bluuebunny/crossref_metadata_2025 huggingface dataset:
Designing shape memory alloy linear actuators: A review
Authors: Mohd Jani Jaronie , Leary Martin , Subic Aleksandar
Published: December 2016

In numerous studies, it was emphasised that only a few of patented shape memory alloy applications are commercially successful due to material limitations combined with a lack of material and design knowledge and associated tools. This work further emphasises that these limitations may be improved or even resolved with proper design approaches and techniques; thus, the functionality and the reliability of shape memory alloy actuators could be realised and optimised. A brief review of the recent progress and development in optimising shape memory alloy linear actuator with different design methods, techniques and/or approaches are presented and discussed in this review.
Untapped Potential of Home Health Care Innovations to Improve Outcomes With Bundled Payment Initiatives
Authors: Lee Teresa , Schiller Jennifer
Published: December 2016

A rapidly changing health care payment system creates opportunities for optimizing home health and home-based care for patients needing cardiac rehabilitation (CR). Home health agencies are poised to play a significant role in episode payment models in the context of post–acute care for patients with cardiovascular conditions. As the Medicare program expands its episode payment models to include patients with cardiovascular conditions, hospitals and other health care stakeholders that will be engaged in these bundled payment arrangements should consider use of home health care in the delivery of CR as a bridge to outpatient therapy and patient self-management.
Effects of Coaching on Teachers’ Implementation of Tier 1 School-Wide Positive Behavioral Interventions and Support Strategies
Authors: Bethune Keri S.
Published: December 2016

Fidelity of implementation of School-Wide Positive Behavioral Interventions and Supports (SWPBIS) procedures within schools is critical to the success of the program. Coaching has been suggested as one approach to helping ensure accuracy of implementation of SWPBIS plans. This study used a multiple baseline across participants design to examine the effects of coaching on elementary schools teachers’ implementation of Tier 1 SWPBIS with their general education students. After providing the coach with an initial training on the SWPBIS and coaching procedures, four elementary schoolteachers were provided with side-by-side coaching during whole-class group instruction. Results indicated that there was a functional relationship between coaching and improved SWPBIS fidelity scores. Implications for practice included the need to consider selecting an appropriate person to act as the coach, scheduling difficulties, and the inability to standardize the number of opportunities for teachers to demonstrate some of the skills based on variability in student performance. However, utilizing school personnel to act as SWPBIS coaches may be a viable option to build sustainability and integrity of SWPBIS procedures within schools.
Performance analysis of a finite noncircular floating ring bearing in turbulent flow regime
Authors: Soni Sandeep , Vakharia DP
Published: December 2016

The present paper investigates the turbulence effect on the steady-state performance of a new variety of journal bearing, i.e. the noncircular floating ring bearing. This particular bearing consists of the journal, floating ring, as well as lower and upper lobes. The shaft and the floating ring are cylindrical while surfaces of the bearing are noncircular. The classical Navier–Stokes equations and continuity equation in cylindrical coordinates are being satisfactorily adapted with the linearized turbulent lubrication model of Ng and Pan. These improved equations are being solved by the finite element method using Galerkin’s technique and an appropriate iteration strategy. The proposed bearing has a length-to-diameter ratio of 1 and operates over different values of the ratio of clearances (i.e. 0.70 and 1.30). The steady-state performance parameters computed are presented in terms of an inner and outer film eccentricity ratios, load-carrying capacity, attitude angle, speed ratio, friction coefficient variable, oil flow, and temperature rise variable for the Reynolds number up to 9000. The present analysis predicts better performance in the turbulent regime as compared to the laminar regime for the noncircular floating ring bearing.
To be or not to be positive: Development of a tool to assess the relationship of negative, positive, and realistic thinking with psychological distress in breast cancer
Authors: Gilbert Émilie , Savard Josée , Gagnon Pierre , Savard Marie-Hélène , Ivers Hans , Foldes-Busque Guillaume
Published: December 2016

There is a widespread belief that positive thinking is a key strategy to cope with cancer. While dispositional optimism is associated with lower psychological distress, the literature supporting the efficacy of cognitive-behavioral therapy indirectly suggests that realistic thinking is also effective. This article describes the development of the Thoughts and Anticipations about Cancer questionnaire designed to directly compare the effect of realistic thinking versus positive thinking on adjustment to cancer. Preliminary data on its relationships with psychological distress gathered in 10 breast cancer patients are promising. The validity of the Thoughts and Anticipations about Cancer questionnaire will need to be confirmed in larger studies.
What If the Rival Drives a Porsche?
Authors: Hennighausen Christine , Hudders Liselot , Lange Benjamin P. , Fink Hanna
Published: December 2016

Previous research found that men conspicuously consume luxury products to attract a mate and to signal their mate value. However, these studies have yet neglected to investigate the function of male conspicuous consumption in same-sex competition. Given that intersexual selection and intrasexual selection are closely related processes, it stands to reason that a further function of male conspicuous consumption could be to impress and deter same-sex rivals. An 2 (intrasexual competition context vs. control) × 2 (conspicuous luxury vs. inconspicuous nonluxury) between-subjects experimental study conducted with an Amazon Mechanical Turk sample ( N = 160) revealed that men reported both higher liking of and an intent to purchase a conspicuous luxury car compared to an inconspicuous nonluxury car due to increased feelings of social status. This effect was stronger in the intrasexual competition than in the control context. An additional perception study using a single-factor between-subjects design (conspicuous luxury vs. inconspicuous nonluxury car) among German men ( N = 405) indicated that male participants rated a man who displayed a conspicuous luxury car more as a rival and mate poacher and less as a friend. They further perceived him to be superior on various mate value characteristics (i.e., attractiveness, intelligence, ambition, and status) and rated him as more oriented toward short-term mating. In sum, our findings add to previous research in the field of evolutionary consumer psychology by suggesting that male conspicuous consumption of luxuries may also serve a function in male–male competition.
Short-term effect of volume recruitment–derecruitment manoeuvre on chest-wall motion in Duchenne muscular dystrophy
Authors: Meric Henri , Falaize Line , Pradon Didier , Lacombe Matthieu , Petitjean Michel , Orlikowski David , Prigent Hélène , Lofaso Frédéric
Published: December 2016

Because progressive respiratory muscle weakness leads to decreased chest-wall motion with eventual ribcage stiffening, the purpose was to compare vital capacity (VC) and contributions of chest-wall compartments before and after volume recruitment–derecruitment manoeuvres (VRDM) in Duchenne muscular dystrophy (DMD). We studied nine patients with DMD and VC lower than 30% of predicted. VRDM was performed using 15 insufflations–exsufflations of +30 to −30 cmH2O. VC and three-dimensional chest-wall motion were measured, as well as oxygen saturation, transcutaneous partial pressure of carbon dioxide and the rapid shallow breathing index (respiratory rate/tidal volume) before (baseline) and immediately and 1 hour after VRDM. VC increased significantly immediately after VRDM (108% ± 7% of baseline, p = 0.018) but returned to baseline within 1 hour, and the rapid shallow breathing index increased significantly. The non-dominant side systematically increased immediately after VRDM ( p = 0.0077), and in the six patients with abnormal breathing asymmetry (difference >10% of VC) at baseline, this asymmetry was corrected immediately and/or 1 hour after VRDM. VRDM improved VC and reduced chest-wall motion asymmetry, but this beneficial effect waned rapidly with respiratory muscle fatigue, suggesting that VRDM may need to be repeated during the day to produce lasting benefits.
Augmentation of Cytolytic Activity in Murine Natural Killer Cells and Inhibition of Tumor Growth by the Ethanol Fraction of Oyster Extract
Authors: Sakaguchi Kaito , Zhong Ming , Kawai Saeko , Shimizu Yoshio , Gohda Eiichi
Published: December 2016

A reduced number and/or reduced activity of natural killer (NK) cells, which are important for defense against a variety of cancers and viral infections, occur under various stress conditions and in patients with various diseases. In this article, we report that the 30% to 50% ethanol precipitate of oyster extract (EPOE50) dose-dependently enhanced the activity of mouse spleen NK cells in vitro and in vivo. The activity of EPOE50 was eluted with a molecular weight of about 2000 by gel filtration and was inactivated by periodate but not by proteinase K. The activity of highly purified NK cells was also augmented by EPOE50 but not by oligodeoxyribonucleotide 1585, which mimics bacterial DNA. Administration of EPOE50 to mice stimulated splenic NK cell activity without a change in splenic NK cell populations. Although the proliferation of B16 tumor cells in vitro was slightly stimulated by EPOE50, the growth of B16 melanoma in vivo was dose-dependently suppressed by administration of EPOE50. Taken together, our results indicate that EPOE50 augmented NK cell activity and that its administration to mice inhibited tumor growth presumably through the activation of NK cells and also suggest that the active substance is a sugar-containing oligomer or polymer and is not of bacterial origin.
Awareness of Prostate Cancer and Screening Modalities Among Long Island Men
Authors: Leonard James A. , Wells Jenna B. , Brandler Ethan S.
Published: December 2016

Despite advances in prostate cancer (PC) treatment and outcomes, it remains one of the most commonly diagnosed cancers and the second leading cause of cancer mortality in men. Furthermore, there exist little data about patient awareness of PC and the frequency of screening. Adult men (470) presenting to the emergency department at a tertiary care center (Stony Brook University) between 2014 and 2015 were surveyed orally for their perceived risk of PC, awareness of PC and screening modalities, and screening history. In a population that mirrors the racial demographics of the United States, it was observed that significant disparities in awareness of PC exist among several populations including those at greatest risk. This study revealed an important opportunity for education on PC and screening modalities among the population of men at risk.
Effect of the thermal sensitivity in modeling of the frictional heating during braking
Authors: Yevtushenko Aleksander , Kuciej Michal , Och Ewa , Yevtushenko Olena
Published: December 2016

The influence of the thermal sensitivity of a coefficient of friction and thermophysical properties of the pad and disk materials on the temperature distribution during single braking has been studied. For this purpose, the corresponding one-dimensional thermal problem of friction at braking has been formulated. The solution to such nonlinear problem has been made in two stages. First, the partial linearization was carried out using Kirchhoff’s substitution, and then, the initial problem for a system of nonlinear ordinary differential equations was obtained by method of lines. Numerical solution to problem was received by Adams’ method realized in the DIFSUB package. For a friction pair, disk (steel)–pad (retinax), an analysis of the evolution of sliding speed and temperature was carried out. The results obtained within the model that took into account the mutual influence between the speed and temperature were compared with those obtained without taking into account such effects.
Theoretical and experimental study of scour depth by submerged water jet
Authors: Hou Jiaoyi , Zhang Lishan , Gong Yongjun , Ning Dayong , Zhang Zengmeng
Published: December 2016

The characteristics and working principles of the impinging by submerged water jet are analyzed, and the relevant mathematical model is optimized based on Rajaratnam’s theoretical and experimental study. A new mathematical model is constructed by adding an important parameter called impinging angle. A new experiment is designed according to the working conditions of various impinging distances and angles. In combination with the experiment data and with the use of the curve fitting method, the functional relationship between the impinging distance and angle as well as the coefficient C4 is obtained. The experiment results show that the scour depth decreases as impinging distance increases, followed by a trend from decline to rise before falling again; those two turning points occur within the range of 20d–25d. The scour depth constantly increases with rising impinging angle, and the maximum and minimum increasing ranges can reach 180% and 50%, respectively, with the impinging angle increasing from 40° to 90°.
Locking it down
Authors: Grindrod Kelly , Boersema Jonathan , Waked Khrystine , Smith Vivian , Yang Jilan , Gebotys Catherine
Published: December 2016

Objective:

To explore the privacy and security of free medication applications (apps) available to Canadian consumers.

Methods:

The authors searched the Canadian iTunes store for iOS apps and the Canadian Google Play store for Android apps related to medication use and management. Using an Apple iPad Air 2 and a Google Nexus 7 tablet, 2 reviewers generated a list of apps that met the following inclusion criteria: free, available in English, intended for consumer use and related to medication management. Using a standard data collection form, 2 reviewers independently coded each app for the presence/absence of passwords, the storage of personal health information, a privacy statement, encryption, remote wipe and third-party sharing. A Cohen’s Kappa statistic was used to measure interrater agreement.

Results:

Of the 184 apps evaluated, 70.1% had no password protection or sign-in system. Personal information, including name, date of birth and gender, was requested by 41.8% (77/184) of apps. Contact information, such as address, phone number and email, was requested by 25% (46/184) of apps. Finally, personal health information, other than medication name, was requested by 89.1% (164/184) of apps. Only 34.2% (63/184) of apps had a privacy policy in place.

Conclusion:

Most free medication apps offer very limited authentication and privacy protocols. As a result, the onus currently falls on patients to input information in these apps selectively and to be aware of the potential privacy issues. Until more secure systems are built, health care practitioners cannot fully support patients wanting to use such apps.
A structured review of chronic care model components supporting transition between healthcare service delivery types for older people with multiple chronic diseases
Authors: Sendall Marguerite , McCosker Laura , Crossley Kristie , Bonner Ann
Published: December 2016

Objective:

Older people with chronic diseases often have complex and interacting needs and require treatment and care from a wide range of professionals and services concurrently. This structured review will identify the components of the chronic care model (CCM) required to support healthcare that transitions seamlessly between hospital and ambulatory settings for people over 65 years of age who have two or more chronic diseases.

Method:

A structured review was conducted by searching six electronic databases combining the terms ‘hospital’, ‘ambulatory’, ‘elderly’, ‘chronic disease’ and ‘integration/seamless’. Four articles meeting the inclusion criteria were included in the review. Study setting, objectives, design, population, intervention, CCM components, outcomes and results were extracted and a process of descriptive synthesis applied.

Results and conclusion:

All four studies reported only using a few components of the CCM – such as clinical information sharing, community linkages and supported self-management – to create an integrated health system. The implementation of these components in a health service seemed to improve the seamless transition between hospital and ambulatory settings, health outcomes and patient experiences. Further research is required to explore the effect of implementing all CCM components to support transition of care between hospital and ambulatory services.
Superordinate Level Processing Has Priority Over Basic-Level Processing in Scene Gist Recognition
Authors: Sun Qi , Ren Yanju , Zheng Yang , Sun Mingxia , Zheng Yuanjie
Published: December 2016

By combining a perceptual discrimination task and a visuospatial working memory task, the present study examined the effects of visuospatial working memory load on the hierarchical processing of scene gist. In the perceptual discrimination task, two scene images from the same (manmade–manmade pairing or natural–natural pairing) or different superordinate level categories (manmade–natural pairing) were presented simultaneously, and participants were asked to judge whether these two images belonged to the same basic-level category (e.g., street–street pairing) or not (e.g., street–highway pairing). In the concurrent working memory task, spatial load (position-based load in Experiment 1) and object load (figure-based load in Experiment 2) were manipulated. The results were as follows: (a) spatial load and object load have stronger effects on discrimination of same basic-level scene pairing than same superordinate level scene pairing; (b) spatial load has a larger impact on the discrimination of scene pairings at early stages than at later stages; on the contrary, object information has a larger influence on at later stages than at early stages. It followed that superordinate level processing has priority over basic-level processing in scene gist recognition and spatial information contributes to the earlier and object information to the later stages in scene gist recognition.
The Role of Vertical Disparity in Distance and Depth Perception as Revealed by Different Stereo-Camera Configurations
Authors: Vienne Cyril , Plantier Justin , Neveu Pascaline , Priot Anne-Emmanuelle
Published: December 2016

Vertical binocular disparity is a source of distance information allowing the portrayal of the layout and 3D metrics of the visual space. The role of vertical disparity in the perception of depth, size, curvature, or slant of surfaces was revealed in several previous studies using cue conflict paradigms. In this study, we varied the configuration of stereo-cameras to investigate how changes in the horizontal and vertical disparity fields, conflicting with the vergence cue, affect perceived distance and depth. In four experiments, observers judged the distance of a cylinder displayed in front of a large fronto-parallel surface. Experiment 1 revealed that the presence of a background surface decreases the uncertainty in judgments of distance, suggesting that observers use the relative horizontal disparity between the target and the background as a cue to distance. Two other experiments showed that manipulating the pattern of vertical disparity affected both distance and depth perception. When vertical disparity specified a nearer distance than vergence (convergent cameras), perceived distance and depth were underestimated as compared with the condition where vertical disparity was congruent with vergence cues (parallel cameras). When vertical disparity specified a further distance than vergence, namely an infinite distance, distance and depth were overestimated. The removal of the vertical distortion lessened the effect on perceived distance. Overall, the results suggest that the vertical disparity introduced by the specific camera configuration is mainly responsible for the effect. These findings outline the role of vertical disparity in distance and depth perception and support the use of parallel cameras for designing stereograms.
A Randomized Controlled Trial of the Effects of Febuxostat Therapy on Adipokines and Markers of Kidney Fibrosis in Asymptomatic Hyperuricemic Patients With Diabetic Nephropathy
Authors: Beddhu Srinivasan , Filipowicz Rebecca , Wang Bin , Wei Guo , Chen Xiaorui , Roy Abinash C. , DuVall Scott L. , Farrukh Hanadi , Habib Arsalan N. , Bjordahl Terrence , Simmons Debra L. , Munger Mark , Stoddard Greg , Kohan Donald E. , Greene Tom , Huang Yufeng
Published: December 2016

Background:

In observational studies, higher uric acid levels are associated with metabolic syndrome, diabetes, and kidney disease.

Objective:

The objective of this study is to examine whether reduction of plasma uric acid with febuxostat, a xanthine oxido reductase inhibitor, impacts adipose tissue oxidative stress, adipokines, and markers of systemic inflammation or kidney fibrosis.

Design:

This was a double-blinded randomized controlled trial.

Setting:

Academic university setting was used.

Patients:

Overweight or obese adults with hyperuricemia and type 2 diabetic nephropathy were included.

Measurements:

Adipose tissue thiobarbituric acid reducing substances (TBARS) and adiponectin concentrations and urinary transforming growth factor–β (TGF-β) were primary endpoints. Plasma C-reactive protein, high molecular weight–adiponectin, interleukin–6, tumor necrosis factor–α, and TBARS and albuminuria were among predefined secondary endpoints.

Methods:

Participants were randomly assigned to febuxostat (n = 40) or matching placebo (n = 40) and followed for 24 weeks.

Results:

Baseline plasma uric acid levels were 426 ± 83 µmol/L; 95% completed the study. Estimated glomerular filtration rate (eGFR) declined from 54 ± 17 mL/min/1.73 m2 at baseline to 51 ± 17 mL/min/1.73 m2 at 24 weeks ( P = .05). In separate mixed-effects models, compared with placebo, febuxostat reduced uric acid by 50% ( P < .001) but had no significant effects on subcutaneous adipose tissue TBARS (−7.4%, 95% confidence interval [CI], 57.4%-101.4%) or adiponectin (6.7%, 95% CI, 26.0%-53.8%) levels or urinary TGF-β/creatinine ratio (18.0%, 95% CI, 10.0%-54.8%) or secondary endpoints.

Limitations:

Relatively modest sample size and short duration of follow-up.

Conclusions:

In this population with progressive diabetic nephropathy, febuxostat effectively reduced plasma uric acid. However, no detectable effects were observed for the prespecified primary or secondary endpoints.

Trial Registration:

The study was registered in clinicaltrials.gov (NCT01350388).
Peritoneal Dialysis–Related Peritonitis Due to Abiotrophia defectiva
Authors: Shah Nikhil , Naidu Prenilla , Pauly Robert P.
Published: December 2016

Background:

Abiotrophia defectiva is a fastidious aerobic gram-positive bacterium which is part of the normal flora of the human oral cavity. It is an unusual cause of peritoneal dialysis–related peritonitis.

Case Presentation:

We present a case of a man in his fifties with end-stage renal failure secondary to polycystic kidney disease who presented with a cloudy peritoneal fluid effluent and a cell count of 35 620 × 106 cells/L with 90% polymorphonuclear cells. The fluid was cultured per unit protocol, and the organism was identified as Abiotrophia defectiva. Post–peritonitis dialysis technique review revealed frequent lapses in the use of facemask and hand washing during cycler connection and disconnection. The patient responded well to vancomycin; however, he subsequently developed ultrafiltration failure and symptoms of fluid overload and uremia and was transferred to home hemodialysis.

Conclusions:

Abiotrophia defectiva is an unusual cause of peritoneal dialysis–related peritonitis. The organism is a normal commensal of the oral cavity and may cause peritonitis in patients with nonadherence to dialysis technique. In our case, the infection was followed by peritoneal membrane failure and transfer to hemodialysis. It remains to be seen if peritonitis with Abiotrophia defectiva heralds a worse outcome.
A computer-assisted systematic quality monitoring method for cervical hip fracture radiography
Authors: Geijer Mats , Laurin Olof , Johnsson Ragnar , Laurin Sven
Published: December 2016

Background

A thorough quality analysis of radiologic performance is cumbersome. Instead, the prevalence of missed cervical hip fractures might be used as a quality indicator.

Purpose

To validate a computer-based quality study of cervical hip fracture radiography.

Material and Methods

True and false negative and positive hip trauma radiography during 6 years was assessed manually. Patients with two or more radiologic hip examinations before surgery were selected by computer analysis of the databases. The first of two preoperative examinations might constitute a missed fracture. These cases were reviewed.

Results

Out of 1621 cervical hip fractures, manual perusal found 51 (3.1%) false negative radiographic diagnoses. Among approximately 14,000 radiographic hip examinations, there were 27 (0.2%) false positive diagnoses. Fifty-seven percent of false negative reports were occult fractures, the other diagnostic mistakes. There were no significant differences over the years. Diagnostic sensitivity was 96.9% and specificity 99.8%. Computer-assisted analysis with a time interval of at least 120 days between the first and the second radiographic examination discovered 39 of the 51 false negative reports.

Conclusion

Cervical hip trauma radiography has high sensitivity and specificity. With computer-assisted analysis, 76% of false negative reports were found.
Can intralesional cryotherapy reshape the management of difficult keloid scars?
Authors: Defty Charlotte , Cubitt Jonathan J , Murison Maxwell SC
Published: December 2016

Keloid scars are notoriously difficult to treat with very high recurrence rates despite a range of treatment options. We present a case report of a 43-year-old man with a resistant keloid scar on his left ear from a piercing. After 15 years of multimodal treatments including surgery, steroid and 5-fluorourcil injections, the keloid persisted. It has responded very well to a single treatment of intralesional cryotherapy (trademark: CryoShape, Etgar Group International Ltd). The authors would now consider intralesional cryotherapy as a useful tool in their armamentarium for prominent, resistant or recurrent keloids. Future experience will guide its clinical applications.
The Relationship Between Pedometer-Determined Ambulatory Activity and Balance Variables Within an Older Adult Population
Authors: Campbell Candice , Kress Jeff , Schroeder Jan , Donlin Ayla , Rozenek Ralph
Published: December 2016

The purpose of this investigation was to determine the differences between gender, physical activity level, and balance in an older adult population. A secondary purpose was to examine the relationship between pedometer-determined ambulatory activity and balance. Forty-six older adults aged 73.7 ± 6.2 years participated in the study. Participants completed the Fullerton Advanced Balance (FAB) Scale and completed a 2-week daily step recording to determine average steps taken per day. Low-level activity participants (<5,000 steps/day) were significantly different from the high-level activity participants (>7,500 steps/day) in weight, age, and the number of medications reported. Males performed better than females on the two-footed jump test and reactive postural test FAB assessments. High-level activity participants performed significantly better than low-level activity participants on all FAB assessments except stand with feet together and eyes closed, reach forward to object, and walk with head turns.
SCIFIO: an extensible framework to support scientific image formats
Authors: Hiner Mark C. , Rueden Curtis T. , Eliceiri Kevin W.
Published: December 2016

Background

No gold standard exists in the world of scientific image acquisition; a proliferation of instruments each with its own proprietary data format has made out-of-the-box sharing of that data nearly impossible. In the field of light microscopy, the Bio-Formats library was designed to translate such proprietary data formats to a common, open-source schema, enabling sharing and reproduction of scientific results. While Bio-Formats has proved successful for microscopy images, the greater scientific community was lacking a domain-independent framework for format translation.

Results

SCIFIO (SCientific Image Format Input and Output) is presented as a freely available, open-source library unifying the mechanisms of reading and writing image data. The core of SCIFIO is its modular definition of formats, the design of which clearly outlines the components of image I/O to encourage extensibility, facilitated by the dynamic discovery of the SciJava plugin framework. SCIFIO is structured to support coexistence of multiple domain-specific open exchange formats, such as Bio-Formats’ OME-TIFF, within a unified environment.

Conclusions

SCIFIO is a freely available software library developed to standardize the process of reading and writing scientific image formats.
The role of nucleotide composition in premature termination codon recognition
Authors: Zahdeh Fouad , Carmel Liran
Published: December 2016

Background

It is not fully understood how a termination codon is recognized as premature (PTC) by the nonsense-mediated decay (NMD) machinery. This is particularly true for transcripts lacking an exon junction complex (EJC) along their 3’ untranslated region (3’UTR), and thus degrade through the EJC-independent NMD pathway.

Results

Here, we analyzed data of transcript stability change following NMD repression and identified over 200 EJC-independent NMD-targets. We examined many features characterizing these transcripts, and compared them to NMD-insensitive transcripts, as well as to a group of transcripts that are destabilized following NMD repression (destabilized transcripts).

Conclusions

We found that none of the known NMD-triggering features, such as the presence of upstream open reading frames, significantly characterizes EJC-independent NMD-targets. Instead, we saw that NMD-targets are strongly enriched with G nucleotides upstream of the termination codon, and even more so along their 3’UTR. We suggest that high G content around the termination codon impedes translation termination as a result of mRNA folding, thus triggering NMD. We also suggest that high G content in the 3’UTR helps to activate NMD by allowing for the accumulation of UPF1, or other NMD-promoting proteins, along the 3’UTR.
Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations
Authors: Mora Osorio Camilo Andrés , González Barrios Andrés Fernando
Published: December 2016

Background

Calculation of the Gibbs free energy changes of biological molecules at the oil-water interface is commonly performed with Molecular Dynamics simulations (MD). It is a process that could be performed repeatedly in order to find some molecules of high stability in this medium.

Here, an alternative method of calculation has been proposed: a group contribution method (GCM) for peptides based on MD of the twenty classic amino acids to obtain free energy change during the insertion of any peptide chain in water-dodecane interfaces. Multiple MD of the twenty classic amino acids located at the interface of rectangular simulation boxes with a dodecane-water medium were performed.

Results

A GCM to calculate the free energy of entire peptides is then proposed. The method uses the summation of the Gibbs free energy of each amino acid adjusted in function of its presence or absence in the chain as well as its hydrophobic characteristics.

Conclusion

Validation of the equation was performed with twenty-one peptides all simulated using MD in dodecane-water rectangular boxes in previous work, obtaining an average relative error of 16%.
ConEVA: a toolbox for comprehensive assessment of protein contacts
Authors: Adhikari Badri , Nowotny Jackson , Bhattacharya Debswapna , Hou Jie , Cheng Jianlin
Published: December 2016

Background

In recent years, successful contact prediction methods and contact-guided ab initio protein structure prediction methods have highlighted the importance of incorporating contact information into protein structure prediction methods. It is also observed that for almost all globular proteins, the quality of contact prediction dictates the accuracy of structure prediction. Hence, like many existing evaluation measures for evaluating 3D protein models, various measures are currently used to evaluate predicted contacts, with the most popular ones being precision, coverage and distance distribution score (Xd).

Results

We have built a web application and a downloadable tool, ConEVA, for comprehensive assessment and detailed comparison of predicted contacts. Besides implementing existing measures for contact evaluation we have implemented new and useful methods of contact visualization using chord diagrams and comparison using Jaccard similarity computations. For a set (or sets) of predicted contacts, the web application runs even when a native structure is not available, visualizing the contact coverage and similarity between predicted contacts. We applied the tool on various contact prediction data sets and present our findings and insights we obtained from the evaluation of effective contact assessments. ConEVA is publicly available at http://cactus.rnet.missouri.edu/coneva/.

Conclusion

ConEVA is useful for a range of contact related analysis and evaluations including predicted contact comparison, investigation of individual protein folding using predicted contacts, and analysis of contacts in a structure of interest.
Molecular control of nitric oxide synthesis through eNOS and caveolin-1 interaction regulates osteogenic differentiation of adipose-derived stem cells by modulation of Wnt/β-catenin signaling
Authors: Bandara Nadeeka , Gurusinghe Saliya , Lim Shiang Yong , Chen Haying , Chen Shuangfeng , Wang Dawei , Hilbert Bryan , Wang Le-Xin , Strappe Padraig
Published: December 2016

Background

Nitric oxide (NO) plays a role in a number of physiological processes including stem cell differentiation and osteogenesis. Endothelial nitric oxide synthase (eNOS), one of three NO-producing enzymes, is located in a close conformation with the caveolin-1 (CAV-1WT) membrane protein which is inhibitory to NO production. Modification of this interaction through mutation of the caveolin scaffold domain can increase NO release. In this study, we genetically modified equine adipose-derived stem cells (eASCs) with eNOS, CAV-1WT, and a CAV-1F92A(CAV-1WTmutant) and assessed NO-mediated osteogenic differentiation and the relationship with the Wnt signaling pathway.

Methods

NO production was enhanced by lentiviral vector co-delivery of eNOS and CAV-1F92Ato eASCs, and osteogenesis and Wnt signaling was assessed by gene expression analysis and activity of a novel Runx2-GFP reporter. Cells were also exposed to a NO donor (NONOate) and the eNOS inhibitor,l-NAME.

Results

NO production as measured by nitrite was significantly increased in eNOS and CAV-1F92Atransduced eASCs +(5.59 ± 0.22 μM) compared to eNOS alone (4.81 ± 0.59 μM) and un-transduced control cells (0.91 ± 0.23 μM) (p < 0.05). During osteogenic differentiation, higher NO correlated with increased calcium deposition, Runx2, and alkaline phosphatase (ALP) gene expression and the activity of a Runx2-eGFP reporter. Co-expression of eNOS and CAV-1WTtransgenes resulted in lower NO production. Canonical Wnt signaling pathway-associated Wnt3a and Wnt8a gene expressions were increased in eNOS-CAV-1F92Acells undergoing osteogenesis whilst non-canonical Wnt5a was decreased and similar results were seen with NONOate treatment. Treatment of osteogenic cultures with 2 mM l-NAME resulted in reduced Runx2, ALP, and Wnt3a expressions, whilst Wnt5a expression was increased in eNOS-delivered cells. Co-transduction of eASCs with a Wnt pathway responsive lenti-TCF/LEF-dGFP reporter only showed activity in osteogenic cultures co-transduced with a doxycycline inducible eNOS. Lentiviral vector expression of canonical Wnt3a and non-canonical Wnt5a in eASCs was associated with induced and suppressed osteogenic differentiation, respectively, whilst treatment of eNOS-osteogenic cells with the Wnt inhibitor Dkk-1 significantly reduced expressions of Runx2 and ALP.

Conclusions

This study identifies NO as a regulator of canonical Wnt/β-catenin signaling to promote osteogenesis in eASCs which may contribute to novel bone regeneration strategies.
Analyzing microtomography data with Python and the scikit-image library
Authors: Gouillart Emmanuelle , Nunez-Iglesias Juan , van der Walt Stéfan
Published: December 2016

The exploration and processing of images is a vital aspect of the scientific workflows of many X-ray imaging modalities. Users require tools that combine interactivity, versatility, and performance. is an open-source image processing toolkit for the Python language that supports a large variety of file formats and is compatible with 2D and 3D images. The toolkit exposes a simple programming interface, with thematic modules grouping functions according to their purpose, such as image restoration, segmentation, and measurements. users benefit from a rich scientific Python ecosystem that contains many powerful libraries for tasks such as visualization or machine learning. combines a gentle learning curve, versatile image processing capabilities, and the scalable performance required for the high-throughput analysis of X-ray imaging data.
Facing Darwin: A Reply to William Flesch
Authors: Fletcher Angus
Published: December 2016

Against the idea that there is one true form of tragedy that can anchor a universal human ethics, Darwinism suggests that life is filled with endless kinds of tragic circumstance. But even as this biological view of tragedy spells the end of moral idealism, it opens up an inclusive practical ethics in which literature can function as a dynamic cognitive toolkit for helping us adapt to the ever-changing tides of life.
Frontier Orbitals in Transition-Metal- and Lanthanide-Mediated Reactions
Authors: Ikeda Hirotaka , Inagaki Satoshi
Published: December 2016

Frontier orbital theory is demonstrated by investigating the appropriately divided parts of transition states, useful for understanding an essential aspect of transition-metal- and lanthanide-mediated reactions. Atomic orbitals are in phase with each other in the outer space of the antibonding orbitals of the bonds between transition-metal and main-group atoms.
C-Ion- and X-ray-Induced Sucrose Radicals Investigated by CW EPR and 9 GHz EPR Imaging
Authors: Nakagawa Kouichi , Hara Hideyuki , Matsumoto Ken-ichiro
Published: December 2016

We investigated stable radical distribution and particle tracks in sucrose irradiated by C-ion irradiation with continuous wave (CW) electron paramagnetic resonance (EPR) and 9 GHz EPR imaging. Both EPR results were compared with X-ray irradiation at a similar dose. Radical distribution in sucrose crystals induced by C-ion and X-ray irradiation were completely different. The 2D EPR imaging results suggested that radical species were mostly located inside the sucrose crystal. Fewer radicals were found on the surface region of the sucrose crystal. The high radical intensities in relation to the C-ion energy deposition are clearly observed at Bragg peak region. No trace of the stable radicals was found after the peak region. The stable radicals of sucrose were distributed as a result of recombination of radicals induced by particle interaction. For the first time, the present EPR images showed the stable radical distribution and particle tracks in the crystal in association with particle-sucrose interaction.
Influence of backscatter radiation on cranial reconstruction implants
Authors: Sakamoto Yoshiaki , Koike Naoyoshi , Takei Hideyuki , Ohno Mari , Miwa Tomoru , Yoshida Kazunari , Shigematsu Naoyuki , Kishi Kazuo
Published: December 2016

Objective:

We aimed to evaluate backscatter dose variations in different cranial bone implant materials in an experimental model designed to simulate post-operative radiotherapy.

Methods:

We assessed the radiation backscatter doses associated with sheet- and mesh-type titanium plates and hydroxyapatite (HAP) samples (porosity: 35%, 50% and 85%). The samples were irradiated with 6- and 10-MV photon beams from a linear accelerator. Measurements were obtained using an ionization chamber and radiochromic films cut from the same batch.

Results:

At 6 MV, the titanium sheet showed the highest peak for backscattered radiation, followed by (in decreasing order) HAP30%, HAP50%, titanium mesh and HAP85%. At 10 MV, HAP30% showed the highest peak, followed by HAP50%, titanium sheet, titanium mesh and HAP85%. The peaks were at different depths in the titanium and HAP samples. The thickness of the human scalp is approximately 7 mm; therefore, measurements were obtained 0–7 mm above the implants to assess the likely dose on the scalp. A comparison of the maximum dose on the scalp showed the titanium sheet had the highest dose at both 6 and 10 MV.

Conclusion:

The backscatter dose differed with the density of the material and the backscatter depth was different for each material.

Advances in knowledge:

Ulcer formation due to radiotherapy after brain tumour depends on not only radiation but also the implant material. Therefore, the density and type of implant material should be considered when planning radiotherapy and selecting bone reconstruction materials.
Image-guided radiotherapy for prostate cancer in the United Kingdom: a national survey
Authors: Ariyaratne Hemal , Chesham Hayley , Alonzi Roberto
Published: December 2016

Objective:

To survey the technology and practice of image-guided radiotherapy (IGRT) for prostate cancer in the UK.

Methods:

A pre-tested semi-structured online questionnaire was sent to National Health Service (NHS) and private radiotherapy providers in the UK between March and April 2014. The survey was carried out on the Opinio© online platform.

Results:

There was a high survey response rate of 83%. There is widespread use of intensity-modulated radiotherapy and advanced verification imaging modalities. Cone-beam CT (CBCT) is the main verification imaging modality in radical prostate radiotherapy, used in 66% of UK centres. Fiducial markers in combination with imaging were used in 30% of centres. Over half the centres used a daily imaging schedule, with a Day 1-3 frequency followed by weekly frequency used less commonly. 26% of centres used daily CBCT.

Conclusion:

There is widespread use of volumetric verification imaging with CBCT for prostate radiotherapy in the UK. There is no consensus on the optimal verification imaging schedule.

Advances in knowledge:

This survey provides an insight into contemporary UK practice of IGRT for prostate cancer, both in the NHS and private sector. It demonstrates the widespread use of CBCT imaging and highlights the need for further research to optimize the practice.
Evaluation of background parenchymal enhancement on breast MRI: a systematic review
Authors: Bignotti Bianca , Signori Alessio , Valdora Francesca , Rossi Federica , Calabrese Massimo , Durando Manuela , Mariscotto Giovanna , Tagliafico Alberto
Published: December 2016

Objective:

To perform a systematic review of the methods used for background parenchymal enhancement (BPE) evaluation on breast MRI.

Methods:

Studies dealing with BPE assessment on breast MRI were retrieved from major medical libraries independently by four reviewers up to 6 October 2015. The keywords used for database searching are “background parenchymal enhancement”, “parenchymal enhancement”, “MRI” and “breast”. The studies were included if qualitative and/or quantitative methods for BPE assessment were described.

Results:

Of the 420 studies identified, a total of 52 articles were included in the systematic review. 28 studies performed only a qualitative assessment of BPE, 13 studies performed only a quantitative assessment and 11 studies performed both qualitative and quantitative assessments. A wide heterogeneity was found in the MRI sequences and in the quantitative methods used for BPE assessment.

Conclusion:

A wide variability exists in the quantitative evaluation of BPE on breast MRI. More studies focused on a reliable and comparable method for quantitative BPE assessment are needed.

Advances in knowledge:

More studies focused on a quantitative BPE assessment are needed.
A prospective evaluation of contrast and radiation dose and image quality in cardiac CT in children with complex congenital heart disease using low-concentration iodinated contrast agent and low tube voltage and current
Authors: Hou Qiao-Ru , Gao Wei , Sun Ai-min , Wang Qian , Qiu Hai-sheng , Wang Fang , Hu Li-wei , Li Jian-ying , Zhong Yu-min
Published: December 2016

Objective:

To the assess image quality, contrast dose and radiation dose in cardiac CT in children with congenital heart disease (CHD) using low-concentration iodinated contrast agent and low tube voltage and current in comparison with standard dose protocol.

Methods:

110 patients with CHD were randomized to 1 of the 2 scan protocols: Group A (n = 45) with 120 mA tube current and contrast agent of 270 mgI/ml in concentration (Visipaque™; GE Healthcare Ireland, Co., Cork, UK); and Group B (n = 65) with the conventional 160 mA and 370 mgI/ml concentration contrast (Iopamiro®; Shanghai Bracco Sine Pharmaceutical Corp Ltd, Shanghai, China). Both groups used 80 kVp tube voltage and were reconstructed with 70% adaptive statistical iterative reconstruction algorithm. The CT value and noise in aortic arch were measured and the signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were calculated. A five-point scale was used to subjectively evaluate image quality. Contrast and radiation dose were recorded.

Results:

There was no difference in age and weight between the two groups (all p > 0.05). The iodine load and radiation dose in Group A were statistically lower (3976 ± 747 mgI vs 5763 ± 1018 mgI in iodine load and 0.60 ± 0.08 mSv vs 0.77 ± 0.10 mSv in effective dose; p < 0.001). However, image noise, CT value, CNR, SNR and subjective image quality for the two groups were similar (all p > 0.05), and with good agreement between the two observers. Comparing the surgery results, the diagnostic accuracy for extracardiac and intracardiac defects for Group A was 96% and 92%, respectively, while the corresponding numbers for Group B were 95% and 93%.

Conclusion:

Compared with the standard dose protocol, the use of low tube voltage (80 kVp), low tube current (120 mA) and low-concentration iodinated contrast agent (270 mgI/ml) enables a reduction of 30% in iodine load and 22% in radiation dose while maintaining compatible image quality and diagnostic accuracy.

Advances in knowledge:

The new cardiac CT scanning protocol can largely reduce the adverse effects of radiation and contrast media to children. Meanwhile, it also can be used effectively to examine complex CHD.