bluuebunny/crossref_metadata_2025 huggingface dataset:
Intermittency and local dissipation scales under strong mean shear
Authors: Morshed Khandakar Niaz , Venayagamoorthy Subhas Karan , Dasi Lakshmi Prasad
Published: January 2013

We experimentally probe the local dissipation scale distribution Q(η) and temporal fluctuations of the turbulent kinetic energy dissipation rate ε in the strongly anisotropic flow past a backward facing step. A shift in Q(η) and corresponding reduction in the relative intermittency of ε is observed with increasing mean shear S. We offer physical arguments to elucidate the role of strong shear on the small-scale structure. A local mean-shear dissipation Reynolds number, ReS ≡ ⟨ε⟩/(S2ν), is proposed that may define a family of universal small-scale structures of turbulence.
On the concentration structure of high-concentration constant-volume fluid mud gravity currents
Authors: Jacobson M. R. , Testik F. Y.
Published: January 2013

An exhaustive laboratory experimental campaign was undertaken in order to elucidate the concentration structure of two-dimensional constant-volume non-Newtonian fluid mud gravity currents. Two sets of experiments were conducted in a lock-exchange tank. The first set of experiments involved measuring the vertical concentration profiles using a siphoning technique; the second set involved auxiliary visual observations. The first set of experiments consisted of 32 experimental runs for four different experimental conditions, with an array of siphoned samples being withdrawn throughout the head and body of the gravity current. From these samples, vertical concentration profiles occurring in constant-volume fluid mud gravity currents were classified and the underlying physical processes that led to the occurrence of observed profiles were discussed. Furthermore, the functional form of the vertical concentration profiles within the head of relatively low-initial-concentration gravity currents was proposed. The relatively high-initial-concentration gravity currents revealed the presence of a lutocline in the current head and body, the presence of which was observed for constant-flux release gravity currents. To our knowledge, this is the first measurement of a lutocline in constant-volume gravity currents. Abrupt transitions, a phenomenon in which the bulk of the suspended sediment in the propagating gravity current drops out, were observed through the concentration profiles and through 15 auxiliary visual experimental runs. It was found that abrupt transitions were caused by the presence of a lutocline. The entrainment of ambient water resulting in the dilution of the gravity current at different concentration contours has been quantified. In a previous work by the authors of this study, it was shown that the initial reduced gravity is directly proportional to the growth rate of the visual area of the two-dimensional current. The analysis of our experimental observations presented in this study, however, showed the initial reduced gravity to be inversely proportional to the growth rate of the area enclosed by concentration contours with higher values than that of the visual area. These seemingly opposing conclusions are rationalized and the considerable practical impacts are discussed.
Development of a high pressure electrical conductivity probe for experimental studies of gas hydrates in electrolytes
Authors: Maeda Nobuo
Published: January 2013

We previously reported the development of a high pressure automated lag time apparatus and a high pressure video cell for experimental study of nucleation and growth of gas hydrates. Here we report the development of a high pressure electrical conductivity probe that monitors the electrical conductivity of an electrolyte that is subjected to a linear cooling ramp at elevated hydrate-forming-gas pressures. The electrical conductivity steadily decreases as the linear cooling progresses because of the increasing viscosity of the electrolyte and the consequently decreasing mobility of the ions. The onset of the formation of methane-propane mixed gas hydrate films at the gas-electrolyte interface is marked by an upward spike in the electrical conductivity. The physical mechanisms behind this phenomenon remain to be elucidated. Continued cooling of the electrolyte to, and subsequent holding of, the temperature at 273 K eventually results in decreased electrical conductivity. This conductivity signal can be used for the detection of the onset of the formation of gas hydrates in optically opaque samples that contain electrolytes.
Binary nature of monolayer boron sheets from ab initio global searches
Authors: Lu Haigang , Mu Yuewen , Bai Hui , Chen Qiang , Li Si-Dian
Published: January 2013

Boron could be the next element after carbon to form two-dimensional monolayer structures. Using the ab initio global searches, we found all low-lying monolayer boron sheets with 1–4 hexagonal holes in each unit cell. The two most stable boron sheets are composed of two kinds of elementary units with isolated-hexagon and twin-hexagon holes, respectively, so that the boron sheets are binary structures in nature. Detailed structural analyses indicate that there exist two types of close-lying stable monolayer boron sheets, revealing the polymorphism of boron sheet. These binary monolayer boron sheets are expected to serve as precursors to build various boron nanotubes, boron fullerenes, and other boron-based low-dimensional nanomaterials.
Orientation-dependent stress relaxation in hetero-epitaxial 3C-SiC films
Authors: Iacopi Francesca , Walker Glenn , Wang Li , Malesys Laura , Ma Shujun , Cunning Benjamin V. , Iacopi Alan
Published: January 2013

Residual stresses in epitaxial 3C-SiC films on silicon, for chosen growth conditions, appear determined by their growth orientation. Stress evaluation locally with Raman spectroscopy, and across a 150 mm wafer with curvature measurements, indicate that thin films can be grown on Si(100) with residual tensile stresses as low as 150 MPa. However, films on Si(111) retain a considerably higher stress, around 900 MPa, with only minor decrease versus film thickness. Stacking faults are indeed geometrically a less efficient relief mechanism for the biaxial strain of SiC films grown on Si(111) with 〈111〉 orientation. Residual stresses can be tuned by the epitaxial process temperatures.
Sieving DNA molecules by length dependence in artificial nano-channel matrices
Authors: Wang Chung-Hsuan , Hua Ho Chia , Chou Y. C.
Published: January 2013

Nano-channel matrices are designed and fabricated for sieving DNA molecules by length. The length dependence is found to change with the size of the channels. Three regimes can be distinguished: (a) for the matrices with the size of the channels comparable to the persistence length (lp) of DNA molecules (45 nm), the mobility of DNA is found to decrease with the length of the molecules, similar to that found for the gel electrophoresis; (b) as the size of the nano-channel increases, the successful attacking frequency increases for the long molecules. The length-dependence of the mobility reverses; and (c) the Ogston mechanism holds for even larger channels. The short DNA molecules drift faster for the channels with diameter larger than 10 lp. Such a variety of the length dependence is observed for the first time in the electrophoresis in the artificial structures.
Step-step interactions on GaAs (110) nanopatterns
Authors: Galiana B. , Benedicto M. , Tejedor P.
Published: January 2013

The step-step interactions on vicinal GaAs (110) surface patterns have been extracted from the quantitative analysis of the terrace width distribution (TWD). We have specifically studied the interactions in near-equilibrium faceting and kinetics-driven step bunching and meandering formed by spontaneous self-organization or through the modification of GaAs growth kinetics by atomic hydrogen. We show that the experimental TWDs determined from atomic force microscopy measurements can be accurately described by a weighed sum of a generalized Wigner distribution and several Gaussians. The results of our calculations indicate that straight facets are formed during high temperature homoepitaxy due to attractive interactions between [11¯0] steps. At low temperatures, steady state attractive interactions in [11¯0] step bunches are preceded by a transition regime dominated by entropic and energetic repulsions between meandering [11¯n]-type steps (n ≥ 2), whose population density exceeds that of the [11¯0] bunched steps. In addition, it has been found that atomic H reduces the attractive interactions between [11¯0] bunched steps and enhances entropic and dipole-induced energetic repulsions between H-terminated [11¯n] steps through the inhibition of As–As bond formation at step edges. Our analysis has evidenced a correlation between the value of the adjustable parameter that accounts in our model for the specific weight of the secondary peaks in the TWD (β) and the extent of transverse meandering on the vicinal surface.
An arbitrary strains carbon nanotube composite piezoresistivity model for finite element integration
Authors: Tallman T. , Wang K. W.
Published: January 2013

Piezoresistive carbon nanotube (CNT) composites can radically enhance structural identification and health monitoring through continuous self-sensing. However, prevailing piezoresistivity models examine only uniaxial strain and are too computationally burdensome to be implemented on a structural scale. This research circumvents these limitations by developing an analytical piezoresistivity model for CNT composites that is adaptable to the finite element formulation enabling the analysis of complicated structures subjected to arbitrary strain. The accuracy of the model is verified by comparison to uniaxial piezoresistivity experiments in existing literature.
Sequentially pulsed fluid delivery to establish soluble gradients within a scalable microfluidic chamber array
Authors: Park Edward S. , DiFeo Michael A. , Rand Jacqueline M. , Crane Matthew M. , Lu Hang
Published: January 2013

This work presents a microfluidic chamber array that generates soluble gradients using sequentially pulsed fluid delivery (SPFD). SPFD produces stable gradients by delivering flow pulses to either side of a chamber. The pulses on each side contain different signal concentrations, and they alternate in sequence, providing the driving force to establish a gradient via diffusion. The device, herein, is significant because it demonstrates the potential to simultaneously meet four important needs that can accelerate and enhance the study of cellular responses to signal gradients. These needs are (i) a scalable chamber array, (ii) low complexity fabrication, (iii) a non-shearing microenvironment, and (iv) gradients with low (near zero) background concentrations. The ability to meet all four needs distinguishes the SPFD device from flow-based and diffusion-based designs, which can only achieve a subset of such needs. Gradients are characterized using fluorescence measurements, which reveal the ability to change the curvature of concentration profiles by simple adjustments to pulsing sequence and flow rate. Preliminary experiments with MDA-MB-231 cancer cells demonstrate cell viability and indicate migrational and morphological responses to a fetal bovine serum gradient. Improved and expanded versions of this technology could form the basis of high-throughput screening tools to study cell migration, development, and cancer.
Self-organized coherent bursts of stimulated Raman scattering and speckle interaction in multi-speckled laser beams
Authors: Yin L. , Albright B. J. , Rose H. A. , Montgomery D. S. , Kline J. L. , Kirkwood R. K. , Michel P. , Bowers K. J. , Bergen B.
Published: January 2013

Nonlinear physics governing the kinetic behavior of stimulated Raman scattering (SRS) in multi-speckled laser beams has been identified in the trapping regime over a wide range of kλD values (here k is the wave number of the electron plasma waves and λD is the Debye length) in homogeneous and inhomogeneous plasmas. Hot electrons from intense speckles, both forward and side-loss hot electrons produced during SRS daughter electron plasma wave bowing and filamentation, seed and enhance the growth of SRS in neighboring speckles by reducing Landau damping. Trapping-enhanced speckle interaction through transport of hot electrons, backscatter, and sidescatter SRS light waves enable the system of speckles to self-organize and exhibit coherent, sub-ps SRS bursts with more than 100% instantaneous reflectivity, resulting in an SRS transverse coherence width much larger than a speckle width and a SRS spectrum that peaks outside the incident laser cone. SRS reflectivity is found to saturate above a threshold laser intensity at a level of reflectivity that depends on kλD: higher kλD leads to lower SRS and the reflectivity scales as ∼(kλD)−4. As kλD and Landau damping increase, speckle interaction via sidescattered light and side-loss hot electrons decreases and the occurrence of self-organized events becomes infrequent, leading to the reduction of time-averaged SRS reflectivity. It is found that the inclusion of a moderately strong magnetic field in the laser direction can effectively control SRS by suppressing transverse speckle interaction via hot electron transport.
Cardiomyocyte proliferation contributes to heart growth in young humans
Authors: Mollova Mariya , Bersell Kevin , Walsh Stuart , Savla Jainy , Das Lala Tanmoy , Park Shin-Young , Silberstein Leslie E. , dos Remedios Cristobal G. , Graham Dionne , Colan Steven , Kühn Bernhard
Published: January 2013

The human heart is believed to grow by enlargement but not proliferation of cardiomyocytes (heart muscle cells) during postnatal development. However, recent studies have shown that cardiomyocyte proliferation is a mechanism of cardiac growth and regeneration in animals. Combined with evidence for cardiomyocyte turnover in adult humans, this suggests that cardiomyocyte proliferation may play an unrecognized role during the period of developmental heart growth between birth and adolescence. We tested this hypothesis by examining the cellular growth mechanisms of the left ventricle on a set of healthy hearts from humans aged 0–59 y (
n
= 36). The percentages of cardiomyocytes in mitosis and cytokinesis were highest in infants, decreasing to low levels by 20 y. Although cardiomyocyte mitosis was detectable throughout life, cardiomyocyte cytokinesis was not evident after 20 y. Between the first year and 20 y of life, the number of cardiomyocytes in the left ventricle increased 3.4-fold, which was consistent with our predictions based on measured cardiomyocyte cell cycle activity. Our findings show that cardiomyocyte proliferation contributes to developmental heart growth in young humans. This suggests that children and adolescents may be able to regenerate myocardium, that abnormal cardiomyocyte proliferation may be involved in myocardial diseases that affect this population, and that these diseases might be treatable through stimulation of cardiomyocyte proliferation.
Two-gate mechanism for phospholipid selection and transport by type IV P-type ATPases
Authors: Baldridge Ryan D. , Graham Todd R.
Published: January 2013

Most P-type ATPases pump specific cations or heavy metals across a membrane to form ion gradients. However, the type IV P-type ATPases evolved the ability to transport specific phospholipid substrates rather than cations and function to establish plasma membrane asymmetry in eukaryotic cells. The mechanism for how a P-type ATPase, or any other transporter, can recognize and flip a phospholipid substrate is unclear. Here, through a combination of genetic screening and directed mutagenesis with the type IV P-type ATPases Dnf1 and Drs2 from budding yeast, we identify more than a dozen residues that determine headgroup specificity for phospholipid transport. These residues cluster at two interfacial regions flanking transmembrane segments 1–4 and lie outside of the canonical substrate binding site operating in cation pumps. Our data imply the presence of two substrate-selecting gates acting sequentially on opposite sides of the membrane: an entry gate, where phospholipid is initially selected from the extracellular leaflet, and an exit gate at the cytosolic leaflet. The entry and exit gates act cooperatively but imperfectly, with neither being able to restrict phosphatidylserine selection completely when the opposing gate is tuned to permit it. This work describes a unique transport mechanism for a P-type ATPase and provides insight into how integral membrane proteins can recognize and transport phospholipid substrate across a lipid bilayer.
Discovery of indolotryptoline antiproliferative agents by homology-guided metagenomic screening
Authors: Chang Fang-Yuan , Brady Sean F.
Published: January 2013

Natural product discovery by random screening of broth extracts derived from cultured bacteria often suffers from high rates of redundant isolation, making it ever more challenging to identify novel biologically interesting natural products. Here we show that homology-based screening of soil metagenomes can be used to specifically target the discovery of new members of traditionally rare, biomedically relevant natural product families. Phylogenetic analysis of oxy-tryptophan dimerization gene homologs found within a large soil DNA library enabled the identification and recovery of a unique tryptophan dimerization biosynthetic gene cluster, which we have termed the
bor
cluster. When heterologously expressed in
Streptomyces albus
, this cluster produced an indolotryptoline antiproliferative agent with CaMKIIδ kinase inhibitory activity (borregomycin A), along with several dihydroxyindolocarbazole anticancer/antibiotics (borregomycins B–D). Similar homology-based screening of large environmental DNA libraries is likely to permit the directed discovery of new members within other previously rare families of bioactive natural products.
CGI-58 knockdown sequesters diacylglycerols in lipid droplets/ER-preventing diacylglycerol-mediated hepatic insulin resistance
Authors: Cantley Jennifer L. , Yoshimura Toru , Camporez Joao Paulo G. , Zhang Dongyan , Jornayvaz Francois R. , Kumashiro Naoki , Guebre-Egziabher Fitsum , Jurczak Michael J. , Kahn Mario , Guigni Blas A. , Serr Julie , Hankin Joseph , Murphy Robert C. , Cline Gary W. , Bhanot Sanjay , Manchem Vara Prasad , Brown J. Mark , Samuel Varman T. , Shulman Gerald I.
Published: January 2013

Comparative gene identification 58 (CGI-58) is a lipid droplet-associated protein that promotes the hydrolysis of triglyceride by activating adipose triglyceride lipase. Loss-of-function mutations in CGI-58 in humans lead to Chanarin–Dorfman syndrome, a condition in which triglyceride accumulates in various tissues, including the skin, liver, muscle, and intestines. Therefore, without adequate CGI-58 expression, lipids are stored rather than used for fuel, signaling intermediates, and membrane biosynthesis. CGI-58 knockdown in mice using antisense oligonucleotide (ASO) treatment also leads to severe hepatic steatosis as well as increased hepatocellular diacylglycerol (DAG) content, a well-documented trigger of insulin resistance. Surprisingly, CGI-58 knockdown mice remain insulin-sensitive, seemingly dissociating DAG from the development of insulin resistance. Therefore, we sought to determine the mechanism responsible for this paradox. Hyperinsulinemic-euglycemic clamp studies reveal that the maintenance of insulin sensitivity with CGI-58 ASO treatment could entirely be attributed to protection from lipid-induced hepatic insulin resistance, despite the apparent lipotoxic conditions. Analysis of the cellular compartmentation of DAG revealed that DAG increased in the membrane fraction of high fat-fed mice, leading to PKCɛ activation and hepatic insulin resistance. However, DAG increased in lipid droplets or lipid-associated endoplasmic reticulum rather than the membrane of CGI-58 ASO-treated mice, and thus prevented PKCɛ translocation to the plasma membrane and induction of insulin resistance. Taken together, these results explain the disassociation of hepatic steatosis and DAG accumulation from hepatic insulin resistance in CGI-58 ASO-treated mice, and highlight the importance of intracellular compartmentation of DAG in causing lipotoxicity and hepatic insulin resistance.
Unanticipated regulatory roles for
Arabidopsis
phytochromes revealed by null mutant analysis
Authors: Hu Wei , Franklin Keara A. , Sharrock Robert A. , Jones Matthew A. , Harmer Stacey L. , Lagarias J. Clark
Published: January 2013

In view of the extensive literature on phytochrome mutants in the L
er
accession of
Arabidopsis
, we sought to secure a phytochrome-null line in the same genetic background for comparative studies. Here we report the isolation and phenotypic characterization of
phyABCDE
quintuple and
phyABDE
quadruple mutants in the L
er
background. Unlike earlier studies, these lines possess a functional allele of
FT
permitting measurements of photoperiod-dependent flowering behavior. Comparative studies of both classes of mutants establish that phytochromes are dispensable for completion of the
Arabidopsis
life cycle under red light, despite the lack of a transcriptomic response, and also indicate that phyC is nonfunctional in the absence of other phytochromes. Phytochrome-less plants can produce chlorophyll for photosynthesis under continuous red light, yet require elevated fluence rates for survival. Unexpectedly, our analyses reveal both light-dependent and -independent roles for phytochromes to regulate the
Arabidopsis
circadian clock. The rapid transition of these mutants from vegetative to reproductive growth, as well as their insensitivity to photoperiod, establish a dual role for phytochromes to arrest and to promote progression of plant development in response to the prevailing light environment.
Good Iranian, Bad Iranian: Representations of Iran and Iranians in Time and Newsweek (1998–2009)
Authors: Fayyaz Sam , Shirazi Roozbeh
Published: January 2013

This article analyzes the ways in which Iran and Iranians are represented in Western news media sources. Through detailed textual analysis of articles in Time and Newsweek between 1998 and 2009, it demonstrates that journalistic representations of Iran and Iranians are not simply efforts aimed at describing the real Iran, but rather form the basis of what Said refers to as a powerful “community of interpretation” that often reflects and reproduces certain xenophobic stereotypes of non-Western foreign subjects. While some shifts in Western media representations of Iranians have occurred in the thirty years since the revolution, the underlying ontological assumptions of these representations have remained remarkably durable. That is to say, the dominant representational discourse found in these newsmagazines depicts the political behavior of Iranians on the basis of essentialized notions of Persian and/or Islamic civilization, while very often emphasizing the taken for granted superiority of the West. Earlier Orientalist discourses focus on the difference of non-Western foreign subjects by denigrating them as fundamentally anti-modern and incapable of political, cultural and economic development without Western intervention. This article presents an unmistakable discursive pattern in American journalism whereby certain Iranians are incorporated into Western civilization by virtue of their embrace of a Western modernity.
Locating Home in a “Digital Age”: An Ethnographic Case Study of Second-Generation Iranian Americans in LA and their Use of Internet Media
Authors: Alinejad Donya
Published: January 2013

This paper explores how children of Iranian immigrants engage with internet media in processes of identity formation. It conceptually centralizes places of home in order to bring together literatures on diaspora and digital media in order to understand the case of the second-generation immigrant home. It argues that this partially mediated home is both connected/mobile and emplaced/embodied. It is in this sense that the article discusses processes of locating home, in the sense of both a narrated discovery and a materially situated formation. The findings are generated from ethnographic fieldwork among second-generation Iranian Americans in Los Angeles carried out over a period of twelve months as part of an ongoing doctoral project with a focus on respondents' everyday practices of internet usage.
Exploring costs and consequences of religious expression in family businesses
Authors: Paterson Ted A. , Specht Dave , Duchon Dennis
Published: January 2013

Although there has been increasing attention given to family businesses in the broader management literature, to date there has been little exploration of the role of religious beliefs in family businesses. We studied the role of religion and the costs and consequences of its expression
in family businesses by conducting 12 interviews with members of family businesses; 6 themes emerged from our qualitative data. The first three themes describe, in the participant’s own words, the experience of religious expression in family businesses: “it’s just the values”,
“it touches everything”, and “we don’t push it on people”. The final three themes describe the positive and negative ramifications of religious expression in family business: “it’s all God’s”, “it’s people, it’s not the
bottom line”, and “it’s a clean lifestyle”. Our informants reported that the inclusion of religious principles in the business fundamentally changes the way that they handle a variety of management issues, the way that they define success, and the fulfillment they experience
through their business.
Age-of-Acquisition Effects in Novel Picture Naming: A Laboratory Analogue
Authors: Catling Jonathan , Dent Kevin , Preece Emma , Johnston Robert
Published: January 2013

Age-of-acquisition (AoA) effects are such that early-acquired items are more quickly recognized and produced than later acquired items. In this laboratory analogue, participants were trained to name a group of Greeble pictures with a novel nonsense name. We manipulated order of acquisition of the stimuli: Half of the stimuli were presented from the onset of training (early acquired) whilst the other half were introduced later in the training schedule (late acquired). At test, when early and late stimuli had equal cumulative frequency, early stimuli were named significantly faster than late items. In a second test, it was also found that visual duration thresholds were significantly smaller for the early items when participants were asked to name the critical items. These findings support the notion that order-of-acquisition effects can be manifest over a short time span in the laboratory, and that the effect of order of acquisition is distinct from mere frequency of exposure. The findings are consistent with the idea that AoA effects occurring over a large temporal scale may be a special case of more general order-of-acquisition effects, and both may be a general property of learning mechanisms.
The PCP effector Fuzzy controls cilial assembly and signaling by recruiting Rab8 and Dishevelled to the primary cilium
Authors: Zilber Yulia , Babayeva Sima , Seo Jung Hwa , Liu Jia Jia , Mootin Steven , Torban Elena
Published: January 2013

The planar cell polarity (PCP) pathway controls multiple cellular processes during vertebrate development. Recently the PCP pathway was implicated in ciliogenesis and in ciliary function. The primary cilium is an apically projecting solitary organelle that is generated via polarized intracellular trafficking. Because it acts as a signaling nexus, defects in ciliogenesis or cilial function cause multiple congenital anomalies in vertebrates. Loss of the PCP effector Fuzzy affects PCP signaling and formation of primary cilia; however, the mechanisms underlying these processes are largely unknown. Here we report that Fuzzy localizes to the basal body and ciliary axoneme and is essential for ciliogenesis by delivering Rab8 to the basal body and primary cilium. Fuzzy appears to control subcellular localization of the core PCP protein Dishevelled, recruiting it to Rab8-positive vesicles and to the basal body and cilium. We show that loss of Fuzzy results in inhibition of PCP signaling and hyperactivation of the canonical WNT pathway. We propose a mechanism by which Fuzzy participates in ciliogenesis and affects both canonical WNT and PCP signaling.
So, what's it really like to work in biotech?
Authors: Belmont Lisa
Published: January 2013

This essay provides insight into the daily life of a scientist in biotechnology, drawing on experience gained from working in companies ranging in size from four to more than 80,000 employees. The basic scientific training in molecular biology required for the work is similar between academia and industry, but the way in which these skills are applied differs. Biologists in industry settings work as part of large, multidisciplinary teams. This requires relinquishing the degree of intellectual freedom allowed in academia but offers an increased opportunity to see the fruits of one's labor translate into products with the potential to positively impact human or environmental health.
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
Authors: Clark Scott C. , Egan Rob , Frazier Peter I. , Wang Zhong
Published: January 2013

Motivation: Researchers need general purpose methods for objectively evaluating the accuracy of single and metagenome assemblies and for automatically detecting any errors they may contain. Current methods do not fully meet this need because they require a reference, only consider one of the many aspects of assembly quality or lack statistical justification, and none are designed to evaluate metagenome assemblies.

Results: In this article, we present an Assembly Likelihood Evaluation (ALE) framework that overcomes these limitations, systematically evaluating the accuracy of an assembly in a reference-independent manner using rigorous statistical methods. This framework is comprehensive, and integrates read quality, mate pair orientation and insert length (for paired-end reads), sequencing coverage, read alignment and k-mer frequency. ALE pinpoints synthetic errors in both single and metagenomic assemblies, including single-base errors, insertions/deletions, genome rearrangements and chimeric assemblies presented in metagenomes. At the genome level with real-world data, ALE identifies three large misassemblies from the Spirochaeta smaragdinae finished genome, which were all independently validated by Pacific Biosciences sequencing. At the single-base level with Illumina data, ALE recovers 215 of 222 (97%) single nucleotide variants in a training set from a GC-rich Rhodobacter sphaeroides genome. Using real Pacific Biosciences data, ALE identifies 12 of 12 synthetic errors in a Lambda Phage genome, surpassing even Pacific Biosciences’ own variant caller, EviCons. In summary, the ALE framework provides a comprehensive, reference-independent and statistically rigorous measure of single genome and metagenome assembly accuracy, which can be used to identify misassemblies or to optimize the assembly process.

Availability: ALE is released as open source software under the UoI/NCSA license at http://www.alescore.org. It is implemented in C and Python.

Contact:  pf98@cornell.edu or ZhongWang@lbl.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine
Authors: Thomas Niclas , Heather James , Ndifon Wilfred , Shawe-Taylor John , Chain Benjamin
Published: January 2013

Summary: High-throughput sequencing provides an opportunity to analyse the repertoire of antigen-specific receptors with an unprecedented breadth and depth. However, the quantity of raw data produced by this technology requires efficient ways to categorize and store the output for subsequent analysis. To this end, we have defined a simple five-item identifier that uniquely and unambiguously defines each TcR sequence. We then describe a novel application of finite-state automaton to map Illumina short-read sequence data for individual TcRs to their respective identifier. An extension of the standard algorithm is also described, which allows for the presence of single-base pair mismatches arising from sequencing error. The software package, named Decombinator, is tested first on a set of artificial in silico sequences and then on a set of published human TcR-β sequences. Decombinator assigned sequences at a rate more than two orders of magnitude faster than that achieved by classical pairwise alignment algorithms, and with a high degree of accuracy (>88%), even after introducing up to 1% error rates in the in silico sequences. Analysis of the published sequence dataset highlighted the strong V and J usage bias observed in the human peripheral blood repertoire, which seems to be unconnected to antigen exposure. The analysis also highlighted the enormous size of the available repertoire and the challenge of obtaining a comprehensive description for it. The Decombinator package will be a valuable tool for further in-depth analysis of the T-cell repertoire.

Availability and implementation: The Decombinator package is implemented in Python (v2.6) and is freely available at https://github.com/uclinfectionimmunity/Decombinator along with full documentation and examples of typical usage.

Contact:  b.chain@ucl.ac.uk
Preregistration of Studies and Mock Reports
Authors: Gelman Andrew
Published: January 2013

The traditional system of scientific and scholarly publishing is breaking down in two different directions.
Dynamics of Southern rice black-streaked dwarf virus in Rice and Implication for Virus Acquisition
Authors: Matsukura Keiichiro , Towata Tomomi , Sakai Junichi , Onuki Masatoshi , Okuda Mitsuru , Matsumura Masaya
Published: January 2013

A novel viral disease of rice caused by Southern rice black-streaked dwarf virus (SRBSDV) has spread throughout East and Southeast Asia since the mid-2000s. Outbreaks of this viral disease occur yearly in southern parts of Japan concurrently with overseas migration of the planthopper vector Sogatella furcifera from southern China during the rainy season (from late June to early July). We examined the dynamics (changes in titer and localization) of SRBSDV on rice using reverse-transcription real-time polymerase chain reaction and determined the relationship between virus titer in plants and virus acquisition by S. furcifera. Under a constant temperature of 27°C, a substantial increase of SRBSDV titer in the leaf sheath together with typical symptoms (stunted growth and twisting of leaf tips) was observed at 20 days after the end of a 7-day exposure of viruliferous S. furcifera. Approximately 40% of S. furcifera acquired SRBSDV through feeding for 5 days on rice plants that were infected following exposure to viruliferous vectors for 10 to 15 days. These results suggest that rice infected by S. furcifera can be a source of SRBSDV before the next generation of S. furcifera emerges.
T-cell epitope vaccine design by immunoinformatics
Authors: Patronov Atanas , Doytchinova Irini
Published: January 2013

Vaccination is generally considered to be the most effective method of preventing infectious diseases. All vaccinations work by presenting a foreign antigen to the immune system in order to evoke an immune response. The active agent of a vaccine may be intact but inactivated (‘attenuated’) forms of the causative pathogens (bacteria or viruses), or purified components of the pathogen that have been found to be highly immunogenic. The increased understanding of antigen recognition at molecular level has resulted in the development of rationally designed peptide vaccines. The concept of peptide vaccines is based on identification and chemical synthesis of B-cell and T-cell epitopes which are immunodominant and can induce specific immune responses. The accelerating growth of bioinformatics techniques and applications along with the substantial amount of experimental data has given rise to a new field, called immunoinformatics. Immunoinformatics is a branch of bioinformatics dealing within silicoanalysis and modelling of immunological data and problems. Different sequence- and structure-based immunoinformatics methods are reviewed in the paper.
Correlation between nucleotide mutation and viral loads of human bocavirus 1 in hospitalized children with respiratory tract infection
Authors: Hao Rui , Ni Ke , Xia Qiuling , Peng Caijing , Deng Yu , Zhao Xiaodong , Fu Zhou , Liu Wei , Liu Enmei
Published: January 2013

The human bocavirus 1 (HBoV1) parvovirus causes respiratory disease and primarily affects children. Despite its worldwide prevalence, the mechanisms of HBoV1 replication and pathogenesis remain largely undefined. In this study of 846 children hospitalized at the Children’s Hospital of Chongqing Medical University in China for respiratory tract infection between June 2009 and May 2011, HBoV1 was detected in 112 (13.2 %) by real-time quantitative PCR. The median age of HBoV1-positive patients was 10 months old. Forty-five (40.2 %) of the HBoV1 cases were monoinfections, and 67 (59.8 %) were viral co-infections. Genotyping of all 112 HBoV1-positive cases yielded 27 full HBoV1 sequences, as well as two NS1 gene sequences, 15 NP1 gene sequences and 10 VP1/VP2 gene sequences harbouring 24, 10 and 43 mutations, respectively. Statistical analysis revealed no relationship between genetic mutations and clinical manifestations of HBoV1-positive patients. However, the viral loads were significantly lower in samples with mutations G236A or A447G in NP1, or G1461A in VP1/VP2, than in samples with wild-type HBoV1. Future studies should investigate whether these mutations in the HBoV1 gene may represent useful markers of disease pathogenesis.
The role of Ran-binding protein 3 during influenza A virus replication
Authors: Predicala Rey , Zhou Yan
Published: January 2013

Influenza A virus vRNP nuclear export is CRM1-dependent. Ran-binding protein 3 (RanBP3) is a Ran-interacting protein that is best known for its role as a cofactor of CRM1-mediated cargo nuclear export. In this study, we investigated the role of RanBP3 during the influenza A virus life cycle. We found that RanBP3 was phosphorylated at Ser58 in the early and late phases of infection. Knockdown of RanBP3 expression led to vRNP nuclear retention, suggesting that RanBP3 is involved in vRNP nuclear export. Moreover, we demonstrated that the function of RanBP3 during vRNP nuclear export is regulated by phosphorylation at Ser58, and that RanBP3 phosphorylation is modulated by both PI3K/Akt and Ras/ERK/RSK pathways in the late phase of viral infection.
Nodes and arcs: concept map, semiotics, and knowledge organization
Authors: Friedman Alon , Smiraglia Richard P.
Published: January 2013

Purpose

The purpose of the research reported here is to improve comprehension of the socially‐negotiated identity of concepts in the domain of knowledge organization. Because knowledge organization as a domain has as its focus the order of concepts, both from a theoretical perspective and from an applied perspective, it is important to understand how the domain itself understands the meaning of a concept.

Design/methodology/approach

The paper provides an empirical demonstration of how the domain itself understands the meaning of a concept. The paper employs content analysis to demonstrate the ways in which concepts are portrayed in KO concept maps as signs, and they are subjected to evaluative semiotic analysis as a way to understand their meaning. The frame was the entire population of formal proceedings in knowledge organization – all proceedings of the International Society for Knowledge Organization's international conferences (1990‐2010) and those of the annual classification workshops of the Special Interest Group for Classification Research of the American Society for Information Science and Technology (SIG/CR).

Findings

A total of 344 concept maps were analyzed. There was no discernible chronological pattern. Most concept maps were created by authors who were professors from the USA, Germany, France, or Canada. Roughly half were judged to contain semiotic content. Peirceian semiotics predominated, and tended to convey greater granularity and complexity in conceptual terminology. Nodes could be identified as anchors of conceptual clusters in the domain; the arcs were identifiable as verbal relationship indicators. Saussurian concept maps were more applied than theoretical; Peirceian concept maps had more theoretical content.

Originality/value

The paper demonstrates important empirical evidence about the coherence of the domain of knowledge organization. Core values are conveyed across time through the concept maps in this population of conference papers.
Does place affect user engagement and understanding?
Authors: Cocciolo Anthony , Rabina Debbie
Published: January 2013

Purpose

The aim of this research project is to uncover if place‐based learning can increase learner engagement and understanding of historical topics.

Design/methodology/approach

To study this, learners will use GeoStoryteller to learn about a historical topic on the places where significant events occurred, and then be interviewed by the researchers. GeoStoryteller is a tool developed by the researchers that runs on smartphones, such as an iPhone or Android. It provides the user multimedia stories about the historical sites, delivered via the mobile web or through Layar, an augmented reality web browser. The initial application of this technology focuses on German immigration to New York City between 1840 and 1945 through a partnership with the Goethe‐Institut, the Federal Republic of Germany's cultural institution. After using GeoStoryteller to learn about this content, n=31 participants were interviewed by the researchers, and transcripts were subjected to a quantitative content analysis.

Findings

Results indicate that the use of place increases learner perceptions of their engagement and understanding of historical topics; however, novel user interfaces like augmented reality impose significant usability issues, and more standard interfaces are preferred by users.

Originality/value

The use of place in mobile learning environments provides a meaningful entry point into historical content. Teachers of history and social studies, as well as those working in memory institutions (museum, libraries, and archives), should be encouraged in using place in their teaching and mobile education initiatives.
Connecting with new information landscapes: information literacy practices of refugees
Authors: Lloyd Annemaree , Anne Kennan Mary , Thompson Kim M. , Qayyum Asim
Published: January 2013

Purpose – The purpose of the research reported in this article is to understand how refugees learn to engage with a complex, multimodal information landscape and how their information literacy practice may be constructed to enable them to connect and be included in their new information landscape. Design/methodology/approach – The study is framed through practice and socio‐cultural theories. A qualitative research design is employed including semi‐structured face‐to‐face interviews and focus groups which are thematically analysed through an information practice lens. Findings – Refugees encounter complex and challenging information landscapes that present barriers to their full participation in their new communities. Social inclusion becomes possible where information is provided via sharing through trusted mediators who assist with navigating the information landscape and information mapping, and through visual and social sources. Research limitations/implications – The study is local and situated and therefore not empirically generalizable. It does however provide rich, deep description and explanation that is instructive beyond the specific research site and contributes to theory building. Practical implications – The study highlights the role, and importance, of social and visual information sources and the key role of service providers as mediators and navigators. Governments, funders and service providers can use these findings to inform their service provision. Originality/value – This is an original research paper in which the results provide practical advice for those working with refugees and which also extends theories of information literacy practice as an information practice.
Readers' perceptions of authors' citation behaviour
Authors: Willett Peter
Published: January 2013

Purpose

The aim of this paper is to determine the extent to which readers perceive correctly the reasons why authors cite items in scholarly texts.

Design/methodology/approach

The authors of ten library and information science articles provided the reasons for citing material in their articles and these reasons were compared with those suggested independently by readers of the articles.

Findings

Readers are able to perceive correctly author reasons for citation only to a very limited extent.

Research limitations/implications

Limitations are a small sample of ten articles and 45 reader assessments of those articles, and the use of a single classification of reasons for citation.

Practical implications

The findings call into question techniques such as citation context analysis that are based on the assumption that readers understand the reasons why authors cite material.

Originality/value

This is the first attempt to compare author and reader reasons for citation and hence to validate the use of citation context analysis.
The measurement of internal supply chain integration
Authors: Basnet Chuda
Published: January 2013

Purpose

Internal supply chain refers to the chain of activities within a company that concludes with providing a product to the customer. This process involves multiple functions within companies such as sales, production, and distribution. It is obvious that a company's performance would be enhanced by the integration of these functions. However, there is no consensus yet on how integration is to be defined and measured. The purpose of this paper is to present research that was conducted with the goal of developing an instrument for the measurement of internal supply chain integration.

Design/methodology/approach

Scale items were identified from current literature and the resulting survey instrument was sent out to a sample of New Zealand manufacturers. Statistical analysis was conducted to purify and validate the instrument.

Findings

In total, three dimensions of integration were identified, labelled coordination, communication, and affective relationship. This paper makes a contribution towards developing a consensus in the understanding and measurement of the integration construct.

Research limitations/implications

The selection and exclusion of measurement items for the survey have followed established principles of survey research, but may have been affected by the personal bias of the author. While every attempt has been made to comprehensively capture the state of the research up to the time of the study, there may be some omissions. The sample for the survey was drawn from a database of New Zealand businesses, thus the results are generalizable only to the extent that these businesses represent the population of all businesses. Another limitation is that no prior survey/case studies were carried out to collect practitioner's definitions/measures for integration.

Practical implications

The authors hope to have made a contribution here towards building a consensus among practitioners and researchers in defining and measuring internal supply chain integration. For practitioners, the measurement instrument offers a self‐assessment tool for internal supply chain integration. This should help them in identifying areas for improvement.

Originality/value

The contribution of this paper consists of: development of an instrument for the measurement of integration, validating the instrument against a criterion, and the identification of three dimensions of integration – communication, coordination, and affective relationship. The unique contributions of this paper are the validation of the instrument against a criterion and the identification of “affective relationship” as a dimension of internal supply chain integration.