bluuebunny/crossref_metadata_2025 huggingface dataset:
A Novel Diastereoselective Synthesis of 6‐Aryl‐5‐hydroxy‐2,3‐dihydropyrano[2,3‐c]pyrazol‐4(1H)‐ones
Authors: Bondock Samir
Published: October 2013

A novel one‐pot diastereoselective synthesis of trans‐6‐aryl‐5‐hydroxy‐2,3‐dihydro[2,3‐c]pyrazol‐4(1H)‐ones 3a, 3b, 3c, 3d, 3e, 3f, 3g, 3h is described via the Darzens condensation reaction of 2‐chloro‐1‐(5‐hydroxy‐3‐methyl‐1‐phenyl‐1H‐pyrazol‐4‐yl)ethanone (2) with different aromatic aldehydes in aqueous basic medium. The structures of the compounds prepared were determined by analytical and spectral analyses.
“Cystic”‐appearing soft tissue masses: What is the role of anatomic, functional, and metabolic MR imaging techniques in their characterization?
Authors: Thawait Gaurav K. , Subhawong Ty K. , Tatizawa Shiga Ney Yoichi , Fayad Laura M.
Published: October 2013

Although conventional MR imaging with contrast‐enhanced T1‐weighted sequences is of paramount importance for evaluating soft tissue masses, noncontrast MR sequences have emerged that facilitate their characterization. In this article, the utility and pitfalls of conventional MR imaging with T1‐weighted, fluid‐sensitive, and contrast‐enhanced sequences will be discussed, along with that of functional (diffusion weighted imaging) and metabolic (proton MR spectroscopy) non–contrast‐enhanced techniques for the purpose of soft tissue mass characterization. In particular, we discuss the application of these techniques to differentiating neoplastic or inflammatory masses that have high fluid content from benign cysts, as this distinction is a common pitfall of conventional sequences. J. Magn. Reson. Imaging 2014;39:504–511. © 2013 Wiley Periodicals, Inc.
Cardiovascular magnetic resonance validation of fractional changes in annulo‐apical angles and tricuspid annular plane systolic excursion for rapid assessment of right ventricular systolic function
Authors: Zakeri Simon A. , Panayotova Rosica , Borg Alexander N. , Miller Christopher A. , Schmitt Matthias
Published: October 2013

Purpose

To evaluate the use of right ventricular (RV) annulo‐apical angle (AA) changes acquired by magnetic resonance imaging (MRI), alongside tricuspid annular plane systolic excursion (TAPSE), for its association with RV systolic function.

Materials and Methods

Thirty patients with varying RV dysfunction and 10 normal controls were enrolled and scanned after obtaining written consent. Systolic change in AAs, alpha (α), beta (β), and theta (θ), subtended by a triangle connecting the septal and lateral extent of the tricuspid valve annulus and RV apex, and TAPSE were measured. Spearman rank correlations of parameters with RV ejection fraction (RVEF) were performed. Receiver operating characteristic (ROC) analysis was used to determine accuracy of these surrogate markers for detecting abnormal RVEF.

Results

Correlations with RVEF included: TAPSE (r = 0.74 P < 0.001), fractional systolic changes in α angle (0.64, P < 0.001), β angle (−0.39, P < 0.05), and θ angle (−0.77, P < 0.001). The best markers for RVEF <50% were fractional θ angle change ≥ –25.5% (eg, −24%) (sensitivity of 97% and specificity of 91%), and TAPSE ≤1.87 cm (sensitivity of 100% and specificity of 82%). Intra‐ and inter‐observer agreement was excellent, with intraclass correlation coefficients for fractional θ angle change (intra = 0.96, inter = 0.94) and TAPSE (intra = 0.98, inter = 0.87).

Conclusion

Fractional θ angle change is a useful semiquantitative parameter associated with the presence and severity of RV systolic dysfunction, with high observer agreement. J. Magn. Reson. Imaging 2014;40:133–139. © 2013 Wiley Periodicals, Inc.
Patient reported outcomes in endoscopic and open transcervical treatment for Zenker's diverticulum
Authors: Seth Rahul , Rajasekaran Karthik , Lee Walter T. , Lorenz Robert R. , Wood Benjamin G. , Kominsky Alan , Scharpf Joseph
Published: October 2013

Objectives/Hypothesis

To compare long‐term symptomatic outcomes between external transcervical (ET) and endoscopic stapling diverticulotomy (ESD) surgeries for Zenker's diverticulum.

Study Design

Retrospective review.

Methods

Patients undergoing surgery for Zenker's diverticulum surgery between 1998 and 2010 with at least 1 year follow‐up were telephoned and questioned for dysphagia, choking, regurgitation, and halitosis based on a validated Gastrointestinal Quality‐of‐Life Index. Symptom degree preoperatively and at phone call was assessed. Patients rated their overall postoperative symptoms as worsened, unchanged, improved, or completely resolved.

Results

A total of 96 patients were eligible for inclusion and 55 were successfully contacted. Of these, 24 underwent ESD and 31 had ET operations. Average follow‐up time was significantly longer for the ET group than the ESD group (5.7 vs. 3.1 years respectively, P < 0.01). Gender, age at operation, diverticulum size, and preoperative symptom scores were not statistically different between the two groups. For both techniques, symptom scores showed significant improvement postoperatively (P < 0.01). A greater proportion of patients undergoing ET procedures reported their symptoms to be completely resolved or improved compared with the ESD group (93% vs. 67%, P = 0.015). Patients undergoing ET demonstrated a greater change or improvement in survey score compared to ESD patients (7.23 vs. 3.42, P = 0.014).

Conclusion

Both the ET and ESD surgeries significantly benefit patients, regardless of diverticulum size. Long‐term symptomatic outcomes between the two populations indicate that patients with ET procedures attain a greater degree of resolution of preoperative symptoms.

Level of Evidence

4. Laryngoscope, 124:119–125, 2014
Novel Bioactive Amino‐Functionalized Cellulose Nanofibers
Authors: Roemhild Katrin , Wiegand Cornelia , Hipler Uta‐Christina , Heinze Thomas
Published: October 2013

Amino‐cellulose‐based nanofibers are prepared by electrospinning of blended solutions of 6‐deoxy‐6‐trisaminoethyl‐amino (TEAE) cellulose and polyvinyl alcohol (PVA). The TEAE cellulose with a degree of substitution of 0.67 is synthesized via a nucleophilic displacement reaction starting from cellulose‐p‐toluenesulfonic acid ester. Several solution characteristics such as polymer concentration, electrical conductivity, and surface tension as well as setup parameters are investigated to optimize the ability of nanofiber formation. These parameters are evaluated using the rheological studies of the solutions. The nanofibers obtained are characterized by scanning electron microscopy (SEM) and show a high antimicrobial activity against Staphylococcus aureus and Klebsiella pneumoniae.

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Reg4‐induced mitogenesis involves Akt‐GSK3β‐β‐Catenin‐TCF‐4 signaling in human colorectal cancer
Authors: Bishnupuri Kumar S , Sainathan Satheesh K , Bishnupuri Kislay , Leahy Devon R , Luo Qizhi , Anant Shrikant , Houchen Courtney W , Dieckgraefe Brian K
Published: October 2013

Upregulation of regenerating gene 4 (Reg4) is observed in many human gastrointestinal malignancies including colorectal cancer (CRC). We previously reported a Reg4‐mediated induction of epidermal growth factor receptor‐Akt‐AP1 signaling regulating CRC cell apoptosis. However, the role of Reg4 in the regulation of CRC cell division is poorly understood. This study tests the hypothesis that Reg4 induces Akt‐GSK3β‐β‐Catenin‐TCF‐4 signaling to regulate CRC cell division. In vitro models of human CRC were used to determine the role of Reg4 in regulation of CRC cell division. Cell cycle studies demonstrated that Reg4 treatment significantly decreased CRC cell number in G1 phase and increased in G2 phase. Subsequently Reg4 significantly increased the mitotic index of CRC cells. As assessed by real‐time RT‐PCR and Western blot analyses, Reg4 significantly increased the expression of cell cycle regulatory genes Cyclin D1 and D3, and associated Cyclin‐dependent kinases (CDK4 and CDK6). Reg4‐mediated increase in these genes involved a pathway that included an induced Akt activity by increasing phosphorylation of Thr308 and Ser473, a reduced glycogen synthase kinase 3β (GSK‐3β) activity by increasing phosphorylation of Ser9, an induced nuclear translocation of β‐Catenin by decreasing phosphorylation of Ser33/37/Thr41, and an increased TCF‐4 transcriptional activity. Furthermore, antagonism of Reg4‐signaling using Reg4‐specific mAbs (2H6 and 3E5) and Akt inhibitor significantly decreased, whereas agonism using GSK‐3β antagonist (SB216763) significantly increased mitotic index and proliferation of CRC cells. These results identify Reg4 as a key regulator of the CRC cell division and proliferation, hence a potential target of human CRC treatment. © 2013 Wiley Periodicals, Inc.
Fluctuations in cognition and alertness vary independently in dementia with Lewy bodies
Authors: Bliwise Donald L. , Scullin Michael K. , Trotti Lynn Marie
Published: October 2013

Fluctuations in mental status are 1 of the core diagnostic criteria for dementia with Lewy bodies (DLB) and are thought to reflect variability in daytime alertness. Previous attempts to study fluctuations have been limited to caregiver reports, observer rating scales, short segments of electroencephalography, or motor‐dependent, reaction time tests. Concordance among such measures is often poor, and fluctuations remain difficult to quantify. We compared fluctuations in cognition and alertness in patients with DLB (n = 13) and idiopathic Parkinson's disease (PD) (n = 64), a condition associated with deficits in daytime alertness. We systematically and repeatedly collected cognitive and physiologic measures during a 48‐hour inpatient protocol in a sound‐attenuated sleep laboratory in a geriatric hospital. Cognitive fluctuations were analyzed using coefficients of variation (COVs) derived from performance on a bedside examination familiar to clinicians (digit span). Alertness fluctuations were assessed objectively using COVs from the polysomnographically‐based Maintenance of Wakefulness Test. Despite predictably lower mean digit span performances, DLB patients demonstrated significantly greater cognitive fluctuations than PD patients (P < 0.001), even when groups were matched on general cognitive impairment. There were no group differences in alertness fluctuations, although DLB patients were less alert than PD patients not receiving dopaminergics. The prevailing assumption that fluctuations in cognition in DLB are reflected in fluctuations in daytime alertness was not supported by objective, physiological measurements. Fluctuating mental status in DLB patients can be detected with repeated administration of a simple bedside exam that can be adapted to a clinic setting. © 2013 International Parkinson and Movement Disorder Society.
Cure kinetics and thermal stability of multifunctional epoxy/anhydride containing release agent and carbon fiber
Authors: Zhou Zhengwei , Li Aijun , Bai Ruicheng , Sun Jinliang
Published: October 2013

The investigations were carried out into the cure kinetics and thermal stability of multifunctional epoxy/anhydride/imidazole/release agent system (matrix) and carbon fiber reinforced matrix composite. Two experimental techniques were applied: dynamic differential scanning calorimetry (DSC) at different heating rates, and non‐isothermal thermogravimetric analysis (TGA). The results were indicated that the two‐parameter model was found to describe the cure kinetics for the matrix and the composite. The kinetic parameters such as pre‐exponential factor, apparent activation energy, and reaction orders were calculated. And, the carbon fiber had a significant effect on the apparent activation energy and the thermal stability. POLYM. COMPOS., 35:596–601, 2014. © 2013 Society of Plastics Engineers
Calendar time‐specific propensity score analysis for observational data: a case study estimating the effectiveness of inhaled long‐acting beta‐agonist on asthma exacerbations
Authors: Dilokthornsakul Piyemeth , Chaiyakunapruk Nathorn , Schumock Glen T. , Lee Todd A.
Published: October 2013

Purpose

Propensity scores (PS) are frequently used in observational studies. PS are usually estimated over the entire study period without consideration of the effect of changing patterns of the included variables over time. This study sought to compare PS estimated using the entire study period (conventional PS) and PS estimated for specific periods (calendar time‐specific PS (CTS‐PS)), and to determine whether there are differences in estimated treatment effects using these approaches.

Methods

We conducted a claims data analysis. Asthmatic patients who received an asthma controller during 1997–2008 were included. Exposed patients were those who received an inhaled long‐acting beta‐2 agonist. Conventional PS used the entire period to estimate a PS for individuals. CTS‐PS approach divided the study period into 1‐year periods and estimated PS separately for each period. Each individual had two PS. Both PS approaches were used to estimate adjusted hazard ratio (HR) for asthma exacerbations using Cox proportional hazard models.

Results

A total of 288,518 patients with an average age of 11.9 ± 5.8 years were included. The difference between conventional PS and CTS‐PS in each period ranged from −0.213 to 0.098. The adjusted HR of conventional PS‐matched cohort was 1.20 (95%CI: 1.18–1.22), whereas the estimate for the CTS‐PS‐matched cohort was 1.24 (95%CI: 1.23–1.37).

Conclusion

Focusing on a specific year, there was a difference between conventional PS estimated versus CTS‐PS for that year. However, there was minimal effect of CTS‐PS on the observed treatment effects compared with conventional PS approach. Copyright © 2013 John Wiley & Sons, Ltd.
Finding the missing link: Disulfide‐containing proteins via a high‐throughput proteomics approach
Authors: Khairallah Ramzi J. , Sadayappan Sakthivel
Published: October 2013

Top‐down proteomics have recently started to gain attention as a novel method to provide insight into the structure of proteins in their native state, specifically the number and location of disulfide bridges. However, previous techniques still relied on complex and time‐consuming protein purification and reduction reactions to yield useful information. In this issue of Proteomics, Zhao et al. (high‐throughput screening of disulfide‐containing proteins in a complex mixture, Proteomics 2013, 13, 3256–3260) devise a clever and rapid method for high‐throughput determination of disulfides in proteins via reduction by tris(2‐carboxyethyl)phosphine. Their work provides the foundation necessary to undertake more complex experiments in biological samples.
The importance of contextual factors and age in association with anxiety and depression in Black breast cancer patients
Authors: Sheppard Vanessa B. , Harper Felicity W. K. , Davis Kimberly , Hirpa Fikru , Makambi Kepher
Published: October 2013

Objectives

Limited research exists on correlates of psychosocial distress in Black breast cancer patients. The goals of the study were to describe the prevalence of distress (anxiety and depression) in Black women with breast cancer and to examine the influence of demographic, clinical, contextual (e.g., self‐efficacy, medical mistrust), and process of care factors (e.g., patient satisfaction) on women's level of anxiety and depression.

Methods

Eighty‐two Black women diagnosed with invasive non‐metastatic breast cancer were interviewed by phone. Collected data included demographic, clinical, contextual, and process of care factors. Bivariate correlations were used to examine relationships between those variables. Multiple linear regressions were used to examine predictors of anxiety and depression.

Results

About one‐third of the women (32%) met cut‐off thresholds for distress. Medical mistrust and positive attitude had significant influences on anxiety levels, whereas age and positive attitude were determinants of levels of depression. Participants with higher medical mistrust reported more anxiety (r = .379; p < .001) and depression (r = .337; p = .002), whereas women with higher self‐efficacy reported less anxiety (r = −.401; p < .001) and depression (r = −.427; p < .001). Age was inversely related to both anxiety and depression (r = −.224; r = −.296, respectively; p < .05).

Conclusions

Findings support national recommendations for routine distress screening in the delivery of cancer care particularly in younger Black patients. Interventions targeted to boost self‐efficacy or reduce medical mistrust through enhanced patient–provider interactions may decrease psychological distress. Psychosocial needs of younger patients warrant particular attention. Copyright © 2013 John Wiley & Sons, Ltd.
An In Vitro and Molecular Informatics Study to Evaluate the Antioxidative and β‐hydroxy‐β‐methylglutaryl‐CoA Reductase Inhibitory Property of Ficus virens Ait
Authors: Iqbal Danish , Khan M. Salman , Khan Mohd. S. , Ahmad Saheem , Srivastava Ashwini K.
Published: October 2013

The present study is initially intended to evaluate antioxidant and β‐hydroxy‐β‐methylglutaryl‐CoA reductase (HMGR) inhibitory property of Ficus virens Ait., first by in vitro analyses followed by a corroboratory molecular informatics study. Our results show that of all the sequentially extracted fraction of F. virens bark and leaves extract, F. virens bark methanol extract exhibits strong radical scavenging, antioxidant and oxidative DNA damage protective activity, which is well correlated with its total phenolic content. In addition, F. virens bark methanol extract, which is non‐cytotoxic, significantly and non‐covalently inhibit the HMGR activity (IC50 = 3.45 ± 0.45 µg/ml) in comparison with other extracts. The mechanistic aspect of this inhibition activity is authenticated by molecular docking study of bioactive compounds as revealed from gas chromatography–mass spectrometry data, with HMGR. The analysis for the first time indicates that quinic acid (ΔG: −8.11 kcal/mol) and paravastatin (ΔG: −8.22 kcal/mol) exhibit almost same binding energy, while other compounds also showed good binding energy, suggesting that quinic acid alone or in combination with other major bioactive compound is probably responsible for HMGR inhibitory property of the extract and plausibly can be used in in vivo system for the management, prevention, and alleviation of hypercholesterolemia as well as hypercholesterolemia‐induced oxidative stress. Copyright © 2013 John Wiley & Sons, Ltd.
Vascular tissue engineering: from in vitro to in situ
Authors: Li Song , Sengupta Debanti , Chien Shu
Published: October 2013

Blood vessels transport blood to deliver oxygen and nutrients. Vascular diseases such as atherosclerosis may result in obstruction of blood vessels and tissue ischemia. These conditions require blood vessel replacement to restore blood flow at the macrocirculatory level, and angiogenesis is critical for tissue regeneration and remodeling at the microcirculatory level. Vascular tissue engineering has focused on addressing these two major challenges. We provide a systematic review on various approaches for vascular graft tissue engineering. To create blood vessel substitutes, bioengineers and clinicians have explored technologies in cell engineering, materials science, stem cell biology, and medicine. The scaffolds for vascular grafts can be made from native matrix, synthetic polymers, or other biological materials. Besides endothelial cells, smooth muscle cells, and fibroblasts, expandable cells types such as adult stem cells, pluripotent stem cells, and reprogrammed cells have also been used for vascular tissue engineering. Cell‐seeded functional tissue‐engineered vascular grafts can be constructed in bioreactors in vitro. Alternatively, an autologous vascular graft can be generated in vivo by harvesting the capsule layer formed around a rod implanted in soft tissues. To overcome the scalability issue and make the grafts available off‐the‐shelf, nonthrombogenic vascular grafts have been engineered that rely on the host cells to regenerate blood vessels in situ. The rapid progress in the field of vascular tissue engineering has led to exciting preclinical and clinical trials. The advancement of micro‐/nanotechnology and stem cell engineering, together with in‐depth understanding of vascular regeneration mechanisms, will enable the development of new strategies for innovative therapies. WIREs Syst Biol Med 2014, 6:61–76. doi: 10.1002/wsbm.1246

This article is categorized under:

Developmental Biology > Stem Cell Biology and Regeneration

Translational, Genomic, and Systems Medicine > Therapeutic Methods

Translational, Genomic, and Systems Medicine > Translational Medicine
A library for polymorphic dynamic typing
Authors: SWIERSTRA WOUTER , VAN NOORT THOMAS
Published: October 2013

This paper presents a library for programming with polymorphic dynamic types in the dependently typed programming language Agda. The resulting library allows dynamically typed values with a polymorphic type to be instantiated to a less general (possibly monomorphic) type without compromising type soundness.
Trade, environment and market access: policy reforms in a small open economy
Authors: Kawahara Shinya
Published: October 2013

This paper investigates how market access and welfare are affected by piecemeal reforms of tariffs and pollution taxes in a small open economy. By constructing a general equilibrium model of international trade, which is extended to allow production-generated pollution, we characterize conditions under which a tariff reform and a pollution tax reform increase the value of the small country's imports. It is shown that uniform proportional cuts in tariffs that increase welfare do not necessarily improve market access, and the Ju–Krishna rule of tariff reforms that improves market access does not necessarily increase welfare. A reduction in all pollution distortions proportional to their degree of distortion can be shown to improve both welfare and market access.
Nutritional quality of food items on fast-food ‘kids’ menus’: comparisons across countries and companies
Authors: Hobin Erin , White Christine , Li Ye , Chiu Maria , O'Brien Mary Fodor , Hammond David
Published: October 2013

Objective

To compare energy (calories), total and saturated fats, and Na levels for ‘kids’ menu’ food items offered by four leading multinational fast-food chains across five countries.

Design

A content analysis was used to create a profile of the nutritional content of food items on kids’ menus available for lunch and dinner in four leading fast-food chains in Australia, Canada, New Zealand, the UK and the USA.

Setting

Food items from kids’ menus were included from four fast-food companies: Burger King, Kentucky Fried Chicken (KFC), McDonald's and Subway. These fast-food chains were selected because they are among the top ten largest multinational fast-food chains for sales in 2010, operate in high-income English-speaking countries, and have a specific section of their restaurant menus labelled ‘kids’ menus’.

Results

The results by country indicate that kids’ menu foods contain less energy (fewer calories) in restaurants in the USA and lower Na in restaurants in the UK. The results across companies suggest that kids’ menu foods offered at Subway restaurants are lower in total fat than food items offered at Burger King and KFC, and food items offered at KFC are lower in saturated fat than items offered at Burger King.

Conclusions

Although the reasons for the variation in the nutritional quality of foods on kids’ menus are not clear, it is likely that fast-food companies could substantially improve the nutritional quality of their kids’ menu food products, translating to large gains for population health.
Comparative tolerances of two Cucumis species to salinity, Rhizoctonia solani and Meloidogyne incognita
Authors: Abu Irmaileh Barakat E. , Mansour Akel N. , Al Banna Luma S. , Badwan Huda O.
Published: October 2013

The search for disease resistance in wild types is continuing, in order to introduce resistant genes from wild relatives. In this study, we found that the wild melon Cucumis prophetarum was comparably more tolerant to salinity, the damping-off disease caused by the fungus Rhizoctonia solani and the root-knot nematode Meloidogyne incognita. The percentage of wild melon survival was 60% compared to that of the cultivated cucumber Cucumis sativus, which was 15%, when irrigated with NaCl at a concentration of 2500 ppm; and 96% for the wild melon compared with 44% for the cultivated cucumber when irrigated with CaSO4.2H2O at a concentration of 1000 ppm. Wild melon plants were more tolerant to R. solani attack, as only 20% of the plants were infested compared with 100% of infestation observed for the cultivated cucumber. The average number of nematode galls was 250 per plant on the cultivated cucumber when compared with 6.3 per plant on the wild species. Wild melon could be a potential source of resistant or tolerant genes that can be transferable to cultivated cucumbers.
Pointing Forward: Typing for Academic Access
Authors: Ashby Christine , Kasa Christi
Published: October 2013

For students who do not demonstrate reliable verbal speech, utilization of augmentative and alternative communication, both low-tech and high-tech, can be an effective way of engaging meaningfully in the academic and social opportunities of the classroom. This article discusses the benefits of drawing on a variety of communication supports, including typing to communicate, and outlines key principles and practices for the successful inclusion of students who type in academic classes. Key principles include universal design, presuming competence, writing effective IEP goals, and successful classroom strategies.
Theoretical physics made easy
Authors: Forinash Kyle , Irick Jeff
Published: October 2013

Advanced undergraduate physics students may benefit from theoretical computational tasks that involve relatively low study time. An example from nuclear physics is given in which packaged subroutines allow efficient computation of a nucleon interaction potential.
Computational method for intrinsic optical bistability: Steady-state solutions and their stability
Authors: Haus Joseph W. , Tran Tuyen K.
Published: October 2013

An efficient numerical algorithm is described for solving problems with coupled nonlinear differential equations with boundary conditions applied at opposite ends of the medium. It is applied to a problem of optical bistability with coupled Maxwell equations and heat-flow equations, and associated boundary conditions. It is shown that the numerical procedure is well suited to perform a stability analysis of the solution.
A note on rendering chaotic ‘‘repeller distance towers’’
Authors: Pickover Clifford A.
Published: October 2013

A simple technique is described for demonstrating graphically interesting behavior in chaotic systems defined by complex dynamics.
On the numerical solution of the Hill–Wheeler equation
Authors: Wampler K. Dean , Wilets Lawrence
Published: October 2013

A particular numerical method is discussed for solving the Hill–Wheeler equation, which is an integral equation that arises in the generator coordinate method analysis of problems in nuclear physics. The method is applicable to scattering problems with finite range potentials and exploits prior knowledge of the asymptotic form of the solution to convert the Hill–Wheeler equation into a Fredholm integral equation of the first kind. The resulting Fredholm equation is ill-posed, which often results in numerically unstable solutions. The method of regularization is used to produce numerically stable, approximate solutions. Optimizing the choice of regularization parameter is discussed and calculations are presented for an example problem.
Predicting multiprocessing efficiency on the Cray multiprocessors in a (CTSS) time-sharing environment/application to a 3-D magnetohydrodynamics code
Authors: Mirin A. A.
Published: October 2013

A formula is derived for predicting multiprocessing efficiency on Cray supercomputers equipped with the Cray Time-Sharing System (CTSS). The model is applicable to an intensive time-sharing environment. The actual efficiency estimate depends on three factors: the code size, task length, and job mix. The implementation of multitasking in a three-dimensional plasma magnetohydrodynamics (MHD) code, TEMCO, is discussed. TEMCO solves the primitive one-fluid compressible MHD equations and includes resistive and Hall effects in Ohm’s law. Virtually all segments of the main time-integration loop are multitasked. The multiprocessing efficiency model is applied to TEMCO. Excellent agreement is obtained between the actual multiprocessing efficiency and the theoretical prediction.
The fractal dimension of cerebral surfaces using magnetic resonance images
Authors: Majumdar Sharmila , Prasad Rahul R.
Published: October 2013

The calculation of the fractal dimension of the surface bounded by the grey matter in the normal human brain using axial, sagittal, and coronal cross-sectional magnetic resonance (MR) images is presented. The fractal dimension in this case is a measure of the convolutedness of this cerebral surface. It is proposed that the fractal dimension, a feature that may be extracted from MR images, may potentially be used for image analysis, quantitative tissue characterization, and as a feature to monitor and identify cerebral abnormalities and developmental changes.
Digital waveform sampling rate converter
Authors: Feibig Peg L. , Brown Leslie I. , Etter Delores M.
Published: October 2013

The digital waveform sampling rate converter is an efficient, easy-to-use software system that allows a user to perform the conversion between sampling rates efficiently and accurately. The user does not need to be concerned with the technical details of the package. The user simply needs to answer the questions presented by the package, specifying certain input and output files. The software takes care of the conversion. The user can easily verify that a desired file has been selected by choosing the option to plot the signal. This package succeeds in making the mathematical process for sampling rate changes efficient and effortless. UFRULE1
Constructive interaction between computer science and physics programs
Authors: Forinash Kyle , Wisman Ray
Published: October 2013

This paper reports on the culmination of a year-long collaborative effort between physics and computer science programs at a small branch campus. The project involved students in a computer science course who wrote generalized software capable of timing and voltage measurements in interfaced physics experiments. The software and experiments were used the following semester in a junior level physics laboratory course.
Spline algorithms for continuum functions
Authors: Froese Fischer Charlotte , Idrees Muhammad
Published: October 2013

Spline algorithms are described for solving the radial equation for continuum states. The Galerkin method leads to a generalized eigenvalue problem for which the eigenvalue is known so that inverse iteration can be used to determine the eigenvector. Three cases are considered: the equation whose solution is sin κr, the Coulomb problem, and the hydrogen scattering problem. Plots are presented for the first two cases that show the dependence of the error in the phase shift on spline parameters and execution time. The results for the scattering problem are compared with earlier values.
On the application of parallel processing to the computation of dose arising from the internal deposition of radionuclides
Authors: Johnson T. K. , Vessella R. L.
Published: October 2013

The advent of monoclonal antibodies has given rise to the possibility of their use as carriers of tumorcidal levels of radiation. The target site—cancerous tissue—is of arbitrary size and location. A tool used for dosimetry must be able to account for the a posteriori definition of these tumor sites. The MABDOS software accomplishes this by performing a simulation of radioactive decay in each of the source organs defined in the standard man model. This solution partitions itself into a number of parallel structures amenable to computation in a true parallel-processing environment. Implementation of these structures on a multiprocessor platform known as ‘‘the simulation machine’’ is described.
Algorithms for molecular dynamics simulations of keV particle bombardment
Authors: Smith R. , Harrison D. E.
Published: October 2013

A variable time step integration algorithm for carrying out molecular dynamics simulations of atomic collision cascades is proposed which evaluates the interaction forces only once per time step. The algorithm is tested on some model problems which have exact solutions and is compared against other common methods. These comparisons show that the method has good stability and accuracy. Applications to Ar+ bombardment of Cu and Si show good accuracy and improved speed to the original method [D. E. Harrison, W. L. Gay, and H. M. Effron, J. Math. Phys. 10, 1179 (1969)].
Use of Monte Carlo techniques to derive yields for n+12C multibody breakup reactions: Programming the computer to simulate collisions by fast neutrons
Authors: Dickens J. K.
Published: October 2013

A computer ‘‘experiment’’ using Monte Carlo sampling methods has been designed to simulate the breaking up of 12C by medium-energy neutrons into final reaction channels having 2, 3, or 4 outgoing charged particles. The calculational nuclear physics concept used in the ‘‘experiment’’ is one of a sequentially decaying, highly excited compound nucleus. Two methods of Monte Carlo sampling, the rejection method and the cumulative-distribution method, are discussed as applied to probability functions developed in the program.
Numerical solution to the Schrödinger equation by constrained optimization
Authors: Garner J.
Published: October 2013

The nonlinear optimization techniques of dynamic simulated annealing and steepest descents make it feasible to solve numerically the Schrödinger equation for systems that have many degrees of freedom. These methods involve finding the solution to a set of quasi-Newtonian equations of motion derived from a fictitious, time-dependent Schrödinger equation. The formalism is reviewed and the methods are illustrated by solving the Schrödinger equation for three simple models: a two-state system, an infinite square well, and the Mathieu equation.
Modeling superconducting networks containing Josephson junctions by means of PC-based circuit simulation software
Authors: Blackburn James A. , Smith H. J. T.
Published: October 2013

Software packages are now available with which complex analog electronic circuits can be simulated on desktop computers. Using Micro Cap III it is demonstrated that the modeling capabilities of such software can be extended to include superconducting networks by means of an appropriate equivalent circuit for a Josephson junction.
Optimization of the controlled separation of biologically active diagnostic magnetic probes
Authors: Sachar Kenneth S. , Goldstein Barry
Published: October 2013

A realistic model is presented that allows rapid calculation and display of both exact, three-dimensional, magnetic flux density lines and the associated trajectories of spherical and ellipsoidal magnetic particles suspended within a viscous liquid. The particles may be saturable and subject to the spatially nonuniform, magnetic flux densities produced by an array of arbitrarily positioned, rectangular, rare-earth, permanent magnets. An iterative technique based on the model is applied to the design of a miniature magnetic separator used in a commercial diagnostic blood assay for HIV (AIDS) infection.
Animating the physics lecture with Amiga BASIC
Authors: Smith Frank A.
Published: October 2013

The use of a Commodore Amiga personal computer in physics lectures to provide full-color simulations of motion is described. The animation capability of Amiga BASIC that allows simulations of motion to be easily programmed is discussed and examples of the program statements are given. Examples using simulations of motion to provide classroom demonstrations, to animate homework problems, and to remedy common misconceptions of motion are presented. The pedagogical benefits of extending the student’s experiences of motion by means of computer simulation are also discussed.
Neuronal activity regulates astrocytic Nrf2 signaling
Authors: Habas Agata , Hahn Junghyun , Wang Xianhong , Margeta Marta
Published: October 2013

Significance

Tripartite synapse, which consists of presynaptic neuron, postsynaptic neuron, and perisynaptic astrocyte, is the central site of intercellular communication in the brain. Here, we show that neuron–astrocyte signaling at the tripartite synapse also regulates activity of nuclear factor erythroid 2-related factor 2 (Nrf2), the transcriptional master regulator of the stress-induced cytoprotective response: through secretion of neurotransmitter glutamate and other soluble messengers, elevated neuronal activity leads to increased expression of Nrf2-regulated genes in neighboring astrocytes. By optimizing astrocyte neuroprotective capacity to the level of adjacent synaptic activity, this regulatory mechanism may contribute to the maintenance of brain health under physiological stress.
Cyclic 100-ka (glacial-interglacial) migration of subseafloor redox zonation on the Peruvian shelf
Authors: Contreras Sergio , Meister Patrick , Liu Bo , Prieto-Mollar Xavier , Hinrichs Kai-Uwe , Khalili Arzhang , Ferdelman Timothy G. , Kuypers Marcel M. M. , Jørgensen Bo Barker
Published: October 2013

Significance

Microbial life beneath the seafloor affects global-scale biogeochemical processes in the ocean, including the carbon and nutrient cycles. Although considered a stable ecosystem, dynamic interaction of this deep biosphere with climate and ocean chemistry remains poorly understood. We used high-resolution geochemical tools to study the sediment archive of the Peru continental shelf and discovered signatures of past changes in subseafloor microbial oxidation of methane. A transient reaction-transport model was used to reconstruct upward and downward migrations of the methane oxidation front according to 100-ka cyclic variations in sediment deposition. The results show for the first time how microbial life beneath the seafloor interacts with changing climate and oceanographic conditions on a glacial-interglacial time scale.
Plus-end tracking proteins, CLASPs, and a viral Akt mimic regulate herpesvirus-induced stable microtubule formation and virus spread
Authors: Naghavi Mojgan H. , Gundersen Gregg G. , Walsh Derek
Published: October 2013

Significance

Viruses exploit their host’s microtubule (MT) transport system to move within infected cells at various stages of their life cycle. The formation and stability of MT networks is controlled by specialized host proteins, which track MT ends. These proteins, called “+TIPs” (plus-end tracking proteins), stabilize subsets of MTs in response to various environmental signals. How viruses influence the organization of these critical intracellular transport networks to facilitate infection remains poorly understood. In this study, we demonstrate that herpes simplex virus type 1 (HSV-1), which infects an estimated 60–90% of the world’s population, encodes a kinase that targets specific +TIPs to stabilize MTs formed at the trans-Golgi network, an alternate MT organizing center and organelle central to viral envelopment, to facilitate HSV-1 spread.
Plasmodium falciparum
phosphoethanolamine methyltransferase is essential for malaria transmission
Authors: Bobenchik April M. , Witola William H. , Augagneur Yoann , Nic Lochlainn Laura , Garg Aprajita , Pachikara Niseema , Choi Jae-Yeon , Zhao Yang O. , Usmani-Brown Sahar , Lee Albert , Adjalley Sophie H. , Samanta Swapna , Fidock David A. , Voelker Dennis R. , Fikrig Erol , Ben Mamoun Choukri
Published: October 2013

Significance

Malaria, caused by intraerythrocytic protozoan parasites of the genus
Plasmodium
, is by far the deadliest and most prevalent parasitic disease. Most fatalities are attributable to infection by
Plasmodium falciparum
. The transmission of
P. falciparum
into
Anopheles
mosquitoes is absolutely dependent on the ability of the parasite to differentiate into mature gametocytes. Here we show that
P. falciparum
requires the plant-like phosphatidylcholine synthesis machinery, which is fueled by host serine, and its key enzyme, phosphoethanolamine
N
-methyltransferase (PfPMT), for gametocyte development, maturation, and transmission. We identified several compounds that inhibit PfPMT activity and gametocyte development. These compounds also inhibited parasite asexual replication. These new chemical entities provide scaffolds for future development of dual-function antimalarials that can block both infection and transmission.
Neonicotinoid clothianidin adversely affects insect immunity and promotes replication of a viral pathogen in honey bees
Authors: Di Prisco Gennaro , Cavaliere Valeria , Annoscia Desiderato , Varricchio Paola , Caprio Emilio , Nazzi Francesco , Gargiulo Giuseppe , Pennacchio Francesco
Published: October 2013

Significance

Honey bees are exposed to a wealth of synergistically interacting stress factors, which may induce colony losses often associated with high infection levels of pathogens. Neonicotinoid insecticides have been reported to enhance the impact of pathogens, but the underlying immune alteration is still obscure. In this study we describe the molecular mechanism through which clothianidin adversely affects the insect immune response and promotes replication of a viral pathogen in honey bees bearing covert infections. Our results shed light on a further level of regulation of the immune response in insects and have implications for bee conservation.
Nitrite produced byMycobacterium tuberculosisin human macrophages in physiologic oxygen impacts bacterial ATP consumption and gene expression
Authors: Cunningham-Bussel Amy , Zhang Tuo , Nathan Carl F.
Published: October 2013

Significance

Most people infected withMycobacterium tuberculosis(Mtb) suppress the pathogen’s replication without eradicating it. It is unknown how Mtb survives for decades in a hostile host environment. Respiration of nitrate to nitrite could help Mtb survive in hypoxic tissues but was not thought to be significant at physiologic oxygen tensions, nor was the resultant nitrite considered consequential to Mtb’s physiology. We found that Mtb infecting human macrophages in vitro produces copious nitrite at physiologic oxygen tensions. This slows Mtb’s growth and consumption of ATP and remodels its transcriptome differently than nitric oxide. Thus, respiration of nitrate and adaptation to nitrite are likely to play a prominent role in Mtb’s pathophysiology, whether or not the Mtb resides in hypoxic sites.
Regulation of onset of female mating and sex pheromone production by juvenile hormone in
Drosophila melanogaster
Authors: Bilen Julide , Atallah Jade , Azanchi Reza , Levine Joel D. , Riddiford Lynn M.
Published: October 2013

Significance

Juvenile hormone (JH) regulates reproductive maturation in insects. In
Drosophila melanogaster
, JH is necessary for egg maturation. We show that the removal of JH delays both mating and the onset of the production of the major female sex pheromones in
D. melanogaster
. Importantly, this action of JH was via the Methoprene-tolerant (Met) JH receptor, rather than its paralog Germ-cell expressed, similar to its action in egg maturation. Thus, JH acting via Met coordinates pheromone production and mating with egg maturation. These studies provide insights into the molecular basis of the hormonal regulation of reproductive behavior in insects that may also be applicable to the coordination of the complex behaviors essential for animal reproduction and thus survival.
Microtubules that form the stationary lattice of muscle fibers are dynamic and nucleated at Golgi elements
Authors: Oddoux Sarah , Zaal Kristien J. , Tate Victoria , Kenea Aster , Nandkeolyar Shuktika A. , Reid Ericka , Liu Wenhua , Ralston Evelyn
Published: October 2013

Skeletal muscle microtubules (MTs) form a nonclassic grid-like network, which has so far been documented in static images only. We have now observed and analyzed dynamics of GFP constructs of MT and Golgi markers in single live fibers and in the whole mouse muscle in vivo. Using confocal, intravital, and superresolution microscopy, we find that muscle MTs are dynamic, growing at the typical speed of ∼9 µm/min, and forming small bundles that build a durable network. We also show that static Golgi elements, associated with the MT-organizing center proteins γ-tubulin and pericentrin, are major sites of muscle MT nucleation, in addition to the previously identified sites (i.e., nuclear membranes). These data give us a framework for understanding how muscle MTs organize and how they contribute to the pathology of muscle diseases such as Duchenne muscular dystrophy.
CD36-specific antibodies block release of HIV-1 from infected primary macrophages and its transmission to T cells
Authors: Berre Stefano , Gaudin Raphaël , Cunha de Alencar Bruna , Desdouits Marion , Chabaud Mélanie , Naffakh Nadia , Rabaza-Gairi Marc , Gobert François-Xavier , Jouve Mabel , Benaroch Philippe
Published: October 2013

HIV-1–infected macrophages likely represent viral reservoirs, as they accumulate newly formed virions in internal virus-containing compartments (VCCs). However, the nature and biogenesis of VCCs remain poorly defined. We show that upon HIV-1 infection of primary human macrophages, Gag is recruited to preexisting compartments containing the scavenger receptor CD36, which then become VCCs. Silencing of CD36 in HIV-1–infected macrophages decreases the amount of virions released. Strikingly, soluble anti-CD36 antibodies, but not the natural ligands of CD36, inhibit release of virions from HIV-1–infected macrophages and the transmission of virus to CD4+ T cells. The effect of the antibodies is potent, rapid, and induces the retention of virions within VCCs. Ectopic expression of CD36 in HeLa cells renders them susceptible to the inhibitory effect of the anti-CD36 mAb upon HIV-1 infection. We show that the anti-CD36 mAb inhibits HIV-1 release by clustering newly formed virions at their site of budding, and that signaling via CD36 is not required. Thus, HIV-1 reservoirs in macrophages may be tackled therapeutically using anti-CD36 antibodies to prevent viral dissemination.
(6-Methoxy-2-oxo-2H-chromen-4-yl)methyl piperidine-1-carbodithioate
Authors: Kumar K. Mahesh , Vinduvahini M. , Mahabhaleshwaraiah N. M. , Kotresh O. , Devarajegowda H. C.
Published: October 2013

In the title compound, C17H19NO3S2, the maximum deviation of atoms in the 2H-chromene ring system is 0.0097 (14) Å and the piperidine ring adopts a chair conformation. The dihedral angle between the 2H-chromene ring and the piperidine ring (all atoms) is 87.59 (8)°. In the crystal, inversion dimers linked by pairs of C—H...O interactions generateR22(22) loops. Further C—H...O hydrogen bonds link the dimers into [110] chains and weak aromatic π–π stacking [shortest centroid–centroid distance = 3.824 (8) Å] is also observed.
N-[(1,3-Benzodioxol-5-yl)methyl]benzenesulfonamide: an analogue of capsaicin
Authors: Maganhi Stella H. , Tavares Maurício T. , Damião Mariana C. F. C. B. , Parise Filho Roberto
Published: October 2013

The title compound, C14H13NO4S, an analogue of capsaicin, differs from the latter by having a 1,3-benzodioxole ring rather than a 2-methoxyphenol moiety, and having a benzenesulfonamide group instead of an aliphatic amide chain. The five-membered ring is in an envelope conformation with the methylene C atom lying 0.221 (6) Å out of the plane formed by the other four atoms. The dihedral angle between the phenyl ring and the mean plane of the 1,3-benzodioxole fused-ring system is 84.65 (4)°. In the crystal, molecules aggregate into supramolecular layers in theacplane through C—H...O, N—H...O and C—H...π interactions.