bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk groups and uptake of influenza and pneumococcal vaccine in Ireland
Authors: Mereckiene J , O’Donnell J , Collins C , Cotter S , Igoe D , O’Flanagan D
Published: October 2017

In Ireland, influenza and pneumococcal vaccines are recommended for adults aged 65 years and over and for those with chronic illness or immunosuppression. Influenza vaccine is recommended for healthcare workers (HCWs) and residents of long stay care facilities. Influenza vaccine uptake is only available for those aged 65 years and over. We conducted a survey to estimate the size of risk groups between 18 and 64 years of age, influenza and pneumococcal vaccine uptake in this group, and to determine possible factors influencing vaccine uptake to improve targeted immunisation programmes. Among respondents aged 18-64 years, 136 of 1,218 (11%) belonged to a health risk group; uptake of influenza and pneumococcal vaccine in these risk groups was 28% (95% CI: 20.9-35.4) and 11% (95% CI: 6.7-17.2) respectively. Uptake among persons aged over 65 years was 69% (95% CI: 62.2-74.4) and 41% (95% CI: 35.0-47.9) for influenza and pneumococcal vaccine, respectively. Influenza vaccine uptake among HCWs was 20% (95% CI: 13.1-28.7). Half (47.6%) of influenza-vaccinated respondents reported that their family doctor had recommended it; 60% of non-vaccinated respondents, for whom influenza vaccine was indicated, saw themselves at low risk of influenza.
SARS update: Additional cases being investigated in Beijing, China
Authors: Goddard N L
Published: October 2017

Since 22 April, the World Health Organization has reported two people who have been classified as probable cases of severe acute respiratory syndrome (SARS), and seven people who remain under investigation for possible SARS infection
First vancomycin-resistant Enterococcus faecium outbreak reported in Hungary
Authors: Böröcz K , Szilágyi Emese , Kurcz A , Libisch B , Glatz K , Gacs M
Published: October 2017

The first healthcare-associated vancomycin-resistant Enterococcus faecium (VRE) outbreak in Hungary occurred between April and September 2004
Xenotransplantation: adequate controls and surveillance of microbial risks needed in all countries
Authors: Editorial team Collective
Published: October 2017

Recent experiments have shown that the transplantation of organs from genetically modified pigs into baboons can yield moderate to good results and has raised hopes of future success of xenotransplantation
MRSA infections increasing in the Nordic countries
Authors: Skov R , SSAC MRSA Working Party Collective
Published: October 2017

Although the incidence of methicillin-resistant Staphylococcus aureus infection is low in the Nordic countries compared with many other European countries, a significant increase has been observed in the last 3-5 years in all of these countries
Infection-related policy oriented research opportunities, including special call on avian influenza
Authors: Editorial team Collective
Published: October 2017

A draft work programme for a call for proposals for policy oriented research has been published under the Sixth Framework Programme
‘The Disease Detectives’: a comic perspective on outbreak investigations
Authors: Burckhardt F , Kissling E
Published: October 2017

Outbreak investigations often share common methodologies and scenarios. One has to confirm the outbreak, establish a case definition, generate hypotheses, decide on a study design, gather data as fast and completely as possible, perform statistical analyses and (hopefully) identify the vehicle and take appropriate control measures.
Predicting Performance of Aluminum - Glass Composite Facade Systems Based on Mechanical Properties of the Connection
Authors: Warszawska Maciej Cwyl , Garbacz Andrzej , Michalczyk Rafał , Grzegorzewska Natalia
Published: October 2017

In this paper, an extensive Finite-Element (FE) numerical study is carried out on a glass framing with point mechanical connectors. The models have been calibrated based on literature studies and field research. The simulations have been performed in order to assess the mechanical behavior of the examined glass-aluminum panels. In frame-support glass structures, such as curtain walls, where glass plates are mounted onto a metal framework, the composite behavior between glass and the supporting aluminum elements is usually a problem. It has been showed that an application of elastomer gaskets decreases the stress concentration at the interface between aluminum and glass while does not significantly change the working scheme of the profile. Based on the proposed models, the failure mechanism for wider set of geometrical configurations can be analyzed.
Molecular Characterization and Genetic Diversity of Aman Rice (Oryza sativa L.) Landraces in Bangladesh
Authors: Siddique MA , Khalequzzaman M , Fatema K , Islam MZ , Islam MM , Chowdhury MAZ
Published: September 2017

Assessment of genetic diversity and molecular characterization among rice landraces of Bangladesh is important for their identification. Genetic diversity of 96 Aman (rainfed, partially irrigated) rice landraces of Bangladesh were evaluated using eight SSR markers to characterize the landraces and also to establish the sovereignty of Bangladeshi rice gene pool. A total of 159 alleles were detected. The number of alleles per locus ranged from 13 (RM60, RM237) to 34 (RM163), with an average of 19.88. The polymorphism information content (PIC) which ranged from 0.86 (RM237) to 0.95 (RM163) with an average of 0.90 revealed much variation among the studied landraces. RM163 was the best marker for identification and diversity estimation of Aman rice landraces as revealed by PIC values. The allele frequency ranged from 8.33% (RM163) to 22.92% (RM60, RM125) with an average of 15.89. The UPGMA dendrogram based on Neis genetic distance revealed seven distinct clusters with a similarity coefficient of 0.09. The two-dimensional graphical view of Principal Coordinate Analysis (PCoA) revealed that the landraces Pankaij, Lotha, Chinigura, Patjag, Chinikanai, Badshabogh, Panati, Jirasail, Joria, Dudhmoni, Jhingasail were found far away and distributed around the centroid of the cluster. The findings of this study are useful for landraces identification to assist plant breeders in selecting suitable genetically diverse parents for breeding programmes.Bangladesh Rice j. 2016, 20(2): 1-11
Effects of NPKS on Yield and Nutrition of BRRI dhan49
Authors: Kamrunnahar - , Ahmad S , Iqbal M , Islam MN , Islam A
Published: September 2017

Nitrogen (N), phosphorus (P), potassium (K) and sulphur (S) strongly influence rice plant nutrition. Present experiment was conducted at the Bangladesh Rice Research Institute (BRRI) farm, Gazipur in a permanent layout in wet season of 2014. Objectives of the research were to study the effects of NPKS on grain yield, plant nutrition, requirement of NPKS to produce one ton grain and to estimate the indigenous nutrient supply of the soil. BRRI dhan49 was tested with NPKS (complete), PKS (-N), NKS (-P), NPS (-K) and NPK (-S) fertilizer packages. The NPKS were applied @ 100-7-80-3 kg ha-1. Omission of each nutrient from the complete treatments significantly reduced grain and straw yields of BRRI dhan49. The highest yield reduction was recorded because of N omission followed by K. Nutrient concentration in grain and straw as well as nutrient uptakes were significantly affected by major plant nutrients. Nutrient uptake was directly related to the biomass production. About 87% of total K uptake remained in straw and thus a good K source for rice cultivation. Nitrogen, P, K, S and Zn required to produce one ton rice were 20.88, 5.04, 18.77, 2.08 and 0.07 kg, respectively. The indigenous N, P, K and S supply capacity of this soil was 37, 13, 41 and 6 kg ha-1, respectively.Bangladesh Rice j. 2016, 20(2): 39-47
Field Evaluation of Brri Usg Applicator in Dry and Wet Season of Rice Cultivation
Authors: Hossen MA , Rahman MA , Zaman MK , Islam MM
Published: September 2017

BRRI (Bangladesh Rice Research Institute) USG (Urea super granule) applicator was developed to apply USG in non-oxidized zone at 6-10 cm depth from surface at desired spacing to maintain the recommended USG fertilizer doses of 118 and 168 kg ha-1 during Aman and Boro season, respectively that could be maintained with the adjustment of the applicator for 20 × 20 cm transplanting spacing. It was designed and fabricated with an adjustable facility for two rows operation in the rice field at spacing of 18 × 20, 20 × 20 and 22 × 20 cm. The modified USG applicator tested in the BRRI regional stations (RS) during Aman 2011 and the farmers fields during Boro 2012 season. Walking speed directly influenced the field capacity of the applicator. Walking speed during field operation of the applicator depends on the soil type, USG placement time and puddled condition of the soil and it was varied 2.46-3.72 km hr-1. Field capacity was observed 0.13 and 0.14 ha hr-1 during Boro and Aman season, respectively whereas manual USG application capacity was observed about 0.02 ha hr-1. The depth of USG placement by the applicator (6.01-6.32 cm) was found more compared to manual application (5.61-5.75 cm). The yield performance of USG plots was identical in all locations during both the seasons either applied by hand or by machine. However, in some cases, USG gave significantly higher grain yield compared to prilled urea applied by hand broadcasting method.Modified BRRI USG applicator saved urea fertilizer, ensured proper placement of USG in subsurface zone and reduced drudgery without sacrificing grain yield.Bangladesh Rice j. 2016, 20(2): 49-59
Density and Distribution of False Smut Balls on Infected Rice Panicles
Authors: Nessa B , Salam MU , Haque AHMM , Biswas JK , Jahan QSA , Khan MAI , Bhuiyan MR , Ara A , Munir MR , Galloway J , Kabir MS , Ali MA
Published: September 2017

Rice false smut (RFSm), considered as a minor importance, has become a serious disease in many rice growing areas of Bangladesh and other parts of the world. Many aspects of its epidemiology still remained unclear, notable the life cycle of RFSm pathogen, its infection site and the smut ball formation on infected panicles. Present research was undertaken to investigate the density and distribution of false smut balls on infected rice panicles aiding to understand on how severe the disease can be in a rice-ecosystem, on which position the smut balls form on infected panicles and likely yield reduction from such disease severity. This study included field observation of natural RFSm infection during 2014, 2015 and 2016, and simulated infection during 2015 in T. Aman rice in the experimental farm of the Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh. While the number of smut balls reached as many as 136 (recorded in one panicle in 2015), the study shows there was 81, 54 and 30% probability that maximum of nine, three and only one smut ball would form, respectively. With the scenarios of density of smut ball formation in the study area, the yield loss was estimated as 0.15% for each 1% incidence level. The level of smut ball density varied between years; this severity was most likely influenced by low daily minimum temperature. In the natural observation 34.4, 53.9 and 11.7% of the smut balls were located at the base, mid and apex part of the infected panicles, respectively. When compared the balls of these three positions in relation to potential grain number, the proportion accounted for the base and mid remained almost similar, whereas the proportion in the apex was much lower. It is concluded that false smut balls predominantly form on the lower half of the infected rice panicles.Bangladesh Rice j. 2016, 20(2): 73-79
Strategies to Automatically Derive a Process Model from a Configurable Process Model Based on Event Data
Authors: Arriagada-Benítez Mauricio , Sepúlveda Marcos , Munoz-Gama Jorge , Buijs Joos C. A. M.
Published: October 2017

Configurable process models are frequently used to represent business workflows and other discrete event systems among different branches of large organizations: they unify commonalities shared by all branches and describe their differences, at the same time. The configuration of such models is usually done manually, which is challenging. On the one hand, when the number of configurable nodes in the configurable process model grows, the size of the search space increases exponentially. On the other hand, the person performing the configuration may lack the holistic perspective to make the right choice for all configurable nodes at the same time, since choices influence each other. Nowadays, information systems that support the execution of business processes create event data reflecting how processes are performed. In this article, we propose three strategies (based on exhaustive search, genetic algorithms and a greedy heuristic) that use event data to automatically derive a process model from a configurable process model that better represents the characteristics of the process in a specific branch. These strategies have been implemented in our proposed framework and tested in both business-like event logs as recorded in a higher educational enterprise resource planning system and a real case scenario involving a set of Dutch municipalities.
HDO of Methyl Palmitate over Silica-Supported Ni Phosphides: Insight into Ni/P Effect
Authors: Deliy Irina , Shamanaev Ivan , Gerasimov Evgeny , Pakharukova Vera , Yakovlev Ilya , Lapina Olga , Aleksandrov Pavel , Bukhtiyarova Galina
Published: October 2017

Two sets of silica-supported nickel phosphide catalysts with a nickel content of about 2.5 and 10 wt % and Ni/P molar ratio 2/1, 1/1 and 1/2 in each set, were prepared by way of a temperature-programmed reduction method using (Ni(CH3COO)2) and ((NH4)2HPO4) as a precursor. The NixPy/SiO2 catalysts were characterized using chemical analysis N2 physisorption, XRD, TEM, 31P MAS NMR. Methyl palmitate hydrodeoxygenation (HDO) was performed in a trickle-bed reactor at 3 MPa and 290 °C with LHSV ranging from 0.3 to 16 h−1. The Ni/P ratio was found to affect the nickel phosphide phase composition, POx groups content and catalytic properties in methyl palmitate HDO with the TOF increased along with a decline of Ni/P ratio and a growth of POx groups’ content. Taking into account the possible routes of methyl palmitate conversion (metal-catalyzed hydrogenolysis or acid-catalyzed hydrolysis), we proposed that the enhancement of acid POx groups’ content with the Ni/P ratio decrease provides an enhancement of the rate of methyl palmitate conversion through the acceleration of acid-catalyzed hydrolysis.
Evidence for Toroidal B-Field Components in AGN Jets on Kiloparsec Scales
Authors: Knuettel Sebastian , Gabuzda Denise , O’Sullivan Shane
Published: October 2017

Though helical magnetic fields are generally believed to arise when the jets of Active Galactic Nuclei (AGN) are launched, it is still unclear what role they play (and if they survive) to the largest jet scales. A helical or toroidal B-field may contribute substantially to the collimation of the jet. This B-field structure can be detected in images of the Faraday rotation measure (RM)—a measure of the change in polarisation angle of an electromagnetic wave as it passes through a magneto-ionic medium. The Faraday rotation measure is directly proportional to the line-of-sight magnetic field; therefore a monotonic gradient in the RM transverse to the jet indicates similar behaviour of the line-of-sight B-field component. This type of analysis has mostly been done on parsec scales using VLBI observations at centimetre wavelengths, while relatively few studies have probed decaparsec to kiloparsec scales. The detection of RM gradients with significances of 3 σ or more on such large scales can demonstrate the presence of a toroidal field component, which may be associated with a helical field that has persisted to these distances from the centre of the AGN. We present the results of new Faraday rotation analyses for 2 AGN on kiloparsec scales based on multiwavelength VLA observations, with robust transverse RM gradients detected in both. Furthermore, the direction of the inferred toroidal B-fields on the sky supports previous results indicating a predominance of outward currents in the jets on kiloparsec scales.
Poly(N-isopropylacrylamide) and Copolymers: A Review on Recent Progresses in Biomedical Applications
Authors: Lanzalaco Sonia , Armelin Elaine
Published: October 2017

The innate ability of poly(N-isopropylacrylamide) (PNIPAAm) thermo-responsive hydrogel to copolymerize and to graft synthetic polymers and biomolecules, in conjunction with the highly controlled methods of radical polymerization which are now available, have expedited the widespread number of papers published in the last decade—especially in the biomedical field. Therefore, PNIPAAm-based hydrogels are extensively investigated for applications on the controlled delivery of active molecules, in self-healing materials, tissue engineering, regenerative medicine, or in the smart encapsulation of cells. The most promising polymers for biodegradability enhancement of PNIPAAm hydrogels are probably poly(ethylene glycol) (PEG) and/or poly(ε-caprolactone) (PCL), whereas the biocompatibility is mostly achieved with biopolymers. Ultimately, advances in three-dimensional bioprinting technology would contribute to the design of new devices and medical tools with thermal stimuli response needs, fabricated with PNIPAAm hydrogels.
Preparation and Molecular Structure of a Cyclopentyl-Substituted Cage Hexasilsesquioxane T6 (T = cyclopentyl-SiO1.5) Starting from the Corresponding Silanetriol
Authors: Kahr Jürgen , Belaj Ferdinand , Pietschnig Rudolf
Published: October 2017

Cyclopentyl substituted silanetriol can be prepared and isolated. Its condensation yields the corresponding disiloxanetetrol as a primary condensation product. Further condensation leads to the hexameric polyhedral silsesquioxane cage T6. The latter has been mentioned in the literature before however, lacking structural data. All compounds have been characterized with multinuclear NMR spectroscopy and, in addition, the molecular structures have been determined in the case of the disiloxanetetrol and the hexasilsesquioxane via single crystal X-ray diffraction.
Regional Quantitative Cover Mapping of Tundra Plant Functional Types in Arctic Alaska
Authors: Macander Matthew , Frost Gerald , Nelson Peter , Swingley Christopher
Published: October 2017

Ecosystem maps are foundational tools that support multi-disciplinary study design and applications including wildlife habitat assessment, monitoring and Earth-system modeling. Here, we present continuous-field cover maps for tundra plant functional types (PFTs) across ~125,000 km2 of Alaska’s North Slope at 30-m resolution. To develop maps, we collected a field-based training dataset using a point-intercept sampling method at 225 plots spanning bioclimatic and geomorphic gradients. We stratified vegetation by nine PFTs (e.g., low deciduous shrub, dwarf evergreen shrub, sedge, lichen) and summarized measurements of the PFTs, open water, bare ground and litter using the cover metrics total cover (areal cover including the understory) and top cover (uppermost canopy or ground cover). We then developed 73 spectral predictors derived from Landsat satellite observations (surface reflectance composites for ~15-day periods from May–August) and five gridded environmental predictors (e.g., summer temperature, climatological snow-free date) to model cover of PFTs using the random forest data-mining algorithm. Model performance tended to be best for canopy-forming PFTs, particularly deciduous shrubs. Our assessment of predictor importance indicated that models for low-statured PFTs were improved through the use of seasonal composites from early and late in the growing season, particularly when similar PFTs were aggregated together (e.g., total deciduous shrub, herbaceous). Continuous-field maps have many advantages over traditional thematic maps, and the methods described here are well-suited to support periodic map updates in tandem with future field and Landsat observations.
Factors Influencing Levels of CSR Disclosure by Forestry Companies in China
Authors: Lu Feifei , Kozak Robert , Toppinen Anne , D’Amato Dalia , Wen Zuomin
Published: October 2017

Abstract: With the international community’s increasing concern for social and environmental problems, the fulfilment and disclosure of corporate social responsibility (CSR) has been advocated and promoted across the world. Forestry companies, which are particularly sensitive to environmental and social issues, are increasingly developing and improving their levels of CSR disclosure. However, information on emerging country contexts is still lacking. To fill this gap, this study focuses on Chinese forestry companies’ CSR disclosure and introduces new disclosure indices through content analysis of annual reports by listed companies between 2011–2015. It then builds a correlation analysis of the factors influencing these companies’ disclosure indices in order to gain a better understanding of the current situation for CSR implementation by forestry companies in emerging economies like China. Although context-specific, our findings can provide a reference for researchers and policy makers, and promote sustainable development via improved CSR disclosure by forestry companies, especially in developing regions.
The Landscape of School Rating Systems
Authors: Dalton Ben
Published: September 2017

The rise of the accountability movement in education has resulted in the proliferation of school report cards, school ratings and rankings, and other kinds of performance reporting for public consumption and policy use. To understand the strengths and limitations of school rating systems and the role they play in shaping public perceptions and school improvement practices, this paper situates rating systems within the broader field of comparative organizational assessments and neo-institutional theory; describes school rankings and rating systems in use by states and consumer-oriented enterprises; and details four aspects of school ratings (measurement, transformation, integration, and presentation) that affect their use and interpretation.
The Development of Conceptual Building Design Technology, Using Quality Function Deployment and Axiomatic Design
Authors: Lapinskienė Vilūnė , Martinaitis Vytautas
Published: October 2017

Understanding issues early in the integrated design process is important, as this is when designers and engineers are able to have the largest impact on the final product. In this article the technology of conceptual architectural design for low energy buildings is proposed to address this issue. Here two methods – Quality function Deployment and Axiomatic design are used to develop the conception and to eliminate the main disadvantages of traditional building design. The integration of BIM, energy modelling (DesignBuilder) help to highlight the issue of energy efficiency at the early stage of building design, resulting in effective and more to posed requirements orientated design process.
Power Generation Technology Based on Piezoelectric Nanocomposite
Authors: Ciganas Justas , Janušas Giedrius
Published: October 2017

A new system based on a piezoelectric effect for electric power generation has been developed. Material used in the new model is flexible and has piezoelectric effect. Using the PRISM stand, it was determined that system of 1 m2 area of such elements would generate a constant 0.36 V voltage. Also the created finite element model and the airflow in the designed system was analysed using CFD software. Two different materials were selected for the numerical investigation: water and air. Calculation shows that turbulent kinetic energy, which is equal to 60 MJ, increases as the obstacle arises. Such energy increases for the short time and quickly decreases and become stable.
Collisional Fragmentation Is Not a Barrier to Close-in Planet Formation
Authors: Wallace Joshua , Tremaine Scott , Chambers John
Published: October 2017

Collisional fragmentation is shown to not be a barrier to rocky planet formation at small distances from the host star. Simple analytic arguments demonstrate that rocky planet formation via collisions of homogeneous gravity-dominated bodies is possible down to distances of order the Roche radius (r
Roche). Extensive N-body simulations with initial bodies ≳1700 km that include plausible models for fragmentation and merging of gravity-dominated bodies confirm this conclusion and demonstrate that rocky planet formation is possible down to ∼1.1r
Roche. At smaller distances, tidal effects cause collisions to be too fragmenting to allow mass buildup to a final, dynamically stable planetary system. We argue that even differentiated bodies can accumulate to form planets at distances that are not much larger than r
Roche.
Why do we continue using social networking sites? The giving loop that feeds computer-mediated social ties
Authors: Mlaiki Alya , Walsh Isabelle , Kalika Michel
Published: September 2017

Cet article étudie la continuité d’usage des réseaux sociaux numériques. Au travers du cadre de la théorie du don (Mauss, 1954), nous proposons une approche basée sur une boucle du don au sein des réseaux sociaux. Nous utilisons des données et techniques de recherche mixtes, avec une approche Glasérienne de la théorie enracinée. A l’aide de données qualitatives et quantitatives, nous définissons et modélisons les composantes du triptyque du don sur les réseaux sociaux ; ces composantes expliquent de manière significative la durabilité des liens sociaux médiatés. Nous mettons en évidence la relation entre les dynamiques du don réciproque et la continuité/discontinuité d’usage de Facebook. Nos résultats nous permettent de mettre en exergue l’importance de l’impact de nouvelles variables sur la continuité d’usage de Facebook. En effet, nous démontrons que la boucle du don-contre-don définie par le triptyque donner-recevoir-rendre explique la continuité d’usage du réseau social puisque les personnes qui entrent dans cette dynamique du don sont les plus enclines à utiliser le réseau social d’une manière continue.
Large Subpectoral Lipoma on Screening Mammography
Authors: Su Andres , Margolies Laurie
Published: September 2017

A 61 year-old woman presenting for bilateral screening mammogram was found to have an oval fat-density mass in the posterior right breast, partially visualized, with anterior displacement and thinning of the pectoralis major muscle. This mass was found on CT and MRI correlation to represent a large fat-containing mass, likely a lipoma, deep to the pectoralis major. On subsequent screening mammograms, the visualized portion of the mass remained stable. Subpectoral lipomas and intramuscular lipomas within the pectoralis major are rare, and their appearance on mammography may not be familiar to most radiologists.  A review of the literature and a discussion of their appearance on multiple imaging modalities is provided.
The Radiologic and Pathologic Diagnosis of Biphasic Pulmonary Blastoma
Authors: Nemeh Fadi , Kuo Anderson , Ross Jenny , Restrepo Carlos S
Published: September 2017

Pulmonary blastomas are rare malignancies, representing 0.25% to 0.5% of all primary lung neoplasms with often aggressive progression and poor prognosis. Clinical management of pulmonary blastomas depends on histologic subtype, staging, and presentation, and may consist of surgery, chemotherapy, and radiation. Biphasic pulmonary blastoma is a subtype of pulmonary blastoma that exhibits biphasic histology, with both epithelial and mesenchymal malignant elements.  We report a case of biphasic pulmonary blastoma in a 33-year-old female with 1 pack per day history of smoking for approximately 16 years, who presented with left-sided pleuritic chest pain on deep inspiration without otherwise significant pat medical history. Imaging evaluation using chest radiography, computed tomography, and magnetic resonance imaging identified a heterogenous, well-circumscribed, left lower lobe mass with extensive necrosis and hemorrhage. No lymphadenopathy or distant metastasis was detected through imaging evaluation. Surgical resection of the tumor followed by histopathological analysis confirmed a biphasic pulmonary blastoma.
Crossed Aphasia in a Patient with Anaplastic Astrocytoma of the Non-Dominant Hemisphere
Authors: Prater Stephanie , Anand Neil , Wei Lawrence , Horner Neil
Published: September 2017

Aphasia describes a spectrum of speech impairments due to damage in the language centers of the brain. Insult to the inferior frontal gyrus of the dominant cerebral hemisphere results in Broca's aphasia - the inability to produce fluent speech. The left cerebral hemisphere has historically been considered the dominant side, a characteristic long presumed to be related to a person's "handedness". However, recent studies utilizing fMRI have shown that right hemispheric dominance occurs more frequently than previously proposed and despite a person's handedness. Here we present a case of a right-handed patient with Broca's aphasia caused by a right-sided brain tumor. This is significant not only because the occurrence of aphasia in right-handed-individuals with right hemispheric brain damage (so-called "crossed aphasia") is unusual but also because such findings support dissociation between hemispheric linguistic dominance and handedness.
Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences
Authors: Negi Surendra S , Braun Werner
Published: October 2017

Background

Precise determination of conformational epitopes of neutralizing antibodies represents a key step in the rational design of novel vaccines. A powerful experimental method to gain insights on the physical chemical nature of conformational epitopes is the selection of linear peptides that bind with high affinities to a monoclonal antibody of interest by phage display technology. However, the structural characterization of conformational epitopes from these mimotopes is not straightforward, and in the past the interpretation of peptide sequences from phage display experiments focused on linear sequence analysis to find a consensus sequence or common sequence motifs.

Results

We present a fully automated search method, EpiSearch that predicts the possible location of conformational epitopes on the surface of an antigen. The algorithm uses peptide sequences from phage display experiments as input, and ranks all surface exposed patches according to the frequency distribution of similar residues in the peptides and in the patch. We have tested the performance of the EpiSearch algorithm for six experimental data sets of phage display experiments, the human epidermal growth factor receptor-2 (HER-2/neu), the antibody mAb Bo2C11 targeting the C2 domain of FVIII, antibodies mAb 17b and mAb b12 of the HIV envelope protein gp120, mAb 13b5 targeting HIV-1 capsid protein and 80R of the SARS coronavirus spike protein. In all these examples the conformational epitopes as determined by the X-ray crystal structures of the antibody-antigen complexes, were found within the highest scoring patches of EpiSearch, covering in most cases more than 50% residues of experimental observed conformational epitopes. Input options of the program include mapping of a single peptide or a set of peptides on the antigen structure, and the results of the calculation can be visualized on our interactive web server.

Availability

Users can access the EpiSearch from our web server http://curie.utmb.edu/episearch.html

Contact

webraun@utmb.edu
Gene Expression Based Leukemia Sub-Classification Using Committee Neural Networks
Authors: Sewak Mihir S. , Reddy Narender P. , Duan Zhong-Hui
Published: October 2017

Analysis of gene expression data provides an objective and efficient technique for sub-classification of leukemia. The purpose of the present study was to design a committee neural networks based classification systems to subcategorize leukemia gene expression data. In the study, a binary classification system was considered to differentiate acute lymphoblastic leukemia from acute myeloid leukemia. A ternary classification system which classifies leukemia expression data into three subclasses including B-cell acute lymphoblastic leukemia, T-cell acute lymphoblastic leukemia and acute myeloid leukemia was also developed. In each classification system gene expression profiles of leukemia patients were first subjected to a sequence of simple preprocessing steps. This resulted in filtering out approximately 95 percent of the non-informative genes. The remaining 5 percent of the informative genes were used to train a set of artificial neural networks with different parameters and architectures. The networks that gave the best results during initial testing were recruited into a committee. The committee decision was by majority voting. The committee neural network system was later evaluated using data not used in training. The binary classification system classified microarray gene expression profiles into two categories with 100 percent accuracy and the ternary system correctly predicted the three subclasses of leukemia in over 97 percent of the cases.
affyPara—a Bioconductor Package for Parallelized Preprocessing Algorithms of Affymetrix Microarray Data
Authors: Schmidberger Markus , Vicedo Esmeralda , Mansmann Ulrich
Published: October 2017

Microarray data repositories as well as large clinical applications of gene expression allow to analyse several hundreds of microarrays at one time. The preprocessing of large amounts of microarrays is still a challenge. The algorithms are limited by the available computer hardware. For example, building classification or prognostic rules from large microarray sets will be very time consuming. Here, preprocessing has to be a part of the cross-validation and resampling strategy which is necessary to estimate the rule's prediction quality honestly.

This paper proposes the new Bioconductor package affyPara for parallelized preprocessing of Affymetrix microarray data. Partition of data can be applied on arrays and parallelization of algorithms is a straightforward consequence. The partition of data and distribution to several nodes solves the main memory problems and accelerates preprocessing by up to the factor 20 for 200 or more arrays.

affyPara is a free and open source package, under GPL license, available form the Bioconductor project at www.bioconductor.org . A user guide and examples are provided with the package.
Gromita: A Fully Integrated Graphical user Interface to Gromacs 4
Authors: Sellis Diamantis , Vlachakis Dimitrios , Vlassi Metaxia
Published: October 2017

Gromita is a fully integrated and efficient graphical user interface (GUI) to the recently updated molecular dynamics suite Gromacs, version 4. Gromita is a cross-platform, perl/tcl-tk based, interactive front end designed to break the command line barrier and introduce a new user-friendly environment to run molecular dynamics simulations through Gromacs. Our GUI features a novel workflow interface that guides the user through each logical step of the molecular dynamics setup process, making it accessible to both advanced and novice users. This tool provides a seamless interface to the Gromacs package, while providing enhanced functionality by speeding up and simplifying the task of setting up molecular dynamics simulations of biological systems. Gromita can be freely downloaded from http://bio.demokritos.gr/gromita/ .
Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences
Authors: Aurahs Ralf , GÖker Markus , Grimm Guido W. , Hemleben Vera , Hemleben Christoph , Schiebel Ralf , Kučera Michal
Published: October 2017

The high sequence divergence within the small subunit ribosomal RNA gene (SSU rDNA) of foraminifera makes it difficult to establish the homology of individual nucleotides across taxa. Alignment-based approaches so far relied on time-consuming manual alignments and discarded up to 50% of the sequenced nucleotides prior to phylogenetic inference. Here, we investigate the potential of the multiple analysis approach to infer a molecular phylogeny of all modern planktonic foraminiferal taxa by using a matrix of 146 new and 153 previously published SSU rDNA sequences. Our multiple analysis approach is based on eleven different automated alignments, analysed separately under the maximum likelihood criterion. The high degree of congruence between the phylogenies derived from our novel approach, traditional manually homologized culled alignments and the fossil record indicates that poorly resolved nucleotide homology does not represent the most significant obstacle when exploring the phylogenetic structure of the SSU rDNA in planktonic foraminifera. We show that approaches designed to extract phylogenetically valuable signals from complete sequences show more promise to resolve the backbone of the planktonic foraminifer tree than attempts to establish strictly homologous base calls in a manual alignment.
A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome
Authors: Kierczak Marcin , Ginalski Krzysztof , Dramiñski Michał , Koronacki Jacek , Rudnicki Witold , Komorowski Jan
Published: October 2017

Reverse transcriptase (RT) is a viral enzyme crucial for HIV-1 replication. Currently, 12 drugs are targeted against the RT. The low fidelity of the RT-mediated transcription leads to the quick accumulation of drug-resistance mutations. The sequence-resistance relationship remains only partially understood. Using publicly available data collected from over 15 years of HIV proteome research, we have created a general and predictive rule-based model of HIV-1 resistance to eight RT inhibitors. Our rough set-based model considers changes in the physicochemical properties of a mutated sequence as compared to the wild-type strain. Thanks to the application of the Monte Carlo feature selection method, the model takes into account only the properties that significantly contribute to the resistance phenomenon. The obtained results show that drug-resistance is determined in more complex way than believed. We confirmed the importance of many resistance-associated sites, found some sites to be less relevant than formerly postulated and—more importantly—identified several previously neglected sites as potentially relevant. By mapping some of the newly discovered sites on the 3D structure of the RT, we were able to suggest possible molecular-mechanisms of drug-resistance. Importantly, our model has the ability to generalize predictions to the previously unseen cases. The study is an example of how computational biology methods can increase our understanding of the HIV-1 resistome.
An Efficient Method to Identify Conditionally Activated Transcription Factors and their Corresponding Signal Transduction Pathway Segments
Authors: Hu Haiyan
Published: October 2017

A signal transduction pathway (STP) is a cascade composed of a series of signal transferring steps, which often activate one or more transcription factors (TFs) to control the transcription of target genes. Understanding signaling pathways is important to our understanding of the molecular mechanisms of disease. Many condition-annotated pathways have been deposited in public databases. However, condition-annotated pathways are far from complete, considering the large number of possible conditions. Computational methods to assist in the identification of conditionally activated pathways are greatly needed. In this paper, we propose an efficient method to identify conditionally activated pathway segments starting from the identification of conditionally activated TFs, by incorporating protein-DNA binding data, gene expression data and protein interaction data. Applying our methods on several microarray datasets, we have discovered many significantly activated TFs and their corresponding pathway segments, which are supported by evidence in the literature.
Software for Quantifying and Simulating Microsatellite Genotyping Error
Authors: Johnson Paul C.D. , Haydon Daniel T.
Published: October 2017

Microsatellite genetic marker data are exploited in a variety of fields, including forensics, gene mapping, kinship inference and population genetics. In all of these fields, inference can be thwarted by failure to quantify and account for data errors, and kinship inference in particular can benefit from separating errors into two distinct classes: allelic dropout and false alleles. Pedant is MS Windows software for estimating locus-specific maximum likelihood rates of these two classes of error. Estimation is based on comparison of duplicate error-prone genotypes: neither reference genotypes nor pedigree data are required. Other functions include: plotting of error rate estimates and confidence intervals; simulations for performing power analysis and for testing the robustness of error rate estimates to violation of the underlying assumptions; and estimation of expected heterozygosity, which is a required input. The program, documentation and source code are available from http://www.stats.gla.ac.uk/~paulj/pedant.html .
Development of the Lymphoma Enterprise Architecture Database: A caBIG™ Silver Level Compliant System
Authors: Huang Taoying , Shenoy Pareen J. , Sinha Rajni , Graiser Michael , Bumpers Kevin W. , Flowers Christopher R.
Published: October 2017

Lymphomas are the fifth most common cancer in United States with numerous histological subtypes. Integrating existing clinical information on lymphoma patients provides a platform for understanding biological variability in presentation and treatment response and aids development of novel therapies. We developed a cancer Biomedical Informatics Grid™ (caBIG™) Silver level compliant lymphoma database, called the Lymphoma Enterprise Architecture Data-system™ (LEAD™), which integrates the pathology, pharmacy, laboratory, cancer registry, clinical trials, and clinical data from institutional databases. We utilized the Cancer Common Ontological Representation Environment Software Development Kit (caCORE SDK) provided by National Cancer Institute's Center for Bioinformatics to establish the LEAD™ platform for data management. The caCORE SDK generated system utilizes an n-tier architecture with open Application Programming Interfaces, controlled vocabularies, and registered metadata to achieve semantic integration across multiple cancer databases. We demonstrated that the data elements and structures within LEAD™ could be used to manage clinical research data from phase 1 clinical trials, cohort studies, and registry data from the Surveillance Epidemiology and End Results database. This work provides a clear example of how semantic technologies from caBIG™ can be applied to support a wide range of clinical and research tasks, and integrate data from disparate systems into a single architecture. This illustrates the central importance of caBIG™ to the management of clinical and biological data.
Hepatitis Infection in the Treatment of Opioid Dependence and Abuse
Authors: Kresina Thomas F. , Sylvestre Diana , Seeff Leonard , Litwin Alain H. , Hoffman Kenneth , Lubran Robert , Clark H. Westley
Published: October 2017

Many new and existing cases of viral hepatitis infections are related to injection drug use. Transmission of these infections can result directly from the use of injection equipment that is contaminated with blood containing the hepatitis B or C virus or through sexual contact with an infected individual. In the latter case, drug use can indirectly contribute to hepatitis transmission through the dis-inhibited at-risk behavior, that is, unprotected sex with an infected partner. Individuals who inject drugs are at-risk for infection from different hepatitis viruses, hepatitis A, B, or C. Those with chronic hepatitis B virus infection also face additional risk should they become co-infected with hepatitis D virus. Protection from the transmission of hepatitis viruses A and B is best achieved by vaccination. For those with a history of or who currently inject drugs, the medical management of viral hepatitis infection comprising screening, testing, counseling and providing care and treatment is evolving. Components of the medical management of hepatitis infection, for persons considering, initiating, or receiving pharmacologic therapy for opioid addiction include: testing for hepatitis B and C infections; education and counseling regarding at-risk behavior and hepatitis transmission, acute and chronic hepatitis infection, liver disease and its care and treatment; vaccination against hepatitis A and B infection; and integrative primary care as part of the comprehensive treatment approach for recovery from opioid abuse and dependence. In addition, participation in a peer support group as part of integrated medical care enhances treatment outcomes. Liver disease is highly prevalent in patient populations seeking recovery from opioid addiction or who are currently receiving pharmacotherapy for opioid addiction. Pharmacotherapy for opioid addiction is not a contraindication to evaluation, care, or treatment of liver disease due to hepatitis virus infection. Successful pharmacotherapy for opioid addiction stabilizes patients and improves patient compliance to care and treatment regimens as well as promotes good patient outcomes. Implementation and integration of effective hepatitis prevention programs, care programs, and treatment regimens in concert with the pharmacological therapy of opioid addiction can reduce the public health burdens of hepatitis and injection drug use.
O PODER POLÍTICO E A MÍDIA DE MASSA: A PERSPECTIVA DA FISCALIZAÇÃO DE CONCESSÕES E OUTORGAS DE RADIODIFUSÃO NO BRASIL
Authors: Barros Bruno Mello Correa de , Oliveira Rafael Santos de
Published: October 2017

Este artigo tem o condão de promover uma observância acerca da conjuntura que atravessam os meios de comunicação no Brasil a partir da interferência do poder político neste meandro. A partir de tal quadro pretende-se visualizar a atuação fiscalizatória do Ministério Público Federal no que diz respeito a concessões e outorgas do serviço de radiodifusão a parlamentares no exercício de mandato eletivo e a pressão política exercida em tal âmbito. Desta forma, a partir dessa narrativa determinada, pretende-se uma visualização representativa dos casos em que há descumprimento do preceito constitucional. Para a feitura do trabalho, utilizou-se o método de abordagem indutivo, por conta da observância dos casos de descumprimento da legislação constitucional gerando a expectativa de uniformização de condutas em um cenário que recai sobre os demais atores, já no que toca ao método de procedimento optou-se pelo monográfico. No que diz respeito à técnica de pesquisa, serviu-se da técnica baseada em fonte documental, com pesquisa em doutrina, artigos e escritos sobre a temática ora apresentada, bem como as posições do MPF acerca do assunto tratado.