bluuebunny/crossref_metadata_2025 huggingface dataset:
Biology of a marine estuarine-opportunist fish species in a microtidal estuary, including comparisons among decades and with coastal waters
Authors: Veale Lauren J. , Coulson Peter G. , Hall Norman G. , Potter Ian C.
Published: August 2015

The biological characteristics of a marine and macrophyte-associated species (Pelates octolineatus) in a large microtidal, eutrophic estuary in 2008–10 were determined. Comparisons are made with those of individuals remaining in coastal waters and during two earlier periods in the estuary when plant biomass differed markedly. P. octolineatus start entering the Peel–Harvey Estuary in mid-summer, soon after metamorphosis, with many remaining there until autumn when they are ~15 months old. These individuals, and older fish that re-entered the estuary in summer, then return to the sea where they spawn from late spring to early summer. Most P. octolineatus in the estuary were less than or equal to the length at maturity and all were <4 years old, whereas individuals up to 10 years old were caught in coastal embayments, emphasising that the estuary acts mainly as a nursery for this terapontid. Growth in the estuary was seasonal and peaked earlier and was greater than in marine waters. Abundance of P. octolineatus in the estuary was greater in 2008–10 and 1980–81 than in 1996–97, when macrophytes were less abundant. The results demonstrate how a marine estuarine-opportunist can benefit from using both estuaries and coastal waters as a nursery area and capitalise on variations in environmental conditions.
Trends in e-commerce for the food marketing system.
Authors: Carpio C. E. , Lange K. Y.
Published: August 2015

E-commerce has emerged as a viable option for connecting agribusinesses and consumers within the food marketing system. The purpose of this review is to assess the current status and impact of e-commerce in the food marketing system. The review comprises issues related to adoption and use of computers and the internet by agribusinesses and the economic impact of e-commerce for these businesses. The review also covers aspects related to the importance of consumers' e-commerce food purchases, the factors affecting its usage and some new developments in the use of e-commerce to market food products using social media and mobile marketing. Regarding the adoption and use of e-commerce by agribusinesses, we find heterogeneous rates of adoption, use and impact across sectors and countries. For example, in the USA even though 67% of farms had access to the internet in 2013, only 14% reported conducting marketing activities over the internet. On the other hand, US Census data show that in 2012 the e-commerce value of food product manufacturing shipments accounted for more than 50% of their total value. Data from the USA and UK, two of the most advanced e-commerce markets in the world, indicate that food internet sales account for less than 4% of total sales. We conclude that while e-commerce has influenced the food marketing system, its impact does not appear to have been as dramatic and swift as had been expected. More research is needed in order to better understand the ways in which e-commerce affects agribusinesses and consumers. The review also identifies a paucity of e-commerce related statistical data.
Growth of local food systems: a review of potential food safety implications.
Authors: Wright K. G. , Sirsat S. A. , Neal J. A. , Gibson K. E.
Published: August 2015

In the USA, local food markets account for a growing share of agriculture production and with this growth come unique food safety challenges. Even though consumers often perceive local foods as safer and more wholesome, there is no evidence that local food products would be less prone to contamination with foodborne pathogens, especially since local foods generally receive less government oversight both at the federal and local levels. This paper reviews the history and growth of direct marketing venues for local food commodities and the food safety issues that have been identified or that could arise with increased growth. In addition, the current knowledge related to food safety education and outreach at local food outlets is discussed. This review concludes that, if left unaddressed, the role of local food commodities as vehicles of foodborne pathogens may become more significant and that food safety training and education that is specific to personnel (i.e. market managers, vendors, farm-to-school buyers) in direct-marketing venues is integral for the protection of public health, specifically consumers of local food commodities.
Optimizing Time of Initiation for Triploid Walleye Production Using Pressure Shock Treatment
Authors: Fetherman Eric R , Lepak Jesse M , Brown Bonnie L , Harris David J
Published: August 2015

Walleyes Sander vitreus support important recreational and commercial fisheries, and have been introduced into many systems throughout the United States and Canada. Use of sterile triploid fish is a valuable management strategy for protecting native fish species from naturally reproducing populations of introduced predators like Walleyes. Hydrostatic pressure is one of the more effective methods for inducing triploidy in Walleyes, and the technique is currently evolving. A 2.7-L capacity electric pressure chamber (TRC-APV Aqua Pressure Vessel; TRC Hydraulics) was used to produce triploid Walleyes using hydrostatic pressure with eggs collected from Pueblo Reservoir, Colorado. The TRC-APV has many advantages over manually operated pressure chambers including its portability, large capacity, and safety. Here, the methods used to create triploid Walleyes using the TRC-APV and the flow cytometric methods for estimating the efficacy of ploidy induction from pooled samples of fry are described. In addition, times of initiation (TIs), the times between fertilization and when eggs were subjected to pressure, were varied to determine the optimal time for maximizing induction and hatching success rates. Results suggest that triploidy in Walleyes is maximized with a TI of approximately 7.5 min, whereas hatching success is maximized with a TI of just over 8 min.
Comparing self‐report and mental chronometry measures of motor imagery ability
Authors: Williams Sarah E , Guillot Aymeric , Di Rienzo Franck , Cumming Jennifer
Published: August 2015

The present study investigated the relationship between two of the most common measures of motor imagery ability, self‐report ratings, and chronometric assessment. This was done for three types of imagery modalities: external visual imagery (EVI), internal visual imagery (IVI), and kinesthetic imagery (KI). Measures of imagery ability (i.e. self‐report and mental chronometry) were also compared across skill levels. Participants (N = 198) completed the Movement Imagery Questionnaire‐3 (MIQ‐3) to generate self‐report ratings. Chronometric assessment was obtained by recording the duration of each MIQ‐3 movement imaged and physically performed and then calculating a discrepancy score. There were no significant correlations between self‐report and mental chronometry for any of the three motor imagery types (p > .05). When assessing the different types of motor imagery ability using self‐report ratings, elite athletes had significantly higher KI than IVI, which was in turn significantly higher than EVI (p < .05). When assessing motor imagery ability using mental chronometry, there were no significant differences in imagery type (p > .05). Findings suggest both measures address different components of MI quality and should be used together to obtain a more comprehensive assessment of motor imagery ability.
Images of manifolds with semi-ample anti-canonical divisor
Authors: Birkar Caucher , Chen Yifei
Published: August 2015

We prove that if

f
:
X
→
Z

f\colon X\to Z

is a smooth surjective morphism between projective manifolds and if

−

K
X

-K_X

is semi-ample, then

−

K
Z

-K_Z

is also semi-ample. This was conjectured by Fujino and Gongyo. We list several counterexamples to show that this fails without the smoothness assumption on

f
f

.

We prove the above result by proving some results concerning the moduli divisor of the canonical bundle formula associated to a klt-trivial fibration

(
X
,
B
)
→
Z

(X,B)\to Z

.
Modulation of receptor dynamics by the regulator of G protein signaling Sst2
Authors: Venkatapurapu Sai Phanindra , Kelley Joshua B. , Dixit Gauri , Pena Matthew , Errede Beverly , Dohlman Henrik G. , Elston Timothy C.
Published: August 2015

G protein–coupled receptor (GPCR) signaling is fundamental to physiological processes such as vision, the immune response, and wound healing. In the budding yeast Saccharomyces cerevisiae, GPCRs detect and respond to gradients of pheromone during mating. After pheromone stimulation, the GPCR Ste2 is removed from the cell membrane, and new receptors are delivered to the growing edge. The regulator of G protein signaling (RGS) protein Sst2 acts by accelerating GTP hydrolysis and facilitating pathway desensitization. Sst2 is also known to interact with the receptor Ste2. Here we show that Sst2 is required for proper receptor recovery at the growing edge of pheromone-stimulated cells. Mathematical modeling suggested pheromone-induced synthesis of Sst2 together with its interaction with the receptor function to reestablish a receptor pool at the site of polarized growth. To validate the model, we used targeted genetic perturbations to selectively disrupt key properties of Sst2 and its induction by pheromone. Together our results reveal that a regulator of G protein signaling can also regulate the G protein–coupled receptor. Whereas Sst2 negatively regulates G protein signaling, it acts in a positive manner to promote receptor retention at the growing edge.
Spindle-to-cortex communication in cleaving, polyspermic Xenopus eggs
Authors: Field Christine M. , Groen Aaron C. , Nguyen Phuong A. , Mitchison Timothy J.
Published: August 2015

Mitotic spindles specify cleavage planes in early embryos by communicating their position and orientation to the cell cortex using microtubule asters that grow out from the spindle poles during anaphase. Chromatin also plays a poorly understood role. Polyspermic fertilization provides a natural experiment in which aster pairs from the same spindle (sister asters) have chromatin between them, whereas asters pairs from different spindles (nonsisters) do not. In frogs, only sister aster pairs induce furrows. We found that only sister asters recruited two conserved furrow-inducing signaling complexes, chromosome passenger complex (CPC) and Centralspindlin, to a plane between them. This explains why only sister pairs induce furrows. We then investigated factors that influenced CPC recruitment to microtubule bundles in intact eggs and a cytokinesis extract system. We found that microtubule stabilization, optimal starting distance between asters, and proximity to chromatin all favored CPC recruitment. We propose a model in which proximity to chromatin biases initial CPC recruitment to microtubule bundles between asters from the same spindle. Next a positive feedback between CPC recruitment and microtubule stabilization promotes lateral growth of a plane of CPC-positive microtubule bundles out to the cortex to position the furrow.
Experimental testing of a new integrated model of the budding yeast Starttransition
Authors: Adames Neil R. , Schuck P. Logan , Chen Katherine C. , Murali T. M. , Tyson John J. , Peccoud Jean
Published: August 2015

The cell cycle is composed of bistable molecular switches that govern the transitions between gap phases (G1 and G2) and the phases in which DNA is replicated (S) and partitioned between daughter cells (M). Many molecular details of the budding yeast G1–S transition (Start) have been elucidated in recent years, especially with regard to its switch-like behavior due to positive feedback mechanisms. These results led us to reevaluate and expand a previous mathematical model of the yeast cell cycle. The new model incorporates Whi3 inhibition of Cln3 activity, Whi5 inhibition of SBF and MBF transcription factors, and feedback inhibition of Whi5 by G1–S cyclins. We tested the accuracy of the model by simulating various mutants not described in the literature. We then constructed these novel mutant strains and compared their observed phenotypes to the model’s simulations. The experimental results reported here led to further changes of the model, which will be fully described in a later article. Our study demonstrates the advantages of combining model design, simulation, and testing in a coordinated effort to better understand a complex biological network.
Modeling the roles of protein kinase Cβ and η in single-cell wound repair
Authors: Holmes William R. , Liao Laura , Bement William , Edelstein-Keshet Leah
Published: August 2015

Wounded cells such as Xenopus oocytes respond to damage by assembly and closure of an array of actin filaments and myosin-2 controlled by Rho GTPases, including Rho and Cdc42. Rho and Cdc42 are patterned around wounds in a characteristic manner, with active Rho concentrating in a ring-like zone inside a larger, ring-like zone of active Cdc42. How this patterning is achieved is unknown, but Rho and Cdc42 at wounds are subject to regulation by other proteins, including the protein kinases C. Specifically, Cdc42 and Rho activity are enhanced by PKCβ and inhibited by PKCη. We adapt a mathematical model of Simon and coworkers to probe the possible roles of these kinases. We show that PKCβ likely affects the magnitude of positive Rho–Abr feedback, whereas PKCη acts on Cdc42 inactivation. The model explains both qualitative and some overall quantitative features of PKC–Rho GTPase regulation. It also accounts for the previous, peculiar observation that ∼20% of cells overexpressing PKCη display zone inversions—that is, displacement of active Rho to the outside of the active Cdc42.
Integrated structure- and ligand-basedin silicoapproach to predict inhibition of cytochrome P450 2D6
Authors: Martiny Virginie Y. , Carbonell Pablo , Chevillard Florent , Moroy Gautier , Nicot Arnaud B. , Vayer Philippe , Villoutreix Bruno O. , Miteva Maria A.
Published: August 2015

Motivation: Cytochrome P450 (CYP) is a superfamily of enzymes responsible for the metabolism of drugs, xenobiotics and endogenous compounds. CYP2D6 metabolizes about 30% of drugs and predicting potential CYP2D6 inhibition is important in early-stage drug discovery.

Results: We developed an original in silico approach for the prediction of CYP2D6 inhibition combining the knowledge of the protein structure and its dynamic behavior in response to the binding of various ligands and machine learning modeling. This approach includes structural information for CYP2D6 based on the available crystal structures and molecular dynamic simulations (MD) that we performed to take into account conformational changes of the binding site. We performed modeling using three learning algorithms --support vector machine, RandomForest and NaiveBayesian --and we constructed combined models based on topological information of known CYP2D6 inhibitors and predicted binding energies computed by docking on both X-ray and MD protein conformations. In addition, we identified three MD-derived structures that are capable all together to better discriminate inhibitors and non-inhibitors compared with individual CYP2D6 conformations, thus ensuring complementary ligand profiles. Inhibition models based on classical molecular descriptors and predicted binding energies were able to predict CYP2D6 inhibition with an accuracy of 78% on the training set and 75% on the external validation set.

Contact:  maria.miteva@univ-paris-diderot.fr

Supplementary information: Supplementary data are available at Bioinformatics online.
Bayexer: an accurate and fast Bayesian demultiplexer for Illumina sequences
Authors: Yi Haisi , Li Zhe , Li Tao , Zhao Jindong
Published: August 2015

Summary: Demultiplexing is used after high-throughput sequencing to in silico assign reads to the samples of origin based on the sequenced reads of the indices. Existing demultiplexing tools based on the similarity between the read index and the reference index sequences may fail to provide satisfactory results on low-quality datasets. We developed Bayexer, a Bayesian demultiplexing algorithm for Illumina sequencers. Bayexer uses the information extracted directly from the contaminant sequences of the targeting reads as the training dataset for a naïve Bayes classifier to assign reads. According to our evaluation, Bayexer provides higher capability, accuracy and speed on various real datasets than other tools.

Availability and  implementation  : Bayexer is implemented in Perl and freely available at https://github.com/HaisiYi/Bayexer.

Contact:  litao@ihb.ac.cn or lizhe@ibcas.ac.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Wedderburn and the Theory of Labour Law: Building on Kahn-Freund
Authors: Dukes Ruth
Published: August 2015

This paper aims to assess the nature and significance of Lord Wedderburn’s contribution to the elaboration of a theory of labour law. Noting the extent to which Wedderburn was influenced, in this respect as in others, by the work of Otto Kahn-Freund, it focuses on the question of whether Wedderburn ever developed a theory of labour law that was clearly distinguishable from Kahn-Freund’s. Were there significant differences in the two scholars’ expositions of abstentionism, or collective laissez-faire? Through a close reading of Wedderburn’s work, it is suggested that Wedderburn was a strong proponent of the principle of collective laissez-fare, in his early as well as his later writing. In the changed political context of the 1980s and 1990s, he undertook the important task of seeking to update or restate the principle as an expression of social-democratic values in the field of work and working relationships.
The Hero’s Journey: Lord Wedderburn and the ‘Political Constitution’ of Labour Law
Authors: Bogg Alan
Published: August 2015

For much of the twentieth century, a functionalist style of scholarship emerged as a critical and dissenting tradition in British constitutional thought. Many of its animating concerns were expressed in J. A. G. Griffith’s famous lecture, ‘The Political Constitution’. This article situates Lord Wedderburn’s work on collective labour law within the broader tradition of political constitutionalism at the London School of Economics. Lord Wedderburn’s intellectual journey in labour law was concerned with the political nature of legal discourse, and the emancipatory potential of fundamental rights discourse as a way of achieving democratic freedoms for working people. The article examines the shifts in Wedderburn’s attitude towards the human rights paradigm, in the light of his passionate commitment to the primacy of politics in the sphere of labour law. In so doing, it concludes with an affirmation of Lord Wedderburn’s remarkable intellectual legacy in framing the virtues and limitations of a ‘political constitution’ for working people.
Data integration of structured and unstructured sources for assigning clinical codes to patient stays
Authors: Scheurwegs Elyne , Luyckx Kim , Luyten Léon , Daelemans Walter , Van den Bulcke Tim
Published: August 2015

Objective Enormous amounts of healthcare data are becoming increasingly accessible through the large-scale adoption of electronic health records. In this work, structured and unstructured (textual) data are combined to assign clinical diagnostic and procedural codes (specifically ICD-9-CM) to patient stays. We investigate whether integrating these heterogeneous data types improves prediction strength compared to using the data types in isolation.

Methods Two separate data integration approaches were evaluated. Early data integration combines features of several sources within a single model, and late data integration learns a separate model per data source and combines these predictions with a meta-learner. This is evaluated on data sources and clinical codes from a broad set of medical specialties.

Results When compared with the best individual prediction source, late data integration leads to improvements in predictive power (eg, overall F-measure increased from 30.6% to 38.3% for International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) diagnostic codes), while early data integration is less consistent. The predictive strength strongly differs between medical specialties, both for ICD-9-CM diagnostic and procedural codes.

Discussion Structured data provides complementary information to unstructured data (and vice versa) for predicting ICD-9-CM codes. This can be captured most effectively by the proposed late data integration approach.

Conclusions We demonstrated that models using multiple electronic health record data sources systematically outperform models using data sources in isolation in the task of predicting ICD-9-CM codes over a broad range of medical specialties.
Antibacterial Activity of Wild Mushroom Extracts on Bacterial Wilt Pathogen Ralstonia solanacearum
Authors: Erjavec Jana , Ravnikar Maja , Brzin Jože , Grebenc Tine , Blejec Andrej , Gosak Mateja Želko , Sabotič Jerica , Kos Janko , Dreo Tanja
Published: August 2015

In total, 150 protein extracts from 94 different basidiomycete and ascomycete wild mushroom species were tested for antibacterial activity against the quarantine plant-pathogen bacterium Ralstonia solanacearum. In in vitro microtiter plate assays, 15 extracts with moderate to high antibacterial activities were identified: 11 completely inhibited bacterial growth and 4 showed partial inhibition. Of these 15 extracts, 5 were further tested and 3 extracts slowed disease progression and reduced disease severity in artificially inoculated tomato and potato plants. However, the in vitro activities of the extracts did not always correlate with their in vivo activities, which emphasizes the importance of performing early screening tests also in vivo. Testing of selected extracts against 12 R. solanacearum strains identified 6 with potential for broader applicability. Further analysis of extracts from Amanita phalloides and Clitocybe geotropa showed that the active substances are proteins with an approximate size of 180 kDa. To our knowledge, this is the first in vitro and in vivo study that demonstrates that mushroom protein extracts can be promising for treatment of bacterial wilt caused by R. solanacearum.
Evaluation of the BlightPro Decision Support System for Management of Potato Late Blight Using Computer Simulation and Field Validation
Authors: Small Ian M. , Joseph Laura , Fry William E.
Published: August 2015

The objective of this study was to evaluate the utility of the BlightPro decision support system (DSS) for late blight management using computer simulation and field tests. Three fungicide schedules were evaluated: (i) calendar-based (weekly) applications, (ii) applications according to the DSS, or (iii) no fungicide. Simulation experiments utilized 14 years of weather data from 59 locations in potato-producing states. In situations with unfavorable weather for late blight, the DSS recommended fewer fungicide applications with no loss of disease suppression; and, in situations of very favorable weather for late blight, the DSS recommended more fungicide applications but with improved disease suppression. Field evaluation was conducted in 2010, 2011, 2012, and 2013. All experiments involved at least two cultivars with different levels of resistance. DSS-guided and weekly scheduled fungicide treatments were successful at protecting against late blight in all field experiments. As expected, DSS-guided schedules were influenced by prevailing weather (observed and forecast) and host resistance and resulted in schedules that maintained or improved disease suppression and average fungicide use efficiency relative to calendar-based applications. The DSS provides an interactive system that helps users maximize the efficiency of their crop protection strategy by enabling well-informed decisions.
Cancer incidence predictions in the North of Portugal: keeping population-based cancer registration up to date
Authors: Castro Clara , Antunes Luís , Lunet Nuno , Bento Maria José
Published: August 2015

Decision making towards cancer prevention and control requires monitoring of trends in cancer incidence and accurate estimation of its burden in different settings. We aimed to estimate the number of incident cases in northern Portugal for 2015 and 2020 (all cancers except nonmelanoma skin and for the 15 most frequent tumours). Cancer cases diagnosed in 1994–2009 were collected by the North Region Cancer Registry of Portugal (RORENO) and corresponding population figures were obtained from Statistics Portugal. JoinPoint regression was used to analyse incidence trends. Population projections until 2020 were derived by RORENO. Predictions were performed using the Poisson regression models proposed by Dyba and Hakulinen. The number of incident cases is expected to increase by 18.7% in 2015 and by 37.6% in 2020, with lower increments among men than among women. For most cancers considered, the number of cases will keep rising up to 2020, although decreasing trends of age-standardized rates are expected for some tumours. Cervix was the only cancer with a decreasing number of incident cases in the entire period. Thyroid and lung cancers were among those with the steepest increases in the number of incident cases expected for 2020, especially among women. In 2020, the top five cancers are expected to account for 82 and 62% of all cases diagnosed in men and women, respectively. This study contributes to a broader understanding of cancer burden in the north of Portugal and provides the basis for keeping population-based incidence estimates up to date.
Are there differences in health information exchange by health system type?
Authors: Opoku-Agyeman William , Menachemi Nir
Published: August 2015

Background:

Despite the potential of health information exchange (HIE) to improve safety and reduce cost, hospitals have been slow to adopt HIE with only 30% of U.S. hospitals doing so in 2012.

Purpose:

The aim of this study was to explore the relationship between different health system types and how they engage in HIE.

Methods:

Data on health system types and engagement in HIE activity were combined with secondary hospital characteristics. Ordinal logistic regression analyses were used to examine the relationship between a scale measuring the level of HIE engagement and health system type controlling for hospital and market characteristics.

Results:

Data from 1552 hospitals were available for analyses. Overall, hospital in a health system of any kind exchanged more patient data elements (e.g., patient demographics, clinical summaries, laboratory results, medication history, and radiology report) compared with stand-alone hospitals (3.82 vs. 1.80, p < .001). Overall, 62.2% of hospitals were part of a health system, and among system hospitals, 125 (8.0%) were in centralized health systems, 75 (4.8%) were in centralized physician/insurance health system, 284 (18.3%) were in moderately centralized health system, 391 (25.2%) were in decentralized health system, and 91 (5.9%) were in independent health system. In regression analyses, hospitals belonging to a health system were more likely to exchange patient health data with other hospitals in the same system (OR = 3.94, p < .001) but not with hospitals outside their system (OR = 1.89, p = .445). Across health system types, there was no significant difference in the exchange of patient health data.

Practice Implications:

Hospital engagement in HIE is associated with health system membership. These findings will assist hospital leaders and managers to better understand how the structure and nature of their system may influence what their individual hospital can and cannot do in their decision to engage in HIE and other decisions that support the overall system objectives.
HER2 Gene Amplification by Fluorescence In Situ Hybridization (FISH) Compared With Immunohistochemistry (IHC) in 122 Equivocal Gastric Cancer Cases
Authors: Liu Xiaoyan , Wang Xiaoling , Wang Bo , Ren Guoping , Ding Wei
Published: August 2015

Objective:

To determine the frequency of HER2/neu amplification and the relationship between HER2/neu expression and clinicopathologic features in gastric cancers scored immunohistochemistry (IHC) 2+.

Methods:

A total of 122 gastric cancer cases scored IHC 2+ were retrospectively analyzed for HER2 amplification by fluorescence in situ hybridization (FISH). The correlation between HER2/neu expression and clinicopathologic features was analyzed.

Results:

HER2/neu gene was amplified in 17 out of the 122 gastric cancer samples. The concordance rate between IHC and FISH was 13.9%. HER2/neu status was correlated with the age of patients (P<0.05). Polysomy of CEP17 was demonstrated in 46 cases, 11 of which (23.91%) were amplified for HER2/neu. Within the subgroups, a correlation between CEP17 polysomy and the depth of invasion was observed (P<0.05).

Conclusions:

The results highlight the necessity of FISH test for further categorization when gastric cancer cases are scored 2+ by IHC. The value of HER2/neu for a potential role as a negative prognostic factor in the equivocal gastric cancer cases is limited.
The Utility of GATA3 in the Diagnosis of Urothelial Carcinomas With Variant Morphologic Patterns
Authors: Verduin Lindsey , Mentrikoski Mark J. , Heitz Christopher T. , Wick Mark R.
Published: August 2015

The transcription factor GATA3 is a recently described biomarker that is highly expressed in bladder and breast carcinomas. Although it has shown sensitivity as a marker of primary bladder carcinomas with purely urothelial differentiation, the ability of GATA3 to label primary bladder carcinomas with variant morphologic patterns has been incompletely assessed to date. The current study was designed to determine whether GATA3 staining is retained in “unconventional” bladder carcinomas. Eighty-eight cases of primary bladder cancers were retrieved from the authors’ institutional archive, and they included the following histomorphologic types: 6 small cell carcinomas, 12 sarcomatoid carcinomas, 17 adenocarcinomas (both primary and urothelial variants with glandular differentiation), 24 micropapillary carcinomas, and 27 squamous cell carcinomas (both primary and urothelial variants with squamous differentiation). A tissue microarray was constructed and automated immunostaining for GATA3 (Clone L50-823, Biocare Medical, Concord, CA) was performed using standard technique. Among the 5 variants of unconventional bladder carcinoma, only the micropapillary and sarcomatoid forms exhibited consistent and strong immunolabeling for GATA3. Hence, the sensitivity of this determinant is diminished in several histologic forms of primary bladder carcinoma. That fact will affect the interpretation of GATA3 stains in the context of possible metastasis from primary bladder carcinomas with variant morphologic patterns, as well as their distinction from secondary bladder involvement by tumors of nonurothelial origin.
Increased FLI-1 Expression is Associated With Poor Prognosis in Non–Small Cell Lung Cancers
Authors: Lin Shiou-Fu , Wu Chun-Chieh , Chai Chee-Yin
Published: August 2015

Friend leukemia integration-1 (FLI-1) antibody, a commercially available antibody directed against the C-terminus of FLI-1 protein-binding domain, has been used as a useful tool in the differential diagnosis of small blue round cell tumors and vascular neoplasms, but shows inconsistent expression in lung cancers. The aims of this study were to evaluate FLI-1 immunohistochemical expression in non–small cell lung cancer (NSCLC), and its relationships between the clinicopathologic parameters and prognosis. We investigated the FLI-1 expression in 108 cases of NSCLC by using multiple tumor microarrays. Correlations between the FLI-1 expression and clinicopathologic parameters and prognostic significance were analyzed. The effect of FLI-1 expression on survival is estimated by Kaplan-Meier survival analysis and Cox proportional hazards models. Our results revealed that patients with high FLI-1 expression had shorter overall survival (P=0.014) than those with low FLI-1 expression. In multivariate analysis, FLI-1 was confirmed as an independent poor prognostic factor in NSCLC (overall survival: hazard ratio, 7.292; 95% confidence interval, 0.294-0.823; P=0.007). In conclusion, this study shows that FLI-1 is expressed variably in different subtypes of NSCLC, and its expression is related to clinicopathologic parameters and poorer prognosis. However, further studies are required to elucidate its function in tumorigenesis of NSCLC.
Fitness-valley crossing with generalized parent-offspring transmission
Authors: Osmond M.M. , Otto S.P.
Published: August 2015

Simple and ubiquitous gene interactions create rugged fitness landscapes composed of coadapted gene complexes separated by “valleys” of low fitness. Crossing such fitness valleys allows a population to escape suboptimal local fitness peaks to become better adapted. This is the premise of Sewall Wright’s shifting balance process. Here we generalize the theory of fitness-valley crossing in the two-locus, bi-allelic case by allowing bias in parent-offspring transmission. This generalization extends the existing mathematical framework to genetic systems with segregation distortion and uniparental inheritance. Our results are also flexible enough to provide insight into shifts between alternate stable states in cultural systems with “transmission valleys”. Using a semi-deterministic analysis and a stochastic diffusion approximation, we focus on the limiting step in valley crossing: the first appearance of the genotype on the new fitness peak whose lineage will eventually fix. We then apply our results to specific cases of segregation distortion, uniparental inheritance, and cultural transmission. Segregation distortion favouring mutant alleles facilitates crossing most when recombination and mutation are rare, i.e., scenarios where crossing is otherwise unlikely. Interactions with more mutable genes (e.g., uniparental inherited cytoplasmic elements) substantially reduce crossing times. Despite component traits being passed on poorly in the previous cultural background, small advantages in the transmission of a new combination of cultural traits can greatly facilitate a cultural transition. While peak shifts are unlikely under many of the common assumptions of population genetic theory, relaxing some of these assumptions can promote fitness-valley crossing.
Re-examining the relationship between virus and microbial cell abundances in the global oceans
Authors: Wigington Charles H. , Sonderegger Derek , Brussaard Corina P.D. , Buchan Alison , Finke Jan F. , Fuhrman Jed , Lennon Jay T. , Middelboe Mathias , Suttle Curtis A. , Stock Charles , Wilson William H. , Eric Wommack K. , Wilhelm Steven W. , Weitz Joshua S.
Published: August 2015

Marine viruses are critical drivers of ocean biogeochemistry and their abundances vary spatiotemporally in the global oceans, with upper estimates exceeding 108per ml. Over many years, a consensus has emerged that virus abundances are typically 10-fold higher than prokaryote abundances. The use of a fixed-ratio suggests that the relationship between virus and prokaryote abundances is both predictable and linear. However, the true explanatory power of a linear relationship and its robustness across diverse ocean environments is unclear. Here, we compile 5671 prokaryote and virus abundance estimates from 25 distinct marine surveys to characterize the relationship between virus and prokaryote abundances. We find that the median virus-to-prokaryote ratio (VPR) is 10:1 and 16:1 in the near-and sub-surface oceans, respectively. Nonetheless, we observe substantial variation in the VPR and find either no or limited explanatory power using fixed-ratio models. Instead, virus abundances are better described as nonlinear, power-law functions of prokaryote abundances - particularly when considering relationships within distinct marine surveys. Estimated power-laws have scaling exponents that are typically less than 1, signifying that the VPR decreases with prokaryote density, rather than remaining fixed. The emergence of power-law scaling presents a challenge for mechanistic models seeking to understand the ecological causes and consequences of marine virus-microbe interactions. Such power-law scaling also implies that efforts to average viral effects on microbial mortality and biogeochemical cycles using “representative” abundances or abundance-ratios need to be refined if they are to be utilized to make quantitative predictions at regional or global ocean scales.
Genome wide estimates of mutation rates and spectrum inSchizosaccharomyces pombeindicate CpG sites are highly mutagenic despite the absence of DNA methylation
Authors: Behringer Megan G. , Hall David W.
Published: August 2015

We accumulated mutations for 1952 generations in 79 initially identical, haploid lines of the fission yeastSchizosaccharomyces pombe and then performed whole-genome sequencing to determine the mutation rates and spectrum. We captured 696 spontaneous mutations across the 79 mutation accumulation lines. We compared the mutation spectrum and rate to another model ascomycetous yeast, the budding yeastSaccharomyces cerevisiae. While the two organisms are approximately 600 million years diverged from each other, they share similar life histories, genome size and genomic G/C content. We found thatSc. pombeandS. cerevisiaehave similar mutation rates, contrary to what was expected givenSc. pombe’s smaller reported effective population size.Sc. pombe’s also exhibits a strong insertion bias in comparison toS. cerevisiae,. Intriguingly, we observed an increased mutation rate at cytosine nucleotides, specifically CpG nucleotides, which is also seen inS. cerevisiae. However, the absence of methylation inSc. pombeand the pattern of mutation at these sites, primarily C→ A as opposed to C→T, strongly suggest that the increased mutation rate is not caused by deamination of methylated cytosines. This result implies that the high mutability of CpG dinucleotides in other species may be caused in part by an additional mechanism than methylation.
Small-angle neutron scattering correlation functions of bulk magnetic materials
Authors: Mettus Denis , Michels Andreas
Published: August 2015

On the basis of the continuum theory of micromagnetics, the correlation function of the spin-misalignment small-angle neutron scattering cross section of bulk ferromagnets (e.g.elemental polycrystalline ferromagnets, soft and hard magnetic nanocomposites, nanoporous ferromagnets, or magnetic steels) is computed. For such materials, the spin disorder which is related to spatial variations in the saturation magnetization and magnetic anisotropy field results in strong spin-misalignment scattering dΣM/dΩ along the forward direction. When the applied magnetic field is perpendicular to the incoming neutron beam, the characteristics of dΣM/dΩ (e.g.the angular anisotropy on a two-dimensional detector or the asymptotic power-law exponent) are determined by the ratio of magnetic anisotropy field strengthHpto the jump ΔMin the saturation magnetization at internal interfaces. Here, the corresponding one- and two-dimensional real-space correlations are analyzed as a function of applied magnetic field, the ratioHp/ΔM, the single-particle form factor and the particle volume fraction. Finally, the theoretical results for the correlation function are compared with experimental data on nanocrystalline cobalt and nickel.
Profex: a graphical user interface for the Rietveld refinement programBGMN
Authors: Doebelin Nicola , Kleeberg Reinhard
Published: August 2015

Profexis a graphical user interface for the Rietveld refinement programBGMN. Its interface focuses on preservingBGMN's powerful and flexible scripting features by giving direct access toBGMNinput files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort.Profexreads and converts a variety of proprietary raw data formats and is thus largely instrument independent.ProfexandBGMNare available under an open-source license for Windows, Linux and OS X operating systems.
Crystal structure of post-perovskite-type CaIrO3reinvestigated: new insights into atomic thermal vibration behaviors
Authors: Nakatsuka Akihiko , Sugiyama Kazumasa , Yoneda Akira , Fujiwara Keiko , Yoshiasa Akira
Published: August 2015

Single crystals of the title compound, the post-perovskite-type CaIrO3[calcium iridium(IV) trioxide], have been grown from a CaCl2flux at atmospheric pressure. The crystal structure consists of an alternate stacking of IrO6octahedral layers and CaO8hendecahedral layers along [010]. Chains formed by edge-sharing of IrO6octahedra (point-group symmetry 2/m..) run along [100] and are interconnected along [001] by sharing apical O atoms to build up the IrO6octahedral layers. Chains formed by face-sharing of CaO8hendecahedra (point-group symmetrym2m) run along [100] and are interconnected along [001] by edge-sharing to build up the CaO8hendecahedral layers. The IrO6octahedral layers and CaO8hendecahedral layers are interconnected by sharing edges. The present structure refinement using a high-power X-ray source confirms the atomic positions determined by Hiraiet al.(2009) [Z. Kristallogr.224, 345–350], who had revised our previous report [Sugaharaet al.(2008).Am. Mineral.93, 1148–1152]. However, the displacement ellipsoids of the Ir and Ca atoms based on the present refinement can be approximated as uniaxial ellipsoids elongating along [100], unlike those reported by Hiraiet al.(2009). This suggests that the thermal vibrations of the Ir and Ca atoms are mutually suppressed towards the Ir...Ca direction across the shared edge because of the dominant repulsion between the two atoms.
Experimenting with dialogic mentoring: a new model
Authors: Nahmad-Williams Lindy , Taylor Carol A
Published: August 2015

Purpose

– The purpose of this paper is to explore mentoring as a dialogic practice in relation to three themes: identity, fear of being judged and respect. It develops Bokenko and Gantt’s (2000) concept of dialogic mentoring to propose a new theorisation of mentoring as a relational, embodied, spatial, affective and ethical practice.

Design/methodology/approach

– The paper reports on a mentoring project that took place in a UK University which was seeking to enhance its research culture. This project used an innovative methodological approach in which mentor and mentee wrote and shared diary entries as means of building more effective and constructive mentoring experiences, and as a vehicle for reflexively analysing the mentoring process.

Findings

– The project outcomes were: first, a deepened appreciation and reflexive evaluation of the role played by diaries and writing in the enactment of dialogic mentoring; second, the development of a theoretical framework to enhance understanding of dialogic mentoring and third, the generation of a dialogic mentoring model encompassing multiple dimensions of the process.

Practical implications

– The paper provides insights to support methodological innovation in mentoring practice; it links mentoring practice with theory development to enhance mentor and mentee collaboration and reflexivity; it offers an example of good mentoring practice that could be scaled up within educational institutions wishing to enhance their research culture.

Originality/value

– The paper offers, first, a reflexive account of a methodologically innovative mentoring practice to enhance mentoring; and second, it proposes a new theorisation and model of dialogic mentoring practices.
The dynamics of favela justice; identity, legitimacy and legality
Authors: Bagnall David
Published: August 2015

Purpose

– The purpose of this paper is to consider and evaluate three models of favela governance structure to appreciate the full extent of the complexity of legislature faced by favela residents and to thereby determine whether any concrete notion of justice can exist within the favela.

Design/methodology/approach

– The paper discusses the relative utilities Donna M. Goldstein’s parallel state theory, Enrique Desmond Arias’ model of state-gang mutual penetration and John Rapley’s notion of neo-medievalism through a process of setting them up in dialogue with one another.

Findings

– The paper finds that the picture of favela governance that emerges through the discussion of the varying theories is one of a delicate equilibrium that depends on a constant process of negotiation and renegotiation and that it is only within this discursive space that any meaningful notion of favela justice can emerge.

Originality/value

– The dialogic aspect of the paper creates a new space, between theories, from which a more nuanced notion of the modern favela, and the subtleties of state-gang relations therein, is able to develop.
Towards a common identity? The harmonisation of identity theft laws
Authors: Clough Jonathan
Published: August 2015

Purpose

– The purpose of this paper is to consider potential criminal law responses to the global challenge of “identity crime”. In particular, it focuses on a specific offence of “identity theft”. It begins with a discussion of the meaning of “identity” in the context of modern transactions, before defining “identity crime” and related terms. Legal responses are then considered before turning to the importance of harmonisation. The transnational nature of modern identity crimes makes it essential that law enforcement agencies not only have suitable offences at their disposal but also the frameworks to facilitate international cooperation.

Design/methodology/approach

– Given the increasingly transnational and organized nature of modern identity crime, this paper adopts a comparative approach. It draws upon provisions from Australia, Canada, the UK and the USA. It also looks at responses to identity crime at the regional and international level.

Findings

– Although there is currently no international instrument which specifically and comprehensively addresses identity theft, it is argued that there is an urgent need for further international discussion as to the desirability and form of identity theft provisions. While international agreement may not be reached, such discussions are important in assisting countries to develop appropriate legal frameworks and capacity to address the modern fraud environment.

Originality/value

– It is hoped that this paper will contribute to, and facilitate, important ongoing discussions as to the most effective ways in which to tackle identity crime at the national and international levels.
Association between having a CA(SA) as CEO and accruals quality
Authors: Mey Elizabeth , de Klerk Marna
Published: August 2015

Purpose

– The purpose of this paper is to examine whether Chartered Accountants South Africa (CAs(SA)) as Chief Executive Officers (CEOs) have an association with accruals quality.

Design/methodology/approach

– The theoretical base of this paper is the link between accounting expertise and accruals quality. The sample consists of 812 observations of Johannesburg Stock Exchange (JSE)-listed firms between 2010 and 2013. The association is tested by regressing the CA(SA) as CEO interest variable and control variables on accruals quality, using three metrics of abnormal accruals.

Findings

– The overall results suggest that less accruals management and estimation error is present when the CEO is a CA(SA).

Originality/value

– This is the first study to test the association between having a CEO with a professional accounting qualification, such as CA(SA), and accruals quality. The findings will be of interest to shareholders and top executives when evaluating the appointment of a CEO.