bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinicopathologic features and pathogenesis of melanocytic colonization in atypical meningioma
Authors: Dehghan Harati Mitra , Yu Andrew , Magaki Shino D. , Perez‐Rosendahl Mari , Im Kyuseok , Park Young K. , Bergsneider Marvin , Yong William H.
Published: August 2017

Only two prior cases of benign dendritic melanocytes colonizing a meningioma have been reported. We add a third case, describe clinicopathologic features shared by the three, and elucidate the risk factors for this very rare phenomenon. A 29 year‐old Hispanic woman presented with headache and hydrocephalus. MRI showed a lobulated enhancing pineal region mass measuring 41 mm in greatest dimension. Subtotal resection of the mass demonstrated an atypical meningioma, WHO grade II, and the patient subsequently underwent radiotherapy. She presented 4 years later with diplopia, and MRI showed an enhancing extra‐axial mass measuring 47 mm in greatest dimension and centered on the tentorial incisura. Subtotal resection showed a brain‐invasive atypical meningioma with melanocytic colonization. The previous two cases in the literature were atypical meningiomas, one of which was also brain invasive. Atypical meningiomas may be at particular risk for melanocytic colonization as they upregulate molecules known to be chemoattractants for melanocytes. We detected c‐Kit expression in a minority of the melanocytes as well as stem cell factor and basic fibroblast growth factor in the meningioma cells, suggesting that mechanisms implicated in normal melanocyte migration may be involved. In some cases, brain invasion with disruption of the leptomeningeal barrier may also facilitate migration from the subarachnoid space into the tumor. Whether there is low‐level proliferation of the dendritic melanocytes is unclear. Given that all three patients were non‐Caucasian, meningiomas in persons and/or brain regions with increased dendritic melanocytes may predispose to colonization. The age range spanned from 6 years old to 70 years old. All three patients were female. The role of gender and estrogen in the pathogenesis of this entity remains to be clarified. Whether melanocytic colonization may also occur in the more common Grade I meningiomas awaits identification of additional cases.
A critical review of knowledge on nurses with problematic substance use: The need to move from individual blame to awareness of structural factors
Authors: Ross Charlotte A. , Berry Nicole S. , Smye Victoria , Goldner Elliot M.
Published: August 2017

Problematic substance use (PSU) among nurses has wide‐ranging adverse implications. A critical integrative literature review was conducted with an emphasis on building knowledge regarding the influence of structural factors within nurses' professional environments on nurses with PSU. Five thematic categories emerged: (i) access, (ii) stress, and (iii) attitudes as contributory factors, (iv) treatment policies for nurses with PSU, and (v) the culture of the nursing profession. Conclusions were that an overemphasis on individual culpability and failing predominates in the literature and that crucial knowledge gaps exist regarding the influence of structural factors on driving and shaping nurses' substance use.
Effects of remifentanil on esophageal and esophagogastric junction (EGJ) bolus transit in healthy volunteers using novel pressure‐flow analysis
Authors: Cock C. , Doeltgen S. H. , Omari T. , Savilampi J.
Published: August 2017

Background

Remifentanil is associated with subjective dysphagia and an objective increase in aspiration risk. Studies of opioid effects have shown decreased lower esophageal sphincter relaxation. We assessed bolus transit through the esophagus and esophagogastric junction (EGJ) during remifentanil administration using objective pressure‐flow analysis.

Methods

Data from 11 healthy young participants (23±3 years, 7 M) were assessed for bolus flow through the esophagus and EGJ using high‐resolution impedance manometry (Manoscan™, Sierra Scientific Instruments, Inc., LES Angeles, CA, USA) with 36 pressure and 18 impedance segments. Data were analyzed for esophageal pressure topography and pressure‐flow analysis using custom Matlab analyses (Mathworks, Natick, USA). Paired t tests were performed with a P‐value of < .05 regarded as significant.

Key Results

Duration of bolus flow through (remifentanil/R 3.0±0.3 vs baseline/B 5.0 ± 0.4 seconds; P < .001) and presence at the EGJ (R 5.1 ± 0.5 vs B 7.1 ± 0.5 seconds; P = .001) both decreased during remifentanil administration. Distal latency (R 5.2 ± 0.4 vs B 7.5 ± 0.2 seconds; P < .001) and distal esophageal distension‐contraction latency (R 3.5 ± 0.1 vs B 4.7 ± 0.2 seconds; P < .001) were both reduced. Intrabolus pressures were increased in both the proximal (R 5.3 ± 0.9 vs B 2.6 ± 1.3 mm Hg; P = .01) and distal esophagus (R 8.6 ± 1.7 vs B 3.1 ± 0.8 mm Hg; P = .001). There was no evidence of increased esophageal bolus residue.

Conclusions and Inferences

Remifentanil‐induced effects were different for proximal and distal esophagus, with a reduced time for trans‐sphincteric bolus flow at the EGJ, suggestive of central and peripheral μ‐opioid agonism. There were no functional consequences in healthy subjects.
Interactions retain the co‐phylogenetic matching that communities lost
Authors: Poisot Timothée , Stouffer Daniel B.
Published: August 2017

Both species and their interactions are affected by changes that occur at evolutionary time‐scales, and these changes shape both ecological communities and their phylogenetic structure. That said, extant ecological community structure is contingent upon random chance, environmental filters and local effects. It is therefore unclear how much ecological signal local communities should retain. Here we show that, in a host–parasite system where species interactions vary substantially over a continental gradient, the ecological significance of individual interactions is maintained across different scales. Notably, this occurs despite the fact that observed community variation at the local scale frequently tends to weaken or remove community‐wide phylogenetic signal. When considered in terms of the interplay between community ecology and coevolutionary theory, our results demonstrate that individual interactions are capable and indeed likely to show a consistent signature of past evolutionary history even when woven into communities that do not.
A framework for understanding human‐driven vegetation change
Authors: Inderjit  , Catford Jane A. , Kalisz Susan , Simberloff Daniel , Wardle David A.
Published: August 2017

Despite a major research focus on human‐mediated reshuffling of plant communities, no coherent framework unites the numerous types of changes in abundances and distributions of native and non‐native species that are driven by human activities. Human driven vegetation change can occur through: non‐native species introductions; population outbreaks or collapses; range expansions or contractions; and range shifts of both native and non‐native species. Boundaries among these different types of floristic changes are not always distinct because of an overlap in the ecological, climatic, and anthropogenic processes that underpin them. We propose a new framework that connects various human‐mediated causes of vegetation change, highlights the spatial scales at which drivers act and the temporal scale at which plant assemblages respond, and provides critical insights for identifying and appropriately managing these changes.
Cares, Identification, and Agency Reductionism
Authors: Franklin Christopher Evan
Published: August 2017

Reductionists about agency maintain that an agent's causing something is reducible to states and events involving the agent causing something. Some worry that reductionism cannot accommodate robust forms of agency, such as self‐determination. One reductionist answer to this worry, which I call ‘identification reductionism,’ contends that self‐governing agents are identified with certain attitudes, and so these attitudes causing a decision count as the agent'sself‐determining the decision. I argue that a prominent species of identification reductionism developed by Harry Frankfurt, Agnieszka Jaworska, Jeffrey Seidman, and David Shoemaker – according to which an agent is identified with his (deepest) cares – is inadequate.
Transcriptomic profile reveals molecular events associated to focal adhesion and invasion in canine mammary gland tumour cell lines
Authors: Cordeiro Y. G. , Xavier P. L. P. , Rochetti A. L. , Alexandre P. A. , Mori C. M. C. , Strefezzi R. F. , Fukumasu H.
Published: August 2017

The prevalence of cancer in animals has increased significantly over the years. Mammary tumours are the most common neoplasia in dogs, in which around 50% are presented in the malignant form. Hence, the development and characterization of in vitro models for the study of canine tumours are important for the improvement of cancer diagnosis and treatment. Thus, the aim of this study was to characterize cell lines derived from canine mammary gland neoplasias which could be further used for basic and applied oncology research. Samples of canine mammary carcinomas were taken for cell culture and 2 cell lines were established and characterized in terms of cell morphology, tumourigenicity and global gene expression. Both cell lines presented spindle‐shape morphology and shown common malignant features as in vitro invasion potential and expression of epithelial and mesenchymal proteins. Also, we found gene expression patterns between the 2 cell cultures in comparison to the normal mammary gland tissue. Cells from M25 culture showed a higher invasion and in vivo tumourigenic potential, associated to the overexpression of genes involved in focal adhesion and extracellular matrix communication, such as FN1, ITGA8 and THBS2. The phenotypic characterization of these cells along with their global gene expression profile potentially determine new therapeutic targets for mammary tumours.
Use of a commercial qPCR assay in 52 high risk shelter cats for disease identification of dermatophytosis and mycological cure
Authors: Moriello Karen A. , Leutenegger Christian M.
Published: August 2017

Background

qPCR is used to test for dermatophytosis.

Objectives

To determine the clinical usefulness of a commercial qPCR for confirming dermatophytosis in lesional cats, and the clinical usefulness of the qPCR Microsporum spp. and/or M. canis assay for confirming mycological cure.

Animals

Fifty two shelter cats with skin lesions.

Methods

qPCR testing of toothbrush fungal culture samples of lesions.

Results

qPCR and fungal culture (FC) matched in 49 of 52 cats. The qPCR correctly identified 45 of 46 and two of four cats with M. canis and Trichophyton spp. infections, respectively. qPCR correctly identified two cats as not infected. No evidence of cross reactivity was noted. The Microsporum spp. qPCR assay was positive in 45 of 46 (97.8%) of infected cats. Results were positive on both Microsporum spp. and M. canis assays in 29 of 45 cats. No cat had a positive qPCR result for M. canis alone. Mycological cure was defined as two negative fungal cultures. There were 92 negative FC from the 46 treated cats and qPCR assay for Microsporum spp. and M. canis was negative in 68 of 92 (73.1%) and 79 of 92 (85.9%) samples, respectively. The number of cats correctly identified with mycological cure via qPCR was 30 of 46 (65.2%) and 39 of 46 (84.8%) cats for the Microsporum spp. and M. canis assays, respectively.

Conclusions and clinical importance

The commercial qPCR assay was a reliable test for confirming disease. The qPCR Microsporum spp. assay was more useful for initial disease confirmation; while the qPCR M. canis assay was more useful for determining mycological cure.
Blood donor show behaviour after an invitation to donate: The influence of collection site factors
Authors: Merz E.‐M. , Zijlstra B. J. H. , de Kort W. L. A. M.
Published: August 2017

Background and Objectives

Show behaviour after invitation to donate varies considerably across donors. More insight into this variation is important for blood banks in achieving stable stocks. This study examined individual factors determining intended show behaviour. Most importantly, however, this study is the first study to account for variation in donor behaviour across different collection sites.

Materials and Methods

We applied a multilevel approach to data from Donor InSight, including 11 889 donors from 257 fixed and mobile collection sites in the Netherlands. The aim of the multilevel models was to account for variance at two levels, that is donors and collection sites. We estimated the likelihood of showing after invitation based on individual predictors, including demographics, donation history and attitude. At the collection site level, we included satisfaction with the blood bank aggregated from individual responses by donors who donate at this site, opening hours and collection site type, that is fixed/mobile.

Results

Most importantly, show behaviour varied considerably across collection sites and depended on characteristics of these sites. Moreover, women, older and more experienced donors had higher odds of showing after invitation than men, younger and less experienced donors. Donors higher on warm glow, self‐efficacy and donor identity more likely showed after an invitation. Higher aggregate satisfaction and donating at fixed collection sites increased the odds of show.

Conclusion

In addition to individual factors, collection site characteristics are important in explaining variation in donor show behaviour, thus presenting clues for blood bank policies and interventions to improve donor show.
The antioxidant capacity of erythrocyte concentrates is increased during the first week of storage and correlated with the uric acid level
Authors: Bardyn M. , Maye S. , Lesch A. , Delobel J. , Tissot J.‐D. , Cortés‐Salazar F. , Tacchini P. , Lion N. , Girault H. H. , Prudent M.
Published: August 2017

Background and Objectives

Red blood cells (RBCs) suffer from lesions during cold storage, depending in part on their ability to counterbalance oxidative stress by activating their antioxidant defence. The aim of this study was to monitor the antioxidant power (AOP) in erythrocyte concentrates (ECs) during cold storage.

Materials and Methods

Six ECs were prepared in saline‐adenine‐glucose‐mannitol (SAGM) additive solution and followed during 43 days. The AOP was quantified electrochemically using disposable electrode strips and compared with results obtained from a colorimetric assay. Haematological data, data on haemolysis and the extracellular concentration of uric acid were also recorded. Additionally, a kinetic model was developed to extract quantitative kinetic data on the AOP behaviour.

Results

The AOP of total ECs and their extracellular samples attained a maximum after 1 week of storage prior to decaying and reaching a plateau, as shown by the electrochemical measurements. The observed trend was confirmed with a colorimetric assay. Uric acid had a major contribution to the extracellular AOP. Interestingly, the AOP and uric acid levels were linked to the sex of the donors.

Conclusion

The marked increase in AOP during the first week of storage suggests that RBCs are impacted early by the modification of their environment. The AOP behaviour reflects the changes in metabolism activity following the adjustment of the extracellular uric acid level. Knowing the origin, interdonor variability and the effects of the AOP on the RBCs could be beneficial for the storage quality, which will have to be further studied.
USE OF THE PHRASE “PERSONAL RELATIONSHIP WITH JESUS”: TOWARD A COMPREHENSIVE INTERDISCIPLINARY EXPLANATION
Authors: Bennett‐Carpenter Benjamin
Published: August 2017

When people use the phrase “personal relationship with Jesus,” how does one explain its significance? Normally attributed to evangelical Protestant Christians, use of the phrase “personal relationship with Jesus” is a complicated phenomenon, and an explanation of it requires drawing upon resources from across multiple disciplines rather than a single discipline only. Attempts to explain exactly what the phrase “personal relationship with Jesus” means frequently can be mystifying, on the one hand, or dismissive and simplistic, on the other hand. This article moves potentially toward a better context for understanding use of the phrase “personal relationship with Jesus” by drawing upon insights from multiple disciplines, including (1) rhetorical and cultural‐historical studies, (2) evolutionary and cognitive psychology, and (3) biological/behavioral and social/anthropological studies in order to set forth some basic lines of explanation for use of the phrase “personal relationship with Jesus.” The article concludes with some possible testable statements for future empirical studies.
ASSESSING THE FIELD OF SCIENCE AND RELIGION: ADVICE FROM THE NEXT GENERATION
Authors: Burdett Michael S.
Published: August 2017

The field of science and religion is undergoing a transition today requiring assessment of its past movements and identifying its future trajectories by the next generation of science and religion scholars. This essay provides such assessment and advice. To focus efforts on the past, I turn to Ian Barbour's own stock taking of the field some forty years ago in an essay entitled “Science and Religion Today” before giving some personal comments where I argue that much of the field has traditionally focused on the conversation between Christianity and the natural sciences. At present, however, we are beginning to see that the future of the conversation lies beyond the dialogue between the natural sciences and Christianity. I suggest that the future dialogue will and ought to expand in several directions: (1) into non‐Christian religions and theology, (2) into the human sciences, (3) into science and technology Studies, and (4) into the humanities more broadly.
NATURALIZING PSYCHEDELIC SPIRITUALITY
Authors: Letheby Chris
Published: August 2017

A pressing philosophical problem is how to respond to the existential, anxiety and disenchantment resulting from a naturalistic worldview that eschews transcendent foundations for meaning and value. This problem is becoming more urgent as the popularization of neuroscientific findings renders a disenchanted conception of human beings ever more vivid, compelling, and widespread. I argue that the study of transformative experiences occasioned by classic psychedelic drugs such as lysergic acid diethylamide and psilocybin may reveal the nature of a viable practical solution to this problem. Despite the apparent centrality of nonnaturalistic metaphysical apprehensions to psychedelic transformation, findings from psychedelic research suggest that key elements of psychedelic or “entheogenic” spirituality are consistent with naturalism. These include disruption to neurocognitive mechanisms underpinning the sense of self, and consequent experiences of self‐transcendence and of the decoupling of attention from personal concerns. This liberation of attention can result in the availability of broader perspectives and the development of wonder and appreciation for life.
THE SCIENTIFIC CHARACTER OF PHILIP HEFNER'S “CREATED CO‐CREATOR”
Authors: Lorrimar Victoria
Published: August 2017

Philip Hefner's understanding of humans as “created co‐creators” has played a key role in the science and religion field, particularly as scholars consider the implications of emerging technologies for the human future. Hefner articulates his “created co‐creator” framework in the form of scientifically testable hypotheses supporting his core understanding of human nature, adopting the structure of Imre Lakatos's scientific research programme. This article provides a brief exposition of Hefner's model, examines his hypotheses in order to assess their scientific character, and evaluates them against the relevant findings of contemporary science. While Hefner's model is largely commensurate with contemporary science, he at times makes claims that cannot be scientifically falsified or corroborated. Hefner's accomplishments in demonstrating the scientific compatibility of many theological notions is admirable; however, his overall position would be strengthened with a more tacit acknowledgment of the limitations of scientific knowledge. His anthropology draws also from extrascientific commitments and is all the richer for it.
SHOULD A CHRISTIAN ADOPT METHODOLOGICAL NATURALISM?
Authors: Torrance Andrew B.
Published: August 2017

It has become standard practice for scientists to avoid the possibility of references to God by adopting methodological naturalism (MN), a method that assumes that the reality of the universe, as it can be accessed by empirical enquiry, is to be explained solely with recourse to natural phenomena. In this essay, I critique the Christian practice of this method, arguing that a Christian's practices should always reflect her belief that the universe is created and sustained by the triune God. This leads me to contend that the Christian should adopt a theologically humble approach to the sciences (instead of MN), with which she humbly acknowledges that special divine action is not discernible by empirical science. To further my critique, I consider three ways in which the practice of MN can be particularly problematic for Christianity.
Children’s Perspective of Game: A Comparison of the Public and Private Schools
Authors: Gündüz Nevin , Taşpinar Tuğçe , Demiş Nurdan
Published: August 2017

The purpose of this research is to determine what the game means from the perspectives of children studying at public and private schools. Four questionnaires were applied to all the third grade parents of four schools; two public and two private schools in Ankara, and questionnaires were completed and sent back by 212 parents. A total of 32 volunteer students from four schools, 4 girls and 4 boys, who were determined according to the results of parents surveys consist of our student research group. Qualitative data were obtained by semi-structured interview technique. Content analysis technique was used for qualitative data and six main themes were created.As a result, children at private and public schools have described as ‘’the meaning of the play’’ theme, as ‘’having fun, being happy, having a good time with friends, ’learning new rules, being healthy and doing sports’’. In the research, they also stated that they play game types such as ’’rope, hide, hide and seek’’ which do not require materials in public schools while they indicated they play games such as ‘’ball, dart, taboo and technological games’’ in private schools. Children indicated that they play at school competitive games prepared by teachers in physical activities lessons. It is concluded that, there is not too much change in the meaning of the game in terms of children who study at private and public schools. Children’s type of game and materials especially change for both girls and boys and schools. Although there are purpose of "enjoy" for both of the two groups, but materials and games that used and played are different.
Evaluation and Application of a Novel BaO–CaO–SiO2–CoO–B2O3 Based Glass-Ceramic Sealing Material for Solid Oxide Fuel Cells
Authors: Li Zhaonan , Yang Jiajun , Yan Dong , Feng Ping , Pu Jian
Published: August 2017

Sealant is used in a solid oxide fuel cell (SOFC) stack to separate fuel and oxygen from burning with each other throughout the stack's lifetime cycle. Various sealing materials have been developed and the glass sealant shows quite a potential for its low leaking rate. However, glass sealants usually suffer from fractures during thermal cycle because of their low-temperature brittleness and mismatched coefficient of thermal expansion. Recently, we have developed a novel glass-based sealant consisting of BaO–CaO–SiO2–CoO and a small amount of Al2O3 powder which is used to adjust the coefficient of thermal expansion (CTE) and reinforce its mechanical performance. The sealant exhibited a good performance with the leaking rates less than 0.04 sccm cm−1 under compressive load of 0.17 MPa at 750 °C and showed stable leak rates over several thermal cycles. The well bonded interfaces and chemical compatibility have been identified by microstructure analysis of the seals. The sealant also demonstrated its applicability in a one-cell stack test.
Stabilization of a Class of Nonlinear Coupled Ordinary Differential Equation–Partial Differential Equation Systems Via Sampled-Data H∞ Fuzzy Controller
Authors: Dharani S. , Rakkiyappan R. , Lakshmanan S.
Published: August 2017

The main intention of this study is to develop a sampled-data H∞ fuzzy controller design to analyze the stability of coupled ordinary differential equation (ODE)–partial differential equation (PDE) systems, where the nonlinear coupled system is expressed by Takagi–Sugeno (T–S) fuzzy models. The coupled ODE–PDE system in this paper constitutes an n–dimensional nonlinear subsystem of ODEs and a scalar linear parabolic subsystem of PDE. Then, in regard to the T–S model representation, Lyapunov technique is utilized to model a sampled-data H∞ fuzzy controller to stabilize the contemplated coupled systems and to attain a desired H∞ disturbance attenuation performance. The formulated time-dependent Lyapunov functional makes full use of the accessible information about the actual sampling pattern. The outcome of the sampled-data H∞ fuzzy control problem is expressed as linear matrix inequality (LMI) optimization problem which can be solved effectively by using any of the available softwares. Finally, hypersonic rocket car model is furnished with simulation results to exhibit the efficacy of the proposed theoretical results.
Effect of Tailoring Martensite Shape and Spatial Distribution on Tensile Deformation Characteristics of Dual Phase Steels
Authors: Ravi Kumar B. , Singh Vishal , Nanda Tarun , Adhikary Manashi , Halder Nimai , Venugopalan T.
Published: August 2017

The authors simulated the industrially used continuous annealing conditions to process dual phase (DP) steels by using a custom designed annealing simulator. Sixty-seven percentage of cold rolled steel sheets was subjected to different processing routes, including the conventional continuous annealing line (CAL), intercritical annealing (ICA), and thermal cycling (TC), to investigate the effect of change in volume fraction, shape, and spatial distribution of martensite on tensile deformation characteristics of DP steels. Annealing parameters were derived using commercial software, including thermo-calc, jmat-pro, and dictra. Through selection of appropriate process parameters, the authors found out possibilities of significantly altering the volume fraction, morphology, and grain size distribution of martensite phase. These constituent variations showed a strong influence on tensile properties of DP steels. It was observed that TC route modified the martensite morphology from the typical lath type to in-grain globular/oblong type and significantly reduced the martensite grain size. This route improved the strength–ductility combination from 590 MPa–33% (obtained through CAL route) to 660 MPa–30%. Finally, the underlying mechanisms of crack initiation/void formation, etc., in different DP microstructures were discussed.
Design of a Magnetic Resonance-Safe Haptic Wrist Manipulator for Movement Disorder Diagnostics
Authors: Bode Dyon , Mugge Winfred , Schouten Alfred C. , van Rootselaar Anne-Fleur , Bour Lo J. , van der Helm Frans C. T. , Lammertse Piet
Published: August 2017

Tremor, characterized by involuntary and rhythmical movements, is the most common movement disorder. Tremor can have peripheral and central oscillatory components which properly assessed may improve diagnostics. A magnetic resonance (MR)-safe haptic wrist manipulator enables simultaneous measurement of proprioceptive reflexes (peripheral components) and brain activations (central components) through functional magnetic resonance imaging (fMRI). The presented design for an MR-safe haptic wrist manipulator has electrohydraulic closed-circuit actuation, optical position and force sensing, and consists of exclusively nonconductive and magnetically compatible materials inside the MR-environment (Zone IV). The MR-safe hydraulic actuator, a custom-made plastic vane motor, is connected to the magnetic parts and electronics located in the shielded control room (Zone III) via hydraulic hoses and optical fibers. Deliberate internal leakage provides backdriveability, damping, and circumvents friction. The manipulator is completely MR-safe and therefore operates safely in any MR-environment while ensuring fMRI imaging quality. Undesired external leakage in the actuator prevented the use of prepressure, limiting the control bandwidth. The compact end effector design fits in the MR-scanner, is easily setup, and can be clamped to the MR-scanner bed. This enables use of the manipulator with the subject at the optimal fMRI location and allows it to be setup quickly, saving costly MR-scanner time. The actuation and sensor solutions performed well inside the MR-environment and did not deteriorate image quality, which allows for various motor control experiments. Enabling prepressure by carrying out the recommendations on fabrication and sealing should improve the bandwidth and fulfill the requirements for proprioceptive reflex identification.
The Application of Different Tripping Techniques to Determine the Characteristics of the Turbulent Boundary Layer Over a Flat Plate
Authors: Silvestri Anton , Ghanadi Farzin , Arjomandi Maziar , Cazzolato Benjamin , Zander Anthony
Published: August 2017

In the present study, the optimal two-dimensional (2D) tripping technique for inducing a naturally fully developed turbulent boundary layer in wind tunnels has been investigated. Various tripping techniques were tested, including wires of different diameters and changes in roughness. Experimental measurements were taken on a flat plate in a wind tunnel at a number of locations along the flat plate and at a variety of flow speeds using hot-wire anemometry to measure the boundary layer resulting from each tripping method. The results have demonstrated that to produce a natural turbulent boundary layer using a 2D protuberance, the height of the trip must be less than the undisturbed boundary layer thickness. Using such a trip was shown to reduce the development length of the turbulent boundary layer by approximately 50%. This was shown to hold true for all Reynolds numbers investigated (Rex=1.2×105−1.5×106). The present study provides an insight into the effect of the investigated trip techniques on the induced transition of a laminar boundary layer into turbulence.
Comparison of Various Pressure Based Boundary Conditions for Three-Dimensional Subsonic DSMC Simulation
Authors: Shah Niraj , Gavasane Abhimanyu , Agrawal Amit , Bhandarkar Upendra
Published: August 2017

Three-dimensional (3D) direct simulation Monte Carlo (DSMC) has been used to simulate flow in a straight microchannel using an in-house parallelized code. In the present work, a comparative study of seven boundary conditions is carried out with respect to time required for achieving steady-state, accuracy in predicting the specified pressure at the boundaries, and the total simulation time required for attaining a statistical error within one percent. The effect of changing the Knudsen number, pressure ratio (PR), and cross aspect ratio (CAR) on these parameters is also studied. The presence of a boundary is seen to affect the simulated pressure in a cell when compared to the specified pressure, the difference being highest for corner cells and least for cells away from walls. All boundary conditions tested work well at the inlet boundary; however, similar results are not obtained at the outlet boundary. For the same cell size, the schemes that employ first- and second-order corrections lead to a smaller pressure difference compared to schemes applying no corrections. The best predictions can be obtained by using first-order corrections with finer cell size close to the boundary. For most of the simulated cases, the boundary condition employing the characteristic scheme with nonequilibrium effect leads to the minimum simulation time. Considering the nonequilibrium effect, prediction of inlet and outlet pressures and the speed of simulation, the characteristic scheme with nonequilibrium effect performs better than all the other schemes, at least over the range of parameters investigated herein.
Adjustable sidewall slopes by electron-beam exposure layout
Authors: Kaspar Corinna , Butschke Jörg , Irmscher Mathias , Martens Stephan , Sailer Holger , Kirchner Robert , Guzenko Vitaliy A. , Schift Helmut , Burghartz Joachim N.
Published: August 2017

Resist sidewall slopes frequently need to be adjusted in micro- and nanofabrication. In this paper, the authors present a straightforward approach to adjust sidewall slopes by using electron beam lithography and applying a background dose in addition to the feature dose. The underlying effect is attributed to an inhomogeneous energy deposition along the resist depth, for which a three-dimensional point spread function is necessary to correctly describe the energy deposition in the resist even for large acceleration voltages and thin resist films. This enables adjacent features with different positive or different negative slopes within a single lithographic step. Corresponding experimental results obtained with the two positive tone resists poly(methyl methacrylate) and ZEP520A are shown, and their opposed sidewall behavior is explained. Moreover, a customized contrast curve is discussed that can, in theory, be used to achieve resist profiles with positive and negative slopes for the same resist. Therefore, a full range tuning on the same substrate becomes feasible.
Atomic layer etching of gallium nitride (0001)
Authors: Kauppinen Christoffer , Khan Sabbir Ahmed , Sundqvist Jonas , Suyatin Dmitry B. , Suihkonen Sami , Kauppinen Esko I. , Sopanen Markku
Published: August 2017

In this work, atomic layer etching (ALE) of thin film Ga-polar GaN(0001) is reported in detail using sequential surface modification by Cl2 adsorption and removal of the modified surface layer by low energy Ar plasma exposure in a standard reactive ion etching system. The feasibility and reproducibility of the process are demonstrated by patterning GaN(0001) films by the ALE process using photoresist as an etch mask. The demonstrated ALE is deemed to be useful for the fabrication of nanoscale structures and high electron mobility transistors and expected to be adoptable for ALE of other materials.
Electrical analyses of GaN PIN diodes grown on patterned sapphire substrates
Authors: Shan Li-Wei , Liu Zhe-Yu , Lin Min-Pang , Yu Chia-Jui , Hsieh Kuang-Chien , Wu Meng-Chyi
Published: August 2017

In this article, the authors report the fabrication and characterization of quasivertical GaN p-i-n diodes with a 3 μm I-layer grown on different sizes of patterned sapphire substrates (PSSs). The diodes were characterized by current–voltage, capacitance–voltage, and deep-level transient spectroscopy. The PIN diodes grown on the smaller-size PSS showed a reverse breakdown voltage of ∼610 V and a defect concentration of 1.0 × 1016 cm−3, both of which are superior to the corresponding measurements of ∼410 V and 1.4 × 1017 cm−3 for the diodes grown on the larger-size PSS. These results indicate that the GaN PIN diodes grown on smaller-size PSS have a better quality of epitaxial layers than those grown on larger-size PSS.
A LEGO Mindstorms Brewster angle microscope
Authors: Fernsler Jonathan , Nguyen Vincent , Wallum Alison , Benz Nicholas , Hamlin Matthew , Pilgram Jessica , Vanderpoel Hunter , Lau Ryan
Published: August 2017

A Brewster Angle Microscope (BAM) built from a LEGO Mindstorms kit, additional LEGO bricks, and several standard optics components, is described. The BAM was built as part of an undergraduate senior project and was designed, calibrated, and used to image phospholipid, cholesterol, soap, and oil films on the surface of water. A BAM uses p-polarized laser light reflected off a surface at the Brewster angle, which ideally yields zero reflectivity. When a film of different refractive index is added to the surface a small amount of light is reflected, which can be imaged in a microscope camera. Films of only one molecule (approximately 1 nm) thick, a monolayer, can be observed easily in the BAM. The BAM was used in a junior-level Physical Chemistry class to observe phase transitions of a monolayer and the collapse of a monolayer deposited on the water surface in a Langmuir trough. Using a photometric calculation, students observed a change in thickness of a monolayer during a phase transition of 7 Å, which was accurate to within 1 Å of the value determined by more advanced methods. As supplementary material, we provide a detailed manual on how to build the BAM, software to control the BAM and camera, and image processing software.
DNA replication–coupled histone modification maintains Polycomb gene silencing in plants
Authors: Jiang Danhua , Berger Frédéric
Published: August 2017

A multifactorial strategy establishes and maintains repressive chromatin marks in plants in response to environmental signals.
Genome Sequence of Lactobacillus sakei LK-145 Isolated from a Japanese Sake Cellar as a High Producer of
d
-Amino Acids
Authors: Kato Shiro , Oikawa Tadao
Published: August 2017

This announcement reports the complete genome sequence of strain LK-145 of
Lactobacillus sakei
isolated from a Japanese sake cellar as a potent strain for the production of large amounts of
d
-amino acids. Three putative genes encoding an amino acid racemase were identified.
Draft Genome Sequence of Chilean Antarctic
Pseudomonas
sp. Strain K2I15
Authors: Orellana Paz , Pavón Alequis , Céspedes Sandra , Salazar Lorena , Gutiérrez Ana , Castillo Daniel , Corsini Gino
Published: August 2017

We announce the draft genome sequence of
Pseudomonas
sp. strain K2I15, isolated from the rhizosphere of
Deschampsia Antarctica
Desv. The genome sequence had 6,645,031 bp with a G+C content of 60.4%. This genome provides insights into the niche adaptation, prophage carriage, and evolution of this specific Antarctic bacteria.
Genome Sequences of Three Novel Isolates of Human Parainfluenza Virus 2 Associated with Acute Respiratory Infection
Authors: Kennedy J. L. , Kincaid J. C. , Schwalm K. C. , Stoner A. N. , Abramo T. J. , Thompson T. M. , Hardin O. , Putt C. , Dinwiddie D. L.
Published: August 2017

Using target capture of viral nucleic acid and next-generation sequencing, we generated the genome sequences of three novel human parainfluenza virus 2 isolates. Isolates ACRI_0185 (GenBank accession number MF077311), ACRI_0230 (MF077312), and ACRI_0248 (MF077313) were collected in October 2016, February 2017, and March 2017, respectively, from pediatric patients with acute respiratory infection in Arkansas.
Draft Genome Sequence of
Bacillus
sp. Strain K2I17, Isolated from the Rhizosphere of
Deschampsia antarctica
Desv
Authors: Pavón Alequis , Orellana Paz , Salazar Lorena , Céspedes Sandra , Muiño Laura , Gutiérrez Ana , Castillo Daniel , Corsini Gino
Published: August 2017

We present here the draft genome sequence of
Bacillus
sp. strain K2I17, which was isolated from the rhizosphere of
Deschampsia antarctica
Desv. The genomic sequence contained 6,113,341 bp. This genome provides insights into the possible new biomedical and biotechnical applications of this specific Antarctic bacterium.
Draft Genome Sequence of
Ideonella
sp. Strain A 288, Isolated from an Iron-Precipitating Biofilm
Authors: Braun Burga , Künzel Sven , Szewzyk Ulrich
Published: August 2017

Here, we report the draft genome sequence of the betaproteobacterium
Ideonella
sp. strain A_228. This isolate, obtained from a bog iron ore-containing floodplain area in Germany, provides valuable information about the genetic diversity of neutrophilic iron-depositing bacteria. The Illumina NextSeq technique was used to sequence the draft genome sequence of the strain.
Draft Genome Sequence of Staphylococcus aureus S681, a Tetracycline-Sensitive Livestock-Associated CC398 MRSA Strain
Authors: Stevens Marc J. A. , Stephan Roger , Johler Sophia
Published: August 2017

We present the draft genome sequence of an atypical tetracycline-susceptible livestock-associated methicillin-resistant
Staphylococcus aureus
(MRSA) strain. It contains 2,817,340 bp and 2,858 coding sequences, including 6 rRNA operons, 56 tRNAs, and 4 noncoding RNA (ncRNA) genes. The strain harbors a
tet
(M) gene, but 15 point mutations in amino acids are present that likely impair the functionality of TetM.
Complete Genome Sequence of Mycobacterium stephanolepidis
Authors: Fukano Hanako , Yoshida Mitsunori , Katayama Yukie , Omatsu Tsutomu , Mizutani Tetsuya , Kurata Osamu , Wada Shinpei , Hoshino Yoshihiko
Published: August 2017

Mycobacterium stephanolepidis
is a rapid-growing nonpigmented species isolated from marine teleost fish (
Stephanolepis cirrhifer
) and is closely related to
Mycobacterium chelonae
. Here, we report the complete sequence of its genome, comprising a 4.9-Mb chromosome. The sequence represents essential data for future phylogenetic and comparative genome studies of this fish pathogen.
Deep Sequencing Reveals a Divergent
Ugandan cassava brown streak virus
Isolate from Malawi
Authors: Mbewe Willard , Winter Stephan , Mukasa Settumba , Tairo Fred , Sseruwagi Peter , Ndunguru Joseph , Duffy Siobain
Published: August 2017

Illumina sequencing of RNA from a cassava cutting from northern Malawi produced a genome of
Ugandan cassava brown streak virus
(UCBSV-MW-NB7_2013). Sequence comparisons revealed stronger similarity to an isolate from nearby Tanzania (93.4% pairwise nucleotide identity) than to those previously reported from Malawi (86.9 to 87.0%).
Complete Genome Sequence of a Naturally Occurring Simian Foamy Virus Isolate from Rhesus Macaque (SFVmmu_K3T)
Authors: Nandakumar Subhiksha , Bae Eunhae H. , Khan Arifa S.
Published: August 2017

The full-length genome sequence of a simian foamy virus (SFVmmu_K3T), isolated from a rhesus macaque (
Macaca mulatta
), was obtained using high-throughput sequencing. SFVmmu_K3T consisted of 12,983 bp and had a genomic organization similar to that of other SFVs, with long terminal repeats (LTRs) and open reading frames for Gag, Pol, Env, Tas, and Bet.
Fungal Genomes and Insights into the Evolution of the Kingdom
Authors: Stajich Jason E.
Published: August 2017

The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute’s Fungal Genome Initiative, and the 1000 Fungal Genomes Project (
http://1000.fungalgenomes.org
). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.
Improved pregnant women’s understanding of research information by an enhanced informed consent form: a randomised controlled study nested in neonatal research
Authors: Koonrungsesomboon Nut , Traivaree Chanchai , Chamnanvanakij Sangkae , Rungtragoolchai Pimchitr , Thanapat Yawana , Karbwang Juntra
Published: August 2017

Objective

This study aimed to test the applicability and effectiveness of the enhanced informed consent form (ICF) methodology, proposed by the Strategic Initiative for Developing Capacity in Ethical Review (SIDCER), in neonatal research requiring maternal consent.

Design

A single-centre open-label randomised controlled study.

Setting

Antenatal care clinics at Phramongkutklao Hospital, Thailand.

Patients

234 pregnant women who were at risk of preterm labour were enrolled; 232 individuals completed the study.

Interventions

The participants were randomly assigned to read either the SIDCER ICF or the conventional ICF.

Main outcome measures

The participants’ understanding of essential trial-related information was assessed using 25 closed-ended questions. The primary endpoint was the proportion of the participants who obtained the satisfactory level of understanding at 80% (score of ≥20/25).

Results

72.5% (87/120) of the participants in the SIDCER ICF group and 59.8% (67/112) of the conventional ICF group achieved the primary endpoint (relative risk (RR)=1.212, 95% CI 1.005 to 1.462, p=0.041). The superiority of the SIDCER ICF over the conventional ICF was significant, particularly among the participants whose education was at the high school level or below (63.5% vs 44.1%, RR=1.441, 95% CI 1.022 to 2.030, p=0.031).

Conclusions

The SIDCER ICF methodology is applicable to neonatal research requiring maternal consent. The SIDCER ICF significantly improved the understanding of pregnant women, particularly among those with lower levels of education. The present study confirms the value of the SIDCER ICF methodology in research involving individuals with a limited academic background.
Reducing social isolation and loneliness in older people: a systematic review protocol
Authors: Landeiro Filipa , Barrows Paige , Nuttall Musson Ellen , Gray Alastair M , Leal José
Published: August 2017

Introduction

Social isolation and loneliness affect approximately one-third to one-half of the elderly population and have a negative impact on their physical and mental health. Group-based interventions where facilitators are well trained and where the elderly are actively engaged in their development seem to be more effective, but conclusions have been limited by weak study designs. We aim to conduct a systematic review to assess the effectiveness of health promotion interventions on social isolation or loneliness in older people.

Methods and analysis

A systematic review was conducted in Medline, Embase, PsycINFO, Cumulative Index to Nursing and Allied Health Literature, Applied Social Sciences Index and Abstracts, LILACS, OpenGrey and the Cochrane Library on peer-reviewed studies and doctoral theses published between 1995 and 2016 evaluating the impact of health promotion interventions on social isolation and/or loneliness for individuals aged 60 and over. Two reviewers will independently assess each study for inclusion and disagreements will be resolved by a third reviewer. Data will be extracted using a predefined pro forma following best practice. Study quality will be assessed with the Effective Public Health Practice Project quality assessment tool. A narrative synthesis of all studies will be presented by type of outcome (social isolation or loneliness) and type of intervention. If feasible, the effectiveness data will be synthesised using appropriate statistical techniques.

Ethics and dissemination

This systematic review is exempt from ethics approval because the work is carried out on published documents. The findings of the review will be disseminated in a related peer-reviewed journal and presented at conferences. They will also contribute to a DPhil thesis.

Trial registration number

CRD42016039650