bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lymphomagenesis‐related gene expression in B cells from sustained virological responders with occult hepatitis C virus infection
Authors: Roque Cuéllar M. C. , García‐Lozano J. R. , Sánchez B. , Praena‐Fernández J. M. , Martínez Sierra C. , Núñez‐Roldán A. , Aguilar‐Reina J. 
Published: March 2016

SummaryThe expression of activation‐induced cytidine deaminase, B‐aggressive lymphoma, cyclin D1 and serine/threonine kinase 15 genes, among others, is increased in B cells from patients with chronic hepatitis C virus (HCV) infection. It is unknown whether the level of expression of these genes in B cells is increased in patients with hepatitis C who have achieved a sustained virological response (SVR) but who have persistent, detectable HCV RNA, so‐called occult infection. Eighty‐three patients who achieved and SVR, 27 with detectable HCV and 56 without detectable HCV RNA, 28 chronic hepatitis C patients and 32 healthy controls were studied. RNA was extracted from B cells, and gene expression levels were measured by RT‐PCR. Patients with chronic HCV and those who achieved an SVR (with and without persistent low‐level HCV RNA) showed a statistically significant higher expression compared to healthy controls, of activation‐induced cytidine deaminase (P = 0.004, P < 0.001 and P = 0.002, respectively), B‐aggressive lymphoma (P < 0.001, P = 0.001 and P = 0.006) and cyclin D1 (P = 0.026, P = 0.001; P = 0.038). For activation‐induced cytidine deaminase patients with an SVR and ‘occult infection’ had a statistically significantly higher expression level than patients with and SVR without ‘occult infection’ (P = 0.014). The higher expression levels found for activation‐induced cytidine deaminase, together with other genes indicates that these B lymphomagenesis‐related genes are upregulated following HCV therapy and this is more marked when HCV can be detected in PBMCs.
WIP: A Web‐based program for indexing planar features in quartz grains and its usage
Authors: Losiak Anna , Golebiowska Izabela , Ferrière Ludovic , Wojciechowski Jacek , Huber Matthew S. , Koeberl Christian 
Published: March 2016

AbstractPlanar deformation features (PDFs) in quartz are the most important diagnostic features that allow the unambiguous identification of impact structures on Earth. In order to confirm that these features (that are characterized by planar character and form along specific crystallographic planes) are indeed PDFs, they need to be properly investigated and indexed. Following universal‐stage measurements, the process of indexing is usually performed manually, using a Wulff stereonet and following a strict procedure, which is time consuming and error prone. In this article, we present WIP, a new Web‐based program for indexing planar deformation features in quartz. The correctness of our program is shown by its application to measurements that had previously been indexed manually. The observed minor differences, especially in the absolute frequency percentage of PDFs, are negligible and not significant enough to influence the estimation of shock pressure that could be calculated from the indexed results. Usability of this program is shown using the spatial relationships between a statistically significant number of 278 quartz grains with 409 sets of PDFs analyzed within the area (~35 mm2) of a single thin section of a meta‐greywacke from the Bosumtwi impact structure. Our program is not only more accurate and faster than the manual (graphical) method but also removes the human error from the plotting process and allows control of several parameters, such as the value of estimated measurement error used in the indexing calculation or method of aggregated error handling. The program also provides information about the angles between the planes of the measured PDF sets present in a grain, which allows determination of the angles between (for example) indexed {} and {} sets.
Interpreting phenotypic antibiotic tolerance and persister cells as evolution via epigenetic inheritance
Authors: Day Troy 
Published: March 2016

AbstractEpigenetic inheritance is the transmission of nongenetic material such as gene expression levels, RNA and other biomolecules from parents to offspring. There is a growing realization that such forms of inheritance can play an important role in evolution. Bacteria represent a prime example of epigenetic inheritance because a large array of cellular components is transmitted to offspring, in addition to genetic material. Interestingly, there is an extensive and growing empirical literature showing that many bacteria can form ‘persister’ cells that are phenotypically resistant or tolerant to antibiotics, but most of these results are not interpreted within the context of epigenetic inheritance. Instead, persister cells are usually viewed as a genetically encoded bet‐hedging strategy that has evolved in response to a fluctuating environment. Here I show, using a relatively simple model, that many of these empirical findings can be more simply understood as arising from a combination of epigenetic inheritance and cellular noise. I therefore suggest that phenotypic drug tolerance in bacteria might represent one of the best‐studied examples of evolution under epigenetic inheritance.
Molecular adaptation of ammonia monooxygenase during independent pH specialization in Thaumarchaeota
Authors: Macqueen Daniel J. , Gubry‐Rangin Cécile 
Published: March 2016

AbstractMicrobes are abundant in nature and often highly adapted to local conditions. While great progress has been made in understanding the ecological factors driving their distribution in complex environments, the underpinning molecular‐evolutionary mechanisms are rarely dissected. Therefore, we scrutinized the coupling of environmental and molecular adaptation in Thaumarchaeota, an abundant archaeal phylum with a key role in ammonia oxidation. These microbes are adapted to a diverse spectrum of environmental conditions, with pH being a key factor shaping their contemporary distribution and evolutionary diversification. We integrated high‐throughput sequencing data spanning a broad representation of ammonia‐oxidizing terrestrial lineages with codon modelling analyses, testing the hypothesis that ammonia monooxygenase subunit A (AmoA) – a highly conserved membrane protein crucial for ammonia oxidation and classical marker in microbial ecology – underwent adaptation during specialization to extreme pH environments. While purifying selection has been an important factor limiting AmoA evolution, we identified episodic shifts in selective pressure at the base of two phylogenetically distant lineages that independently adapted to acidic conditions and subsequently gained lasting ecological success. This involved nonconvergent selective mechanisms (positive selection vs. selection acting on variants fixed during an episode of relaxed selection) leading to unique sets of amino acid substitutions that remained fixed across the radiation of both acidophilic lineages, highlighting persistent adaptive value in acidic environments. Our data demonstrates distinct trajectories of AmoA evolution despite convergent phenotypic adaptation, suggesting that microbial environmental specialization can be associated with diverse signals of molecular adaptation, even for marker genes employed routinely by microbial ecologists.
Relapsing polychondritis‐associated limbic encephalitis preceding the emergence of systemic inflammation
Authors: Kawabe Miho , Tachi Rintaro , Hideyama Takuto , Yagi Masato , Kishida Yukiko , Maekawa Risa , Shima Sayuri , Mutoh Tatsuro , Shiio Yasushi 
Published: March 2016

AbstractA 67‐year‐old man presented with limbic encephalitis diagnosed from clinical symptoms and abnormal findings on brain magnetic resonance imaging. No abnormalities in laboratory measures of systemic inflammation were observed on admission. Fluorodeoxyglucose‐positron emission tomography/computed tomography showed mild uptake in the right auricle. Histological examination of biopsy specimens showed abnormalities consistent with relapsing polychondritis. Subsequently, the patient developed bilateral auricular erythema, an elevated erythrocyte sedimentation rate and a raised serum C‐reactive protein level. The early diagnosis of relapsing polychondritis in the present case was clinically challenging, as limbic encephalitis preceded the development of elevated systemic inflammation parameters and typical symptoms of relapsing polychondritis. Fluorodeoxyglucose‐positron emission tomography/computed tomography has utility in the systemic evaluation of limbic encephalitis when the underlying cause is unknown.
Importance of high sensitivity C‐reactive protein in the evaluation of wheezing in children
Authors: Bostanci Ilknur , Ozmen Serap , Susam Sen Hilal , Misirlioglu Dibek Emine , Zorlu Pelin 
Published: March 2016

AbstractBackgroundIt is important to determine the presence of asthma in children under the age of 3 with recurrent wheezing. Inflammatory markers have been investigated in the diagnosis and treatment of asthma. The aim of the present study was to investigate the relationship between recurrent wheezing with or without modified asthma predictive index (mAPI) positivity and high‐sensitivity‐C reactive protein (hs‐CRP) level in children aged 6–36 months.MethodsNinety‐nine children with recurrent wheezing and 47 healthy children aged 6–36 months were included in the present cross‐sectional, case–control study. Those children with wheezing were divided into two groups according to mAPI positivity.ResultsMean serum hs‐CRP was higher in the recurrent wheezers than in the control group (0.89 ± 1.7 mg/dL vs 0.12 ± 1.3 mg/dL, respectively; P = 0.002). There was a positive correlation between serum total IgE and hs‐CRP (P = 0,003; r = 0348). mAPI positivity was detected in 46 of the recurrent wheezers (46.5%). There was no significant difference in hs‐CRP between the mAPI‐positive and ‐negative groups. The best hs‐CRP cut‐off for differentiating between the patient and control groups was 0.11 mg/dL on receiver operating characteristic analysis (area under curve, 0.658; 95%CI: 0.571–0.744; P < 0.05; sensitivity, 60%; specificity, 61.7%).ConclusionsHigh‐sensitivity CRP can be used to indicate respiratory and systemic inflammation independently of mAPI positivity in wheezy children.
Accelerated Regeneration of ATP Level after Irradiation in Human Skin Fibroblasts by Coenzyme Q10
Authors: Schniertshauer Daniel , Müller Sonja , Mayr Tobias , Sonntag Tanja , Gebhard Daniel , Bergemann Jörg 
Published: March 2016

AbstractHuman skin is exposed to a number of harmful agents of which the ultraviolet (UV) component of solar radiation is most important. UV‐induced damages include direct DNA lesions as well as oxidative damage in DNA, proteins and lipids caused by reactive oxygen species (ROS). Being the main site of ROS generation in the cell, mitochondria are particularly affected by photostress. The resulting mitochondrial dysfunction may have negative effects on many essential cellular processes. To counteract these effects, coenzyme Q10 (CoQ10) is used as a potent therapeutic in a number of diseases. We analyzed the mitochondrial respiration profile, the mitochondrial membrane potential and cellular ATP level in skin fibroblasts after irradiation. We observed an accelerated regeneration of cellular ATP level, a decrease in mitochondrial dysfunction as well as a preservation of the mitochondrial membrane potential after irradiation in human skin fibroblasts by treatment with CoQ10. We conclude that the faster regeneration of the ATP level was achieved by a preservation of mitochondrial function by the addition of CoQ10 and that the protective effect of CoQ10 is primarily mediated via its antioxidative function. We suggest also that it might be further dependent on a stimulation of DNA repair enzymes by CoQ10.
Impact of Low Maternal Education on Early Childhood Overweight and Obesity in Europe
Authors: Ruiz Milagros , Goldblatt Peter , Morrison Joana , Porta Daniela , Forastiere Francesco , Hryhorczuk Daniel , Antipkin Youriy , Saurel‐Cubizolles Marie‐Josèphe , Lioret Sandrine , Vrijheid Martine , Torrent Maties , Iñiguez Carmen , Larrañaga Isabel , Bakoula Chryssa , Veltsista Alexandra , van Eijsden Manon , Vrijkotte Tanja G. M. , Andrýsková Lenka , Dušek Ladislav , Barros Henrique , Correia Sofia , Järvelin Marjo‐Riitta , Taanila Anja , Ludvigsson Johnny , Faresjö Tomas , Marmot Michael , Pikhart Hynek 
Published: March 2016

AbstractBackgroundComparable evidence on adiposity inequalities in early life is lacking across a range of European countries. This study investigates whether low maternal education is associated with overweight and obesity risk in children from distinct European settings during early childhood.MethodsProspective data of 45 413 children from 11 European cohorts were used. Children's height and weight obtained at ages 4–7 years were used to assess prevalent overweight and obesity according to the International Obesity Task Force definition. The Relative/Slope Indices of Inequality (RII/SII) were estimated within each cohort and by gender to investigate adiposity risk among children born to mothers with low education as compared to counterparts born to mothers with high education. Individual‐data meta‐analyses were conducted to obtain aggregate estimates and to assess heterogeneity between cohorts.ResultsLow maternal education yielded a substantial risk of early childhood adiposity across 11 European countries. Low maternal education yielded a mean risk ratio of 1.58 (95% confidence interval (CI) 1.34, 1.85) and a mean risk difference of 7.78% (5.34, 10.22) in early childhood overweight, respectively, measured by the RII and SII. Early childhood obesity risk by low maternal education was as substantial for all cohorts combined (RII = 2.61 (2.10, 3.23)) and (SII = 4.01% (3.14, 4.88)). Inequalities in early childhood adiposity were consistent among boys, but varied among girls in a few cohorts.ConclusionsConsiderable inequalities in overweight and obesity are evident among European children in early life. Tackling early childhood adiposity is necessary to promote children's immediate health and well‐being and throughout the life course.
Engineering C4 photosynthesis into C3 chassis in the synthetic biology age
Authors: Schuler Mara L. , Mantegazza Otho , Weber Andreas P.M. 
Published: March 2016

SummaryC4 photosynthetic plants outperform C3 plants in hot and arid climates. By concentrating carbon dioxide around Rubisco C4 plants drastically reduce photorespiration. The frequency with which plants evolved C4 photosynthesis independently challenges researchers to unravel the genetic mechanisms underlying this convergent evolutionary switch. The conversion of C3 crops, such as rice, towards C4 photosynthesis is a long‐standing goal. Nevertheless, at the present time, in the age of synthetic biology, this still remains a monumental task, partially because the C4 carbon‐concentrating biochemical cycle spans two cell types and thus requires specialized anatomy. Here we review the advances in understanding the molecular basis and the evolution of the C4 trait, advances in the last decades that were driven by systems biology methods. In this review we emphasise essential genetic engineering tools needed to translate our theoretical knowledge into engineering approaches. With our current molecular understanding of the biochemical C4 pathway, we propose a simplified rational engineering model exclusively built with known C4 metabolic components. Moreover, we discuss an alternative approach to the progressing international engineering attempts that would combine targeted mutagenesis and directed evolution.
Open‐angle glaucoma in the Petit Basset Griffon Vendeen
Authors: Bedford Peter G. C. 
Published: March 2016

AbstractObjectivesTo report the prevalence and clinical characteristics of an open‐angle glaucoma in Petit Basset Griffon Vendeen (PBGV) dogs in the United Kingdom (UK).Animals studied and methodsAt breed society clinics extending over a 6‐year period, 366 dogs of varying ages and both sexes were clinically examined for signs of glaucoma using slit‐lamp biomicroscopy, indirect and direct ophthalmoscopy, tonometry, and gonioscopy.ResultsThe prevalence of glaucoma was 10.4% (38 dogs). Clinical signs of the disease presented from 3 years of age onwards, the commonest initial feature being the elevation of intraocular pressure (IOP) in 15 dogs (39.4%). In addition to elevated IOP, another 13 dogs (34.2%) presented with other features of glaucoma, some with lens subluxation and globe enlargement and all with possible or known vision defects. In the remaining 10 dogs (26.3%), phacodonesis or lens subluxation was observed before subsequent elevation of IOP.ConclusionsHigh prevalence and similarity to the primary open‐angle glaucoma (POAG) seen in the Beagle and Elkhound breeds indicate that an open‐angle glaucoma is present in the PBGV in the UK and that this disease may be genetically determined in this breed. Although increased IOP is the commonest early diagnostic feature, lens instability prior to an increase in IOP may be part of the clinical picture.
Parallel workflow manager for non-parallel bioinformatic applications to solve large-scale biological problems on a supercomputer
Authors: Suplatov Dmitry , Popova Nina , Zhumatiy Sergey , Voevodin Vladimir , Švedas Vytas 
Published: March 2016

Rapid expansion of online resources providing access to genomic, structural, and functional information associated with biological macromolecules opens an opportunity to gain a deeper understanding of the mechanisms of biological processes due to systematic analysis of large datasets. This, however, requires novel strategies to optimally utilize computer processing power. Some methods in bioinformatics and molecular modeling require extensive computational resources. Other algorithms have fast implementations which take at most several hours to analyze a common input on a modern desktop station, however, due to multiple invocations for a large number of subtasks the full task requires a significant computing power. Therefore, an efficient computational solution to large-scale biological problems requires both a wise parallel implementation of resource-hungry methods as well as a smart workflow to manage multiple invocations of relatively fast algorithms. In this work, a new computer software mpiWrapper has been developed to accommodate non-parallel implementations of scientific algorithms within the parallel supercomputing environment. The Message Passing Interface has been implemented to exchange information between nodes. Two specialized threads — one for task management and communication, and another for subtask execution — are invoked on each processing unit to avoid deadlock while using blocking calls to MPI. The mpiWrapper can be used to launch all conventional Linux applications without the need to modify their original source codes and supports resubmission of subtasks on node failure. We show that this approach can be used to process huge amounts of biological data efficiently by running non-parallel programs in parallel mode on a supercomputer. The C++ source code and documentation are available from http://biokinet.belozersky.msu.ru/mpiWrapper .
The New Face of the Development: Social Capital
Authors: SAÇIK Sinem YAPAR , CEYLAN Onur , ALAGÖZ Mehmet 
Published: March 2016

Classical models were insufficient in measuring development differences in countries because of focusing only capital stocks. On the other hand, new approaches discuss development with countries’ social capital. Social capital which shows relations between countries depend on confidence and affect a country’s economic, politic and social success.The confidence element has an important role in the social capital. The researches show that a society is called an underdeveloped one when the confidence is weak in that society. The existence of the social capital is mentioned in the societies with high confidence levels. Societies with the high level social capital together with human capital experience a rise in their life qualities. Many elements in the researches done come into prominence when the standards of the social capital are examined. When these are examined generally, the existing number of institutions and confidence elements are found. Although many researches are shown as a standard of the social capital, it is the confidence element that occupies an important place among them. At the same time, the existence of the social capital and the confidence element provide a decrease in temporal and monetary costs. The works operate in a busier and more rational way when in that society people’s and institutions’ reliability arise. The interaction here completely relies on confidence. Since this element exists in most of the developed countries, their level of success is higher.
Does iPad technology bolster art teaching and learning?
Authors: Wang Tingting Windy 
Published: March 2016

Abstract
Despite the availability of iPads in a large number of school districts, as well as the popularity of teaching with iPads in art classrooms, evidenced by presentations that featured iPad teaching methods at National Art Education Association annual conventions during recent years, little research has been conducted to explore the practicability and effectiveness of the utilization of mobile tablet technology such as iPads in actual art teaching scenarios for kindergarten to middle school students. I hereby present an exploratory study about how the mobile tablet technology including iPads and artistic applications (mainly Sketchbook pro) can assist in a specific art education teaching and learning practice. Results of this study suggested that through using iPads, students achieved the expected comprehension and performance of artistic skills and knowledge, gained more interest in artistic learning, aroused creative abilities, and generated innovative forms of artistic practices.
Is the critique relevant? The function of critique in a studio art classroom, told three times
Authors: Doren Mariah 
Published: March 2016

Abstract
Is the critique relevant? Art and design education is changing as we move deeper into the twenty-first century. This article will describe and investigate the critique from three vantage points: The first is a common sense narrative, the mythical ideal of critique presented in stories of how art should be taught. The second works to take apart this ideal, looking at how this formalized assessment is experienced by students and the symbolic ‘violence’ of authority-driven educational practices. The third perspective unpacks how we, as practitioners and educators in the field of art and design, understand meaning in artworks and what is described as valuable in assessment. The focus here is on the presentation of originality and the problem with a lingering adherence to Modernist notions of linear progress. ‘The function of critique in a studio art classroom’ re-examines critique and asks us to reframe classroom conversations of student artwork.
A propósito de duas encomendas: conversa com José Fonseca e Costa
Authors: Sampaio Sofia , Mota Gonçalo , E Sá Sérgio Bordalo 
Published: March 2016

Entrevista ao realizador José Fonseca e Costa (1933-2015) sobre duas curtas-metragens suas: ...E era o Mar (1966) e A Cidade (1968), que têm como tema, respetivamente, o Hotel do Mar, em Sesimbra, projetado pelo arquiteto Conceição Silva, e a cidade de Évora. A entrevista foi realizada no dia 24 de fevereiro de 2015, no âmbito do projeto de investigação “Atrás da câmara: práticas de visualidade e mobilidade no filme turístico português” (EXPL/IVC-ANT/1706/2013), financiado por fundos nacionais através da FCT/MCTES.