bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinematic and Microphysical Significance of Lightning Jumps versus Nonjump Increases in Total Flash Rate
Authors: Schultz Christopher J. , Carey Lawrence D. , Schultz Elise V. , Blakeslee Richard J. 
Published: December 2016

Abstract
Thirty-nine thunderstorms are examined using multiple-Doppler, polarimetric, and total lightning observations to understand the role of mixed-phase kinematics and microphysics in the development of lightning jumps. This sample size is larger than those of previous studies on this topic. The principal result of this study is that lightning jumps are a result of mixed-phase updraft intensification. Larger increases in intense updraft volume (≥10 m s−1) and larger changes in peak updraft speed are observed prior to lightning jump occurrence when compared to other nonjump increases in total flash rate. Wilcoxon–Mann–Whitney rank sum testing yields p values ≤ 0.05, indicating statistical independence between lightning jump and nonjump distributions for these two parameters. Similar changes in mixed-phase graupel mass magnitude are observed prior to lightning jumps and nonjump increases in total flash rate. The p value for the graupel mass change is p = 0.096, so jump and nonjump distributions for the graupel mass change are not found to be statistically independent using the p = 0.05 significance level. The timing of updraft volume, speed, and graupel mass increases is found to be 4–13 min in advance of lightning jump occurrence. Also, severe storms without lightning jumps lack robust mixed-phase updrafts, demonstrating that mixed-phase updrafts are not always a requirement for severe weather occurrence. Therefore, the results of this study show that lightning jump occurrences are coincident with larger increases in intense mixed-phase updraft volume and peak updraft speed than smaller nonjump increases in total flash rate.
Attempted suicide by ingestion of hair dye containing p-phenylenediamine: a case report
Authors: Beshir Lamis , Kaballo Babiker , Young Donald 
Published: December 2016

Para-phenylenediamine is widely used as a chemical in hair dyes and in combination with henna. This dye is used to paint the body for decorative reasons, to speed the processing time of henna and to intensify the results. Para-phenylenediamine is widely used in the Middle East, North Africa and India. Several reports have been published of the fatal ingestion of hair dye containing para-phenylenediamine. Here, we describe the case of a 14-year-old girl who ingested the compound but whose prompt treatment prevented her death. Ingestion of para-phenylenediamine produces a typical triad of angioneurotic oedema, rhabdomyolysis and acute tubular necrosis. Awareness of signs of these associated conditions in our patient, together with a comprehensive history, facilitated appropriate treatment to be instituted. We document the steps we took to enable her complete physical recovery.
Reflective Tape Applied to Bicycle Frame and Conspicuity Enhancement at Night
Authors: Costa Marco , Bonetti Leonardo , Bellelli Manuela , Lantieri Claudio , Vignali Valeria , Simone Andrea 
Published: December 2016

Objective: Four studies were conducted to assess bicyclist conspicuity enhancement at night by the application of reflective tape (ECE/ONU 104) to the bicycle rear frame and to pedal cranks. Background: Previous studies have tested the benefits of reflective markings applied to bicyclist clothing. Reflective jackets however need to be available and worn while reflective markings enhance conspicuity without any active behavior by the bicyclist. Method: In the first study, reflective tape was applied to the rear frame. Detection distance was compared in four conditions: control, rear red reflector, high visibility jacket, and reflective tape. In the second study, the same conditions were studied with night street lighting on and off. In the third study, detection and recognition distances were evaluated in rainy conditions. In the fourth study, visibility was assessed with the reflective tape applied to pedal cranks. Results: In the first study, the application of reflective markings resulted in a detection distance of 168.28 m. In the second study, the detection distance with reflective markings was 229.74 m with public street light on and 256.41 m with public street light off. In rainy conditions, detection distance using the reflective markings was 146.47 m. Reflective tape applied to pedal cracks resulted in a detection distance of 168.60 m. Conclusion: Reflective tape applied to the rear bicycle frame can considerably increase bicyclist conspicuity and safety at night. Application: Reflective tape is highly recommended to complement anterior and rear lights in bicycle riding at night.
Short-Form Audit Instrument for Assessing Corner Store Healthfulness
Authors: DeWeese Robin S. , Todd Michael , Karpyn Allison , Yedidia Michael J. , Kennedy Michelle , Bruening Meg , Wharton Christopher M. , Ohri-Vachaspati Punam 
Published: December 2016

Purpose: To develop a valid and feasible short-form corner store audit tool (SCAT) that could be used in-store or over the phone to capture the healthfulness of corner stores. Design: Nonexperimental. Setting: Four New Jersey cities. Subjects: Random selection of 229 and 96 corner stores in rounds 1 and 2, respectively. Measures: An adapted version of the Nutrition Environment Measures Survey for Corner Stores (NEMS-CS) was used to conduct in-store audits. The 7-item SCAT was developed and used for round 2 phone audits. Analysis: Exploratory factor analysis and item response theory were used to develop the SCAT. Results: The SCAT was highly correlated with the adapted NEMS-CS ( r = .79). Short-form corner store audit tool scores placed stores in the same healthfulness categories as did the adapted NEMS-CS in 88% of the cases. Phone response matches indicated that store owners did not distinguish between 2% and low-fat milk and tended to round up the fruit and vegetable count to 5 if they had fewer varieties. Conclusion: The SCAT discriminates between higher versus lower healthfulness scores of corner stores and is feasible for use as a phone audit tool.
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.
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.
SCIFIO: an extensible framework to support scientific image formats
Authors: Hiner Mark C. , Rueden Curtis T. , Eliceiri Kevin W. 
Published: December 2016

Abstract
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

Abstract
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

Abstract
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

Abstract
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

AbstractBackgroundNitric 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.MethodsNO 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.ResultsNO 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.ConclusionsThis 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.