bluuebunny/crossref_metadata_2025_split huggingface dataset:
High–low reflectivity enhancement based retinal vessel projection for SD‐OCT images
Authors: Chen Qiang , Niu Sijie , Yuan Songtao , Fan Wen , Liu Qinghuai 
Published: September 2016

PurposeThe retinal vessel visualization from spectral‐domain optical coherence tomography (SD‐OCT) images is important for ocular disease diagnosis and multimodal retinal image processing. The purpose is to display the retinal vessel in a single projection image from 3D SD‐OCT images by using the light absorption and shadow characteristics of the retinal vessel.MethodsThe authors present a novel retinal vessel projection method for SD‐OCT images, which utilizes the light absorption and shadow characteristics of the retinal vessel, called high–low reflectivity enhancement (HLRE) method. The reflectivity of the retinal vessel increases between the internal limiting membrane and inner nuclear layer‐outer plexiform layer (INL‐OPL) layers because of the light absorption, and the reflectivity below the retinal vessel decreases because of the influence of the retinal vessel shadow. A retinal vessel mask image generated based on the reflectivity characteristics of the retinal vessel is used to enhance the subvolume projection image restricted between the INL‐OPL and Bruch's membrane layers.ResultsExperimental results with 22 SD‐OCT cubes from 12 patients and 10 normal persons demonstrate that the authors’ method is more effective in displaying the retinal vessel than the summed‐voxel projection and other five region restriction based projection methods. The average of the mean difference between the retinal vessel and background regions based on their HLRE method is 0.1921.ConclusionsThe proposed HLRE method was more effective for the visualization of the retinal vessels than the state‐of‐art methods because it provides higher contrast and distinction.
DNA Supercoiling Regulates the Motility of Campylobacter jejuni and Is Altered by Growth in the Presence of Chicken Mucus
Authors: Shortt Claire , Scanlan Eoin , Hilliard Amber , Cotroneo Chiara E. , Bourke Billy , Ó Cróinín Tadhg 
Published: September 2016

ABSTRACT

Campylobacter jejuni
is the leading cause of bacterial gastroenteritis in humans, but relatively little is known about the global regulation of virulence factors during infection of chickens or humans. This study identified DNA supercoiling as playing a key role in regulating motility and flagellar protein production and found that this supercoiling-controlled regulon is induced by growth in chicken mucus. A direct correlation was observed between motility and resting DNA supercoiling levels in different strains of
C. jejuni
, and relaxation of DNA supercoiling resulted in decreased motility. Transcriptional analysis and Western immunoblotting revealed that a reduction in motility and DNA supercoiling affected the two-component regulatory system FlgRS and was associated with reduced FlgR expression, increased FlgS expression, and aberrant expression of flagellin subunits. Electron microscopy revealed that the flagellar structure remained intact. Growth in the presence of porcine mucin resulted in increased negative supercoiling, increased motility, increased FlgR expression, and reduced FlgS expression. Finally, this supercoiling-dependent regulon was shown to be induced by growth in chicken mucus, and the level of activation was dependent on the source of the mucus from within the chicken intestinal tract. In conclusion, this study reports for the first time the key role played by DNA supercoiling in regulating motility in
C. jejuni
and indicates that the induction of this supercoiling-induced regulon in response to mucus from different sources could play a critical role in regulating motility
in vivo
.

IMPORTANCE
Although
Campylobacter jejuni
is the leading cause of bacterial gastroenteritis, very little is understood about how this pathogen controls the expression of genes involved in causing disease. This study for the first time identifies DNA supercoiling as a key regulator of motility in
C. jejuni
, which is essential for both pathogenesis and colonization. Altering the level of DNA supercoiling results in changes in motility levels, as well as changes in the expression of genes involved in flagellar gene regulation. Furthermore, spontaneous clones of the organism with different motility profiles have altered DNA supercoiling levels. Finally, mucus was identified as a key stimulator of changes in DNA supercoiling, and it was shown that mucus from different sites in the chicken intestine induced different levels of DNA supercoiling. In conclusion, this study implicates DNA supercoiling as a key regulator of motility in
C. jejuni in vivo
during colonization of the mucus layer.
Examining a DNA Replication Requirement for Bacteriophage λ Red- and Rac Prophage RecET-Promoted Recombination in Escherichia coli
Authors: Thomason Lynn C. , Costantino Nina , Court Donald L. 
Published: September 2016

ABSTRACT

Recombineering,
in vivo
genetic engineering with bacteriophage homologous recombination systems, is a powerful technique for making genetic modifications in bacteria. Two systems widely used in
Escherichia coli
are the Red system from phage λ and RecET from the defective Rac prophage. We investigated the
in vivo
dependence of recombineering on DNA replication of the recombining substrate using plasmid targets. For λ Red recombination, when DNA replication of a circular target plasmid is prevented, recombination with single-stranded DNA oligonucleotides is greatly reduced compared to that under replicating conditions. For RecET recombination, when DNA replication of the targeted plasmid is prevented, the recombination frequency is also reduced, to a level identical to that seen for the Red system in the absence of replication. The very low level of oligonucleotide recombination observed in the absence of any phage recombination functions is the same in the presence or absence of DNA replication. In contrast, both the Red and RecET systems recombine a nonreplicating linear dimer plasmid with high efficiency to yield a circular monomer. Therefore, the DNA replication requirement is substrate dependent. Our data are consistent with recombination by both the Red and RecET systems occurring predominately by single-strand annealing rather than by strand invasion.

IMPORTANCE
Bacteriophage homologous recombination systems are widely used for
in vivo
genetic engineering in bacteria. Single- or double-stranded linear DNA substrates containing short flanking homologies to chromosome targets are used to generate precise and accurate genetic modifications when introduced into bacteria expressing phage recombinases. Understanding the molecular mechanism of these recombination systems will facilitate improvements in the technology. Here, two phage-specific systems are shown to require exposure of complementary single-strand homologous targets for efficient recombination; these single-strand regions may be created during DNA replication or by single-strand exonuclease digestion of linear duplex DNA. Previously,
in vitro
studies reported that these recombinases promote the single-strand annealing of two complementary DNAs and also strand invasion of a single DNA strand into duplex DNA to create a three-stranded region. Here,
in vivo
experiments show that recombinase-mediated annealing of complementary single-stranded DNA is the predominant recombination pathway in
E. coli
.
Tandemly Integrated HPV16 Can Form a Brd4-Dependent Super-Enhancer-Like Element That Drives Transcription of Viral Oncogenes
Authors: Dooley Katharine E. , Warburton Alix , McBride Alison A. 
Published: September 2016

ABSTRACT
In cancer cells associated with human papillomavirus (HPV) infections, the viral genome is very often found integrated into the cellular genome. The viral oncogenes E6 and E7 are transcribed from the viral promoter, and integration events that alter transcriptional regulation of this promoter contribute to carcinogenic progression. In this study, we detected highly enriched binding of the super-enhancer markers Brd4, MED1, and H3K27ac, visible as a prominent nuclear focus by immunofluorescence, at the tandemly integrated copies of HPV16 in cells of the cervical neoplasia cell line W12 subclone 20861. Tumor cells are often addicted to super-enhancer-driven oncogenes and are particularly sensitive to disruption of transcription factor binding to the enhancers. Treatment of 20861 cells with bromodomain inhibitors displaced Brd4 from the HPV integration site, greatly decreased E6/E7 transcription, and inhibited cellular proliferation. Thus, Brd4 activates viral transcription at this integration site, and strong selection for E6/E7 expression can drive the formation of a super-enhancer-like element to promote oncogenesis.

IMPORTANCE
Oncogenic human papillomaviruses play an essential role in the development of cervical cancer, and growth of these cancer cells requires continued expression of the viral E6 and E7 oncogenes. Integration of the virus into the host genome often results in deregulation of E6 and E7 expression, which provides a selective growth advantage and increases genetic instability of infected cells. We show here that tandemly integrated copies of the viral genome can form a super-enhancer-like element that drives E6/E7 transcription. Targeted disruption of factors binding to this element decreases viral transcription and causes cell death. Thus, cancer cells that harbor integrated HPV could be targeted by therapeutics that disrupt super-enhancer function.
All-cause mortality risk in elderly individuals with disabilities: a retrospective observational study
Authors: Wu Li-Wei , Chen Wei-Liang , Peng Tao-Chun , Chiang Sheng-Ta , Yang Hui-Fang , Sun Yu-Shan , Chan James Yi-Hsin , Kao Tung-Wei 
Published: September 2016

ObjectivesDisability is considered an important issue that affects the elderly population. This study aimed to explore the relationship between disability and all-cause mortality in US elderly individuals.DesignRetrospective and longitudinal designs.SettingData from the National Health and Nutrition Examination Survey (NHANES 1999–2002) conducted by the National Center for Health Statistics of the Centers for Disease Control and Prevention.ParticipantsA total of 1834 participants in the age range 60–84 years from NHANES 1999–2002.Main outcome measuresWe acquired five major domains of disability (activities of daily living (ADL), general physical activities (GPA), instrumental ADL (IADL), lower extremity mobility (LEM) and leisure and social activities (LSA)) through self-reporting. We applied an extended-model approach with Cox (proportional hazards) regression analysis to investigate the relationship between different features of disability and all-cause mortality risk in the study population.ResultsDuring a mean follow-up of 5.7 years, 77 deaths occurred. An increased risk of all-cause mortality was identified in elderly individuals with disability after adjustment for potential confounders (HR 2.23; 95% CI 1.29 to 3.85; p=0.004). Participants with more than one domain of disability were associated with a higher risk of mortality (ptrend=0.047). Adjusted HRs and 95% CIs for each domain of disability were 2.53 (1.49 to 4.31), 1.99 (0.93 to 4.29), 1.74 (0.72 to 4.16), 1.57 (0.76 to 3.27) and 1.52 (0.93 to 2.48) for LEM, LSA, ADL, IADL and GPA, respectively.ConclusionsThe results of this study support an increased association between disability and all-cause mortality in the elderly in the USA. Disability in LEM may be a good predictor of high risk of all-cause mortality in elderly subjects.
Study protocol for a randomised controlled trial of invasive versus conservative management of primary spontaneous pneumothorax
Authors: Brown Simon G A , Ball Emma L , Perrin Kyle , Read Catherine A , Asha Stephen E , Beasley Richard , Egerton-Warburton Diana , Jones Peter G , Keijzers Gerben , Kinnear Frances B , Kwan Ben C H , Lee Y C Gary , Smith Julian A , Summers Quentin A , Simpson Graham ,   the PSP Study Group
Published: September 2016

IntroductionCurrent management of primary spontaneous pneumothorax (PSP) is variable, with little evidence from randomised controlled trials to guide treatment. Guidelines emphasise intervention in many patients, which involves chest drain insertion, hospital admission and occasionally surgery. However, there is evidence that conservative management may be effective and safe, and it may also reduce the risk of recurrence. Significant questions remain regarding the optimal initial approach to the management of PSP.Methods and analysisThis multicentre, prospective, randomised, open label, parallel group, non-inferiority study will randomise 342 participants with a first large PSP to conservative or interventional management. To maintain allocation concealment, randomisation will be performed in real time by computer and stratified by study site. Conservative management will involve a period of observation prior to discharge, with intervention for worsening symptoms or physiological instability. Interventional treatment will involve insertion of a small bore drain. If drainage continues after 1 hour, the patient will be admitted. If drainage stops, the drain will be clamped for 4 hours. The patient will be discharged if the lung remains inflated. Otherwise, the patient will be admitted. The primary end point is the proportion of participants with complete lung re-expansion by 8 weeks. Secondary end points are as follows: days in hospital, persistent air leak, predefined complications and adverse events, time to resolution of symptoms, and pneumothorax recurrence during a follow-up period of at least 1 year. The study has 95% power to detect an absolute non-inferiority margin of 9%, assuming 99% successful expansion at 8 weeks in the invasive treatment arm. The primary analysis will be by intention to treat.Ethics and disseminationLocal ethics approval has been obtained for all sites. Study findings will be disseminated by publication in a high-impact international journal and presentation at major international Emergency Medicine and Respiratory meetings.Trial registration numberACTRN12611000184976; Pre-results.
Performance of p16INK4aELISA as a primary cervical cancer screening test among a large cohort of HIV-infected women in western Kenya: a 2-year cross-sectional study
Authors: Wu Tara J , Smith-McCune Karen , Reuschenbach Miriam , von Knebel Doeberitz Magnus , Maloba May , Huchko Megan J 
Published: September 2016

ObjectiveA biomarker with increased specificity for cervical dysplasia compared with human papillomavirus (HPV) testing would be an attractive option for cervical cancer screening among HIV-infected women in resource-limited settings. p16INK4ahas been explored as a biomarker for screening in general populations.DesignA 2-year cross-sectional study.Setting2 large HIV primary care clinics in western Kenya.Participants1054 HIV-infected women in western Kenya undergoing cervical cancer screening as part of routine HIV care from October 2010 to November 2012.InterventionsParticipants underwent p16INK4aspecimen collection and colposcopy. Lesions with unsatisfactory colposcopy or suspicious for cervical intraepithelial neoplasia 2+ (CIN2+; including CIN2/3 or invasive cervical cancer) were biopsied. Following biopsy, disease status was determined by histopathological diagnosis.Primary and secondary outcome measuresWe measured the sensitivity, specificity and predictive values of p16INK4aELISA for CIN2+ detection among HIV-infected women and compared them to the test characteristics of current screening methods used in general as well as HIV-infected populations.ResultsAverage p16INK4aconcentration in cervical samples was 37.4 U/mL. After colposcopically directed biopsy, 127 (12%) women were determined to have CIN2+. Receiver operating characteristic analysis showed an area under the curve of 0.664 for p16INK4ato detect biopsy-proven CIN2+. At a p16INK4acut-off level of 9 U/mL, sensitivity, specificity, positive and negative predictive values were 89.0%, 22.9%, 13.6% and 93.8%, respectively. The overall p16INK4apositivity at a cut-off level of 9 U/mL was 828 (78.6%) women. There were 325 (30.8%) cases of correct p16INK4aprediction to detect or rule out CIN2+, and 729 (69.2%) cases of incorrect p16INK4aprediction.Conclusionsp16INK4aELISA did not perform well as a screening test for CIN2+ detection among HIV-infected women due to low specificity. Our study contributes to the ongoing search for a more specific alternative to HPV testing for CIN2+ detection.
Exploring the experiences of substitute decision-makers with an exception to consent in a paediatric resuscitation randomised controlled trial: study protocol for a qualitative research study
Authors: Parker Melissa J , de Laat Sonya , Schwartz Lisa 
Published: September 2016

IntroductionProspective informed consent is required for most research involving human participants; however, this is impracticable under some circumstances. The Tri-Council Policy Statement: Ethical Conduct for Research Involving Humans (TCPS) outlines the requirements for research involving human participants in Canada. The need for an exception to consent (deferred consent) is recognised and endorsed in the TCPS for research in individual medical emergencies; however, little is known about substitute decision-maker (SDM) experiences. A paediatric resuscitation trial (SQUEEZE) (NCT01973907) using an exception to consent process began enrolling at McMaster Children's Hospital in January 2014. This qualitative research study aims to generate new knowledge on SDM experiences with the exception to consent process as implemented in a randomised controlled trial.Methods and analysisThe SDMs of children enrolled into the SQUEEZE pilot trial will be the sampling frame from which ethics study participants will be derived.Design:Qualitative research study involving individual interviews and grounded theory methodology.Participants:SDMs for children enrolled into the SQUEEZE pilot trial.Sample size:Up to 25 SDMs.Qualitative methodology:SDMs will be invited to participate in the qualitative ethics study. Interviews with consenting SDMs will be conducted in person or by telephone, taped and professionally transcribed. Participants will be encouraged to elaborate on their experience of being asked to consent after the fact and how this process occurred.Analysis:Data gathering and analysis will be undertaken simultaneously. The investigators will collaborate in developing the coding scheme, and data will be coded using NVivo. Emerging themes will be identified.Ethics and disseminationThis research represents a rare opportunity to interview parents/guardians of critically ill children enrolled into a resuscitation trial without their knowledge or prior consent. Findings will inform implementation of the exception to consent process in the planned definitive SQUEEZE trial and support development of evidence-based ethics guidelines.
Pharmacological Inhibition of Centrosome Clustering by Slingshot-Mediated Cofilin Activation and Actin Cortex Destabilization
Authors: Konotop Gleb , Bausch Elena , Nagai Tomoaki , Turchinovich Andrey , Becker Natalia , Benner Axel , Boutros Michael , Mizuno Kensaku , Krämer Alwin , Raab Marc Steffen 
Published: September 2016

AbstractCentrosome amplification is a hallmark of virtually all types of cancers, including solid tumors and hematologic malignancies. Cancer cells with extra centrosomes use centrosome clustering (CC) to allow for successful division. Because normal cells do not rely on this mechanism, CC is regarded as a promising target to selectively eradicate cells harboring supernumerary centrosomes. To identify novel inhibitors of CC, we developed a cell-based high-throughput screen that reports differential drug cytotoxicity for isogenic cell populations with different centrosome contents. We identified CP-673451 and crenolanib, two chemically related compounds originally developed for the inhibition of platelet-derived growth factor receptor β (PDGFR-β), as robust inhibitors of CC with selective cytotoxicity for cells with extra centrosomes. We demonstrate that these compounds induce mitotic spindle multipolarity by activation of the actin-severing protein cofilin, leading to destabilization of the cortical actin network, and provide evidence that this activation is dependent on slingshot phosphatases 1 and 2 but unrelated to PDGFR-β inhibition. More specifically, we found that although both compounds attenuated PDGF-BB–induced signaling, they significantly enhanced the phosphorylation of PDGFR-β downstream effectors, Akt and MEK, in almost all tested cancer cell lines under physiologic conditions. In summary, our data reveal a novel mechanism of CC inhibition depending on cofilin-mediated cortical actin destabilization and identify two clinically relevant compounds interfering with this tumor cell–specific target. Cancer Res; 76(22); 6690–700. ©2016 AACR.
Exploring unmet needs in venous and arterial thromboembolism with rivaroxaban
Authors: Cappato Riccardo , Welsh Robert 
Published: September 2016

SummaryThe vast clinical research programme for the direct, oral factor Xa inhibitor rivaroxaban has generated a wealth of data since the first rivaroxaban approval in 2008 for the prevention of venous thrombo embolism (VTE) in patients undergoing elective hip or knee replacement surgery. While rivaroxaban is widely used across a spectrum of seven indications, there is continuous commitment to investigating its wider benefits in new indications and attempts to refine current evidence. Key data from recently completed randomised controlled trials (RCTs) have shown that rivaroxaban is a feasible anticoagulation option for patients with non-valvular atrial fibrillation (NVAF) undergoing cardioversion or catheter ablation. Now, a number of Phase II and III RCTs are underway that seek to uncover further roles for rivaroxaban in patients at risk of thrombosis and aim to improve quality of life. This article will introduce and provide context for these RCTs in the contemporary management of arterial and venous thromboembolism in the following underserved areas: Patients with both NVAF and acute coronary syndrome (ACS) requiring percutaneous coronary intervention (PCI); patients with embolic stroke of undetermined source (ESUS); patients who require transcatheter aortic valve replacement (TAVR); patients with acute or chronic coronary artery disease (CAD; including those with heart failure [HF]); those at risk of or suffering from cancer-associated thrombosis (CAT) and those requiring long-term anticoagulation. It is hoped that this collection of studies provides clarity around the use of rivaroxaban as a fundamental component of antithrombotic therapy in an array of clinical situations.