bluuebunny/crossref_metadata_2025 huggingface dataset:
Prohibition and Repeal: A Short History of the Wine Industry's Regulation in the United States
Authors: Beliveau Barbara C. , Rouse M. Elizabeth
Published: June 2012

The United States wine industry has experienced tremendous growth in the past twenty-five years. The number of wineries in the United States has grown to almost 5000, located in all fifty states, and creating over a million full time jobs. Alcohol distribution laws that hinge on the Supreme Court's reconciliation of the Twenty-first Amendment and the Commerce Clause have significantly hindered the industry's ability to expand. Current interpretations of the 21stAmendment give states unprecedented freedom to regulate interstate commerce in alcoholic beverages. The resulting regulatory diversity presents problems both domestically and internationally. (JEL Classification: K2, L5, N4)
The Economic Impact of the Wine Industry on Hotels and Restaurants: Evidence from Washington State
Authors: Storchmann Karl
Published: June 2012

Washington State enjoys an extraordinarily fast growing wine industry and is now the second largest wine producing state in the U.S. This paper examines the impact of this growth on the revenue of hotels and restaurants. Employing a dynamic quarterly panel model at the county level we show that the regional reputation as high quality wine county, as expressed by critical wine points in the national wine press, has a significant effect on the tourism industry. For Walla Walla, the most prominent wine county in the state, less than 17% of all restaurant and approximately 40% of all hotel revenue is tied to the wine cluster (2007). However, regional reputation is not long-living and needs constant replenishment. (JEL Classification: R11, R15, Q19)
Beer in Good Times and Bad: A U.S. State-Level Analysis of Economic Conditions and Alcohol Consumption
Authors: Freeman Donald G.
Published: June 2012

Data on U.S. state-level beer shipments from 1970 to 2007 provided by The Beer Institute are used to estimate pooled time-series models of annual consumption regressed on economic and demographic variables, using the common correlated effects (CCE) estimators to control for unobserved common effects and to allow for heterogeneous responses across units. Beer is found to be a procyclical good, varying negatively with the state unemployment rate. Previous findings for the negative effect of excise taxes on consumption are supported, though the estimated elasticities are smaller than those reported in earlier research. Demographics have a significant and material effect on consumption, with larger shares of young adults in the population implying greater consumption of beer per capita. (JEL Classification: D12, C23)
Fluid upwelling beneath arc volcanoes above the subducting Philippine Sea Plate: Evidence from regional electrical resistivity structure
Authors: Hata Maki , Oshiman Naoto , Yoshimura Ryokei , Tanaka Yoshikazu , Uyeshima Makoto
Published: June 2012

At subduction zones, aqueous fluids released from the subducting slab play an important role in island arc volcanism, triggering partial melting and accretion magmatism. We used the Network‐magnetotelluric (MT) method to obtain the deep (>100 km), large‐scale electrical resistivity structure beneath Kyushu, Japan, with the aim of identifying regions of deep fluids and magma that feeds subduction zone volcanoes in the region. Network‐MT observations, in which dipoles of about 10–30 km in length were used to measure the electric potential difference, were performed over all of Kyushu, in the Southwest Japan Arc, where the Philippine Sea Plate (PSP) is subducting beneath the Eurasian Plate at a high angle. Using the Network‐MT data, we obtained the large‐scale electrical resistivity structure along four profiles across each of four Quaternary active volcanoes at the volcanic front of the Kyushu subduction zone. The resistivity models have two features in common: a conductor beneath each volcano, whose base extends to the backarc side, and a resistor along the hinge line of the subducting PSP in the forearc. The conductor indicates regions of fluid released from the slab or partial melting of the mantle, representing a magma source for subduction zone volcanoes in this region.
Tackling challenges in assessing air quality over South America
Authors: Gallardo Laura , Jorquera Hector , Molina Luisa T.
Published: June 2012

Towards an Integrated Observing System for South America: Air Quality Assessment and Forecasting in Mega Cities; Santiago, Chile, 9–12 January 2012
Williams to become new AGU director of science
Authors: Ambrogio Olivia
Published: June 2012

Billy Williams, who will join AGU as its new director of science on 15 June, will work to raise AGU's profile and impact and shape AGU's scientific activities and the development of scientific careers for AGU student members. As director of science, Williams will facilitate working relationships and communication of scientific information and resources between and among the AGU Board and Council, committees, sections and focus groups, AGU members (including students), staff, and external partners. In addition, he will facilitate and coordinate the development and implementation of memorandums of understanding and other collaborations with various scientific societies, and he will provide leadership for AGU's efforts to develop resources designed to assist students in preparing for scientific careers. Williams also will serve as senior staff member to the AGU Council.
Hurricane feedback research may improve intensity forecasts
Authors: Schultz Colin
Published: June 2012

Forecasts of a hurricane's intensity are generally much less accurate than forecasts of its most likely path. Large‐scale atmospheric patterns dictate where a hurricane will go and how quickly it will get there. The storm's intensity, however, depends on small‐scale shifts in atmospheric stratification, upwelling rates, and other transient dynamics that are difficult to predict. Properly understanding the risk posed by an impending storm depends on having a firm grasp of all three properties: translational speed, intensity, and path. Drawing on 40 years of hurricane records representing 3090 different storms, Mei et al. propose that a hurricane's translational speed and intensity may be closely linked.
Cattle waste tops cars as source of Southern California smog
Authors: Schultz Colin
Published: June 2012

A new study shows that cows, not cars, are the more substantial source of ammonia that leads to ammonium nitrate in California's South Coast Air Basin, the smoggiest place in the United States. Within the region, which consists of the area surrounding and downwind of Los Angeles, a large proportion of the fine‐grained particulate matter that makes up smog is formed from ammonium nitrate. Nowak et al. found two main sources of ammonium nitrate: small gas‐powered vehicles and dairy farms. Catalytic converters designed to stem the emissions of carbon monoxide, nitrogen oxides, and hydrocarbons from the region's 9.9 million vehicles can produce gaseous ammonia as an unwanted by‐product. Bacteria decomposing organic wastes from the region's 298,000 dairy cattle, on the other hand, also account for a sizable source of ammonia emissions.
Transport of thermal‐energy ionospheric oxygen (O+) ions between the ionosphere and the plasma sheet and ring current at quiet times preceding magnetic storms
Authors: Yau Andrew W. , Howarth Andrew , Peterson W. K. , Abe Takumi
Published: June 2012

The presence of energetic O+ ions in the ring current at the onset of a magnetic storm prompts the question of the possible role of “in‐transit” ionospheric O+ ions between the ionosphere and the plasma sheet and ring current in the quiet periods immediately preceding the main phase of a magnetic storm. Thermal‐energy O+ ions are often observed in the quiet time high‐altitude (>7000 km) polar ionosphere on Akebono, at temperatures of ∼0.2–0.3 eV and flow velocities of a few km/s. In this paper, we use single‐particle trajectory simulation to study the transport of these ions in the periods preceding a number of large magnetic storms (Dst < −100 nT). Our simulation shows that due to centrifugal ion acceleration at higher altitudes (above ∼3 RE altitude), about 10–20% of polar wind and other low‐energy O+ ions reaches the plasma sheet during such periods; the actual percentage is a factor of ∼3 larger in the dusk sector on average compared with the dawn sector and dependent on the IMF and the O+ ion temperature. This provides a low but non‐negligible flux of O+ ions between the ionosphere and the plasma sheet and ring current, which is believed to constitute a significant “in‐transit” oxygen ion population over a period of a few (∼4) hours preceding a magnetic storm. Such a population could explain the presence of energetic O+ ions at the onset of the main phase of the storm, when the heavy ions could potentially modify the evolution of the ring current.
Evaluation of MOPITT retrievals of lower‐tropospheric carbon monoxide over the United States
Authors: Deeter M. N. , Worden H. M. , Edwards D. P. , Gille J. C. , Andrews A. E.
Published: June 2012

The new Version 5 MOPITT (Measurements of Pollution in the Troposphere) product for carbon monoxide (CO) is the first satellite product to exploit simultaneous near‐infrared and thermal‐infrared observations to enhance retrieval sensitivity in the lower troposphere. This feature is important to air quality analyses and studies of CO sources. However, because of the influence of both thermal contrast and geophysical noise, the retrieval characteristics for this new multispectral product are highly variable. New V5 products for surface‐level CO concentrations have been evaluated over the contiguous United States using both in situ vertical profiles and NOAA ground‐based “Tall Tower” measurements. Validation results based on the in situ profiles indicate that retrieval biases are on the order of a few percent. However, direct comparisons with the Tall Tower measurements demonstrate that smoothing error, which depends on both the retrieval averaging kernels and CO variability in the lower troposphere, exhibits significant geographical and seasonal variability.
Methane flux response to nitrogen amendment in an upland pine forest soil and riparian zone
Authors: Aronson E. L. , Vann D. R. , Helliker B. R.
Published: June 2012

Methane (CH4) is an important anthropogenic greenhouse gas, up to 15% of which is consumed by terrestrial soils. In this field study of the CH4cycle of a pine forest, 18 plots were established at each of two sites, located 40 m apart. The upper site was well‐drained and the lower site was poorly drained, but they shared similar overstory tree composition. Nitrogen was added as NH4NO3 incrementally across the 2009 growing season in a high (67 kg NH4NO3 ha−1 yr−1) and a low (5 kg NH4NO3 ha−1 yr−1) concentration. The sites were monitored for soil and air temperature, soil moisture, precipitation, air pressure, and NH4 and NO2+NO3 concentrations throughout the growing season. Across all treatments for the duration of the field season, average CH4 flux showed consumption of −0.84 kg CH4 ha−1 yr−1, but CH4 flux differed between the upper and lower sites. Across all treatments, upper site CH4 flux averaged −5.38 kg CH4 ha−1 yr−1, while lower site flux averaged 3.72 kg CH4 ha−1 yr−1, with greater variance than was observed at the upper site. High N treatments caused greater CH4 release than the control in the lower, but not the upper, site. The main correlated variable with CH4 flux was soil moisture; however, it accounted for <14% of the variation. Statistics were run several different ways, resulting in multiple environmental factors contributing up to 84% of the variation in CH4flux. Long‐term drainage differences between the sites likely drove the differences in CH4 flux.
In the nature of twins: a study of the archetypal realm of universal duality, opposition and imitation between the ‘first’ and ‘other’ in creation myths
Authors: Brodersen E.
Published: June 2012

This paper explores the complex, archetypal world of twins through creation myths. Twins are special cases of ‘two’, in that their relationship is qualitative not quantitative: they enact the relationship between the ‘first’ and the ‘other’. I present two early creation myths to explore the primacy of this dyadic relationship before it was superseded by patrilineal primogeniture (c. 3000 BCE), which designated ethical, fixed gender specificity to one twin over the other. I examine which gender has been negatively affected and speculate about the reasons behind the devaluation and disassociation. Analytical psychology, in particular the individuation process, is relevant to this paper because Jung saw the creative value of working experientially with the unconscious ‘shadow’ and intra-psychic contra-sexual twin ‘other’ to help bring taboo, disassociative emotions into mainstream cultural life.1
Alexey Khodjakov: Diving into the mitotic apparatus
Authors: Sedwick Caitlin
Published: June 2012

Khodjakov uses cutting-edge microscopy to study how the mitotic spindle is organized.
Integrity of the P-site is probed during maturation of the 60S ribosomal subunit
Authors: Bussiere Cyril , Hashem Yaser , Arora Sucheta , Frank Joachim , Johnson Arlen W.
Published: June 2012

Eukaryotic ribosomes are preassembled in the nucleus and mature in the cytoplasm. Release of the antiassociation factor Tif6 by the translocase-like guanosine triphosphatase Efl1 is a critical late maturation step. In this paper, we show that a loop of Rpl10 that embraces the P-site transfer ribonucleic acid was required for release of Tif6, 90 Å away. Mutations in this P-site loop blocked 60S maturation but were suppressed by mutations in Tif6 or Efl1. Molecular dynamics simulations of the mutant Efl1 proteins suggest that they promote a conformation change in Efl1 equivalent to changes that elongation factor G and eEF2 undergo during translocation. These results identify molecular signaling from the P-site to Tif6 via Efl1, suggesting that the integrity of the P-site is interrogated during maturation. We propose that Efl1 promotes a functional check of the integrity of the 60S subunit before its first round of translation.
Weighted pooling—practical and cost-effective techniques for pooled high-throughput sequencing
Authors: Golan David , Erlich Yaniv , Rosset Saharon
Published: June 2012

Motivation: Despite the rapid decline in sequencing costs, sequencing large cohorts of individuals is still prohibitively expensive. Recently, several sophisticated pooling designs were suggested that can identify carriers of rare alleles in large cohorts with a significantly smaller number of pools, thus dramatically reducing the cost of such large-scale sequencing projects. These approaches use combinatorial pooling designs where each individual is either present or absent from a pool. One can then infer the number of carriers in a pool, and by combining information across pools, reconstruct the identity of the carriers.

Results: We show that one can gain further efficiency and cost reduction by using ‘weighted’ designs, in which different individuals donate different amounts of DNA to the pools. Intuitively, in this situation, the number of mutant reads in a pool does not only indicate the number of carriers, but also their identity.

We describe and study a powerful example of such weighted designs, using non-overlapping pools. We demonstrate that this approach is not only easier to implement and analyze but is also competitive in terms of accuracy with combinatorial designs when identifying rare variants, and is superior when sequencing common variants.

We then discuss how weighting can be incorporated into existing combinatorial designs to increase their accuracy and demonstrate the resulting improvement using simulations. Finally, we argue that weighted designs have enough power to facilitate detection of common alleles, so they can be used as a cornerstone of whole-exome sequencing projects.

Contact:  saharon@post.tau.ac.il
Identification of sequence–structure RNA binding motifs for SELEX-derived aptamers
Authors: Hoinka Jan , Zotenko Elena , Friedman Adam , Sauna Zuben E. , Przytycka Teresa M.
Published: June 2012

Motivation: Systematic Evolution of Ligands by EXponential Enrichment (SELEX) represents a state-of-the-art technology to isolate single-stranded (ribo)nucleic acid fragments, named aptamers, which bind to a molecule (or molecules) of interest via specific structural regions induced by their sequence-dependent fold. This powerful method has applications in designing protein inhibitors, molecular detection systems, therapeutic drugs and antibody replacement among others. However, full understanding and consequently optimal utilization of the process has lagged behind its wide application due to the lack of dedicated computational approaches. At the same time, the combination of SELEX with novel sequencing technologies is beginning to provide the data that will allow the examination of a variety of properties of the selection process.

Results: To close this gap we developed, Aptamotif, a computational method for the identification of sequence–structure motifs in SELEX-derived aptamers. To increase the chances of identifying functional motifs, Aptamotif uses an ensemble-based approach. We validated the method using two published aptamer datasets containing experimentally determined motifs of increasing complexity. We were able to recreate the author's findings to a high degree, thus proving the capability of our approach to identify binding motifs in SELEX data. Additionally, using our new experimental dataset, we illustrate the application of Aptamotif to elucidate several properties of the selection process.

Contact:  przytyck@ncbi.nlm.nih.gov, Zuben.Sauna@fda.hhs.gov
A conditional neural fields model for protein threading
Authors: Ma Jianzhu , Peng Jian , Wang Sheng , Xu Jinbo
Published: June 2012

Motivation: Alignment errors are still the main bottleneck for current template-based protein modeling (TM) methods, including protein threading and homology modeling, especially when the sequence identity between two proteins under consideration is low (<30%).

Results: We present a novel protein threading method, CNFpred, which achieves much more accurate sequence–template alignment by employing a probabilistic graphical model called a Conditional Neural Field (CNF), which aligns one protein sequence to its remote template using a non-linear scoring function. This scoring function accounts for correlation among a variety of protein sequence and structure features, makes use of information in the neighborhood of two residues to be aligned, and is thus much more sensitive than the widely used linear or profile-based scoring function. To train this CNF threading model, we employ a novel quality-sensitive method, instead of the standard maximum-likelihood method, to maximize directly the expected quality of the training set. Experimental results show that CNFpred generates significantly better alignments than the best profile-based and threading methods on several public (but small) benchmarks as well as our own large dataset. CNFpred outperforms others regardless of the lengths or classes of proteins, and works particularly well for proteins with sparse sequence profiles due to the effective utilization of structure information. Our methodology can also be adapted to protein sequence alignment.

Contact:  j3xu@ttic.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
SEQuel: improving the accuracy of genome assemblies
Authors: Ronen Roy , Boucher Christina , Chitsaz Hamidreza , Pevzner Pavel
Published: June 2012

Motivation: Assemblies of next-generation sequencing (NGS) data, although accurate, still contain a substantial number of errors that need to be corrected after the assembly process. We develop SEQuel, a tool that corrects errors (i.e. insertions, deletions and substitution errors) in the assembled contigs. Fundamental to the algorithm behind SEQuel is the positional de Bruijn graph, a graph structure that models k-mers within reads while incorporating the approximate positions of reads into the model.

Results: SEQuel reduced the number of small insertions and deletions in the assemblies of standard multi-cell Escherichia coli data by almost half, and corrected between 30% and 94% of the substitution errors. Further, we show SEQuel is imperative to improving single-cell assembly, which is inherently more challenging due to higher error rates and non-uniform coverage; over half of the small indels, and substitution errors in the single-cell assemblies were corrected. We apply SEQuel to the recently assembled Deltaproteobacterium SAR324 genome, which is the first bacterial genome with a comprehensive single-cell genome assembly, and make over 800 changes (insertions, deletions and substitutions) to refine this assembly.

Availability: SEQuel can be used as a post-processing step in combination with any NGS assembler and is freely available at http://bix.ucsd.edu/SEQuel/.

Contact:  ppevzner@cs.ucsd.edu
Minimum message length inference of secondary structure from protein coordinate data
Authors: Konagurthu Arun S. , Lesk Arthur M. , Allison Lloyd
Published: June 2012

Motivation: Secondary structure underpins the folding pattern and architecture of most proteins. Accurate assignment of the secondary structure elements is therefore an important problem. Although many approximate solutions of the secondary structure assignment problem exist, the statement of the problem has resisted a consistent and mathematically rigorous definition. A variety of comparative studies have highlighted major disagreements in the way the available methods define and assign secondary structure to coordinate data.

Results: We report a new method to infer secondary structure based on the Bayesian method of minimum message length inference. It treats assignments of secondary structure as hypotheses that explain the given coordinate data. The method seeks to maximize the joint probability of a hypothesis and the data. There is a natural null hypothesis and any assignment that cannot better it is unacceptable. We developed a program SST based on this approach and compared it with popular programs, such as DSSP and STRIDE among others. Our evaluation suggests that SST gives reliable assignments even on low-resolution structures.

Availability:  http://www.csse.monash.edu.au/~karun/sst

Contact:  arun.konagurthu@monash.edu (or lloyd.allison@monash.edu)
Protein subcellular location pattern classification in cellular images using latent discriminative models
Authors: Li Jieyue , Xiong Liang , Schneider Jeff , Murphy Robert F.
Published: June 2012

Motivation: Knowledge of the subcellular location of a protein is crucial for understanding its functions. The subcellular pattern of a protein is typically represented as the set of cellular components in which it is located, and an important task is to determine this set from microscope images. In this article, we address this classification problem using confocal immunofluorescence images from the Human Protein Atlas (HPA) project. The HPA contains images of cells stained for many proteins; each is also stained for three reference components, but there are many other components that are invisible. Given one such cell, the task is to classify the pattern type of the stained protein. We first randomly select local image regions within the cells, and then extract various carefully designed features from these regions. This region-based approach enables us to explicitly study the relationship between proteins and different cell components, as well as the interactions between these components. To achieve these two goals, we propose two discriminative models that extend logistic regression with structured latent variables. The first model allows the same protein pattern class to be expressed differently according to the underlying components in different regions. The second model further captures the spatial dependencies between the components within the same cell so that we can better infer these components. To learn these models, we propose a fast approximate algorithm for inference, and then use gradient-based methods to maximize the data likelihood.

Results: In the experiments, we show that the proposed models help improve the classification accuracies on synthetic data and real cellular images. The best overall accuracy we report in this article for classifying 942 proteins into 13 classes of patterns is about 84.6%, which to our knowledge is the best so far. In addition, the dependencies learned are consistent with prior knowledge of cell organization.

Availability:  http://murphylab.web.cmu.edu/software/.

Contact:  Jeff.Schneider@cs.cmu.edu, murphy@cmu.edu
Incorporating prior information into association studies
Authors: Darnell Gregory , Duong Dat , Han Buhm , Eskin Eleazar
Published: June 2012

Summary: Recent technological developments in measuring genetic variation have ushered in an era of genome-wide association studies which have discovered many genes involved in human disease. Current methods to perform association studies collect genetic information and compare the frequency of variants in individuals with and without the disease. Standard approaches do not take into account any information on whether or not a given variant is likely to have an effect on the disease. We propose a novel method for computing an association statistic which takes into account prior information. Our method improves both power and resolution by 8% and 27%, respectively, over traditional methods for performing association studies when applied to simulations using the HapMap data. Advantages of our method are that it is as simple to apply to association studies as standard methods, the results of the method are interpretable as the method reports p-values, and the method is optimal in its use of prior information in regards to statistical power.

Availability: The method presented herein is available at http://masa.cs.ucla.edu

Contact:  eeskin@cs.ucla.edu
Revisiting the syntactic abilities of non-human animals: natural vocalizations and artificial grammar learning
Authors: ten Cate Carel , Okanoya Kazuo
Published: June 2012

The domain of syntax is seen as the core of the language faculty and as the most critical difference between animal vocalizations and language. We review evidence from spontaneously produced vocalizations as well as from perceptual experiments using artificial grammars to analyse animal syntactic abilities, i.e. abilities to produce and perceive patterns following abstract rules. Animal vocalizations consist of vocal units (elements) that are combined in a species-specific way to create higher order strings that in turn can be produced in different patterns. While these patterns differ between species, they have in common that they are no more complex than a probabilistic finite-state grammar. Experiments on the perception of artificial grammars confirm that animals can generalize and categorize vocal strings based on phonetic features. They also demonstrate that animals can learn about the co-occurrence of elements or learn simple ‘rules’ like attending to reduplications of units. However, these experiments do not provide strong evidence for an ability to detect abstract rules or rules beyond finite-state grammars. Nevertheless, considering the rather limited number of experiments and the difficulty to design experiments that unequivocally demonstrate more complex rule learning, the question of what animals are able to do remains open.
Formal language theory: refining the Chomsky hierarchy
Authors: Jäger Gerhard , Rogers James
Published: June 2012

The first part of this article gives a brief overview of the four levels of the Chomsky hierarchy, with a special emphasis on context-free and regular languages. It then recapitulates the arguments why neither regular nor context-free grammar is sufficiently expressive to capture all phenomena in the natural language syntax. In the second part, two refinements of the Chomsky hierarchy are reviewed, which are both relevant to the extant research in cognitive science: the mildly context-sensitive languages (which are located between context-free and context-sensitive languages), and the sub-regular hierarchy (which distinguishes several levels of complexity within the class of regular languages).
Distinctive signatures of recursion
Authors: Martins Maurício Dias
Published: June 2012

Although recursion has been hypothesized to be a necessary capacity for the evolution of language, the multiplicity of definitions being used has undermined the broader interpretation of empirical results. I propose that only a definition focused on representational abilities allows the prediction of specific behavioural traits that enable us to distinguish recursion from non-recursive iteration and from hierarchical embedding: only subjects able to represent recursion, i.e. to represent different hierarchical dependencies (related by parenthood) with the same set of rules, are able to generalize and produce new levels of embedding beyond those specifieda priori(in the algorithm or in the input). The ability to use such representations may be advantageous in several domains: action sequencing, problem-solving, spatial navigation, social navigation and for the emergence of conventionalized communication systems. The ability to represent contiguous hierarchical levels with the same rules may lead subjects to expect unknown levels and constituents to behave similarly, and this prior knowledge may bias learning positively. Finally, a new paradigm to test for recursion is presented. Preliminary results suggest that the ability to represent recursion in the spatial domain recruits both visual and verbal resources. Implications regarding language evolution are discussed.
Production and perception rules underlying visual patterns: effects of symmetry and hierarchy
Authors: Westphal-Fitch Gesche , Huber Ludwig , Gómez Juan Carlos , Fitch W. Tecumseh
Published: June 2012

Formal language theory has been extended to two-dimensional patterns, but little is known about two-dimensional pattern perception. We first examined spontaneous two-dimensional visual pattern production by humans, gathered using a novel touch screen approach. Both spontaneous creative production and subsequent aesthetic ratings show that humans prefer ordered, symmetrical patterns over random patterns. We then further explored pattern-parsing abilities in different human groups, and compared them with pigeons. We generated visual plane patterns based on rules varying in complexity. All human groups tested, including children and individuals diagnosed with autism spectrum disorder (ASD), were able to detect violations of all production rules tested. Our ASD participants detected pattern violations with the same speed and accuracy as matched controls. Children's ability to detect violations of a relatively complex rotational rule correlated with age, whereas their ability to detect violations of a simple translational rule did not. By contrast, even with extensive training, pigeons were unable to detect orientation-based structural violations, suggesting that, unlike humans, they did not learn the underlying structural rules. Visual two-dimensional patterns offer a promising new formally-grounded way to investigate pattern production and perception in general, widely applicable across species and age groups.
How semantic biases in simple adjacencies affect learning a complex structure with non-adjacencies in AGL: a statistical account
Authors: Poletiek Fenna H. , Lai Jun
Published: June 2012

A major theoretical debate in language acquisition research regards the learnability of hierarchical structures. The artificial grammar learning methodology is increasingly influential in approaching this question. Studies using an artificial centre-embedded AnBngrammar without semantics draw conflicting conclusions. This study investigates the facilitating effect of distributional biases in simple AB adjacencies in the input sample—caused in natural languages, among others, by semantic biases—on learning a centre-embedded structure. A mathematical simulation of the linguistic input and the learning, comparing various distributional biases in AB pairs, suggests that strong distributional biases might help us to grasp the complex AnBnhierarchical structure in a later stage. This theoretical investigation might contribute to our understanding of how distributional features of the input—including those caused by semantic variation—help learning complex structures in natural languages.
Artificial grammar learning meets formal language theory: an overview
Authors: Fitch W. Tecumseh , Friederici Angela D.
Published: June 2012

Formal language theory (FLT), part of the broader mathematical theory of computation, provides a systematic terminology and set of conventions for describing rules and the structures they generate, along with a rich body of discoveries and theorems concerning generative rule systems. Despite its name, FLT is not limited to human language, but is equally applicable to computer programs, music, visual patterns, animal vocalizations, RNA structure and even dance. In the last decade, this theory has been profitably used to frame hypotheses and to design brain imaging and animal-learning experiments, mostly using the ‘artificial grammar-learning’ paradigm. We offer a brief, non-technical introduction to FLT and then a more detailed analysis of empirical research based on this theory. We suggest that progress has been hampered by a pervasive conflation of distinct issues, including hierarchy, dependency, complexity and recursion. We offer clarifications of several relevant hypotheses and the experimental designs necessary to test them. We finally review the recent brain imaging literature, using formal languages, identifying areas of convergence and outstanding debates. We conclude that FLT has much to offer scientists who are interested in rigorous empirical investigations of human cognition from a neuroscientific and comparative perspective.
Phosphoglucose isomerase genotype effects on life history depend on latitude and food stress
Authors: De Block Marjan , Stoks Robby
Published: June 2012

1.Phosphoglucose isomerase (Pgi) genotypes differ in life‐history traits and shifts in their frequencies are thought to contribute to latitudinal gradients in life history. Yet, it is unstudied whether the life‐history effects of Pgi are invariant across latitudes. Further, while genetic variation at the Pgi locus is thought to be maintained by genotype‐by‐environment interactions and by life‐history trade‐offs involving resource allocation, the effects of food stress on Pgi genotype effects are largely unstudied.

2.We compared Pgi allozyme genotype effects on life history between northern and southern populations of the damselfly Ischnura elegans in a common garden experiment where we manipulated food stress.

3.Pgi genotypes differed in larval development time and body mass, but neither in larval growth rates nor in adult life span.

4.The effect of the Pgi genotype on larval development time differed between latitudes, suggesting interactions with the latitude‐specific genetic background and/or maternal effects. Pgi genotype effects on both development time and body mass were dependent on food stress and indicated a trade‐off between both fitness‐related traits associated with the Pgi gene.

5.The newly identified interaction between the Pgi genotype and latitude, the poorly studied Pgi genotype‐by‐food stress interactions and the observed life‐history trade‐offs associated with the Pgi genotypes can all potentially contribute to maintaining genetic variation at the Pgi locus and to latitudinal patterns in life history. Both types of interactions may also explain the poorly understood differences in the Pgi genotype effects on life history among studies of the same species.
Feasibility of short message service to document bleeding episodes in children with haemophilia
Authors: Broderick C. R. , Herbert R. D. , Latimer J. , Mathieu E. , van Doorn N. , Curtin J. A.
Published: June 2012

The increasing emphasis on home‐based treatment for the management of children with haemophilia has meant that many of these children no longer regularly report to a medical facility. Consequently, it is difficult to monitor incidence of bleeding episodes. The aim of this study was to assess the feasibility of using a short message service (SMS) to monitor incidence of bleeding episodes in children with haemophilia. One hundred and four children with moderate and severe haemophilia A or B took part in a 1‐year prospective study between 2008 and 2010. Children or their parents were asked to maintain a bleeds diary. They received a weekly SMS asking whether there had been a bleeding episode in the preceding week. Response rates were calculated. Children were followed for a total of 4839 person‐weeks. SMS replies were received for 4201 weeks. Thus, the rate of follow‐up was 86.8%. Median responses rates were 94.2% (IQR: 86.1–100%). Weekly SMS is a feasible reporting tool for documenting bleeding episodes in children with haemophilia. It is associated with high response rates and minimal expense and intrusion. The use of SMS could be extended to encourage compliance to prophylactic treatment, particularly in adolescents with haemophilia.
Daily dosing prophylaxis for haemophilia: a randomized crossover pilot study evaluating feasibility and efficacy
Authors: Lindvall K. , Astermark J. , Björkman S. , Ljung R. , Carlsson K. S. , Persson S. , Berntorp E.
Published: June 2012

Regular replacement therapy (prophylaxis) for haemophilia has been shown to prevent development of disabling arthropathy and to provide a better quality of life compared to treatment on demand; however, at a substantially higher cost. Calculations based on pharmacokinetic principles have shown that shortening dose intervals may reduce cost. The aim of this prospective, randomized, crossover pilot study was to address whether daily dosing is feasible, if it reduces concentrate consumption and is as effective in preventing bleeding as the standard prophylactic dosing regimen. In a 12 + 12 month crossover study, 13 patients were randomized to start either their own previously prescribed standard dose, or daily dosing adjusted to maintain at least the same trough levels as obtained with the standard dose. Ten patients completed the study. A 30% reduction in cost of factor concentrates was achieved with daily prophylaxis. However, the number of bleeding events increased in some patients in the daily dosing arm and patients reported decreased quality of life during daily prophylaxis. Daily treatment had a greater impact on daily life, and the patients found it more stressful.Prophylaxis with daily dosing may be feasible and efficacious in some patients. A substantial reduction of factor consumption and costs can be realized, but larger studies are needed before the introduction of daily prophylaxis into clinical routine can be recommended.
Extrapulmonary small cell carcinoma: a clinicopathological study with identification of potential diagnostic mimics
Authors: Quinn Anne Marie , Blackhall Fiona , Wilson Godfrey , Danson Sarah , Clamp Andrew , Ashcroft Linda , Brierley Judith , Hasleton Philip
Published: June 2012

Quinn A M, Blackhall F, Wilson G, Danson S, Clamp A, Ashcroft L, Brierley J & Hasleton P  (2012) Histopathology 61, 454–464

Extrapulmonary small cell carcinoma: a clinicopathological study with identification of potential diagnostic mimics

Aims:  To evaluate the clinicopathological features of small cell carcinoma arising outside the lung.

Methods and results:  Thirty‐seven cases with a pathology diagnosis of extrapulmonary small cell carcinoma (EPSCC) were selected. The clinical notes were reviewed and tumour blocks were selected for a fresh haematoxylin and eosin (H&E) section and immunohistochemical stains. The most common tumour locations were cervix and bladder. Twenty‐five cases (68%) were finally diagnosed as EPSCC, nine of which were found with coexisting non small cell carcinoma. Two cases (5%) were diagnosed as large cell neuroendocrine carcinoma (LCNEC) of the cervix. The remainder was classified as 10 poorly differentiated carcinomas (PDCs) (27%). Positive staining for thyroid transcription factor 1 (TTF‐1) was noted in nine cases of EPSCC and in none of the cases of PDC (P = 0.034). Synaptophysin immunoreactivity was found in 20 cases of EPSCC and two cases of PDC with neuroendocrine differentiation (P = 0.002), as well as two cases of LCNEC. 34βE12 was positive in eight cases of SCC and two cases of PDC.

Conclusions:  Based on this series, EPSCC may be overdiagnosed. Immunohistochemistry for TTF‐1, used in combination with synaptophysin, may help to discriminate EPSCC from PDC.
Brewer’s spent grain as a functional ingredient for breadsticks
Authors: Ktenioudaki Anastasia , Chaurin Valérie , Reis Sofia F. , Gallagher Eimear
Published: June 2012

Brewer’s spent grain (BSG) was evaluated for its potential as a functional baking ingredient. Scanning electron microscopy (SEM) was used to examine the microstructure of BSG and wheat flours. Baked snacks (breadsticks) were prepared using 15%, 25% and 35% BSG and evaluated for their baking quality and fibre and protein content (over a period of 3 months). The addition of BSG altered the baking characteristics of the breadsticks by affecting their structure and texture. The snacks appeared to lack in cellular structure and crispiness. However, they had quite a stable shelf‐life, as changes in texture, moisture and aw progressed at a low rate. Addition of 25% and 35% BSG significantly increased the protein content of the snacks, and addition of 15% BSG more than doubled the content of dietary fibre in the samples.
The effect of UV‐C in combination with H2O2 treatments on microbial response and quality parameters of fresh cut pear discs
Authors: Schenk Marcela , García Loredo Analía , Raffellini Silvia , Alzamora Stella Maris , Guerrero Sandra
Published: June 2012

The response of Escherichia coli ATCC 11229, Listeria innocua ATCC 33090 and Zygosaccharomyces bailii NRRL 7256 in fresh‐cut pear to simultaneous and serial combined treatments involving H2O2 immersion (3% w/v; pH 3.0; 25 °C; 2.0 or 5.0 min) and UV‐C exposure (7.5 min; 3.7 kJ m−2) was investigated. For selected treatments, native flora, sensory and colour changes were also evaluated. E. coli and L. innocua were more sensitive than Z. bailii. Serial H2O2/UV‐C treatments were more effective than the simultaneous arrangement. The single effect of UV‐C was enhanced by the combination with 5 min H2O2, hence avoiding the recovery of the surviving population. The combined treatment kept optimal microbial stability and exhibited more luminosity than the single UV‐C treatment. Texture profile analysis conducted using a trained panel showed that H2O2/UV‐C processed pear discs were perceived with significantly less hardness and fracturability but as juicy as untreated discs. Consumers found them pleasant.
Recovery of sporamin from naturally fermented sweet potato starch slurry by foam fractionation
Authors: Li Peng‐Gao , Mu Tai‐Hua
Published: June 2012

To recover sporamin, the major storage protein in sweet potato (Ipomoea batatas L. Lam.), from the wastewater generated by starch extracting industry by foam fractionation, the pH of the wastewater must be decreased to near three. This work explores a novel strategy where natural fermentation of the starch slurry was used to lower the pH without adding any acids. This work shows that after fermenting for 7 days the pH in the slurry significantly decreased from 6.57 ± 0.15 to 3.40 ± 0.00 (P < 0.05). Subsequently, sporamin was successfully recovered from the slurry with a peak recovery and enrichment of 87.9 ± 6.07% and 1.55 ± 0.11, respectively, at day 7. However, the concentration of protein in the slurry decreased correlatively with the decrease in pH value (r = 0.828, P = 0.042). Taken together, we concluded that the new strategy is feasible for recovering sporamin from the wastewater and fermentation for 4−7 days was recommended.
Weaning practices of mothers attending United Nations Relief and Works Agency health centres in the Gaza Governorates
Authors: Abu Hamad Bassam A. , Sammour Huda K.
Published: June 2012

Abu Hamad B.A. & Sammour H.K. (2013) Weaning practices of mothers attending United Nations Relief and Works Agency health centres in the Gaza Governorates. Journal of Advanced Nursing69(4), 773–781. doi: 10.1111/j.1365‐2648.2012.06057.x

Aim.  To report a study about weaning patterns and practices among Palestinian mothers attending health centres managed by the United Nations Relief and Works Agency in the Gaza Strip.

Background.  Although breastfeeding and weaning are important domains in child health, weaning has gained little attention from healthcare providers and researchers. In Arab culture, weaning practices are problematic and information gaps exist in relation to how and when weaning takes place.

Design.  A descriptive/analytical cross‐sectional study.

Methods.  A multi‐stage stratified random sample of 285 mothers of infants from 6–24 months, attending six health centres, was selected and completed an interviewed questionnaire in 2009. The Statistical Package for Social Sciences Program was used to conduct descriptive and analytical analysis.

Results.  The rate of exclusive breastfeeding for infants from 0–6 months of age was low. Pregnancy was reported as the main reason for weaning. The mean weaning age was 13·5 months. The vast majority of mothers used sudden weaning, from them, the majority used traditional methods. The most popular traditional methods used by mothers were putting substances with bad taste especially aloe vera (Subra Murra) on the nipples, using of alternatives as pacifiers, putting red substances, and placing coffee on the nipples. Variations were found in the use of traditional methods in reference to mothers’ demographic characteristics.

Conclusion.  During counselling mothers, nurses should focus on promoting gradual weaning practices and abstain from using traditional methods. Also, nurses should receive training and supervision on the appropriate weaning practices.