bluuebunny/crossref_metadata_2025 huggingface dataset:
Intraoperative Arthrogram Predicts Residual Dysplasia after Successful Closed Reduction of DDH
Authors: Zhang Zhong‐li , Fu Zhe , Yang Jian‐ping , Wang Kan , Xie Li‐wei , Deng Shu‐zhen , Chen Zhao‐qiang
Published: September 2016

Objective

To determine the incidence of residual dysplasia after closed reduction (CR) of developmental dysplasia of the hip (DDH) and assess correlations between quality of arthrogram‐guided CR and residual dysplasia using a new intraoperative radiographic criterion.

Methods

Data of a consecutive series of 126 patients with DDH in 139 hips treated at our institution by arthrogram‐guided CR from March 2006 to June 2013 were reviewed in this retrospective study. There were 23 boys and 103 girls with 88 affected left hips and 51 right hips. The average age at closed reduction was 14 months (range, 7–19 months) and average duration of follow‐up 36 months (range, 24–100 months). Femoral head coverage (FHC) and arthrography type (A/B/C) on best reduced arthrographic images, acetabular index (AI) and Wiberg Center‐Edge (CE) angle on anteroposterior (AP) pelvis radiograph at latest follow‐up were measured. Residual hip dysplasia was determined according to the Harcke acetabular dysplasia radiographic standard. Patients were divided into non‐late acetabular dysplasia (non‐LACD) and late acetabular dysplasia (LACD) groups according to final results and age at reduction, sex and side compared between these two groups. Correlations between FHC and arthrography type and residual hip dysplasia were analyzed. Multiple logistic regression analysis was used to analyze sex, AI at CR, arthrography type and FHC with LACD. Receiver operating characteristic (ROC) curve analysis was used to determine the cutoff value for FHC.

Results

Forty‐five of 139 hips (32.4%) had residual hip dysplasia. Avascular necrosis of the femoral head occurred in 11 hips (7.9%), nine of which had acetabular dysplasia. There were no significant differences between the two groups in age at reduction, sex or side. FHC differed significantly between the two groups (51.2% ± 15.3% vs
. 28.5% ± 15.9%, t = 4.718, P = 0.000). A significantly greater percentage of the arthrography Type C group than Type A and B groups had LACD (χ2 = 17.170, P = 0.017). According to multiple logistic regression analysis, FHC was the only prognostic factor for LACD. There was a clear cutoff value for FHC (30%), under which 81.8% hips were determined as having LACD according to ROC curve analysis.

Conclusions

Intraoperative arthrogram‐determined FHC is an alternative predictor of residual hip dysplasia after CR of DDH and FHC ≤30% can be considered the criterion for unacceptable reduction.
Feeling bad and doing good: The effect of customer mistreatment on service employee's daily display of helping behaviors
Authors: Yue Yumeng , Wang Karyn L. , Groth Markus
Published: September 2016

Mistreatment by customers is a common occurrence for many frontline service employees. Although some evidence suggests that employees engage in dysfunctional workplace behaviors as a result of mistreatment, others studies have suggested that employees may cope with such negative experiences by helping others. Drawing on negative state relief theory, we conducted 2 studies to test these relationships and examine whether service employees cope with negative emotions arising from such daily customer mistreatment by engaging in helping others. In Study 1, daily surveys from 70 restaurant employees showed that daily customer mistreatment predicted the experience of negative moods the next morning, which, in turn, led to higher levels of coworker helping the next day. In Study 2, daily surveys from 54 retail employees showed that daily customer mistreatment led to higher customer helping the next day, but only when customer orientation was high. Our results further show that helping behavior was associated with elevated positive affective experiences and that the proposed relationships differ depending on whether customer mistreatment is measured at a daily or a cumulative perspective. Specifically, cumulative customer mistreatment over time decreased general helping. These findings are discussed in relation to employees' coping strategies towards acute and cumulative mistreatment.
Juvenile Hormone and the endocrine regulation of wing polymorphism in insects: new insights from circadian and functional‐genomic studies in Gryllus crickets
Authors: Zera Anthony J.
Published: September 2016

For decades, Juvenile Hormone (JH) has been a major focus of studies investigating the endocrine regulation of wing‐polymorphism. The most general model postulates a single threshold, above which JH causes the expression of traits that define the short‐winged morph (SW), and below which JH causes the expression of traits that define the long‐winged morph (LW). Early studies in aphids and crickets reported ambiguous results as a result of the small size of aphids or the very low JH titre in nymphal crickets. Detailed studies in wing morphs of adult Gryllus firmus Scudder uncovered an unexpected and novel morph‐specific JH titre circadian cycle (cycling in LW but not in SW) in both the laboratory and field. This finding clearly contradicts the classic model. Morph‐specific daily rhythms in global gene expression are strongly associated with (and are possibly caused by) the morph‐specific JH titre rhythm. Daily rhythms for hormonal traits and gene expression, which are largely ignored in studies of life‐history evolution, may be common and play an important role in adaptation. Juvenile Hormone has likely evolved a specialized within‐morph function in G. firmus, regulating aspects of daily flight in the LW morph, which exhibits circadian flight. Other hormones, such as insulin‐like peptides and ecdysteroids, possibly regulate the expression of chronic (long‐term, noncircadian) differences between LW and SW morphs. Future studies should aim to investigate JH titres in more detail, as well as other hormones, most notably peptides and biogenic amines, which are largely ignored in endocrine studies of wing polymorphism.
Phytophthora caryae sp. nov., a new species recovered from streams and rivers in the eastern United States
Authors: Brazee N. J. , Yang X. , Hong C. X.
Published: September 2016

Members of the Phytophthora citricola complex (Phytophthora clade 2c), such as P. plurivora, are destructive pathogens of trees and shrubs in nursery, landscape and forest settings worldwide. During surveys of Phytophthora species from streams and rivers in Massachusetts and North Carolina, a novel species in the P. citricola complex was recovered. Based on sequences from three nuclear (ITS, β‐tub and tef1) and two mitochondrial (cox1 and nadh1) loci, morphological characters, temperature–growth relationships and host plant inoculations, this novel species is described as Phytophthora caryae sp. nov. Phytophthora caryae resembles several other species in the P. citricola complex, demonstrating homothallism and producing paragynous antheridia and semipapillate and noncaducous sporangia. However, P. caryae exhibits smaller sexual structures, higher rates of oogonia with a tapered base and sporangia with an offset attachment of the sporangiophores. Phylogenetic analyses using maximum likelihood and Bayesian inference placed isolates of P. caryae into a unique clade with significant statistical support. Based on the mitochondrial dataset, P. caryae is most closely related to P. pini and P. citricola III, which are believed to be native in eastern North America. Inoculations of P. caryae on 1‐year‐old twigs of 12 tree species representing nine genera resulted in under‐bark lesions on species of Carya and Juglans. Sapling inoculations under greenhouse conditions suggest that P. caryae may be pathogenic to shagbark hickory (Carya ovata) but not to black walnut (Juglans nigra).
Cuneiform Sources for Judeans in Babylonia in the Neo‐Babylonian and Achaemenid Periods: An Overview
Authors: Pearce Laurie E.
Published: September 2016

Cuneiform Sources for Judeans in Babylonia in the Neo‐Babylonian and Achaemenid Periods: An Overview

Cuneiform documents written in Babylonia provide valuable evidence for the experience of the Judeans who came there during the Exile and who remained throughout the Neo‐Babylonian and Achaemenid periods. Recent publications add significant data to the corpus previously known. The article describes and summarizes the relevant cuneiform evidence that informs an understanding of the Judeans' role in the social and economic history of Babylonia. Comparanda make clear that the Judeans occupied a place in the Babylonian economy and social order similar to that of other deportee populations in Babylonia.
‘Lying by authority’: travel dissimulations in Fynes Moryson's Itinerary
Authors: Pfannebecker Mareile
Published: September 2016

The sixteenth and seventeenth centuries in Europe have long been recognized as an ‘Age of Dissimulation’; in the period, their compatriots often depicted English travellers to the Continent as the ultimate liars and dissemblers. This article suggests that Fynes Moryson's An Itinerary of a Journey (1617) is one important example of how travel writers engaged with the charge of dissimulation made against them by opponents to European travel, beginning in the 1570s with Roger Ascham's The Scholemaster (1571). With particular focus on the role of Catholic Italy in the travel debate, the article shows how An Itinerary negotiates what was perceived as a hostile and infectious Catholic Italian reality to develop its own approach to travel observation at a moment of generic and epistemic fluidity. Via a number of textual tricks, Itinerary turns the threat of the Inquisition into a strategic advantage; ultimately, the travel report represents strategies of ‘honest dissimulation’ as the basis of the traveller's claim to truthful observation.
Ice slurry ingestion does not enhance self‐paced intermittent exercise in the heat
Authors: Gerrett N. , Jackson S. , Yates J. , Thomas G.
Published: September 2016

This study aimed to determine if ice slurry ingestion improved self‐paced intermittent exercise in the heat. After a familiarisation session, 12 moderately trained males (30.4 ± 3.4 year, 1.8 ± 0.1 cm, 73.5 ± 14.3 kg, O2max 58.5 ± 8.1 mL/kg/min) completed two separate 31 min self‐paced intermittent protocols on a non‐motorised treadmill in 30.9 ± 0.9 °C, 41.1 ± 4.0% RH. Thirty minutes prior to exercise, participants consumed either 7.5 g/kg ice slurry (0.1 ± 0.1 °C) (ICE) or 7.5 g/kg water (23.4 ± 0.9 °C) (CONTROL). Despite reductions in Tc (ΔTc: −0.51 ± 0.3 °C, P < 0.05) and thermal sensation prior to exercise, ICE did not enhance self‐paced intermittent exercise compared to CONTROL. The average speed during the walk (CONTROL: 5.90 ± 1.0 km, ICE: 5.90 ± 1.0 km), jog (CONTROL: 8.89 ± 1.7 km, ICE: 9.11 ± 1.5 km), run (CONTROL: 12.15 ± 1.7 km, ICE: 12.54 ± 1.5 km) and sprint (CONTROL: 17.32 ± 1.3 km, ICE: 17.18 ± 1.4 km) was similar between conditions (P > 0.05). Mean Tsk, Tb, blood lactate, heart rate and RPE were similar between conditions (P > 0.05). The findings suggest that lowering Tc prior to self‐paced intermittent exercise does not translate into an improved performance.
CENH3 morphogenesis reveals dynamic centromere associations during synaptonemal complex formation and the progression through male meiosis in hexaploid wheat
Authors: Sepsi Adél , Higgins James D. , Heslop‐Harrison John S. (Pat) , Schwarzacher Trude
Published: September 2016

During meiosis, centromeres in some species undergo a series of associations, but the processes and progression to homologous pairing is still a matter of debate. Here, we aimed to correlate meiotic centromere dynamics and early telomere behaviour to the progression of synaptonemal complex (SC) construction in hexaploid wheat (2n = 42) by triple immunolabelling of CENH3 protein marking functional centromeres, and SC proteins ASY1 (unpaired lateral elements) and ZYP1 (central elements in synapsed chromosomes). We show that single or multiple centromere associations formed in meiotic interphase undergo a progressive polarization (clustering) at the nuclear periphery in early leptotene, leading to formation of the telomere bouquet. Critically, immunolabelling shows the dynamics of these presynaptic centromere associations and a structural reorganization of the centromeric chromatin coinciding with key events of synapsis initiation from the subtelomeric regions. As short stretches of subtelomeric synapsis emerged at early zygotene, centromere clusters lost their strong polarization, gradually resolving as individual centromeres indicated by more than 21 CENH3 foci associated with unpaired lateral elements. Only following this centromere depolarization were homologous chromosome arms connected, as observed by the alignment and fusion of interstitial ZYP1 loci elongating at zygotene so synapsis at centromeres is a continuation of the interstitial synapsis. Our results thus reveal that centromere associations are a component of the timing and progression of chromosome synapsis, and the gradual release of the individual centromeres from the clusters correlates with the elongation of interstitial synapsis between the corresponding homologues.
Heat‐shock protein 70 expression in the equine cornea
Authors: Peterson Cornelia , Driskell Elizabeth , Wilkie David , Premanandan Christopher , Hamor Ralph
Published: September 2016

Objective

Expression of the 70‐kDa heat‐shock protein (HSP70) has been demonstrated in normal canine corneal epithelium, and inducible expression has been suggested to facilitate wound resolution through organized migration, proliferation, and adhesion of the corneal epithelial cells. Diminished expression ofHSP70 may therefore contribute to prolonged healing in the pathologic cornea of other companion animal species, including the horse.

Animal studied

Normal and pathologic equine cornea was evaluated to determine whether the expression ofHSP70 is correlated with appropriate corneal epithelial wound healing.

Procedures

Paraffin‐embedded tissue from normal equine cornea and therapeutic keratectomies of sterile keratopathies was subject to routine immunohistochemistry forHSP70.

Results

Normal equine corneas exhibited the baseline expression ofHSP70 in the nuclei of all epithelial cells as well as the cytoplasm of the basal epithelium. Expression ofHSP70 in suspected immune‐mediated keratitis was localized to the cytoplasm of basal epithelial cells and nuclei of all epithelial cells, similar to the normal equine cornea. Expression in indolent ulcers was diminished; weak, diffuse staining was noted in the cytoplasm of all epithelial cells.

Conclusions

These findings suggest the expression ofHSP70 is induced in the normal equine cornea during re‐epithelialization and may be altered in sterile keratopathies.
Resilient and Robust Control of Time-Delay Wind Energy Conversion Systems
Authors: Wang Xin , Alden Mohammed Jamal
Published: September 2016

Wind energy is the fastest growing and the most promising renewable energy resource. High efficiency and reliability are required for wind energy conversion systems (WECSs) to be competitive within the energy market. Difficulties in achieving the maximum level of efficiency in power extraction from the available wind energy resources warrant the collective attention of control and power system engineers. A strong movement toward sustainable energy resources and advances in control system methodologies make previously unattainable levels of efficiency possible. In this paper, we design a general resilient and robust control framework for a time-delay variable speed permanent magnet synchronous generator (PMSG)-based WECS. A linear matrix inequality-based control approach is developed to accommodate the unstructured model uncertainties, L2 type of external disturbances, and time delays in input and state feedback variables. Computer simulation results have shown the efficacy of the proposed approach of achieving asymptotic stability and H∞ performance objectives.
Influencing Parameters of Tip Blowing Interacting With Rotor Tip Flow
Authors: Guinet Cyril , Inzenhofer André , Gümmer Volker
Published: September 2016

The design space of axial-flow compressors is restricted by stability issues. Different axial-type casing treatments (CTs) have shown their ability to enhance compressor stability and to influence efficiency. Casing treatments have proven to be effective, but there still is need for more detailed investigations and gain of understanding for the underlying flow mechanism. Casing treatments are known to have a multitude of effects on the near-casing 3D flow field. For transonic compressor rotors, these are more complex, as super- and subsonic flow regions alternate while interacting with the casing treatment. To derive design rules, it is important to quantify the influence of the casing treatment on the different tip flow phenomena. Designing a casing treatment in a way that it antagonizes only the deteriorating secondary flow effects can be seen as a method to enhance stability while increasing efficiency. The numerical studies are carried out on a tip-critical rotor of a 1.5-stage transonic axial compressor. The examined recirculating tip blowing casing treatment (TBCT) consists of a recirculating channel with an air off-take above the rotor and an injection nozzle in front of the rotor. The design and functioning of the casing treatment are influenced by various parameters. A variation of the geometry of the tip blowing, more specifically the nozzle aspect ratio, the axial position, or the tangential orientation of the injection port, was carried out to identify key levers. The tip blowing casing treatment is defined as a parameterized geometric model and is automatically meshed. A sensitivity analysis of the respective design parameters of the tip blowing is carried out on a single rotor row. Their impact on overall efficiency and their ability to improve stall margin are evaluated. The study is carried out using unsteady Reynolds-averaged Navier–Stokes (URANS) simulations.
Dynamical Properties of Combustion Instability in a Laboratory-Scale Gas-Turbine Model Combustor
Authors: Gotoda Hiroshi , Hayashi Kenta , Tsujimoto Ryosuke , Domen Shohei , Tachibana Shigeru
Published: September 2016

We present an experimental study on the nonlinear dynamics of combustion instability in a lean premixed gas-turbine model combustor with a swirl-stabilized turbulent flame. Intermittent combustion oscillations switching irregularly back and forth between burst and pseudo-periodic oscillations exhibit the deterministic nature of chaos. This is clearly demonstrated by considering two nonlinear forecasting methods: an extended version (Gotoda et al., 2015, “Nonlinear Forecasting of the Generalized Kuramoto-Sivashinsky Equation,” Int. J. Bifurcation Chaos, 25, p. 1530015) of the Sugihara and May algorithm (Sugihara and May, 1990, “Nonlinear Forecasting as a Way of Distinguishing Chaos From Measurement Error in Time Series,” Nature, 344, pp. 734–741) as a local predictor, and a generalized radial basis function (GRBF) network as a global predictor (Gotoda et al., 2012, “Characterization of Complexities in Combustion Instability in a Lean Premixed Gas-Turbine Model Combustor,” Chaos, 22, p. 043128; Gotoda et al., 2016 (unpublished)). The former enables us to extract the short-term predictability and long-term unpredictability of chaos, while the latter can produce surrogate data to test for determinism by a free-running approach. The permutation entropy based on a symbolic sequence approach is estimated for the surrogate data to test for determinism and is also used as an online detector to prevent lean blowout.
Toxicological evaluation of dextran stabilized iron oxide nanoparticles in human peripheral blood lymphocytes
Authors: Easo Sheeja Liza , Mohanan Parayanthala Valappil
Published: September 2016

Iron oxide nanoparticles present an attractive choice for carcinogenic cell destruction via hyperthermia treatment due to its small size and magnetic susceptibility. Dextran stabilized iron oxide nanoparticles (DIONPs) synthesized and characterized for this purpose were used to evaluate its effect on cellular uptake, cytotoxicity, and oxidative stress response in human peripheral blood lymphocytes. In the absence of efficient internalization and perceptible apoptosis, DIONPs were still capable of inducing significant levels of reactive oxygen species formation shortly after exposure. Although these particles did not cause any genotoxic effect, they enhanced the expression of a few relevant oxidative stress and antioxidant defense related genes, accompanied by an increase in the glutathione peroxidase activity. These results indicate that under the tested conditions, DIONPs induced only minimal levels of oxidative stress in lymphocytes. Understanding the biological interaction of DIONPs, the consequences as well as the associated mechanisms in vitro, together with information obtained from systemic studies, could be expected to advance the use of these particles for further clinical trials.
Simultaneous 4D‐CBCT reconstruction with sliding motion constraint
Authors: Dang Jun , Yin Fang‐Fang , You Tao , Dai Chunhua , Chen Deyu , Wang Jing
Published: September 2016

Purpose

Current approaches using deformable vector field (DVF) for motion‐compensated 4D‐cone beam CT (CBCT) reconstruction typically utilize an isotropically smoothed DVF between different respiration phases. Such isotropically smoothed DVF does not work well if sliding motion exists between neighboring organs. This study investigated an anisotropic motion modeling scheme by extracting organ boundary local motions (e.g., sliding) and incorporated them into 4D‐CBCT reconstruction to optimize the motion modeling and reconstruction methods.

Methods

Initially, a modified simultaneous algebraic reconstruction technique (mSART) was applied to reconstruct high quality reference phase CBCT using all phase projections. The initial DVFs were precalculated and subsequently updated to achieve the optimized solution. During the DVF update, sliding motion estimation was performed by matching the measured projections to the forward projection of the deformed reference phase CBCT. In this process, each moving organ boundary was first segmented. The normal vectors of the boundary DVF were then extracted and incorporated for further DVF optimization. The regularization term in the objective function adaptively regularizes the DVF by (1) isotopically smoothing the DVF within each organ; (2) smoothing the DVF at boundary along the normal direction; and (3) leaving the tangent direction of boundary DVF unsmoothed (i.e., allowing for sliding motion). A nonlinear conjugate gradient optimizer was used. The algorithm was validated on a digital cubic tube phantom with sliding motion, nonuniform rotational B‐spline based cardiac‐torso (NCAT) phantom, and two anonymized patient data. The relative reconstruction error (RE), the motion trajectory's root mean square error (RMSE) together with its maximum error (MaxE), and the Dice coefficient of the lung boundary were calculated to evaluate the algorithm performance.

Results

For the cubic tube and NCAT phantom tests, the REs are 10.2% and 7.4% with sliding motion compensation, compared to 13.4% and 8.9% without sliding modeling. The motion trajectory's RMSE and MaxE for NCAT phantom tests are 0.5 and 0.8 mm with sliding motion constraint compared to 3.5 and 7.3 mm without sliding motion modeling. The Dice coefficients for both NCAT phantom and the patients show a consistent trend that sliding motion constraint achieves better similarity for segmented lung boundary compared with the ground truth or patient reference.

Conclusions

A sliding motion‐compensated 4D‐CBCT reconstruction and the motion modeling scheme was developed. Both phantom and patient study demonstrated the improved accuracy and motion modeling accuracy in reconstructed 4D‐CBCT.
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

Purpose

The 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.

Methods

The 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.

Results

Experimental 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.

Conclusions

The 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.
Enhanced T cell responses to IL-6 in type 1 diabetes are associated with early clinical disease and increased IL-6 receptor expression
Authors: Hundhausen Christian , Roth Alena , Whalen Elizabeth , Chen Janice , Schneider Anya , Long S. Alice , Wei Shan , Rawlings Rebecca , Kinsman MacKenzie , Evanko Stephen P. , Wight Thomas N. , Greenbaum Carla J. , Cerosaletti Karen , Buckner Jane H.
Published: September 2016

T cells from diabetic individuals are hyperresponsive to IL-6 stimulation, which could contribute to disease pathogenesis and may be an avenue for therapeutic intervention.
Pairing the right ingredients for the perfect drug cocktail
Authors: Bhakta Nirav R.
Published: September 2016

A computer model of combination drug therapy improves predictive accuracy, requires less experimental data, and may reduce the barrier to developing multidrug regimens.
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

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

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

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.
Microbial Communities Are Well Adapted to Disturbances in Energy Input
Authors: Fernandez-Gonzalez Nuria , Huber Julie A. , Vallino Joseph J.
Published: September 2016

Within the broader ecological context, biological communities are often viewed as stable and as only experiencing succession or replacement when subject to external perturbations, such as changes in food availability or the introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic “unstable” communities may be important for ecosystem functional stability, with rare organisms playing an important role in community restructuring. Understanding the mechanisms responsible for internal community dynamics will certainly be required for understanding and manipulating microbiomes in both host-associated and natural ecosystems.
The Copenhagen Consensus Conference 2016: children, youth, and physical activity in schools and during leisure time
Authors: Bangsbo Jens , Krustrup Peter , Duda Joan , Hillman Charles , Andersen Lars Bo , Weiss Maureen , Williams Craig A , Lintunen Taru , Green Ken , Hansen Peter Riis , Naylor Patti-Jean , Ericsson Ingegerd , Nielsen Glen , Froberg Karsten , Bugge Anna , Lundbye-Jensen Jesper , Schipperijn Jasper , Dagkas Symeon , Agergaard Sine , von Seelen Jesper , Østergaard Charlotte , Skovgaard Thomas , Busch Henrik , Elbe Anne-Marie
Published: September 2016

From 4 to 7 April 2016, 24 researchers from 8 countries and from a variety of academic disciplines gathered in Snekkersten, Denmark, to reach evidence-based consensus about physical activity in children and youth, that is, individuals between 6 and 18 years. Physical activity is an overarching term that consists of many structured and unstructured forms within school and out-of-school-time contexts, including organised sport, physical education, outdoor recreation, motor skill development programmes, recess, and active transportation such as biking and walking. This consensus statement presents the accord on the effects of physical activity on children's and youth's fitness, health, cognitive functioning, engagement, motivation, psychological well-being and social inclusion, as well as presenting educational and physical activity implementation strategies. The consensus was obtained through an iterative process that began with presentation of the state-of-the art in each domain followed by plenary and group discussions. Ultimately, Consensus Conference participants reached agreement on the 21-item consensus statement.
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

Objectives

Disability 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.

Design

Retrospective and longitudinal designs.

Setting

Data 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.

Participants

A total of 1834 participants in the age range 60–84 years from NHANES 1999–2002.

Main outcome measures

We 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.

Results

During 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.

Conclusions

The 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

Introduction

Current 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 analysis

This 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 dissemination

Local 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 number

ACTRN12611000184976; 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

Objective

A 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.

Design

A 2-year cross-sectional study.

Setting

2 large HIV primary care clinics in western Kenya.

Participants

1054 HIV-infected women in western Kenya undergoing cervical cancer screening as part of routine HIV care from October 2010 to November 2012.

Interventions

Participants 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 measures

We 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.

Results

Average 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.

Conclusions

p16INK4aELISA 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

Introduction

Prospective 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 analysis

The 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 dissemination

This 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.
Evaluation of the Performance of C. Diff Quik Chek Complete and its Usefulness in a Hospital Setting with a High Prevalence of Clostridium Difficile Infection
Authors: Chung Hae-Sun , Lee Miae
Published: September 2016

Rapid and accurate diagnosis of Clostridium difficile infection (CDI) is crucial for patient care, infection control, and efficient surveillance. We evaluated C. DIFF QUIK CHEK COMPLETE (QCC; TechLab), which detects glutamate dehydrogenase (GDH) antigen (QCC-Ag) and toxin A/B (QCC-Tox) simultaneously, and compared it to the laboratory diagnostics for CDI currently in use in a tertiary hospital setting with a high prevalence of CDI. QCC, RIDASCREEN C. difficile toxin A/B assay (Toxin EIA; R-Biopharm AG), chromID C. difficile agar (bioMérieux) culture (ChromID culture), and Xpert C. difficile PCR assay (Xpert PCR; Cepheid) were performed according to the manufacturers' instructions. Performances of the assays were compared against that of Xpert PCR as a reference. Of the 231 loose stool specimens, 83 (35.9%) were positive by Xpert PCR. The sensitivity, specificity, and positive and negative predictive values were 97.6%, 93.9%, 90.0%, and 98.6%, respectively, for QCC-Ag and 55.4%, 100%, 100%, and 80.0%, respectively, for QCC-Tox. The median threshold cycle values of the QCC-Tox(+) specimens were lower than those of the QCC-Tox(−) specimens. Results of QCC as an initial screening test were confirmed in 81.0% (187/231) of samples; these specimens did not require further testing. QCC is a rapid, easy, and cost-effective method that would be a useful first-line screening assay for laboratory diagnosis of CDI in a tertiary hospital with a high prevalence of CDI. A two-step algorithm using QCC as an initial screening tool, followed by Xpert PCR as a confirmatory test, is a practical and cost-effective approach.