bluuebunny/crossref_metadata_2025 huggingface dataset:
Tenofovir Plasma Concentrations According to Companion Drugs: a Cross-Sectional Study of HIV-Positive Patients with Normal Renal Function
Authors: Calcagno A. , Gonzalez de Requena D. , Simiele M. , D'Avolio A. , Tettoni M. C. , Salassa B. , Orofino G. , Bramato C. , Libanore V. , Motta I. , Bigliano P. , Orsucci E. , Di Perri G. , Bonora S.
Published: February 2013

As the risk of tenofovir-associated renal toxicity has been found to be proportional to the drug plasma concentration, our aim was to measure the determinants of tenofovir plasma exposure in HIV-positive patients with normal renal function. A cross-sectional analysis was conducted in HIV-positive patients chronically receiving tenofovir-containing highly active antiretroviral therapies (HAARTs). Patients on tenofovir-containing antiretroviral regimens, presenting 22 to 26 h after drug intake, having estimated glomerular filtration rates above 60 ml/min, reporting high adherence to antiretroviral medications (above 95% of the doses), and signing a written informed consent were included. Plasma tenofovir concentrations were measured through a validated high-performance liquid chromatography–mass spectrometry (HPLC/LC-MS) method. The tenofovir trough concentrations in 195 patients (median, 50 ng/ml, and interquartile range, 35 to 77 ng/ml) were significantly associated with the estimated glomerular filtration rate, body mass index, and third-drug class (protease-containing versus protease-sparing regimens) (with the highest exposure in unboosted-atazanavir recipients). The results of multivariate analysis showed that the third-drug class and the weight/creatinine ratio were independent predictors of tenofovir trough concentrations. This cross-sectional study shows that tenofovir trough concentrations are predicted by the weight/creatinine ratio and by the coadministered antiretrovirals, with protease inhibitors (whether boosted or unboosted) being associated with the highest plasma exposure. These data, previously available in healthy subjects or for some drugs only, could be useful for designing strategies to manage tenofovir-associated toxicity, since this toxicity has been reported to be dose dependent.
Macrolides Inhibit Fusobacterium nucleatum-Induced MUC5AC Production in Human Airway Epithelial Cells
Authors: Nagaoka Kentaro , Yanagihara Katsunori , Harada Yosuke , Yamada Koichi , Migiyama Yohei , Morinaga Yoshitomo , Hasegawa Hiroo , Izumikawa Koichi , Kakeya Hiroshi , Nishimura Masaharu , Kohno Shigeru
Published: February 2013

Fusobacterium nucleatum
is one of the most common anaerobic bacteria in periodontitis and is responsible for several extraoral infections, including respiratory tract diseases. In this study, we examined whether
F. nucleatum
induces mucin secretion in airway epithelial cells. We also examined the effects of macrolides on
F. nucleatum
-induced mucus production compared with the effects of other antibiotics that exert anti-anaerobic activities. The production of MUC5AC, the major core protein of mucin secreted from the airway surface epithelium, in bronchial epithelial cells after stimulation with culture supernatants (Sup) of
F. nucleatum
was analyzed by performing enzyme-linked immunosorbent assay and quantitative RT-PCR. The cell-signaling pathway of
F. nucleatum
Sup stimulation was also analyzed by Western blotting. For inhibition studies, cells were treated with azithromycin, clarithromycin, clindamycin (CLDM), and metronidazole (MTZ). The
F. nucleatum
Sup induced NCI-H292 cells to express MUC5AC at both the protein level and the mRNA level in both a time- and dose-dependent manner. Macrolides inhibited
F. nucleatum
Sup-induced MUC5AC production, while CLDM and MTZ were less effective.
F. nucleatum
Sup induced the phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2), and this induction was suppressed by macrolides.
F. nucleatum
Sup-induced MUC5AC production was blocked by the ERK pathway inhibitor U0126.
F. nucleatum
is likely to contribute to excessive mucin production, which suggests that periodontitis may correlate with the pathogenesis of chronic respiratory tract infection. Macrolides seem to reduce this mucin production and might represent an additional means of therapeutic intervention for
F. nucleatum
respiratory tract infections other than CLDM and MTZ.
Ferric Uptake Regulator and Its Role in the Pathogenesis of Nontypeable Haemophilus influenzae
Authors: Harrison Alistair , Santana Estevan A. , Szelestey Blake R. , Newsom David E. , White Peter , Mason Kevin M.
Published: February 2013

NontypeableHaemophilus influenzae(NTHi) is a commensal microorganism of the human nasopharynx, and yet is also an opportunistic pathogen of the upper and lower respiratory tracts. Host microenvironments influence gene expression patterns, likely critical for NTHi persistence. The host sequesters iron as a mechanism to control microbial growth, and yet iron limitation influences gene expression and subsequent production of proteins involved in iron homeostasis. Careful regulation of iron uptake, via theferricuptakeregulator Fur, is essential in multiple bacteria, including NTHi. We hypothesized therefore that Fur contributes to iron homeostasis in NTHi, is critical for bacterial persistence, and likely regulates expression of virulence factors. Toward this end,furwas deleted in the prototypic NTHi clinical isolate, 86-028NP, and we assessed gene expression regulated by Fur. As expected, expression of the majority of genes that encode proteins with predicted roles in iron utilization was repressed by Fur. However, 14 Fur-regulated genes encode proteins with no known function, and yet may contribute to iron utilization or other biological functions. In a mammalian model of human otitis media, we determined that Fur was critical for bacterial persistence, indicating an important role for Fur-mediated iron homeostasis in disease progression. These data provide a profile of genes regulated by Fur in NTHi and likely identify additional regulatory pathways involved in iron utilization. Identification of such pathways will increase our understanding of how this pathogen can persist within host microenvironments, as a common commensal and, importantly, as a pathogen with significant clinical impact.
Epicutaneous Model of Community-Acquired Staphylococcus aureus Skin Infections
Authors: Prabhakara Ranjani , Foreman Oded , De Pascalis Roberto , Lee Gloria M. , Plaut Roger D. , Kim Stanley Y. , Stibitz Scott , Elkins Karen L. , Merkel Tod J.
Published: February 2013

Staphylococcus aureus
is one of the most common etiological agents of community-acquired skin and soft tissue infection (SSTI). Although the majority of
S. aureus
community-acquired SSTIs are uncomplicated and self-clearing in nature, some percentage of these cases progress into life-threatening invasive infections. Current animal models of
S. aureus
SSTI suffer from two drawbacks: these models are a better representation of hospital-acquired SSTI than community-acquired SSTI, and they involve methods that are difficult to replicate. For these reasons, we sought to develop a murine model of community-acquired methicillin-resistant
S. aureus
SSTI (CA-MRSA SSTI) that can be consistently reproduced with a high degree of precision. We utilized this model to begin to characterize the host immune response to this type of infection. We infected mice via epicutaneous challenge of the skin on the outer ear pinna using Morrow-Brown allergy test needles coated in
S. aureus
USA300. When mice were challenged in this model, they developed small, purulent, self-clearing lesions with predictable areas of inflammation that mimicked a human infection. CFU in the ear pinna peaked at day 7 before dropping by day 14. The T
h
1 and T
h
17 cytokines gamma interferon (IFN-γ), interleukin-12 (IL-12) p70, tumor necrosis factor alpha (TNF-α), IL-17A, IL-6, and IL-21 were all significantly increased in the draining lymph node of infected mice, and there was neutrophil recruitment to the infection site.
In vivo
neutrophil depletion demonstrated that neutrophils play a protective role in preventing bacterial dissemination and fatal invasive infection.
An unexpected Holter monitor result: multiple sinus arrests in a patient with lateral medullary syndrome
Authors: Koay Shiwen , Dewan Bikash
Published: February 2013

A 52-year-old man presented with vomiting, dysphagia, left-sided ataxia and dissociated sensory loss. Diffusion-weighted MRI showed evidence of acute infarct in the left lateral medulla and left medial cerebellar hemisphere, probably secondary to thromboembolism from left vertebral artery dissection. While making an uneventful recovery as an inpatient, a routine 24 h ECG was performed 2 weeks after the stroke to investigate possible paroxysmal atrial fibrillation. The recording instead revealed 56 asymptomatic episodes of sinus arrest, necessitating implantation of a permanent pacemaker to prevent sudden cardiac death. The medulla contains key structures involved in autonomic regulation, including the dorsal vagal nucleus and the nucleus tractus solitarius. Acute infarction may disrupt cardiac autonomic regulation pathways, resulting in altered parasympathetic and sympathetic outflow to the sinoatrial and atrioventricular nodes, with potentially life-threatening effects.
S-1-induced lung injury combined with pneumocystis pneumonia
Authors: Yano Shuichi
Published: February 2013

Pulmonary injuries due to S-1 have been reported, and these reports have shown an increase in lung cancer following the increased usage of S-1 in treating lung cancer. We report the first case of lung injury due to S-1 in combination with pneumocystis pneumonia (PCP), because the radiological findings and clinical courses were compatible with S-1-induced lung injury combined with PCP. We should consider that S-1 might induce lung injuries which might occur with PCP, especially with a history of drug-induced or radiation-induced lung injuries.
Physical activity and television watching in relation to semen quality in young men
Authors: Gaskins Audrey Jane , Mendiola Jaime , Afeiche Myriam , Jørgensen Niels , Swan Shanna H , Chavarro Jorge E
Published: February 2013

Background

Semen quality appears to have declined over the past decades but reasons for this decline are unresolved. The concurrent increase in sedentary behaviour may be a contributing factor. The objective of this study was to evaluate the relationship of physical activity and television (TV) watching with sperm parameters in a population of young, healthy men.

Methods

Men aged 18–22 years (n=189) from the Rochester Young Men's Study (2009–2010) participated in this analysis. Physical activity (h/week of moderate and vigorous exercise) and TV watching (h/week of TV, video or DVD watching) over the past 3 months were assessed via questionnaire. Semen quality was assessed by sperm concentration, motility, morphology and total sperm count.

Results

Sperm concentration and total sperm count were directly related to physical activity after multivariable adjustment (p-trend=0.01 and 0.04); men in the highest quartile of moderate-to-vigorous activity (≥15 h/week) had 73% (95% CI 15% to 160%) higher sperm concentration than men in the lowest quartile (<5 h/week). TV watching was inversely associated with sperm concentration and total sperm count in multivariable analyses (p-trend=0.05 and 0.06); men in the highest quartile of TV watching (>20 h/week) had 44% (95% CI 15 to 63%) lower sperm concentration than men in the lowest quartile (0 h/week). These measures of physical and leisure time activities were not significantly associated with sperm motility or morphology.

Conclusions

In this population of healthy men, higher moderate-to-vigorous activity and less TV watching were significantly associated with higher total sperm count and sperm concentration.
Frequent alcohol, nicotine or cannabis use is common in young persons presenting for mental healthcare: a cross-sectional study
Authors: Hermens Daniel F , Scott Elizabeth M , White Django , Lynch Marta , Lagopoulos Jim , Whitwell Bradley G , Naismith Sharon L , Hickie Ian B
Published: February 2013

Objectives

To determine the prevalence of recent alcohol, nicotine or cannabis use in young persons presenting for mental healthcare.

Design

A cross-sectional study of young people seeking mental healthcare completed self-report questionnaires regarding their use of alcohol, nicotine or cannabis.

Setting

Data were collected from two sites as part of the nationalheadspaceservices programme.

Participants

2122 young people aged 12–30 years provided information as part of a patient register; a subset of N=522 participants also provided more detailed information about their patterns of alcohol use.

Outcome measures

Prevalence levels of recent alcohol, nicotine or cannabis use within relevant age bands (12–17, 18–19 and 20–30) or primary diagnostic categories.

Results

The rates for useat least weeklyof alcohol for the three age bands were 12%, 39% and 45%, and for cannabis 7%, 14% and 18%, respectively. The rates ofdailynicotine use for the three age bands were 23%, 36% and 41%. The pattern of alcohol use was characterised by few abstainers as well as many risky drinkers. Age of onset across all three substances was approximately 15 years. Individuals who used any of the three substances more frequently were likely to be older, male or have psychotic or bipolar disorders.

Conclusions

Frequent use of alcohol, nicotine or cannabis in young people seeking mental healthcare is common. Given the restricted legal access, the patterns of use in those aged 12–17 years are particularly notable. Reductions in substance use needs to be prioritised within services for at-risk young people.
Oophorectomy hinders antioxidant adaptation promoted by swimming in Wistar rats
Authors: Macedo Ulisvaldo Brunno de Oliveira , Martins Rand Randall , Freire Neto Francisco Paulo , Oliveira Yonara Monique da Costa , Medeiros Aldo da Cunha , Brandão-Neto José , Rezende Adriana Augusto de , Almeida Maria das Graças
Published: February 2013

Oxidative stress is associated with postmenopause and is also responsible for various metabolic alterations. The redox imbalance observed during ovarian decline can be induced experimentally by bilateral ovariectomy in rats. In addition to hormone replacement, regular moderate physical exercise is indicated to prevent several common postmenopausal diseases. This study aimed to assess the effect of daily swimming on the antioxidant defense system of oophorectomized Wistar rats. Control and oophorectomized groups were submitted to 1 h of daily swimming for 90 days. Levels of lipid peroxidation and glutathione content and the activities of superoxide dismutase enzyme and glutathione peroxidase in erythrocytes, liver, and brain were assessed every 30 days. The control group exhibited lower lipoperoxidation that was associated with a significant increase in superoxide dismutase enzyme activity, glutathione peroxidase activity, and glutathione content in erythrocytes and liver; however, swimming did not cause changes in antioxidant parameters in the brain over time. The oophorectomized group showed no antioxidant adaptation to daily swimming and had greater oxidative damage in the liver and blood. Our results suggest that ovariectomy hinders antioxidant adaptation in Wistar rats submitted to daily swimming.
Exploring diffractive features of elastic scattering of 6Li by different target nuclei at different energies
Authors: Badran R.I. , Al-Masri Dana
Published: February 2013

The diffractive aspects of angular distribution have been investigated by analyzing the experimental data for a set of elastic scattering processes of 6Li by different target nuclei at different laboratory energies. The analysis of experimental data of angular distribution for elastic scattering process is performed using both Frahn–Venter and McIntyre models. The theoretical models can reasonably reproduce the general pattern of the data, thus allowing us to extract geometrical parameters from elastic scattering processes. It is found that interpretation of the diffraction features of the data is model-independent. The values of extracted parameters, from both models, are found to be comparable to each other and to those of others. The correlation between the total reaction cross section and the incident laboratory energy for each scattering is discernible and values of total reaction cross section are found to be comparable with those of others.
DYNAMICAL ANALYSIS OF DRUG EFFICACY AND MECHANISM OF ACTION USING GFP REPORTERS
Authors: HUA JIANPING , SIMA CHAO , CYPERT MILANA , GOODEN GERALD C. , SHACK SONSOLES , ALLA LALITAMBA , SMITH EDWARD A. , TRENT JEFFREY M. , DOUGHERTY EDWARD R. , BITTNER MICHAEL L.
Published: February 2013

Two issues are critical to the development of effective cancer-drug combinations. First, it is necessary to determine common combinations of alterations that exert strong control over proliferation and survival regulation for the general type of cancer being considered. Second, it is necessary to have a drug testing method that allows one to assess the variety of responses that can be provoked by drugs acting at key points in the cellular processes dictating proliferation and survival. Utilizing a previously reported GFP (green fluorescent protein) reporter-based technology that provides dynamic measurements of individual reporters in individual cells, the present paper proposes a dynamical systems approach to these issues. It involves a three-state experimental design: (1) formulate an oncologic pathway model of relevant processes; (2) perturb the pathways with the test drug and drugs with known effects on components of the pathways of interest; and (3) measure process activity indicators at various points on cell populations. This design addresses the fundamental problems in the design and analysis of combinatorial drug treatments. We apply the dynamical approach to three issues in the context of colon cancer cell lines: (1) identification of cell subpopulations possessing differing degrees of drug sensitivity; (2) the consequences of different drug dosing strategies on cellular processes; and (3) assessing the consequences of combinatorial versus monotherapy. Finally, we illustrate how the dynamical systems approach leads to a mechanistic hypothesis in the colon cancer HCT116 cell line.
PREDICTION OF SECONDARY STRUCTURE OF RNAs WITH PSEUDOKNOTS USING MATCHED FILTERS
Authors: KAKUMANI RAJASEKHAR , AHMAD M. OMAIR , DEVABHAKTUNI VIJAY KUMAR
Published: February 2013

Prediction of ribonucleic acid (RNA) secondary structure is an important task in bioinformatics. The RNA structure is known to influence its biological functionality. RNA secondary structure contains many substructures such as stems, loops and pseudoknots. The substructure pseudoknot occurs in several classes of RNAs, and plays a vital role in many biological processes. Prediction of pseudoknots in RNA is challenging and still an open research problem. Several computational methods based on dynamic programming, genetic algorithms, statistical models, etc., have been proposed with varying success. In this paper, we employ matched filtering approach to determine the RNA secondary structure containing pseudoknots. The central idea is to use a matched filter to identify the longest possible stem patterns in the base-pairing matrix of an RNA. The stem patterns obtained are then used to determine the locations of the other substructures such as loops and pseudoknots present in the RNA. Comparison of the prediction results, for RNA sequences derived from PseudoBase, illustrate the effectiveness and the accuracy of our proposed approach as compared to some of the existing popular RNA secondary structure prediction methods.
AN INVESTIGATION ON THE EFFECT OF ELECTROCHEMICAL ADSORBATES ON PROPERTIES OF ELECTRODEPOSITED NANOCRYSTALLINE Fe–Ni ALLOYS
Authors: SANATY-ZADEH A. , RAEISSI K. , SAIDI A.
Published: February 2013

Iron–Nickel nanocrystalline alloys were electrodeposited from a simple chloride bath using different current densities. The composition and grain size of deposited alloys were in the range of 29–42% Ni and 8–11 nm, respectively. The alloy deposited at lower current density showed higher microhardness, which is most probably due to its higher Fe content and lower grain size. EIS measurements showed that the iron hydroxide species can be formed and adsorbed onto the cathode surface during the deposition. Such species showed an inhibitive effect not only on Ni ion reduction but also on grain growth. By increasing the deposition current density, the adsorption tendency of iron hydroxide was reduced which caused an increase in grain size and Ni percentage of the alloy produced.
MECHANICAL SYSTEMS ON ALMOST PARA/PSEUDO-KÄHLER–WEYL MANIFOLDS
Authors: KASAP ZEKİ , TEKKOYUN MEHMET
Published: February 2013

The paper aims to introduce Lagrangian and Hamiltonian formalism for mechanical systems using para/pseudo-Kähler manifolds, representing an interesting multidisciplinary field of research. Moreover, the geometrical, relativistical, mechanical and physical results related to para/pseudo-Kähler mechanical systems are given, too.
HAMPI
Authors: Kiezun Adam , Ganesh Vijay , Artzi Shay , Guo Philip J. , Hooimeijer Pieter , Ernst Michael D.
Published: February 2013

Many automatic testing, analysis, and verification techniques for programs can be effectively reduced to a constraint-generation phase followed by a constraint-solving phase. This separation of concerns often leads to more effective and maintainable software reliability tools. The increasing efficiency of off-the-shelf constraint solvers makes this approach even more compelling. However, there are few effective and sufficiently expressive off-the-shelf solvers for string constraints generated by analysis of string-manipulating programs, so researchers end up implementing their own ad-hoc solvers.

To fulfill this need, we designed and implemented Hampi, a solver for string constraints over bounded string variables. Users of Hampi specify constraints using regular expressions, context-free grammars, equality between string terms, and typical string operations such as concatenation and substring extraction. Hampi then finds a string that satisfies all the constraints or reports that the constraints are unsatisfiable.

We demonstrate Hampi's expressiveness and efficiency by applying it to program analysis and automated testing. We used Hampi in static and dynamic analyses for finding SQL injection vulnerabilities in Web applications with hundreds of thousands of lines of code. We also used Hampi in the context of automated bug finding in C programs using dynamic systematic testing (also known as concolic testing). We then compared Hampi with another string solver, CFGAnalyzer, and show that Hampi is several times faster. Hampi's source code, documentation, and experimental data are available at http://people.csail.mit.edu/akiezun/hampi
1
Named entity recognition for tweets
Authors: Liu Xiaohua , Wei Furu , Zhang Shaodian , Zhou Ming
Published: February 2013

Two main challenges of Named Entity Recognition (NER) for tweets are the insufficient information in a tweet and the lack of training data. We propose a novel method consisting of three core elements: (1) normalization of tweets; (2) combination of a K-Nearest Neighbors (KNN) classifier with a linear Conditional Random Fields (CRF) model; and (3) semisupervised learning framework. The tweet normalization preprocessing corrects common ill-formed words using a global linear model. The KNN-based classifier conducts prelabeling to collect global coarse evidence across tweets while the CRF model conducts sequential labeling to capture fine-grained information encoded in a tweet. The semisupervised learning plus the gazetteers alleviate the lack of training data. Extensive experiments show the advantages of our method over the baselines as well as the effectiveness of normalization, KNN, and semisupervised learning.
Improving recency ranking using twitter data
Authors: Chang Yi , Dong Anlei , Kolari Pranam , Zhang Ruiqiang , Inagaki Yoshiyuki , Diaz Fernanodo , Zha Hongyuan , Liu Yan
Published: February 2013

In Web search and vertical search,
recency ranking
refers to retrieving and ranking documents by both relevance and freshness. As impoverished in-links and click information is the the biggest challenge for recency ranking, we advocate the use of Twitter data to address the challenge in this article. We propose a method to utilize Twitter TinyURL to detect fresh and high-quality documents, and leverage Twitter data to generate novel and effective features for ranking. The empirical experiments demonstrate that the proposed approach effectively improves a commercial search engine for both Web search ranking and tweet vertical ranking.
Reorder user's tweets
Authors: Shen Keyi , Wu Jianmin , Zhang Ya , Han Yiping , Yang Xiaokang , Song Li , Gu Xiao
Published: February 2013

Twitter displays the tweets a user received in a reversed chronological order, which is not always the best choice. As Twitter is full of messages of very different qualities, many informative or relevant tweets might be flooded or displayed at the bottom while some nonsense buzzes might be ranked higher. In this work, we present a supervised learning method for personalized tweets reordering based on user interests. User activities on Twitter, in terms of tweeting, retweeting, and replying, are leveraged to obtain the training data for reordering models. Through exploring a rich set of social and personalized features, we model the relevance of tweets by minimizing the pairwise loss of relevant and irrelevant tweets. The tweets are then reordered according to the predicted relevance scores. Experimental results with real twitter user activities demonstrated the effectiveness of our method. The new method achieved above 30% accuracy gain compared with the default ordering in twitter based on time.
Mining contextual movie similarity with matrix factorization for context-aware recommendation
Authors: Shi Yue , Larson Martha , Hanjalic Alan
Published: February 2013

Context-aware recommendation seeks to improve recommendation performance by exploiting various information sources in addition to the conventional user-item matrix used by recommender systems. We propose a novel context-aware movie recommendation algorithm based on joint matrix factorization (JMF). We jointly factorize the user-item matrix containing general movie ratings and other contextual movie similarity matrices to integrate contextual information into the recommendation process. The algorithm was developed within the scope of the mood-aware recommendation task that was offered by the Moviepilot mood track of the 2010 context-aware movie recommendation (CAMRa) challenge. Although the algorithm could generalize to other types of contextual information, in this work, we focus on two: movie mood tags and movie plot keywords. Since the objective in this challenge track is to recommend movies for a user given a specified mood, we devise a novel mood-specific movie similarity measure for this purpose. We enhance the recommendation based on this measure by also deploying the second movie similarity measure proposed in this article that takes into account the movie plot keywords. We validate the effectiveness of the proposed JMF algorithm with respect to the recommendation performance by carrying out experiments on the Moviepilot challenge dataset. We demonstrate that exploiting contextual information in JMF leads to significant improvement over several state-of-the-art approaches that generate movie recommendations without using contextual information. We also demonstrate that our proposed mood-specific movie similarity is better suited for the task than the conventional mood-based movie similarity measures. Finally, we show that the enhancement provided by the movie similarity capturing the plot keywords is particularly helpful in improving the recommendation to those users who are significantly more active in rating the movies than other users.
Using clouds for MapReduce measurement assignments
Authors: Rabkin Ariel , Reiss Charles , Katz Randy , Patterson David
Published: February 2013

We describe our experiences teaching MapReduce in a large undergraduate lecture course using public cloud services and the standard Hadoop API. Using the standard API, students directly experienced the quality of industrial big-data tools. Using the cloud, every student could carry out scalability benchmarking assignments on realistic hardware, which would have been impossible otherwise. Over two semesters, over 500 students took our course. We believe this is the first large-scale demonstration that it is feasible to use pay-as-you-go billing in the cloud for a large undergraduate course. Modest instructor effort was sufficient to prevent students from overspending. Average per-pupil expenses in the Cloud were under $45. Students were excited by the assignment: 90% said they thought it should be retained in future course offerings.
A model-driven approach to teaching concurrency
Authors: Carro Manuel , Herranz Ángel , Mariño Julio
Published: February 2013

We present an undergraduate course on concurrent programming where formal models are used in different stages of the learning process. The main practical difference with other approaches lies in the fact that the ability to develop correct concurrent software relies on a systematic transformation of formal models of inter-process interaction (so called
shared resources
), rather than on the specific constructs of some programming language. Using a resource-centric rather than a language-centric approach has some benefits for both teachers and students. Besides the obvious advantage of being independent of the programming language, the models help in the early validation of concurrent software design, provide students and teachers with a
lingua franca
that greatly simplifies communication at the classroom and during supervision, and help in the automatic generation of tests for the practical assignments. This method has been in use, with slight variations, for some 15 years, surviving changes in the programming language and course length. In this article, we describe the components and structure of the current incarnation of the course—which uses Java as target language—and some tools used to support our method. We provide a detailed description of the different outcomes that the model-driven approach delivers (validation of the initial design, automatic generation of tests, and mechanical generation of code) from a teaching perspective. A critical discussion on the perceived advantages and risks of our approach follows, including some proposals on how these risks can be minimized. We include a statistical analysis to show that our method has a positive impact in the student ability to understand concurrency and to generate correct code.
Approximate Recall Confidence Intervals
Authors: Webber William
Published: February 2013

Recall, the proportion of relevant documents retrieved, is an important measure of effectiveness in information retrieval, particularly in the legal, patent, and medical domains. Where document sets are too large for exhaustive relevance assessment, recall can be estimated by assessing a random sample of documents, but an indication of the reliability of this estimate is also required. In this article, we examine several methods for estimating two-tailed recall confidence intervals. We find that the normal approximation in current use provides poor coverage in many circumstances, even when adjusted to correct its inappropriate symmetry. Analytic and Bayesian methods based on the ratio of binomials are generally more accurate but are inaccurate on small populations. The method we recommend derives beta-binomial posteriors on retrieved and unretrieved yield, with fixed hyperparameters, and a Monte Carlo estimate of the posterior distribution of recall. We demonstrate that this method gives mean coverage at or near the nominal level, across several scenarios, while being balanced and stable. We offer advice on sampling design, including the allocation of assessments to the retrieved and unretrieved segments, and compare the proposed beta-binomial with the officially reported normal intervals for recent TREC Legal Track iterations.
Adaptive request batching for byzantine replication
Authors: de Sá Alírio Santos , Silva Freitas Allan Edgard , de Araújo Macêdo Raimundo José
Published: February 2013

Castro and Liskov proposed in 1999 a successful solution for byzantine fault-tolerant replication, named PBFT, which overcame performance drawbacks of earlier byzantine faulttolerant replication protocols. Other proposals extended PBFT with further optimizations, improving PBFT performance in certain conditions. One of the key optimizations of PBFT-based protocols is the use a request batching mechanism. If the target distributed system is dynamic, that is, if its underlying characteristics change dynamically, such as workload, channel QoS, network topology, etc., the configuration of the request batching mechanism must follow the dynamics of the system or it may not yield the desired performance improvement. This paper addresses this challenge by proposing an innovative solution to the dynamic configuration of request batching parameters inspired on feedback control theory. In order to evaluate its efficiency, the proposed solution is simulated in various scenarios and compared with the original version used in the PBFT-family protocols.
Report on the fourth workshop on hot topics in software upgrades (HotSWUp 2012)
Authors: Saur Karla , Neamtiu Iulian
Published: February 2013

The Fourth Workshop on Hot Topics in Software Upgrades (HotSWUp 2012) was held on June 3, 2012 in Zurich, Switzerland. The workshop was co-located with ICSE 2012. The goal of HotSWUp is to identify, through interdisciplinary collaboration, cutting-edge research ideas for implementing software upgrades. The workshop combined presentations of peer-reviewed research papers with a keynote speech on how empirical software engineering can help reduce update-induced failures. The audience included researchers and practitioners from academia and industry. In addition to the technical presentations, the program allowed ample time for discussions, which were driven by debate questions provided in advance by the presenters. HotSWUp provides a premier forum for discussing problems that are often considered niche topics in the established research communities. For example, the technical discussions at HotSWUp'12 covered dynamic software updates, package management tools, using model-checking and verification to verify updates, empirical software engineering and repository mining, and highlighted many synergies among these and other topics.
Induction of Apoptosis by Luteolin Involving Akt Inactivation in Human 786-O Renal Cell Carcinoma Cells
Authors: Ou Yen-Chuan , Kuan Yu-Hsiang , Li Jian-Ri , Raung Shue-Ling , Wang Chung-Chiang , Hung Yu-Yeh , Chen Chun-Jung
Published: February 2013

There is a growing interest in the health-promoting effects of natural substances obtained from plants. Although luteolin has been identified as a potential therapeutic and preventive agent for cancer because of its potent cancer cell-killing activity, the molecular mechanisms have not been well elucidated. This study provides evidence of an alternative target for luteolin and sheds light on the mechanism of its physiological benefits. Treatment of 786-O renal cell carcinoma (RCC) cells (as well as A498 and ACHN) with luteolin caused cell apoptosis and death. This cytotoxicity was caused by the downregulation of Akt and resultant upregulation of apoptosis signal-regulating kinase-1 (Ask1), p38, and c-Jun N-terminal kinase (JNK) activities, probably via protein phosphatase 2A (PP2A) activation. In addition to being a concurrent substrate of caspases and event of cell death, heat shock protein-90 (HSP90) cleavage might also play a role in driving further cellular alterations and cell death, at least in part, involving an Akt-related mechanism. Due to the high expression of HSP90 and Akt-related molecules in RCC and other cancer cells, our findings suggest that PP2A activation might work in concert with HSP90 cleavage to inactivate Akt and lead to a vicious caspase-dependent apoptotic cycle in luteolin-treated 786-O cells.
Role of New Biomarkers: Functional and Structural Damage
Authors: Tsigou Evdoxia , Psallida Vasiliki , Demponeras Christos , Boutzouka Eleni , Baltopoulos George
Published: February 2013

Traditional diagnosis of acute kidney injury (AKI) depends on detection of oliguria and rise of serum creatinine level, which is an unreliable and delayed marker of kidney damage. Delayed diagnosis of AKI in the critically ill patient is related to increased morbidity and mortality, prolonged length of stay, and cost escalation. The discovery of a reliable biomarker for early diagnosis of AKI would be very helpful in facilitating early intervention, evaluating the effectiveness of therapy, and eventually reducing cost and improving outcome. Innovative technologies such as genomics and proteomics have contributed to the discovery of new biomarkers, such as neutrophil gelatinase-associated lipocalin (NGAL), cystatin C (Cys C), kidney injury molecule-1 (KIM-1), interleukin-18 (IL-18), and liver-type fatty acid binding protein (L-FABP). The current status of the most promising of these novel AKI biomarkers, including NGAL, Cys C, KIM-1, L-FABP, and IL-18, is reviewed.
Quality of Life in Persons with Intellectual Disabilities and Mental Health Problems: An Explorative Study
Authors: Morisse Filip , Vandemaele Eleonore , Claes Claudia , Claes Lien , Vandevelde Stijn
Published: February 2013

The field of intellectual disability (ID) is strongly influenced by the Quality of Life paradigm (QOL). We aimed at investigating whether or not the QOL paradigm also applies to clients with ID and cooccurring mental health problems. This paper aims at stimulating a debate on this topic, by investigating whether or not QOL domains are universal. Focus groups with natural and professional network members were organized to gather qualitative data, in order to answer two questions: (1) Are the QOL dimensions conceptualized in the model of Schalock et al. applicable for persons with ID and mental health problems? (2) What are indicators relating to the above‐mentioned dimensions in relation to persons with ID and mental health problems? The results offer some proof for the assumption that the QOL construct seems to have universal properties. With regard to the second question, the study revealed that the natural and professional network members are challenged to look for the most appropriate support strategies, taking specific indicators of QOL into account. When aspects of empowerment and regulation are used in an integrated manner, the application of the QOL paradigm could lead to positive outcomes concerning self‐determination, interdependence, social inclusion, and emotional development.
Performance Recognition for Sulphur Flotation Process Based on Froth Texture Unit Distribution
Authors: He Mingfang , Yang Chunhua , Gui Weihua , Ling Yiqiu
Published: February 2013

As an important indicator of flotation performance, froth texture is believed to be related to operational condition in sulphur flotation process. A novel fault detection method based on froth texture unit distribution (TUD) is proposed to recognize the fault condition of sulphur flotation in real time. The froth texture unit number is calculated based on texture spectrum, and the probability density function (PDF) of froth texture unit number is defined as texture unit distribution, which can describe the actual textual feature more accurately than the grey level dependence matrix approach. As the type of the froth TUD is unknown, a nonparametric kernel estimation method based on the fixed kernel basis is proposed, which can overcome the difficulty when comparing different TUDs under various conditions is impossible using the traditional varying kernel basis. Through transforming nonparametric description into dynamic kernel weight vectors, a principle component analysis (PCA) model is established to reduce the dimensionality of the vectors. Then a threshold criterion determined by theTQstatistic based on the PCA model is proposed to realize the performance recognition. The industrial application results show that the accurate performance recognition of froth flotation can be achieved by using the proposed method.
An Unusual Case Report of Erupted Odontoma
Authors: Mehta Dhaval , Raval Nilesh , Udhani Sneha , Parekh Viral , Modi Chintan
Published: February 2013

Odontomas are the most common of the odontogenic tumors of the jaws, which are benign, slow growing, and nonaggressive. They are usually asymptomatic and found in routine dental radiographic examination. Odontomas are usually associated with tooth eruption disturbances. Eruption of odontoma in oral cavity is rare entity. Here we report a case of an unusual erupted compound odontoma.
Perspectives in Molecular Imaging Using Staging Biomarkers and Immunotherapies in Alzheimer’s Disease
Authors: Leclerc Benoît , Abulrob Abedelnasser
Published: February 2013

Sporadic Alzheimer’s disease (AD) is an emerging chronic illness characterized by a progressive pleiotropic pathophysiological mode of actions triggered during the senescence process and affecting the elderly worldwide. The complex molecular mechanisms of AD not only are supported by cholinergic, beta‐amyloid, and tau theories but also have a genetic basis that accounts for the difference in symptomatology processes activation among human population which will evolve into divergent neuropathological features underlying cognitive and behaviour alterations. Distinct immune system tolerance could also influence divergent responses among AD patients treated by immunotherapy. The complexity in nature increases when taken together the genetic/immune tolerance with the patient’s brain reserve and with neuropathological evolution from early till advance AD clinical stages. The most promising diagnostic strategies in today’s world would consist in performing high diagnostic accuracy of combined modality imaging technologies using beta‐amyloid 42 peptide‐cerebrospinal fluid (CSF) positron emission tomography (PET), Pittsburgh compound B‐PET, fluorodeoxyglucose‐PET, total and phosphorylated tau‐CSF, and volumetric magnetic resonance imaging hippocampus biomarkers for criteria evaluation and validation. Early diagnosis is the challenge task that needs to look first at plausible mechanisms of actions behind therapies, and combining them would allow for the development of efficient AD treatment in a near future.
Albumin-Like Proteins Are Critical Regulators of Vascular Redox Signaling
Authors: Ramos Kenneth S. , Stribinskis Vilius , Steffen Marlene C. , Nanez Adrian , Montoya-Durango Diego , He Qiang
Published: February 2013

This laboratory previously identified an albumin-like protein (denoted as p70) as a component of the macromolecular complex assembled within the 5′-regulatory region of redox-sensitive genes in vascular smooth muscle cells (vSMCs). Here we show that p70 is present in the cytosolic and nuclear compartments of vSMCs and dynamically responsive to redox status. Intense cytoplasmic and perinuclear staining, coupled with enhanced nuclear localization, was observed in vSMCs, but not HepG2 cells, treated with benzo(a)pyrene (BaP), H2O2, or N-acetylcysteine, agents known to modulate redox status. 3′ RACE indicated that p70 is not generated as a product of endogenous gene expression, but rather taken up from the extracellular compartment. While p70 was undetectable in cells grown for 24 hours under serum-free conditions, cell-associated, acid-resistant albumin was detected 30 min after the addition of exogenous albumin. vSMCs incubated at 4°C with 100 μg/mL unlabeled BSA and 10 μg/mL FITC-BSA for 60 minutes and switched to 37°C to examine temperature-sensitive label uptake showed punctate structures throughout the cell consistent with albumin internalization at the higher temperature. Albumin was found to influence redox-signaling, as evidenced by modulation of cyp1a1 gsta1 and Ha-ras gene inducibility. Together, these results implicate albumin and albumin-like proteins as critical regulators of vascular redox signaling.
Reuse Feasibility of Electrocoagulated Metal Hydroxide Sludge of Textile Industry in the Manufacturing of Building Blocks
Authors: Adyel Tanveer Mehedi , Rahman Syed Hafizur , Zaman Mohammad Moniruz , Sayem Hossain Md. , Khan Mala , Abdul Gafur Md. , Islam S. M. Nazrul
Published: February 2013

During the last decade, the growing load of sludge from textile industries, the top foreign exchange earning sector of Bangladesh, is a common nuisance to environmental system and community health. The present study was aimed to minimize the environmental impact from the disposal of Electrocoagulated Metal Hydroxide Sludge (EMHS) by using it as a partial substitute of clay in the manufacturing of construction material like building blocks (BBs). Different batches of normal and pressurized building blocks (NBBs and PBBs, resp.) were prepared using up to 50% EMHS with clay and then fired at a particular temperature. EMHS proportion in the mixture and firing temperature were two key factors determining the quality of BB. BB did not show any deformation or uneven surfaces at any of the examined firing temperature. At higher firing temperature and EMHS proportion, more weight loss and shrinkage of BB were noticed. Higher compressive strength and lower water adsorption were found at lower EMHS content and higher firing temperature. It was explored that NBB and PBB with 20 and 30% EMHS in clay, respectively, and fired at 1050 °C would be usable for nonloading applications; namely, ornamental bricks, decoration purposes, and fence of garden.
A CD90+ Tumor-Initiating Cell Population with an Aggressive Signature and Metastatic Capacity in Esophageal Cancer
Authors: Tang Kwan Ho , Dai Yong Dong , Tong Man , Chan Yuen Piu , Kwan Pak Shing , Fu Li , Qin Yan Ru , Tsao Sai Wah , Lung Hong Lok , Lung Maria L. , Tong Daniel K. , Law Simon , Chan Kwok Wah , Ma Stephanie , Guan Xin Yuan
Published: February 2013

Tumor-initiating cells (TIC), also known as cancer stem cells, are regarded widely as a specific subpopulation of cells needed for cancer initiation and progression. TICs have yet to be identified in esophageal tumors that have an increasing incidence in developed countries. Here, we report a CD90+ cell population found in esophageal squamous cell carcinoma (ESCC), which is endowed with stem cell–like properties and high tumorigenic and metastatic potential. mRNA profiling of these cells suggested pathways through which they drive tumor growth and metastasis, with deregulation of an Ets-1/MMP signaling pathway and epithelial–mesenchymal transition figuring prominently. These cells possessed higher self-renewal activity and were sufficient for tumor growth, differentiation, metastasis, and chemotherapeutic resistance. CD90+ TICs were isolated and characterized from ESCC clinical specimens as well as ESCC cell lines. In freshly resected clinical specimens, they represented a rare cell population, the levels of which correlated with strong family histories and lymph node metastasis. Our results prompt further study of this CD90+ population of esophageal TICs as potential therapeutic targets. Cancer Res; 73(7); 2322–32. ©2013 AACR.