bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations
Authors: Shirai Hiroki , Ikeda Kazuyoshi , Yamashita Kazuo , Tsuchiya Yuko , Sarmiento Jamica , Liang Shide , Morokata Tatsuaki , Mizuguchi Kenji , Higo Junichi , Standley Daron M. , Nakamura Haruki 
Published: April 2014

ABSTRACTIn the second antibody modeling assessment, we used a semiautomated template‐based structure modeling approach for 11 blinded antibody variable region (Fv) targets. The structural modeling method involved several steps, including template selection for framework and canonical structures of complementary determining regions (CDRs), homology modeling, energy minimization, and expert inspection. The submitted models for Fv modeling in Stage 1 had the lowest average backbone root mean square deviation (RMSD) (1.06 Å). Comparison to crystal structures showed the most accurate Fv models were generated for 4 out of 11 targets. We found that the successful modeling in Stage 1 mainly was due to expert‐guided template selection for CDRs, especially for CDR‐H3, based on our previously proposed empirical method (H3‐rules) and the use of position specific scoring matrix‐based scoring. Loop refinement using fragment assembly and multicanonical molecular dynamics (McMD) was applied to CDR‐H3 loop modeling in Stage 2. Fragment assembly and McMD produced putative structural ensembles with low free energy values that were scored based on the OSCAR all‐atom force field and conformation density in principal component analysis space, respectively, as well as the degree of consensus between the two sampling methods. The quality of 8 out of 10 targets improved as compared with Stage 1. For 4 out of 10 Stage‐2 targets, our method generated top‐scoring models with RMSD values of less than 1 Å. In this article, we discuss the strengths and weaknesses of our approach as well as possible directions for improvement to generate better predictions in the future. Proteins 2014; 82:1624–1635. © 2014 Wiley Periodicals, Inc.
Modeling market valuation of offshore drilling contractors
Authors: Kaiser Mark J. 
Published: April 2014

Abstract
Offshore drilling is big business, and on a worldwide basis, contractor revenues have ranged between $25 and 50 billion a year over the past decade. The industry is organized through public, private, and state-owned companies, and in 2012 public companies Seadrill, Transocean, Ensco, Noble, and Diamond dominated the market, followed by mid-market players Rowan, Hercules, and Aban. The industry is competitive and dynamic, and contractor business strategies evolve in response to changing market demands and competitor activity. Contractors derive their cash flow and earnings by leasing rigs for exploration and development and attempt to maximize their revenue through scale economies, specialization, geographic diversity, and safe and efficient operations. The market value of contractors depends upon their rig fleet, contract backlog, and operational and financial characteristics. Market valuations change as supply and demand conditions change and companies upgrade their fleet portfolio and relocate rigs to satisfy demand. The purpose of this paper is to describe the factors that impact contractor value and to develop quantitative models of market valuation for a cross-section of public firms. A high-level overview of the offshore contract market and business strategies of firms is described. Fleet value, contract backlog, revenue, and earnings are significant predictors of market capitalization and enterprise value, and fleet value is the best predictor of firm value.
Clinical experience of large colorectal laterally spreading tumor in a regional hospital: 2‐year results
Authors: Hsu Wen‐Hsin , Sun Meng‐Shun , Lo Hoi‐Wan , Tsai Ching‐Yang , Tsai Yu‐Jou , Chen Pao‐Huei 
Published: April 2014

SummaryBackgroundNonpolypoid colorectal neoplasm has been widely recognized in the past few years. Among nonpolypoid colorectal neoplasms, laterally spreading tumor (LST) is a unique and distinct category in that the tumor grows horizontally with a size >1 cm. It may be easily overlooked during colonoscopy. If the size of the colorectal LST is >2 cm, achieving definite management is also another concerning issue. The aim of this study was to improve our understanding of LST by reviewing its clinical manifestations.MethodsAll the large colorectal LSTs that were diagnosed and managed at our hospital in the past 2 years were reviewed. Basic demographic data were recorded. LSTs were divided into granular (G) and nongranular types (NG), then further subdivided into nodular mixed and homogeneous types for the G group and flat elevated and pseudodepressed types for the NG group.ResultsA total of 28 LST in 28 patients were enrolled, with males being more predominant than females (male/female: 18/10). Mean age of the patients and mean size of the LST were 62.6 ± 9.75 years and 3.4 ± 1.257 cm, respectively. Concerning morphology, 14 were diagnosed as NG and 14 as G group. The rate of malignant change was 28.6% (8/28). Twenty‐three of our patients received endoscopic treatment (5 for endoscopic piecemeal mucosal resection 18 for endoscopic submucosal dissection) and five for laparoscopy‐assisted colectomy. The cost and length of admission analysis between the endoscopic and operation treatment groups showed significant cost reduction (endoscopy/operation: NTD 28172/82516, p < 0.001) and fewer admission days in the endoscopy therapy group (4.74/9.00, days, p < 0.001). Subgroup comparison between the G and NG groups did not reveal statistical significance in age, sex ratio, tumor size, rate of malignant change, or location.ConclusionAlthough long‐term outcome comparison was lacking, endoscopic treatment should be considered firstly for colorectal LST under the consideration of shorter hospitalization. Most of our analyses between the G and NG groups were statistically insignificant, which is likely to be due to the small population base.
Fatou components with punctured limit sets
Authors: BOC-THALER LUKA , FORNÆSS JOHN ERIK , PETERS HAN 
Published: April 2014

We study invariant Fatou components for holomorphic endomorphisms in $\mathbb{P}^{2}$. In the recurrent case these components were classified by Fornæss and Sibony [Classification of recurrent domains for some holomorphic maps. Math. Ann. 301(4) (1995), 813–820]. Ueda [Holomorphic maps on projective spaces and continuations of Fatou maps. Michigan Math J.56(1) (2008), 145–153] completed this classification by proving that it is not possible for the limit set to be a punctured disk. Recently Lyubich and Peters [Classification of invariant Fatou components for dissipative Hénon maps. Preprint] classified non-recurrent invariant Fatou components, under the additional hypothesis that the limit set is unique. Again all possibilities in this classification were known to occur, except for the punctured disk. Here we show that the punctured disk can indeed occur as the limit set of a non-recurrent Fatou component. We provide many additional examples of holomorphic and polynomial endomorphisms of $\mathbb{C}^{2}$ with non-recurrent Fatou components on which the orbits converge to the regular part of arbitrary analytic sets.
Superhydrophobic turbulent drag reduction as a function of surface grating parameters
Authors: Park Hyungmin , Sun Guangyi , Kim Chang-Jin “CJ” 
Published: April 2014

AbstractDespite the confirmation of slip flows and successful drag reduction (DR) in small-scaled laminar flows, the full impact of superhydrophobic (SHPo) DR remained questionable because of the sporadic and inconsistent experimental results in turbulent flows. Here we report a systematic set of bias-free reduction data obtained by measuring the skin-friction drags on a SHPo surface and a smooth surface at the same time and location in a turbulent boundary layer (TBL) flow. Each monolithic sample consists of a SHPo surface and a smooth surface suspended by flexure springs, all carved out from a$2.7 \times 2.7 {\mathrm{mm}}^{2}$silicon chip by photolithographic microfabrication. The flow tests allow continuous monitoring of the plastron on the SHPo surfaces, so that the DR data are genuine and consistent. A family of SHPo samples with precise profiles reveals the effects of grating parameters on turbulent DR, which was measured to be as much as${\sim }75\, \%$.
On the need for a nonlinear subscale turbulence term in POD models as exemplified for a high-Reynolds-number flow over an Ahmed body
Authors: Östh Jan , Noack Bernd R. , Krajnović Siniša , Barros Diogo , Borée Jacques 
Published: April 2014

AbstractWe investigate a hierarchy of eddy-viscosity terms in proper orthogonal decomposition (POD) Galerkin models to account for a large fraction of unresolved fluctuation energy. These Galerkin methods are applied to large eddy simulation (LES) data for a flow around a vehicle-like bluff body called an Ahmed body. This flow has three challenges for any reduced-order model: a high Reynolds number, coherent structures with broadband frequency dynamics, and meta-stable asymmetric base flow states. The Galerkin models are found to be most accurate with modal eddy viscosities as proposed by Rempfer & Fasel (J. Fluid Mech., vol. 260, 1994a, pp. 351–375;J. Fluid Mech.vol. 275, 1994b, pp. 257–283). Robustness of the model solution with respect to initial conditions, eddy-viscosity values and model order is achieved only for state-dependent eddy viscosities as proposed by Noack, Morzyński & Tadmor (Reduced-Order Modelling for Flow Control, CISM Courses and Lectures, vol. 528, 2011). Only the POD system with state-dependent modal eddy viscosities can address all challenges of the flow characteristics. All parameters are analytically derived from the Navier–Stokes-based balance equations with the available data. We arrive at simple general guidelines for robust and accurate POD models which can be expected to hold for a large class of turbulent flows.
Multifractality in combustion noise: predicting an impending combustion instability
Authors: Nair Vineeth , Sujith R. I. 
Published: April 2014

AbstractThe transition in dynamics from low-amplitude, aperiodic, combustion noise to high-amplitude, periodic, combustion instability in confined, combustion environments was studied experimentally in a laboratory-scale combustor with two different flameholding devices in a turbulent flow field. We show that the low-amplitude, irregular pressure fluctuations acquired during stable regimes, termed ‘combustion noise’, display scale invariance and have a multifractal signature that disappears at the onset of combustion instability. Traditional analysis often treats combustion noise and combustion instability as acoustic problems wherein the irregular fluctuations observed in experiments are often considered as a stochastic background to the dynamics. We demonstrate that the irregular fluctuations contain useful information of prognostic value by defining representative measures such as Hurst exponents that can act as early warning signals to impending instability in fielded combustors.
Sociability and support in online eating disorder communities: Evidence from personal networks
Authors: TUBARO PAOLA , MOUNIER LISE 
Published: April 2014

AbstractWe study how people select their health support ties from their broader personal networks, taking into account the interplay of web-based and face-to-face interactions. We focus on users of self-styled Internet communities on eating disorders, often dubbed “pro-ana” and “pro-mia” and widely feared to contribute to maintaining and spreading these disorders. Despite the controversial anti-medical stances of some of them, “ana-mia” websites may channel mutual assistance, advice, and psychological and emotional support, with ultimate benefits for health.In 2011–12 we fielded an online survey of users of French- and English-language “ana-mia” websites, mapping the composition and structure of their personal networks both online and face-to-face, and their health and eating-related support networks, for two types of health issues. We estimate binary choice models for these data and find that different health needs call for different types of support, embedded in different parts of personal networks. Specifically, online groups provide distinctive sources of help, which partly compensate for perceived shortcomings in healthcare services, although members do not overwhelmingly reject standard health systems and norms. We discuss how web-based groups constitute an important source of social support, and a potential resource for enhanced public health services provision.
Geology and geochemistry of the Baijiantan–Baikouquan ophiolitic mélanges: implications for geological evolution of west Junggar, Xinjiang, NW China
Authors: ZHU YONGFENG , CHEN BO , QIU TIAN 
Published: April 2014

AbstractWe report two newly identified Ordovician ophiolite belts in west Junggar, NW China: Tajin–Tarbahatai–Kujibai–Honguleleng (TTKH) and Tangbale–Baijiantan–Baikouquan (TBB) ophiolitic belts. These two ophiolitic belts provide constraints for the Palaeozoic reconstruction of Central Asia and the geological evolution of this region. The TTKH and TBB ophiolitic belts are dismembered parts of different ophiolitic belts which represent relics of Ordovician oceanic floor; they subducted to the north under the Chingiz–Tarbahatai arc and to the south under the Junggar plate, respectively. The Baijiantan–Baikouquan ophiolite mélanges comprise the major part of the TBB. Flat rare Earth element (REE) patterns with positive Eu anomalies and insignificant depletion of high-field-strength elements (HFSE) relative to melts of primitive mantle suggest a mid-ocean-ridge basalt (MORB) origin for the metagabbro. Lherzolite samples define a Sm–Nd isotopic isochron with age of 474 Ma andɛNd(t)of +8.9. Lherzolite samples with positiveɛNd(t)values of +8.8 to +9.1 and initial87Sr/86Sr ratios of 0.7037–0.7040 are rather homogeneous in Sr–Nd isotopic composition, whereas metagabbro samples show wider Sr–Nd isotopic compositional ranges withɛNd(t)of +5.9 to +11.0. The Sm–Nd isotopic isochron age (c.380 Ma) for garnet amphibolite samples, consistent with a zircon U–Pb age (c.385 Ma) for metagabbro, represents a magmatic event prior to subduction. Thermodynamic calculations for garnet amphibolite yield a clockwise pressure–temperature path with peak metamorphic condition ofc.15 kbar and 520–560°C at 342 Ma, indicating a subduction-channel setting. The Rb–Sr isochron ages (335 Ma, 333 Ma) for metagabbro represent a metamorphic event during exhumation.
How Does the Market Value Toxic Assets?
Authors: Longstaff Francis A. , Myers Brett W. 
Published: April 2014

AbstractHow does the market value “toxic” structured-credit securities? We study the valuation of what is possibly the most toxic of all toxic assets: the equity tranche of a collateralized debt obligation (CDO). In theory, CDO equity should be similar in nature to bank stock since both represent residual claims on a portfolio of loans. We find CDO equity returns are much more related to stock returns than to fixed-income returns. CDO equity returns track the returns of financial stocks much more closely than any other industry. Nearly two-thirds of the variation in CDO returns can be explained by fundamentals.
Impacted dentures in the oesophagus
Authors: Bandyopadhyay S N , Das S , Das S K , Mandal A 
Published: April 2014

AbstractObjective:This study presents the incidence of denture impaction in the oesophagus, and discusses the difficulties of managing such cases.Method:A total of 262 patients with a history of foreign body ingestion (between 1999 and 2010) were reviewed; 46 of these patients had dentures impacted in the oesophagus.Results:The cervical section of the oesophagus was the commonest site of impaction. Dysphagia and tracheal tenderness were the most consistent features when dentures became impacted in the upper oesophagus. In most cases, rigid oesophagoscopy enabled successful removal of the impacted denture. Locating an impacted denture hidden within the oesophageal mucosal folds sometimes proved difficult.Conclusion:In cases of impacted dentures in the oesophagus, a positive history helps in the diagnosis, but a high degree of clinical suspicion aids early detection. Conventional radiographs are important but may not always be of assistance. Early intervention reduces complications. Dentures that are poorly maintained and old are more likely to be swallowed accidentally. The inclusion of radiopaque filler within dentures would assist localisation following accidental swallowing.
Materiam superabat opus: Lucretius Metamorphosed
Authors: Schiesaro Alessandro 
Published: April 2014

AbstractOvid's narrative of Phaethon's failed attempt prematurely to emulate his father in his unique expertise can be read as a reflection on the virtues and limits of Lucretius' philosophical poetry. The paper suggests that, while he gives much credit to theDe Rerum Natura's literary quality and its striving for the sublime, Ovid also critiques the hubristic connotations of Lucretius' rejection of divine authority and agency from the workings of nature. The second part of the article explores how this particular version of the myth touches upon issues of poetic authority, political positioning, and Oedipal competition.
Transporting functions across ornaments
Authors: DAGAND PIERRE-ÉVARISTE , McBRIDE CONOR 
Published: April 2014

AbstractProgramming with dependent types is a blessing and a curse. It is a blessing to be able to bake invariants into the definition of datatypes: We can finally write correct-by-construction software. However, this extreme accuracy is also a curse: A datatype is the combination of a structuring medium together with a special purpose logic. These domain-specific logics hamper any attempt to reuse code across similarly structured data. In this paper, we capitalise on the structural invariants of datatypes. To do so, we first adapt the notion of ornament to our universe of inductive families. We then show how code reuse can be achieved by ornamenting functions. Using these functional ornaments, we capture the relationship between functions such as the addition of natural numbers and the concatenation of lists. With this knowledge, we demonstrate how the implementation of the former informs the implementation of the latter: The users can ask the definition of addition to be lifted to lists and they will only be asked the details necessary to carry on adding lists rather than numbers. Our presentation is formalised in the type theory with a universe of datatypes and all our constructions have been implemented as generic programs, requiring no extension to the type theory.
Why do firms oppose entry-deterring policies? Environmental regulation and entry deterrence
Authors: Espínola-Arredondo Ana , Muñoz-García Félix 
Published: April 2014

AbstractThis paper investigates the design of environmental regulation under different regimes: flexible and inflexible policies. We analyze under which settings strict emission fees can be used as an entry-deterring tool, and become socially optimal. Furthermore, we demonstrate that the incentives of the social planner and the incumbent firm are aligned regarding policy regimes ifentry can be easily deterred by setting a stringent regulation. Their incentives, however, can bemisaligned when entry becomes more costly to deter, leading the incumbent to actually preferenvironmental policies that attract entry.
In-Situ Electrochemical Transmission Electron Microscopy for Battery Research
Authors: Layla Mehdi B. , Gu Meng , Parent Lucas R. , Xu Wu , Nasybulin Eduard N. , Chen Xilin , Unocic Raymond R. , Xu Pinghong , Welch David A. , Abellan Patricia , Zhang Ji-Guang , Liu Jun , Wang Chong-Min , Arslan Ilke , Evans James , Browning Nigel D. 
Published: April 2014

AbstractThe recent development of in-situ liquid stages for (scanning) transmission electron microscopes now makes it possible for us to study the details of electrochemical processes under operando conditions. As electrochemical processes are complex, care must be taken to calibrate the system before any in-situ/operando observations. In addition, as the electron beam can cause effects that look similar to electrochemical processes at the electrolyte/electrode interface, an understanding of the role of the electron beam in modifying the operando observations must also be understood. In this paper we describe the design, assembly, and operation of an in-situ electrochemical cell, paying particular attention to the method for controlling and quantifying the experimental parameters. The use of this system is then demonstrated for the lithiation/delithiation of silicon nanowires.
Quantitative Strain and Compositional Studies of InxGa1−xAs Epilayer in a GaAs-based pHEMT Device Structure by TEM Techniques
Authors: Sridhara Rao Duggi V. , Sankarasubramanian Ramachandran , Muraleedharan Kuttanellore , Mehrtens Thorsten , Rosenauer Andreas , Banerjee Dipankar 
Published: April 2014

AbstractIn GaAs-based pseudomorphic high-electron mobility transistor device structures, strain and composition of the InxGa1−xAs channel layer are very important as they influence the electronic properties of these devices. In this context, transmission electron microscopy techniques such as (002) dark-field imaging, high-resolution transmission electron microscopy (HRTEM) imaging, scanning transmission electron microscopy-high angle annular dark field (STEM-HAADF) imaging and selected area diffraction, are useful. A quantitative comparative study using these techniques is relevant for assessing the merits and limitations of the respective techniques. In this article, we have investigated strain and composition of the InxGa1−xAs layer with the mentioned techniques and compared the results. The HRTEM images were investigated with strain state analysis. The indium content in this layer was quantified by HAADF imaging and correlated with STEM simulations. The studies showed that the InxGa1−xAs channel layer was pseudomorphically grown leading to tetragonal strain along the [001] growth direction and that the average indium content (x) in the epilayer is ~0.12. We found consistency in the results obtained using various methods of analysis.
Which Level of Government Do the ASEAN People Think that Environmental Issues Should Be Decided By? An Analysis of the ASEAN-Barometer Survey of 2009
Authors: FUJII SEIJI 
Published: April 2014

AbstractThis paper explores preferences and attitudes related to fiscal federalism held by the ASEAN people in the context of environmental issues. Fiscal federalism would predict that local environmental problems will be handled more efficiently by local governments, while national environmental problems will be solved more efficiently by the national government. But it is not obvious whether citizens consider in the same way as economics theory predicts. To unveil this point, I address questions of whether those who have higher consciousness toward environmental issues at the neighbor or local level prefer local governments to decide environment policies, whether those who have more consciousness about environmental issues at the national level prefer the national government to decide the policies, and whether those who have higher consciousness toward environmental problems at global level prefer higher levels government such as the United Nations to decide the policies. By fitting multi-level probit regressions to cross-national survey data collected in ASEAN countries, I found the results supporting the hypotheses. The country analyses show the results which support the hypotheses in Brunei, Indonesia, and the Philippines.