bluuebunny/crossref_metadata_2025 huggingface dataset:
Exhaust gas recirculation stratification to control diesel homogeneous charge compression ignition combustion
Authors: André Mathieu , Walter Bruno , Bruneaux Gilles , Foucher Fabrice , Mounaïm–Rousselle Christine
Published: March 2012

A single-cylinder diesel engine was used to investigate the potential of exhaust gas recirculation dilution stratification as a control technique for homogeneous charge compression ignition combustion with early direct injections. Experimental studies on both all-metal and optically accessible engines were performed to understand the processes involved when exhaust gas recirculation is introduced separately in the intake ports. Laser-induced fluorescence diagnostics were carried out in the optical engine in order to provide fuel and exhaust gas recirculation distributions.

The results indicate that depending on the intake configuration, the exhaust gas recirculation stratification can be maintained until late timings corresponding to the combustion event, leading to decreased maxima of heat-release rates, as well as decreased combustion noise levels. This result suggests that exhaust gas recirculation stratification may be used as a control parameter for combustion speed and therefore may contribute to the extension of the homogeneous charge compression ignition operating range.

However, although exhaust gas recirculation stratification appears to be an interesting new control technique for homogeneous charge compression ignition combustion, its effect on the combustion was shown to be very sensitive to parameters such as the intake system configuration or the exhaust gas recirculation composition, showing that industrial use of this control technique requires further understanding of the physical phenomena involved.
Effect of an ethanol–diesel blend on a common-rail injection system
Authors: Armas Octavio , Mata Carmen , Martínez-Martínez Simón
Published: March 2012

This research paper presents a comparative experimental study for determining the functionality of a common-rail injection system used in light-duty diesel vehicles. Two Bosch fuel-injection systems were chosen to be tested using a low sulphur diesel fuel and an ethanol–diesel blend (7.7% v/v). Both systems were composed of a high-pressure injection pump Bosch (320 CDI), a common-rail and a Bosch piezoelectric fuel injector, and were tested during an accelerated durability test. In both cases, the injection systems were mounted in an injection test bench and run for 12 hours/day for 600 hours. An injection pressure of 1500 bar, a pump rotation speed of 2500 min−1 and an injection time of 1 ms were selected to simulate critical engine operating conditions. The selected test conditions were equivalent to driving a light-duty vehicle for over 120,000 km. This work employed several analysis equipment and techniques, including a surface tester for surface roughness characterization of the elements, an optical microscope for observation of the workpiece surface microstructure, a shadow comparator for geometrical characterization of elements, an analytical balance for weighing parts and, finally, a scanning electronic microscopy to determine nozzle dimensions. In both cases, the total fuel delivery was determined using an injection test bench. Results show that the use of the ethanol–diesel blend tested produced a similar effect on the durability of the injection pump parts as that produced when using diesel fuel. However, the effect on the injector nozzle was dissimilar.
Pantomime and politics: the story of a performance ethnography
Authors: Foster Victoria
Published: March 2012

The article looks at the alternative forms of knowledge that can be generated by a participatory, arts-based social research process. It draws on a project carried out with working-class women in the North West of England, UK, during the course of which a performance ethnography was developed depicting women’s experiences of motherhood and their interactions with a local Sure Start programme. The transcript of the play produced during the research process, The Wizard of Us, is interspersed here with discussion of how the research was carried out and the motives underlying the methodological approach taken. It looks at the extent to which a process involving stories, theatrics and ‘artifice’ can make claims of validity and authenticity and concludes by questioning the potential of the work to transform lives.
Photographic strain monitoring during full-scale failure testing of Örnsköldsvik bridge
Authors: Sas Gabriel , Blanksvärd Thomas , Enochsson Ola , Täljsten Björn , Elfgren Lennart
Published: March 2012

Full-scale failure tests are rarely performed on structures, primarily due to their high costs and the lack of suitable test objects. This article reports the results of a ‘test-to-failure’ performed using a real bridge. The results obtained in such tests are valuable for assessing analytical models, updating finite element models and investigating the real behaviour of structures. The specific intention in these experiments was to study the shear failure of the bridge, which is a less well-understood mode of failure than is bending. To this end, it was necessary to strengthen the bridge using near-surface-mounted reinforcements made of carbon fibre–reinforced polymer bars in order to prevent bending failure. The bridge was heavily monitored during the test, using both traditional sensors such as electrical strain gauges and linear variable differential transducers alongside new monitoring systems such as fibre-optic sensors, strain rosette linear variable differential transducers and a novel photographic monitoring system. This article presents the photographic strain measurements and describes the use of the photographic tools in monitoring and characterizing the behaviour of the failure zone during the full-scale test. The strains measured using the photographic method were found to agree well with those measured using classical strain gauges. In addition, the strain contour plots generated using the photographic method provided crucial insights into the strains within the bridge’s failure zone. This study was conducted under the remit of the EU ‘Sustainable Bridges’ Project.
Arm exercise training in chronic obstructive pulmonary disease
Authors: McKeough Zoe J , Bye Peter TP , Alison Jennifer A
Published: March 2012

The aim of this study was to compare the effects of arm endurance training, arm strength training, a combination of arm endurance and strength training, and no arm training on endurance arm exercise capacity. A randomised controlled trial was undertaken with chronic obstructive pulmonary disease subjects randomised into one of four groups to complete 8 weeks of training: (a) arm endurance training (endurance group) consisting of supported and unsupported arm exercises, (b) arm strength training (strength group) using weight machines, (c) a combination of arm endurance and arm strength training (combined group), or (d) no arm training (control group). The primary outcome measurement was endurance arm exercise capacity measured by an endurance arm crank test. Secondary outcomes included functional arm exercise capacity measured by the incremental unsupported arm exercise test and health-related quality of life. A total of 52 subjects were recruited and 38 (73%) completed the study. When comparing the arm endurance group to the control group, there was a significant increase in endurance time of 6 min (95% CI 2–10, p < 0.01) following the interventions. When comparing the combined group to each of the control, endurance and strength groups, there was a significantly greater reduction in dyspnoea and rate of perceived exertion at the end of the functional arm exercise test for the combined group following the interventions. The mode of training to be favoured to increase endurance arm exercise capacity is arm endurance training. However, combined arm endurance and strength training may also be very useful to reduce the symptoms during everyday arm tasks.
Better Learning Through Instructional Science
Authors: Freedman Ariela M. , Echt Katharina V. , Cooper Hannah L. F. , Miner Kathleen R. , Parker Ruth
Published: March 2012

Health education and behavior change interventions typically pay little attention to the intervention’s instructional foundation. Combining the fields of health literacy, cognitive psychology, and adult learning theory, this article provides an integrative scientific approach, called the BEAN (Better Education and iNnovation) model, to creating an instructional foundation based on how individuals acquire knowledge and skills. The article uses a case study example from an adult literacy center’s health literacy class to explore how environmental factors and instructional strategies can be applied to health education and behavior change interventions. Data for this case study were derived through 20 hours of classroom observation and qualitative interviews with 21 adult education students and 3 instructors. Results provide practical examples of environmental factors and instructional strategies designed to facilitate learning, such as fostering autonomy, activating prior knowledge, and fostering perspective change. Results also describe the resulting health behavior changes of students attending the health literacy class, such as increased medication adherence and physical activity, improved nutritional habits, and increased question asking of health practitioners. This article serves as a first step to encouraging researchers and educators to consider the importance of drawing on cognitive psychology and theories of adult learning to create a scientifically based instructional foundation for health behavior change programs. Additionally, by drawing on the expertise of adult educators well versed in the science of instructional design, this article also demonstrates that the adult education classroom is an excellent setting for conducting health education and behavior change interventions.
Health Reform and the Constitutionality of the Individual Mandate
Authors: Lee Jeffrey J. , Kelly Deena , McHugh Matthew D.
Published: March 2012

The Patient Protection and Affordable Care Act (ACA) of 2010 is landmark legislation designed to expand access to health care for virtually all legal U.S. residents. A vital but controversial provision of the ACA requires individuals to maintain health insurance coverage or face a tax penalty—the individual mandate. We examine the constitutionality of the individual mandate by analyzing relevant court decisions. A critical issue has been defining the “activities” Congress is authorized to regulate. Some judges determined that the mandate was constitutional because the decision to go without health insurance, that is, to self-insure, is an activity with substantial economic effects within the overall scheme of the ACA. Opponents suggest that Congress overstepped its authority by regulating “inactivity,” that is, compelling people to purchase insurance when they otherwise would not. The U.S. Supreme Court is set to review the issues and the final ruling will shape the effectiveness of health reform.
School Nursing in New Zealand
Authors: Buckley Susan , Gerring Zachary , Cumming Jacqueline , Mason David , McDonald Janet , Churchward Marianna
Published: March 2012

There are universal concerns about youth health and recognition of the potential of school health services but little consensus internationally as to how these are best configured. Limited information about nursing services in New Zealand secondary schools, changing patterns of youth health needs and expanding roles for nurses in primary health care indicated a need to research school nursing services. This study found that within New Zealand schools there was wide variation in the types of health services and their funding; that nurses are well qualified and highly experienced, although some lack clinical supervision; that students present most commonly for sexual health and injuries or sickness; and that they choose school health services for accessibility and confidentiality. It concludes that one way forward would be to develop a national-level policy for nurse-led school health centers, with appropriate funding, that allows for local flexibility and includes a career pathway for school nurses.
A Conceptual Model for Developing Mindsets for Strategic Insight Under Conditions of Complexity and High Uncertainty
Authors: Yorks Lyle , Nicolaides Aliki
Published: March 2012

This article addresses an important, yet often underattended to, aspect of the strategy development process: fostering the use of strategic learning practices in the simultaneous practice of developing strategy and cultivating strategic mindset awareness. The need for addressing this aspect of the strategy development process is increasingly important because of the intensifying complexity of the task environment. Following a framing of this context in terms of a complex adaptive systems perspective, a conceptual model for addressing this strategic HRD challenge is presented. The model is based on two distinct, yet in terms of potential implications for HRD practice, interconnected streams of literature: strategic learning practices, and adult development theory (specifically, constructive developmental theory and developmental action inquiry). The implications for HRD practices seeking to address this need, along with implications for future research, are also discussed.
EEG From a Single-Channel Dry-Sensor Recording Device
Authors: Johnstone Stuart J. , Blackman Russell , Bruggemann Jason M.
Published: March 2012

While a laboratory setting and research-grade electroencephalogram (EEG) equipment allow control of variables and high-quality multiple-channel EEG recording, there are situations and populations for which this is not suitable. The present studies examined the validity of a new method of single-channel EEG measurement that is portable and uses dry-sensor technology. In study 1, EEG was recorded simultaneously from the portable device and 4 standard EEG electrodes from a research system, during eyes open (EO) and eyes closed (EC) resting conditions, with 20 adult participants. Average correlations with the research system frequency spectra were highest at site F3 for portable device data processed onboard of the device ( r = .90), and for device data processed in a standard manner ( r = .89). Further, predictable variations in EO versus EC comparisons were observed. In study 2, twenty-three healthy children had EEGs recorded from the portable device during EO and EC resting conditions, and 3 EO active conditions (ie, relaxation, attention, and cognitive load). Absolute and relative EEG band power differed between conditions in predicted ways, including a reduction in relative theta power and an increase in relative alpha power in EC compared to EO resting conditions. Overall, the results suggest that, while limited in terms of scalp recording locations, the portable device has potential utility in certain EEG recording situations where ease of use is a priority.
The Formal Qualities of the Video Game
Authors: Cremin Colin
Published: March 2012

Approaching the video game Super Mario Galaxy on the Nintendo Wii console using Deleuzian concepts, the article identifies a series of formal qualities it is argued pertain to all video games. Concepts from Gilles Deleuze’s books on Francis Bacon and cinema are appropriated for this purpose. Three qualities in particular are identified; they center on the role of the player in contributing to the finished form, the nature of the player’s canvas, and the sensations that return back to the player when traversing the video game field. It is argued that the concepts used to define the formal qualities of the video game can be deployed to distinguish where a video game succeeds or fails. On the basis of the position developed here, it is argued that Super Mario Galaxy is a masterpiece of the form.
Boceprevir in chronic hepatitis C infection: a perspective review
Authors: Ascione Antonio
Published: March 2012

Boceprevir (Victrelis), from the oral α-ketoamide class of slow-binding reversible hepatitis C virus (HCV)-NS3 protease inhibitors, creates a new class of drugs: direct acting antivirals (DDAs). Boceprevir is highly selective against HCV serine protease. Its use is restricted to genotype 1 HCV infection and it must not be used as monotherapy. Boceprevir is given orally, rapidly absorbed, reaching plasma peak concentration within 1–2 h and is metabolized by aldo-ketoreductase and partly by the cytochrome P450 enzyme CYP3A4/5. Administration with drugs that induce or inhibit CYP3A4/5 could decrease or increase its plasma concentration. The optimal dosage is 800 mg three times daily; capsules should be taken with food. Boceprevir was approved by the US Food and Drug Administration and the European Medicines Agency and is indicated in combination with peginterferon plus ribavirin for the treatment of patients with genotype 1 HCV who have not received previous treatment or whose condition has failed to respond to previous therapy. In the Serine Protease Inhibitor Therapy 2 (SPRINT-2) trial (treatment-naïve patients) and RESPOND-2 trial (patients whose condition relapsed or did not respond to previous treatment), the boceprevir-containing regimen was always more effective than standard of care (SOC). Adverse events were similar in the treatment groups, but in the boceprevir treated group, anemia was more frequent, requiring erythropoietin in nearly 40% of cases. Discontinuation of therapy because of adverse events was identical in all treated groups. As for cost effectiveness, two studies showed that boceprevir plus SOC is cost effective with regard to the lifetime incidence of liver complications, quality of life years, and the incremental cost-effectiveness ratio. The management of this therapy is more complex than before for physicians and patients. The educational role of the physician is crucial for successful therapy and counseling should be carefully given, especially for adherence to the assigned treatment.
Impact of prescribed medications on patient safety in older people
Authors: Anathhanam Sujo , Powis Rachel A. , Cracknell Alison L. , Robson Jeremy
Published: March 2012

Appropriate prescribing for older adults presents unique challenges to the prescriber. An understanding of the scale of the problems and contributing factors is essential when designing interventions to improve patient safety. The altered pharmacology of ageing, the existence of multiple medical conditions and the exclusion of elderly patients from many trials render this subgroup of the population particularly vulnerable to underprescribing and overprescribing. Adverse drug events are common, causing significant morbidity and mortality as well as having economic implications. ‘High-risk’ medications such as opioids, anticoagulants and antipsychotics can have benefits in this group of patients but strategies to optimize their safety are required. Tools exist that help to identify those at risk of adverse drug reactions and to screen for inappropriate prescribing. Developments in information technology are ongoing, and it is hoped that these may enhance the process of medication reconciliation across healthcare transitions and alert the prescriber to potential adverse drug events. This review addresses commonly encountered issues when prescribing for older people, considers strategies to improve medication safety and offers a list of ‘top tips’ to aid the clinician.
Comparative study of fatigue behaviour in dissimilar Al alloy/steel and Mg alloy/steel friction stir spot welds fabricated by scroll grooved tool without probe
Authors: Uematsu Y , Kakiuchi T , Tozaki Y , Kojin H
Published: March 2012

Aluminium alloy A6061-T6 or magnesium alloy AZ31 sheet was welded to steel sheet by a friction stir spot welding technique using a scroll grooved tool without a probe. The material flow in the nugget of the Mg/steel weld was less than that in the Al/steel one. The Al/steel weld exhibited higher static tensile–shear strength than the Al/Al weld, while the strengths of Mg/steel and Mg/Mg welds were comparable. Tensile–shear fatigue tests were performed using lap shear specimens of both dissimilar and similar welds. The dissimilar welds exhibited nearly the same fatigue strengths as the similar ones. The effective nugget size in the dissimilar welds was defined as the area where Al or Mg alloy remained on the steel side after static fracture. When the fatigue strengths of dissimilar welds were evaluated based on the effective nugget size, the normalised fatigue strengths of Al/steel and Mg/steel welds were comparable.
Autophagy is required for CSF-1–induced macrophagic differentiation and acquisition of phagocytic functions
Authors: Jacquel Arnaud , Obba Sandrine , Boyer Laurent , Dufies Maeva , Robert Guillaume , Gounon Pierre , Lemichez Emmanuel , Luciano Frederic , Solary Eric , Auberger Patrick
Published: March 2012

Autophagy is the process by which superfluous or damaged macromolecules or organelles are degraded by the lysosome. Pharmacologic and genetic evidence indicates that autophagy plays pleiotropic functions in cellular homeostasis, development, survival, and differentiation. The differentiation of human blood monocytes into macrophages is a caspase-dependent process when triggered ex vivo by colony stimulating factor-1. We show here, using pharmacologic inhibitors, siRNA approaches, and Atg7−/− mice, that autophagy initiated by ULK1 is required for proper colony stimulating factor-1–driven differentiation of human and murine monocytes. We also unravel a role for autophagy in macrophage acquisition of phagocytic functions. Collectively, these findings highlight an unexpected and essential role of autophagy during monocyte differentiation and acquisition of macrophage functions.
Primates and mouse NumtS in the UCSC Genome Browser
Authors: Calabrese Francesco Maria , Simone Domenico , Attimonelli Marcella
Published: March 2012

Background

NumtS (N uclear M iT ochondrial S equences) are mitochondrial DNA sequences that, after stress events involving the mitochondrion, colonized the nuclear genome. Accurate mapping of NumtS avoids contamination during mtDNA PCR amplification, thus supplying reliable bases for detecting false heteroplasmies. In addition, since they commonly populate mammalian genomes (especially primates) and are polymorphic, in terms of presence/absence and content of SNPs, they may be used as evolutionary markers in intra- and inter-species population analyses.

Results

The need for an exhaustive NumtS annotation led us to produce the Reference Human NumtS compilation, followed, as reported in this paper, by those for chimpanzee, rhesus macaque and mouse ones. Identification of NumtS inside the UCSC Genome Browser and their inter-species comparison required the design and the implementation of NumtS tracks, starting from the compilation data. NumtS retrieval through the UCSC Genome Browser, in the species examined, is now feasible at a glance.

Conclusions

Analyses involving NumtS tracks, together with other genome element tracks publicly available at the UCSC Genome Browser, can provide deep insight into genome evolution and comparative genomics, thus improving studies dealing with the mechanisms that drove the generation of NumtS. In addition, the NumtS tracks constitute a useful tool in the design of mitochondrial DNA primers.
Intuitive representation of surface properties of biomolecules using BioBlender
Authors: Andrei Raluca Mihaela , Callieri Marco , Zini Maria Francesca , Loni Tiziana , Maraziti Giuseppe , Pan Mike Chen , Zoppè Monica
Published: March 2012

Background

In living cells, proteins are in continuous motion and interaction with the surrounding medium and/or other proteins and ligands. These interactions are mediated by protein features such as electrostatic and lipophilic potentials. The availability of protein structures enables the study of their surfaces and surface characteristics, based on atomic contribution. Traditionally, these properties are calculated by physico-chemical programs and visualized as range of colors that vary according to the tool used and imposes the necessity of a legend to decrypt it. The use of color to encode both characteristics makes the simultaneous visualization almost impossible, requiring these features to be visualized in different images. In this work, we describe a novel and intuitive code for the simultaneous visualization of these properties.

Methods

Recent advances in 3D animation and rendering software have not yet been exploited for the representation of biomolecules in an intuitive, animated form. For our purpose we use Blender, an open-source, free, cross-platform application used professionally for 3D work.

On the basis Blender, we developed BioBlender, dedicated to biological work: elaboration of protein motion with simultaneous visualization of their chemical and physical features.

Electrostatic and lipophilic potentials are calculated using physico-chemical software and scripts, organized and accessed through BioBlender interface.

Results

A new visual code is introduced for molecular lipophilic potential: a range of optical features going from smooth-shiny for hydrophobic regions to rough-dull for hydrophilic ones. Electrostatic potential is represented as animated line particles that flow along field lines, proportional to the total charge of the protein.

Conclusions

Our system permits visualization of molecular features and, in the case of moving proteins, their continuous perception, calculated for each conformation during motion. Using real world tactile/sight feelings, the nanoscale world of proteins becomes more understandable, familiar to our everyday life, making it easier to introduce "un-seen" phenomena (concepts) such as hydropathy or charges. Moreover, this representation contributes to gain insight into molecular functions by drawing viewer's attention to the most active regions of the protein. The program, available for Windows, Linux and MacOS, can be downloaded freely from the dedicated website http://www.bioblender.eu
PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL
Authors: Bramucci Emanuele , Paiardini Alessandro , Bossa Francesco , Pascarella Stefano
Published: March 2012

Background

In recent years, an exponential growing number of tools for protein sequence analysis, editing and modeling tasks have been put at the disposal of the scientific community. Despite the vast majority of these tools have been released as open source software, their deep learning curves often discourages even the most experienced users.

Results

A simple and intuitive interface, PyMod, between the popular molecular graphics system PyMOL and several other tools (i.e., [PSI-]BLAST, ClustalW, MUSCLE, CEalign and MODELLER) has been developed, to show how the integration of the individual steps required for homology modeling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks. Sequence similarity searches, multiple sequence and structural alignments generation and editing, and even the possibility to merge sequence and structure alignments have been implemented in PyMod, with the aim of creating a simple, yet powerful tool for sequence and structure analysis and building of homology models.

Conclusions

PyMod represents a new tool for the analysis and the manipulation of protein sequences and structures. The ease of use, integration with many sequence retrieving and alignment tools and PyMOL, one of the most used molecular visualization system, are the key features of this tool.

Source code, installation instructions, video tutorials and a user's guide are freely available at the URL http://schubert.bio.uniroma1.it/pymod/index.html
BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments
Authors: Consiglio Arianna , Carella Massimo , De Caro Giorgio , Delle Foglie Gianfranco , Giovannelli Candida , Grillo Giorgio , Ianigro Massimo , Licciulli Flavio , Palumbo Orazio , Piepoli Ada , Ranieri Elena , Liuni Sabino
Published: March 2012

Background

It is known from recent studies that more than 90% of human multi-exon genes are subject to Alternative Splicing (AS), a key molecular mechanism in which multiple transcripts may be generated from a single gene. It is widely recognized that a breakdown in AS mechanisms plays an important role in cellular differentiation and pathologies. Polymerase Chain Reactions, microarrays and sequencing technologies have been applied to the study of transcript diversity arising from alternative expression. Last generation Affymetrix GeneChip Human Exon 1.0 ST Arrays offer a more detailed view of the gene expression profile providing information on the AS patterns. The exon array technology, with more than five million data points, can detect approximately one million exons, and it allows performing analyses at both gene and exon level. In this paper we describe BEAT, an integrated user-friendly bioinformatics framework to store, analyze and visualize exon arrays datasets. It combines a data warehouse approach with some rigorous statistical methods for assessing the AS of genes involved in diseases. Meta statistics are proposed as a novel approach to explore the analysis results. BEAT is available at http://beat.ba.itb.cnr.it.

Results

BEAT is a web tool which allows uploading and analyzing exon array datasets using standard statistical methods and an easy-to-use graphical web front-end. BEAT has been tested on a dataset with 173 samples and tuned using new datasets of exon array experiments from 28 colorectal cancer and 26 renal cell cancer samples produced at the Medical Genetics Unit of IRCCS Casa Sollievo della Sofferenza.

To highlight all possible AS events, alternative names, accession Ids, Gene Ontology terms and biochemical pathways annotations are integrated with exon and gene level expression plots. The user can customize the results choosing custom thresholds for the statistical parameters and exploiting the available clinical data of the samples for a multivariate AS analysis.

Conclusions

Despite exon array chips being widely used for transcriptomics studies, there is a lack of analysis tools offering advanced statistical features and requiring no programming knowledge. BEAT provides a user-friendly platform for a comprehensive study of AS events in human diseases, displaying the analysis results with easily interpretable and interactive tables and graphics.
Improving biomarker list stability by integration of biological knowledge in the learning process
Authors: Sanavia Tiziana , Aiolli Fabio , Da San Martino Giovanni , Bisognin Andrea , Di Camillo Barbara
Published: March 2012

Background

The identification of robust lists of molecular biomarkers related to a disease is a fundamental step for early diagnosis and treatment. However, methodologies for biomarker discovery using microarray data often provide results with limited overlap. It has been suggested that one reason for these inconsistencies may be that in complex diseases, such as cancer, multiple genes belonging to one or more physiological pathways are associated with the outcomes. Thus, a possible approach to improve list stability is to integrate biological information from genomic databases in the learning process; however, a comprehensive assessment based on different types of biological information is still lacking in the literature. In this work we have compared the effect of using different biological information in the learning process like functional annotations, protein-protein interactions and expression correlation among genes.

Results

Biological knowledge has been codified by means of gene similarity matrices and expression data linearly transformed in such a way that the more similar two features are, the more closely they are mapped. Two semantic similarity matrices, based on Biological Process and Molecular Function Gene Ontology annotation, and geodesic distance applied on protein-protein interaction networks, are the best performers in improving list stability maintaining almost equal prediction accuracy.

Conclusions

The performed analysis supports the idea that when some features are strongly correlated to each other, for example because are close in the protein-protein interaction network, then they might have similar importance and are equally relevant for the task at hand. Obtained results can be a starting point for additional experiments on combining similarity matrices in order to obtain even more stable lists of biomarkers. The implementation of the classification algorithm is available at the link: http://www.math.unipd.it/~dasan/biomarkers.html.
RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts
Authors: Driver Ashley M , Peñagaricano Francisco , Huang Wen , Ahmad Khawaja R , Hackbart Katie S , Wiltbank Milo C , Khatib Hasan
Published: March 2012

Background

A valuable tool for both research and industry, in vitro fertilization (IVF) has applications range from gamete selection and preservation of traits to cloning. Although IVF has achieved worldwide use, with approximately 339,685 bovine embryos transferred in 2010 alone, there are still continuing difficulties with efficiency. It is rare to have more than 40% of fertilized in vitro cattle oocytes reach blastocyst stage by day 8 of culture, and pregnancy rates are reported as less than 45% for in vitro produced embryos. To investigate potential influences in-vitro fertilization (IVF) has on embryonic development, this study compares in vivo- and in vitro-derived bovine blastocysts at a similar stage and quality grade (expanded, excellent quality) to determine the degree of transcriptomic variation beyond morphology using RNA-Seq.

Results

A total of 26,906,451 and 38,184,547 fragments were sequenced for in vitro and in vivo embryo pools, respectively. We detected expression for a total of 17,634 genes, with 793 genes showing differential expression between the two embryo populations with false discovery rate (FDR) < 0.05. There were also 395 novel transcribed units found, of which 45 were differentially expressed (FDR < 0.05). In addition, 4,800 genes showed evidence of alternative splicing, with 873 genes displaying differential alternative splicing between the two pools (FDR < 0.05). Using GO enrichment analysis, multiple biological pathways were found to be significantly enriched for differentially expressed genes (FDR < 0.01), including cholesterol and sterol synthesis, system development, and cell differentiation.

Conclusions

Thus, our results support that IVF may influence at the transcriptomic level and that morphology is limited in full characterization of bovine preimplantation embryos.
Altered expression of testis-specific genes, piRNAs, and transposons in the silkworm ovary masculinized by a W chromosome mutation
Authors: Hara Kahori , Fujii Tsuguru , Suzuki Yutaka , Sugano Sumio , Shimada Toru , Katsuma Susumu , Kawaoka Shinpei
Published: March 2012

Background

In the silkworm, Bombyx mori, femaleness is strongly controlled by the female-specific W chromosome. Originally, it was presumed that the W chromosome encodes female-determining gene(s), accordingly called Fem. However, to date, neither Fem nor any protein-coding gene has been identified from the W chromosome. Instead, the W chromosome is occupied with numerous transposon-related sequences. Interestingly, the silkworm W chromosome is a source of female-enriched PIWI-interacting RNAs (piRNAs). piRNAs are small RNAs of 23-30 nucleotides in length, which are required for controlling transposon activity in animal gonads. A recent study has identified a novel mutant silkworm line called KG, whose mutation in the W chromosome causes severe female masculinization. However, the molecular nature of KG line has not been well characterized yet.

Results

Here we molecularly characterize the KG line. Genomic PCR analyses using currently available W chromosome-specific PCR markers indicated that no large deletion existed in the KG W chromosome. Genetic analyses demonstrated that sib-crosses within the KG line suppressed masculinization. Masculinization reactivated when crossing KG females with wild type males. Importantly, the KG ovaries exhibited a significantly abnormal transcriptome. First, the KG ovaries misexpressed testis-specific genes. Second, a set of female-enriched piRNAs was downregulated in the KG ovaries. Third, several transposons were overexpressed in the KG ovaries.

Conclusions

Collectively, the mutation in the KG W chromosome causes broadly altered expression of testis-specific genes, piRNAs, and transposons. To our knowledge, this is the first study that describes a W chromosome mutant with such an intriguing phenotype.
Dietary habits in women with recurrent idiopathic calcium nephrolithiasis
Authors: Meschi Tiziana , Nouvenne Antonio , Ticinesi Andrea , Prati Beatrice , Guerra Angela , Allegri Franca , Pigna Federica , Soldati Laura , Vezzoli Giuseppe , Gambaro Giovanni , Lauretani Fulvio , Maggio Marcello , Borghi Loris
Published: March 2012

Background

Nutrition has been widely recognized to influence the risk of kidney stone formation. Therefore the aim of our study was to assess: a) whether usual diet of women with idiopathic calcium nephrolithiasis (ICN) living in Parma (Northern-Italy) is different compared to healthy controls, b) how their diet differs from Italian National guidelines and c) whether it is related to nephrolithiasis clinical course.

Methods

143 women with recurrent ICN (mean age 43 ± 13 ys) and 170 healthy women (mean age 42 ± 11 ys) were enrolled. All women completed a food frequency questionnaire for the last 60-days and a 3-day dietary diary analysed with a dedicated software.

Results

Stone formers showed a higher consumption of sausages, ham, meat and sweets than healthy controls (43.1% vs 11.1%, 29.4% vs 13.9%, 21.6% vs 4.2%, 66.7% vs 18.1%, p < 0.001). The 3-day diary analysis showed an intake of calories, carbohydrates, lipids and non-discretionary sodium about 10% higher than healthy controls (p < 0.001). Finally, after dividing the population into 3 age groups (≤30, 31-40, > 40 years), the differences described above were amplified in the class ≤30 years, where nephrolithiasis presented a more serious course (shorter recurrence interval, greater stone-rate). In this age group the intake of fruit and vegetables was notably lower than guideline recommendations.

Conclusions

We conclude that the usual diet of women with recurrent ICN is different from controls and characterized by low intake of fruits and vegetables and higher consumption of simple sugars and foods with high protein and salt content. This dietary imbalance could play a role in the ICN pathogenesis, especially in younger women.

This work was financed by grants from Italian Ministry of University and Research as part of a larger project about the prevention of kidney stones (PRIN 2005063822) and by Fondazione per la Ricerca Scientifica Termale (FoRST). No potential conflict of interest relevant to this paper was reported.
Effects of dihydropyridine calcium channel blockers on oxidized low-density lipoprotein induced proliferation and oxidative stress of vascular smooth muscle cells
Authors: Zou Jun , Li Yan , Fan Hong-Qi , Wang Ji-Guang
Published: March 2012

Background

Dihydropyridine calcium channel blockers (CCBs) are more effective in reducing carotid intima-media thickness (IMT) than other classes of antihypertensive drugs due to their vascular effects. However, the mechanism remains to be elucidated.

Findings

Ox-LDL induced HUVSMCs proliferation in a time- and dose-dependent manner. When pretreated with three CCBs before 50 μg/ml ox-LDL stimulation, 30 μM lacidipine and 3 μM amlodipine exhibited 27% and 18% decrease of pro-proliferative effect induced by ox-LDL, whereas (S-)-amlodipine did not have any anti-proliferative effect. 30 μM lacidipine inhibited about two-thirds of the ox-LDL induced ROS production in HUVSMCs, whereas amlodipine and (S-)-amlodipine did not have influence on ROS production. The MAPKs pathway inhibitors inhibited the ox-LDL induced proliferation of HUVSMCs.

Conclusion

Our study has demonstrated that lipophilic CCBs, such as lacidipine may inhibit ox-LDL induced proliferation and oxidative stress of VSMCs, and that the ROS-MAPKs pathway might be involved in the mechanism.
Nimesulide inhibited the growth of hypopharyngeal carcinoma cells via suppressing Survivin expression
Authors: Jia-Jun Tian , Su-Mei Lu , Liang Yu , Ju-Ke Ma , Ya-Kui Mu , Hai-Bo Wang , Wei Xu
Published: March 2012

Background

The objective of this study was to evaluate the efficacy of Nimesulide, a selective cyclooxygenase-2 (COX-2) inhibitor, on the growth of hypopharyngeal carcinoma cells (FaDu) in vitro, and investigate its potential mechanism.

Methods

After FaDu cells were treated with graded concentrations of Nimesulide for divergent time, sensitivity of cells to drug treatment was analyzed by MTT assay. Morphological changes of FaDu cells in the presence of Nimesulide were observed by acridine orange cytochemistry staining. Proliferating cells were detected using the 5-Bromo-2'-deoxy-uridine (BrdU) incorporation assay. Following cells were subjected to Nimesulide (500 μmol/l) for 6 h, 12 h and 24 h, the percentage of apoptosis was examined by flow cytometry. We detected COX-2 and Survivin expression change by RT-PCR and Western blot, and analyzed the correlation of them with the growth of FaDu cells. Additionally, we also analyzed Caspase-3, Bcl-2 and Bax expressions as markers to investigate the related pathway of Nimesulide-indued apoptosis.

Results

Compared with the control group, the viabilities rates were decreased by Nimesulide in time- and dose-dependent manners, typical morphological changes of apoptotic cells were observed in the Nimesulide-treatment groups, Nimesulide could suppress the proliferation of FaDu cells significantly. The percentage of apoptosis in FaDu cells were markedly increased after Nimesulide-treatment for 6 h, 12 h and 24 h. Nimesulide down-regulated the Survivin and COX-2 expressions at mRNA and protein levels in FaDu cells. Additional analyses indicated that Bcl-2 expression was significantly decreased and the expressions of Caspase-3 as well as Bax were increased at both mRNA and protein levels.

Conclusions

Based on the induction of apoptosis and suppression of proliferation, Nimesulide could inhibit the growth of FaDu cells. Furthermore, the suppression of Survivin expression may play an important role in Nimesulide-induced growth inhibition. Nimesulide could act as an effective therapeutic agent for hypopharyngeal carcinoma therapy.
The R337H mutation in TP53 and breast cancer in Brazil
Authors: Gomes Magda CB , Kotsopoulos Joanne , de Almeida Gutemberg Leão , Costa Mauricio M , Vieira Roberto , Filho Firmino de AG , Pitombo Marcos B , F Leal Paulo Roberto , Royer Robert , Zhang Phil , Narod Steven A
Published: March 2012

Background

Germline mutations in p53 are associated with the Li-Fraumeni Syndrome which is characterized by childhood cancers, including pediatric adrenal cortical carcinomas and early onset breast cancer. The high incidence of adrenal cortical carcinomas in southern Brazil is mostly attributed to the R337H mutation in TP53. The relatively high population frequency of this mutation in southern Brazil, along with the clustering of early onset breast cancer in Li-Frameni families, suggests this mutation may also be a low-penetrance breast cancer susceptibility polymorphism.

Methods

We undertook this study to evaluate the frequency of the R337H mutation in breast cancer patients from Rio de Janeiro, Brazil. R337H mutation status was determined in 390 unselected breast cases and 324 controls identified from clinics in Rio de Janeiro, Brazil using a PCR-based assay.

Results

Two of the breast cancer cases (0.5%) and none of the controls carried the mutation. Both cases had an early age at diagnosis (< 40 years old) and a family history of breast and other cancers.

Conclusions

These data suggest genetic screening of young onset breast cancer patients should include testing for the R337H mutation.
Usage of skin care products and risk of rheumatoid arthritis: results from the Swedish EIRA study
Authors: Sverdrup Berit M , Källberg Henrik , Klareskog Lars , Alfredsson Lars ,   Epidemiological Investigation of Rheumatoid Arthritis Study Group
Published: March 2012

Introduction

The aim of this study was to investigate the association between exposure to cosmetics, often containing mineral oil, and the risk of developing rheumatoid arthritis (RA). The study was performed against the background that occupational exposure to mineral oil has recently been shown to be associated with an increased risk for RA in man, and that injection of or percutaneous exposure to mineral-oil-containing cosmetics can induce arthritis in certain rat strains.

Methods

A population-based case-control study of incident cases of RA was performed among the population aged 18 to 70 years in a defined area of Sweden during May 1996 to December 2003. A case was defined as an individual from the study base, who received for the first time a diagnosis of RA according to the 1987 American College of Rheumatology criteria. Controls were randomly selected from the study base with consideration taken for age, gender and residential area. Cases (n = 1,419) and controls (n = 1,674) answered an extensive questionnaire regarding environmental and lifestyle factors including habits of cosmetic usage. The relative risk of developing RA was calculated for subjects with different cosmetic usage compared with subjects with low or no usage. Analysis was also performed stratifying the cases for presence/absence of rheumatoid factor and antibodies to citrulline-containing peptides.

Results

The relative risks of developing RA associated with use of cosmetics were all close to one, both for women and men, for different exposure categories, and in relation to different subgroups of RA.

Conclusion

This study does not support the hypothesis that ordinary usage of common cosmetics as body lotions, skin creams, and ointments, often containing mineral oil, increase the risk for RA in the population in general. We cannot exclude, however, that these cosmetics can contribute to arthritis in individuals carrying certain genotypes or simultaneously being exposed to other arthritis-inducing environmental agents.