bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of Stochastic Delay Predator-Prey System with Impulsive Toxicant Input in Polluted Environments
Authors: Liu Meng
Published: October 2013

A stochastic delay predator-prey model in a polluted environment with impulsive toxicant input is proposed and studied. The thresholds between stability in time average and extinction of each population are obtained. Some recent results are extended and improved greatly. Several simulation figures are introduced to support the conclusions.
Optical Coherence Tomography Noise Reduction Using Anisotropic Local Bivariate Gaussian Mixture Prior in 3D Complex Wavelet Domain
Authors: Rabbani Hossein , Sonka Milan , Abramoff Michael D.
Published: October 2013

In this paper, MMSE estimator is employed for noise-free 3D OCT data recovery in 3D complex wavelet domain. Since the proposed distribution for noise-free data plays a key role in the performance of MMSE estimator, a priori distribution for the pdf of noise-free 3D complex wavelet coefficients is proposed which is able to model the main statistical properties of wavelets. We model the coefficients with a mixture of two bivariate Gaussian pdfs with local parameters which are able to capture the heavy-tailed property and inter- and intrascale dependencies of coefficients. In addition, based on the special structure of OCT images, we use an anisotropic windowing procedure for local parameters estimation that results in visual quality improvement. On this base, several OCT despeckling algorithms are obtained based on using Gaussian/two-sided Rayleigh noise distribution and homomorphic/nonhomomorphic model. In order to evaluate the performance of the proposed algorithm, we use 156 selected ROIs from 650 × 512 × 128 OCT dataset in the presence of wet AMD pathology. Our simulations show that the best MMSE estimator using local bivariate mixture prior is for the nonhomomorphic model in the presence of Gaussian noise which results in an improvement of 7.8 ± 1.7 in CNR.
Two-Layer Predictive Control of a Continuous Biodiesel Transesterification Reactor
Authors: Shi Hongyan , Wang Dingding , Yuan Decheng , Wang Tianran
Published: October 2013

A novel two-layer predictive control scheme for a continuous biodiesel transesterification reactor is presented. Based on a validated mechanistic model, the least squares (LS) algorithm is used to identify the finite step response (FSR) process model adapted in the controller. The two-layer predictive control method achieves the steady-state optimal setpoints and resolves the multivariable dynamic control problems synchronously. Simulation results show that the two-layer predictive control strategy leads to a significant improvement of control performance in terms of the optimal set-points tracking and disturbances rejection, as compared to conventional PID controller within a multiloop framework.
Interaction of Normal and Sickle Hemoglobins for Sodium Dodecylsulphate and Hydrogen Peroxide at pH 5.0 and 7.2
Authors: Ezebuo Fortunatus C. , Eze Sabinus Oscar O. , Lukong Colin B. , Chilaka Ferdinand C.
Published: October 2013

Clinical manifestations of malaria primarily result from proliferation of the parasite within the hosts’ erythrocytes. The malaria parasite digests hemoglobin within its digestive vacuole through a sequential metabolic process involving multiple proteases. The activities of these proteases could lead to the production of ROS which could lead to the death of the parasites due to the destruction of their membrane. The action of SDS on hemoglobins can be likened to the way malarial proteases destabilizes host hemoglobin. Hence, the study was designed to determine the binding parameters of SDS and H2O2 for normal, sickle trait carrier and sickle hemoglobins at pH 5.0 and 7.2 using UV-VIS Titration Spectrophotometry. Hb-SDS interactions were significantly different at pH 5.0 but were not at pH 7.2. Also, Hb-H2O2 interactions were statistically different at pH 5.0 and 7.2. The interactions suggest that HbA and HbS are easily destabilized than HbAS and that HbAS has more affinity for H2O2. These suggest a production of more ferryl intermediates or hydroxyl radicals. All these interactions may hinder the development of the malaria parasite at the intraerythrocytic stage and could likely account for a significant proportion of the mechanism that favours the resistance to malaria by individuals with HbAS.
Ethnic Background and Overweight among 5-Year-Old Children: The “Be Active, Eat Right” Study
Authors: Veldhuis Lydian , van Dooremaal Mara , Kroeze Willemieke , Renders Carry M. , HiraSing Remy A. , Raat Hein
Published: October 2013

Introduction. This study investigates the association between ethnic background and overweight (obesity included) among 5 year olds. Methods. We used baseline data from 5 year olds (n=7801) and their parents collected for the “Be active, eat right” study. A child was considered to be of non-Dutch ethnic background when at least one of the parents was born abroad. Odds ratios (ORs) were adjusted for sociodemographic characteristics. Results. Compared to children of Dutch ethnic background, for children with a Moroccan ethnic background the OR for being overweight (obesity included) was 2.27 (95% CI 1.48–3.47), for Turkish children the OR was 3.63 (95% confidence interval (CI) 2.46–5.35), for Antillean children the OR was 1.97 (95% CI 1.01–3.86), and for Surinamese children the OR was 0.47 (95% CI 0.20–1.06). Addition of parental overweight decreased the ORs for Moroccan and Turkish children by 10.2% and 12.5%, and addition of watching TV and having breakfast by the child decreased the ORs by 7.9% and 12.2%. Conclusion. Already at a young age, children of Moroccan and Turkish ethnic background are at increased risk for being overweight compared to Dutch children. Parental overweight, watching TV, and not having breakfast by the child are contributing factors in this association.
Modeling and Analysis of Bifurcation in a Delayed Worm Propagation Model
Authors: Yao Yu , Zhang Nan , Xiang Wenlong , Yu Ge , Gao Fuxiang
Published: October 2013

A delayed worm propagation model with birth and death rates is formulated. The stability of the positive equilibrium is studied. Through theoretical analysis, a critical valueτ0of Hopf bifurcation is derived. The worm propagation system is locally asymptotically stable when time delay is less thanτ0. However, Hopf bifurcation appears when time delayτpasses the thresholdτ0, which means that the worm propagation system is unstable and out of control. Consequently, time delay should be adjusted to be less thanτ0to ensure the stability of the system stable and better prediction of the scale and speed of Internet worm spreading. Finally, numerical and simulation experiments are presented to simulate the system, which fully support our analysis.
New Connections between Old Pathways: PDK1 Signaling Promotes Cellular Transformation through PLK1-Dependent MYC Stabilization
Authors: Cunningham John T. , Ruggero Davide
Published: October 2013

Summary: Limited understanding of the functional link between multiple oncogenic pathways is a major barrier in the ongoing effort of cancer biologists to design an effective therapeutic approach to treat malignancies characterized by driver oncogenic network signals. In this issue of Cancer Discovery, Tan and colleagues elucidate a novel PDK1–PLK1–MYC signaling pathway connecting two fundamental oncogenic programs, phosphoinositide 3-kinase and MYC. They define the functional role for PDK1–PLK1–MYC signaling in cancer cell survival and tumor formation and show the therapeutic benefit of inhibiting PDK1 and PLK1 pharmacologically in cancer, tackling the most undruggable tumors defined by elevated levels of the MYC oncoprotein. Cancer Discov; 3(10); 1099–1102. ©2013 AACR.

See related article by Tan et al., p. 1156
Soluble Concentrations of the Interleukin Receptor Family Member ST2 and β-Blocker Therapy in Chronic Heart Failure
Authors: Gaggin Hanna K. , Motiwala Shweta , Bhardwaj Anju , Parks Kimberly A. , Januzzi James L.
Published: October 2013

Background—

Concentrations of soluble (s)ST2 predict prognosis in heart failure. We recently found changing doses of β-blocker (BB) may affect sST2 concentrations. It remains unclear whether sST2 concentrations identify benefit of BB therapy, however.

Methods and Results—

A total of 151 subjects with heart failure attributable to left ventricular systolic dysfunction were examined in this post hoc analysis; >96% were taking BB at enrollment. Medication regimen and sST2 values were obtained during 10 months. Cardiovascular events were examined as a function of baseline sST2 status (low ≤35 versus high >35 ng/mL) and final achieved BB dose (high ≥50 versus low <50 mg daily equivalent dose of metoprolol succinate). Patients with low sST2 titrated to high-dose BB had the lowest cardiovascular event rate at 0.53 events (
P
=0.001), and lowest cumulative hazard (
P
=0.003). Those with low sST2/low-dose BB, or high sST2/high-dose BB had intermediate outcomes (0.92 and 1.19 events). Patients with high sST2 treated with low-dose BB had the highest cardiovascular event rate (2.08 events) and the highest cumulative hazard. Compared with low sST2/high-dose BB, those with high sST2 treated with low-dose BB had an odds ratio of 6.77 (
P
<0.001) for a cardiovascular event. Patients with low sST2/low-dose BB or high sST2/high-dose BB had intermediate odds ratios for cardiovascular events (
P
=0.18 and 0.02). Similar results were found for heart failure hospitalization and cardiovascular death.

Conclusions—

Although BB therapy exerted dose-related benefits across all study participants, sST2 measurement identifies patients with chronic heart failure who may particularly benefit from higher BB doses.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT00351390.
Age and Ethnic Disparities in Incidence of Stroke Over Time
Authors: Wang Yanzhong , Rudd Anthony G. , Wolfe Charles D.A.
Published: October 2013

Background and Purpose—

Data on continuous monitoring of stroke risk among different age and ethnic groups are lacking. We aimed to investigate age and ethnic disparities in stroke incidence over time from an inner-city population–based stroke register.

Methods—

Trends in stroke incidence and before-stroke risk factors were investigated with the South London Stroke Register, a population-based register covering a multiethnic population of 357 308 inhabitants. Age-, ethnicity-, and sex-specific incidence rates with 95% confidence intervals were calculated, assuming a Poisson distribution and their trends over time tested by the Cochran–Armitage test.

Results—

Four thousand two hundred forty-five patients with first-ever stroke were registered between 1995 and 2010. Total stroke incidence reduced by 39.5% during the 16-year period from 247 to 149.5 per 100 000 population (
P
<0.0001). Similar declines in stroke incidence were observed in men, women, white groups, and those aged >45 years, but not in those aged 15 to 44 years (12.6–10.1;
P
=0.2034) and black groups (310.1–267.5;
P
=0.3633). The mean age at stroke decreased significantly from 71.7 to 69.6 years (
P
=0.0001). The reduction in prevalence of before-stroke risk factors was mostly seen in white patients aged >55 years, whereas an increase in diabetes mellitus was observed in younger black patients aged 15 to 54 years.

Conclusions—

Total stroke incidence decreased during the 16-year time period. However, this was not seen in younger age groups and black groups. The advances in risk factor reduction observed in white groups aged >55 years failed to be transferred to younger age groups and black groups.
CoCoTools: Open-source Software for Building Connectomes Using the CoCoMac Anatomical Database
Authors: Blumenfeld Robert S. , Bliss Daniel P. , Perez Fernando , D'Esposito Mark
Published: October 2013

Neuroanatomical tracer studies in the nonhuman primate macaque monkey are a valuable resource for cognitive neuroscience research. These data ground theories of cognitive function in anatomy, and with the emergence of graph theoretical analyses in neuroscience, there is high demand for these data to be consolidated into large-scale connection matrices (“macroconnectomes”). Because manual review of the anatomical literature is time consuming and error prone, computational solutions are needed to accomplish this task. Here we describe the “CoCoTools” open-source Python library, which automates collection and integration of macaque connectivity data for visualization and graph theory analysis. CoCoTools both interfaces with the CoCoMac database, which houses a vast amount of annotated tracer results from 100 years (1905–2005) of neuroanatomical research, and implements coordinate-free registration algorithms, which allow studies that use different parcellations of the brain to be translated into a single graph. We show that using CoCoTools to translate all of the data stored in CoCoMac produces graphs with properties consistent with what is known about global brain organization. Moreover, in addition to describing CoCoTools' processing pipeline, we provide worked examples, tutorials, links to on-line documentation, and detailed appendices to aid scientists interested in using CoCoTools to gather and analyze CoCoMac data.
Molecular and morphological characterisation of Scutellonema bradys from yam in Costa Rica and development of specific primers for its detection
Authors: Humphreys-Pereira Danny A. , Williamson Valerie Moroz , Lee Sooung , Coyne Daniel L. , Salazar Luis , Gómez-Alpízar Luis
Published: October 2013

The yam nematode, Scutellonema bradys, which can cause dry rot disease of yam (Dioscorea spp.), was recorded for the first time from Costa Rica in four species of yam occurring in the Atlantic and north regions. Morphometric measurements from two populations from each region using ten female and 11 male characters corresponded with previous descriptions of this species. Canonical discriminant analysis of the female morphometric data separated the populations by region, whereas no separation by region was evident using the male data. Analysis of DNA sequences from the ITS region indicated that populations from Costa Rica were monophyletic with S. bradys from West Africa and clearly distinct from other Scutellonema species. No genetic separation by geographic region or Dioscorea species host was observed between Costa Rica populations. Species-specific primers were developed from the ITS region and supported the identity of 17 populations from 15 locations in Costa Rica as S. bradys: 14 populations from D. alata (greater or water yam) and one each from D. trifida (white yampee), D. cayenensis (yellow yam) and D. rotundata (white yam). Yam production in Costa Rica began in the Atlantic region, where the yam nematode was likely introduced from the Caribbean, progressively spreading to other locations through the use of infected vegetative planting material.
Phylogenetic position and taxonomy of the enigmatic Orobanche krylowii (Orobanchaceae), a predominatly Asian species newly found in Albania (SE Europe)
Authors: Frajman Božo , Carlón Luis , Kosachev Petr , Sánchez Pedraja Óscar , Schneeweiss Gerald M. , Schönswetter Peter
Published: October 2013

We report on the occurrence of Orobanche krylowii in the Alpet Shqiptare (Prokletije, Albanian Alps) mountain range in northern Albania (Balkan Peninsula). The species was previously known only from eastern-most Europe (Volga-Kama River in Russia), more than 2500 km away, and from adjacent Siberia and Central Asia. We used morphological evidence as well as nuclear ribosomal ITS sequences to show that the Albanian population indeed belongs to O. krylowii and that its closest relative is the European O. lycoctoni, but not O. elatior as assumed in the past. Both Orobanche krylowii and O. lycoctoni parasitize Ranunculaceae (Thalictrum spp. and Aconitum lycoctonum, respectively). We provide an identification key and a taxonomic treatment for O. krylowii, and suggest the IUCN category CE (critically endangered) for the highly disjunct Albanian population.
Minding the Gap
Authors: Connelly Brian L. , Haynes Katalin Takacs , Tihanyi Laszlo , Gamache Daniel L. , Devers Cynthia E.
Published: October 2013

Management researchers have long been concerned with the antecedents and consequences of managerial compensation. More recently, scholarly and popular attention has turned to the gap in pay between workers at the highest and lowest levels of the organization, or “pay dispersion.” This study investigates the performance implications of pay dispersion on a longitudinal (10-year) sample of publicly traded firms from multiple industries. We combine explanations based on tournament theory and equity theory to develop a model wherein pay dispersion has opposing effects on a firm’s short-term performance and their trend in performance over time. We also show that ownership is a key antecedent of pay dispersion. Specifically, transient institutional investors (who have short time horizons and equity stakes in a wide variety of firms) positively influence pay dispersion whereas dedicated institutional investors (who have longer investment time horizons and equity stakes in fewer firms) negatively influence pay dispersion. We discuss the wide-ranging implications of these findings for scholars, managers, and policy makers alike.
Social Media in Employee-Selection-Related Decisions
Authors: Roth Philip L. , Bobko Philip , Van Iddekinge Chad H. , Thatcher Jason B.
Published: October 2013

Social media (SM) pervades our society. One rapidly growing application of SM is its use in personnel decision making. Organizations are increasingly searching SM (e.g., Facebook) to gather information about potential employees. In this article, we suggest that organizational practice has outpaced the scientific study of SM assessments in an area that has important consequences for individuals (e.g., being selected for work), organizations (e.g., successfully predicting job performance or withdrawal), and society (e.g., consequent adverse impact/diversity). We draw on theory and research from various literatures to advance a research agenda that addresses this gap between practice and research. Overall, we believe this is a somewhat rare moment in the human resources literature when a new class of selection methods arrives on the scene, and we urge researchers to help understand the implications of using SM assessments for personnel decisions.
The Work–Family Interface and Promotability
Authors: Paustian-Underdahl Samantha C. , Halbesleben Jonathon R. B. , Carlson Dawn S. , Kacmar K. Michele
Published: October 2013

Based on role accumulation theory and boundary theory we propose and examine a model that represents the process by which family involvement influences promotability through enrichment, and the moderating roles of employees’ boundary management preferences (i.e., segmentation/integration) in that process. Data collected from 347 registered nurses and their supervisors ( N = 40) across three periods showed that as employees’ family involvement increases, they are able to accumulate resources from their family role and transfer them to the workplace. This increase in family-to-work enrichment (FWE) benefits employees by increasing supervisor perceptions of employees’ promotability. As hypothesized, an integrating boundary management preference serves as a double-edged sword for employees such that it strengthens the positive influence of family involvement on FWE, but weakens the relationship between FWE and supervisor perceptions of promotability.
Clinical Results and MRI Evolution of a Nano-Composite Multilayered Biomaterial for Osteochondral Regeneration at 5 Years
Authors: Kon Elizaveta , Filardo Giuseppe , Di Martino Alessandro , Busacca Maurizio , Moio Antonio , Perdisa Francesco , Marcacci Maurilio
Published: October 2013

Background:

Several cartilage lesions involve the subchondral bone, and there is a need for biphasic scaffolds to treat the entire osteochondral unit to reproduce the different biological and functional requirements and guide the growth of the 2 tissues.

Purpose:

To evaluate the results of a cell-free collagen-hydroxyapatite osteochondral scaffold at midterm, and to use magnetic resonance imaging (MRI) analysis to document the imaging evolution of the tissue regeneration process through 5 years of follow-up.

Study Design:

Case series; Level of evidence, 4.

Methods:

Twenty-seven patients (9 women, 18 men; mean age, 34.9 ± 10.2 years) treated for knee chondral or osteochondral lesions (size, 1.5-6 cm2) were followed for 2 and 5 years and were clinically evaluated using the International Knee Documentation Committee (IKDC) and Tegner scores. An MRI evaluation was performed at both follow-ups in 23 lesions, and the magnetic resonance observation of cartilage repair tissue (MOCART) score and specific subchondral bone parameters (bone regeneration, bone signal quality, osteophytes or upcoming bone front, sclerotic areas, and edema) were analyzed.

Results:

A statistically significant improvement in all clinical scores was observed from the initial evaluation to the 2- and 5-year follow-ups, and the results were stable over time. The mean IKDC subjective score improved from 40.0 ± 15.0 to 76.5 ± 14.5 (2-year follow-up) and 77.1 ± 18.0 (5-year follow-up) and the mean Tegner score from 1.6 ± 1.1 to 4.0 ± 1.8 (2-year follow-up) and 4.1 ± 1.9 (5-year follow-up). The MRI evaluation showed a significant improvement in both the MOCART score and subchondral bone status from 2 to 5 years. At 5 years, complete filling of the cartilage was shown in 78.3% of the lesions, complete integration of the graft was detected in 69.6% of cases, the repair tissue surface was intact in 60.9%, and the structure of the repair tissue was homogeneous in 60.9% of the cases. No correlation was found between MRI findings and clinical outcome.

Conclusion:

This osteochondral scaffold was used for the treatment of chondral and osteochondral knee defects with a single-step procedure. The study results highlighted the safety and potential of this procedure, which offered a good clinical outcome with stable results at midterm follow-up. Although the MRI findings improved over time, some abnormalities persisted, but no correlation was found between the imaging and clinical results.
Long-Term Follow-Up in Infantile-Onset Lambert-Eaton Myasthenic Syndrome
Authors: Portaro S. , Parisi D. , Polizzi A. , Ruggieri M. , Andreetta F. , Bernasconi P. , Toscano A. , Rodolico C.
Published: October 2013

Lambert-Eaton myasthenic syndrome is a neuromuscular junction disorder characterized by proximal limb muscle weakness, fatigability, decreased deep-tendon reflexes, and autonomic symptoms. There are 2 forms of Lambert-Eaton myasthenic syndrome: one most frequently associated with small-cell lung cancer (P–Lambert-Eaton myasthenic syndrome) and the other that is a pure autoimmune form (NP–Lambert-Eaton myasthenic syndrome). Lambert-Eaton myasthenic syndrome is a very rare disorder in children younger than age 12 years. Herein, we report a 25-year-old man with NP–Lambert-Eaton myasthenic syndrome, which onset was at the age of 10 years. To date, this is the most long-term follow-up of NP–Lambert-Eaton myasthenic syndrome in childhood. In our patient, the only symptomatic treatment with 3,4-diaminopyridine phosphate has been sufficient to guarantee him a good quality of life. Our data remind physicians to keep in mind the diagnosis of Lambert-Eaton myasthenic syndrome in children with a proximal myopathic pattern and they confirm the specificity of compound muscle action potential incremental pattern after brief maximal effort in Lambert-Eaton myasthenic syndrome.
The Aeolus project: Science outreach through art
Authors: Drumm Ian A. , Belantara Amanda , Dorney Steve , Waters Timothy P. , Peris Eulalia
Published: October 2013

With a general decline in people’s choosing to pursue science and engineering degrees there has never been a greater need to raise the awareness of lesser known fields such as acoustics. Given this context, a large-scale public engagement project, the ‘Aeolus project’, was created to raise awareness of acoustics science through a major collaboration between an acclaimed artist and acoustics researchers. It centred on touring the large singing sculpture Aeolus during 2011/12, though the project also included an extensive outreach programme of talks, exhibitions, community workshops and resources for schools. Described here are the motivations behind the project and the artwork itself, the ways in which scientists and an artist collaborated, and the public engagement activities designed as part of the project. Evaluation results suggest that the project achieved its goal of inspiring interest in the discipline of acoustics through the exploration of an otherworldly work of art.
Beyond dichotomies: Towards a more encompassing view of learning
Authors: Snoeren Miranda MWC , Niessen Theo JH , Abma Tineke A
Published: October 2013

In organisations, learning is generally seen as a dynamic, collective and often conscious process that occurs by reflecting on real work experiences. In this article, we discuss these assumptions about learning in the context of work by presenting a case study in the care for older people. The case illustrates that learning in and through work is predominantly an embodied and responsive phenomenon that usually occurs implicitly while acting. We argue that a learning perspective grounded in the worldview of enactivism encapsulates this pragmatic and embodied character of learning and at the same time provides a reality and language helpful in encouraging a critical attitude towards assumptions about learning in organisations. Understanding learning from an enactive point of view carries consequences for studying and organising learning within organisations. These are outlined within this article to challenge managers’ meanings of learning in health care and comparable settings and to encourage further dialogue on this issue.
Analysis of mechanical properties and cost of glass/jute fiber-reinforced hybrid polyester composites
Authors: Kumar Amit , Singh Satnam
Published: October 2013

Polymers and their composites are one of the most advanced and adaptable engineering materials. The strength of any composite depends upon number of factors such as volume/weight fraction of reinforcement, L/D ratio of fibers, types of fibers, orientation angles, chemical treatment of reinforcement, and many others. The present work focuses on the analysis of mechanical properties (tensile, flexural, and impact) of synthetic and natural fiber (glass/jute)-reinforced polyester composites. An attempt is made to reduce the usage of synthetic glass fibers by incorporating natural jute fibers such that the resultant hybrid composite shows increased strength when compared with single reinforcements of glass or jute fibers. The test specimens were prepared and tested according to ASTM standards. Experimental results revealed that reinforcement of natural fibers up to some extent increases the mechanical properties and reduces the overall cost of fabrication of composites.
From Rawlsian autonomy to sufficient opportunity in education
Authors: Shields Liam
Published: October 2013

Equality of Opportunity is widely thought of as the normative ideal most relevant to the design of educational institutions. One widely discussed interpretation of this ideal is Rawls' principle of Fair Equality of Opportunity. In this paper I argue that theories, like Rawls, that give priority to the achievement of individual autonomy, are committed to giving that same priority to a principle of sufficient opportunity. Thus, the Rawlsian's primary focus when designing educational institutions should be on sufficiency and not equality. The paper then argues this commitment has at least three attractive implications. Firstly, it enables defenders of Fair Equality of Opportunity to overcome Richard Arneson's powerful objections. Secondly, it suggests a revised version of the principle of Fair Equality of Opportunity that is more plausible. Thirdly, it has attractive practical implications for educational provision.
Badgrlz? Exploring Sex Differences in Cyberbullying Behaviors
Authors: Connell Nadine M. , Schell-Busey Natalie M. , Pearce Allison N. , Negro Pamela
Published: October 2013

Research on bullying suggests that traditional bullying is gendered such that males participate in physical acts while females engage in relational attacks, but the nature of the relationship between gender and cyberbullying is less defined. Because the Internet is an ideal environment for the relational forms of bullying favored by females, we hypothesize that females engage in more cyberbullying than males. We also hypothesize that there are gender differences in predictors of cyberbullying and cybervictimization. In order to better understand these gender dynamics, we examine self-reported bullying and victimization experiences in a sample of 3,867 middle school students in a northeastern state. Contrary to recent findings, our results show support for the gendered nature of cyberbullying and suggest that females engage in more cyberbullying than males. We also find gender variation in predictors of cybervictimization. We discuss the implication of these findings, especially in light of prevention and intervention needs.
Electrical Source Imaging of Sleep Spindles
Authors: Del Felice Alessandra , Arcaro Chiara , Storti Silvia Francesca , Fiaschi Antonio , Manganotti Paolo
Published: October 2013

To identify and compare cortical source generators of slow and fast sleep spindles in healthy subjects, electroencephalographic (EEG) signals were obtained from 256 channels, and sources on neuroanatomical Montreal Neurological Institute (MNI) space estimated with low-resolution brain electromagnetic tomography analysis (LORETA). Spindle activity was recorded in 18 healthy volunteers during daytime napping. Because of lack of sleep or excessive artifacts, data from 13 subjects were analyzed off-line. Spindles were visually scored, marked, and bandpass filtered (slow 10-12 Hz or fast 12-14 Hz). EEG was segmented on the marker, and segments separately averaged. LORETA projected cortical sources on the MNI brain. Maximal intra- and inter-individual intensities were compared using the Wilcoxon test ( P< .05) and cortical sources distribution compared using a χ2 test. Two to three slow spindles generators were consistently identified in frontal lobes, with additional sources in parietal and limbic lobes in half cases. Fast spindles had multiple temporo-parietal sources, with an inconstant frontal source. Inter-individual ( P = 0.44), and intra-individual ( P = 0.09 slow and P = 0.10 fast spindles) source intensities were comparable. Slow spindles sources were preferentially concentrated over frontal cortices in comparison with fast spindles ( P = 0.0009). Our results demonstrate multiple, synchronous, and equipotent spindles cortical generators in healthy subjects, with more anterior generators for slow spindles.
An Uncommon Cause of Transient Neurological Dysfunction
Authors: Farooq Muhammad U. , Bhatt Archit , Chang Howard T.
Published: October 2013

Transient neurological dysfunction may be associated with uncommon disorders and should prompt consideration of a broad differential diagnosis when assessing patients with episodic symptoms. The most common causes of transient neurological dysfunction include transient ischemic attack (TIA), seizure disorder, and migraine and its variants. However, underlying unusual pathophysiological processes such as brain tumors can also cause transient neurological dysfunction. Here we present a case of a 68-year-old male with oligodendroglial gliomatosis cerebri (OGC) who presented with TIA-like symptoms. Brain magnetic resonance imaging revealed multiple diffuse T2 hyperintensities within the white and gray matter. Magnetic resonance spectroscopy was suggestive of gliomatosis cerebri and was particularly helpful in this case. The diagnosis of OGC was confirmed by histopathology and molecular genetic studies on brain biopsy tissue. In this report, we discuss the clinical and radiological characteristics of OGC and highlight the unusual presentation of this case.
cudaMap: a GPU accelerated program for gene expression connectivity mapping
Authors: McArt Darragh G , Bankhead Peter , Dunne Philip D , Salto-Tellez Manuel , Hamilton Peter , Zhang Shu-Dong
Published: October 2013

Background

Modern cancer research often involves large datasets and the use of sophisticated statistical techniques. Together these add a heavy computational load to the analysis, which is often coupled with issues surrounding data accessibility. Connectivity mapping is an advanced bioinformatic and computational technique dedicated to therapeutics discovery and drug re-purposing around differential gene expression analysis. On a normal desktop PC, it is common for the connectivity mapping task with a single gene signature to take > 2h to complete using sscMap, a popular Java application that runs on standard CPUs (Central Processing Units). Here, we describe new software, cudaMap, which has been implemented using CUDA C/C++ to harness the computational power of NVIDIA GPUs (Graphics Processing Units) to greatly reduce processing times for connectivity mapping.

Results

cudaMap can identify candidate therapeutics from the same signature in just over thirty seconds when using an NVIDIA Tesla C2050 GPU. Results from the analysis of multiple gene signatures, which would previously have taken several days, can now be obtained in as little as 10 minutes, greatly facilitating candidate therapeutics discovery with high throughput. We are able to demonstrate dramatic speed differentials between GPU assisted performance and CPU executions as the computational load increases for high accuracy evaluation of statistical significance.

Conclusion

Emerging ‘omics’ technologies are constantly increasing the volume of data and information to be processed in all areas of biomedical research. Embracing the multicore functionality of GPUs represents a major avenue of local accelerated computing. cudaMap will make a strong contribution in the discovery of candidate therapeutics by enabling speedy execution of heavy duty connectivity mapping tasks, which are increasingly required in modern cancer research. cudaMap is open source and can be freely downloaded from http://purl.oclc.org/NET/cudaMap.
Experimental hybridization and backcrossing reveal forces of reproductive isolation in Microbotryum
Authors: Büker Britta , Petit Elsa , Begerow Dominik , Hood Michael E
Published: October 2013

Background

Hybridization and reproductive isolation are central to the origin and maintenance of species, and especially for sympatric species, gene flow is often inhibited through barriers that depend upon mating compatibility factors. The anther-smut fungi (genus Microbotryum) serve as models for speciation in the face of sympatry, and previous studies have tested for but not detected assortative mating. In addition, post-mating barriers are indicated by reduced fitness of hybrids, but sources of those barriers (i.e. ecological maladaptation or genetic incompatibilities) have not yet been detected. Here, backcrossing experiments, specifically controlling for the fungal species origins of the mating compatibility factors, were used to investigate reproductive isolation in the recently-derived species Microbotryum lychnidis-dioicae and Microbotryum silenes-dioicae.

Results

Assortative mating was detected during backcrossing and was manifested by the preferential conjugation of the hybrid-produced gametes with non-hybrid gametes containing mating compatibility factors from the same parental species. Patterns of post-mating performance supported either a level of extrinsic isolation mechanism, where backcross progeny with a higher proportion of the pathogen genome adapted to the particular host environment were favored, or an infection advantage attributed to greater genetic contribution to the hybrid from the M. lychnidis-dioicae genome.

Conclusion

The use of controlled backcrossing experiments reveals significant species-specific mating type effects on conjugations between recently-derived sister species, which are likely to play important roles in both maintaining species separation and the nature of hybrids lineages that emerge in sympatry between Microbotryum species.
Use of transcriptome sequencing to understand the pistillate flowering in hickory (Carya cathayensis Sarg.)
Authors: Huang You-Jun , Liu Li-Li , Huang Jian-Qin , Wang Zheng-Jia , Chen Fang-Fang , Zhang Qi-Xiang , Zheng Bing-Song , Chen Ming
Published: October 2013

Background

Different from herbaceous plants, the woody plants undergo a long-period vegetative stage to achieve floral transition. They then turn into seasonal plants, flowering annually. In this study, a preliminary model of gene regulations for seasonal pistillate flowering in hickory (Carya cathayensis) was proposed. The genome-wide dynamic transcriptome was characterized via the joint-approach of RNA sequencing and microarray analysis.

Results

Differential transcript abundance analysis uncovered the dynamic transcript abundance patterns of flowering correlated genes and their major functions based on Gene Ontology (GO) analysis. To explore pistillate flowering mechanism in hickory, a comprehensive flowering gene regulatory network based on Arabidopsis thaliana was constructed by additional literature mining. A total of 114 putative flowering or floral genes including 31 with differential transcript abundance were identified in hickory. The locations, functions and dynamic transcript abundances were analyzed in the gene regulatory networks. A genome-wide co-expression network for the putative flowering or floral genes shows three flowering regulatory modules corresponding to response to light abiotic stimulus, cold stress, and reproductive development process, respectively. Totally 27 potential flowering or floral genes were recruited which are meaningful to understand the hickory specific seasonal flowering mechanism better.

Conclusions

Flowering event of pistillate flower bud in hickory is triggered by several pathways synchronously including the photoperiod, autonomous, vernalization, gibberellin, and sucrose pathway. Totally 27 potential flowering or floral genes were recruited from the genome-wide co-expression network function module analysis. Moreover, the analysis provides a potential FLC-like gene based vernalization pathway and an 'AC’ model for pistillate flower development in hickory. This work provides an available framework for pistillate flower development in hickory, which is significant for insight into regulation of flowering and floral development of woody plants.
Improving prokaryotic transposable elements identification using a combination of de novo and profile HMM methods
Authors: Kamoun Choumouss , Payen Thibaut , Hua-Van Aurélie , Filée Jonathan
Published: October 2013

Background

Insertion Sequences (ISs) and their non-autonomous derivatives (MITEs) are important components of prokaryotic genomes inducing duplication, deletion, rearrangement or lateral gene transfers. Although ISs and MITEs are relatively simple and basic genetic elements, their detection remains a difficult task due to their remarkable sequence diversity. With the advent of high-throughput genome and metagenome sequencing technologies, the development of fast, reliable and sensitive methods of ISs and MITEs detection become an important challenge. So far, almost all studies dealing with prokaryotic transposons have used classical BLAST-based detection methods against reference libraries. Here we introduce alternative methods of detection either taking advantages of the structural properties of the elements (de novo methods) or using an additional library-based method using profile HMM searches.

Results

In this study, we have developed three different work flows dedicated to ISs and MITEs detection: the first two use de novo methods detecting either repeated sequences or presence of Inverted Repeats; the third one use 28 in-house transposase alignment profiles with HMM search methods. We have compared the respective performances of each method using a reference dataset of 30 archaeal and 30 bacterial genomes in addition to simulated and real metagenomes. Compared to a BLAST-based method using ISFinder as library, de novo methods significantly improve ISs and MITEs detection. For example, in the 30 archaeal genomes, we discovered 30 new elements (+20%) in addition to the 141 multi-copies elements already detected by the BLAST approach. Many of the new elements correspond to ISs belonging to unknown or highly divergent families. The total number of MITEs has even doubled with the discovery of elements displaying very limited sequence similarities with their respective autonomous partners (mainly in the Inverted Repeats of the elements). Concerning metagenomes, with the exception of short reads data (<300 bp) for which both techniques seem equally limited, profile HMM searches considerably ameliorate the detection of transposase encoding genes (up to +50%) generating low level of false positives compare to BLAST-based methods.

Conclusion

Compared to classical BLAST-based methods, the sensitivity of de nov o and profile HMM methods developed in this study allow a better and more reliable detection of transposons in prokaryotic genomes and metagenomes. We believed that future studies implying ISs and MITEs identification in genomic data should combine at least one de novo and one library-based method, with optimal results obtained by running the two de novo methods in addition to a library-based search. For metagenomic data, profile HMM search should be favored, a BLAST-based step is only useful to the final annotation into groups and families.
Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots
Authors: Vidal Elena A , Moyano Tomás C , Krouk Gabriel , Katari Manpreet S , Tanurdzic Milos , McCombie W Richard , Coruzzi Gloria M , Gutiérrez Rodrigo A
Published: October 2013

Background

Nitrate and other nitrogen metabolites can act as signals that regulate global gene expression in plants. Adaptive changes in plant morphology and physiology triggered by changes in nitrate availability are partly explained by these changes in gene expression. Despite several genome-wide efforts to identify nitrate-regulated genes, no comprehensive study of the Arabidopsis root transcriptome under contrasting nitrate conditions has been carried out.

Results

In this work, we employed the Illumina high throughput sequencing technology to perform an integrated analysis of the poly-A + enriched and the small RNA fractions of the Arabidopsis thaliana root transcriptome in response to nitrate treatments. Our sequencing strategy identified new nitrate-regulated genes including 40 genes not represented in the ATH1 Affymetrix GeneChip, a novel nitrate-responsive antisense transcript and a new nitrate responsive miRNA/TARGET module consisting of a novel microRNA, miR5640 and its target, AtPPC3.

Conclusions

Sequencing of small RNAs and mRNAs uncovered new genes, and enabled us to develop new hypotheses for nitrate regulation and coordination of carbon and nitrogen metabolism.
The role and prognostic value of apoptosis in colorectal carcinoma
Authors: Alcaide Julia , Funez Rafael , Rueda Antonio , Perez-Ruiz Elisabeth , Pereda Teresa , Rodrigo Isabel , Coveñas Rafael , Muñoz Miguel , Redondo Maximino
Published: October 2013

Background

Alterations to apoptosis are a common occurrence in human tumours. The aim of our study was to determine the influence of apoptotic variations on the carcinogenesis and prognosis of colorectal carcinomas (CRCs).

Methods

A TUNEL assay was performed on archival material from 103 colorectal carcinomas, 26 adenomas and 20 samples of normal epithelia.

Results

The number of apoptotic cells was higher in CRCs (1.09 ± 0.13) than in adenomas (0.38 ± 0.23, p = 0.059) and normal epithelium (0.06 ± 0.04, p = 0.001). In addition, the apoptotic index (AI) was greater in metastatic disease (stage IV) than in other stages (p = 0.017). No relationship was found between apoptotic rates and age, gender or tumour grade. However, patients with tumours that showed higher AI values had a significantly lower disease-free survival (DFS) and overall survival (OS) than those with tumours that had lower AIs (p = 0.020 and p = 0.027). In a multivariate Cox proportional hazards model, AI remained a significant independent predictor of survival.

Conclusions

We conclude that disregulated apoptosis is an important event during CRC development and progression. Higher AIs are associated with more aggressive tumours and a poorer prognosis for patients with CRC.
MiRNA-497 regulates cell growth and invasion by targeting cyclin E1 in breast cancer
Authors: Luo Qifeng , Li Xiaoyu , Gao Yan , Long Yin , Chen Lei , Huang Yixiang , Fang Lin
Published: October 2013

Background

MicroRNAs are a class of endogenous single strand non-coding RNAs that are involved in many important physiological and pathological processes. The purpose of this study was to examine the expression levels of miR-497 in human breast cancer and its function in MDA-MB-231 breast cancer cells.

Methods

Quantitative polymerase chain reaction was used to measure the expression levels of miR-497 in 40 breast cancer specimens and adjacent normal breast tissues. MTT assays, colony formation assays, wound healing assays, transwell assays and cell cycle assays were used to explore the potential function of miR-497 in MDA-MB-231 breast cancer cells. Dual-luciferase reporter assays were performed to analyze the regulation of putative target of miR-497, and western blot assays were used to validate the dual-luciferase results.

Results

The expression of miR-497 in breast cancer specimens was lower than adjacent normal tissues (P < 0.05). Overexpression of miR-497 inhibited cellular growth, suppressed cellular migration and invasion, and caused a G1 arrest. Dual-luciferase reporter assays showed that miR-497 binds the 3′-untranslated region (3′-UTR) of cyclin E1, suggesting that cyclin E1 is a direct target of miR-497. Western blot assays confirmed that overexpression of miR-497 reduced cyclin E1 protein levels.

Conclusions

MiR-497 may act as a tumor suppressor gene in breast cancer. Inhibited cellular growth, suppressed cellular migration and invasion, and G1 cell cycle arrest were observed upon overexpression of miR-497 in cells, possibly by targeting cyclin E1. These results indicate miR-497 could be considered a therapeutic target for the development of treatment for breast cancer.