bluuebunny/crossref_metadata_2025 huggingface dataset:
From directionals to telics
Authors: Martín Arista Javier , Cortés-Rodriguez Francisco J.
Published: July 2014

This chapter deals with the evolution of preverbs and discusses the development
of a telic function by directionals after a process of lexicalization and grammaticalization.
The main language of analysis is Old English and the discussion
includes a comparison with Sanskrit, Gothic and Old Icelandic. The theoretical
background is provided by Role and Reference Grammar. The conclusion
is reached that a cline of lexicalization and grammaticalization free adverb >
preverbal
adverb > bound prefix > no prefix can be defined with respect to
Sanskrit, Gothic, Old English and Old Icelandic, in such a way that Sanskrit
represents the earliest stage of the cline and Old Icelandic the latest.
Principal or Father? A Survey of the Novel Modir-e Madreseh (The School Principal) Based on Critical Discourse Analysis
Authors: Khalilinejad Meisam , Ardakani Negar Davari
Published: July 2014

In this research, linguistics is applied to the study of novels through critical discourse analysis. Critical discourse analysts take into consideration those elements of discourse which are hidden in order to preserve power hierarchy. Clearly contrary to descriptive-formal surveys of language, they contend that language can be used intentionally in order to support dominance, inequality and struggle against them as well. The novel Modir-e Madreseh (The School Principal) by Jalal Al-e Ahmad is analyzed based on Theo Van Leeuwen's research indexes, namely activation and passivation, nomination and categorization, identification and functionalization, personalization and impersonalization. The analysis illustrates how examination of the linguistic form used in the novel leads to deeper knowledge of the author who tries to alleviate people's miseries while they themselves do not play any significant role in doing so.
Down-regulated miR-15a mediates the epithelial–mesenchymal transition in renal tubular epithelial cells promoted by high glucose
Authors: Sun Tingli , Yang Jun , Dong Wenpeng , Wang Ruiyan , Ma Peilong , Kang Ping , Zhang Hongbo , Xie Changying , Du Juan , Zhao Lijie
Published: July 2014

High glucose (HG) has been reported to be associated with renal dysfunction. And one potential mechanism underlining the dysfunction is the epithelial–mesenchymal transition (EMT) of renal tubular epithelial cells. Present study showed that EMT was induced in the HG-treated renal tubular epithelial cells by promoting the expression of mesenchymal phenotype molecules, such as α-SMA and collagen I, and down-regulating the expression of epithelial phenotype molecule E-cadherin. Moreover, we have identified the down-regulation of miR-15a which was accompanied with the HG-induced EMT. And the miR-15a overexpression inhibited the α-SMA, collagen I expression, and the promotion of E-cadherin expression by targeting and down-regulating AP4 which was also significantly promoted by the HG in the renal tubular epithelial cells. Thus, this study revealed that the weakening regulation on the AP4 expression by miR-15a might contribute to the HG-induced EMT in the renal tubular epithelial cells.
Cognitive processing of moral and social judgements: A comparison of offenders, students, and control participants
Authors: Lahat Ayelet , Gummerum Michaela , Mackay Lorna , Hanoch Yaniv
Published: July 2014

Examining cognitive processes related to offenders’ moral and social judgements is important in order to better understand their criminal behaviour. In the present study, 30 offenders, 30 students, and 24 control participants were administered the moral-conventional judgements computer task, which requires responding under strict time constraints. Participants read scenarios and were asked to judge whether the act was acceptable or unacceptable when rules were either assumed or removed. Additionally, participants completed an executive function (EF) task in order to examine the relation between EF and moral and social judgements. The findings revealed that, as expected, controls and students had faster reaction times (RTs) and a higher percentage of normative judgements than offenders. Additionally, offenders had a low percentage of normative judgements, particularly in the conventional rule removed condition. Finally, RTs of moral and conventional judgements in most conditions were related to EF among students but not controls or offenders. We conclude that offenders, as compared to controls and students, may rely more on rule-oriented responding and may rely less on EF when making moral and social judgements.
Contrast Constancy Revisited: The Perceived Contrast of Sinusoidal Gratings above Threshold
Authors: Smith Wayne S.
Published: July 2014

The contrast sensitivity function of the human visual system, measured with sinusoidal luminance gratings, has an inverted U shape with a peak around 2–4 c/deg. Above threshold, it is thought that luminance gratings of equal physical contrasts but of distinguishably different spatial frequencies are all perceived as having similar contrasts, a phenomenon that has been termed contrast constancy. However, when suprathreshold contrast matches were measured for pairs of luminance gratings whose spatial frequencies were indistinguishable, the matching curves were not flat and followed a similar inverted U shape form as the contrast sensitivity function at threshold. It was therefore suggested that contrast constancy may only be revealed when matching the contrasts of clearly distinguishable spatial frequencies. Here, observers matched the perceived contrasts of suprathreshold luminance gratings of similar but visibly different spatial frequencies between 0.25 and 16 c/deg. The results show that, much like the contrast sensitivity function at threshold, observers are more sensitive to intermediate spatial frequencies (1–6 c/deg) than they are to either higher or to lower spatial frequencies. This tuning is evident when matching reference contrasts of 30–80%, implying a significant role in everyday vision. To demonstrate that these results were not due to local adaptation, the experiment was repeated with shorter stimulus duration, producing the same results. The extent of departure from contrast constancy found in the present study is compared to previously reported suprathreshold measurements. The results are also discussed with consideration to limitations with display apparatus such as monitor blur.
Optimal time discrimination
Authors: Çoşkun Filiz , Sayalı Zeynep Ceyda , Gürbüz Emine , Balcı Fuat
Published: July 2014

In the temporal bisection task, participants categorize experienced stimulus durations as short or long based on their similarity to previously acquired reference durations. Reward maximization in this task requires integrating endogenous timing uncertainty as well as exogenous probabilities of the reference durations into temporal judgements. We tested human participants on the temporal bisection task with different short and long reference duration probabilities (exogenous probability) in two separate test sessions. Incorrect categorizations were not penalized in Experiment 1 but were penalized in Experiment 2, leading to different levels of stringency in the reward functions that participants tried to maximize. We evaluated the judgements within the framework of optimality. Our participants adapted their choice behaviour in a nearly optimal fashion and earned nearly the maximum possible expected gain they could attain given their level of endogenous timing uncertainty and exogenous probabilities in both experiments. These results point to the optimality of human temporal risk assessment in the temporal bisection task. The long categorization response times (RTs) were overall faster than short categorization RTs, and short but not long categorization RTs were modulated by reference duration probability manipulations. These observations suggested an asymmetry between short and long categorizations in the temporal bisection task.
Categorization by movement direction: Retrieval-induced forgetting of motor sequences grouped by motion features
Authors: Tempel Tobias , Frings Christian
Published: July 2014

We investigated the organized storage of motor sequences in memory by assuming that processes related to interference at retrieval are indicative of memory organization. Effects resulting from these processes, thus, would allow inferences on how motor sequences are represented and organized. Participants learned motor sequences that were categorized by the direction of the initial movement. The subsequent selective retrieval of a subset of sequences of one category resulted in retrieval-induced forgetting (RIF) for the non-retrieved sequences of the same category. RIF occurred in an explicit recall test (Experiment 1), as well in an implicit test assessing memory with novel cues (Experiment 2). The results suggest that RIF affected motor programmes and that other cues as the used effectors (here movement direction) can be used for the organization of procedural memory. Basic retrieval dynamics apparently operate within the declarative and procedural systems in a similar way.
Scaling laws of free magnetic energy stored in a solar emerging flux region
Authors: Magara Tetsuya
Published: July 2014

This Letter reports scaling laws of free magnetic energy stored in a solar emerging flux region which is a key to understanding the energetics of solar active phenomena such as solar flares and coronal mass ejections. By performing three-dimensional magnetohydrodynamic simulations that reproduce several emerging flux regions of different magnetic configurations, we derive power-law relationships among emerged magnetic flux, free magnetic energy and relative magnetic helicity in these emerging flux regions. Since magnetic flux is an observable quantity, the scaling law between magnetic flux and free magnetic energy may give a way to estimate invisible free magnetic energy responsible for solar active phenomena.
Effect of Stabilized Rice Bran Fractions on the Formation of Rice Flour Pasting Properties
Authors: Saleh Mohammed I. , Abu‐Waar Ziad Y. , Akash Muhanad W. , Al‐Dabbas Maher
Published: July 2014

Rice flour composition played a key role in determining the changes in pasting properties of rice flour. The influence of incorporating defatted rice bran (DFRB), rice bran fiber (RBF), rice bran protein (RBP), and stabilized rice bran (SRB) fractions on the mechanism of rice flour pasting viscosities was investigated. Pasting properties of long‐ and medium‐grain rice flour substituted with 5, 10, 15, 20, and 100% bran fractions resulted in a significant decrease (P < 0.05) in rice flour pasting property values. Flour substituted with RBP had the lowest pasting property measurements compared with other fractions, and the greater the percentage substituted, the lower the pasting property values. DFRB and RBF were least affected properties when used as a replacement. Results were attributed to the contribution of rice starch in the mechanism of rice paste formation, in which decreasing starch in a rice flour sample, as a result of substituting with fractions of SRB, may have resulted in faster swelling of starch granules to the maximum extent and increased their susceptibility to be disrupted by shear, resulting in low paste viscosities. Results also suggested that protein structural integrity and the nature of starch–protein bonding affected rice flour pasting mechanism formation.
Comparison of Quality‐Related Alleles Among Australian and North American Wheat Classes Exported to Japan
Authors: Ikeda Tatsuya M. , Yanaka Mikiko , Takata Kanenori
Published: July 2014

Grain hardness, amylose content, and glutenin subunit composition are critical determinants for end‐use properties of wheat. To improve the end‐use properties of domestic wheats, we studied these traits between the Australian and North American wheat classes exported to Japan in 2009 and 2011 by analyzing the corresponding alleles. Most hard classes had Pina‐D1b or Pinb‐D1b. A partial waxy allele (Wx‐B1b) was found in all Australian Standard White (ASW) seeds in 2009 and two‐thirds of ASW seeds in 2011. All or most American hard wheat seeds had Glu‐D1d. Most U.S. Western White (WW) seeds had a null allele (Glu‐A1c) or alleles that lacked one of the two Glu‐B1 subunits. Most hard red winter (HRW) seeds had Glu‐B3b or Glu‐B3g. Quality characteristics of these classes seemed to be consistent with these results. In addition, we also found new Glu‐1 and Glu‐3 alleles in HRW and WW. These results suggested that although there are variations in its allelic composition from year to year, each class has unique quality‐related alleles corresponding to its end use. We proposed two matrices for classification of starch properties on the basis of Pin and Wx allelic combinations and for classification of gluten strength on the basis of glutenin allelic combinations.
Pathogenicity and Host Susceptibility of Penicillium spp. on Citrus
Authors: Louw Johannes Petrus , Korsten Lise
Published: July 2014

Citrus fruit are exposed to numerous postharvest pathogens throughout the fresh produce supply chain. Well-known postharvest citrus fruit pathogens are Penicillium digitatum and P. italicum. Lesser-known pathogens include P. crustosum and P. expansum. This study examined pathogenicity and aggressiveness of Penicillium spp. present in fresh fruit supply chains on various Citrus spp. and cultivars. The impact of different inoculation methods and storage conditions on decay were also assessed. P. digitatum and P. italicum were the most aggressive Penicillium spp. on citrus but aggressiveness varied significantly over the evaluated citrus range. Decay and tissue-response lesions caused by P. crustosum were observed on ‘Nules Clementine’, ‘Nova’, ‘Owari Satsuma’, ‘Delta Valencia’, ‘Cambria Navel’, ‘Eureka’ seeded, and ‘Star Ruby’ for the first time. Likewise, these lesions caused by P. expansum were noted on Nules Clementine, Owari Satsuma, Delta Valencia, ‘Midknight Valencia’, and Eureka seeded for the first time. Tissue-response lesions affect fruit quality and some Penicillium spp. sporulated from the lesions, causing the inoculated species to complete their life cycle. New citrus–Penicillium spp. interactions were observed and the importance of monitoring inoculum loads of pathogens and nonhost pathogens were highlighted.
A Novel Phellinidium sp. Causes Laminated Root Rot on Qilian Juniper (Sabina przewalskii) in Northwest China
Authors: Cui Bao-Kai , Dai Yu-Cheng , He Shuang-Hui , Zhou Li-Wei , Yuan Hai-Sheng
Published: July 2014

A laminated root rot on Qilian juniper (Sabina przewalskii) caused by a species of Phellinidium (Basidiomycota) was observed in northwest China. Seventeen fungal samples collected from Qinghai Province during 2012 and 2013 were used for taxonomic and pathogenicity tests. The fungal pathogen was identified by morphological characters and phylogenetic analyses based on nLSU sequences. A new fungus is described herein as Phellinidium qilianense sp. nov. One-year-old Qilian juniper seedlings were wound-inoculated under controlled conditions to test pathogenicity of the fungal species. The fungus was successfully reisolated from decayed tissue of tested seedlings. P. qilianense is a new forest pathogen on coniferous trees in China.
First Report of Phakopsora pachyrhizi on Soybean Causing Rust in Tanzania
Authors: Murithi H. M. , Beed F. D. , Madata C. S. , Haudenshield J. S. , Hartman G. L.
Published: July 2014

Phakopsora pachyrhizi Syd. was reported on legume hosts other than soybean in Tanzania as early as 1979 (1). Soybean rust (SBR), caused by P. pachyrhizi, was first reported on soybean in Africa in Uganda in 1996 (3), and its introduction into Africa was proposed to occur through urediniospores blowing from western India to the African east coastal areas by moist northeast monsoon winds (4). The fungus rapidly spread and was reported on soybean in South Africa in 2001, in western Cameroon in 2003, and in Ghana and the Democratic Republic of the Congo in 2007 (5). A second species causing SBR on soybean, P. meibomiae, has not been reported in Africa or elsewhere, outside of the Americas. From 2012 to 2014, symptomatic leaf samples were collected in the major soybean growing areas of the Tanzanian Southern Highlands (Iringa, Mbeya, and Ruvuma regions). Symptoms of SBR included yellowing of leaves and tan sporulating lesions. These symptoms were observed at flowering through seed maturity. From fields surveyed in 2012, 2013, and 2014, SBR was observed in 5 of 14, 7 of 11, and 14 of 31 fields, respectively. Some of the leaves sampled had up to 80% of the leaf area affected. When microscopically examined, urediniospores were elliptical, echinulate, and hyaline to pale yellowish brown. In 2014, sporuliferous uredinia were observed on leaf material collected from the Iringa and Ruvuma regions of Tanzania, and a subset of these samples was sent by APHIS permit to the University of Illinois. To confirm the pathogen, symptomatic soybean leaf tissue of approximately 1 cm2 was excised from each of the samples, and DNA was extracted using the FastDNA Spin Kit (MP Biomedicals, Solon, OH), with further purification using the MicroElute DNA Clean-up Kit (Omega Bio-Tek, Norcross, GA). The DNA was subjected to quantitative PCR using published Taqman assays for P. pachyrhizi, P. meibomiae, and a multiplexed exogenous internal control reaction to validate negative results (2). P. pachyrhizi DNA was detected in excess of 66,000 genome equivalents/cm2 in all samples, and P. meibomiae DNA was determined to be absent from all samples (limit of quantification ~2 pg DNA/cm2). Free surviving urediniospores were dislodged from 12 samples and inoculated onto susceptible soybean cultivar Williams 82, which produced sporulating SBR lesions after 2 weeks of incubation in a detached-leaf assay. Thus, Koch's postulates were completed. This is the first report of P. pachyrhizi causing rust on soybean in Tanzania. In vivo cultures have been established from most of these samples, and ongoing research includes an evaluation of the P. pachyrizi virulence on a differential set, and characterization of the genetic diversity.

References: (1) D. L. Ebbels and D. J. Allen. Phytopath. Pap. 22:1-89. (2) J. S. Haudenshield and G. L. Hartman. Plant Dis. 95:343, 2011. (3) R. Kawuki et al. Afr. Crop Sci. J. 11:301, 2003. (4) C. Levy. Plant Dis. 89:669, 2005. (5) P. S. Ojiambo et al. Plant Dis. 91:1204, 2007.
First Report of Sweet potato leaf curl Georgia virus Infecting Tall Morning Glory (Ipomoea purpurea) in China
Authors: Zhang S. B. , Du Z. G. , Wang Z. , Tang Y. F. , She X. M. , Lan G. B. , He Z. F.
Published: July 2014

In September 2013, tall morning glory (Ipomoea purpurea) plants showing vein yellowing and leaf curl symptoms typical of a begomovirus infection were observed in Jingzhou, Hubei Province, China. Total nucleic acids were extracted from a symptomatic plant using cetyltrimethylammonium bromide (CTAB). Rolling circle amplification (RCA) was conducted using TempliPhi kit (GE Healthcare) to recover the genome of a putative begomovirus. Digestion of the RCA product with PstI yielded a ~2.8 kbp DNA fragment suggestive of a monomerized begomoviral genome. The fragment was cloned and sequenced and the sequence was deposited in GenBank under accession no. KF769447. SDTv1.0 (species demarcation tool) analysis revealed that the putative begomovirus showed 98.5 and 92.0% nucleotide sequence identity with Sweet potato leaf curl Georgia virus (SPLCGV)-[China:Hebei:2011] (GenBank Accession No. JX448368) and SPLCGV-[US:Geo:16] (AF326775), respectively. The virus contained six ORFs, which encoded proteins showing 96.5 to 100% and 90.6 to 95.6% amino acid sequence identity with their counterparts of SPLCGV-[China:Hebei:2011] and SPLCGV-[US:Geo:16], respectively. Thus, the virus should be considered as an isolate of SPLCGV-[China:Hebei:2011]. Tall glory morning in a nearby field (which covers an area of 3 square kilometers) was surveyed and 70 to 100% of plants were found showing symptoms reminiscent of begomoviral infection. Total nucleic acid was extracted from 13 randomly selected (10 symptomatic and 3 healthy) plants and used as templates for PCR with a pair of specific primers (5′-CGCAGCCTTTCCACACTATC-3′/5′-AAAACAGTTTGGGCTCGGTC-3′) designed according to the sequence described above. Positive results were obtained for all of the symptomatic, but none of the healthy-looking tall morning glory plants. SPLCGV (genus Begomovirus, family Geminiviridae) was reported to infect sweet potato (I. batatas) in the United States (4), India (2), and China (3). To our knowledge, this is the first report of SPLCGV infecting tall morning glory in China. Also, it is the first report of a geminivirus in Hubei, a province of central China. Whereas the finding of SPLCGV in sweet potato (3) may be a result of vegetative propagation of this crop, the detection of SPLCGV in tall morning glory, an annual plant, raises the possibility that this virus is transmissible and is spreading in China.

References: (1) B. Muhire et al. Arch. Virol. 158:1411, 2013. (2) G. Prasanth and V. Hegde. Plant Dis. 92:311, 2008. (3) Y. Qin et al. Plant Dis. 97:1388, 2013. (4) R. A. Valverde and D. L. Gutierrez. Rev. Mex. Fitopatol. 21:128, 2003.
Effect of Mini-plate Fixation on Hinge Fracture and Bony Fusion in Unilateral Open-door Cervical Expansive Laminoplasty
Authors: Chen Hua , Liu Hao , Zou Li , Li Tao , Gong Quan , Song Yueming , Zeng Jiancheng , Liu Limin , Kong Qingquan
Published: July 2014

Study Design:

This was a retrospective study.

Objective:

The aim of this study was to investigate the effect of Centerpiece mini-plate fixation on the complete fracture and bony fusion of the hinge side in unilateral open-door cervical expansive laminoplasty.

Summary of Background Data:

Cervical laminoplasty is an effective and safe surgery for cervical canal stenosis. The Centerpiece mini-plate is an instrument used to secure the laminae and maintain the cervical canal expansion. Stability of the new laminae is largely dependent on healing of the hinge side bone fracture and the degree of bony fusion. To date, few studies have reported on the effects of mini-plate fixation on these 2 important factors.

Materials and Methods:

Between September 2009 and March 2011, 58 patients received unilateral open-door cervical expansive laminoplasty at the authors’ hospital. The group included 47 male and 11 female patients, with a mean age of 61 (range, 35–81) years. Two hundred twenty-five laminae were fixed using the Centerpiece mini-plate (group A), whereas 62 laminae were fixed using suture suspension (group B). The rates of fracture and bony fusion of the hinge were observed using computed tomography scan and compared between the 2 groups. The complete fractures were subdivided into 4 groups based on the degree of displacement of the fractured ends: type I (no displacement), type II (mild to moderate displacement), type III (complete displacement or separation), or type IV (the hinge had collapsed into the cervical canal).

Results:

The number of incomplete fractures and type I to IV fractures in group A were 95, 93, 25, 8, and 4 and 29, 25, 4, 2, 2 in group B, respectively. There were no significant differences between the 2 groups in terms of complete fracture rates (P=0.309) and complete fracture type distribution (P=0.694). Group A had a significantly higher rate of bony fusion of the hinge 3 months after surgery (82% vs. 70%, P=0.042); however, this rate was not statistically significant 6 months after surgery (P=0.141). For type I complete hinge fracture, group A had higher bony fusion rates, both 3 months (86% vs. 57%, P=0.004) and 6 months (92% vs. 85%, P=0.048) postoperatively. The rates of bony fusion were also significantly different among all complete fracture types 3 months (P<0.001) and 6 months (P<0.001) postoperatively.

Conclusions:

Centerpiece mini-plate fixation in unilateral open-door cervical expansive laminoplasty might not increase the complete fracture rate compared with suture suspension and might promote bony fusion of type I complete hinge fractures.
Large eddy simulation of flows in industrial compressors: a path from 2015 to 2035
Authors: Gourdain N. , Sicot F. , Duchaine F. , Gicquel L.
Published: July 2014

A better understanding of turbulent unsteady flows is a necessary step towards a breakthrough in the design of modern compressors. Owing to high Reynolds numbers and very complex geometry, the flow that develops in such industrial machines is extremely hard to predict. At this time, the most popular method to simulate these flows is still based on a Reynolds-averaged Navier–Stokes approach. However, there is some evidence that this formalism is not accurate for these components, especially when a description of time-dependent turbulent flows is desired. With the increase in computing power, large eddy simulation (LES) emerges as a promising technique to improve both knowledge of complex physics and reliability of flow solver predictions. The objective of the paper is thus to give an overview of the current status of LES for industrial compressor flows as well as to propose future research axes regarding the use of LES for compressor design. While the use of wall-resolved LES for industrial multistage compressors at realistic Reynolds number should not be ready before 2035, some possibilities exist to reduce the cost of LES, such as wall modelling and the adaptation of the phase-lag condition. This paper also points out the necessity to combine LES to techniques able to tackle complex geometries. Indeed LES alone, i.e. without prior knowledge of such flows for grid construction or the prohibitive yet ideal use of fully homogeneous meshes to predict compressor flows, is quite limited today.
Lack of a surface layer in Tannerella forsythia mutants deficient in the type IX secretion system
Authors: Narita Yuka , Sato Keiko , Yukitake Hideharu , Shoji Mikio , Nakane Daisuke , Nagano Keiji , Yoshimura Fuminobu , Naito Mariko , Nakayama Koji
Published: July 2014

Tannerella forsythia, a Gram-negative anaerobic bacterium, is an important pathogen in periodontal disease. This bacterium possesses genes encoding all known components of the type IX secretion system (T9SS). T. forsythia mutants deficient in genes orthologous to the T9SS-encoding genes porK, porT and sov were constructed. All porK, porT and sov single mutants lacked the surface layer (S-layer) and expressed less-glycosylated versions of the S-layer glycoproteins TfsA and TfsB. In addition, these mutants exhibited decreased haemagglutination and increased biofilm formation. Comparison of the proteins secreted by the porK and WT strains revealed that the secretion of several proteins containing C-terminal domain (CTD)-like sequences is dependent on the porK gene. These results indicate that the T9SS is functional in T. forsythia and contributes to the translocation of CTD proteins to the cell surface or into the extracellular milieu.
Stress-Induced Mutagenesis and Complex Adaptation
Authors: Ram Yoav , Hadany Lilach
Published: July 2014

Because mutations are mostly deleterious, mutation rates should be reduced by natural selection. However, mutations also provide the raw material for adaptation. Therefore, evolutionary theory suggests that the mutation rate must balance between adaptability - the ability to adapt - and adaptedness - the ability to remain adapted. We model an asexual population crossing a fitness valley and analyze the rate of complex adaptation with and without stress-induced mutagenesis - the increase of mutation rates in response to stress or maladaptation. We show that stress-induced mutagenesis increases the rate of complex adaptation without reducing the population mean fitness, thus breaking the evolutionary trade-off between adaptability and adaptedness. Our theoretical results support the hypothesis that stress-induced mutagenesis promotes adaptation and provide quantitative predictions of the rate of complex adaptation with different mutational strategies.
Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction
Authors: Gomes Antonio L.C. , Abeel Thomas , Peterson Matthew , Azizi Elham , Lyubetskaya Anna , Carvalho Luís , Galagan James
Published: July 2014

The comprehension of protein and DNA binding in vivo is essential to understand gene regulation. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) provides a global map of the regulatory binding network. Most ChIP-seq analysis tools focus on identifying binding regions from coverage enrichment. However, less work has been performed to infer the physical and regulatory details inside the enriched regions. This research extends a previous blind-deconvolution approach to develop a post-peak–calling algorithm that improves binding site resolution and predicts cooperative interactions. At the core of our new method is a physically motivated model that characterizes the binding signal as an extreme value distribution. This model suggests a mathematical framework to study physical properties of DNA shearing from the ChIP-seq coverage. The model explains the ChIP-seq coverage with two signals: The first considers DNA fragments with only a single binding event, whereas the second considers fragments with two binding events (a double-binding signal). The model incorporates motif discovery and is able to detect multiple sites in an enriched region with single-nucleotide resolution, high sensitivity, and high specificity. Our method improves peak caller sensitivity, from less than 45% up to 94%, at a false positive rate <11% for a set of 47 experimentally validated prokaryotic sites. It also improves resolution of highly enriched regions of large-scale eukaryotic data sets. The double-binding signal provides a novel application in ChIP-seq analysis: the identification of cooperative interaction. Predictions of known cooperative binding sites show a 0.85 area under an ROC curve.
A novel extracellular protease of Vibrio mimicus that mediates maturation of an endogenous hemolysin
Authors: Mizuno Tamaki , Nanko Ayako , Maehara Yoko , Shinoda Sumio , Miyoshi Shin‐Ichi
Published: July 2014

Vibrio mimicus, a human pathogen that causes gastroenteritis, produces an enterotoxic hemolysin as a virulence factor. The hemolysin is secreted extracellularly as an inactive protoxin and converted to a mature toxin through removal of the N‐terminal propeptide, which comprises 151 amino acid residues. In this study, a novel protease having the trypsin‐like substrate specificity was purified from the bacterial culture supernatant. The N‐terminal amino acid sequence of the purified protein was identical with putative trypsin VMD27150 of V. mimicus strain VM573. The purified protease was found to cause maturation of the protoxin by cleavage of the Arg151Ser152 bond. Deletion of the protease gene resulted in increased amounts of the protoxin in the culture supernatant. In addition, expression of the hemolysin and protease genes was detected during the logarithmic growth phase. These findings indicate that the protease purified may mediate maturation of the hemolysin.
Antigen itself antibody: an alternative one‐step immunoassay for measuring the anti‐idiotypic antibody titer
Authors: Kabir M. Enamul , Krishnaswamy Senthilkumar , Selvakumar Dakshnamurthy , Miyamoto Masahiko , Furuichi Yasuhiro , Komiyama Tadazumi
Published: July 2014

Immunoassay designs rely on the great specificity of antibodies and a suitable marker that facilitates generation of a quantitative signal. Currently, there is no reliable method for measuring the titers of an anti‐idiotypic antibody. Our initial attempt to measure titers of mouse anti‐idiotypic antibody after idiotypic vaccination with HM‐1 killer toxin neutralizing monoclonal antibody (nmAb‐KT) failed. Because the injected antigen, nmAb‐KT, is a mouse IgG, using a commercial antibody to measure the antibody titer always gave a false positive signal against control mouse serum antibody in parallel with the antigen‐treated immunized serum antibodies. To get a reliable and clearly differentiable signal by ELISA, idiotypic antigen was labeled with HRP and HRP‐conjugated‐nmAb‐KT used to measure the antibody titers in the antigen‐treated mice. Compared with control mice, signals were found in high anti‐nmAb‐KT IgG responses in test mice; however, untreated control mice had a significant amount of purified non‐specific IgG. This method is amenable to long read lengths and will likely enable anti‐idiotypic antibody titer measurement in a more specific and cost effective way without requiring commercial antibody.
Non‐convex compressed sensing with frequency mask for seismic data reconstruction and denoising
Authors: Gholami Ali
Published: July 2014

Compressed Sensing has recently proved itself as a successful tool to help address the challenges of acquisition and processing seismic data sets. Compressed sensing shows that the information contained in sparse signals can be recovered accurately from a small number of linear measurements using a sparsity‐promoting regularization. This paper investigates two aspects of compressed sensing in seismic exploration: (i) using a general non‐convex regularizer instead of the conventional one‐norm minimization for sparsity promotion and (ii) using a frequency mask to additionally subsample the acquired traces in the frequency‐space () domain. The proposed non‐convex regularizer has better sparse recovery performance compared with one‐norm minimization and the additional frequency mask allows us to incorporate a priori information about the events contained in the wavefields into the reconstruction. For example, (i) seismic data are band‐limited; therefore one can use only a partial set of frequency coefficients in the range of reflections band, where the signal‐to‐noise ratio is high and spatial aliasing is low, to reconstruct the original wavefield, and (ii) low‐frequency characteristics of the coherent ground rolls allow direct elimination of them during reconstruction by disregarding the corresponding frequency coefficients (usually bellow 10 Hz) via a frequency mask. The results of this paper show that some challenges of reconstruction and denoising in seismic exploration can be addressed under a unified formulation. It is illustrated numerically that the compressed sensing performance for seismic data interpolation is improved significantly when an additional coherent subsampling is performed in the domain compared with the domain case. Numerical experiments from both simulated and real field data are included to illustrate the effectiveness of the presented method.
Trade, Remittances and Economic Growth in Nigeria: Any Causal Relationship?
Authors: Olubiyi Ebenezer Adesoji
Published: July 2014

This study examined the causal relationships among GDP, export, imports and remittances. The study, among others, investigated the validity of export‐led and remittances‐led growth hypotheses. Specifically, the study investigated the causal relationship between remittances and GDP, remittances and export and remittances and imports. Employing a VECM Granger Causality for data spanning between 1980 and 2012, imports and remittances significantly Granger‐caused GDP in the short run. Also, there were reverse causalities running from GDP to export and imports. This implies that export‐led growth hypothesis holds in Nigeria. Furthermore, there was a unidirectional causation running from remittances to GDP, implying that remittances matter for economic growth. But since the effect was more from the demand side, it could lead to inflationary pressure. The policy recommendation is that the authorities should intensify efforts on the export base of the economy. The monetary authorities should implement necessary policy to cool the pressure arising from conspicuous spending of remittances.
Knowledge Economy and Financial Sector Competition in African Countries
Authors: Asongu Simplice A.
Published: July 2014

The goal of this paper is to assess how knowledge economy (KE) plays out in financial sector competition. It suggests a practicable way to disentangle the effects of different components of KE on various financial sectors. The variables identified under the World Bank's four knowledge economy index (KEI) are employed. An endogeneity robust panel instrumental variable fixed‐effects estimation strategy is employed on data from 53 African countries for the period 1996–2010. The following findings are established. First, education and innovation in terms of scientific and technical publications broadly bear an inverse nexus with financial development. Second, the incidence of information and communication technologies is positive on all financial sectors but increases the non‐formal sectors to the detriment of the formal sector. Third, economic incentives have positive implications for all sectors though the formal financial sector benefits most. Fourth, institutional regime is positive (negative) for the semi‐formal (informal) financial sector. The findings contribute at the same time to the macroeconomic literature on measuring financial development and respond to the growing fields of informal sector importance, microfinance and mobile banking by means of KE promotion. Policy implications and future research directions are discussed.
Impact of Real Exchange Rate on Trade Balance in Nigeria
Authors: Igue Nkenchor Neville , Ogunleye Toyin Segun
Published: July 2014

The study investigated whether the depreciation of exchange rate has a favourable impact on trade balance in Nigeria, based on the Marshall–Lerner (ML) condition. The Johansen method of cointegration and vector error correction methodology (VECM) was employed to investigate the existence of a long‐run relationship between trade balance and the specified set of independent variables. The results confirm the satisfaction of the Marshall–Lerner condition in Nigeria, implying that depreciation of the exchange rate has a positive effect on trade balance in the long run. The study also established that a one per cent depreciation in the exchange rate would improve trade balance by 1.16 per cent. In the light of these findings, the study recommends a gradual depreciation of the exchange rate, which should be accompanied with export policy that encourages domestic production of non‐oil products for exports.
Facteurs Microéconomiques du Déficit de Financement des PME au Cameroun
Authors: Tsafack Nanfosso Christian Lambert Nguena et Roger
Published: July 2014

La présente étude a pour but d'effectuer une évaluation économétrique des facteurs microéconomiques responsables du problème de financement externe des PME au Cameroun. A l'aide d'un modèle logit multinomial l'on a estimé la variable «Principale source de financement» sur la base des données d'enquête auprès des acteurs du financement portant sur un échantillon de 413 PME du Cameroun. Les résultats montrent que le déficit de financement externe est expliqué par l'absence d'information comptable, le statut juridique Société à Responsabilité Limité (SARL) et Société Anonyme (SA), l'appartenance au secteur industriel, le faible effectif d'employé, le taux d'intérêt élevé et les demandes de crédit à long terme. Ces deux dernières causes étant renforcées par la toute dernière crise financière. Ces résultats conduisent à interpeller Les différents acteurs sur les décisions à prendre en fonction de leur niveau de responsabilité dans ces éléments de frein au financement des PME.
La pauvreté monétaire au Sénégal entre 2002–2006: Disparités régionales et effets de décomposition de la pauvreté
Authors: Sy Ibrahima
Published: July 2014

Cet article propose une analyse de la pauvreté monétaire au Sénégal. La pauvreté est estimée non pas à travers un seuil de pauvreté national mais des seuils de pauvreté régionaux. Nous présentons les outils méthodologiques nécessaires à l'appréhension de la dynamique de pauvreté monétaire avec la formule générique des indices proposée par Foster, Greer et Thorbecke (FGT, 1984) afin d'estimer et analyser la pauvreté monétaire au Sénégal sur la période 2002–2006. Partant delà, et supposant l'existence notoire de disparités de la variation de pauvreté, nous explorons la décomposition sectorielle des changements de la pauvreté en fonction de la localisation géographique en utilisant la méthode de décomposition proposée par Ravallion et Huppi (), en vue d'évaluer la contribution des facteurs explicatifs potentiels des disparités de pauvreté. Les résultats obtenus dévoilent d'abord que les disparités en termes de seuil de pauvreté montrent la non pertinence de l'utilisation d'un seuil unique de pauvreté au Sénégal. Ensuite, ils suggèrent une baisse de la pauvre monétaire au plan national, mais avec de fortes disparités entre les régions et une stabilisation des inégalités de pauvreté au cours de la période étudiée. En enfin, l'effet des changements de la localisation de la population contribue à augmenter la pauvreté dans certaines régions et dans la pauvreté globale.
Aid Categories that Foster Pro‐Poor Growth: The Case of Sierra Leone
Authors: Kargbo Philip Michael , Sen Kunal
Published: July 2014

This paper examines the effect of different categories of foreign aid on poverty reduction. It uses a country case study for Sierra Leone to explore the impact of different aid types on pro‐poor growth as a dimension of poverty reduction. Using annual time series data spanning from 1970 to 2007 and employing the bounds test approach to cointegration by Pesaran and Shin (), the study finds strong evidence to suggest that only aid in the form of grants do have a pro‐poor effect. This result is more obvious in the long run than in the short run. Aid in the forms of loans and technical assistance could not prove signficant for fostering pro‐poor growth in the country. Thus, even though total aid reveals a highly significant long‐run impact in improving pro‐poor growth in Sierra Leone, when disaggregated, only aid in the form of grants shows strong evidence of reducing poverty in the country. The implication of these findings is that for reducing poverty in typically poor and fagile states, aid in the form of grants should be encouraged. The increasing donor interest in technical assistance aid in recent years should be reconsidered as there is no strong evidence that it reduces poverty.
What Is the Value of Adding Medicare Data in Estimating VA Hospital Readmission Rates?
Authors: O'Brien William J. , Chen Qi , Mull Hillary J. , Shwartz Michael , Borzecki Ann M. , Hanchate Amresh , Rosen Amy K.
Published: July 2014

Objective

To determine the effects of including diagnostic and utilization data from a secondary payer on readmission rates and hospital profiles.

Data Sources/Study Setting

Veterans Health Administration (VA) and Medicare inpatient and outpatient administrative data for veterans discharged from 153 VA hospitals during FY 2008–2010 with a principal diagnosis of acute myocardial infarction, heart failure, or pneumonia.

Study Design

We estimated hospital‐level risk‐standardized readmission rates derived using VA data only. We then used data from both VA and Medicare to reestimate readmission rates and compared hospital profiles using two methods: Hospital Compare and the CMS implementation of the Hospital Readmissions Reduction Program (HRRP).

Data Collection/Extraction Methods

Retrospective data analysis using VA hospital discharge and outpatient data matched with Medicare fee‐for‐service claims by scrambled Social Security numbers.

Principal Findings

Less than 2 percent of hospitals in any cohort were classified discordantly by the Hospital Compare method when using VA‐only compared with VA/Medicare data. In contrast, using the HRRP method, 13 percent of hospitals had differences in whether they were flagged as having excessive readmission rates in at least one cohort.

Conclusions

Inclusion of secondary payer data may cause changes in hospital profiles, depending on the methodology used. An assessment of readmission rates should include, to the extent possible, all available information about patients' utilization of care.
Funding emergency care: Australian style
Authors: Bell Anthony , Crilly Julia , Williams Ged , Wylie Kate , Toloo Ghasem (Sam) , Burke John , FitzGerald Gerry
Published: July 2014

The ongoing challenge for ED leaders is to remain abreast of system‐wide changes that impact on the day‐to‐day management of their departments. Changes to the funding model creates another layer of complexity and this introductory paper serves as the beginning of a discussion about the way in which EDs are funded and how this can and will impact on business decisions, models of care and resource allocation within Australian EDs. Furthermore it is evident that any funding model today will mature and change with time, and moves are afoot to refine and contextualise ED funding over the medium term. This perspective seeks to provide a basis of understanding for our current and future funding arrangements in Australian EDs.
Disengaging from engagement
Authors: Purcell John
Published: July 2014

Two basic approaches to engagement are contrasted. Work engagement relates to an individual's psychological state of mind while at work. The problems with this and its limited relevance to HRM are considered: its concern with a minority of employees, the way non‐engaged staff are portrayed, the airbrushing out of conflict and the pernicious use of positive psychology. Employee or behavioural engagement is more relevant to HRM and employment relations but suffers from a lack of definition and a failure to specify the components that are associated with higher levels of employee engagement. It is usually a‐contextual and lacks the subtlety of earlier work on HR and performance, while covering the same ground. Problems remain with research seeking to show the connections with financial performance. Boiling engagement measures down to one score is particularly worrying. The management of employee engagement in the UK National Health Service illustrates that properly constructed studies of employee engagement can inform policies and practices to improve work relations, employee well‐being and aspects of performance.
Effect of Curing Agents on the Oxidative and Nitrosative Damage to Meat Proteins during Processing of Fermented Sausages
Authors: Villaverde A. , Morcuende D. , Estévez M.
Published: July 2014

The effect of increasing concentrations of curing agents, ascorbate (0, 250, and 500 ppm), and nitrite (0, 75, and 150 ppm), on the oxidative and nitrosative damage to proteins during processing of fermented sausages was studied. The potential influence of these reactions on color and texture of the fermented sausages was also addressed. Nitrite had a pro‐oxidant effect on tryptophan depletion and promoted the formation of protein carbonyls and Schiff bases. The nitration degree in the fermented sausages was also dependent on nitrite concentration. On the other hand, ascorbate acted as an efficient inhibitor of the oxidative and nitrosative damage to meat proteins. As expected, nitrite clearly favored the formation of the cured red color and ascorbate acted as an enhancer of color formation. Nitrite content was positively correlated with hardness. The chemistry behind the action of nitrite and ascorbate on muscle proteins during meat fermentation is thoroughly discussed. The results suggest that ascorbate (500 ppm) may be required to compensate the pro‐oxidant impact of nitrite on meat proteins.