bluuebunny/crossref_metadata_2025 huggingface dataset:
Intraspecies Competition in Serratia marcescens Is Mediated by Type VI-Secreted Rhs Effectors and a Conserved Effector-Associated Accessory Protein
Authors: Alcoforado Diniz Juliana , Coulthurst Sarah J.
Published: May 2015

The type VI secretion system (T6SS) is widespread in Gram-negative bacteria and can deliver toxic effector proteins into eukaryotic cells or competitor bacteria. Antibacterial T6SSs are increasingly recognized as key mediators of interbacterial competition and may contribute to the outcome of many polymicrobial infections. Multiple antibacterial effectors can be delivered by these systems, with diverse activities against target cells and distinct modes of secretion. Polymorphic toxins containing Rhs repeat domains represent a recently identified and as-yet poorly characterized class of T6SS-dependent effectors. Previous work had revealed that the potent antibacterial T6SS of the opportunistic pathogen
Serratia marcescens
promotes intraspecies as well as interspecies competition (S. L. Murdoch, K. Trunk, G. English, M. J. Fritsch, E. Pourkarimi, and S. J. Coulthurst, J Bacteriol 193:6057–6069, 2011,
http://dx.doi.org/10.1128/JB.05671-11
). In this study, two new Rhs family antibacterial effectors delivered by this T6SS have been identified. One of these was shown to act as a DNase toxin, while the other contains a novel, cytoplasmic-acting toxin domain. Importantly, using
S. marcescens
, it has been demonstrated for the first time that Rhs proteins, rather than other T6SS-secreted effectors, can be the primary determinant of intraspecies competition. Furthermore, a new family of accessory proteins associated with T6SS effectors has been identified, exemplified by
S. marcescens
EagR1, which is specifically required for deployment of its associated Rhs effector. Together, these findings provide new insight into how bacteria can use the T6SS to deploy Rhs-family effectors and mediate different types of interbacterial interactions.

IMPORTANCE
Infectious diseases caused by bacterial pathogens represent a continuing threat to health and economic prosperity. To counter this threat, we must understand how such organisms survive and prosper. The type VI secretion system is a weapon that many pathogens deploy to compete against rival bacterial cells by injecting multiple antibacterial toxins into them. The ability to compete is vital considering that bacteria generally live in mixed communities. We aimed to identify new toxins and understand their deployment and role in interbacterial competition. We describe two new type VI secretion system-delivered toxins of the Rhs class, demonstrate that this class can play a primary role in competition between closely related bacteria, and identify a new accessory factor needed for their delivery.
Replication Restart after Replication-Transcription Conflicts Requires RecA in Bacillus subtilis
Authors: Million-Weaver Samuel , Samadpour Ariana Nakta , Merrikh Houra
Published: May 2015

Efficient duplication of genomes depends on reactivation of replication forks outside the origin. Replication restart can be facilitated by recombination proteins, especially if single- or double-strand breaks form in the DNA. Each type of DNA break is processed by a distinct pathway, though both depend on the RecA protein. One common obstacle that can stall forks, potentially leading to breaks in the DNA, is transcription. Though replication stalling by transcription is prevalent, the nature of DNA breaks and the prerequisites for replication restart in response to these encounters remain unknown. Here, we used an engineered site-specific replication-transcription conflict to identify and dissect the pathways required for the resolution and restart of replication forks stalled by transcription in
Bacillus subtilis
. We found that RecA, its loader proteins RecO and AddAB, and the Holliday junction resolvase RecU are required for efficient survival and replication restart after conflicts with transcription. Genetic analyses showed that RecO and AddAB act in parallel to facilitate RecA loading at the site of the conflict but that they can each partially compensate for the other's absence. Finally, we found that RecA and either RecO or AddAB are required for the replication restart and helicase loader protein, DnaD, to associate with the engineered conflict region. These results suggest that conflicts can lead to both single-strand gaps and double-strand breaks in the DNA and that RecA loading and Holliday junction resolution are required for replication restart at regions of replication-transcription conflicts.

IMPORTANCE
Head-on conflicts between replication and transcription occur when a gene is expressed from the lagging strand. These encounters stall the replisome and potentially break the DNA. We investigated the necessary mechanisms for
Bacillus subtilis
cells to overcome a site-specific engineered conflict with transcription of a protein-coding gene. We found that the recombination proteins RecO and AddAB both load RecA onto the DNA in response to the head-on conflict. Additionally, RecA loading by one of the two pathways was required for both replication restart and efficient survival of the collision. Our findings suggest that both single-strand gaps and double-strand DNA breaks occur at head-on conflict regions and demonstrate a requirement for recombination to restart replication after collisions with transcription.
Conflict escalation in paediatric services: findings from a qualitative study
Authors: Forbat Liz , Teuten Bea , Barclay Sarah
Published: May 2015

Objective

To explore clinician and family experiences of conflict in paediatric services, in order to map the trajectory of conflict escalation.

Design

Qualitative interview study, employing extreme-case sampling. Interviews were analysed using an iterative thematic approach to identify common themes regarding the experience and escalation of conflict.

Participants

Thirty-eight health professionals and eight parents. All participants had direct experience of conflict, including physical assault and court proceedings, at the interface of acute and palliative care.

Setting

Two teaching hospitals, one district general hospital and two paediatric hospices in England, in 2011.

Results

Conflicts escalate in a predictable manner. Clearly identifiable behaviours by both clinicians and parents are defined as mild, moderate and severe. Mild describes features like the insensitive use of language and a history of unresolved conflict. Moderate involves a deterioration of trust, and a breakdown of communication and relationships. Severe marks disintegration of working relationships, characterised by behavioural changes including aggression, and a shift in focus from the child's best interests to the conflict itself. Though conflicts may remain at one level, those which escalated tended to move sequentially from one level to the next.

Conclusions

Understanding how conflicts escalate provides clinicians with a practical, evidence-based framework to identify the warning signs of conflict in paediatrics.
Muscle metabolism changes with age and maturation: How do they relate to youth sport performance?
Authors: Armstrong Neil , Barker Alan R , McManus Alison M
Published: May 2015

Aim

To provide an evidence-based review of muscle metabolism changes with sex-, age- and maturation with reference to the development of youth sport performance.

Methods

A narrative review of data from both invasive and non-invasive studies, from 1970 to 2015, founded on personal databases supported with computer searches of PubMed and Google Scholar.

Results

Youth sport performance is underpinned by sex-, age- and maturation-related changes in muscle metabolism. Investigations of muscle size, structure and metabolism; substrate utilisation; pulmonary oxygen uptake kinetics; muscle phosphocreatine kinetics; peak anaerobic and aerobic performance; and fatigue resistance; determined using a range of conventional and emerging techniques present a consistent picture. Age-related changes have been consistently documented but specific and independent maturation-related effects on muscle metabolism during exercise have proved elusive to establish. Children are better equipped for exercise supported primarily by oxidative metabolism than by anaerobic metabolism. Sexual dimorphism is apparent in several physiological variables underpinning youth sport performance. As young people mature there is a progressive but asynchronous transition into an adult metabolic profile.

Conclusions

The application of recent developments in technology to the laboratory study of the exercising child and adolescent has both supplemented existing knowledge and provided novel insights into developmental exercise physiology. A sound foundation of laboratory-based knowledge has been established but the lack of rigorously designed child-specific and sport-specific testing environments has clouded the interpretation of the data in real life situations. The primary challenge remains the translation of laboratory research into the optimisation of youth sports participation and performance.
Anti-VEGF therapies in the treatment of choroidal neovascularisation secondary to non-age-related macular degeneration: a systematic review
Authors: Stuart Arabella , Ford John A , Duckworth Susan , Jones Colin , Pereira Augustine
Published: May 2015

Objectives

The aim of this study is to systematically review the evidence for anti-vascular endothelial growth factor (VEGF) therapy in choroidal neovascularisation secondary to conditions other than age-related macular degeneration.

Data sources

MEDLINE, MEDLINE in-process, EMBASE and CENTRAL databases and conference abstracts were searched (from inception to Jan 2014).

Study eligibility criteria, participants and interventions

Randomised and non-randomised comparative studies with follow-up of at least 6 months were included and were used to assess clinical effectiveness.

Study appraisal and synthesis method

Risk of bias was assessed using the Cochrane risk of bias tool and modified Newcastle-Ottawa Scale. Meta-analysis was not possible due to methodological heterogeneity.

Results

16 studies met the inclusion criteria (1091 eyes; 963 pathological myopia, 74 other conditions). There was large variation in risk of bias across studies. An improvement in best-corrected visual acuity in anti-VEGF arms over comparators was reported in all studies. The proportion of patients improving by at least 15 letters in anti-VEGF arms ranged from 27.3% to 70%. There were no significant differences between bevacizumab and ranibizumab.

Limitations

Owing to the rarity of choroidal neovascularisation secondary to conditions other than age-related macular degeneration or pathological myopia, there are unlikely to ever be sufficiently powered trials in these populations.

Conclusions

Bevacizumab and ranibizumab appear to be effective in improving visual acuity for patients with choroidal neovascularisation secondary to conditions other than age-related macular degeneration. The evidence base is strongest for choroidal neovascularisation secondary to pathological myopia, however, based on current evidence and likely pharmacological pathways, clinicians should consider treatment with either bevacizumab or ranibizumab for rarer causes.
The feasibility of using manual segmentation in a multifeature computer-aided diagnosis system for classification of skin lesions: a retrospective comparative study
Authors: Chang Wen-Yu , Huang Adam , Chen Yin-Chun , Lin Chi-Wei , Tsai John , Yang Chung-Kai , Huang Yin-Tseng , Wu Yi-Fan , Chen Gwo-Shing
Published: May 2015

Objectives

To investigate the feasibility of manual segmentation by users of different backgrounds in a previously developed multifeature computer-aided diagnosis (CADx) system to classify melanocytic and non-melanocytic skin lesions based on conventional digital photographic images.

Methods

In total, 347 conventional photographs of melanocytic and non-melanocytic skin lesions were retrospectively reviewed, and manually segmented by two groups of physicians, dermatologists and general practitioners, as well as by an automated segmentation software program, JSEG. The performance of CADx based on inputs from these two groups of physicians and that of the JSEG program was compared using feature agreement analysis.

Results

The estimated area under the receiver operating characteristic curve for classification of benign or malignant skin lesions based were comparable on individual segmentation by the gold standard (0.893, 95% CI 0.856 to 0.930), dermatologists (0.886, 95% CI 0.863 to 0.908), general practitioners (0.883, 95% CI 0.864 to 0.903) and JSEG (0.856, 95% CI 0.812 to 0.899). The agreement in the malignancy probability scores among the physicians was excellent (intraclass correlation coefficient: 0.91). By selecting an optimal cut-off value of malignancy probability score, the sensitivity and specificity were 80.07% and 81.47% for dermatologists and 79.90% and 80.20% for general practitioners.

Conclusions

This study suggests that manual segmentation by general practitioners is feasible in the described CADx system for classifying benign and malignant skin lesions.
Validation of the MD Anderson Symptom Inventory—Head-and-Neck—Filipino (MDASI—HN—F): clinical utility of symptom screening among patients with head-and-neck cancer
Authors: Bacorro Warren R , Sy Ortin Teresa T , Suarez Consuelo G , Mendoza Tito R , Que Jocelyn C
Published: May 2015

Context

Symptom burden and quality of life (QOL) are of particular importance in head-and-neck cancer treatment. The MD Anderson Symptom Inventory—Head-and-Neck (MDASI-HN) is a simple symptom assessment tool practicable for patient follow-up, but a validated Filipino translation was previously unavailable.

Objectives

The objectives of this study were to develop a valid Filipino translation of the MDASI-HN, to test the sensitivity of the validated MDASI core-F, and to report the prevalence and pattern of head-and-neck symptoms in our cohort.

Methods

An MDASI-HN-Filipino (MDASI-HN-F) version was developed and examined for convergent validity, internal consistency, test-retest reliability, known-group validity and sensitivity to change. Eligible participants were aged 18–80 years, with histopathologically-proven head-and-neck (except thyroid) cancer, able to understand and read English and Filipino, and without cognitive impairment or other conditions precluding self-administration of the questionnaire.

Results

Participants (n=100) were aged 18–76 years; the majority were aged <60, male, married, had college schooling, or were from a Tagalog-speaking region. The validity of the MDASI HN-F was demonstrated in all parameters. Age or educational attainment did not affect convergent validity or test-retest reliability. At baseline, 48% had multiple moderate/severe symptoms and 38% had at least one severe symptom.

Conclusions

The MDASI-HN-F is valid, reliable and sensitive. The sensitivity of the MDASI core-F is demonstrated, and its validity and reliability reaffirmed. Moderate and severe head-and-neck symptoms are prevalent in early-stage and advanced-stage head-and-neck cancers, reflecting the utility of symptom screening for improvement of symptom management, QOL and compliance to treatment.
A multisource feedback tool to assess ward round leadership skills of senior paediatric trainees: (1) Development of tool
Authors: Lakshminarayana Indumathy , Wall David , Bindal Taruna , Goodyear Helen M
Published: May 2015

Background

Leading a ward round is an essential skill for hospital consultants and senior trainees but is rarely assessed during training.

Objectives

To investigate the key attributes for ward round leadership and to use these results to develop a multisource feedback (MSF) tool to assess the ward round leadership skills of senior specialist trainees.

Methods

A panel of experts comprising four senior paediatric consultants and two nurse managers were interviewed from May to August 2009. From analysis of the interview transcripts, 10 key themes emerged. A structured questionnaire based on the key themes was designed and sent electronically to paediatric consultants, nurses and trainees at a large university hospital (June–October 2010).

Results

81 consultants, nurses and trainees responded to the survey. The internal consistency of this tool was high (Cronbach's α 0.95). Factor analysis showed that five factors accounted for 72% of variance. The five key areas for ward round leadership were communication skills, preparation and organisation, teaching and enthusiasm, team working and punctuality; communication was the most important key theme. A MSF tool for ward round leadership skills was developed with these areas as five domains.

Conclusions

We believe that this tool will add to the current assessment tools available by providing feedback about ward round leadership skills.
Anti-inflammatory effects of PGE2 in the lung: role of the EP4 receptor subtype
Authors: Birrell Mark A , Maher Sarah A , Dekkak Bilel , Jones Victoria , Wong Sissie , Brook Peter , Belvisi Maria G
Published: May 2015

Background

Asthma and chronic obstructive pulmonary disease (COPD) are chronic inflammatory diseases of the airway. Current treatment options (long acting β-adrenoceptor agonists and glucocorticosteroids) are not optimal as they are only effective in certain patient groups and safety concerns exist regarding both compound classes. Therefore, novel bronchodilator and anti-inflammatory strategies are being pursued. Prostaglandin E2 (PGE2) is an arachidonic acid-derived eicosanoid produced by the lung which acts on four different G-protein coupled receptors (EP1–4) to cause an array of beneficial and deleterious effects. The aim of this study was to identify the EP receptor mediating the anti-inflammatory actions of PGE2 in the lung using a range of cell-based assays and in vivo models.

Methods and results

It was demonstrated in three distinct model systems (innate stimulus, lipopolysaccharide (LPS); allergic response, ovalbumin (OVA); inhaled pollutant, cigarette smoke) that mice missing functional EP4 (Ptger4−/−) receptors had higher levels of airway inflammation, suggesting that endogenous PGE2 was suppressing inflammation via EP4 receptor activation. Cell-based assay systems (murine and human monocytes/alveolar macrophages) demonstrated that PGE2 inhibited cytokine release from LPS-stimulated cells and that this was mimicked by an EP4 (but not EP1–3) receptor agonist and inhibited by an EP4 receptor antagonist. The anti-inflammatory effect occurred at the transcriptional level and was via the adenylyl cyclase/cAMP/ cAMP-dependent protein kinase (PKA) axis.

Conclusion

This study demonstrates that EP4 receptor activation is responsible for the anti-inflammatory activity of PGE2 in a range of disease relevant models and, as such, could represent a novel therapeutic target for chronic airway inflammatory conditions.
Determination of the tensile strength of unsaturated tailings using bending tests
Authors: Narvaez Bibiana , Aubertin Michel , Saleh-Mbemba Faustin
Published: May 2015

Bending tests were conducted on specimens of unsaturated tailings from three hard rock mines to evaluate their tensile strength. Saturated samples were prepared at an initial water content, w0, of 40% and then naturally dried under ambient conditions to pre-selected degrees of saturation, Sr, which can be related to the corresponding suction using the water retention curve. The basic interpretation of the bending tests results is based on an elastic–brittle behavior. The results show how the tensile strength, σt, of unsaturated tailings varies with water content, w (and Sr). The experimental data are also used to evaluate Young’s modulus in tension, Et, and to estimate the apparent cohesion, capp, as a function of Sr. Predictive equations are also applied to estimate the values of σtof unsaturated tailings using the water retention curve.
Renormalized vacuum polarization of rotating black holes
Authors: Ferreira Hugo R. C.
Published: May 2015

Quantum field theory on rotating black hole spacetimes is plagued with technical difficulties. Here, we describe a general method to renormalize and compute the vacuum polarization of a quantum field in the Hartle–Hawking state on rotating black holes. We exemplify the technique with a massive scalar field on the warped AdS3 black hole solution to topologically massive gravity, a deformation of (2 + 1)-dimensional Einstein gravity. We use a "quasi-Euclidean" technique, which generalizes the Euclidean techniques used for static spacetimes, and we subtract the divergences by matching to a sum over mode solutions on Minkowski spacetime. This allows us, for the first time, to have a general method to compute the renormalized vacuum polarization, for a given quantum state, on a rotating black hole, such as the physically relevant case of the Kerr black hole in four dimensions.
Particle creation in global de Sitter space: Bulk space consideration
Authors: Tanhayi M. Reza
Published: May 2015

Recently in [P. R. Anderson and E. Mottola, Phys. Rev. D 89 (2014) 104039, arXiv:1310.1963 [gr-qc] and P. R. Anderson and E. Mottola, Phys. Rev. D 89 (2014) 104038, arXiv:1310.0030 [gr-qc].], it was shown that global de Sitter space is unstable even to the massive particle creation with no self-interactions. In this paper, we study the instability by making use of the coordinate-independent plane wave in de Sitter space. Within this formalism, we show that the previous results of instability of de Sitter space due to the particle creation can be generalized to higher-spin fields in a straightforward way. The so-called plane wave is defined globally in de Sitter space and de Sitter invariance is manifest since such modes are deduced from the group theoretical point of view by means of the Casimir operators. In fact, we employ the symmetry of embedding space namely the 4 + 1-dimensional flat space to write the field equations and the solutions can be obtained in terms of the plane wave in embedding space.
Method Application in New Product Development and the Impact on Product Success
Authors: Graner Marc , Mißler-Behr Magdalena
Published: May 2015

The purpose of this paper is to analyze the use of methods in new product development and their impact on product success. Based on a large sample totaling 410 development projects, we show which methods are used with the greatest frequency. For each method, we also highlight the differences in application between particularly successful and unsuccessful product development projects. Additionally, we identify methods whose adoption correlates strongly with the success of the developed product. Further, we examine which combinations of methods promise to deliver the most successful outcomes, thus showing how the success rates for new products can be improved systematically.
Belief Dynamics and Biases in Web Search
Authors: White Ryen W. , Horvitz Eric
Published: May 2015

We investigate how beliefs about the efficacy of medical interventions are influenced by searchers' exposure to information on retrieved Web pages. We present a methodology for measuring participants' beliefs and confidence about the efficacy of treatment before, during, and after search episodes. We consider interventions studied in the Cochrane collection of meta-analyses. We extract related queries from search engine logs and consider the Cochrane assessments as ground truth. We analyze the dynamics of belief over time and show the influence of prior beliefs and confidence at the end of sessions. We present evidence for confirmation bias and for anchoring-and-adjustment during search and retrieval. Then, we build predictive models to estimate postsearch beliefs using sets of features about behavior and content. The findings provide insights about the influence of Web content on the beliefs of people and have implications for the design of search systems.
Impact of Diabetes Status and Medication on Presentation, Treatment, and Outcome of Stage II Colon Cancer Patients
Authors: Bae Susie , Wong Hui-Li , Tie Jeanne , Desai Jayesh , Field Kathryn , Kosmider Suzanne , Fourlanos Spiros , Jones Ian , Skinner Iain , Gibbs Peter
Published: May 2015

Diabetes is a risk factor for colorectal cancer and several reports suggest worse cancer-specific outcomes in diabetes patients. Recent studies in multiple tumour types indicate metformin may positively impact on cancer-specific and overall survival. A population-based series of stage II colorectal cancer patients treated and followed from 2000 to 2013 were analysed for baseline characteristics, treatment, and outcomes. 1116 patients with stage II colon cancer were identified, 55.5% were male and median age was 70.9 years (range 20.5–101.2). The diabetes patients (21.6%,n= 241) were older than nondiabetes patients (median 74.0 versus 69.6,p= 0.0001). There was no impact of diabetes on cancer presentation or pathology. Diabetes patients were less likely to receive adjuvant treatment (13.7 versus 24.8%,p= 0.002) but were equally likely to complete treatment (69.7 versus 67.7%,p= 1.00). Diabetes did not significantly impact cancer recurrence (HR = 1.07, 95% CI 0.71–1.63) or overall survival (HR = 1.23, 95% CI 0.88–1.72), adjusted for age. Diabetes medication did not impact cancer recurrence or survival. Cancer presentation and outcomes in diabetes patients are comparable to those of nondiabetes patients in those with stage II colon cancer. The effect of metformin merits further evaluation in patients with colon cancer.
Assessing Apoptosis Gene Expression Profiling with a PCR Array in the Hippocampus of Ts65Dn Mice
Authors: Yu Bin , Zhang Bin , Zhou Wen-bo , Wang Qiu-wei , Yuan Pei , Yang Yu-qi , Kong Jing
Published: May 2015

It is well known that Down syndrome (DS) is a condition in which extra genetic material causes delays in the way a child develops, both mentally and physically. Intellectual disability is the foremost and most debilitating trait, which caused loss of cognitive abilities and the development of early onset Alzheimer’s disease (AD). Ts65Dn mice were used in this study. We isolated the hippocampus. First, we used transmission scanning electron microscopy to directly observe the hippocampus and confirm if apoptosis had occurred. Second, we customized a PCR array with 53 genes, including several important genes related to cell apoptosis. Gene expression was detected by RT-PCR. There were varying degrees of changes characteristic of apoptosis in the hippocampus of Ts65Dn mice, which mainly included the following: nuclear membrane thinning, unevenly distributed chromosomes, the production of chromatin crescents, and pyknosis of the nuclei with some nuclear fragmentation. Meanwhile, three genes (API5, AIFM1, and NFκB1) showed changes of expression in the hippocampus of Ts65Dn mice compared with normal mice. Only NFκB1 expression was significantly increased, while the expressions of API5 and AIFM1 were notably decreased. The fold changes in the expression of API5, AIFM1, and NFκB1 were 11.55, 5.94, and 3.11, respectively. However, some well-known genes related to cell apoptosis, such as the caspase family, Bcl-2, Bad, Bid, Fas, and TNF, did not show changes in expression levels. The genes we found which were differentially expressed in the hippocampus of Ts65Dn mice may be closely related to cell apoptosis. PCR array technology can assist in the screening and identification of genes involved in apoptosis.
Synthesis of PAMAM Dendrimers Loaded with Mycophenolic Acid to Be Studied as New Potential Immunosuppressants
Authors: Guazzelli Lorenzo , D’Andrea Felicia , Giorgelli Francesco , Catelani Giorgio , Panattoni Alessandra , Luvisi Andrea
Published: May 2015

The terminalN-Boc protected diamino PAMAM7was condensed (EDC-DMAP) with two units of mycophenolic acid (MPA) giving theN-Boc protected dendron8in a good yield (76%). The ammonium trifluoroacetate9was prepared from8by acid treatment (TFA-THF-H2O) and was split into two equal parts. The first half was treated with di-2-pyridyl thionocarbonate (DPT) in the presence of Et3N to give the corresponding isothiocyanate10. This was reacted with the second half of9providing the symmetrical dendrimer11(68% yield), exposing four MPA units around the thioureido-PAMAM core.
Log-Spiral Keypoint: A Robust Approach toward Image Patch Matching
Authors: Paek Kangho , Yao Min , Liu Zhongwei , Kim Hun
Published: May 2015

Matching of keypoints across image patches forms the basis of computer vision applications, such as object detection, recognition, and tracking in real-world images. Most of keypoint methods are mainly used to match the high-resolution images, which always utilize an image pyramid for multiscale keypoint detection. In this paper, we propose a novel keypoint method to improve the matching performance of image patches with the low-resolution and small size. The location, scale, and orientation of keypoints are directly estimated from an original image patch using a Log-Spiral sampling pattern for keypoint detection without consideration of image pyramid. A Log-Spiral sampling pattern for keypoint description and two bit-generated functions are designed for generating a binary descriptor. Extensive experiments show that the proposed method is more effective and robust than existing binary-based methods for image patch matching.
Modeling and Simulation Based on the Hybrid System of Leasing Equipment Optimal Allocation
Authors: Tian Ying , Zhong Wei-qing
Published: May 2015

Modeling of the hybrid system of leasing equipment optimal allocation and its optimal control methods are put forward based on the hybrid characteristics of succession and dispersion. After studying equipment unit’s hybrid automata model (the hybrid and basic structure), the hybrid system facing manufacture demand can be considered as the synthesis of some hybrid and basic structures, which efficiently avoid combination explosion of models due to the increase of systematic scale. On this basis, we study the hybrid and optimal control methods that meet the demand for some equipment and achieve the usage rate maximization. Following that, calculating methods of performance optimization and simulation are put forward based on the first- and second-order subsection linear model. At last, we also have made the numerical simulating calculation on the equipment’s optimal matching of some leasing company.
Diagnostic Accuracy Comparison of Artificial Immune Algorithms for Primary Headaches
Authors: Çelik Ufuk , Yurtay Nilüfer , Koç Emine Rabia , Tepe Nermin , Güllüoğlu Halil , Ertaş Mustafa
Published: May 2015

The present study evaluated the diagnostic accuracy of immune system algorithms with the aim of classifying the primary types of headache that are not related to any organic etiology. They are divided into four types: migraine, tension, cluster, and other primary headaches. After we took this main objective into consideration, three different neurologists were required to fill in the medical records of 850 patients into our web-based expert system hosted on our project web site. In the evaluation process, Artificial Immune Systems (AIS) were used as the classification algorithms. The AIS are classification algorithms that are inspired by the biological immune system mechanism that involves significant and distinct capabilities. These algorithms simulate the specialties of the immune system such as discrimination, learning, and the memorizing process in order to be used for classification, optimization, or pattern recognition. According to the results, the accuracy level of the classifier used in this study reached a success continuum ranging from 95% to 99%, except for the inconvenient one that yielded 71% accuracy.
Highlight on the Mathematical Modeling of Controlled Free Radical Polymerization
Authors: Al-Harthi Mamdouh A.
Published: May 2015

Over the last quarter century, controlled free radical polymerization (CFRP) has received great attention by the researchers of polymer science and engineering. In addition to the experimental studies, many publications in the literature dealt with the modeling of CFRP processes. A review of acknowledged and well-received researches on mathematical modeling in the area of CFRP is presented in this work. Three main categories of CFRP (namely, ATRP, RAFT, and NMP) are taken into consideration in the review. The different techniques used in modeling CFRP processes are also enumerated with more emphasis on Monte Carlo simulation and the method of moments. The review provides a better understanding of the processes and the recent efforts to model CFRP.
Comparison of Adsorption Capability of Activated Carbon and Metal Doped TiO2 for Geosmin and 2‐MIB Removal from Water
Authors: Asghar Aisha , Khan Zahiruddin , Maqbool Nida , Qazi Ishtiaq A. , Awan Muhammad Ali
Published: May 2015

This study stemmed from consumer complaints about earthy and musty off‐flavours in treated water of Rawal Lake Filtration Plant. In recent years, several novel adsorbents have been developed from nanomaterials for enhancing the contaminant removal efficiency. This paper presents preparation and the use of new adsorbents Pt doped titania and Fe doped titania, for the adsorption capacity of Geosmin and 2‐MIB from water under laboratory conditions and their comparison, with most widely used activated carbon, under batch and column experiments. Stock solutions were prepared by using Geosmin and 2‐MIB standards, procured by Sigma Aldrich (England). Samples were analysed using SPME‐GC‐FID. The adsorption of Geosmin and 2‐MIB on GAC conformed to the Freundlich isotherm, while that of adsorption on metal doped titania fit equally well to both Langmuir and Freundlich isotherms. Moreover, data, generated for the kinetic isotherm, confirmed that Geosmin and 2‐MIB removal is a function of contact time. Breakthrough column tests using 125 mg/L Pt doped titania nanoparticles, coated on glass beads against 700 ng/L of off‐flavours, attained later breakthrough and exhaustion points and removed 98% of Geosmin and 97% of 2‐MIB at room temperature. All columns could be regenerated using 50 mL 0.1 molar sodium hydroxide.
Influence of NaCl-Induced Salinity and Cd Toxicity on Respiration Activity and Cd Availability to Barley Plants in Farmyard Manure-Amended Soil
Authors: Usman Adel R. A.
Published: May 2015

The objective of this study was to evaluate the Cd availability and toxicity as affected by NaCl-induced salinity and farmyard manure addition. The Cd availability and toxicity were investigated in greenhouse pot and incubation experiments were conducted on a calcareous loamy sand soil contaminated with Cd (0.5, 1.5, 3, 6, 12, and 24 mg kg−1of soil) and amended with two rates of 0.0 and 30 g farmyard manure (FYM) kg−1. Barley seeds (Hordeum vulgareL.) were sown in pots and irrigated with water containing different levels of salinity (0, 30, 60, and 120 mM NaCl). The results revealed that the DTPA-extractable Cd and its content in barley plant shoots tended to increase in line as Cd was applied and salt levels increased. Elevated decreases in the soil basal respiration with increased Cd applied and NaCl-induced salinity were found. However, applying FYM significantly reduced Cd availability and increased plant growth and soil respiration activity. The results clearly showed that adding farmyard manure as soil organic amendment decreased the availability of Cd to barley plants and mitigated the toxicity of both Cd and salinity to soil microbial activity.
Piecewise Model and Parameter Obtainment of Governor Actuator in Turbine
Authors: Zhao Jie , Wang Li , Liu Dichen , Wang Jun
Published: May 2015

The governor actuators in some heat-engine plants have nonlinear valves. This nonlinearity of valves may lead to the inaccuracy of the opening and closing time constants calculated based on the whole segment fully open and fully close experimental test curves of the valve. An improved mathematical model of the turbine governor actuator is proposed to reflect the nonlinearity of the valve, in which the main and auxiliary piecewise opening and closing time constants instead of the fixed oil motive opening and closing time constants are adopted to describe the characteristics of the actuator. The main opening and closing time constants are obtained from the linear segments of the whole fully open and close curves. The parameters of proportional integral derivative (PID) controller are identified based on the small disturbance experimental tests of the valve. Then the auxiliary opening and closing time constants and the piecewise opening and closing valve points are determined by the fully open/close experimental tests. Several testing functions are selected to compare genetic algorithm and particle swarm optimization algorithm (GA-PSO) with other basic intelligence algorithms. The effectiveness of the piecewise linear model and its parameters are validated by practical power plant case studies.
A New Paradigm in Cardiac Regeneration: The Mesenchymal Stem Cell Secretome
Authors: Gallina Clara , Turinetto Valentina , Giachino Claudia
Published: May 2015

The potentialities to apply mesenchymal stem cells (MSCs) in regenerative medicine have been extensively studied over the last decades. In the cardiovascular disease (CVD) field, MSCs-based therapy is the subject of great expectations. Its therapeutic potential has been already shown in several preclinical models and both the safety and efficacy of MSCs-based therapy are being evaluated in humans. It is now clear that the predominant mechanism by which MSCs participate in heart tissue repair is through a paracrine activity. Via the production of a multitude of trophic factors endowed with different properties, MSCs can reduce tissue injury, protect tissue from further adverse effects, and enhance tissue repair. The present review discusses the current understanding of the MSCs secretome as a therapy for treatment of CVD. We provide insights into the possible employment of the MSCs secretome and their released extracellular vesicles as novel approaches for cardiac regeneration that would have certain advantages over injection of living cells.
High Accuracy GPS-Free Vehicle Localization Framework via an INS-Assisted Single RSU
Authors: Khattab Ahmed , Fahmy Yasmine A. , Abdel Wahab Ahmed
Published: May 2015

Collision avoidance and road safety applications require highly accurate vehicle localization techniques. Unfortunately, the existing localization techniques are not suitable for road safety applications as they rely on the error-prone Global Positioning System (GPS). Likewise, cooperative localization techniques that use intervehicle communications experience high errors due to hidden vehicles and the limited sensing/communication range. Recently, GPS-free localization based on vehicle communication with a low cost infrastructure installed on the roadsides has emerged as a more accurate alternative. However, existing techniques require the vehicle to communicate with two roadside units (RSUs) in order to achieve high localization accuracy. In contrast, this paper presents a GPS-free localization framework that uses two-way time of arrival to locate the vehicles based on communication with a single RSU. Furthermore, our framework uses the vehicle kinematics information obtained via the vehicle's onboard inertial navigation system (INS) to further improve the accuracy of the vehicle location using Kalman filters. Our results show that the localization error of the proposed framework is as low as 1.8 meters. The resulting localization accuracy is up to 65% and 47.5% better than GPS-based techniques used without/with INS, respectively. This accuracy gain becomes around 73.3% when compared to existing RSU-based techniques.
Risk Factors and Scoring System for Predicting Bacterial Resistance to Cefepime as Used Empirically in Haematology Wards
Authors: El Maaroufi Hicham , Goubard Agathe , Redjoul Rabah , Legrand Patrick , Pautas Cécile , Mikdame Mohamed , Doghmi Kamal , Toma Andréa , Maury Sébastien , Schwarzinger Michael , Cordonnier Catherine
Published: May 2015

Objectives. Bacterial resistance is of growing concern in haematology wards. As the inappropriate administration of empirical antibacterial may alter survival, we studied risk factors for resistance to our usual empirical first-line antibacterial therapy, cefepime.Methods. We retrospectively studied 103 first episodes of bacteraemia recorded in our haematology department over 2.5 years. Risk factors for cefepime-resistance were identified by multivariate logistic regression with backward selection (P<0.05). A scoring system for predicting cefepime-resistance was built on independent factor, with an internal validation by the bootstrap resampling technique.Results. 38 (37%) episodes were due to Gram-negative bacteria. Fifty (49%) were due to bacteria resistant to cefepime. Cefepime resistance was significantly associated with a decreased survival at day 30 (P<0.05). Three risk factors were independently associated with cefepime-resistance: acute lymphoblastic leukaemia; ≥18 days since hospital admission; and receipt of anyβ-lactam in the last month. Patients with ≥2 of these risk factors had a probability of 86% (CI 95%, 25 to 100%) to carry a cefepime-resistant strain.Conclusion. Using our scoring system should reduce the indication of very broad antibacterial regimens in the empirical, first-line treatment of febrile hematology patients in more than 80% of the cases.
Abstract 3434: Genomic exome DNA sequencing identifies top driver genetic alterations in head and neck cancer cell lines of different HPV status
Authors: Cheng Hui , Yang Xinping , Si Han , Saleh Anthony , Coupar Jamie , Ferris Robert L. , Yarbrough Wendell G. , Prince Mark E. , Carey Thomas E. , Waes Carter Van , Chen Zhong
Published: May 2015

Head and neck squamous cell carcinoma (HNSCC) is among the top cancer types with high frequencies of genetic alterations, including mutation and copy number variation (CNV). The Cancer Genome Atlas (TCGA) has characterized 279 HNSCC tumors to provide a landscape of comprehensive genomic alterations. To identify cell line models which mimic HNSCC subtypes of genetic alterations, we have conducted genome-wide exome DNA sequencing (exome DNA-seq) and whole transcriptome sequencing (RNA-seq) on 16 HPV negative and 8 HPV positive HNSCC lines, in comparison with three normal human oral mucosa lines and 8 matched blood samples. Exome DNA-seq and RNA-seq were performed using an ABI SOLiD sequencer, and the data were analyzed with LifeScope2.5 and an in-house developed computation program. An average of 87X coverage in each cell line was achieved by exome DNA-seq. Deleterious mutations that negatively affect protein function were identified in each cell line using ANNOVAR software, in combination with multiple functional prediction tools, such as SIFT, PolyPhen-2, Likelihood Ratio Test (LRT), MutationTaster and MutationAssessor. The top deleterious mutations include TP53 in 42% of cell lines (56% in HPV- and 13% in HPV+ cell lines), and FAT1 and NOTCH1 mutations in 83% and 42% cell lines, respectively. These mutations are cross-validated through RNA-seq, which has an average of 168 million mapped reads with an estimated mean of 44X coverage per sample. In addition, we identified 261 putative CNV calls using the CoNIFER (copy number inference from exome reads) analysis. Among these putative CNV calls, 12 of them occur inside of the over 30 significant somatic copy number alteration (SCNA) sites identified in TCGA, including amplification of FADD, BIRC2/3, YAP1 and TP63. Our sequencing results identified the HNSCC cell lines with specific genetic alterations, which resemble many defects found from tumor specimens in TCGA project. These cell lines provided experimental models, which are amenable for future investigation of molecular mechanisms and targeted therapy, and could benefit preclinical drug evaluation and provide rationales for future clinical trials with genetic testing.

Supported by NIDCD intramural projects ZIA-DC-000016, 73 and 74.

Citation Format: Hui Cheng, Xinping Yang, Han Si, Anthony Saleh, Jamie Coupar, Robert L. Ferris, Wendell G. Yarbrough, Mark E. Prince, Thomas E. Carey, Carter Van Waes, Zhong Chen. Genomic exome DNA sequencing identifies top driver genetic alterations in head and neck cancer cell lines of different HPV status. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3434. doi:10.1158/1538-7445.AM2014-3434
Abstract 3447: Role of fibroblast growth factor receptors in esophageal squamous cell carcinoma
Authors: Shimada Yutaka , Okumura Tomoyuki , Nagata Takuya , Takei Yoshinori , Tsukada Kazuhiro , Shimizu Kazuharu
Published: May 2015

Introduction:

MicroRNA-210 regulates cancer cell proliferation by targeting fibroblast growth factor receptor-like 1 (FGFRL1) in esophageal squamous cell cancer (ESCC) (JBC 2011). The expression of FGFRL1 has been associated with tumor growth and lymph node metastasis. In the present study, we analyzed and compared the expression of FGFR1, FGFR2, FGFR3, and FGFR4 with that of FGFRL1 using a tissue microarray. We also examined whether antibodies for FGFRL1 inhibited the growth and motility of ESCC cells.

Material and Methods:

A squamous cell carcinoma tissue microarray established in Toyama University was used to evaluate the expression of the 5 FGFRs. Sixty-nine specimens of ESCC were obtained from 62 male and 7 female patients, with an average age of 64.4 years old, that underwent surgery between 1990 and 2008. The TNM stages of these patients were as follows; stage 1: 7, stage 2a; 10, stage 2b; 10, stage 3; 35, stage 4; 7. The immunohistochemical results of these patients were scored according to intensity and distribution after a careful examination by two independent researchers. The ESCC cell line KYSE520 was used for experimental analyses. Polyclonal and monoclonal antibodies for FGFRL1 were used to evaluate the function of FGFRL1.

Results:

The percentage of patients who tested positive for the expression of the different FGFRs was as follows: FGFRL-1, 81% (56/69); FGFR1, 65% (37/57); FGFR2, 36% (22/61); FGFR3, 21% (12/57); FGFR4, 39% (22/56). The prognosis of FGFRL1 positive patients was significantly worse than that of FGFRL1 negative patients. (P=0.0311). Both polyclonal and monoclonal antibodies inhibited the growth (50% reduction) and motility (25% reduction) of ESCC cells. However, no association was observed between the expression of the other FGFRs and patient prognosis. Regarding combination analysis of the expression of each FGFR, patients that co-expressed FGFRL1 and FGFR1 had the worst prognosis, while patients who tested negative for the expression of both FGFRL1 and FGFR4 had the best prognosis.

Conclusions:

Among the 5 FGFRs, the expression of FGFRL1 was the main oncogenic driving factor in ESCC patients. The expression of FGFR1 and FGFR4 may be a sub-driving factor of ESCC.

Citation Format: Yutaka Shimada, Tomoyuki Okumura, Takuya Nagata, Yoshinori Takei, Kazuhiro Tsukada, Kazuharu Shimizu. Role of fibroblast growth factor receptors in esophageal squamous cell carcinoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3447. doi:10.1158/1538-7445.AM2014-3447