bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased microRNA-223 in Helicobacter pylori-associated gastric cancer contributed to cancer cell proliferation and migration
Authors: Ma Lianjun , Chen Yan , Zhang Bin , Liu Guifeng 
Published: May 2014

Abstract
Dysregulation of microRNA-223 (miR-223) was associated with gastric cancer (GC), in which Helicobacter pylori (H. pylori) played important roles. However, the mechanism of relationships between miR-223 and H. pylori-associated GC was largely undiscovered. Here, we found the overexpression of miR-223 was related with H. pylori positive infection in vivo and in vitro in GC by relative quantification of qRT-PCR. Upregulated miR-223 was responsible for the poorer prognosis of GC with H. pylori positive, also. The result indicated not only overexpression of miR-223 stimulated the proliferation by CCK-8 assays and colony formation of H. pylori associated GC cells, but also migration and invasion by scratch assay and transwell invasion assays in vitro. Above all, all our data declared H. pylori infection played an important role in developing GC according to overexpression of miR-223, which increased cancer cell proliferation and migration.
Presence of osteoinductive factors in bovine colostrum
Authors: Mussano Federico , Bartorelli Cusani Alberto , Brossa Alessia , Carossa Stefano , Bussolati Gianni , Bussolati Benedetta 
Published: May 2014

AbstractNew approaches in the treatment of skeletal defects may benefit from the use of soluble biological factors. We previously standardized a derivative of bovine colostrum (SBCD), deprived of casein and fat and rich in cytokines. In the present study, we tested its possible use as an adjuvant in bone healing. SBCD contained factors involved in stromal cell stimulation and differentiation and induced cytokine production from stimulated mesenchymal stem cells (MSCs). In vitro, SBCD promoted proliferation, migration and, in association with osteogenic factors, osteogenic differentiation of osteoblastic and MSCs. In in vivo experiments of subcutaneous Matrigel injection in mice, SBCD plus hydroxyapatite, but not hydroxyapatite nor SBCD alone, induced recruitment of macrophages and stromal cells. After 60 days, plugs containing SBCD and hydroxyapatite were densely calcified and diffusely positive for osteocalcin, supporting the occurrence of an early osteogenic process. These results indicate that SBCD is a rich source of factors with osteoinductive properties.
SAMBLASTER: fast duplicate marking and structural variant read extraction
Authors: Faust Gregory G. , Hall Ira M. 
Published: May 2014

Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the requirement to read, write, sort and compress large BAM files multiple times.
Results: We present SAMBLASTER, a tool that reduces the number of times such costly operations are performed. SAMBLASTER is designed to mark duplicates in read-sorted SAM files as a piped post-pass on DNA aligner output before it is compressed to BAM. In addition, it can simultaneously output into separate files the discordant read-pairs and/or split-read mappings used for structural variant calling. As an alignment post-pass, its own runtime overhead is negligible, while dramatically reducing overall pipeline complexity and runtime. As a stand-alone duplicate marking tool, it performs significantly better than PICARD or SAMBAMBA in terms of both speed and memory usage, while achieving nearly identical results.
Availability and implementation: SAMBLASTER is open-source C++ code and freely available for download from https://github.com/GregoryFaust/samblaster.
Contact: imh4y@virginia.edu
SEK: sparsity exploiting k-mer-based estimation of bacterial community composition
Authors: Chatterjee Saikat , Koslicki David , Dong Siyuan , Innocenti Nicolas , Cheng Lu , Lan Yueheng , Vehkaperä Mikko , Skoglund Mikael , Rasmussen Lars K. , Aurell Erik , Corander Jukka 
Published: May 2014

Motivation: Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. As the sample sequence data typically harbors reads of variable lengths and different levels of biological and technical noise, accurate statistical analysis of such data is challenging. Currently popular estimation methods are typically time-consuming in a desktop computing environment.
Results: Using sparsity enforcing methods from the general sparse signal processing field (such as compressed sensing), we derive a solution to the community composition estimation problem by a simultaneous assignment of all sample reads to a pre-processed reference database. A general statistical model based on kernel density estimation techniques is introduced for the assignment task, and the model solution is obtained using convex optimization tools. Further, we design a greedy algorithm solution for a fast solution. Our approach offers a reasonably fast community composition estimation method, which is shown to be more robust to input data variation than a recently introduced related method.
Availability and implementation: A platform-independent Matlab implementation of the method is freely available at http://www.ee.kth.se/ctsoftware; source code that does not require access to Matlab is currently being tested and will be made available later through the above Web site.
Contact: sach@kth.se
Bioinformatics-driven discovery of rational combination for overcoming EGFR-mutant lung cancer resistance to EGFR therapy
Authors: Kim Jihye , Vasu Vihas T. , Mishra Rangnath , Singleton Katherine R. , Yoo Minjae , Leach Sonia M. , Farias-Hesson Eveline , Mason Robert J. , Kang Jaewoo , Ramamoorthy Preveen , Kern Jeffrey A. , Heasley Lynn E. , Finigan James H. , Tan Aik Choon 
Published: May 2014

Motivation: Non–small-cell lung cancer (NSCLC) is the leading cause of cancer death in the United States. Targeted tyrosine kinase inhibitors (TKIs) directed against the epidermal growth factor receptor (EGFR) have been widely and successfully used in treating NSCLC patients with activating EGFR mutations. Unfortunately, the duration of response is short-lived, and all patients eventually relapse by acquiring resistance mechanisms.
Result: We performed an integrative systems biology approach to determine essential kinases that drive EGFR-TKI resistance in cancer cell lines. We used a series of bioinformatics methods to analyze and integrate the functional genetics screen and RNA-seq data to identify a set of kinases that are critical in survival and proliferation in these TKI-resistant lines. By connecting the essential kinases to compounds using a novel kinase connectivity map (K-Map), we identified and validated bosutinib as an effective compound that could inhibit proliferation and induce apoptosis in TKI-resistant lines. A rational combination of bosutinib and gefitinib showed additive and synergistic effects in cancer cell lines resistant to EGFR TKI alone.
Conclusions: We have demonstrated a bioinformatics-driven discovery roadmap for drug repurposing and development in overcoming resistance in EGFR-mutant NSCLC, which could be generalized to other cancer types in the era of personalized medicine.
Availability and implementation: K-Map can be accessible at: http://tanlab.ucdenver.edu/kMap.
Contact: aikchoon.tan@ucdenver.edu or finiganj@njhealth.org
Supplementary information: Supplementary Data are available at Bioinformatics online.
Injecting Charter School Best Practices into Traditional Public Schools: Evidence from Field Experiments
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Authors: Fryer Roland G. 
Published: May 2014

Abstract
This study examines the impact on student achievement of implementing a bundle of best practices from high-performing charter schools into low-performing, traditional public schools in Houston, Texas, using a school-level randomized field experiment and quasi-experimental comparisons. The five practices in the bundle are increased instructional time, more effective teachers and administrators, high-dosage tutoring, data-driven instruction, and a culture of high expectations. The findings show that injecting best practices from charter schools into traditional Houston public schools significantly increases student math achievement in treated elementary and secondary schools—by 0.15 to 0.18 standard deviations a year—and has little effect on reading achievement. Similar bundles of practices are found to significantly raise math achievement in analyses for public schools in a field experiment in Denver and program in Chicago.
Workplace stress in libraries: a case study
Authors: Farler Liz , Broady‐Preston Judith 
Published: May 2014

PurposeThis paper seeks to analyse the results of a case study conducted in 2008/2009 investigating workplace stress in a further education college library service.Design/methodology/approachResults from questionnaires and a series of semi‐structured interviews held with library staff are analysed and discussed in the paper.FindingsLibrarians reported that interaction with students can be stressful or enjoyable, depending on context. The need to control noise levels, modify student behaviour and balance the needs of different user groups are cited as stressors. The results also show that the library staff exhibit a degree of humour and self‐awareness in their work and employ a range of methods to cope with stress.Research limitations/implicationsRepeating the study more widely amongst a range of differing library services would add credibility to the findings.Practical implicationsThis study shows that positive stress may motivate librarians to engage actively with students and thus create job satisfaction. Negative stress may be managed by measures such as zoning and flexible governance.Originality/valueThe study contributes to knowledge and understanding of stress in the library profession by contributing a case study of stress in the college sector.
Living and lurking on LiveJournal
Authors: Kate Merry Sarah , Simon Anoush 
Published: May 2014

PurposeThis paper aims to report on research investigating the benefits of membership of the online community LiveJournal, for both active and non‐active participants (lurkers). It also aims to build on and develop previous research on this topic in a new context and to present some alternative perspectives on how lurking is understood by both active participants and lurkers themselves.Design/methodology/approachData were gathered using an online questionnaire made available to members of two different LiveJournal communities.FindingsThe data indicate that both active participants and lurkers receive similar benefits from their membership of LiveJournal in terms of their sense of community and satisfaction with experience of the community. The percentage of lurkers who felt a sense of community and high levels of satisfaction was lower than that of the respondents who posted regularly to the community, but nonetheless represented the majority of the lurkers. The majority of overall respondents said that lurkers are members of the community, in contrast to earlier research in this area.Social implicationsThe research contributes to an understanding of the fast‐developing world of online communities, including individuals' reasons for joining and participating in communities.Originality/valueThe research builds on an earlier research in a new context; the findings present a different, developing understanding of how non‐active participants are viewed as part of the community of LiveJournal.
Analysis of effective parameters on ablative PPT performance
Authors: Rezaeiha Abdolrahim , Schönherr Tony 
Published: May 2014

PurposeThe purpose of this paper is to comprehensively review most of the significant works ever done worldwide to study the effects of essential parameters on pulsed plasma thruster (PPT) performance and to analyze the effects of each parameter on PPT performance.Design/methodology/approachAll the important works studying PPT performance are categorized by the parameter they have studied and its effect on the thruster performance, and their works have been reviewed to analyze the influence of each parameter.FindingsThe analysis leads to elucidation of the effects of different geometrical parameters including aspect ratio, electrode width, electrode spacing, electrode shape, electrode length, and flare angle, in addition to the effects of other parameters such as electrode material, propellant type, propellant temperature, spark distance from propellant, pulse repetition frequency, discharge energy, capacitance, and hood angle on PPT performance.Research limitations/implicationsThe analysis is mainly focused on parallel‐rail breech‐fed PPTs and side‐fed PPTs and does not deal with co‐axial PPTs.Originality/valueThe paper reviews and analyses many of the considerable works ever done to contribute to clarify the effects of different parameters on PPT performance. The results of the current analysis can be of invaluable assistance in PPT design and optimization procedure and help the designer to develop a system with better performance characteristics.
Dynamics analysis of satellite cluster non‐coplanar orbit transfer based on geometric method
Authors: Zhang Wei , Deng Zhongmin , Li Jingsheng 
Published: May 2014

PurposeThe purpose of this paper is to propose strategies for satellite cluster non‐coplanar orbit transfer to reduce fuel cost of formation maintenance and orbit maneuver.Design/methodology/approachThis research tries to use geometric method model to describe the relative motion of satellites in the cluster non‐coplanar orbit transfer, and genetic algorithm (GA) to optimize the proposed maneuver strategies.FindingsCompared with the C‐W equations, the geometric method model is found to be more precise. Three strategies are proposed and optimized to maintain the relative orbit and a strategy of indefinite phase and non‐synchronous costs least fuel.Practical implicationsGeometric method model can be used to describe the relative motion of satellite cluster, especially on elliptical orbits considering the effects of perturbation, with a simple form and good accuracy. Fuel cost minimization is one of the most important issues in formation flight mission.Originality/valueThis paper provides dynamics analysis about formation non‐coplanar orbit transfer, which is involved in minor researches.
Optimal virtual center selection for formation flying maintenance
Authors: Wang Jihe , Cao Xibin , Zhang Jinxiu 
Published: May 2014

PurposeThe purpose of this paper is to propose a fuel‐optimal virtual centre selection method for formation flying maintenance in the J2 perturbed environment.Design/methodology/approachBased on the relative orbital elements (ROE) theory, the J2 perturbed relative motions between different satellites in the formation are analyzed, and then the fuel‐optimal virtual centre selection issue for formation flying maintenance are parameterized in terms of ROE. In order to determine the optimal virtual centre, two theories are proposed in terms of ROE.FindingsNumerical simulations demonstrate that the fuel‐optimal virtual centre selection method is valid, and the control of the ROE of each satellite with respect to a virtual optimal centre of the formation is more efficient regarding the fuel consumption than the control of all satellites with respect to a satellite belonging to the formation.Research limitations/implicationsThe fuel‐optimal virtual centre selection method is valid for formation flying mission whose member satellite in circular or near circular orbit.Practical implicationsThe fuel‐optimal virtual centre selection approach can be used to solve formation flying maintenance problem which involves multiple satellites in the formation.Originality/valueThe paper proposes a fuel‐optimal virtual centre selection method in terms of ROE, and shows that keeping the formation with respect the optimal virtual centre is more fuel efficient.
Corrosion resistance and electrodeposition behavior of electrodeposited nickel‐cobalt‐iron alloys
Authors: Abou‐Krisha M.M. , Assaf F.H. , Khodari M. , Elkady E.M. 
Published: May 2014

PurposeThe purpose of this paper is to investigate the corrosion resistance and the electrodeposition behavior of electrodeposited nickel‐cobalt‐iron alloys. Also, to compare the electrodeposition of ternary nickel‐cobalt‐iron alloy from acidic sulfate bath onto a steel substrate with the characteristics of Co‐Fe electrodeposits.Design/methodology/approachThe investigation of electrodeposition was carried out using cyclic voltammetry and galvanostatic techniques, while potentiodynamic polarization resistance and anodic linear sweep voltammetry techniques were used for corrosion study. The phase structure was characterized by means of X‐ray diffraction analysis. The surface morphology and chemical composition of the deposits were examined by using scanning electron microscopy and atomic absorption spectroscopy, respectively.FindingsThe obtained results revealed that the Ni‐Co‐Fe alloys consisted of a mixture of iron (Fe10.8Ni) and (FeCo) phases. It was found that the obtained Ni‐Co‐Fe alloy exhibited a more‐preferred surface appearance and better corrosion resistance, compared to the Co‐Fe alloy that was electrodeposited under similar conditions.Practical implicationsNi‐Co‐Fe alloy was successfully electroplated from a sulfate bath. This alloy showed better anticorrosion properties compared to Co‐Fe deposits. The Ni‐Co‐Fe alloy could be used advantageously in industry, e.g. the automotive industry. The coating also has particular interest due to it is ability to exhibit stable magnetic properties.Originality/valueThe paper evaluates the effect of electrodeposition of the ternary alloy on the corrosion behavior of electroplated steel. To date, there has been little research on this issue. It was found that the presence of Ni could increase the corrosion resistance of steel.
Socio‐emotional support of apprentices during the school‐to‐work transition
Authors: Du Plessis Karin , Corney Tim , Broadbent Robyn , Papadopoulos Theo 
Published: May 2014

PurposeThe aim of the paper is to locate the role of social and emotional support during the school‐to‐work transitions of apprentices, within the Australian vocational education and training context.Design/methodology/approachThe research reported here is based on an independent evaluation of an apprentice suicide prevention and support program. This program has been implemented in rural and regional Australia, and findings highlight the program's retention of key messages in the long‐term (i.e. 6 months to 2 years post‐completion). The work is based on both quantitative questionnaires from 119 apprentices as well as 18 face‐to‐face interviews.FindingsThe research showed that apprentices’ resilience to face school‐to‐work transitional challenges can be enhanced by increasing knowledge of suicide risk factors and sources of social and emotional support had increased. Findings indicate that a number of apprentices had made significant changes in their lives as a result of participating in the program. While 10 per cent of apprentices identify as “socially isolated”, it was encouraging to note that peer support, as a result of the program, can be considered an informal referral point to formal help‐provision and support.Research limitations/implicationsWhile the program has been successfully applied to building and construction industry apprentices, there is overlap in school‐to‐work transition issues of other types of apprenticeships/traineeships; this merits consideration of wider application of apprentice support programs within the Australian vocational education sector.Originality/valueThis paper draws together a focus on school‐to‐work vulnerabilities and social‐emotional support (similar to that found in youth development programs) as it can be applied to the vocational education and training sector.
Robots for space exploration
Authors: Bogue Robert 
Published: May 2014

PurposeThis paper aims to provide a technical description of the robots that have been deployed in space, primarily on the Moon and Mars.Design/methodology/approachFollowing an introduction, this paper describes the robotic devices that have been deployed on the Moon and Mars. It also considers the latest Mars robot mission, the humanoid robot recently deployed on the International Space Station and robotic developments for use during proposed future planetary missions. It concludes with a brief consideration of the impact of space robots on terrestrial robotic technology.FindingsThe paper shows that robots have been developed which can withstand the hostile environment of space. They have made a significant contribution to lunar and Martian science and some of the technology has had an impact on terrestrial robots.Originality/valueThis paper provides a technical insight into the robots that have operated on the surfaces of the Moon and Mars.
RFID tag localization by using adaptive neuro‐fuzzy inference for mobile robot applications
Authors: Cicirelli Grazia , Milella Annalisa , Di Paola Donato 
Published: May 2014

PurposeThe purpose of this paper is to address the use of passive RFID technology for the development of an autonomous surveillance robot. Passive RFID tags can be used for labelling both valued objects and goal‐positions that the robot has to reach in order to inspect the surroundings. In addition, the robot can use RFID tags for navigational purposes, such as to keep track of its pose in the environment. Automatic tag position estimation is, therefore, a fundamental task in this context.Design/methodology/approachThe paper proposes a supervised fuzzy inference system to learn the RFID sensor model; Then the obtained model is used by the tag localization algorithm. Each tag position is estimated as the most likely among a set of candidate locations.FindingsThe paper proves the feasibility of RFID technology in a mobile robotics context. The development of a RFID sensor model is first required in order to provide a functional relationship between the spatial attitude of the device and its responses. Then, the RFID device provided with this model can be successfully integrated in mobile robotics applications such as navigation, mapping and surveillance, just to mention a few.Originality/valueThe paper presents a novel approach to RFID sensor modelling using adaptive neuro‐fuzzy inference. The model uses both Received Signal Strength Indication (RSSI) and tag detection event in order to achieve better accuracy. In addition, a method for global tag localization is proposed. Experimental results prove the robustness and reliability of the proposed approach.
Formulation and procedure to treat a discrete particle model as a continuum
Authors: del Olmo D. , Serrano A. 
Published: May 2014

PurposeThe purpose of this paper is to continue the path opened by previous researches that focused on the stress and deformation behaviour of discrete particle models, along with mechanical and morphological analyses.Design/methodology/approachThis work presents a formulation that allows the study of discrete particle models as if they were continuum. By knowing forces, torques, displacements and rotations that occur inside a particle media whenever a force is loading it, this formulation permits to obtain the stress, the torque, strain and rotation tensors of the media.FindingsThese tensors are equivalent to the ones that would have been obtained by treating a discrete media as if it were a continuum. In addition, a procedure to apply the formulas to a numerical model has been detailed in the text. Finally, these formulas are compared to the one obtained from an energy balance approach to establish a connection between the forces and the increase of the energy produced inside the media.Originality/valueThis paper presents a proposal of formulation to calculate the stress, torque, deformation and curvature tensor for discrete particle medias, welded or non‐welded, in order to study them as if they were continuous.