bluuebunny/crossref_metadata_2025 huggingface dataset:
1. What is science?
Authors: Okasha Samir
Published: September 2013

‘What is science?’ asks what it is that makes something a science and shows that one of the key problems in philosophy of science is to understand how techniques such as experimentation, observation, and theory-construction have enabled scientists to unravel so many of nature's secrets. The origins of modern science lie in the scientific revolution between 1500 and 1750 with the work of Nicolas Copernicus, Johannes Kepler, Galileo Galilei, and Isaac Newton. In biology, the breakthroughs of Charles Darwin and James Watson and Francis Crick are outlined. Philosophy of science is then described and the difference between science and pseudo-science explained using Karl Popper's views of Marx and Freud as examples.
2. Scientific reasoning
Authors: Okasha Samir
Published: September 2013

‘Scientific reasoning’ asks how much confidence should be placed in the inferences scientists make. What exactly is the nature of scientific reasoning? The important distinction between deductive and inductive patterns of reasoning is explained before Hume's problem is outlined. Science relies on induction and Hume's argument seems to show that induction cannot be rationally justified. Darwin's theory of evolution and Einstein's work on Brownian motion are provided as examples of inference to the best explanation. Finally, the interest of philosophers of science in probability and induction is shown and the frequency, subjective, and logical interpretations of probability are described.
5. Scientific change and scientific revolutions
Authors: Okasha Samir
Published: September 2013

‘Scientific change and scientific revolutions’ discusses the work of Thomas Kuhn who, in 1963, published The Structure of Scientific Revolutions, the most influential work of philosophy of science in the last fifty years. Firstly, the logical positivist philosophy of science and structure of scientific revolutions are explained. Kuhn's doctrine of paradigm shifts, of incommensurability, and of the theory-ladenness of data are then examined. He argued that his aim was not to cast doubt on the rationality of science, but rather to offer a more realistic, historically accurate picture of how science actually develops. Kuhn's work also played a role in the rise of cultural relativism in the humanities and social sciences.
1. The context of American elections and political parties
Authors: Maisel L. Sandy
Published: September 2013

‘The context of American elections and political parties’ explains the framework under which elections are run in the US. This is laid out in the Constitution which outlines the basic tenets of democracy in America. The most important aspects of that framework are the separation of powers, with a single executive separate from and elected separately from the legislature, and the federal system with residual powers left to the states. The electoral college system, unique to the US, is a result of the initial decisions made at the time of the framing of the Constitution.
2. The Presidency Finds Its Place
Authors: Jones Charles O.
Published: September 2013

An important issue with respect to setting up the new system of government was where to put the presidency. The capital city, it was decided, would be central between North and South. Congress and the presidency would be in the same city, separated by a swamp. ‘The Presidency Finds Its Place’ looks at how the location was decided and evolved over time. Presidential candidates were not required to go through Congress to win. They were to be independently elected. Three governing centers were established in the new capital: one each for the Congress, the presidency, and the courts at Judiciary Square. The President's House was designed to be both a residence and a workplace.
Trust: A Very Short Introduction
Authors: Hawley Katherine
Published: September 2013

Trust: A Very Short Introduction explores key ideas about trust and distrust. Trust is indispensable, yet it can be damaging. Without trusting others, we cannot function in society, or even stay alive for very long, but being overly-trustful can also be a bad strategy. Trust is pragmatic, but it also has a moral dimension: trustworthiness is a virtue, and well-placed trust benefits us all. Why do we value trust? Why do we want to be trusted? Trust is important both in the personal and public spheres, including in family and relationships as well as politics and society.
BSeQC: quality control of bisulfite sequencing experiments
Authors: Lin Xueqiu , Sun Deqiang , Rodriguez Benjamin , Zhao Qian , Sun Hanfei , Zhang Yong , Li Wei
Published: September 2013

Motivation: Bisulfite sequencing (BS-seq) has emerged as the gold standard to study genome-wide DNA methylation at single-nucleotide resolution. Quality control (QC) is a critical step in the analysis pipeline to ensure that BS-seq data are of high quality and suitable for subsequent analysis. Although several QC tools are available for next-generation sequencing data, most of them were not designed to handle QC issues specific to BS-seq protocols. Therefore, there is a strong need for a dedicated QC tool to evaluate and remove potential technical biases in BS-seq experiments.

Results: We developed a package named BSeQC to comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases that may result in inaccurate methylation estimation. BSeQC takes standard SAM/BAM files as input and generates bias-free SAM/BAM files for downstream analysis. Evaluation based on real BS-seq data indicates that the use of the bias-free SAM/BAM file substantially improves the quantification of methylation level.

Availability and implementation: BSeQC is freely available at: http://code.google.com/p/bseqc/.

Contact:  wl1@bcm.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells
Authors: Fisher Ciarán P. , Plant Nicholas J. , Moore J. Bernadette , Kierzek Andrzej M.
Published: September 2013

Motivation: Dynamic simulation of genome-scale molecular interaction networks will enable the mechanistic prediction of genotype–phenotype relationships. Despite advances in quantitative biology, full parameterization of whole-cell models is not yet possible. Simulation methods capable of using available qualitative data are required to develop dynamic whole-cell models through an iterative process of modelling and experimental validation.

Results: We formulate quasi-steady state Petri nets (QSSPN), a novel method integrating Petri nets and constraint-based analysis to predict the feasibility of qualitative dynamic behaviours in qualitative models of gene regulation, signalling and whole-cell metabolism. We present the first dynamic simulations including regulatory mechanisms and a genome-scale metabolic network in human cell, using bile acid homeostasis in human hepatocytes as a case study. QSSPN simulations reproduce experimentally determined qualitative dynamic behaviours and permit mechanistic analysis of genotype–phenotype relationships.

Availability and implementation: The model and simulation software implemented in C++ are available in supplementary material and at http://sysbio3.fhms.surrey.ac.uk/qsspn/.

Contact:  a.kierzek@surrey.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Interaction rules underlying group decisions in homing pigeons
Authors: Pettit Benjamin , Perna Andrea , Biro Dora , Sumpter David J. T.
Published: September 2013

Travelling in groups gives animals opportunities to share route information by following cues from each other's movement. The outcome of group navigation will depend on how individuals respond to each other within a flock, school, swarm or herd. Despite the abundance of modelling studies, only recently have researchers developed techniques to determine the interaction rules among real animals. Here, we use high-resolution GPS (global positioning system) tracking to study these interactions in pairs of pigeons flying home from a familiar site. Momentary changes in velocity indicate alignment with the neighbour's direction, as well as attraction or avoidance depending on distance. Responses were stronger when the neighbour was in front. From the flocking behaviour, we develop a model to predict features of group navigation. Specifically, we show that the interactions between pigeons stabilize a side-by-side configuration, promoting bidirectional information transfer and reducing the risk of separation. However, if one bird gets in front it will lead directional choices. Our model further predicts, and observations confirm, that a faster bird (as measured from solo flights) will fly slightly in front and thus dominate the choice of homing route. Our results explain how group decisions emerge from individual differences in homing flight behaviour.
An encapsulated drug delivery system for recalcitrant urinary tract infection
Authors: Labbaf Sheyda , Horsley Harry , Chang Ming-Wei , Stride Eleanor , Malone-Lee James , Edirisinghe Mohan , Rohn Jennifer L.
Published: September 2013

One of the hallmarks of urinary tract infection, a serious global disease, is its tendency to recur. Uropathogenic bacteria can invade cells lining the bladder, where they form longer-term intracellular reservoirs shielded from antibiotics, re-emerging at a later date to initiate flare-ups. In these cases, only lengthy systemic antibiotic treatment can eradicate all the reservoirs. Yet, long courses of antibiotics are not ideal, as they can lead to side effects and an increase in antibiotic resistance. Moreover, most antibiotics lose some potency by the time they reach the bladder, and many cannot permeate cells, so they cannot access intracellular reservoirs. Here, using coaxial electrohydrodynamic forming, we developed novel core–shell capsules containing antibiotics as a prototype for a future product that could be infused directly into the bladder. Gentamicin was encapsulated in a polymeric carrier (polymethylsilsesquioxane) and these capsules killed
Enterococcus faecalis
, a common chronic uropathogen,
in vitro
in a dose-responsive, slow-release manner. Capsules containing a fluorescent tracer dye in place of gentamicin penetrated human bladder cells and released their dye cargo with no apparent toxicity, confirming their ability to successfully permeate cells. These results suggest that such antibiotic capsules could prove useful in the treatment of recalcitrant UTI.
Flavobacterium tructae sp. nov. and Flavobacterium piscis sp. nov., isolated from farmed rainbow trout (Oncorhynchus mykiss)
Authors: Zamora L. , Vela A. I. , Sánchez-Porro C. , Palacios M. A. , Moore E. R. B. , Domínguez L. , Ventosa A. , Fernández-Garayzábal J. F.
Published: September 2013

Four Gram-staining-negative, catalase- and oxidase-positive, pale-orange pigmented bacterial strains (435-08T, 47B-3-09, 412R-09T and 60B-3-09) were isolated from diseased rainbow trout. Analysis of their 16S rRNA gene sequences suggested their adscription to the genus

Flavobacterium

. Strains formed two phylogenetic groups represented by strains 435-08T and 47B-3-09 (group A), and strains 412R-09T and 60B-3-09 (group B) displaying 16S rRNA sequence similarities greater than 99.8–99.9 % within their respective groups. Strain 435-08T exhibited the highest levels of similarity with

Flavobacterium aquidurense

WB-1.1.56T (98.6 % sequence similarity) and strain 412R-09T with

Flavobacterium frigidimaris

KUC-1T and

Flavobacterium aquidurense

WB-1.1.56T (98.9 % and 98.6 % sequence similarity, respectively). DNA–DNA hybridization studies showed low levels of relatedness between strain 435-08T and strain 412R-09T and between both strains and the most closely related species of the genus

Flavobacterium

. The genomic DNA G+C contents of strains 435-08T and 412R-09T were 36.2 and 34.3 mol%, respectively. The predominant respiratory quinone of both strains was MK-6 and the major fatty acids were iso-C15 : 0, C16 : 1ω7c and C15 : 0. The two groups of strains could be distinguished from each other and from related species of the genus

Flavobacterium

by a number of phenotypic properties. Phylogenetic, genotypic and phenotypic evidence indicated that strains of groups A and B represent two novel species of the genus

Flavobacterium

, for which the names Flavobacterium tructae sp. nov. (type strain 435-08T = CECT 7791T = CCUG 60100T) and Flavobacterium piscis sp. nov. (type strain 412R-09T = CECT 7911T = CCUG 60099T) are proposed.
Nonlabens
antarcticus sp. nov., a psychrophilic bacterium isolated from glacier ice, and emended descriptions of Nonlabens marinus Park et al. 2012 and Nonlabens agnitus Yi and Chun 2012
Authors: Kwon Yong Min , Yang Sung-Hyun , Kwon Kae Kyoung , Kim Sang-Jin
Published: September 2013

A Gram-negative, proteorhodopsin-containing, orange pigmented, rod-shaped and strictly aerobic bacterium, designated strain AKS622T, was isolated from a glacier core collected from the coast of King George Island, Antarctica. 16S rRNA gene sequence analysis revealed that strain AKS622T was affiliated to the genus

Nonlabens

of the family

Flavobacteriaceae

and showed highest similarity to

Nonlabens marinus

S1-08T (97.9 %). The level of DNA–DNA relatedness between strain AKS622T and

N. marinus

S1-08T was 46 %. Optimal growth of strain AKS622T was observed at pH 7.0, at 15 °C and with 2.0 % NaCl. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0, iso-C16 : 0 3-OH, C17 : 0 2-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content was 37.9 mol%. The major respiratory quinone was MK-6. Phosphatidylethanolamine, four unidentified glycolipids, three unidentified aminolipids and one unidentified lipid were detected as major polar lipids. On the basis of the data from this polyphasic taxonomic study, it was concluded that strain AKS622T represents a novel species within the genus

Nonlabens

, for which the name Nonlabens antarcticus sp. nov. is proposed. The type strain is AKS622T ( = KCCM 43019T = JCM 14068T). Emended descriptions of

N. marinus

Park et al. 2012 and

Nonlabens agnitus

Yi and Chun 2012 are given.
H3.3 actively marks enhancers and primes gene transcription via opening higher-ordered chromatin
Authors: Chen Ping , Zhao Jicheng , Wang Yan , Wang Min , Long Haizhen , Liang Dan , Huang Li , Wen Zengqi , Li Wei , Li Xia , Feng Hongli , Zhao Haiyong , Zhu Ping , Li Ming , Wang Qian-fei , Li Guohong
Published: September 2013

The histone variants H3.3 and H2A.Z have recently emerged as two of the most important features in transcriptional regulation, the molecular mechanism of which still remains poorly understood. In this study, we investigated the regulation of H3.3 and H2A.Z on chromatin dynamics during transcriptional activation. Our in vitro biophysical and biochemical investigation showed that H2A.Z promoted chromatin compaction and repressed transcriptional activity. Surprisingly, with only four to five amino acid differences from the canonical H3, H3.3 greatly impaired higher-ordered chromatin folding and promoted gene activation, although it has no significant effect on the stability of mononucleosomes. We further demonstrated that H3.3 actively marks enhancers and determines the transcriptional potential of retinoid acid (RA)-regulated genes via creating an open chromatin signature that enables the binding of RAR/RXR. Additionally, the H3.3-dependent recruitment of H2A.Z on promoter regions resulted in compaction of chromatin to poise transcription, while RA induction results in the incorporation of H3.3 on promoter regions to activate transcription via counteracting H2A.Z-mediated chromatin compaction. Our results provide key insights into the mechanism of how histone variants H3.3 and H2A.Z function together to regulate gene transcription via the modulation of chromatin dynamics over the enhancer and promoter regions.
Random replication of the inactive X chromosome
Authors: Koren Amnon , McCarroll Steven A.
Published: September 2013

In eukaryotic cells, genomic DNA replicates in a defined temporal order. The inactive X chromosome (Xi), the most extensive instance of facultative heterochromatin in mammals, replicates later than the active X chromosome (Xa), but the replication dynamics of inactive chromatin are not known. By profiling human DNA replication in an allele-specific, chromosomally phased manner, we determined for the first time the replication timing along the active and inactive chromosomes (Xa and Xi) separately. Replication of the Xi was different from that of the Xa, varied among individuals, and resembled a random, unstructured process. The Xi replicated rapidly and at a time largely separable from that of the euchromatic genome. Late-replicating, transcriptionally inactive regions on the autosomes also replicated in an unstructured manner, similar to the Xi. We conclude that DNA replication follows two strategies: slow, ordered replication associated with transcriptional activity, and rapid, random replication of silent chromatin. The two strategies coexist in the same cell, yet are segregated in space and time.
The BRASSINOSTEROID INSENSITIVE1–LIKE3 Signalosome Complex Regulates Arabidopsis Root Development
Authors: Fàbregas Norma , Li Na , Boeren Sjef , Nash Tara E. , Goshe Michael B. , Clouse Steven D. , de Vries Sacco , Caño-Delgado Ana I.
Published: September 2013

Brassinosteroid (BR) hormones are primarily perceived at the cell surface by the leucine-rich repeat receptor-like kinase BRASSINOSTEROID INSENSITIVE1 (BRI1). In Arabidopsis thaliana, BRI1 has two close homologs, BRI1-LIKE1 (BRL1) and BRL3, respectively, which are expressed in the vascular tissues and regulate shoot vascular development. Here, we identify novel components of the BRL3 receptor complex in planta by immunoprecipitation and mass spectrometry analysis. Whereas BRI1 ASSOCIATED KINASE1 (BAK1) and several other known BRI1 interactors coimmunoprecipitated with BRL3, no evidence was found of a direct interaction between BRI1 and BRL3. In addition, we confirmed that BAK1 interacts with the BRL1 receptor by coimmunoprecipitation and fluorescence microscopy analysis. Importantly, genetic analysis of brl1 brl3 bak1-3 triple mutants revealed that BAK1, BRL1, and BRL3 signaling modulate root growth and development by contributing to the cellular activities of provascular and quiescent center cells. This provides functional relevance to the observed protein–protein interactions of the BRL3 signalosome. Overall, our study demonstrates that cell-specific BR receptor complexes can be assembled to perform different cellular activities during plant root growth, while highlighting that immunoprecipitation of leucine-rich repeat receptor kinases in plants is a powerful approach for unveiling signaling mechanisms with cellular resolution in plant development.
An Arabidopsis Soil-Salinity–Tolerance Mutation Confers Ethylene-Mediated Enhancement of Sodium/Potassium Homeostasis
Authors: Jiang Caifu , Belfield Eric J. , Cao Yi , Smith J. Andrew C. , Harberd Nicholas P.
Published: September 2013

High soil Na concentrations damage plants by increasing cellular Na accumulation and K loss. Excess soil Na stimulates ethylene-induced soil-salinity tolerance, the mechanism of which we here define via characterization of an Arabidopsis thaliana mutant displaying transpiration-dependent soil-salinity tolerance. This phenotype is conferred by a loss-of-function allele of ETHYLENE OVERPRODUCER1 (ETO1; mutant alleles of which cause increased production of ethylene). We show that lack of ETO1 function confers soil-salinity tolerance through improved shoot Na/K homeostasis, effected via the ETHYLENE RESISTANT1–CONSTITUTIVE TRIPLE RESPONSE1 ethylene signaling pathway. Under transpiring conditions, lack of ETO1 function reduces root Na influx and both stelar and xylem sap Na concentrations, thereby restricting root-to-shoot delivery of Na. These effects are associated with increased accumulation of RESPIRATORY BURST OXIDASE HOMOLOG F (RBOHF)–dependent reactive oxygen species in the root stele. Additionally, lack of ETO1 function leads to significant enhancement of tissue K status by an RBOHF-independent mechanism associated with elevated HIGH-AFFINITY K+ TRANSPORTER5 transcript levels. We conclude that ethylene promotes soil-salinity tolerance via improved Na/K homeostasis mediated by RBOHF-dependent regulation of Na accumulation and RBOHF-independent regulation of K accumulation.
Mental health recovery and voting: why being treated as a citizen matters and how we can do it
Authors: Lawn S. , McMillan J. , Comley Z. , Smith A. , Brayley J.
Published: September 2013

Accessible summary

It helps people with mental illnesses to recover if they are not deprived of their rights of citizenship. The right to vote is an important marker of citizenship.

Ensuring citizenship through the right to vote is especially important when someone is committed under mental health legislation, yet it is unclear how and whether this occurs in practice.

This paper discusses what occurs for this population in Australia and overseas and reviews the role of capacity and supported decision making in the context of the right to vote.

Solutions are offered for how mental health practice can protect the interest that Australians with mental illnesses have in voting.

A central feature of recovery‐based practice for people with mental illness is that they are able to exercise rights and experience membership of a community. This notion of citizenship is especially important when someone has had rights removed after being committed under mental health legislation. The right to vote is a central marker of citizenship. Supporting a person's right to vote is important for recovery‐based practice. In this paper, we review the issue of voting for people who have been committed under mental health legislation, why it matters for recovery, and what occurs from the Australian and international perspective. We briefly review the concepts of capacity and supported decision making in the context of the right to vote. We also consider the usefulness of the American ‘Doe Standard’, which has been used with the Competency Assessment Tool (CAT‐V), to determine capacity to vote. Some solutions are offered that would protect the interest that Australians with mental illnesses have in voting.
Numerical Investigation of the Unsteady Interaction Within a Close-Coupled Centrifugal Compressor Used in an Aero Engine
Authors: Wilkosz Benjamin , Zimmermann Markus , Schwarz Philipp , Jeschke Peter , Smythe Caitlin
Published: September 2013

The present work forms part of a research project of the Institute of Jet Propulsion and Turbomachinery at the RWTH Aachen University in collaboration with GE Aviation. The subject is the detailed numerical analysis of the unsteady flow field, focusing on the interaction between the impeller and the passage diffuser of a close-coupled transonic centrifugal compressor used in an aero engine. The centrifugal compressor investigated is characterized by a close-coupled impeller and passage diffuser with a radial gap of only 3.6%. The close coupling tends to provide a high aerodynamic efficiency but simultaneously cause a high unsteady interaction between the impeller and the diffuser. These unsteady effects can have a significant impact on the performance of both components and present a challenge to state-of-the-art numerical methods. With increasing compressor efficiency, the more important it is to have an understanding of the detailed unsteady flow physics. Experimental data was obtained from a state-of-the art centrifugal compressor test rig located at the Institute of Jet Propulsion. Steady and unsteady pressure measurements within the impeller and diffuser are used to gain detailed information on the temporal, time-averaged, and spectral pressure distributions within the stage to validate the CFD. The work presented here shows the unsteady phenomena caused by the interaction and the location and propagation of these phenomena within the centrifugal stage. Within the impeller, the exducer is in first order excited by the blade passing frequency (BPF) of the diffuser, whereas in the diffuser both the BPF and the passage passing frequency (PPF), are present up until the end of the pipe-diffuser. Significant effects on the integral component performance could only be identified for the impeller. Special focus is paid to evaluate the diffuser upstream pressure field, since this is the major source of unsteadiness within the impeller. The performance of the rotor decreases due to the unsteady interaction. This effect is traced back to the unsteady tip-clearance flow, in which the time-averaged mass transport decreases, whereas the specific entropy production increases in a nonlinear way. Within the diffuser, local effects counteracting with respect to the integral performance are found. In front of the throat, there is less decay in the total pressure as a result of tangentially expanding pressure waves. Within the passage a decrease in flow uniformity in the unsteady flow is identified as the reason for the lower diffusion up until the throat and higher losses within the downstream diffuser passage.
Nonlinear Time and Frequency Domain Methods for Multirow Aeromechanical Analysis
Authors: Rahmati M. T. , He L. , Wang D. X. , Li Y. S. , Wells R. G. , Krishnababu S. K.
Published: September 2013

An unsteady Navier–Stokes solution system for aeromechanical analysis of multiple blade row configurations is presented. A distinctive feature of the solver is that unified numerical methods and boundary condition treatments are consistently used for both a nonlinear time-domain solution mode and a frequency-domain one. This not only enables a wider range of physical aeromechanical problems to be tackled, but also provides a consistent basis for validating different computational models, identifying and understanding their relative merits and adequate working ranges. An emphasis of the present work is on a highly efficient frequency-domain method for multirow aeromechanical analysis. With a new interface treatment, propagations and reflections of pressure waves between adjacent blade rows are modeled within a domain consisting of only a single passage in each blade row. The computational model and methods are firstly described. Then, extensive validations of the frequency-domain method against both experimental data and the nonlinear time-domain solutions are described. Finally, the computational analysis and demonstration of the intrarow reflection effects on the rotor aerodynamic damping are presented.
On the Design of a Mechanically Programmable Underactuated Anthropomorphic Prosthetic Gripper
Authors: Baril Mathieu , Laliberté Thierry , Gosselin Clément , Routhier François
Published: September 2013

This paper introduces a novel underactuated anthropomorphic gripper for prosthetic applications. In order to extend the grasping capabilities of underactuated prosthetic grippers and improve the force transmission ratio, a mechanical lever is mounted inside the palm that allows a proper distribution of the forces and provides mechanical advantage. A static model is developed and the possibilities offered by the lever transmission are investigated. Also, a compact mechanism is introduced to synchronize the motion of the four fingers. Additionally, a mechanical selector is designed that functions as a means of mechanically programming the motion of the fingers by selectively blocking their closing motion. Finally, a prototype, including all the above features, is described and experimental validation is briefly reported.
Stable Nanofluids for Convective Heat Transfer
Applications
Authors: Chiney Abhinandan , Ganvir Vivek , Rai Beena , Pradip
Published: September 2013

Nanofluids are stable dispersions of ultrafine or nanoscale metallic, metal oxide, ceramic particles in a given base fluid. It is reported that nanofluids register an extraordinarily high level of thermal conductivity, and thus possess immense potential in improvement of heat transfer and energy efficiency of several industrial applications including vehicular cooling in transportation, nuclear reactors, and microelectronics. The key issues with nanofluids are: (i) a robust, cost-effective and scalable method to produce nanofluids to industrial scale has not yet been developed, (ii) stability in industrial applications is not yet established, and (iii) meaningful data in flow based heat transfer process do not exist. The present work attempts to address all these three issues. We have developed an in-situ technique for preparation of stable nanofluids by wet-milling of the metal oxide powder in the base fluid, and in the presence of a suitable dispersant. The nanofluids thus produced are tested for heat transfer efficiency under flow conditions in double pipe heat exchangers. Alumina nanofluids have been found to show enhancements of around 10–60% for various base fluids flown under different flow conditions. Thermal enhancements have been found to depend on the flow-rate, particle concentration, type of base fluid, and material of the thermal contact surface of the heat exchanger. The nanofluids thus obtained exhibit sustained stability (>30 months) and their stability remains unaltered for several heating-cooling cycles.
Kinetogami: A Reconfigurable, Combinatorial, and Printable Sheet Folding
Authors: Gao Wei , Ramani Karthik , Cipra Raymond J. , Siegmund Thomas
Published: September 2013

As an ancient paper craft originating from Japan, origami has been naturally embedded and contextualized in a variety of applications in the fields of mathematics, engineering, food packaging, and biological design. The computational and manufacturing capabilities today urge us to develop significantly new forms of folding as well as different materials for folding. In this paper, by allowing line cuts with crease patterns and creating folded hinges across basic structural units (BSU), typically not done in origami, we achieve a new multiprimitive folding framework such as using tetrahedral, cuboidal, prismatic, and pyramidal components, called “Kinetogami.” “Kinetogami” enables one to fold up closed-loop(s) polyhedral mechanisms (linkages) with multi-degree-of-freedom and self-deployable characteristics in a single build. This paper discusses a set of mathematical and design theories to enable design of 3D structures and mechanisms all folded from preplanned printed sheet materials. We present prototypical exploration of folding polyhedral mechanisms in a hierarchical manner as well as their transformations through reconfiguration that reorients the material and structure. The explicit 2D fabrication layout and construction rules are visually parameterized for geometric properties to ensure a continuous folding motion free of intersection. As a demonstration artifact, a multimaterial sheet is 3D printed with elastomeric flexure hinges connecting the rigid plastic facets.
A Thermodynamic Consistent Model for Coupled Strain-Gradient Plasticity With Temperature
Authors: Faghihi Danial , Voyiadjis George Z.
Published: September 2013

The mechanical responses of small volume metallic compounds are addressed in this work through developing a nonlocal continuum theory. In this regard, a thermodynamic-based higher-order strain-gradient plasticity framework for coupled thermoviscoplasticity modeling is presented. The concept of thermal activation energy and the dislocations interaction mechanisms are taken into consideration to describe the choice of thermodynamic potentials such as Helmholtz free energy and rate of dissipation. The theory is developed based on the decomposition of the thermodynamic conjugate forces into energetic and dissipative counterparts, which provides the constitutive equations to have both energetic and dissipative gradient length scales. The derived constitutive model is calibrated against the experimental data of bulge test conducted on thin films.
A New Modeling Approach to Forecast Building Energy Demands During Extreme Heat Events in Complex Cities
Authors: Gutiérrez Estatio , González Jorge E. , Bornstein Robert , Arend Mark , Martilli Alberto
Published: September 2013

The thermal response of a large and complex city including the energy production aspects of it are explored using urbanized atmospheric mesoscale modeling. The Weather Research and Forecasting (WRF) Mesocale model is coupled to a multilayer urban canopy model that considers thermal and mechanical effects of the urban environment including a building scale energy model to account for anthropogenic heat contributions due to indoor–outdoor temperature differences. This new urban parameterization is used to evaluate the evolution and the resulting urban heat island (UHI) formation associated to a 3-day heat wave in New York City (NYC) during the summer of 2010. High-resolution (250 m) urban canopy parameters (UCPs) from the National Urban Database were employed to initialize the multilayer urban parameterization. The precision of the numerical simulations is evaluated using a range of observations. Data from a dense network of surface weather stations, wind profilers, and Lidar measurements are compared to model outputs over Manhattan and its surroundings during the 3-days event. The thermal and drag effects of buildings represented in the multilayer urban canopy model improves simulations over urban regions giving better estimates of the 2 m surface air temperature and 10 m wind speed. An accurate representation of the nocturnal urban heat island registered over NYC in the event was obtained from the improved model. The accuracy of the simulation is further assessed against more simplified urban parameterizations models with positive results with new approach. Results are further used to quantify the energy consumption of the buildings during the heat wave, and to explore alternatives to mitigate the intensity of the UHI during the extreme event.
Dynamic Modeling of a Solar Reactor for Zinc Oxide Thermal Dissociation and Experimental Validation Using IR Thermography
Authors: Villasmil W. , Meier A. , Steinfeld A.
Published: September 2013

A dynamic numerical model of a solar cavity-type reactor for the thermal dissociation of ZnO is formulated based on a detailed radiative heat transfer analysis combining the Monte Carlo ray-tracing technique and the radiosity enclosure theory. The quartz window is treated as a semitransparent glass layer with spectrally and directionally dependent optical properties. Model validation is accomplished by comparison with experimental results obtained with a 10-kW solar reactor prototype in terms of cavity temperatures, reaction extents, and quartz window temperature distribution measured by IR thermography. The solar-to-fuel energy conversion efficiencies obtained experimentally are reported, and the various energy flows are quantified.
Polarization and Electrocatalyst Selection for Polybenzimidazole Direct Methanol Fuel Cells
Authors: García-Díaz Brenda L. , Colón-Mercado Héctor R. , Herrington Kevin , Fox Elise B.
Published: September 2013

High temperature direct methanol fuel cells (DMFCs) using polybenzimidazole (PBI) membranes could improve the energy density of portable power sources. This study examines the polarization of vapor phase PBI DMFCs constructed with commercial membranes manufactured by a sol-gel method. The polarization of the high temperature DMFCs is compared to similar low temperature membrane electrode assemblies (MEAs) using Nafion® membranes. The results showed that the cathode of the PBI DMFC had higher kinetic losses that are likely due to phosphate poisoning of the Pt electrocatalyst. At the tested conditions, the membrane conductivity of the PBI MEAs was comparable to the Nafion® MEA even with no humidification. Higher cell temperatures significantly improved PBI DMFC performance for Pt electrocatalyst electrodes. In full cell tests, the PBI DMFC MEAs had higher performance than Nafion® MEAs with similar catalyst loadings. The Pt and PtRu catalysts were tested for methanol oxidation and oxygen reduction activity by a rotating disk electrode (RDE) under 0.5 M H2SO4 and 0.5 M H3PO4. The combination of the polarization and RDE results for the PBI and Nafion® DMFCs suggest that Pt is a more active electrocatalyst for methanol oxidation in PBI than in Nafion®.
Full Parametric Characterization of LSM/LSM-YSZ Cathodes by Electrochemical Impedance Spectroscopy
Authors: Antunes Rui , Jewulski Janusz , Golec Tomasz
Published: September 2013

The contributions of the individual process steps of the cathode resistance were determined experimentally, directly from impedance spectra obtained from symmetrical cells. The symmetrical cells have architecture/structure consisting of YSZ electrolyte and a double layer cathode LSM-LSM/YSZ. The investigations were carried out in the temperature interval from 650 to 900 °C. The cathode processes steps activation energies obtained were 1.16 eV, 1.1 eV, and 0.09 eV (diffusion), respectively, which is in relatively good agreement with literature values. To understand the role of layer cathode thickness on electrochemical performance, electrical impedance spectra from symmetric LSM/YSZ/LSM cells were deconvoluted to obtain the key electrochemical components of electrode performance, namely ohmic resistance (RΩ), two low frequency processes related with chemical adsorption and dissociative reaction of O2 (Rp1 and Rp2), and bulk gas diffusion (W, finite warburg) through the electrode pores. The model used has Voight structure with three times constant. These parameters were then related to features, such as contact layer thickness, function layer thickness, and temperature. It was found that polarization resistance is highly dependent on the thickness of the contact layer (Rp1 and Rp2). All deconvoluted parameters are validated by using the appropriate physicochemical model.
Effective detective quantum efficiency for two mammography systems: Measurement and comparison against established metrics
Authors: Salvagnini Elena , Bosmans Hilde , Struelens Lara , Marshall Nicholas W.
Published: September 2013

Purpose:

The aim of this paper was to illustrate the value of the new metric effective detective quantum efficiency (eDQE) in relation to more established measures in the optimization process of two digital mammography systems. The following metrics were included for comparison against eDQE: detective quantum efficiency (DQE) of the detector, signal difference to noise ratio (SdNR), and detectability index (d′) calculated using a standard nonprewhitened observer with eye filter.

Methods:

The two systems investigated were the Siemens MAMMOMAT Inspiration and the Hologic Selenia Dimensions. The presampling modulation transfer function (MTF) required for the eDQE was measured using two geometries: a geometry containing scattered radiation and a low scatter geometry. The eDQE, SdNR, andd′ were measured for poly(methyl methacrylate) (PMMA) thicknesses of 20, 40, 60, and 70 mm, with and without the antiscatter grid and for a selection of clinically relevant target/filter (T/F) combinations. Figures of merit (FOMs) were then formed from SdNR and d′ using the mean glandular dose as the factor to express detriment. Detector DQE was measured at energies covering the range of typical clinically used spectra.

Results:

The MTF measured in the presence of scattered radiation showed a large drop at low spatial frequency compared to the low scatter method and led to a corresponding reduction in eDQE. The eDQE for the Siemens system at 1 mm−1 ranged between 0.15 and 0.27, depending on T/F and grid setting. For the Hologic system, eDQE at 1 mm−1 varied from 0.15 to 0.32, again depending on T/F and grid setting. The eDQE results for both systems showed that the grid increased the system efficiency for PMMA thicknesses of 40 mm and above but showed only small sensitivity to T/F setting. While results of the SdNR and d′ based FOMs confirmed the eDQE grid position results, they were also more specific in terms of T/F selection. For the Siemens system at 20 mm PMMA, the FOMs indicated Mo/Mo (grid out) as optimal while W/Rh (grid in) was the optimal configuration at 40, 60, and 70 mm PMMA. For the Hologic, the FOMs pointed to W/Rh (grid in) at 20 and 40 mm of PMMA while W/Ag (grid in) gave the highest FOM at 60 and 70 mm PMMA. Finally, DQE at 1 mm−1 averaged for the four beam qualities studied was 0.44 ± 0.02 and 0.55 ± 0.03 for the Siemens and Hologic detectors, respectively, indicating only a small influence of energy on detector DQE.

Conclusions:

Both the DQE and eDQE data showed only a small sensitivity to T/F setting for these two systems. The eDQE showed clear preferences in terms of scatter reduction, being highest for the grid‐in geometry for PMMA thicknesses of 40 mm and above. The SdNR andd′ based figures of merit, which contain additional weighting for contrast and dose, pointed to specific T/F settings for both systems.
Drug Synergy Screen and Network Modeling in Dedifferentiated Liposarcoma Identifies CDK4 and IGF1R as Synergistic Drug Targets
Authors: Miller Martin L. , Molinelli Evan J. , Nair Jayasree S. , Sheikh Tahir , Samy Rita , Jing Xiaohong , He Qin , Korkut Anil , Crago Aimee M. , Singer Samuel , Schwartz Gary K. , Sander Chris
Published: September 2013

Drug screening and computational modeling of oncogenic signaling pathways identifies synergistic drug pairs for liposarcoma.
Profiles of Basal and Stimulated Receptor Signaling Networks Predict Drug Response in Breast Cancer Lines
Authors: Niepel Mario , Hafner Marc , Pace Emily A. , Chung Mirra , Chai Diana H. , Zhou Lili , Schoeberl Birgit , Sorger Peter K.
Published: September 2013

Activity of receptor tyrosine kinase networks may serve as an effective means to classify breast cancers and predict their sensitivity to therapeutic drugs.
siRNA Screen for Genes That Affect Junín Virus Entry Uncovers Voltage-Gated Calcium Channels as a Therapeutic Target
Authors: Lavanya Madakasira , Cuevas Christian D. , Thomas Monica , Cherry Sara , Ross Susan R.
Published: September 2013

Voltage-gated calcium channel blockers may prevent fusion and cell entry of New World arenaviruses.
Refractures of the paediatric forearm with the intramedullary nail in situ
Authors: van Egmond Pim W , van der Sluijs Hans A , van Royen Barend J , Saouti Rachid
Published: September 2013

Forearm fractures in children are common. When conservative treatment fails, internal fixation with Elastic Stable Intramedullary Nailing (ESIN) become the first choice in the operative treatment of diaphyseal forearm shaft fractures. Refractures with the intramedullary nail in situ are known to occur but formal guidelines to guide management in such fractures are lacking. We present a well-documented case of a radius midshaft refracture in a 12-year-old boy with the intramedullary nail in situ, managed by closed reduction. Literature is reviewed for this type of complication, the treatment of 30 similar cases is discussed and a treatment strategy is defined.

The refracture of the paediatric forearm fracture with the intramedullary nail in situ is a rare, but probably under recognised complication which is observed in approximately 2.3% of the study population. Closed reduction may be considered in these cases.
Trial-based cost-effectiveness analysis comparing surgical and endoscopic drainage in patients with obstructive chronic pancreatitis
Authors: Laramée Philippe , Wonderling David , Cahen Djuna L , Dijkgraaf Marcel G , Gouma Dirk J , Bruno Marco J , Pereira Stephen P
Published: September 2013

Objective

Published evidence indicates that surgical drainage of the pancreatic duct was more effective than endoscopic drainage for patients with chronic pancreatitis. This analysis assessed the cost-effectiveness of surgical versus endoscopic drainage in obstructive chronic pancreatitis.

Design

This trial-based cost-utility analysis (ISRCTN04572410) was conducted from a UK National Health Service (NHS) perspective and during a 79-month time horizon. During the trial the details of the diagnostic and therapeutic procedures, and pancreatic insufficiency were collected. The resource use was varied in the sensitivity analysis based on a review of the literature. The health outcome was the Quality-Adjusted Life Year (QALY), generated using EQ-5D data collected during the trial. There were no pancreas-related deaths in the trial. All-cause mortality from the trial was incorporated into the QALY estimates in the sensitivity analysis.

Setting

Hospital.

Participants

Patients with obstructive chronic pancreatitis.

Primary and secondary outcome measures

Costs, QALYs and cost-effectiveness.

Results

The result of the base-case analysis was that surgical drainage dominated endoscopic drainage, being both more effective and less costly. The sensitivity analysis varied mortality and resource use and showed that the surgical option remained dominant in all scenarios. The probability of cost-effectiveness for surgical drainage was 100% for the base case and 82% in the assessed most conservative case scenario.

Conclusions

In obstructive chronic pancreatitis, surgical drainage is highly cost-effective compared with endoscopic drainage from a UK NHS perspective.
Reducing delay to stroke thrombolysis—lessons learnt from the Stroke 90 Project
Authors: Kendall Jason , Dutta Dipankar , Brown Elsa
Published: September 2013

Background

The Stroke 90 Project was implemented to reduce delays to stroke thrombolysis and involved 7 hospitals and 2 ambulance services in the Avon, Gloucester, Wiltshire and Somerset regional network. Interventions included a direct to CT (DtoCT) protocol for paramedics to transport patients directly to the CT scanner. Coincidentally, there were severe winter pressures on all participating emergency departments during this period.

Methods

Comparison of data from 2 groups across all 7 hospitals: preintervention (n=136) and postintervention patients (n=215) thrombolysed from August 2012 to January 2013. The χ2test, t tests, multiple and linear regression were used for analysis.

Results

Ambulance transport times were 56.8 min for preintervention versus 57.5 min for postintervention patients (p=0.78). 11.7% of preintervention patients received thrombolysis within 90 min of call for help versus 23.7% of postintervention cases (p=0.0135). 44% of postintervention patients entered the DtoCT pathway and achieved a mean reduction in door to CT time of 17 min (95% CI 11.5 to 21.5; p<0.0001) and a 19 min reduction in door to needle time (95% CI 10.8 to 26.8; p<0.0001). CT to needle times were 43.8 min preintervention and 42.1 min postintervention (p=0.57).

Conclusions

The DtoCT pathway was successful in reducing delays to thrombolysis and should be implemented routinely. The call to door and CT to needle times were not improved by our interventions and further work is required to streamline these. Factors beyond the control of most hospitals may play a role in delaying treatment, but local changes can be implemented to mitigate this.
Prestressed near-surface mounted fibre reinforced polymer reinforcement for concrete structures — a review
Authors: El-Hacha Raafat , Soudki Khaled
Published: September 2013

The specialized application of prestressing the near-surface mounted (NSM) fibre reinforced polymer (FRP) reinforcement for strengthening reinforced concrete (RC) structures combines the benefits of the FRP reinforcement with the advantages associated with external prestressing. By applying a prestress to the NSM FRP the material is used more efficiently since a greater portion of its tensile capacity is employed. This paper presents a comprehensive review on the performance of RC members strengthened using prestressed NSM FRP reinforcement. Several techniques and anchorage systems developed to prestress the NSM FRP are presented. The static flexural and fatigue performance of RC beams strengthened using prestressed NSM FRP in comparison to non-prestressed NSM is presented. Research on the long-term performance under freeze–thaw exposures and sustained loading is also presented.