bluuebunny/crossref_metadata_2025 huggingface dataset:
The Listeria monocytogenes Hibernation-Promoting Factor Is Required for the Formation of 100S Ribosomes, Optimal Fitness, and Pathogenesis
Authors: Kline Benjamin C. , McKay Susannah L. , Tang William W. , Portnoy Daniel A.
Published: November 2014

During exposure to certain stresses, bacteria dimerize pairs of 70S ribosomes into translationally silent 100S particles in a process called ribosome hibernation. Although the biological roles of ribosome hibernation are not completely understood, this process appears to represent a conserved and adaptive response that contributes to optimal survival during stress and post-exponential-phase growth. Hibernating ribosomes are formed by the activity of one or more highly conserved proteins; gammaproteobacteria produce two relevant proteins, ribosome modulation factor (RMF) and hibernation promoting factor (HPF), while most Gram-positive bacteria produce a single, longer HPF protein. Here, we report the formation of 100S ribosomes by an HPF homolog inListeria monocytogenes.L. monocytogenes100S ribosomes were observed by sucrose density gradient centrifugation of bacterial extracts during mid-logarithmic phase, peaked at the transition to stationary phase, and persisted at lower levels during post-exponential-phase growth. 100S ribosomes were undetectable in bacteria carrying anhpf::Himar1transposon insertion, indicating that HPF is required for ribosome hibernation inL. monocytogenes. Additionally, epitope-tagged HPF cosedimented with 100S ribosomes, supporting its previously described direct role in 100S formation. We examinedhpfmRNA by quantitative PCR (qPCR) and identified several conditions that upregulated its expression, including carbon starvation, heat shock, and exposure to high concentrations of salt or ethanol. Survival of HPF-deficient bacteria was impaired under certain conditions bothin vitroand during animal infection, providing evidence for the biological relevance of 100S ribosome formation.
Identification of Determinants of the Utilisation of Acupuncture Treatment Using Andersen's Behavioural Model
Authors: Lee Ye-Seul , Lee In-Seon , Kim Song-Yi , Lee Hyangsook , Park Hi-Joon , Lee Hyejung , Kim Sung-Hoon , Chae Younbyoung
Published: November 2014

Objectives

The utilisation of healthcare services is the result of a complex decision-making process with different determinants. This study aims to identify the determinants of the utilisation of acupuncture treatment using Andersen's behavioural model and quality of life.

Methods

In this study we reviewed Korean Health Panel data, a nationally representative set of data, and analysed the utilisation of outpatient acupuncture services during 2011. A two-part model, which included predisposing, enabling and need factors of Andersen's behavioural model in model 1 and the additional factor of health-related quality of life (HRQOL, EQ-5D Korean index) in model 2, was analysed by logistic analysis to identify determinants of acupuncture service usage among subjects who visited traditional Korean medical clinics.

Results

The higher frequency of acupuncture service usage among patients who visited traditional Korean medical clinics was associated with gender, age, number of chronic diseases, physical disabilities and HRQOL of the subjects.

Conclusions

This study shows that the important determinants of the frequency of acupuncture treatment utilisation are gender, age, number of chronic diseases and the presence of physical disabilities. Our findings contribute to understanding the characteristics of patients who use acupuncture treatment and may be used as a basic resource for related policy making by government officials and medical professionals.
Left ventricular pseudoaneurysm after myocardial infarction detected by cardiac MRI
Authors: Orsborne Christopher , Schmitt Matthias
Published: November 2014

Left ventricular free wall rupture (LVFWR) is a grave complication of acute myocardial infarction. Acutely, it has an extremely high rate of mortality, especially if undetected. Chronically, there is paucity of data on how to manage the pathology, especially if detected as an incidental finding. We present a unique case of initially undetected LVFWR in a patient who presented with repeated chest pain. Cardiac MRI enabled the diagnosis and localisation of the original site of LVFWR and provided highly relevant volume calculations. Measurement of both absolute and virtual volumes indicated that aneurysm resection, including the original site of rupture, was surgically feasible without reducing postoperative stroke volume.
Oral ketamine analgesia in chronic pain and problematic rise in blood pressure
Authors: van Hecke Oliver , Guthrie Bruce
Published: November 2014

Hospitals and specialists in the UK are increasingly prescribing and dispensing off-license drugs such as ketamine which are not routinely included in the prescribing record of the general practitioner (GP). We present the case of a 67-year-old woman who developed an episode of uncontrolled raised blood pressure (BP) (224/124 mm Hg) following hospital introduction of oral ketamine for chronic pain. This raised BP was not followed up, and she was then found to be persistently hypertensive in the community some months later. No obvious cause for the patient's increase in BP could be identified. Only on reduction of the ketamine dose and introduction of additional antihypertensive medication, did her BP normalise. We postulate that long-term ketamine use may have been associated with this unexpected and persistent rise in BP. Clinicians should monitor BP closely during ketamine therapy and be wary of new hypertension associated with its long-term use. Further research is needed on the long-term effects of ketamine on BP.
A systematic review of associations between environmental exposures and development of asthma in children aged up to 9 years
Authors: Dick S , Friend A , Dynes K , AlKandari F , Doust E , Cowie H , Ayres J G , Turner S W
Published: November 2014

Objectives

Childhood asthma is a complex condition where many environmental factors are implicated in causation. The aim of this study was to complete a systematic review of the literature describing associations between environmental exposures and the development of asthma in young children.

Setting

A systematic review of the literature up to November 2013 was conducted using key words agreed by the research team. Abstracts were screened and potentially eligible papers reviewed. Papers describing associations between exposures and exacerbation of pre-existing asthma were not included. Papers were placed into the following predefined categories: secondhand smoke (SHS), inhaled chemicals, damp housing/mould, inhaled allergens, air pollution, domestic combustion, dietary exposures, respiratory virus infection and medications.

Participants

Children aged up to 9 years.

Primary outcomes

Diagnosed asthma and wheeze.

Results

14 691 abstracts were identified, 207 papers reviewed and 135 included in the present review of which 15 were systematic reviews, 6 were meta-analyses and 14 were intervention studies. There was consistent evidence linking exposures to SHS, inhaled chemicals, mould, ambient air pollutants, some deficiencies in maternal diet and respiratory viruses to an increased risk for asthma (OR typically increased by 1.5–2.0). There was less consistent evidence linking exposures to pets, breast feeding and infant dietary exposures to asthma risk, and although there were consistent associations between exposures to antibiotics and paracetamol in early life, these associations might reflect reverse causation. There was good evidence that exposures to house dust mites (in isolation) was not associated with asthma risk. Evidence from observational and intervention studies suggest that interactions between exposures were important to asthma causation, where the effect size was typically 1.5–3.0.

Conclusions

There are many publications reporting associations between environmental exposures and modest changes in risk for asthma in young children, and this review highlights the complex interactions between exposures that further increase risk.
Driven to distraction: a prospective controlled study of a simulated ward round experience to improve patient safety teaching for medical students
Authors: Thomas Ian , Nicol Laura , Regan Luke , Cleland Jennifer , Maliepaard Drieka , Clark Lindsay , Walker Kenneth , Duncan John
Published: November 2014

Background

Distraction and interruption are endemic in the clinical environment and contribute to error. This study assesses whether simulation-based training with targeted feedback can improve undergraduate management of distractions and interruptions to reduce error-making.

Design

A prospective non-randomised controlled study.

Methods

28 final year medical students undertook a simulated baseline ward round. 14 students formed an intervention group and received immediate feedback on distractor management and error. 14 students in a control group received no feedback. After 4 weeks, students participated in a post-intervention ward round of comparable rigour. Changes in medical error and distractor management between simulations were assessed with Mann-Whitney U tests using SPSS V.21.

Results

At baseline, error rates were high. The intervention group committed 72 total baseline errors (mean of 5.1 errors/student; median 5; range 3–7). The control group exhibited a comparable number of errors—with a total of 76 observed (mean of 5.4 errors/student; median 6; range 4–7). Many of these errors were life-threatening. At baseline distractions and interruptions were poorly managed by both groups. All forms of simulation training reduced error-making. In the intervention group the total number of errors post-intervention fell from 72 to 17 (mean 1.2 errors/student; median 1; range 0–3), representing a 76.4% fall (p<0.0001). In the control group the total number of errors also fell—from 76 to 44 (mean of 3.1 errors/student; median 3; range 1–5), representing a 42.1% reduction (p=0.0003).

Conclusions

Medical students are not inherently equipped to manage common ward-based distractions to mitigate error. These skills can be taught—with simulation and feedback conferring the greatest benefit. Curricular integration of simulated ward round experiences is recommended.
Operational biomass recovery of small trees: equations for six central Ontario tree species
Authors: Thiel Matt , Basiliko Nathan , Caspersen John , Fera Jeff , Jones Trevor
Published: November 2014

Accurate estimates of the amount of biomass that can be recovered at the roadside are needed to make informed decisions about whether to implement an increased utilization harvesting system to supply additional bioenergy feedstocks. Current estimates of recovery are based on total aboveground biomass equations that do not always account for the volume lost to the unharvested stumps or to tops and branches broken during forestry operations. The study took place in a white pine (Pinus strobus L.) mixedwood forest at the Petawawa Research Forest in central Ontario. Equations to describe recoverable biomass were developed from 371 cut and skidded trees, which ranged from 3 to 24 cm in diameter at breast height, across six species. For each species and diameter size class, we evaluated the difference between estimates produced by locally developed equations and those from published equations produced for other locations and forest types. Our recovered biomass estimates were generally higher than the Canadian national averages but within the observed range of published values from across North America. We report that small trees are recovered nearly in their entirety, with little breakage and loss during operations. The high degree of variability among estimates produced by the various equations poses one of the biggest challenges in accurately estimating roadside biomass in an operational setting.
New atomic probes for dark matter detection: Axions, axion-like particles and topological defects
Authors: Stadnik Yevgeny V. , Flambaum Victor V.
Published: November 2014

We present a brief overview of recently proposed detection schemes for axion, axion-like pseudoscalar particle and topological defect dark matter. We focus mainly on the possibility of using atomic and molecular systems for dark matter detection. For axions and axion-like particles, these methods are complementary probes to ongoing photon–axion interconversion experiments and astrophysical observations. For topological defects, these methods are complementary to conventional astrophysical search schemes based on gravitational signatures.
Probing for leptophilic gauge boson Zl at ILC with $\sqrt{s} = 1~{\rm TeV}$ by using ANN
Authors: Kara S. Okan , Akkoyun Serkan , Bayram Tuncay
Published: November 2014

We search for leptophilic gauge boson Zl via the process e+e- → μ+μ- at ILC with [Formula: see text]. In the leptonic extension of SM [Formula: see text] we have predicted that ILC with [Formula: see text] will enable searching Zl with masses up to the center-of-mass energy if the related coupling constant gl exceeds 10-3 for 3σ observations and 5σ discovery. Furthermore similar results have been obtained by using artificial neural network (ANN) method.
Spin radiation effects in the BMT model of spinning charge
Authors: Lebedev S. L.
Published: November 2014

The radiation processes emerging as a result of interaction between spin and orbit degrees of freedom of spinning charge are investigated with the use of the Bargmann–Michel–Telegdi (BMT) model. The spin contribution to the self-energy of the ultrarelativistic particle is imaginary and proportional to invariant constructed from the derivatives of the worldline and from the spin. This invariant determines up to negative numerical factor of the QED spin contribution to the imaginary part of the mass shift (MS). Particular cases of crossed, electric and magnetic external fields are considered in detail. The influence of an ideal boundary upon the self-energy of the particle is analyzed for the crossed field case. In the presence of the "mirror" the imaginary part of the MS gets an addition and the nonzero spin dependent real part appears, both however giving the small corrections to no-boundary MS. An alternative method to obtain the spin magnetic moment correction to the power of synchrotron radiation entails in generalization of the result known for the planar motion. Special attention is given to disagreement between classical and quantum pictures of spin radiation.
An inquiry on hindrance to heavy-ion sub-barrier fusion
Authors: Mişicu Şerban
Published: November 2014

Since more than a decade the phenomenon of hindrance to fusion in collisions of heavy-ions at energies much lower than the Coulomb barrier is systematically investigated both experimentally and theoretically. The accumulated data for fusion excitation functions is not confirming a unique trend for the cross-section reduction with decreasing energy. I review shortly the theoretical contribution I did together with my collaborators, aiming to explain this new low-energy phenomenon based on the inclusion of an additional repulsion due to the incompressibility of nuclear matter in the nuclear interaction of two strongly overlapping nuclei. I show that for reactions at extremely low energy, the hindrance to fusion is mainly caused by a thicker Coulomb barrier due to the incompressibility of nuclear matter. A strict association of a maximum in the astrophysical S-factor near the threshold to the onset of hindrance is discarded by our long series of studies on the subject. We succeeded to obtain an excellent agreement to the fusion cross-sections data for a significative number of systems: medium-heavy projectile-target combinations, medium-heavy projectile and medium-light target, medium-light projectile and target, light projectile and heavy target. Fusion reactions relevant for the carbon and oxygen burning cycles in highly evolved stars are also set under scrutiny and we conclude that hindrance is absent in this case.
Quantum inversion with elastic phase shifts to discrete different energies
Authors: Scheid Werner , Apagyi Barnabas
Published: November 2014

We consider the inverse quantum scattering problem with phase shifts of different discrete energies belonging to a real energy-independent radial potential for elastic scattering. The solution of this problem is essential for atomic and nuclear physics. The two procedures investigated are based on the modified Newton–Sabatier method. The first procedure leads to angular-momentum dependent potentials with poles. The second one carries out an inversion at a fixed energy by varying the phase shifts of the other energies and leads finally to the correct energy-independent potential.
DANCING WITH THE PARADOX — SOCIAL MEDIA IN INNOVATION THROUGH COMPLEXITY LENS
Authors: JALONEN HARRI
Published: November 2014

This paper discusses the social media paradox in the context of innovation. Innovation is defined as a knowledge intensive process of seeing and doing things differently, whereas social media refers to new ways of being connected. Social media has revolutionised the ways how knowledge is produced, shared and accumulated through social interactions within the organisation and across the organisation's boundaries. From an organisational perspective, this raises the question of how social media influences — enabling or inhibiting — its ability to see and do things differently. Social media offers tempting opportunities but also poses new threats. It is a paradox involving contradictory forces. Despite growing interest among academics, there is a lack of understanding of the possibilities of social media in the specific context of innovation. This paper fills the research gap by arguing that complexity concepts offer a new type of language to understand social media. Seeing interaction as intrinsic to innovation activity, complexity thinking opens the paradox of being in charge but not in control.
Comparative Immunology of Allergic Responses
Authors: Gershwin Laurel J.
Published: November 2014

Allergic responses occur in humans, rodents, non-human primates, avian species, and all of the domestic animals. These responses are mediated by immunoglobulin E (IgE) antibodies that bind to mast cells and cause release/synthesis of potent mediators. Clinical syndromes include naturally occurring asthma in humans and cats; atopic dermatitis in humans, dogs, horses, and several other species; food allergies; and anaphylactic shock. Experimental induction of asthma in mice, rats, monkeys, sheep, and cats has helped to reveal mechanisms of pathogenesis of asthma in humans. All of these species share the ability to develop a rapid and often fatal response to systemic administration of an allergen—anaphylactic shock. Genetic predisposition to development of allergic disease (atopy) has been demonstrated in humans, dogs, and horses. Application of mouse models of IgE-mediated allergic asthma has provided evidence for a role of air pollutants (ozone, diesel exhaust, environmental tobacco smoke) in enhanced sensitization to allergens.
Signaling to Actin Stochastic Dynamics
Authors: Li Jiejie , Blanchoin Laurent , Staiger Christopher J.
Published: November 2014

Advances in microscopy techniques applied to living cells have dramatically transformed our view of the actin cytoskeleton as a framework for cellular processes. Conventional fluorescence imaging and static analyses are useful for quantifying cellular architecture and the network of filaments that support vesicle trafficking, organelle movement, and response to biotic stress. However, new imaging techniques have revealed remarkably dynamic features of individual actin filaments and the mechanisms that underpin their construction and turnover. In this review, we briefly summarize knowledge about actin and actin-binding proteins in plant systems. We focus on the quantitative properties of the turnover of individual actin filaments, highlight actin-binding proteins that participate in actin dynamics, and summarize the current genetic evidence that has been used to dissect specific aspects of the stochastic dynamics model. Finally, we describe some signaling pathways in which recent data implicate changes in actin filament dynamics and the associated cytoplasmic responses.
Economic Value of Biological Control in Integrated Pest Management of Managed Plant Systems
Authors: Naranjo Steven E. , Ellsworth Peter C. , Frisvold George B.
Published: November 2014

Biological control is an underlying pillar of integrated pest management, yet little focus has been placed on assigning economic value to this key ecosystem service. Setting biological control on a firm economic foundation would help to broaden its utility and adoption for sustainable crop protection. Here we discuss approaches and methods available for valuation of biological control of arthropod pests by arthropod natural enemies and summarize economic evaluations in classical, augmentative, and conservation biological control. Emphasis is placed on valuation of conservation biological control, which has received little attention. We identify some of the challenges of and opportunities for applying economics to biological control to advance integrated pest management. Interaction among diverse scientists and stakeholders will be required to measure the direct and indirect costs and benefits of biological control that will allow farmers and others to internalize the benefits that incentivize and accelerate adoption for private and public good.
Antimicrobial Food Equipment Coatings: Applications and Challenges
Authors: Bastarrachea Luis J. , Denis-Rohr Anna , Goddard Julie M.
Published: November 2014

Emerging technologies in antimicrobial coatings can help improve the quality and safety of our food supply. The goal of this review is to survey the major classes of antimicrobial agents explored for use in coatings and to describe the principles behind coating processes. Technologies from a range of fields, including biomedical and textiles research, as well as current applications in food contact materials, are addressed, and the technical hurdles that must be overcome to enable commercial adaptation to food processing equipment are critically evaluated.
Colloids in Food: Ingredients, Structure, and Stability
Authors: Dickinson Eric
Published: November 2014

This article reviews progress in the field of food colloids with particular emphasis on advances in novel functional ingredients and nanoscale structuring. Specific aspects of ingredient development described here are the stabilization of bubbles and foams by the protein hydrophobin, the emulsifying characteristics of Maillard-type protein–polysaccharide conjugates, the structural and functional properties of protein fibrils, and the Pickering stabilization of dispersed droplets by food-grade nanoparticles and microparticles. Building on advances in the nanoscience of biological materials, the application of structural design principles to the fabrication of edible colloids is leading to progress in the fabrication of functional dispersed systems—multilayer interfaces, multiple emulsions, and gel-like emulsions. The associated physicochemical insight is contributing to our mechanistic understanding of oral processing and textural perception of food systems and to the development of colloid-based strategies to control delivery of nutrients during food digestion within the human gastrointestinal tract.
Archaeal DNA Replication
Authors: Kelman Lori M. , Kelman Zvi
Published: November 2014

DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed.
Cellular and Molecular Mechanisms of Single and Collective Cell Migrations in Drosophila: Themes and Variations
Authors: Pocha Shirin M. , Montell Denise J.
Published: November 2014

The process of cell migration is essential throughout life, driving embryonic morphogenesis and ensuring homeostasis in adults. Defects in cell migration are a major cause of human disease, with excessive migration causing autoimmune diseases and cancer metastasis, whereas reduced capacity for migration leads to birth defects and immunodeficiencies. Myriad studies in vitro have established a consensus view that cell migrations require cell polarization, Rho GTPase–mediated cytoskeletal rearrangements, and myosin-mediated contractility. However, in vivo studies later revealed a more complex picture, including the discovery that cells migrate not only as single units but also as clusters, strands, and sheets. In particular, the role of E-Cadherin in cell motility appears to be more complex than previously appreciated. Here, we discuss recent advances achieved by combining the plethora of genetic tools available to the Drosophila geneticist with live imaging and biophysical techniques. Finally, we discuss the emerging themes such studies have revealed and ponder the puzzles that remain to be solved.
Impact of the Obesity Epidemic on Cancer
Authors: Goodwin Pamela J. , Stambolic Vuk
Published: November 2014

There is growing appreciation that the current obesity epidemic is associated with increases in cancer incidence at a population level and may lead to poor cancer outcomes; concurrent decreases in cancer mortality at a population level may represent a paradox, i.e., they may also reflect improvements in the diagnosis and treatment of cancer that mask obesity effects. An association of obesity with cancer is biologically plausible because adipose tissue is biologically active, secreting estrogens, adipokines, and cytokines. In obesity, adipose tissue reprogramming may lead to insulin resistance, with or without diabetes, and it may contribute to cancer growth and progression locally or through systemic effects. Obesity-associated changes impact cancer in a complex fashion, potentially acting directly on cells through pathways, such as the phosphoinositide 3-kinase (PI3K) and Janus kinase–signal transducer and activator of transcription (JAK-STAT) pathways, or indirectly via changes in the tumor microenvironment. Approaches to obesity management are discussed, and the potential for pharmacologic interventions that target the obesity–cancer link is addressed.
Emerging Technologies for Point-of-Care Management of HIV Infection
Authors: Shafiee Hadi , Wang ShuQi , Inci Fatih , Toy Mehlika , Henrich Timothy J. , Kuritzkes Daniel R. , Demirci Utkan
Published: November 2014

The global HIV/AIDS pandemic has resulted in 39 million deaths to date, and there are currently more than 35 million people living with HIV worldwide. Prevention, screening, and treatment strategies have led to major progress in addressing this disease globally. Diagnostics is critical for HIV prevention, screening and disease staging, and monitoring antiretroviral therapy (ART). Currently available diagnostic assays, which include polymerase chain reaction (PCR), enzyme-linked immunosorbent assay (ELISA), and western blot (WB), are complex, expensive, and time consuming. These diagnostic technologies are ill suited for use in low- and middle-income countries, where the challenge of the HIV/AIDS pandemic is most severe. Therefore, innovative, inexpensive, disposable, and rapid diagnostic platform technologies are urgently needed. In this review, we discuss challenges associated with HIV management in resource-constrained settings and review the state-of-the-art HIV diagnostic technologies for CD4+ T lymphocyte count, viral load measurement, and drug resistance testing.
The Inflammasomes and Autoinflammatory Syndromes
Authors: Broderick Lori , De Nardo Dominic , Franklin Bernardo S. , Hoffman Hal M. , Latz Eicke
Published: November 2014

Inflammation, a vital response of the immune system to infection and damage to tissues, can be initiated by various germline-encoded innate immune-signaling receptors. Among these, the inflammasomes are critical for activation of the potent proinflammatory interleukin-1 cytokine family. Additionally, inflammasomes can trigger and maintain inflammatory responses aimed toward excess nutrients and the numerous danger signals that appear in a variety of chronic inflammatory diseases. We discuss our understanding of how inflammasomes assemble to trigger caspase-1 activation and subsequent cytokine release, describe how genetic mutations in inflammasome-related genes lead to autoinflammatory syndromes, and review the contribution of inflammasome activation to various pathologies arising from metabolic dysfunction. Insights into the mechanisms that govern inflammasome activation will help in the development of novel therapeutic strategies, not only for managing genetic diseases associated with overactive inflammasomes, but also for treating common metabolic diseases for which effective therapies are currently lacking.
Birth and Pathogenesis of Rogue Respiratory Viruses
Authors: Safronetz David , Feldmann Heinz , de Wit Emmie
Published: November 2014

Emerging infectious diseases of zoonotic origin are shaping today's infectious disease field more than ever. In this article, we introduce and review three emerging zoonotic viruses. Novel hantaviruses emerged in the Americas in the mid-1990s as the cause of severe respiratory infections, designated hantavirus pulmonary syndrome, with case fatality rates of around 40%. Nipah virus emerged a few years later, causing respiratory infections and encephalitis in Southeast Asia, with case fatality rates ranging from 40% to more than 90%. A new coronavirus emerged in 2012 on the Arabian Peninsula with a clinical syndrome of acute respiratory infections, later designated as Middle East respiratory syndrome (MERS), and an initial case fatality rate of more than 40%. Our current state of knowledge on the pathogenicity of these three severe, emerging viral infections is discussed.
Identifying Predictive Features in Drug Response Using Machine Learning: Opportunities and Challenges
Authors: Vidyasagar Mathukumalli
Published: November 2014

This article reviews several techniques from machine learning that can be used to study the problem of identifying a small number of features, from among tens of thousands of measured features, that can accurately predict a drug response. Prediction problems are divided into two categories: sparse classification and sparse regression. In classification, the clinical parameter to be predicted is binary, whereas in regression, the parameter is a real number. Well-known methods for both classes of problems are briefly discussed. These include the SVM (support vector machine) for classification and various algorithms such as ridge regression, LASSO (least absolute shrinkage and selection operator), and EN (elastic net) for regression. In addition, several well-established methods that do not directly fall into machine learning theory are also reviewed, including neural networks, PAM (pattern analysis for microarrays), SAM (significance analysis for microarrays), GSEA (gene set enrichment analysis), and k-means clustering. Several references indicative of the application of these methods to cancer biology are discussed.
Crystal Structure and Prediction
Authors: Thakur Tejender S. , Dubey Ritesh , Desiraju Gautam R.
Published: November 2014

The notion of structure is central to the subject of chemistry. This review traces the development of the idea of crystal structure since the time when a crystal structure could be determined from a three-dimensional diffraction pattern and assesses the feasibility of computationally predicting an unknown crystal structure of a given molecule. Crystal structure prediction is of considerable fundamental and applied importance, and its successful execution is by no means a solved problem. The ease of crystal structure determination today has resulted in the availability of large numbers of crystal structures of higher-energy polymorphs and pseudopolymorphs. These structural libraries lead to the concept of a crystal structure landscape. A crystal structure of a compound may accordingly be taken as a data point in such a landscape.
Reaction Dynamics in Astrochemistry: Low-Temperature Pathways to Polycyclic Aromatic Hydrocarbons in the Interstellar Medium
Authors: Kaiser Ralf I. , Parker Dorian S.N. , Mebel Alexander M.
Published: November 2014

Bimolecular reactions of phenyl-type radicals with the C4 and C5 hydrocarbons vinylacetylene and (methyl-substituted) 1,3-butadiene have been found to synthesize polycyclic aromatic hydrocarbons (PAHs) with naphthalene and 1,4-dihydronaphthalene cores in exoergic and entrance barrierless reactions under single-collision conditions. The reaction mechanism involves the initial formation of a van der Waals complex and addition of a phenyl-type radical to the C1 position of a vinyl-type group through a submerged barrier. Investigations suggest that in the hydrocarbon reactant, the vinyl-type group must be in conjugation with a –C≡CH or –HC=CH2 group to form a resonantly stabilized free radical intermediate, which eventually isomerizes to a cyclic intermediate followed by hydrogen loss and aromatization (PAH formation). The vinylacetylene-mediated formation of PAHs might be expanded to more complex PAHs, such as anthracene and phenanthrene, in cold molecular clouds via barrierless reactions involving phenyl-type radicals, such as naphthyl, which cannot be accounted for by the classical hydrogen abstraction–acetylene addition mechanism.
Polymorphisms in Glutathione S-Transferase M1, T1, and P1 in Patients with Chronic Periodontitis: A Pilot Study
Authors: Camargo Ortega Victor Raul , Bravo López Leliette Deyanira , Visoso Salgado Angel , Mejia Sanchez Fernando , Castillo Cadena Julieta
Published: November 2014

Background. Although the direct cause of chronic periodontitis is bacterial infection, the progression of this disease depends on genetic and environmental factors, and smoking is a known risk factor in the development and severity of the disease. An individual’s susceptibility may be influenced by polymorphisms in the glutathione S-transferase genes. These genes encode enzymes that metabolize xenobiotic compounds. The aim of this study was to determine the frequency of GSTM1, GSTT1, and GSTP1 polymorphisms in Mexicans with chronic periodontitis. Methods. 60 Mexicans with chronic periodontitis (30 smokers and 30 nonsmokers) were studied. A peripheral blood sample was taken for subsequent DNA extraction. The genetic material was PCR-amplified followed by restriction fragment length polymorphism with the aim of identifying GST polymorphisms. Results. Polymorphisms in the GSTT1 and GSTP1 genes were not significantly different between the smokers and nonsmokers. However, there were significant differences (P=0.05) between groups in polymorphisms in the GSTM1 gene. The patients with chronic periodontitis have a higher frequency of null and mutant polymorphisms in GSTM1, GSTT1, and GSTP1 compared with historical data from a healthy Mexican population. Conclusions. The presence of these polymorphisms may be a risk factor for the development of chronic periodontitis.
Temperature Effect on Mechanical Properties and Damage Identification of Concrete Structure
Authors: Jiao Yubo , Liu Hanbing , Wang Xianqiang , Zhang Yuwei , Luo Guobao , Gong Yafeng
Published: November 2014

Static and dynamic mechanical properties of concrete are affected by temperature effect in practice. Therefore, it is necessary to investigate the corresponding influence law and mechanism. This paper demonstrates the variation of mechanical properties of concrete at temperatures from −20°C to 60°C. Temperature effects on cube compressive strength, splitting tensile strength, prism compressive strength, modulus of elasticity, and frequency are conducted and discussed. The results indicate that static mechanical properties such as compressive strength (cube and prism), splitting tensile strength, and modulus of elasticity have highly linear negative correlation with temperature; this law is also applied to the first order frequency of concrete slab. The coupling effect of temperature and damage on change rate of frequency reveals that temperature effect cannot be ignored in damage identification of structure. Mechanism analysis shows that variation of elastic modulus of concrete caused by temperature is the primary reason for the change of frequency.
Production Scheduling of Open Pit Mines Using Particle Swarm Optimization Algorithm
Authors: Khan Asif , Niemann-Delius Christian
Published: November 2014

Determining an optimum long term production schedule is an important part of the planning process of any open pit mine; however, the associated optimization problem is demanding and hard to deal with, as it involves large datasets and multiple hard and soft constraints which makes it a large combinatorial optimization problem. In this paper a procedure has been proposed to apply a relatively new and computationally less expensive metaheuristic technique known as particle swarm optimization (PSO) algorithm to this computationally challenging problem of the open pit mines. The performance of different variants of the PSO algorithm has been studied and the results are presented.
Enhanced Photocatalytic Performance of NiO-Decorated ZnO Nanowhiskers for Methylene Blue Degradation
Authors: Abdul Rahman I. , Ayob M. T. M. , Radiman S.
Published: November 2014

ZnO nanowhiskers were used for photodecomposition of methylene blue in aqueous solution under UV irradiation. The rate of methylene blue degradation increased linearly with time of UV irradiation. 54% of degradation rate was observed when the ZnO nanowhiskers were used as photocatalysts for methylene blue degradation for 80 min under UV irradiation. The decoration of p-type NiO nanoparticles on n-type ZnO nanowhiskers significantly enhanced photocatalytic activity and reached 72% degradation rate of methylene blue by using the same method. NiO-decorated ZnO was recycled for second test and shows 66% degradation from maximal peak of methylene blue within the same period. The increment of photocatalytic activity of NiO-decorated ZnO nanowhiskers was explained by the extension of the electron depletion layer due to the formation of nanoscale p-n junctions between p-type NiO and n-type ZnO. Hence, these products provide new alternative proficient photocatalysts for wastewater treatment.
Potential Lung Nodules Identification for Characterization by Variable Multistep Threshold and Shape Indices from CT Images
Authors: Iqbal Saleem , Iqbal Khalid , Arif Fahim , Shaukat Arslan , Khanum Aasia
Published: November 2014

Computed tomography (CT) is an important imaging modality. Physicians, surgeons, and oncologists prefer CT scan for diagnosis of lung cancer. However, some nodules are missed in CT scan. Computer aided diagnosis methods are useful for radiologists for detection of these nodules and early diagnosis of lung cancer. Early detection of malignant nodule is helpful for treatment. Computer aided diagnosis of lung cancer involves lung segmentation, potential nodules identification, features extraction from the potential nodules, and classification of the nodules. In this paper, we are presenting an automatic method for detection and segmentation of lung nodules from CT scan for subsequent features extraction and classification. Contribution of the work is the detection and segmentation of small sized nodules, low and high contrast nodules, nodules attached with vasculature, nodules attached to pleura membrane, and nodules in close vicinity of the diaphragm and lung wall in one-go. The particular techniques of the method are multistep threshold for the nodule detection and shape index threshold for false positive reduction. We used 60 CT scans of “Lung Image Database Consortium-Image Database Resource Initiative” taken by GE medical systems LightSpeed16 scanner as dataset and correctly detected 92% nodules. The results are reproducible.
A Decomposition Model for HPLC-DAD Data Set and Its Solution by Particle Swarm Optimization
Authors: Cui Lizhi , Ling Zhihao , Poon Josiah , Poon Simon K. , Gao Junbin , Kwan Paul
Published: November 2014

This paper proposes a separation method, based on the model of Generalized Reference Curve Measurement and the algorithm of Particle Swarm Optimization (GRCM-PSO), for the High Performance Liquid Chromatography with Diode Array Detection (HPLC-DAD) data set. Firstly, initial parameters are generated to construct reference curves for the chromatogram peaks of the compounds based on its physical principle. Then, a General Reference Curve Measurement (GRCM) model is designed to transform these parameters to scalar values, which indicate the fitness for all parameters. Thirdly, rough solutions are found by searching individual target for every parameter, and reinitialization only around these rough solutions is executed. Then, the Particle Swarm Optimization (PSO) algorithm is adopted to obtain the optimal parameters by minimizing the fitness of these new parameters given by the GRCM model. Finally, spectra for the compounds are estimated based on the optimal parameters and the HPLC-DAD data set. Through simulations and experiments, following conclusions are drawn: (1) the GRCM-PSO method can separate the chromatogram peaks and spectra from the HPLC-DAD data set without knowing the number of the compounds in advance even when severe overlap and white noise exist; (2) the GRCM-PSO method is able to handle the real HPLC-DAD data set.
Subclinical Ketosis on Dairy Cows in Transition Period in Farms with Contrasting Butyric Acid Contents in Silages
Authors: Vicente Fernando , Rodríguez María Luisa , Martínez-Fernández Adela , Soldado Ana , Argamentería Alejandro , Peláez Mario , de la Roza-Delgado Begoña
Published: November 2014

This study examines the relationship between subclinical ketosis (SCK) in dairy cows and the butyric acid content of the silage used in their feeding. Twenty commercial farms were monitored over a period of 12 months. The feed at each farm and the silages used in its ration were sampled monthly for proximal analysis and for volatile fatty acid analysis. A total of 2857 urine samples were taken from 1112 cows to examine the ketonuria from about 30 days prepartum to 100 postpartum. Wide variation was recorded in the quality of silages used in the preparation of diets. Approximately 80% of the urine samples analyzed had no detectable ketone bodies, 16% returned values indicative of slight SCK, and the remainder, 4%, showed symptoms of ketosis. Most of the cases of hyperkenuria were associated with the butyric acid content of the silage used (r2=0.56;P<0.05). As the metabolizable energy content of the feed was similar, no relationship was observed between the proportion of cows with SCK and the energy content of the feed. In our study, the probability of dairy cows suffering SCK is higher when they are eating feed made from silage with a high butyric acid content (35.2 g/kg DM intake).
Robot Trajectories Comparison: A Statistical Approach
Authors: Ansuategui A. , Arruti A. , Susperregi L. , Yurramendi Y. , Jauregi E. , Lazkano E. , Sierra B.
Published: November 2014

The task of planning a collision-free trajectory from a start to a goal position is fundamental for an autonomous mobile robot. Although path planning has been extensively investigated since the beginning of robotics, there is no agreement on how to measure the performance of a motion algorithm. This paper presents a new approach to perform robot trajectories comparison that could be applied to any kind of trajectories and in both simulated and real environments. Given an initial set of features, it automatically selects the most significant ones and performs a statistical comparison using them. Additionally, a graphical data visualization named polygraph which helps to better understand the obtained results is provided. The proposed method has been applied, as an example, to compare two different motion planners,FM2and WaveFront, using different environments, robots, and local planners.
Compliance of Healthcare Workers with Hand Hygiene Practices in Neonatal and Pediatric Intensive Care Units: Overt Observation
Authors: Karaaslan Ayşe , Kepenekli Kadayifci Eda , Atıcı Serkan , Sili Uluhan , Soysal Ahmet , Çulha Gülcan , Pekru Yasemin , Bakır Mustafa
Published: November 2014

Background.The objective of this study was to assess the compliance of hand hygiene (HH) of healthcare workers (HCWs) in the neonatal and pediatric intensive care unit in a tertiary university hospital in Istanbul.Methods.An observational study was conducted on the compliance of HH for the five World Health Organization (WHO) indications. HCWs were observed during routine patient care in day shift. The authors also measured the technique of HH through hand washing or hand hygiene with alcohol-based disinfectant.Results.A total of 704 HH opportunities were identified during the observation period. Overall compliance was 37.0% (261/704). Compliance differed by role: nurses (41.4%) and doctors (31.9%) [P=0.02, OR: 1.504, CI 95%: 1.058–2.137]. HCWs were more likely to use soap and water (63.6%) compared to waterless-alcohol-based hand hygiene (36.3%) [P<0.05].Conclusion.Adherence to hand hygiene practice and use of alcohol-based disinfectant was found to be very low. Effective education programs that improve adherence to hand hygiene and use of disinfectants may be helpful to increase compliance.
A Novel Complementary Method for the Point-Scan Nondestructive Tests Based on Lamb Waves
Authors: Gorgin Rahim , Wu Zhanjun , Zheng Yuebin
Published: November 2014

This study presents a novel area-scan damage identification method based on Lamb waves which can be used as a complementary method for point-scan nondestructive techniques. The proposed technique is able to identify the most probable locations of damages prior to point-scan test which lead to decreasing the time and cost of inspection. The test-piece surface was partitioned with some smaller areas and the damage probability presence of each area was evaluated.A0mode of Lamb wave was generated and collected using a mobile handmade transducer set at each area. Subsequently, a damage presence probability index (DPPI) based on the energy of captured responses was defined for each area. The area with the highest DPPI value highlights the most probable locations of damages in test-piece. Point-scan nondestructive methods can then be used once these areas are found to identify the damage in detail. The approach was validated by predicting the most probable locations of representative damages including through-thickness hole and crack in aluminum plates. The obtained experimental results demonstrated the high potential of developed method in defining the most probable locations of damages in structures.
Influence of Grain Size and Texture on the Yield Strength of Mg Alloys Processed by Severe Plastic Deformation
Authors: Lin Jinbao , Ren Weijie , Wang Qudong , Ma Lifeng , Chen Yongjun
Published: November 2014

Severe plastic deformation (SPD) has been widely employed to refine the grain size of Mg alloys, with the main objective to improve the strength and ductility of Mg alloys, since the well-known Hall-Petch equation suggests that a decreased grain size leads to an increased yield strength. However, the yield strength of Mg alloys processed by SPD is often decreased even though the grain size is effectively reduced. The abnormal flow behavior in Mg alloys processed by SPD has attracted great attention although this mechanism is still unclear, due to its complex and extensive influence factors. In this paper, the relationships between the processing conditions, grain refinement, and mechanical properties of the SPD treated Mg alloys are reviewed, with the emphasis on the effects of grain size and texture on the yield strength.