bluuebunny/crossref_metadata_2025 huggingface dataset:
Embracing the population health framework in nursing research
Authors: MacDonald Shannon E , Newburn‐Cook Christine V , Allen Marion , Reutter Linda
Published: December 2012

MACDONALD SE, NEWBURN‐COOK CV, ALLEN M and REUTTER L.Nursing Inquiry2013;20: 30–41  Embracing the population health framework in nursing research

Individuals’ health outcomes are influenced not only by their knowledge and behavior, but also by complex social, political and economic forces. Attention to these multi‐level factors is necessary to accurately and comprehensively understand and intervene to improve human health. The population health framework is a valuable conceptual framework to guide nurse researchers in identifying and targeting the broad range of determinants of health. However, attention to the intermediate processes linking multi‐level factors and use of appropriate multi‐level theory and research methodology is critical to utilizing the framework effectively. Nurse researchers are well equipped to undertake such investigations but need to consider a number of political, societal, professional and organizational barriers to do so. By fully embracing the population health framework, nurse researchers have the opportunity to explore the multi‐level influences on health and to develop, implement and evaluate interventions that target immediate needs, more distal factors and the intermediate processes that connect them.
Cortical visual areas process intestinal information during slow‐wave sleep
Authors: Pigarev I. N. , Bagaev V. A. , Levichkina E. V. , Fedorov G. O. , Busigina I. I.
Published: December 2012

Background Previously we have shown that, during sleep, electrical and magnetic stimulation of areas of the stomach and small intestine evoked neuronal and EEG responses in various cortical areas. In this study we wanted to correlate natural myoelectrical activity of the duodenum with cortical neuronal activity, and to investigate whether there is a causal link between them during periods of slow‐wave sleep.

Methods We have recorded the myoelectrical activity from the wall of the duodenum and activity of single neurons from three cortical visual areas in naturally sleeping cats and investigated causal interrelationship between these structures during slow‐wave sleep.

Key Results About 30% of the cortical neurons studied changed their firing rate dependent on the phases of the peristaltic cycle and demonstrated selectivity to particular pattern of duodenal myoelectrical activity during slow‐wave sleep. This interrelationship was never seen when awake.

Conclusions & Inferences This observation supports the hypothesis that, during sleep, the cerebral cortex switches from processing of exteroceptive and proprioceptive information to processing of interoceptive information.
Effect of DA‐9701, a novel prokinetic agent, on stress‐induced delayed gastric emptying and hormonal changes in rats
Authors: Jung Y.‐S. , Kim M.‐Y. , Lee H. S. , Park S. L. , Lee K. J.
Published: December 2012

Background  DA‐9701 is a novel prokinetic agent formulated with Pharbitis Semen and Corydalis Tuber. This study aimed to evaluate the effect of DA‐9701 on stress‐induced delay in gastric emptying and changes in plasma adrenocorticotropic hormone and ghrelin levels in rats.

Methods  Changes in gastric emptying in response to different durations of stress were evaluated. Gastric emptying was compared between the following groups: (i) nonstressed vehicle‐ or DA‐9701‐treated group, (ii) nonstressed vehicle‐ or mosapride‐treated group, (iii) 2‐h stressed vehicle‐ or DA‐9701‐treated group, and (iv) 2‐h stressed vehicle‐ or mosapride‐treated group. Water immersion restraint stress was used as the stressor. DA‐9701 or mosapride at 3 mg kg−1 was administered to the rats after subjecting them to 2‐h stress, and then gastric emptying was measured using the phenol red method.

Key Results  Gastric emptying was significantly delayed in the 2‐h stressed group compared with the nonstressed group. Mosapride administration resulted in significant recovery from the stress‐induced delay in gastric emptying. Gastric emptying in the rats that underwent 2‐h stress followed by DA‐9701 administration was not significantly different from that in the nonstressed group. The plasma adrenocorticotropic hormone and active ghrelin levels in the 2‐h stressed group were significantly higher than those in the nonstressed group. These increases were significantly inhibited by DA‐9701.

Conclusions & Inferences  The administration of DA‐9701 improved delayed gastric emptying and inhibited the hormonal changes induced by stress, suggesting that DA‐9701 can be used as a gastroprokinetic agent for the treatment of delayed gastric emptying, particularly that associated with stress.
Internal aeration of paddy field rice (Oryza sativa) during complete submergence – importance of light and floodwater O2
Authors: Winkel Anders , Colmer Timothy D. , Ismail Abdelbagi M. , Pedersen Ole
Published: December 2012

Flash floods can submerge paddy field rice (Oryza sativa), with adverse effects on internal aeration, sugar status and survival. Here, we investigated the in situ aeration of roots of rice during complete submergence, and elucidated how underwater photosynthesis and floodwater pO2 influence root aeration in anoxic soil.

In the field, root pO2 was measured using microelectrodes during 2 d of complete submergence. Leaf gas films that formed on the superhydrophobic leaves were left intact, or experimentally removed, to elucidate their effect on internal aeration.

In darkness, root pO2 declined to very low concentrations (0.24 kPa) and was strongly correlated with floodwater pO2. In light, root pO2 was high (14 kPa) and primarily a function of the incident light determining the rates of underwater net photosynthesis. Plants with intact leaf gas films maintained higher underwater net photosynthesis relative to plants without gas films when the submerged shoots were in light.

During complete submergence, internal aeration of rice in the field relies on underwater photosynthesis during the day and entry of O2 from the floodwater during the night. Leaf gas films enhance photosynthesis during submergence leading to improved O2 production and sugar status, and therefore contribute to the submergence tolerance of rice.
Towards an integrative approach to understanding the role of chemerin in human health and disease
Authors: Rourke J. L. , Dranse H. J. , Sinal C. J.
Published: December 2012

Chemerin is an adipocyte‐secreted protein with autocrine/paracrine roles on adipose development and function as well as endocrine roles in metabolism and immunity. Following prochemerin secretion, protease‐mediated generation of chemerin isoforms with a range of biological activities is a key regulatory mechanism controlling local, context‐specific chemerin bioactivity. Together, experimental and clinical data indicate that localized and/or circulating chemerin expression and activation are elevated in numerous metabolic and inflammatory diseases including psoriasis, obesity, type 2 diabetes, metabolic syndrome and cardiovascular disease. These elevations are positively correlated with deleterious changes in glucose, lipid, and cytokine homeostasis, and may serve as a link between obesity, inflammation and other metabolic disorders. This review highlights the current state of knowledge regarding chemerin expression, processing, biological function and relevance to human disease, particularly with respect to adipose tissue development, inflammation, glucose homeostasis and cardiovascular disease. Furthermore, it discusses study variability, deficiencies in current measurement, and questions concerning chemerin function in disease, with a special emphasis on techniques and tools used to properly assess chemerin biology. An integration of basic and clinical research is key to understanding how chemerin influences disease pathobiology, and whether modulation of chemerin levels and/or activity may serve as a potential method to prevent and treat metabolic diseases.
Linking evolution and development: Synchrotron Radiation X‐ray tomographic microscopy of planktic foraminifers
Authors: SCHMIDT DANIELA N. , RAYFIELD EMILY J. , COCKING ALEXANDRA , MARONE FEDERICA
Published: December 2012

Abstract:  Making the link between evolutionary processes and development in extinct organisms is usually hampered by the lack of preservation of ontogenetic stages in the fossil record. Planktic foraminifers, which grow by adding chambers, are an ideal target organism for such studies as their test incorporates all prior developmental stages. Previously, studies of development in these organisms were limited by the small size of their early chambers. Here, we describe the application of synchrotron radiation X‐ray tomographic microscopy (SRXTM) to document the ontogenetic history of the foraminifers Globigerinoides sacculifer and Globorotalia menardii. Our SRXTM scans permit resolution at submicrometre scale, thereby displaying additional internal structures such as pores, dissolution patterns and complexity of the wall growth. Our methods provide a powerful tool to pick apart the developmental history of these microfossils and subsequently assist in inferring phylogenetic relationships and evolutionary processes.
History of pediatric anesthesia timeline
Authors: Mai Christine L. , Firth Paul G. , Yaster Myron
Published: December 2012

This editorial comments on the History of Pediatric Anethesia Timeline article by Mai et al on pages 3–8 of this issue
Evidence for contribution of autophagy to Rubisco degradation during leaf senescence in Arabidopsis thaliana
Authors: ONO YUKI , WADA SHINYA , IZUMI MASANORI , MAKINO AMANE , ISHIDA HIROYUKI
Published: December 2012

Rubisco is degraded during leaf senescence, and its components are recycled within the plant. Although Rubisco can be mobilized to the vacuole by autophagy via specific autophagic bodies, the importance of this process in Rubisco degradation has not been shown directly. Using an assay based on the processing of fluorescent protein‐tagged Rubisco, here, we provide further evidence for the contribution of autophagy to Rubisco degradation during both natural and promoted leaf senescence in Arabidopsis.
Reversible inhibition of CO2 fixation by ribulose 1,5‐bisphosphate carboxylase/oxygenase through the synergic effect of arsenite and a monothiol
Authors: SUDHANI HEMANTH P. K. , GARCíA‐MURRIA MARíA‐JESúS , MORENO JOAQUíN
Published: December 2012

The photosynthetic carbon‐fixing enzyme, ribulose 1,5‐bisphosphate carboxylase/oxygenase (Rubisco), is reversibly inhibited by micromolar arsenite in the presence of an enhancer monothiol such as cysteine, cysteamine, 2‐mercaptoethanol or N‐acetylcysteine, but not glutathione. Arsenite reacts specifically with the vicinal Cys172‐Cys192 from the large subunit of Rubisco and with the monothiol to establish a ternary complex. The combination of arsenite and monothiol stops also the carbon fixation in illuminated cultures of
Chlamydomonas reinhardtii but the in vivo arrest appears to be driven by an undetermined effector that is even more sensitive to the arsenite‐thiol synergism than Rubisco.
Maternal Prepregnancy Obesity is an Independent Risk Factor for Frequent Wheezing in Infants by Age 14 Months
Authors: Guerra Stefano , Sartini Claudio , Mendez Michelle , Morales Eva , Guxens Mònica , Basterrechea Mikel , Arranz Leonor , Sunyer Jordi
Published: December 2012

Background:  Maternal prepregnancy obesity has been linked to the offspring's risk for subsequent asthma. We determined whether maternal obesity is associated with increased risk of wheezing phenotypes early in life.

Methods:  We used data on 1107 mother–child pairs from two birth cohorts from the INMA–INfancia y Medio Ambiente project. Maternal height was measured and prepregnancy weight self‐reported at enrolment (on average at 13.7 ± 2 weeks of gestation). Maternal prepregnancy body mass index was categorised as underweight, normal, overweight and obese according to WHO recommendations. Information on child's wheezing was obtained through questionnaires up to the age of 14 (±1) months. Wheezing was classified as infrequent (<4 reported wheezing episodes) or frequent (≥4 episodes). Weight and length of infants were measured by trained study staff at 14.6 (±1) months of age and weight‐for‐length z‐scores computed.

Results:  Although maternal obesity did not increase the risk of the child to have any or infrequent wheezing, children of obese mothers were more likely to have frequent wheezing than children of normal‐weight mothers (11.8% vs. 3.8%; P = 0.002). In fully adjusted multinomial logistic regression models, including infants' weight‐for‐length z‐scores and other covariates, maternal prepregnancy obesity was associated with increased risk of frequent [adjusted relative risk (RR) 4.18, 95% confidence interval (CI) 1.55, 11.3] but not infrequent (RR 1.05 [95% CI 0.55, 2.01]) wheezing in their children.

Conclusions:  Maternal prepregnancy obesity is independently associated with an increased risk of frequent wheezing in the infant by the age of 14 months. These findings add evidence on the potential effects of in utero exposures on asthma‐related phenotypes.
Identification and Avoidance of Systematic Measurement Errors in Lamb Wave Observation With One‐Dimensional Scanning Laser Vibrometry
Authors: Neumann M. N. , Hennings B. , Lammering R.
Published: December 2012

Abstract:  Scanning laser vibrometry is a widely used tool to observe Lamb wave fields for structural health monitoring (SHM) purposes. Lamb waves propagate over long distances in thin‐walled structures and interact with structural inhomogeneities, for example, damages, in spite of wavelengths several times of the damage size. In SHM of sheets and glass‐ or carbon‐fibre‐reinforced plastic plates, this effect is used for determining the position as well as the size of structural faults. With the often employed one‐dimensional vibrometry, a geometrically induced, systematic error occurs when measuring oblique‐angled motion. This error can be, in the specific case of Lamb waves, of a non‐negligible quantity. The nature of this geometrical measurement error in general and concerning Lamb waves in special is discussed analytically for both amplitude and phase data. It is shown that this matter should be taken into account in some applications.
Identification of a new HLA‐B*13 allele, HLA‐B*13:23
Authors: Gong Z. , Zhang Z. X. , Shan X. , Wang L. , Liu N.
Published: December 2012

The HLA‐B*13:23 allele differs from the B*13:01:01 by one nucleotide substitution in exon 2 at nt 97.
HLA antigen, allele and haplotype frequencies and their use in virtual panel reactive antigen calculations in the Finnish population
Authors: Haimila K. , Peräsaari J. , Linjama T. , Koskela S. , Saarinenl T. , Lauronen J. , Auvinen M.‐K. , Jaatinen T.
Published: December 2012

The human leukocyte antigen (HLA) antigen, allele and haplotype frequencies of the Finnish population are quite unique because of a rather restricted and homogeneous gene pool. This has a strong influence on finding suitable donors for transplant patients; hence knowledge about the HLA frequencies of the patient population is essential. Here we report the HLA antigen frequencies for a large population sample and show high resolution HLA allele frequencies for 11 loci, including the rarely typed DPA1 and DQA1 loci. Furthermore, the most common Finnish high resolution haplotypes are presented for five HLA loci. The study shows that there are fewer HLA haplotypes in the Finnish population compared with mixed populations, and the common Finnish HLA haplotypes are more frequent. Using HLA antibody identification and panel reactive antibody calculations we show that a virtual population‐specific panel, combined with single antigen testing, gives a more accurate and reliable estimate of the reactivity of the recipient serum against potential solid organ donors within the Finnish population. The results can be directly used to improve donor search for patients waiting for stem cell transplantation and to allocate highly immunised patients accurately to acceptable mismatch programs.
Identification and sequence analysis of a novel human leukocyte antigen allele B*51:141
Authors: Caggiari L. , De Zorzi M. , Izzo F. , Tornesello M. L. , Buonaguro F. M. , De Re V.
Published: December 2012

The newly detected HLA‐B*51:141 is distinguished from HLA‐B*51:08 by a single‐nucleotide exchange at codon 30 where D is replaced by Y.
Molecular phylogeny and systematics of Dipodoidea: a test of morphology‐based hypotheses
Authors: Lebedev Vladimir S. , Bannikova Anna A. , Pagès Marie , Pisano Julie , Michaux Johan R. , Shenbrot Georgy I.
Published: December 2012

Lebedev, V.S., Bannikova, A.A., Pagès, M., Pisano, J., Michaux, J.R. & Shenbrot, G.I. (2012). Molecular phylogeny and systematics of Dipodoidea: a test of morphology‐based hypotheses. —Zoologica Scripta, 42, 231–249.

The superfamily Dipodoidea (Rodentia, Myomorpha) in its current interpretation contains a single family subdivided into six subfamilies. Four of them include morphologically specialized bipedal arid‐dwelling jerboas (Dipodinae – three‐toed jerboas, Allactaginae – five‐toed jerboas, Cardiocraniinae – pygmy jerboas and Euchoreutinae – long‐eared jerboas), the other two are represented by more generalized quadrupedal taxa (Zapodinae – jumping mice and Sminthinae – birch mice). Despite considerable effort from morphologists, the taxonomy as well as the phylogeny of the Dipodoidea remains controversial. Strikingly, molecular approach has never been envisaged to investigate these questions. In this study, the phylogenetic relationships among the main dipodoid lineages were reconstructed for the first time using DNA sequence data from four nuclear genes (IRBP, GHR, BRCA1, RAG1). No evidence of conflict among genes was revealed. The same robustly supported tree topology was inferred from the concatenated alignment whatever the phylogenetic methods used (maximum parsimony, maximum‐likelihood and Bayesian phylogenetic methods). Sminthinae branches basally within the dipodoids followed by Zapodinae. Monophyletic Cardiocraniinae is sister to all other jerboas. Within the latter, the monophyly of both Dipodinae and Allactaginae is highly supported. The relationships between Dipodinae, Allactaginae and Euchoreutinae should be regarded as unresolved trichotomy. Morphological hypotheses were confronted to findings based on the presented molecular data. As a result, previously proposed sister group relationships between Euchoreutes and Sicista, Paradipus and Cardiocraniinae as well as the monophyly of Cardiocaniinae + Dipodinae were rejected. However, the latter association is consistently supported by most morphological analyses. The basis of the obvious conflict between genes and morphology remains unclear. Suggested modifications to the taxonomy of Dipodoidea imply recognition of three families: Sminthidae, Zapodidae and Dipodidae, the latter including Cardiocraniinae, Euchoreutinae, Allactaginae and Dipodinae as subfamilies.
Statistical approaches for morphological continuous characters: a conceptual model applied to Phytoseiidae (Acari: Mesostigmata)
Authors: Marie‐Stephane Tixier
Published: December 2012

Marie‐Stephane, T. (2012). Statistical approaches for morphological continuous characters: a conceptual model applied to Phytoseiidae (Acari: Mesostigmata). —Zoologica Scripta, 42, 327–334.

Species discrimination is certainly the most current and essential taxonomic task. Despite molecular development, species continue to be delimited using morphological characters. This study provides statistical approaches to assess decision rules, using continuous morphological characters, to determine whether specimens examined belong or not to a same species. As species discrimination is usually based on no overlapping between intraspecific distributions, a general statistical approach has been developed to assess, for a character x, the relation between intraspecific overlapping and (i) the differences between the means of specimen lots corresponding to two species and (ii) the differences between the values borne by two specimens belonging to two species. Then, this conceptual approach was applied to the predatory mite family Phytoseiidae, highlighting that the minimal difference between means of two specimen lots belonging to two species should be of 10.58 μm (for setae <65 μm) and 33.99 μm (for setae >65 μm). When no specimen sets are available but only two specimens compared, the model shows that a difference of 13.24 μm (for setae <65 μm) and 31.74 μm (for setae >65 μm) would be sufficient to conclude that these specimens belong to two species. The presently proposed decision rules are assumed to improve species discrimination and to limit synonymies. Further developments will consist in applying this approach to databases containing species features in order to automatically extract the putative synonyms. Furthermore, such decision rules would also be useful to determine whether a species newly described is really new for science.
Microstructure and Mechanical Properties of Fiber Laser-Metal Active Gas Hybrid Weld of X80 Pipeline Steel
Authors: Zhenglong Lei , Caiwang Tan , Yanbin Chen , Zhongshao Sun
Published: December 2012

Fiber laser-metal active gas (MAG) hybrid welding process was explored to join X80 pipeline steel to improve the efficiency and performance of pipeline welding. During the hybrid welding process, five different positions are applied to simulate the practical pipe girth welding. The weldability is evaluated concerning the bead shape, hardness, tensile, impact properties, and microstructures of welded joints. The results reveal that the tensile strength is higher than that of the base metal and the weld has a good impact ductility and an excellent bend performance. At the same time, the difference in microstructure between the laser zone and arc zone of laser-MAG hybrid welding of X80 pipeline steel is observed. Compared with the arc zone, the laser zone has finer weld grains and a narrower heat affected zone (HAZ). The fusion zone microstructure of the arc zone mainly consists of columnar proeutectoid ferrite (PF) and fine acicular ferrite (AF), whereas that of laser zone comprises acicular ferrite, upper bainite (Bu), and granular bainite (BG), which verifies technical feasibility of hybrid welding in pipeline steel and lays a good foundation for practical application.
Flowforce in a Safety Relief Valve Under Incompressible, Compressible, and Two-Phase Flow Conditions (PVP-2011-57896)
Authors: Kourakos Vasilios , Rambaud Patrick , Buchlin Jean-Marie , Chabane Saïd
Published: December 2012

The use of relief valves is crucial for the safety of power plants. Indeed, these valves, simple but robust in their design, provide the ultimate protection when all other safety systems are inadequate. This study is focused on valve opening characteristics which can be studied through the determination of flowforces applied on the valve disk. A spring-loaded safety relief valve (SRV) (1½ in. G 3 in.) and its transparent model are tested under static conditions. The spring is removed and the forces, exerted at the valve disk for different inlet pressures and lift positions, are measured in compressible, incompressible, and two-phase flows. Results indicate that even for relatively small qualities (i.e., 5–10%), two-phase mixtures approach compressible flow behavior (especially for the higher lifts) in terms of disk force. Additionally, an inverse flowforce of air and water is noticed above a certain value of valve lift. Numerical simulations with a commercial computation fluid dynamics (CFD) code are performed in a 2D axisymmetric model of the valve for validation purposes. The main motivation of these computations is to obtain the qualitative physical explanation of this phenomenon revealing the displacement of the sonic line which occurs in air flow simulations. Finally, the importance of precise adjustment of the valve ring (in the smallest valve opening) for its optimal use is stressed by quantitative analysis using CFD simulations.
Critical Assessment of a Local Strain-Based Fatigue Crack Growth Model Using Experimental Data Available for the P355NL1 Steel
Authors: De Jesus Abílio M. P. , Correia José A. F. O.
Published: December 2012

Fatigue crack growth models based on elastic–plastic stress–strain histories at the crack tip region and strain-life damage models have been proposed in the literature. The UniGrow model fits this particular class of fatigue crack propagation models. The residual stresses developed at the crack tip play a central role in these models, since they are used to assess the actual crack driving force, taking into account mean stress and loading sequence effects. The performance of the UniGrow model is assessed based on available experimental constant amplitude crack propagation data, derived for the P355NL1 steel. Key issues in fatigue crack growth prediction using the UniGrow model are discussed; in particular, the assessment of the elementary material block size, the elastoplastic analysis used to estimate the residual stress distribution ahead of the crack tip and the adopted strain-life damage relation. The use of finite element analysis to estimate the residual stress field, in lieu of a simplified analysis based on the analytical multi-axial Neuber's approach, and the use of the Morrow's strain-life equation, resulted in fatigue crack propagation rates consistent with the experimental results available for P355NL1 steel, for several stress R-ratios. The use of the Smith–Watson–Topper (SWT) (=σmax.Δɛ/2) damage parameter, which has often been proposed in the literature, over predicts the stress R-ratio effects.
Spinoff Challenges for Computational Fluid Dynamics
Authors: Harlow Francis H.
Published: December 2012

This paper describes extensions of computational fluid dynamics (CFD) to fields of analysis lying well beyond their current realms of application. In particular, three examples are presented. The first is to the collective behavior of mobs of people interacting with sources of danger and/or opportunity to which each individual responds by actions that depend strongly on the inducement of fear and/or excitement, depending on the intrinsic susceptibilities of the person. This behavior results in both individual activities (agent-based) and collective behaviors (crowd-based stochastic) with consequences of potentially great significance. Extensions are also described for which various other emotional developments are important to the behavior of a mob. The second example is to the processes of biological evolution, in particular to the driving forces that influence the directions of species alterations through a succession of characteristics that are tested for survivability in classical Darwinian fashion. The key to the analysis lies in the newly emerging field of epigenetics, in which numerous important experimental studies are producing astonishing results leading to major challenges to the creation of computational models of the collective fluid-like dynamics of interacting biological species. The third example explores an alternative to the Big Bang theory for describing the origin of our universe. The idea is that a parent universe exists, being composed of energy, matter, and antimatter in various forms. In some region a perturbation occurs, which locally has an excess of matter over antimatter. An enormous gravitational buildup of matter and energy in the region leads to a black hole, in which there is distortion in the fourth dimension. The result then leads to an offspring entity (universe) that becomes completely detached from the parent. To apply computational fluid dynamics to the analysis of this process requires formulations that include a major component of relevant physical representations. In all three of these examples, instabilities, fluctuations, and turbulence play major roles. These arise naturally in agent-based numerical formulations (the first and second of our examples), but are much more challenging to describe in a stochastic representation (e.g., the Navier–Stokes equations). Some promising spectral analysis extensions for stochastic formulations are included in this paper.
A Parallel Universe: Contributions to the Initial Development of Computational Heat Transfer
Authors: Churchill Stuart W.
Published: December 2012

Computational heat transfer developed in parallel time-wise with computational fluid dynamics because they were both prompted by the emergence of electronic devices for computation in the middle of the twentieth century and by the subsequent rapid growth in capability and availability of those devices. The development of numerical methodologies for natural convection followed a somewhat different path because the fluid motion is generated by and intimately coupled with the thermal transport. The minihistories presented herein are representative rather than definitive because they trace the contributions of only one thread of investigators. They also differ from a review by virtue of identification of the human element, which is ordinarily excluded from archival technical accounts although it usually plays a critical role. They differ in a still another sense from the contributions of Spalding and of Harlow and their associates in that most of the advances were motivated by specific practical considerations rather than by computation itself.
A Fast Hybrid Fourier–Boltzmann Transport Equation Solver for Nongray Phonon Transport
Authors: Loy James M. , Murthy Jayathi Y. , Singh Dhruv
Published: December 2012

Nongray phonon transport solvers based on the Boltzmann transport equation (BTE) are being increasingly employed to simulate submicron thermal transport in semiconductors and dielectrics. Typical sequential solution schemes encounter numerical difficulties because of the large spread in scattering rates. For frequency bands with very low Knudsen numbers, strong coupling between other BTE bands result in slow convergence of sequential solution procedures. This is due to the explicit treatment of the scattering kernel. In this paper, we present a hybrid BTE-Fourier model which addresses this issue. By establishing a phonon group cutoff Knc, phonon bands with low Knudsen numbers are solved using a modified Fourier equation which includes a scattering term as well as corrections to account for boundary temperature slip. Phonon bands with high Knudsen numbers are solved using the BTE. A low-memory iterative solution procedure employing a block-coupled solution of the modified Fourier equations and a sequential solution of BTEs is developed. The hybrid solver is shown to produce solutions well within 1% of an all-BTE solver (using Knc = 0.1), but with far less computational effort. Speedup factors between 2 and 200 are obtained for a range of steady-state heat transfer problems. The hybrid solver enables efficient and accurate simulation of thermal transport in semiconductors and dielectrics across the range of length scales from submicron to the macroscale.
Optimization Under Uncertainty Applied to Heat Sink Design
Authors: Bodla Karthik K. , Murthy Jayathi Y. , Garimella Suresh V.
Published: December 2012

Optimization under uncertainty (OUU) is a powerful methodology used in design and optimization to produce robust, reliable designs. Such an optimization methodology, employed when the input quantities of interest are uncertain, yields output uncertainties that help the designer choose appropriate values for input parameters to produce safe designs. Apart from providing basic statistical information, such as mean and standard deviation in the output quantities, uncertainty-based optimization produces auxiliary information, such as local and global sensitivities. The designer may thus decide the input parameter(s) to which the output quantity of interest is most sensitive, and thereby design better experiments based on just the most sensitive input parameter(s). Another critical output of such a methodology is the solution to the inverse problem, i.e., finding the allowable uncertainty (range) in the input parameter(s), given an acceptable uncertainty (range) in the output quantities of interest. We apply optimization under uncertainty to the problem of heat transfer in fin heat sinks with uncertainties in geometry and operating conditions. The analysis methodology is implemented using DAKOTA, an open-source design and analysis kit. A response surface is first generated which captures the dependence of the quantity of interest on inputs. This response surface is then used to perform both deterministic and probabilistic optimization of the heat sink, and the results of the two approaches are compared.
Flash sample heating for scanning tunneling microscopy: Desorption of 1-octanethiolate self-assembled monolayers in air
Authors: Jobbins Matthew M. , Agostino Christopher J. , Michel Jolai D. , Caponigri-Guerra Guido , Nees Sean B. , Alex Kandel S.
Published: December 2012

The authors have developed a method of performing scanning tunneling microscopy experiments with a sample that can be controllably heated and quickly cooled. Temperatures in excess of 100 °C are achievable, and the same scanning area can be imaged multiple times before and after repeated heating cycles. This opens up for study any physical process or chemical reaction where the reactants, products, and/or intermediates can be kinetically trapped on a conductive surface at room temperature. As a demonstration of this approach, the authors have investigated desorption from 1-octanethiolate self-assembled monolayers on Au(111).
Ultraviolet curable branched siloxanes as low-k dielectrics for imprint lithography
Authors: Ogawa Tsuyoshi , Takei Satoshi , Grant Willson C.
Published: December 2012

A methacrylate-based, UV curable branched siloxane (MA-Si-12) was designed for use as a low-k dielectric that can be directly patterned by step and flash imprint lithography. MA-Si-12 has the properties of low viscosity (20 cP) and low vapor pressure (1.3 Torr), which make the material suitable for imprint processes based on an inkjet dispensing system. However, the mechanical strength of UV cured MA-Si-12 is too low (0.4 GPa Young's modulus by nanoindentation) for use with chemical mechanical polishing. Therefore, a methacrylate-based, UV curable cyclic siloxane (8-ring) was synthesized to be blended with the siloxane and improve the modulus. A formulation consisting of a mixture of MA-Si-12 and 8-ring (50 wt. % respectively) provides patterned structures with a modulus of 2.0 GPa. This formulation still has a viscosity (19 cP) and vapor pressure (1.3 Torr) low enough for inkjet dispensing. The UV cured resin has a dielectric constant of 2.8 at 1 MHz, low water absorption (0.7 wt. % after 24 h), and low UV cure shrinkage (5.6%). It provides high resolution, high fidelity imprint patterns. Mixing or blending of branched and cyclic siloxanes is a valuable approach to the design of imprint resist formulations with low dielectric constants.
Interleaved acquisition for cross scatter avoidance in dual cone‐beam CT
Authors: Giles William , Bowsher James , Li Hao , Yin Fang‐Fang
Published: December 2012

Purpose:

Cone‐beam x‐ray imaging with flat panel detectors is used for target localization in image guided radiation therapy. This imaging includes cone‐beam computed tomography (CBCT) and planar imaging. Use of two orthogonal x‐ray systems could reduce imaging time for CBCT, provide simultaneous orthogonal views in planar imaging, facilitate dual‐energy methods, and be useful in alleviating cone‐beam artifacts by providing two axially offset focal‐spot trajectories. However, the potential advantages of a second cone‐beam system come at the cost of cross scatter, i.e., scatter of photons originating from one tube into the noncorresponding detector. Herein, cross scatter is characterized for dual cone‐beam imaging, and a method for avoiding cross scatter is proposed and evaluated.

Methods:

A prototype dual‐source CBCT system has been developed that models the geometry of a gantry‐mounted kV imaging device used in radiation therapy. Cross scatter was characterized from 70 to 145 kVp in projections and reconstructed images using this system and three cylindrical phantoms (15, 20, and 30 cm) with a common Catphan core. A novel strategy for avoiding cross scatter in dual CBCT was developed that utilized interleaved data acquisition on each imaging chain. Interleaving, while maintaining similar angular sampling, can be achieved by either doubling the data acquisition rate or, as presented herein, halving the rotation speed.

Results:

The ratio of cross scatter to the total detected signal was found to be as high as 0.59 in a 30 cm diameter phantom. The measured scatter‐to‐primary ratio in some cases exceeded 4. In the 30 cm phantom, reconstructed contrast was reduced across all ROIs by an average of 48.7% when cross scatter was present. These cross‐scatter degradations were almost entirely avoided by the method of interleaved exposures.

Conclusions:

Cross scatter is substantial in dual cone‐beam imaging, but its effects can be largely removed by interleaved acquisition, which can be achieved at the same angular sampling rate either by doubling the data acquisition rate or halving the rotation speed.
On the coherent components of low-frequency ambient noise in the Indian Ocean
Authors: Sabra Karim G. , Fried Stephanie , Kuperman W. A. , Prior Mark
Published: December 2012

This letter demonstrates that the dominant coherent component of low-frequency (1 Hz < f < 20 Hz) ambient noise propagating between hydrophone pairs of the same hydroacoustic station, deployed in the deep sound channel of the Indian Ocean, is directional and mainly originates from Antarctica. However, the amplitude of the peak coherent noise arrivals, obtained using a 4-month-long averaging interval, was relatively low given the small hydrophones spacing hydrophones (<2 km). Hence, extracting similar coherent arrivals between two distinct hydroacoustic stations separated instead by thousands of kilometers for noise-based acoustic thermometry purposes seems unlikely, even using a year-long averaging.
Tuning the Electronic Absorption of Protein-Embedded All-
trans
-Retinal
Authors: Wang Wenjing , Nossoni Zahra , Berbasova Tetyana , Watson Camille T. , Yapici Ipek , Lee Kin Sing Stephen , Vasileiou Chrysoula , Geiger James H. , Borhan Babak
Published: December 2012

Seeing the Light

Rhodopsins respond to a range of electromagnetic radiation—allowing visual perception over a broad wavelength range in animals and facilitating light-driven ion transport and phototaxis in microorganisms. All rhodopsins contain an embedded retinal chromophore in which absorbance is tuned by the protein environment. To gain insight into how the protein tunes absorbance,

Wang
et al.

(p.
1340
; see the Perspective by

Sakmar

) turned to a smaller soluble protein, cellular retinol binding protein II. They engineered the protein to fully encapsulate and covalently bind all-
trans
-retinal as a Schiff base. From this starting point, they used rational mutagenesis to vary the absorption maximum over a range of more than 200 nanometers by altering the electrostatic environment of the protein-binding pocket.
Drought in Africa Caused Delayed Arrival of European Songbirds
Authors: Tøttrup A. P. , Klaassen R. H. G. , Kristensen M. W. , Strandberg R. , Vardanis Y. , Lindström Å. , Rahbek C. , Alerstam T. , Thorup K.
Published: December 2012

A severe drought in the Horn of Africa delayed the spring arrival in Europe of two migratory species.
Taming of Fluoroform: Direct Nucleophilic Trifluoromethylation of Si, B, S, and C Centers
Authors: Prakash G. K. Surya , Jog Parag V. , Batamack Patrice T. D. , Olah George A.
Published: December 2012

CF
3
from Fluoroform

Fluoroform (CF
3
H) is a by-product from the manufacture of fluorocarbon-based materials used, for example, in nonstick coatings and refrigerants. Fluoroform's potency as a greenhouse gas is a growing concern as supplies continue to accumulate. In this context,

Prakash
et al.

(p.
1324
; see the Perspective by

Haufe

) show that fluoroform can be used to transfer CF
3
to silicon, sulfur, and carbon centers in the development of CF
3
-bearing pharmaceutical and agrochemical structures.
Mapping Local Charge Recombination Heterogeneity by Multidimensional Nanospectroscopic Imaging
Authors: Bao Wei , Melli M. , Caselli N. , Riboli F. , Wiersma D. S. , Staffaroni M. , Choo H. , Ogletree D. F. , Aloni S. , Bokor J. , Cabrini S. , Intonti F. , Salmeron M. B. , Yablonovitch E. , Schuck P. J. , Weber-Bargioni A.
Published: December 2012

Mind the Gap

Near-field microscopy has benefited from subwavelength near-field plasmonic probes that make use of the field-concentrating properties of gaps. These probes achieve maximum enhancement only in the tip-substrate gap mode, which can yield large near-field signals, but only for a metallic substrate and for very small tip-substrate gap distances.

Bao
et al.

(p.
1317
) designed a probe that unites broadband field enhancement and confinement with bidirectional coupling between far-field and near-field electromagnetic energy. Their tips primarily rely on the internal gap modes of the tip itself, thereby enabling it to image nonmetallic samples.
Redder Than Red
Authors: Sakmar Thomas P.
Published: December 2012

Molecular engineering of a retinol binding protein defies prediction.
Atomic Layer Electrodeposition
Authors: Switzer Jay A.
Published: December 2012

An electrochemical process provides a cheap and simple route to layer-by-layer growth of metal films.
Inflammation to Rebuild a Brain
Authors: Stella Nephi
Published: December 2012

Inflammation in the zebrafish brain stimulates neurogenesis and tissue regeneration.
Final Report on Stapel Also Blames Field As a Whole
Authors: Enserink Martin
Published: December 2012

The blame for social psychologist Diederik Stapel's "blatant" fraud goes far beyond him and the three Dutch universities where he worked, a joint report reveals.
Proposed H5N1 Research Reviews Raise Concerns
Authors: Malakoff David
Published: December 2012

Researchers are giving a mixed reception to a draft U.S. government plan to do more stringent funding reviews of certain kinds of H5N1 avian influenza research—and perhaps even keep some studies secret.
River Basin Management Plan Secures Water for the Environment
Authors: Finkel Elizabeth , Normile Dennis
Published: December 2012

A new plan to balance societal and ecological needs is under way at Australia's Murray-Darling basin.
Growing Pains in the Desert
Authors: Mervis Jeffrey
Published: December 2012

A 3-year-old graduate research university in Saudi Arabia is finding that it will take more than money to create a global research powerhouse.
LIFE SCIENCE TECHNOLOGIES: The New Technologies of Chromatin Analysis
Authors: Dove Alan
Published: December 2012

Scientists have been culturing mammalian cells in flat petri dishes for decades, but a new generation of tools and techniques is now letting them grow three-dimensional cultures that more closely mimic the biology of real tissues.
Host Responses to Persistent Mycobacterium avium Subspecies
paratuberculosis
Infection in Surgically Isolated Bovine Ileal Segments
Authors: Charavaryamath Chandrashekhar , Gonzalez-Cano Patricia , Fries Patrick , Gomis Susantha , Doig Kimberley , Scruten Erin , Potter Andrew , Napper Scott , Griebel Philip J.
Published: December 2012

A lack of appropriate disease models has limited our understanding of the pathogenesis of persistent enteric infections with
Mycobacterium avium
subsp.
paratuberculosis
. A model was developed for the controlled delivery of a defined dose of
M. avium
subsp.
paratuberculosis
to surgically isolated ileal segments in newborn calves. The stable intestinal segments enabled the characterization of host responses to persistent
M. avium
subsp.
paratuberculosis
infections after a 9-month period, including an analysis of local mucosal immune responses relative to an adjacent uninfected intestinal compartment.
M. avium
subsp.
paratuberculosis
remained localized at the initial site of intestinal infection and was not detected by PCR in the mesenteric lymph node.
M. avium
subsp.
paratuberculosis
-specific T cell proliferative responses included both CD4 and γδ T cell receptor (γδTcR) T cell responses in the draining mesenteric lymph node. The levels of CD8
+
and γδTcR
+
T cells increased significantly (
P
< 0.05) in the lamina propria, and
M. avium
subsp.
paratuberculosis
-specific tumor necrosis factor alpha (TNF-α) and gamma interferon secretion by lamina propria leukocytes was also significantly (
P
< 0.05) increased. There was a significant (
P
< 0.05) accumulation of macrophages and dendritic cells (DCs) in the lamina propria, but the expression of mucosal toll-like receptors 1 through 10 was not significantly changed by
M. avium
subsp.
paratuberculosis
infection. In conclusion, surgically isolated ileal segments provided a model system for the establishment of a persistent and localized enteric
M. avium
subsp.
paratuberculosis
infection in cattle and facilitated the analysis of
M. avium
subsp.
paratuberculosis
-specific changes in mucosal leukocyte phenotype and function. The accumulation of DC subpopulations in the lamina propria suggests that further investigation of mucosal DCs may provide insight into host responses to
M. avium
subsp.
paratuberculosis
infection and improve vaccine strategies to prevent
M. avium
subsp.
paratuberculosis
infection.
Impaired Toll-Like Receptor 3-Mediated Immune Responses from Macrophages of Patients Chronically Infected with Hepatitis C Virus
Authors: Qian Feng , Bolen Christopher R. , Jing Chunxia , Wang Xiaomei , Zheng Wei , Zhao Hongyu , Fikrig Erol , Bruce R. Douglas , Kleinstein Steven H. , Montgomery Ruth R.
Published: December 2012

Hepatitis C virus (HCV) is the most common chronic blood-borne infection in the United States, with the majority of patients becoming chronically infected and a subset (20%) progressing to cirrhosis and hepatocellular carcinoma. Individual variations in immune responses may help define successful resistance to infection with HCV. We have compared the immune response in primary macrophages from patients who have spontaneously cleared HCV (viral load negative [VL−],n= 37) to that of primary macrophages from HCV genotype 1 chronically infected (VL+) subjects (n= 32) and found that macrophages from VL− subjects have an elevated baseline expression of Toll-like receptor 3 (TLR3). Macrophages from HCV patients were stimulatedex vivothrough the TLR3 pathway and assessed using gene expression arrays and pathway analysis. We found elevated TLR3 response genes and pathway activity from VL− subjects. Furthermore, macrophages from VL− subjects showed higher production of beta interferon (IFN-β) and related IFN response genes by quantitative PCR (Q-PCR) and increased phosphorylation of STAT-1 by immunoblotting. Analysis of polymorphisms in TLR3 revealed a significant association of intronic TLR3 polymorphism (rs13126816) with the clearance of HCV and the expression of TLR3. Of note, peripheral blood mononuclear cells (PBMCs) from the same donors showed opposite changes in gene expression, suggesting ongoing inflammatory responses in PBMCs from VL+ HCV patients. Our results suggest that an elevated innate immune response enhances HCV clearance mechanisms and may offer a potential therapeutic approach to increase viral clearance.
Legionella micdadei Brain Abscess
Authors: Charles Marthe , Johnson Edward , Macyk-Davey Andrea , Henry Monica , Nilsson Jan-Erik , Miedzinski Lil , Zahariadis George
Published: December 2012

We describe an immunocompromised patient who developed a large frontal brain abscess caused by
Legionella micdadei
. This is, to our knowledge, a rare case of culture-proven
Legionella
central nervous system infection.