bluuebunny/crossref_metadata_2025 huggingface dataset:
Lumbar Discitis Caused by Clostridium perfringens
Authors: Lotte Romain , Popoff M. R. , Degand Nicolas , Lotte Laurene , Bouvet Philippe , Baudin Guillaume , Cua Eric , Roger Pierre-Marie , Ruimy Raymond
Published: July 2014

We report here a rare case of chronic lumbar discitis caused by
Clostridium perfringens
in an elderly patient that was treated with a combination of β-lactams and clindamycin. Molecular analysis performed on the strain revealed an unusual toxin gene pattern.
Comparison of Amplicor and GeneXpert MTB/RIF Tests for Diagnosis of Tuberculous Meningitis
Authors: Patel Vinod B. , Connolly Cathy , Singh Ravesh , Lenders Laura , Matinyenya Brian , Theron Grant , Ndung'u Thumbi , Dheda Keertan
Published: July 2014

There are no data about the comparative accuracy of commercially available nucleic acid amplification tests (GeneXpert MTB/RIF and Roche Amplicor) for the diagnosis of tuberculous meningitis (TBM). A total of 148 patients with suspected TBM were evaluated, and cultures served as the reference standard. The sensitivities and specificities (95% confidence interval [CI]) for the Amplicor and Xpert MTB/RIF tests were similar: 46 (31–60) versus 50 (33–67) and 99 (93–100) and 94 (84–99), respectively.
Detection of Respiratory Viruses in Sputum from Adults by Use of Automated Multiplex PCR
Authors: Branche Angela R. , Walsh Edward E. , Formica Maria A. , Falsey Ann R.
Published: July 2014

Respiratory tract infections (RTI) frequently cause hospital admissions among adults. Diagnostic viral reverse transcriptase PCR (RT-PCR) of nose and throat swabs (NTS) is useful for patient care by informing antiviral use and appropriate isolation. However, automated RT-PCR systems are not amenable to utilizing sputum due to its viscosity. We evaluated a simple method of processing sputum samples in a fully automated respiratory viral panel RT-PCR assay (FilmArray). Archived sputum and NTS samples collected in 2008-2012 from hospitalized adults with RTI were evaluated. A subset of sputum samples positive for 10 common viruses by a uniplex RT-PCR was selected. A sterile cotton-tip swab was dunked in sputum, swirled in 700 μL of sterile water (dunk and swirl method) and tested by the FilmArray assay. Quantitative RT-PCR was performed on “dunked” sputum and NTS samples for influenza A (Flu A), respiratory syncytial virus (RSV), coronavirus OC43 (OC43), and human metapneumovirus (HMPV). Viruses were identified in 31% of 965 illnesses using a uniplex RT-PCR. The sputum sample was the only sample positive for 105 subjects, including 35% (22/64) of influenza cases and significantly increased the diagnostic yield of NTS alone (302/965 [31%] versus 197/965 [20%];
P
= 0.0001). Of 108 sputum samples evaluated by the FilmArray assay using the dunk and swirl method, 99 (92%) were positive. Quantitative RT-PCR revealed higher mean viral loads in dunked sputum samples compared to NTS samples for Flu A, RSV, and HMPV (
P
= 0.0001,
P
= 0.006, and
P
= 0.011, respectively). The dunk and swirl method is a simple and practical method for reliably processing sputum samples in a fully automated PCR system. The higher viral loads in sputa may increase detection over NTS testing alone.
Inducible Gene Expression in Tumors Colonized by Modified Oncolytic Vaccinia Virus Strains
Authors: Stritzker Jochen , Huppertz Sascha , Zhang Qian , Geissinger Ulrike , Härtl Barbara , Gentschev Ivaylo , Szalay Aladar A.
Published: July 2014

Exogenous gene induction of therapeutic, diagnostic, and safety mechanisms could be a considerable improvement in oncolytic virotherapy. Here, we introduced a doxycycline-inducible promoter system (comprised of a tetracycline repressor, several promoter constructs, and a
tet
operator sequence) into oncolytic recombinant vaccinia viruses (rVACV), which were further characterized in detail. Experiments in cell cultures as well as in tumor-bearing mice were analyzed to determine the role of the inducible-system components. To accomplish this, we took advantage of the optical reporter construct, which resulted in the production of click-beetle luciferase as well as a red fluorescent protein. The results indicated that each of the system components could be used to optimize the induction rates and had an influence on the background expression levels. Depending on the given gene to be induced in rVACV-colonized tumors of patients, we discuss the doxycycline-inducible promoter system adjustment and further optimization.

IMPORTANCE
Oncolytic virotherapy of cancer can greatly benefit from the expression of heterologous genes. It is reasonable that some of those heterologous gene products could have detrimental effects either on the cancer patient or on the oncolytic virus itself if they are expressed at the wrong time or if the expression levels are too high. Therefore, exogenous control of gene expression levels by administration of a nontoxic inducer will have positive effects on the safety as well as the therapeutic outcome of oncolytic virotherapy. In addition, it paves the way for the introduction of new therapeutic genes into the genome of oncolytic viruses that could not have been tested otherwise.
Virus-Specific Memory CD8 T Cells Provide Substantial Protection from Lethal Severe Acute Respiratory Syndrome Coronavirus Infection
Authors: Channappanavar Rudragouda , Fett Craig , Zhao Jincun , Meyerholz David K. , Perlman Stanley
Published: July 2014

Severe acute respiratory syndrome coronavirus (SARS-CoV) caused an acute human respiratory illness with high morbidity and mortality in 2002-2003. Several studies have demonstrated the role of neutralizing antibodies induced by the spike (S) glycoprotein in protecting susceptible hosts from lethal infection. However, the anti-SARS-CoV antibody response is short-lived in patients who have recovered from SARS, making it critical to develop additional vaccine strategies. SARS-CoV-specific memory CD8 T cells persisted for up to 6 years after SARS-CoV infection, a time at which memory B cells and antivirus antibodies were undetectable in individuals who had recovered from SARS. In this study, we assessed the ability of virus-specific memory CD8 T cells to mediate protection against infection in the absence of SARS-CoV-specific memory CD4 T or B cells. We demonstrate that memory CD8 T cells specific for a single immunodominant epitope (S436 or S525) substantially protected 8- to 10-month-old mice from lethal SARS-CoV infection. Intravenous immunization with peptide-loaded dendritic cells (DCs) followed by intranasal boosting with recombinant vaccinia virus (rVV) encoding S436 or S525 resulted in accumulation of virus-specific memory CD8 T cells in bronchoalveolar lavage fluid (BAL), lungs, and spleen. Upon challenge with a lethal dose of SARS-CoV, virus-specific memory CD8 T cells efficiently produced multiple effector cytokines (gamma interferon [IFN-γ], tumor necrosis factor alpha [TNF-α], and interleukin 2 [IL-2]) and cytolytic molecules (granzyme B) and reduced lung viral loads. Overall, our results show that SARS-CoV-specific memory CD8 T cells protect susceptible hosts from lethal SARS-CoV infection, but they also suggest that SARS-CoV-specific CD4 T cell and antibody responses are necessary for complete protection.

IMPORTANCE
Virus-specific CD8 T cells are required for pathogen clearance following primary SARS-CoV infection. However, the role of SARS-CoV-specific memory CD8 T cells in mediating protection after SARS-CoV challenge has not been previously investigated. In this study, using a prime-boost immunization approach, we showed that virus-specific CD8 T cells protect susceptible 8- to 10-month-old mice from lethal SARS-CoV challenge. Thus, future vaccines against emerging coronaviruses should emphasize the generation of a memory CD8 T cell response for optimal protection.
Exosomes from Human Immunodeficiency Virus Type 1 (HIV-1)-Infected Cells License Quiescent CD4
+
T Lymphocytes To Replicate HIV-1 through a Nef- and ADAM17-Dependent Mechanism
Authors: Arenaccio Claudia , Chiozzini Chiara , Columba-Cabezas Sandra , Manfredi Francesco , Affabris Elisabetta , Baur Andreas , Federico Maurizio
Published: July 2014

Resting CD4
+
T lymphocytes resist human immunodeficiency virus (HIV) infection. Here, we provide evidence that exosomes from HIV-1-infected cells render resting human primary CD4
+
T lymphocytes permissive to HIV-1 replication. These results were obtained with transwell cocultures of HIV-1-infected cells with quiescent CD4
+
T lymphocytes in the presence of inhibitors of exosome release and were confirmed using exosomes purified from supernatants of HIV-1-infected primary CD4
+
T lymphocytes. We found that the expression of HIV-1 Nef in exosome-producing cells is both necessary and sufficient for cell activation as well as HIV-1 replication in target CD4
+
T lymphocytes. We also identified a Nef domain important for the effects we observed, i.e., the
62
EEEE
65
acidic cluster domain. In addition, we observed that ADAM17, i.e., a disintegrin and metalloprotease converting pro-tumor necrosis factor alpha (TNF-α) in its mature form, associates with exosomes from HIV-1-infected cells, and plays a key role in the HIV-1 replication in quiescent CD4
+
T lymphocytes. Treatment with an inhibitor of ADAM17 abolished both activation and HIV-1 replication in resting CD4
+
T lymphocytes. TNF-α is the downstream effector of ADAM17 since the treatment of resting lymphocytes with anti-TNF-α antibodies blocked the HIV-1 replication. The data presented here are consistent with a model where Nef induces intercellular communication through exosomes to activate bystander quiescent CD4
+
T lymphocytes, thus stimulating viral spread.

IMPORTANCE
Overall, our findings support the idea that HIV evolved to usurp the exosome-based intercellular communication network to favor its spread in infected hosts.
Short Self-Interacting N-Terminal Region of Rubella Virus Capsid Protein Is Essential for Cooperative Actions of Capsid and Nonstructural p150 Proteins
Authors: Sakata Masafumi , Otsuki Noriyuki , Okamoto Kiyoko , Anraku Masaki , Nagai Misato , Takeda Makoto , Mori Yoshio
Published: July 2014

Nucleocapsid formation is a primary function of the rubella virus capsid protein, which also promotes viral RNA synthesis via an unknown mechanism. The present study demonstrates that in infected cells, the capsid protein is associated with the nonstructural p150 protein via the short self-interacting N-terminal region of the capsid protein. Mutational analyses indicated that hydrophobic amino acids in this N-terminal region are essential for its N-terminal self-interaction, which is critical for the capsid-p150 association. An analysis based on a subgenomic replicon system demonstrated that the self-interacting N-terminal region of the capsid protein plays a key role in promoting viral gene expression. Analyses using a virus-like particle (VLP) system also showed that the self-interacting N-terminal region of the capsid protein is not essential for VLP production but is critical for VLP infectivity. These results demonstrate that the close cooperative actions of the capsid protein and p150 require the short self-interacting N-terminal region of the capsid protein during the life cycle of the rubella virus.

IMPORTANCE
The capsid protein of rubella virus promotes viral RNA replication via an unknown mechanism. This protein interacts with the nonstructural protein p150, but the importance of this interaction is unclear. In this study, we demonstrate that the short N-terminal region of the capsid protein forms a homo-oligomer that is critical for the capsid-p150 interaction. These interactions are required for the viral-gene-expression-promoting activity of the capsid protein, allowing efficient viral growth. These findings provide information about the mechanisms underlying the regulation of rubella virus RNA replication via the cooperative actions of the capsid protein and p150.
Careers in Virology: Teaching at a Primarily Undergraduate Institution
Authors: Kushner David B.
Published: July 2014

A faculty position at a primarily undergraduate institution requires working with undergraduates in both the classroom and the research lab. Graduate students and postdoctoral fellows who are interested in such a career should understand that faculty at these institutions need to teach broadly and devise research questions that can be addressed safely and with limited resources compared to a research I university. Aspects of, and ways to prepare for, this career will be reviewed herein.
Annexin A11 (ANXA11) gene polymorphisms are associated with sarcoidosis in a Han Chinese population: a case–control study
Authors: Feng Xianjun , Zang Shuzhi , Yang Yanrong , Zhao Shasha , Li Yunxia , Gao Xinyuan , Zhang Ligong
Published: July 2014

Objectives

To further identify the single-nucleotide polymorphisms (SNPs) that contribute to the genetic susceptibility to sarcoidosis, we examined the potential association between sarcoidosis and 15 SNPs of the ANXA11 gene.

Design

A case–control study.

Setting

A tuberculosis unit in a hospital of the university in China.

Participants

Participants included 412 patients with sarcoidosis and 418 healthy controls.

Methods

The selected SNPs were genotyped using the MALDI-TOF in the MassARRAY system.

Results

Statistically significant differences were found in the allelic or genotypic frequencies of the rs2789679, rs1049550 and rs2819941 in the ANXA11 gene between patients with sarcoidosis and controls. The rs2789679 A allele (p=0.00004, OR=1.42, 95% CI 1.17 to 1.73) and rs2819941 T allele (p=0.0006, OR=1.41, 95% CI 1.16 to 1.71) were significantly more frequent in patients with sarcoidosis compared with controls. The frequency of the rs1049550 T allele (p=0.000002, OR=0.61, 95% CI 0.49 to 0.74) in patients with sarcoidosis was significantly lower than that in controls. The multi-SNP model reveals that rs1049550 is the only independent SNP association effect after accounting for the other two marginally associated SNPs. In block 2 (rs1049550–rs2573351), the T–C haplotype occurred significantly less frequently (p=0.001), whereas the C–C haplotypes occurred more frequently (p=0.0001) in patients with sarcoidosis than controls. Furthermore, genotype frequency distribution revealed that, in rs1049550, the CC genotype was significantly more in patients with chest X-ray (CXR) stage I sarcoidosis than in patients with CXR stage II–IV sarcoidosis (p=0.012).

Conclusions

These findings point to a role for the polymorphisms of ANXA11 in sarcoidosis in a Chinese Han population, and may be informative for future genetic studies on sarcoidosis.
Patient and public involvement in the early stages of clinical trial development: a systematic cohort investigation
Authors: Gamble Carrol , Dudley Louise , Allam Alison , Bell Philip , Goodare Heather , Hanley Bec , Preston Jennifer , Walker Alison , Williamson Paula , Young Bridget
Published: July 2014

Background

Randomised controlled trials (RCTs) are considered particularly likely to benefit from patient and public involvement (PPI). Decisions made by professional researchers at the outset may go on to have a significant impact on the potential for PPI contributions.

Objective

To increase knowledge of PPI within the early development of RCTs by systematically describing the reported level, nature and acceptability of proposed PPI to the funders.

Methods

Documentation from the outline application process for all RCTs that received funding from the Health Technology Assessment (HTA) Programme 2006–2010 was requested. For each application, data were extracted on trial characteristics, references to PPI in the development of the outline application and funding Board feedback, and plans for PPI in the full application and after the trial was funded.

Results

110 applications were eligible with outline applications available for 90 (82%). The cohort covered a wide range of interventions and conditions. 54% (49/90) provided some information about PPI. 26 (28.9%) indicated PPI within the development of the outline application itself; 32 (35.6%) planned involvement in the full application and 43 (48%) once the trial was funded. Recruitment at diagnosis and surgical interventions were less likely to describe PPI. Blinded trials and trials in which participants may receive placebo only, more frequently described PPI activity. The HTA commissioning Board feedback rarely referred to PPI.

Conclusions

Incorporation of PPI within the development of the outline application or specification of plans for future involvement was low. Funder requests for applicants to provide information on PPI and justification for its absence should be welcomed but further research is needed to identify the impact of this on its contributions to research. Comments on PPI by reviewers should be directional rather than state that an increase is required. Challenges facing applicants in initiating PPI prior to funding need to be addressed.
Brazilian medicinal plants to treat upper respiratory tract and bronchial illness: systematic review and meta-analyses—study protocol
Authors: Lopes Luciane C , Silva Maria Carolina O , Motta Cristiane Bergamashi , Macho Quirós Antonio , Biavatti Maique Weber , de Oliveira Jardel Corrêa , Guyatt Gordon
Published: July 2014

Introduction

Respiratory illness, often associated with cough and sputum, is frequent. In Brazil, herbal medicines are often recommended as a first-line treatment for respiratory illness. There exists uncertainty regarding the effectiveness of these treatments. No systematic review has evaluated Brazilian medicinal plants (BMP) to treat upper respiratory tract and bronchial illness (URTI).

Methods and analysis

We will conduct a systematic review and, if appropriate, a series of meta-analyses evaluating the safety and effectiveness of BMP for URTI. Eligible randomised controlled trials and observational studies will enrol adult or paediatric patients presenting with URTI treated by BMP approved by the Brazilian Health Surveillance Agency compared with placebo, no treatment or an alternative therapy. Our search will include the Cochrane Central Register of Controlled Trials (CENTRAL), which contains the Cochrane Acute Respiratory Illness Group's Specialized Register; MEDLINE; EMBASE; CINAHL (Cumulative Index to Nursing and Allied Health Literature); Web of Science; AMED; LILACS; CAB abstracts; clinical trial.gov; the WHO Trial Register and the Brazilian thesis database (CAPES) without any language restrictions. Outcomes of interest are time to resolution of clinical symptoms and/or signs (cough, sputum production or activity limitations), severity of symptoms prior to resolution and major/minor adverse events. Teams of reviewers will, independently and in duplicate, screen titles and abstracts and the complete full text to determine eligibility. For eligible studies, reviewers will perform data abstraction and assess risk of bias of eligible trials. When appropriate, we will conduct meta-analyses. We will also assess the quality of body of evidence (confidence in estimates of effect) for each of the outcomes using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach.

Ethics and dissemination

The systematic review will be published in a peer-reviewed journal. Brief reports of review findings will be disseminated directly to appropriate audiences via email and other modes of communication. The review will guide healthcare practice and policy in Brazil.

Trial registration number

Prospero CRD42014007057.
Perceptions of chronically ill and healthy consumers about electronic personal health records: a comparative empirical investigation
Authors: Cocosila Mihail , Archer Norm
Published: July 2014

Objective

To develop a model of consumer perceptions of electronic personal health records (PHRs) and validate it in a comparative study between consumers who report having a chronic illness and those who report being well.

Materials and methods

A model of PHR use motivators and barriers was built and tested through a national survey across Canada. Data were collected from 800 individuals, 18 years or older. Half reported having a chronic illness or disability and half reported being well. Analyses were performed with structural equation modelling techniques.

Results

A total of 389 answers from chronically ill and 383 from well participants were collected. Perceived usefulness was the key explanation of the intention to use PHRs for both ill and well people (total effect of 0.601 and 0.565, respectively) followed by security, privacy and trust in PHRs (total effect of 0.377 and 0.479, respectively). Conversely, computer anxiety was perceived as a significant barrier (total effect of −0.327 for ill individuals and −0.212 for well individuals).

Discussion

The model proposed was appropriate in explaining key consumer positive and negative perceptions on electronic PHR use. We found little difference in perceptions of electronic PHRs between chronically ill and well individuals, although self-reporting their health status might have influenced the results.

Conclusions

To increase the adoption rate of electronic PHRs among both chronically ill and well consumers it is necessary to reinforce consumer perceptions of the usefulness of and trust in these eHealth technologies while mitigating their anxieties about computer use in general.
Mapping patient pathways and estimating resource use for point of care versus standard testing and treatment of chlamydia and gonorrhoea in genitourinary medicine clinics in the UK
Authors: Adams Elisabeth J , Ehrlich Alice , Turner Katherine M E , Shah Kunj , Macleod John , Goldenberg Simon , Meray Robin K , Pearce Vikki , Horner Patrick
Published: July 2014

Objectives

We aimed to explore patient pathways using a chlamydia/gonorrhoea point-of-care (POC) nucleic acid amplification test (NAAT), and estimate and compare the costs of the proposed POC pathways with the current pathways using standard laboratory-based NAAT testing.

Design/participants

Workshops were conducted with healthcare professionals at four sexual health clinics representing diverse models of care in the UK. They mapped out current pathways that used chlamydia/gonorrhoea tests, and constructed new pathways using a POC NAAT. Healthcare professionals' time was assessed in each pathway.

Outcome measure

The proposed POC pathways were then priced using a model built in Microsoft Excel, and compared to previously published costs for pathways using standard NAAT-based testing in an off-site laboratory.

Results

Pathways using a POC NAAT for asymptomatic and symptomatic patients and chlamydia/gonorrhoea-only tests were shorter and less expensive than most of the current pathways. Notably, we estimate that POC testing as part of a sexual health screen for symptomatic patients, or as stand-alone chlamydia/gonorrhoea testing, could reduce costs per patient by as much as £16 or £6, respectively. In both cases, healthcare professionals' time would be reduced by approximately 10 min per patient.

Conclusions

POC testing for chlamydia/gonorrhoea in a clinical setting may reduce costs and clinician time, and may lead to more appropriate and quicker care for patients. Further study is warranted on how to best implement POC testing in clinics, and on the broader clinical and cost implications of this technology.
Clinical significance of low forced expiratory flow between 25% and 75% of vital capacity following treated pulmonary tuberculosis: a cross-sectional study
Authors: Pefura-Yone Eric Walter , Kengne Andre Pascal , Tagne-Kamdem Pierre Eugene , Afane-Ze Emmanuel
Published: July 2014

Objectives

The aim of this study was to assess the prevalence and determinants of post-tuberculosis chronic respiratory signs, as well as the clinical impact of a low forced expiratory flow between 25% and 75% (FEF25–75%) in a group of individuals previously treated successfully for pulmonary tuberculosis.

Design

This was a cross-sectional study involving individuals in their post-tuberculosis treatment period. They all underwent a spirometry following the 2005 criteria of the American Thoracic Society/European Respiratory Society. Distal airflow obstruction (DAO) was defined by an FEF25–75%<65% and a ratio forced expiratory volume during the first second (FEV1)/forced vital capacity (FVC) ≥ 0.70. Logistic regression models were used to investigate the determinants of persisting respiratory symptoms following antituberculous treatment.

Setting

This study was carried out in the tuberculosis diagnosis and treatment centre at Yaounde Jamot Hospital, which serves as a referral centre for tuberculosis and respiratory diseases for the capital city of Cameroon (Yaounde) and surrounding areas.

Participants

All consecutive patients in their post-tuberculosis treatment period were consecutively enrolled between November 2012 and April 2013.

Results

Of the 177 patients included, 101 (57.1%) were men, whose median age (25th-75th centiles) was 32 (24–45.5) years. At least one chronic respiratory sign was present in 110 (62.1%) participants and DAO was found in 67 (62.9%). Independent determinants of persisting respiratory signs were the duration of symptoms prior to tuberculosis diagnosis higher than 12 weeks (adjusted OR 2.91; 95% CI 1.12 to 7.60, p=0.029) and presence of DAO (2.22; 1.13 to 4.38, p=0.021).

Conclusions

FEF25–75%<65% is useful for the assessment and diagnosis of post-tuberculous DAO. Mass education targeting early diagnosis of pulmonary tuberculosis can potentially reduce the prevalence of post-tuberculosis respiratory signs and distal airflow obstruction.
Are we exposing patients with a mildly elevated faecal calprotectin to unnecessary investigations?
Authors: Seenan J P , Thomson F , Rankin K , Smith K , Gaya D R
Published: July 2014

Objective

Faecal calprotectin (FC) is a non-invasive marker used to differentiate irritable bowel syndrome from inflammatory bowel disease (IBD). However, false positives are common. We sought to determine the diagnostic yield of investigation in patients presenting with new lower gastrointestinal (GI) symptoms and a mildly elevated FC (100–200 µg/g).

Design

Retrospective study of electronic patient records.

Patients

Patients aged 16–50 years with new lower GI symptoms and an FC 100–200 µg/g were identified from our biochemistry laboratory database between September 2009 and 2011. Patients were excluded if they had a previous FC >200 µg/g, were taking non-steroidal anti-inflammatory drugs (NSAIDs), had IBD, positive stool cultures or ‘alarm’ symptoms.

Setting

Secondary care gastroenterology clinics.

Results

161 patients (103 female patients) were identified. Mean age was 37.3 years with a mean FC of 147 µg/g. 398 endoscopic, radiological and histological investigations were undertaken in 141 patients (an average of 2.8 investigations per patient). 131 colonoscopies were performed with abnormalities in only 24 (18.3%). In patients with a macroscopically normal upper GI endoscopy and colonoscopy, the diagnostic yield of any further investigation was only 7.3%. The negative predictive value (NPV) of an FC 100–200 µg/g was 86.7% for any pathology and 97.5% for significant luminal pathology (IBD, advanced adenoma or colorectal carcinoma). After a mean follow-up of 172.4 weeks, IBD was the final diagnosis in only 4 (2.5%) of patients.

Conclusions

In adult patients under 50 years old presenting with new lower GI symptoms, the NPV of an FC between 100 and 200 µg/g in excluding significant organic GI disease is high.
The significance of autophagy in colorectal cancer pathogenesis and implications for therapy
Authors: Lai K , Killingsworth M C , Lee C S
Published: July 2014

Colorectal cancer (CRC) is one of the most common cancers in developed countries with poor survival outcome in advanced stages of the disease due to its resistance to chemotherapy and other forms of treatment. New and alternative approaches are needed to overcome the tumour cells’ capacity for survival and to drive the tumour towards cell death. Autophagy is a mechanism involved in the elimination of damaged cellular components through lysosomal degradation and is capable of inducing programmed cell death. The process has recently gained much interest in understanding the pathogenesis of CRC and its potential for treatment of the disease due to its role in host protection and anticancer activity. This review describes and illustrates the fundamental mechanisms of autophagy, its importance as a prognostic marker and the current approaches to harness its protective and anticancer activity in CRC therapy.
Pregnancy intentions among female sex workers: recognising their rights and wants as mothers
Authors: Duff Putu , Shoveller Jeannie , Feng Cindy , Ogilvie Gina , Montaner Julio , Shannon Kate
Published: July 2014

Objective

To better understand the prevalence and correlates of pregnancy intentions among female sex workers (FSWs).

Design

Cross-sectional analysis using data from an open prospective cohort of street and off-street FSWs in Vancouver, Canada, in partnership with local sex work and community agencies.

Methods

FSWs were recruited through outreach to street and off-street locations (e.g. massage parlours, micro-brothels) and completed interviewer-administered questionnaires and HIV/sexually transmitted infection testing. Bivariable and multivariable logistic regression was used to evaluate correlates of pregnancy intention, based on a ‘yes’ or ‘no’ response to the question “Are you planning on have any (any more) children in the future?”.

Results

Of the 510 women, 394 (77.3%) reported prior pregnancy, with 140 (27.5%) of the entire sample reporting positive pregnancy intentions. Regarding ethnicity, 35.3% were Caucasian and 26.3% were Asian/visible minority, with no differences in pregnancy intention by ethnicity or HIV status; 38.4% reported Canadian Aboriginal ancestry. In our final multivariable model, servicing clients in formal indoor settings, inconsistent condom use by clients, younger age, and intimate partner violence (IPV) were associated with pregnancy intention.

Conclusions

FSWs may have pregnancy intention levels similar to that of women in other occupations. Policy changes are needed to improve FSWs’ access to integrated HIV and reproductive health services and harm reduction services, particularly for FSWs experiencing IPV.
Modified plasma–fluid equations from nonstandard Lagrangians with applications to nuclear fusion
Authors: El-Nabulsi Rami Ahmad
Published: July 2014

Nonstandard Lagrangian dynamics have gained great interest recently, in particular within the theory of nonlinear differential equations and dissipative dynamical systems. In this paper, we address their implications in plasma–fluid dynamics. The mathematical settings are constructed starting from the modified Vlasov–Boltzmann transport equation, which is derived from modified Euler–Lagrange equations of motion. Far from giving a self-consistent nonstandard Lagrangian theory of plasma–fluid dynamics, in this paper we have just introduced the basic settings and discussed some illustrative examples that such a modified theory should have in plasma–fluid theory and nuclear fusion.
The little desert? Some subfactors with index in the interval $(5, 3+\sqrt{5})$
Authors: Morrison Scott , Peters Emily
Published: July 2014

Progress on classifying small index subfactors has revealed an almost empty landscape. In this paper we give some evidence that this desert continues up to index [Formula: see text]. There are two known quantum-group subfactors with index in this interval, and we show that these subfactors are the only way to realize the corresponding principal graphs. One of these subfactors is 1-supertransitive, and we demonstrate that it is the only 1-supertransitive subfactor with index between 5 and [Formula: see text]. Computer evidence shows that any other subfactor in this interval would need to have rank at least 38. We prove our uniqueness results by showing that there is a unique flat connection on each graph. The result on 1-supertransitive subfactors is proved by an argument using intermediate subfactors, running the "odometer" from the FusionAtlas' Mathematica package and paying careful attention to dimensions. This is the published version of arXiv:1205.2742.
Modality transition-based network from multivariate time series for characterizing horizontal oil–water flow patterns
Authors: Ding Mei-Shuang , Jin Ning-De , Gao Zhong-Ke
Published: July 2014

The simultaneous flow of oil and water through a horizontal pipe is a common occurrence during petroleum industrial processes. Characterizing the flow behavior underlying horizontal oil–water flows is a challenging problem of significant importance. In order to solve this problem, we carry out experiment to measure multivariate signals from different flow patterns and then propose a novel modality transition-based network to analyze the multivariate signals. The results suggest that the local betweenness centrality and weighted shortest path of the constructed network can characterize the transitions of flow conditions and further allow quantitatively distinguishing and uncovering the dynamic flow behavior underlying different horizontal oil–water flow patterns.
DECOMPOSING 3D OBJECTS IN SIMPLE PARTS CHARACTERIZED BY RECTILINEAR SPINES
Authors: SERINO LUCA , ARCELLI CARLO , SANNITI DI BAJA GABRIELLA
Published: July 2014

The distance labeled curve skeleton of a 3D object is used to guide the decomposition of the object into disjoint parts. To this aim, the skeleton is polygonally approximated by taking into account spatial coordinates and distance values of its voxels. The obtained skeleton segments are characterized by the absence of significant changes of curvature. Moreover, along each skeleton segment distance values are constant or show a linearly changing trend. Each segment can be interpreted as the spine of a simple part, which is characterized by the absence of significant curvature changes along its boundary, and by local thickness that is constant or evolves linearly along the part. By using exclusively the spatial coordinates and distance values of the vertices of the spines, quantitative information on shape, size, position and orientation of the corresponding simple parts can be obtained. Alternative decompositions of the object can be computed by selecting different values for the threshold used during polygonal approximation of the skeleton. Some criteria are also discussed for the selection of optimal threshold values originating approximated skeletons having a small number of segments, but still producing decompositions rather well adapting the input object boundary.
Ontology for Systems Development
Authors: Hallberg Niklas , Jungert Erland , Pilemalm Sofie
Published: July 2014

Software-intensive information systems have a major impact on our lives, both privately and professionally. Development of these systems is a complex activity that requires the involvement of people with different competences and skills. Even though software-intensive systems have been developed since the 1960s, the success rate is still low. A major hindrance to successful system development projects is the lack of consistent terminology. Since systems development is a collaborative activity, involving not only systems developers but also domain experts and user representatives, the understanding of each other is a prerequisite for an effective collaboration. The aim of this paper is to explore and present definitions, dependencies, and relationships of the most fundamental concepts in systems development in the form of an ontology. The ontology consists of four categories of concepts: General concepts, Description concepts, Realization concepts, and Appearance concepts. The two core concepts in the ontology are Systems and Systems development.
Combining the Strengths of BPEL and Mule ESB
Authors: Jongtaveesataporn Aimrudee , Takada Shingo
Published: July 2014

Service Oriented Architecture (SOA) provides an application framework which integrates variety of technology services in a loosely coupled way. Mule Enterprise Service Bus (ESB) is a widely-used ESB product that provides important functions such as message routing, message transformation, protocol-mediation, and event handling. These functions enable Mule ESB to integrate services implemented on various platforms and technologies. However, Mule ESB does not support business logic at all. Another approach to integrate services is to use a business process language such as BPEL (Business Process Execution Language). BPEL is used to define activities along with control flow. It is limited to Web service connections. One major difference is that BPEL is capable of orchestrating a business process with programming constructs, whereas Mule ESB is capable of processing messages in many protocal connections. Both BPEL and Mule ESB have different advantages. Unfortunately, neither one is powerful enough to solve some classes of business problems. In this paper we present the COMBO framework, which merges the strengths of Mule ESB and BPEL. We develop a tool to translate an extended BPEL file to a Mule ESB configuration file. The configuration file is used within a Mule ESB to execute the process that has been described within the BPEL document. We add extension modules to the standard Mule ESB for supporting BPEL functions that Mule ESB does not provide. The extended ESB has capabilities for supporting variable assignment and conditional branches in complex business processes. Our translation can cover frequently used activities in business processes. We also present case studies that use many business activities to show how the COMBO framework supports various activity translation.
NMMp: A Model-Driven UML Extension for the Description of Navigation Maps for Web Applications
Authors: Cortés Humberto , Navarro Antonio
Published: July 2014

With the advent of multitier and service-oriented architectures, the presentation tier is more detached from the rest of the web application than ever. Moreover, complex web applications can have thousands of linked web pages built using different technologies. As a result, the description of navigation maps has become more complex in recent years. This paper presents NMMp, a UML extension that: (i) provides an abstract vision of the navigation structure of the presentation tier of web applications, independently of architectural details or programming languages; (ii) can be automatically transformed into UML-WAE class diagrams, which can be easily integrated with the design of the other tiers of the web application; (iii) encourages the use of architectural and multitier design patterns; and (iv) has been developed according to OMG standards, thus facilitating its use with general purpose UML CASE tools in industry.
Enhancing Navigability in Websites Built Using Web Content Management Systems
Authors: Distante Damiano , Risi Michele , Scanniello Giuseppe
Published: July 2014

Websites built using Web Content Management Systems (WCMSs) usually provide their users with three types of access structures to surf their contents: indexes of categories, breadcrumb trails, and sitemaps. In addition, to find contents of his/her interest, a user can perform more or less advanced full-text searches. In this paper we propose an automatic approach to extend the navigation structure of websites developed using WCMSs with Semantic Navigation Maps (SNMs), a complementary navigation structure that enables linking and navigating contents based on their lexical similarity. The approach uses an information retrieval technique (namely, Latent Semantic Indexing) to identify lexical similarities between textual contents, and a fuzzy clustering algorithm to form groups of similar web pages. For each page of the website, a set of navigation links towards pages showing similar content and a measure of such similarity is provided. The paper presents the approach to generate SNMs, an implementation for the Joomla! open source WCMS, and the results of an empirical evaluation involving two real world websites built using this WCMS.
A diagrammatic definition of Uq(𝔰𝔩2)
Authors: Bigelow Stephen J.
Published: July 2014

We give a diagrammatic definition of Uq(𝔰𝔩2) when q is not a root of unity, including the Hopf algebra structure and relationship with the Temperley–Lieb category.
On Set Covering Based on Biclustering
Authors: Panteli Antiopi , Boutsinas Basilis , Giannikos Ioannis
Published: July 2014

In this paper, we present a clustering heuristic for solving demand covering models where the objective is to determine locations for servers that optimally cover a given set of demand points. This heuristic is based on the concept of biclusters and processes the set of demand points as well as the set of potential servers and determines biclusters that result in smaller problems. Given a coverage matrix, a bicluster is defined as a sub-matrix spanned by both a subset of rows and a subset of columns, such that rows are the most similar to each other when compared over columns. The algorithm starts by using any biclustering algorithm in order to identify appropriate biclusters of the coverage matrix and then combines selected biclusters to define an aggregate solution to the original problem. The algorithm can be easily adapted to address a whole family of covering problems including set covering, maximal covering and backup covering problems. The proposed algorithm is tested in a series of widely known test datasets for various such problems. The main objective of this paper is to introduce the concept of biclustering as an efficient and effective approach to tackle covering problems and to stimulate further research in this area.
Widespread Cretaceous secondary magnetization in the High Atlas (Morocco). A common origin for the Cretaceous remagnetizations in the western Tethys?
Authors: Torres-López S. , Villalaín J. J. , Casas A. M. , EL Ouardi H. , Moussaid B. , Ruiz-Martínez V. C.
Published: July 2014

In this paper, we present the first palaeomagnetic data (51 sites) for Mesozoic (Lower–Middle Jurassic) sediments of the Moroccan Central High Atlas and address the study of a widespread remagnetization. The remagnetization is characterized by a very stable component with systematic normal polarity, carried by magnetite. The relationship between the magnetic properties and location within the basin suggests that the acquisition of the remagnetization is controlled by basin geometry. Fold-tests indicate that the overprint acquisition is syn-folding in some structures but clearly predates the Tertiary compressional stage. Using the small circle intersection method we have calculated the remagnetization direction (
D
= 336.4°,
I
= 29.2°). Comparison with the global apparent polar wander path indicates that the remagnetization was acquired during the Late Cretaceous (probably Cenomanian). Considering both the basinal confinement of remagnetization and the connection with other remagnetization events in the western Tethys, we propose a scenario explaining widespread remagnetizations in the region, concerning both basin-scale conditions mainly related to sediment thickness and a regional-scale thermal event acting as catalyst of remagnetizations in those sedimentary basins that satisfy the basin-scale conditions.
Efficient maximum flow algorithms
Authors: Goldberg Andrew V. , Tarjan Robert E.
Published: July 2014

Though maximum flow algorithms have a long history, revolutionary progress is still being made.
LoCo—A Logic for Configuration Problems
Authors: Aschinger Markus , Drescher Conrad , Gottlob Georg , Vollmer Heribert
Published: July 2014

In this work, we present LoCo, a fragment of classical first-order logic carefully tailored for expressing technical product configuration problems. The core feature of LoCo is that the number of components used in configurations does not have to be finitely bounded explicitly, but instead is bounded implicitly through the axioms. Computing configurations is equivalent to the task of model finding. We present the language, related algorithms, and complexity results as well as a prototypical implementation via answer set programming.
Bringing arbitrary compute to authoritative data
Authors: Cavage Mark , Pacheco David
Published: July 2014

Many disparate use cases can be satisfied with a single storage system.
Puzzled: Paths and Matchings
Authors: Winkler Peter
Published: July 2014

Consider two simple games played by Alice and Bob on a checkerboard or, more generally, on a graph. The games look different, but, as we know, looks can be deceiving…
Hello, my name is…
Authors: Klarreich Erica
Published: July 2014

Facial recognition and privacy concerns.
Private then shared?
Authors: Coward Chris
Published: July 2014

Designing for the mobile phone to shared PC pipeline.
Forked over
Authors: Neville-Neil George V.
Published: July 2014

Shortchanged by open source.
Example-based learning in computer-aided STEM education
Authors: Gulwani Sumit
Published: July 2014

Example-based reasoning techniques developed for programming languages also help automate repetitive tasks in education.
The excretion of NaCl and KCl loads in mosquitoes. 1. Control data
Authors: Hine Rebecca M. , Rouhier Matthew F. , Park Seokhwan Terry , Qi Zhijun , Piermarini Peter M. , Beyenbach Klaus W.
Published: July 2014

The handling of Na+and K+loads was investigated in isolated Malpighian tubules and in whole mosquitoes of Aedes aegypti. Isolated Malpighian tubules bathed in Na+-rich Ringer solution secreted Na+-rich fluid, and tubules bathed in K+-rich Ringer solution secreted K+-rich fluid. Upon Na+loading the hemolymph, the mosquito removed 77% the injected Na+within the next 30 min. The rapid onset and magnitude of this diuresis and the excretion of more Na+than can be accounted for by tubular secretion in vitro is consistent with the release of the calcitonin-like diuretic hormone in the mosquito to remove the Na+load from the hemolymph. Downstream, K+was reabsorbed with water in the hindgut, which concentrated Na+in excreted urine hyperosmotic to the hemolymph. Upon K+loading the hemolymph, the mosquito took 2 h to remove 100% of the injected K+from the hemolymph. The excretion of K+-rich isosmotic urine was limited to clearing the injected K+from the hemolymph with a minimum of Cl−and water. As a result, 43.3% of the injected Cl−and 48.1% of the injected water were conserved. The cation retained in the hemolymph with Cl−was probably N-methyl-d-glucamine, which replaced Na+in the hemolymph injection of the K+load. Since the tubular secretion of K+accounts for the removal of the K+load from the hemolymph, the reabsorption of K+, Na+, Cl−, and water must be inhibited in the hindgut. The agents mediating this inhibition are unknown.