then tested using Snort and MalwareAnalysis. The tested IDSs were not able to catch many of the generated port scanning attacks, specifically the slow and distributed ones. We also measured the attack detection efficiency of the IDSs under different loads of background activities. Hence, the proposed framework and the annotated benchmarks will provide researchers and industry with an effective way of testing the power of IDSs' port scanning detection modules. Copyright © 2014 John Wiley & Sons, Ltd.
Using symbols: developmental perspectives
Authors: Uttal David H. , Yuan Lei
Published: February 2014

The frequent and fluent use of symbols is a distinguishing characteristic of human thought and communication. Symbols free us from the bounds of our own direct experience and allow us to learn about the world from others. To use a symbol, children need to (1) understand the intention that led to the creation and use of the symbol, and (b) how the symbol relates to its referent. For example, to use a map, children need to know that it is intended to communicate spatial information, and how locations on the map correspond to locations in the world. In some cases, even very young children are capable of meeting both requirements. For example, infants quickly learn that people intend to communicate when they use words. Moreover, they quickly learn the meanings of many specific words and the objects or concepts that they stand for. In other cases, such as learning to use maps of large‐scale space, children may struggle to understand what the symbol is intended to communicate and the specific relations between elements of the symbol and their referents in the world. Here we review the development of children's understanding of words, photographs, scale models, maps, and text. We consider when and how children gain insight into the communicative intent of each of these symbols and how they learn to establish connections between the symbol and what it represents. This review helps to integrate research on the development of children's understanding of a variety of symbol systems.

This article is categorized under:

Linguistics > Language in Mind and Brain

Psychology > Development and Aging

Psychology > Learning
Understanding the mind from an evolutionary perspective: an overview of evolutionary psychology
Authors: Shackelford Todd K. , Liddle James R.
Published: February 2014

The theory of evolution by natural selection provides the only scientific explanation for the existence of complex adaptations. The design features of the brain, like any organ, are the result of selection pressures operating over deep time. Evolutionary psychology posits that the human brain comprises a multitude of evolved psychological mechanisms, adaptations to specific and recurrent problems of survival and reproduction faced over human evolutionary history. Although some mistakenly view evolutionary psychology as promoting genetic determinism, evolutionary psychologists appreciate and emphasize the interactions between genes and environments. This approach to psychology has led to a richer understanding of a variety of psychological phenomena, and has provided a powerful foundation for generating novel hypotheses. Critics argue that evolutionary psychologists resort to storytelling, but as with any branch of science, empirical testing is a vital component of the field, with hypotheses standing or falling with the weight of the evidence. Evolutionary psychology is uniquely suited to provide a unifying theoretical framework for the disparate subdisciplines of psychology. An evolutionary perspective has provided insights into several subdisciplines of psychology, while simultaneously demonstrating the arbitrary nature of dividing psychological science into such subdisciplines. Evolutionary psychologists have amassed a substantial empirical and theoretical literature, but as a relatively new approach to psychology, many questions remain, with several promising directions for future research.

This article is categorized under:

Cognitive Biology > Evolutionary Roots of Cognition

Cognitive Biology > Genes and Environment

Psychology > Theory and Methods
Pneumococcal empyema and complicated pneumonias: global trends in incidence, prevalence, and serotype epidemiology
Authors: Fletcher M. A. , Schmitt H.-J. , Syrochkina M. , Sylvester G.
Published: February 2014

This review evaluates the serotype epidemiology of complicated pneumococcal pneumonia (CPP) during the period 1990–2012. PubMed and EMBASE were searched using the terms “empyema”, “complicated pneumonia”, “pleural infection”, “necrotizing pneumonia”, “pleural effusion”, “parapneumonic effusion”, “pneumatocele”, or “lung abscess”; “pneumococcal” or “Streptococcus pneumoniae”; and “serotype” for studies on the epidemiology of complicated pneumonias published from January 1, 1990 to October 1, 2013. Studies with data on incidence and serotypes were included; reviews, case reports, and conference abstracts were excluded. Of 152 papers, 84 fitted the inclusion criteria. A few pneumococcal serotypes were predominant causes of CPP, particularly serotypes 1, 19A, 3, 14, and 7F. CPP was a more common manifestation of pneumococcal disease among older (>2 years old) than younger children. The data support increases in both reported incidence rates and proportions of CPP in children and adults during the period 1990–2012; specific increases varied by geographic region. The proportions of serotype 3 and, particularly in Asia, serotype 19A CPP have increased, whereas most studies show declines in serotype 14. Serotype 1 has been a predominant cause of CPP since 1990, while antibiotic resistance was infrequent among serotype 1 isolates. The reported incidence and proportions of CPP among pneumonia cases steadily increased from 1990 to 2012. Several factors might account for these increases, including enhanced disease detection due to a higher index of suspicion, more sophisticated diagnostic assays, and changes in the prevalence of serotypes with capacity to invade the pleural space that were not targeted by the 7-valent pneumococcal conjugate vaccine (PCV7).
Effects of oxytetracycline on populations and community metabolism of an aquatic microcosm
Authors: Shibata Kenichi , Amemiya Takashi , Itoh Kiminori
Published: February 2014

To investigate the ecological impacts of a widely‐used antibiotic agent oxytetracycline (OTC), we prepared an aquatic microcosm consisting of two green algae (Chlorella sp. and Scenedesmus sp.), a blue‐green alga (Tolypothrix sp.), a protozoan (Cyclidium sp.), two rotifers (Philodina sp. and Lecane sp.), an aquatic oligochaete (Aeolosoma hemprichi), and bacteria. We investigated the effects of OTC on population abundance of composite species, gross primary production (GPP), and community respiration (CR). We linked population abundance, GPP and CR to understand the relationship between these measures. First, ‘experimental respiration rate of heterotrophs’ (HRexp) was obtained by CR minus algal respiration that is calculated by 0.35 × GPP. Next, the population respiration of each heterotroph was calculated from the direct measure of population abundance and the assumed constant of per‐capita respiration. We defined the sum of the population respirations across all heterotrophs as ‘theoretical respiration rate of heterotrophs’ (HRtheo). Finally, relative community metabolism (RCM) of the heterotrophic community was obtained by calculating the ratio of HRexp to HRtheo that indicates changes in specific respiration rates as a whole in the community. The influence of OTC on RCM was larger than on CR, thus the effect of OCT on the metabolism of heterotrophs was far more severe than expected from CR. RCM can magnify the rate of change in the original data, and facilitate the detection of influences in ecotoxicological studies.
Reflections on having a ‘calling’ as a medical doctor
Authors: Westerman Michiel
Published: February 2014

None
Predicting Variation in Repertoire Size with the NBD Model
Authors: Trinh Giang
Published: February 2014

This paper proposes and validates the negative binomial distribution (NBD) to predict the variation in repertoire size (the number of brands purchased by a consumer in a specific time period) within a category. From a managerial perspective, the variation is crucial for brand managers who would like to know the nature and intensity of competition that is facing their brands. Empirical findings across multiple datasets from UK consumer packaged goods demonstrate that the NBD model predicts variations in repertoire size very well in different time periods (1year, 18months and 3years), and different buyer groups (light and heavy category buyers). The paper then suggests a simple method to predict those who are brand exclusively loyal, those who are loyal to a few brands, and those who are diversified to buy multiple brands, based on very little information such as category and brand penetrations, using the parameters of the NBD model.
Analysis of covalent flavinylation using thermostable succinate dehydrogenase from Thermus thermophilus and Sulfolobus tokodaii lacking SdhE homologs
Authors: Kounosu Asako
Published: February 2014

Recent studies have indicated that post‐translational flavinylation of succinate dehydrogenase subunit A (SdhA) in eukaryotes and bacteria require the chaperone‐like proteins Sdh5 and SdhE, respectively. How does covalent flavinylation occur in prokaryotes, which lack SdhE homologs? In this study, I showed that covalent flavinylation in two hyperthermophilic bacteria/archaea lacking SdhE, Thermus thermophilus and Sulfolobus tokodaii, requires heat and dicarboxylic acid. These thermophilic bacteria/archaea inhabit hot environments and are said to be genetically far removed from mesophilic bacteria which possess SdhE. Since mesophilic bacteria have been effective at covalent bonding in temperate environments, they may have caused the evolution of SdhE.
Ursolic acid, a natural pentacyclic triterpenoid, inhibits intracellular trafficking of proteins and induces accumulation of intercellular adhesion molecule‐1 linked to high‐mannose‐type glycans in the endoplasmic reticulum
Authors: Mitsuda Satoshi , Yokomichi Tomonobu , Yokoigawa Junpei , Kataoka Takao
Published: February 2014

Ursolic acid (3β‐hydroxy‐urs‐12‐en‐28‐oic acid) is a natural pentacyclic triterpenoid that is present in many plants, including medicinal herbs, and foods. Ursolic acid was initially identified as an inhibitor of the expression of intercellular adhesion molecule‐1 (ICAM‐1) in response to interleukin‐1α (IL‐1α). We report here a novel biological activity: ursolic acid inhibits intracellular trafficking of proteins. Ursolic acid markedly inhibited the IL‐1α‐induced cell‐surface ICAM‐1 expression in human cancer cell lines and human umbilical vein endothelial cells. By contrast, ursolic acid exerted weak inhibitory effects on the IL‐1α‐induced ICAM‐1 expression at the protein level. Surprisingly, we found that ursolic acid decreased the apparent molecular weight of ICAM‐1 and altered the structures of N‐linked oligosaccharides bound to ICAM‐1. Ursolic acid induced the accumulation of ICAM‐1 in the endoplasmic reticulum, which was linked mainly to high‐mannose‐type glycans. Moreover, in ursolic‐acid‐treated cells, the Golgi apparatus was fragmented into pieces and distributed over the cells. Thus, our results reveal that ursolic acid inhibits intracellular trafficking of proteins and induces the accumulation of ICAM‐1 linked to high‐mannose‐type glycans in the endoplasmic reticulum.
A dynamic view of cultural influence: A review
Authors: Briley Donnel , Wyer Robert S. , Li En
Published: February 2014

Static models of culture's influence have given way to a dynamic view, which identifies not only differences across cultures in people's judgments and decisions, but also the situations and conditions in which these differences do or do not appear. Theory and evidence developed from a cognitive psychological perspective underlie this dynamic approach, including research emerging from the “dynamic constructivist” and “situated cognition” models. In the present review, we focus on findings that confirm the utility of this cognitively oriented approach, and briefly discuss the advantages and complementary nature of the “social collective” and neuroscience approaches to understanding culture.
A Study of the Predictive Value of the Modified Tokuhashi Score in Metastatic Spinal Tumour Causing Cord Compression in a Southern Chinese Population
Authors: Yuk-Nam Yeung , Ka-Kin Cheung , Tai-Chung Lam , Hung-On Cheng , Yuk-Yin Chow
Published: February 2014

Introduction

It is generally agreed that operative intervention is beneficial in carefully selected groups of patients with metastatic spinal cord compression (MSCC). Tokuhashi et al have presented a preoperative scoring system to predict patient survival, which is widely used as a guideline for making a decision on whether to operate or not. However, only limited data are available regarding the validity of the Tokuhashi score in Southern Chinese populations.

Materials and methods

We report a series of 128 patients treated in our hospital from 2000 to 2010. All patients were diagnosed to have spinal metastasis of different origins with cord compression. Of the 128, 59 underwent operation and the remaining 69 received conservative treatments. The Tokuhashi score was then calculated retrospectively. The survival rate was analysed and p < 0.05 was considered statistically significant.

Results

In our series, the accuracy of the modified Tokuhashi scoring for predicting the survival rate in patients with MSCC was demonstrated to be 79% (101/128). The poor prognostic group showed statistically significant worse survival than the two better prognostic groups. The type of primary cancer (p = 0.0015), visceral metastasis (p = 0.006), and the general condition (p < 0.001) were confirmed as significant survival prognostic factors. Nasopharyngeal carcinoma (NPC) had the most favourable outcome with a mean survival of 20.1 months.

Conclusion

The modified Tokuhashi score was statistically correlated to the overall survival of MSCC patients in a Southern Chinese population. The type of primary cancer, visceral metastasis, and the general condition were statistically significant survival factors. We recommend weighting a higher score for NPC in the modified Tokuhashi scoring system in view of its favourable prognosis.
Antibody‐independent targeted quantification of TMPRSS2‐ERG fusion protein products in prostate cancer
Authors: He Jintang , Sun Xuefei , Shi Tujin , Schepmoes Athena A. , Fillmore Thomas L. , Petyuk Vladislav A. , Xie Fang , Zhao Rui , Gritsenko Marina A. , Yang Feng , Kitabayashi Naoki , Chae Sung-Suk , Rubin Mark A. , Siddiqui Javed , Wei John T. , Chinnaiyan Arul M. , Qian Wei-Jun , Smith Richard D. , Kagan Jacob , Srivastava Sudhir , Rodland Karin D. , Liu Tao , Camp David G.
Published: February 2014

Fusions between the transmembrane protease serine 2 (TMPRSS2) and ETS related gene (ERG) represent one of the most specific biomarkers that define a distinct molecular subtype of prostate cancer. Studies of TMPRSS2‐ERG gene fusions have seldom been performed at the protein level, primarily due to the lack of high‐quality antibodies suitable for quantitative studies. Herein, we applied a recently developed PRISM (high‐pressure high‐resolution separations with intelligent selection and multiplexing)‐SRM (selected reaction monitoring) strategy for quantifying ERG protein in prostate cancer cell lines and tumors. The highly sensitive PRISM‐SRM assays provided confident detection of 6 unique ERG peptides in both TMPRSS2‐ERG positive cell lines and tissues, but not in cell lines or tissues lacking the TMPRSS2‐ERG rearrangement, clearly indicating that ERG protein expression is significantly increased in the presence of the TMPRSS2‐ERG gene fusion. Significantly, our results provide evidence that two distinct ERG protein isoforms are simultaneously expressed in TMPRSS2‐ERG positive samples as evidenced by the concomitant detection of two mutually exclusive peptides in two patient tumors and in the VCaP prostate cancer cell line. Three peptides, shared across almost all fusion protein products, were determined to be the most abundant peptides, providing “signature” peptides for detection of ERG over‐expression resulting from TMPRSS2‐ERG gene fusion. The PRISM‐SRM assays provide valuable tools for studying TMPRSS2‐ERG gene fusion protein products in prostate cancer.
Kilowatt high average power narrow-linewidth nanosecond all-fiber laser
Authors: Su Rongtao , Zhou Pu , Wang Xiaolin , Tao Rumao , Xu Xiaojun
Published: February 2014

A high power narrow-linewidth nanosecond all-fiber laser based on the master oscillator power amplifier (MOPA) configuration is demonstrated. A pulsed seed with high repetition rate of 10 MHz was generated by modulating a continuous-wave (CW) single-frequency fiber laser at $\sim $1064 nm by using an electro-optic intensity modulator (EOIM). After multi-stage cascaded power amplification, the average power was boosted to be kilowatt level. The pulses from the main amplifier had a pulse width of $\sim $3 ns and an average/peak power of 913 W/28.6 kW. Further power scaling of the pulses was limited by stimulated Raman scattering (SRS) for the moment, method for SRS suppression and further power scaling was briefly discussed.
Effects ofLactobacillus rhamnosusLA68 on the immune system of C57BL/6 mice upon oral administration
Authors: Dimitrijevic Rajna , Ivanovic Nevena , Mathiesen Geir , Petrusic Vladimir , Zivkovic Irena , Djordjevic Brizita , Dimitrijevic Ljiljana
Published: February 2014

Probiotic bacteria have been used in human nutrition for centuries and are now attracting more attention. In order to examine the immunological aspects of probiotic consumption,Lactobacillus rhamnosusLA68 was orally administrated using gavage to healthy C57BL/6 mice. After one month splenocytes were isolated, and analysed by flow cytometry. The magnitude of splenocyte proliferation upon stimulation with lipopolysaccharide and peptidoglycan and cytokine levels (IFN-γ, IL-6, IL-10 and IL-17) was assessed. Cytokine levels in the serum were also analysed. Oral application of strain LA68 leads to a significant decrease of CD3+, CD25+ and CD19+ cells, and an increase of CD11b+ and CD16/CD32+ positive cell populations in the mouse spleen. Increased sensitivity to stimulation through proliferation and IL-6 secretion was detected. Increased serum IFN-γ and decreased IL-10 levels were found. Our results show increased responsiveness of splenocytes, activation of the Th1 type of immune response, and a shift of leucocyte populations towards monocyte/granulocyte populations.
Relativistic shock waves induced by ultra-high laser pressure
Authors: Eliezer Shalom , Nissim Noaz , Raicher Erez , Martínez-Val José Maria
Published: February 2014

This paper analyzes the one dimensional shock wave created in a planar target by the ponderomotive force induced by very high laser irradiance. The laser-induced relativistic shock wave parameters, such as compression, pressure, shock wave and particle flow velocities, sound velocity and temperature are calculated here for the first time in the context of relativistic hydrodynamics. For solid targets and laser irradiance of about 2 × 1024 W/cm2, the shock wave velocity is larger than 50% of the speed of light, the shock wave compression is larger than 4 (usually of the order of 10) and the targets have a pressure of the order of 1015 atmospheres. The estimated temperature can be larger than 1 MeV in energy units and therefore very excited physics (like electron positron formation) is expected in the shocked area. Although the next generation of lasers might allow obtaining relativistic shock waves in the laboratory this possibility is suggested in this paper for the first time.
Non-linear interaction of ultra-intense ultra-short laser pulse with a relativistic flying double-sided dense plasma slab/mirror
Authors: Jain Vineeta , Maheshwari K.P. , Jaiman N.K. , Malav Harish
Published: February 2014

Analytical and numerical investigation of the reflection and transmission of a counter-propagating relativistically strong laser pulse from a relativistically flying dense plasma double-sided mirror is studied. We assume that the incident laser pulse is short, so that we can neglect the slow ion dynamics and consider the electron motion only. Numerical results of the amplitudes of the reflected/transmitted electric fields from a uniformly moving mirror, accelerated mirror, and oscillating mirror are obtained. Fourier spectrum of the reflected intensity from the moving mirror shows that the intensity decreases with increase in the frequency. The reflected pulse has an up-shifted frequency and increased intensity. It is seen that the first few cycles of the reflected radiation exhibit presence of high harmonics, while the later cycles are compressed together with harmonics in comparison with the earlier cycles. The variation of the reflection coefficient for a uniformly moving mirror as a function of the thin foil plasma-density parameter is numerically studied.
PETER C.B. PHILLIPS’S CONTRIBUTIONS TO PANEL DATA METHODS
Authors: Moon Hyungsik Roger , Perron Benoit
Published: February 2014

This paper discusses Peter Phillips’s contributions to panel data methods. These include contributions in the areas of seemingly unrelated regressions, nonstationary panel data, dynamic panels, and the development of multiple index asymptotic theory. We also discuss his empirical contributions in the area of economic growth and convergence that use macro panel data.
The influence of forest fragmentation on clonal diversity and genetic structure inHeliconia angusta, an endemic understorey herb of the Brazilian Atlantic rain forest
Authors: Stein Katharina , Rosche Christoph , Hirsch Heidi , Kindermann Anke , Köhler Julia , Hensen Isabell
Published: February 2014

Fragmented populations are usually exposed to the negative effects of reduced gene flow, genetic drift and population differentiation. These effects result in the collective loss of genetic variation, thereby reducing the probability of population adaptation to new environmental conditions and increasing the risk of extinction. Forest fragments commonly exhibit suboptimal site conditions, which can result in enhanced clonal reproduction, and a potential reduction in clonal diversity due to increased selfing and inbreeding depression. The clonal diversity, genetic diversity and structure ofHeliconia angusta(Heliconiaceae) were assessed using AFLP-markers. We analysed six patches in the continuous forest (Atlantic rain forest, State of Rio de Janeiro) and eight patches (155 leaf samples in total) in five nearby forest fragments (age of oldest fragment:c. 50 y; size range: < 5–100 ha). Clonal diversity (Pd) of patches was slightly, yet significantly, lower in forest fragments compared with continuous forest. Measures of genetic diversity of patches in forest fragments did not differ from those in the continuous forest. A STRUCTURE analysis did not show any clear clustering of patches in the continuous forest and forest fragments. Our results suggest thatH. angustahas not yet suffered from the anticipated negative effects of fragmentation.
Links not concordant to the Hopf link
Authors: FRIEDL STEFAN , POWELL MARK
Published: February 2014

We give new Casson–Gordon style obstructions for a two–component link to be topologically concordant to the Hopf link.
TWO NEW SPECIES OF STREPTOCARPUS (GESNERIACEAE) FROM TROPICAL AFRICA
Authors: Darbyshire I. , Massingue A. O.
Published: February 2014

Two new species are described in the genus Streptocarpus (Gesneriaceae) from eastern tropical Africa. The first, Streptocarpus mazumbaiensis I.Darbysh. from the Usambara Mts of Tanzania, was treated as Streptocarpus sp. A in the Flora of Tropical East Africa account of the Gesneriaceae. The second, Streptocarpus acicularis I.Darbysh. & Massingue, is known from a single collection from the lower Chimanimani massif in Mozambique, previously misidentified as S. eylesii S.Moore. Both species are illustrated, their likely affinities are discussed and their conservation status is assessed.
A SYNOPSIS OF THE GENUS COLUTEA (FABACEAE) IN IRAN
Authors: Pooyan P. , Ghahremaninejad F. , Assadi M.
Published: February 2014

The genus Colutea (Fabaceae) has been revised in preparation for the Flora of Iran treatment and a synopsis is presented here. In Iran the genus includes four sections, three subsections and nine species. An identification key, notes and distributions are given for the taxa. Two new subsections are described: Colutea sect. Rostrata subsect. Gifana and Colutea sect. Rostrata subsect. Uniflora.
A NEW SPECIES OF HEDYOTIS (RUBIACEAE) FROM INDIA
Authors: Karuppusamy S. , Ravichandran V.
Published: February 2014

A new species, Hedyotis rajasekaranii Karupp. & Ravichandran (Rubiaceae), is described from the Megamalai Hills of the Western Ghats in Tamil Nadu, southern India.
THE GENUS CENTAUREA (ASTERACEAE, CARDUEAE) IN IRAN: TWO NEW SPECIES AND A LECTOTYPIFICATION
Authors: Ranjbar M. , Negaresh K.
Published: February 2014

Two new species of Centaurea sect. Cynaroides (Asteraceae) from western Iran, C. shehbazii Ranjbar & Negaresh and C. solitaria Ranjbar & Negaresh, are described. In addition, Centaurea aziziana is typified.
Rational design of catalysts for asymmetric diamination reaction using transition state modeling
Authors: Jindal Garima , Sunoj Raghavan B.
Published: February 2014

DFT calculations have been used to design chiral phosphoramidite ligands for the asymmetric diamination of vicinal diamines. The substituents at both the 3,3′ positions of the binol framework and the amido nitrogen play a vital role in the stereochemical outcome.
Acyclic CB[n]-type molecular containers: effect of solubilizing group on their function as solubilizing excipients
Authors: Zhang Ben , Zavalij Peter Y. , Isaacs Lyle
Published: February 2014

Acyclic CB[n]-type receptors with sulfonate solubilizing groups function best as hosts for soluble guests and solubilizing agents for insoluble drugs.
An efficient facile and one-pot synthesis of benzodiazepines and chemoselective 1,2-disubstituted benzimidazoles using a magnetically retrievable Fe3O4 nanocatalyst under solvent free conditions
Authors: Jamatia Ramen , Saha Mithu , Pal Amarta Kumar
Published: February 2014

An efficient facile and one-pot synthesis of benzodiazepines and chemoselective 1,2-disubstituted benzimidazoles using magnetically retrievable Fe3O4 nanocatalyst under solvent free condition.
Coordination-triggered NO release from a dinitrosyl iron complex leads to anti-inflammatory activity
Authors: Skodje Kelsey M. , Kwon Min-Young , Chung Su Wol , Kim Eunsuk
Published: February 2014

The appropriate control of redox and coordination chemistry of dinitrosyl iron complexes enables them to become anti-inflammatory agents.
Facile synthesis of highly fluorescent BF2 complexes bearing isoindolin-1-one ligand
Authors: Gao Naixun , Cheng Chi , Yu Changjiang , Hao Erhong , Wang Shengyuan , Wang Jun , Wei Yun , Mu Xiaolong , Jiao Lijuan
Published: February 2014

A new class of isoindolin-1-one based BF2 complexes containing pyridine or benzothiazole groups has been prepared from a “one-pot” reaction.
Facile chemical solution deposition of nanocrystalline CrN thin films with low magnetoresistance
Authors: Hui Zhenzhen , Tang Xianwu , Wei Renhuai , Hu Ling , Yang Jie , Luo Hongmei , Dai Jianming , Song Wenhai , Liu Xingzhao , Zhu Xuebin , Sun Yuping
Published: February 2014

Polycrystalline CrN thin films were first prepared by a facile chemical solution deposition method.
IBX works efficiently under solvent free conditions in ball milling
Authors: Achar Tapas Kumar , Maiti Saikat , Mal Prasenjit
Published: February 2014

Under ball-milling, the organo-oxidant IBX efficiently works at room temperature, in solvent free conditions and in milligram to gram scale.
Larger π-extended anti-/syn-aroylenediimidazole polyaromatic compounds: synthesis, physical properties, self-assembly, and quasi-linear conjugation effect
Authors: Zhao Jianfeng , Wong Jen It , Gao Junkuo , Li Gang , Xing Guichuan , Zhang Huacheng , Sum Tze Chien , Yang Hui Ying , Zhao Yanli , Ake Kjelleberg Staffan Lars , Huang Wei , Joachim Loo Say Chye , Zhang Qichun
Published: February 2014

Four polyaromatic compounds with 11- or 13-fused rings have been synthesized and their physical properties have been studied.
Hierarchical WO3@SnO2core–shell nanowire arrays on carbon cloth: a new class of anode for high-performance lithium-ion batteries
Authors: Gao Lina , Qu Fengyu , Wu Xiang
Published: February 2014

Hybrid WO3@SnO2nanowire array/carbon cloth electrodes exhibit a high reversible capacity of 1000 mA h g−1after 200 cycles.
Cryogenic dual‐temperature low noise amplifier in K band
Authors: Pasian Marco , Chambon Cedric , Bozzi Maurizio , Perregrini Luca , Rayet Remi , Fauroux Benoit , Rawson Steve
Published: February 2014

Future ground stations will require a high level of operational flexibility and, for this reason, the possibility to adjust their receiving performance (i.e. signal‐over‐noise) is beneficial. This study presents an approach to achieve this flexibility based on a dual‐temperature low‐noise amplifier, which can be normally operated at room temperature (300 K), reducing the operational and maintenance costs, and at cryogenic temperature (103 K) only when required, for example, for critical mission supports. To demonstrate the effectiveness of this solution, a dual‐temperature K‐band low‐noise amplifier is designed, manufactured and measured for the first time. Critical aspects, such as the stability of the electromagnetic response over the entire temperature range, and the reduction of the thermal load from the entire assembly, fundamental for a fast transition between room and cryogenic temperatures, are discussed. In particular, the low‐noise amplifier exhibits a minimum gain of 20 dB over the entire working bandwidth (18–22 GHz) and a maximum noise figure of 2.2 at 300 K and 1.4 at 103 K, with a transition time between room and cryogenic temperature of <120 min because of a total thermal load lower than 1 W.