bluuebunny/crossref_metadata_2025_split huggingface dataset:
A molecular dynamics study of C1r and C1s dimers: Implications for the structure of the C1 complex
Authors: Beveridge Allan J , Wallis Russell , Samani Nilesh J. 
Published: April 2012

AbstractComplement is an important part of the immune system. It is initiated through three different pathways known as the classical, lectin, and alternative pathway. The multimolecular C1 complex of the classical pathway consists of a subcomponent, C1q, which binds to a tetramer comprising two C1r and two C1s proteases. A detailed description of the structure of the C1 complex is essential to fully understand how the complex acts on pathogens. A variety of different models have been proposed, which differ mainly in the way the proteases interact with C1q. In this study, we have used a combination of homology‐based structure prediction and molecular dynamics to predict a partial structure of the C1s/C1r/C1r/C1s tetramer. For computational expediency the study was restricted to the CUB1‐EGF‐CUB2 domains which are directly involved in the formation of the tetramer and its interaction with C1q; the catalytic fragments (CCP1‐CCP2‐SP), which mediate C1 activation and subsequent cleavage of substrates, were omitted. A systematic molecular dynamics (MD) study of several possible dimeric combinations suggest that the tetramer is formed when a pair of C1r/C1s dimers form a “doughnut” via a C1s/C1s head‐to‐tail interaction, which is stabilized by several putative salt bridges at the dimer interface. This result is consistent with biochemical data which have shown that self assembly requires the formation of C1r‐C1s contacts and that electrostatic interactions play a key role. Furthermore, it identifies a number of putative binding residues that can be tested using site‐directed mutagenesis. Proteins 2012. © 2012 Wiley Periodicals, Inc
Inhibition of interdomain motion in g‐actin by the natural product latrunculin: A molecular dynamics study
Authors: Rennebaum Sandra , Caflisch Amedeo 
Published: April 2012

AbstractAs part of the cytoskeleton, actin is essential for the morphology, motility, and division of eukaryotic cells. Recent X‐ray fiber diffraction studies have shown that the conformation of monomeric actin is flattened upon incorporation into the filament by a relative rotation of its two major domains. The antiproliferative activity of latrunculin, a macrolide toxin produced by sponges, seems to be related to its binding to monomeric actin and inhibition of polymerization. Yet, the mechanism of inhibition is not known in detail. Here, multiple explicit water molecular dynamics simulations show that latrunculin binding hinders the conformational transition related to actin polymerization. In particular, the presence of latrunculin at the interface of the two major domains of monomeric actin reduces the correlated displacement of Domain 2 with respect to Domain 1. Moreover, higher rotational flexibility between the two major domains is observed in the absence of ATP as compared to ATP‐bound actin, offering a possible explanation as to why actin polymerizes more favorably in the absence of nucleotides. Proteins 2012; © 2012 Wiley Periodicals, Inc.
Simulation‐based investigations on noise characteristics of redox‐cycling sensors
Authors: Kätelhön Enno , Wolfrum Bernhard 
Published: April 2012

AbstractWe describe a simulation framework for the modeling of electrochemical processes within nanocavity redox‐cycling devices. Nanocavity devices feature two closely spaced and individually biased electrodes that are incorporated into a nanofluidic channel. This setup enables the repeated participation of certain molecules in subsequent redox reactions at the two electrodes, hence leading to a strong amplification of the electrochemical signal. Our simulation is based on stochastic random walks that represent single molecule trajectories; electrochemical reactions are modeled on the molecular level. The presented approach reveals insight into the dependency of the sensor's current noise characteristics on geometrical features. We describe the simulation of two key geometries and identify two distinct types of noise that can be discriminated by their characteristics in the frequency domain. magnified imageSchematic of a random‐walk approach for the simulation of the redox‐cycling effect. A single molecule trajectory is indicated, differently colored spheres specify the molecule occupying different oxidation states throughout its pathway.
Electrospun copper oxide nanofibers for H2S dosimetry
Authors: Hennemann Jörg , Sauerwald Tilman , Kohl Claus‐Dieter , Wagner Thorsten , Bognitzki Michael , Greiner Andreas 
Published: April 2012

AbstractWe present the preparation and characterization of a novel copper(II)oxide (CuO) nanofiber based sensor with very high sensitivity and selectivity to hydrogen sulfide (H2S). The working principle is based on the phase transition of semiconducting p‐type CuO to strongly degenerated p‐type copper sulfide (CuS) with metallic conductivity. Electrospun polymer fiber networks of polyvinyl butyrate (PVB) and Cu(NO3)2 were attached on standard gas sensing substrates and calcined to CuO at 600 °C in ambient air for 24 h. Continuous exposure to H2S (0.1–5 ppm) as well as a sequence of 1 ppm H2S pulses result in a dosimeter type behavior of the nanofiber sensors. Triggered by a certain dose (gas concentration multiplied by time) a steep conductance increase of the sensitive layer over several orders of magnitude is observed. After reaching this percolation threshold only small conductance changes were observed. These fiber based sensors show a remarkably high specificity, there is no response to carbon monoxide, hydrogen, and methane at 160 °C. The fiber network can be regenerated by raising the operating temperature to 350 °C for 30 min in absence of H2S. magnified image
Conductance change under exposure to various gases. Continuous recording with one measurement per second.
A novel approach for increasing sensitivity in lateral flow assays: Development of an enrichment module based on polyethylene sintered bodies
Authors: Kehrel Marcus , Dassinger Nina , Merkl Stefan , Vornicescu Doru , Keusgen Michael 
Published: April 2012

AbstractLateral flow assays (LFAs, e.g. the well established pregnancy test) are frequently used, fast and easy‐to‐handle immunoassays with a broad application range. Nevertheless, the restriction to small sample volumes is one of the major drawbacks and can be the reason for lack of sensitivity. In order to detect even small amounts of analyte in big sample volumes without the need for time consuming sample preparation or sophisticated labelling or detection technologies, the aim of the here presented research was the development of an ‘enrichment module’, which can be integrated into the workflow of a LFA. The core element of this enrichment module was a cleavable biological interface structure. A fusion protein, which was expressed recombinant and consisted of a monomeric concanavalin A (Con A) domain and a monomeric streptavidin domain (SAv), was used as interface structure. For the construction of the entire module, the polysaccharide mannan was firstly covalently attached to a porous polyethylene (PE) sintered body in a four‐stage procedure. This immobilisation procedure was monitored by a modified Bradford assay. In the next step, the Con A–SAv fusion protein was added. In order to assess the functionality of the enrichment module, a model assay was developed. The SAv domain of the attached fusion protein was specifically recognised by a primary and a secondary, horseradish peroxidase (HRP)‐labelled, antibody. The HRP‐reaction was used for photometric detection in order to characterise binding properties of the enrichment module and to prove binding characteristics of the fusion protein.
Optical, structural, and mechanical properties of different valence‐cation‐doped bismuth vanadate oxides
Authors: Kaur G. , Pandey O. P. , Singh K. 
Published: April 2012

AbstractThe optical, structural, and mechanical properties of Bi4V2 − xMxO11 − δ (0 ≤ x ≤ 0.4 in the steps of 0.1, M = Mn, Ga, As) oxides have been investigated. The parameters like band gap (Eg), Urbach energy (Eu), grain size, hardness (H), and fracture strength (K) have been calculated as a function of dopant concentration, i.e., 0 ≤ x ≤ 0.4. In addition to this, the infrared spectra have been obtained for all the dopant oxides with different dopant concentrations. The results are discussed in light of correlation of these optical and mechanical parameters to their electrical properties. The fractured surface is analyzed by X‐ray dot mapping to check the segregation of elements and their effect on mechanical properties.
Cu2ZnSnSe4 absorbers processed from solution deposited metal salt precursors under different selenization conditions
Authors: Fella Carolin M. , Uhl Alexander R. , Romanyuk Yaroslav E. , Tiwari Ayodhya N. 
Published: April 2012

AbstractCu2ZnSnSe4 (CZTSe) thin film solar cells are fabricated by a simple, non‐vacuum deposition of metal salts dissolved in non‐hazardous solvents followed by selenization in Se atmosphere. Despite a residual carbon‐rich layer between the back contact and the CZTSe absorber layer, solar cells with up to 4.28% conversion efficiency are obtained for Cu‐poor and Zn‐rich CZTSe absorbers. A frequently reported problem, the loss of tin, is investigated with respect to the influence of the selenization conditions such as substrate temperature and selenium partial pressure. EDX point measurements directly confirm that the remaining decomposed layer consists of a mixture of binary ZnSe and Cu2−xSe phases if the substrate temperature is too high and not sufficient Se is supplied.magnified image
Determination of ultrathin diamond films by Raman spectroscopy
Authors: Chernozatonskii Leonid A. , Mavrin Boris N. , Sorokin Pavel B. 
Published: April 2012

AbstractThe study of Raman spectra of recently predicted ultrathin diamond films (diamanes) with nanometer thickness, transformed from multilayered graphenes by the adsorption of hydrogen is presented. Here we studied the phonon spectra of diamane structures in detail by ab initio method, especially the Raman and infrared (IR) vibrational modes. In particular, two‐layered diamanes display Raman peaks near 1110, 1260, 1320, 2860 cm−1, and three‐layered diamanes have a broad region (1110–1340 cm−1) of Raman shifts and peaks near 2830–2860 cm−1. The spectra are radically distinguished from the similar spectra of one to three layered graphenes and graphane. magnified imageLeft side: Atomic structure and vibration pattern of optical modes of ultrathin diamond (diamane). Right: Phonon densities of the states of graphane and diamanes.
Variability of the thermal structure of the atmosphere during wet and dry spells over southeast India
Authors: Satyanarayana Mohan T. , Narayana Rao T. 
Published: April 2012

AbstractSurface and upper‐air observations of meteorological parameters at Gadanki (13.5°N, 79.2°E) are utilized to understand the thermal structure of the atmosphere in dry and wet spells and its effect on draught core statistics. The temperature and humidity variations from wet to dry spell are quite pronounced near the surface and in the atmospheric boundary layer (ABL), but not above the ABL. Interestingly, convective available potential energy (CAPE) is found to be higher during wet spells than during dry spells, in contrast to the earlier studies made elsewhere over warm oceans and tropical land masses. The stratified CAPE values based on rainfall occurrence are also larger during wet spells than during dry spells, irrespective of whether the sounding is made before, during or after the rain occurrence. Surprisingly, large CAPE values are observed after the rain occurrence in both spells. The high CAPE during wet spells (and also after rain occurrence) corresponds well with larger surface equivalent potential temperature (θe). During wet spells, the positive buoyancy is not only larger but also vertically extended to higher altitudes. On the other hand, buoyancy profiles during dry spells are punctuated by several negative buoyancies (associated with stable layers), reducing CAPE values in those spells.A synthesis of all measurements reveals that favourable environmental conditions (high CAPE, humid atmosphere and weak stable layers) allow the convection to grow into a deep system in wet spells. On the other hand, strong stable layers, weak CAPE coupled with relatively less humidity above the ABL inhibits the growth of convective cloud during dry spells. These observations explain the differences in draught core statistics in wet and dry spells. Copyright © 2012 Royal Meteorological Society
Conceptual design of a novel multi‐DoF manual instrument for laparoscopic surgery
Authors: Wang Xiaofei , Wang Shuxin , Li Jianmin , Zhang Guokai , Wu Zhiliang 
Published: April 2012

AbstractBackgroundLaparoscopic surgery is becoming increasingly popular throughout the world. But the conventional instruments used in many surgeries are not flexible enough to be operated. Challenging tasks, such as suturing and knot‐tying tasks are difficult to complete using conventional instruments with limited degrees of freedom (DoFs). In the paper, a novel cable‐driven multi‐DoF manual instrument is presented with a simple structure but strong functionality.MethodsThe proposed instrument has been developed with a wristlike operation end (OE), a wristlike end effector (EE), and the transmission system. It can be operated intuitively. The orientation and the position of the EE are directly controlled by surgeons due to the one‐to‐one motion mapping structure. The clamp structure and tension device are reasonably designed. The pitch, yaw, and the open and close motion are actuated by cables. Based on the optimization index Global Condition Index (GCI), four cables are used to actuate the pitch and yaw motions, while other two are used for the open and close motion. The layout of the cables is also determined by the GCI.ResultsExperiments carried out with a prototype show that tasks such as suturing and knot‐tying can be completed comfortably. Due to the intuitive control and multi‐DoFs, surgeons can use the prototype to finish the tasks with ease.ConclusionsThe instrument developed herein with intuitive control and dexterity can be used alone or together with a robotic system to accomplish some challenging tasks that are difficult for conventional instruments. Copyright © 2012 John Wiley & Sons, Ltd.
Best practices for describing, consuming, and discovering web services: a comprehensive toolset
Authors: Rodriguez Juan Manuel , Crasso Marco , Mateos Cristian , Zunino Alejandro 
Published: April 2012

SUMMARYThe service‐oriented computing (SOC) paradigm has recently gained a lot of attention in the software industry because SOC represents a novel and a fresh way of architecting distributed applications. SOC is usually materialized via web services, which allows developers to structure applications exposing a clear, public interface to their capabilities. Although conceptually and technologically mature, SOC still lacks adequate development support from a methodological point of view. In this paper, we present the EasySOC project, a set of guidelines to simplify the development of service‐oriented applications and services. EasySOC is a synthesized catalog of best SOC development practices that arise as a result of several years of research in fundamental Services Computing topics, that is, Web Service Description Language‐based technical specification, Web Service discovery, and Web Service outsourcing. In addition, we describe a materialization of the guidelines for the Java language, which has been implemented as a plug‐in for the Eclipse IDE. We believe that both the practical nature of the guidelines and the availability of this software that enforces them may help software practitioners to rapidly exploit our ideas for building real SOC applications. Copyright © 2012 John Wiley & Sons, Ltd.
Rightward convexity of the great vessel arising from the anterior ventricle: a novel fetal marker for transposition of the great arteries
Authors: Menahem S. , Rotstein A. , Meagher S. 
Published: April 2012

ABSTRACTObjectivesTraditionally transposition of the great arteries (TGA) is suggested by bifurcation of the great vessel arising from the posterior ventricle and the parallel course of the great vessels as they leave the heart. These findings may be difficult to demonstrate, requiring additional fetal echocardiographic features to indicate TGA. In this study, we investigated a new marker of TGA, namely rightward convexity of the great vessel arising from the anterior ventricle.MethodsWe reviewed fetal studies from 2006 to 2010 in which an antenatal diagnosis of TGA was confirmed postnatally. We specifically viewed images obtained by scanning the great vessel arising from the anterior ventricle cranially to the superior mediastinum at the level of the three vessels and trachea view and compared them with similar views in normal hearts.ResultsIn 21 cases of confirmed TGA, the great vessel arising from the anterior ventricle (aorta) coursing cranially demonstrated an abnormal convexity to the right. This was in contrast to convexity to the left or lack of convexity of the great vessel (pulmonary artery) arising from the anterior ventricle in fetuses with a normal heart. In two fetuses rightward vessel convexity from the anterior ventricle was the clue on the initial scan suggesting TGA, which was subsequently confirmed. In addition, only two vessels, the superior vena cava and aorta, were demonstrated in fetuses with TGA, the pulmonary artery and ductus arteriosus lying below (caudal to) the transverse arch.ConclusionsNoting the rightward convexity of the great vessel arising from the anterior ventricle may aid in the prenatal diagnosis of TGA. Furthermore, the relative simplicity of this sign may make it valuable in fetal screening for this cardiac defect.
Effects of Abdominal Fat Distribution Parameters on Severity of Acute Pancreatitis
Authors: O’Leary D. P. , O’Neill D. , McLaughlin P. , O’Neill S. , Myers E. , Maher M. M. , Redmond H. P. 
Published: April 2012

AbstractBackgroundObesity is a well‐established risk factor for acute pancreatitis. Increased visceral fat has been shown to exacerbate the pro‐inflammatory milieu experienced by patients.This study aimed to investigate the relationship between the severity of acute pancreatitis and abdominal fat distribution parameters measured on computed tomography (CT) scan.MethodsConsecutive patients admitted to Cork University Hospital with acute pancreatitis between January 2005 and December 2010 were evaluated for inclusion in the study. An open source image analysis software (Osirix, v 3.9) was used to calculate individual abdominal fat distribution parameters from CT scans by segmentation of abdominal tissues.ResultsA total of 214 patients were admitted with pancreatitis between January 2005 and December 2010. Sixty‐two of these patients underwent a CT scan and were thus eligible for inclusion. Visceral fat volume was the volumetric fat parameter that had the most significant association with severe acute pancreatitis (P = 0.003). There was a significant association between visceral fat volume and subsequent development of systemic complications of severe acute pancreatitis (P = 0.003). There was a strong association between mortality and visceral fat volume (P = 0.019). Multivariate regression analysis, adjusted for gender, did not identify any individual abdominal fat distribution index as an independent risk factor for severe acute pancreatitis.ConclusionsOverall, estimation of abdominal fat distribution parameters from CT scans performed on patients with acute pancreatitis indicates a strong association between visceral fat, severe acute pancreatitis, and the subsequent development of systemic complications. These data suggest that visceral fat volume should be incorporated into future predictive scoring systems.
Diagnostic Role of Procalcitonin in Patients with Suspected Appendicitis
Authors: Wu Jiunn‐Yih , Chen Hang‐Cheng , Lee Si‐Huei , Chan Rai‐Chi , Lee Chien‐Chang , Chang Shy‐Shin 
Published: April 2012

AbstractBackgroundThe aim of this study was to assess the diagnostic value of procalcitonin (PCT) in emergency department (ED) patients with suspected appendicitis.MethodsA prospective observational study was carried out inthe emergency department of a university hospital between July 2007 and June 2008. Adult patients who presented to the ED with clinically suspected appendicitis were enrolled. Each patient underwent serum PCT, C‐reactive protein (CRP), and Alvarado score evaluation on admission. The results of these three measurements were analyzed in relation to the final diagnosis determined by histopathological findings or compatible computed tomography findings.ResultsOf the 214 study patients, 113 (52.8 %) had a confirmed diagnosis of appendicitis and 58 had complicated appendicitis (phlegmon, perforation, or gangrene). For the diagnosis of appendicitis, the area under the receiving operating characteristic (ROC) curve is 0.74 for Alvarado score, 0.69 for PCT, and 0.61 for CRP. Overall, the Alvarado score has the best discriminative capability among the three tested markers. We adopted two cutoff point approaches to harness both ends of the diagnostic value of a biomarker. PCT levels were significantly higher in patients with complicated appendicitis. For diagnosis of complicated appendicitis, a cutoff value of 0.5 ng/mL had a sensitivity of 29 % and a specificity of 95 %, while a cutoff value of 0.05 ng/ml had a sensitivity of 85 % and a specificity of 30 % in diagnosing complicated appendicitis. For those with a PCT value in the gray zone, clinical findings may play a more important role.ConclusionThe study does not support the hypothesis that the PCT test may be useful for screening ED patients for appendicitis. However, determination of the PCT level may be useful for risk assessment of ED patients with suspected complicated appendicitis.
Developing a Prevention Synthesis and Translation System to Promote Science‐Based Approaches to Teen Pregnancy, HIV and STI Prevention
Authors: Lewis Kelly M. , Lesesne Catherine A. , Zahniser S. Christine , Wilson Mary Martha , Desiderio Gina , Wandersman Abraham , Green Diane C. 
Published: April 2012

AbstractThe Interactive Systems Framework for Dissemination and Implementation (ISF) is a multi‐system framework that can guide research‐to‐practice efforts by building and supporting the work of three interacting systems: the Prevention Delivery, Support, and Synthesis and Translation Systems. The Synthesis and Translation system is vital to bridging science and practice, yet how to develop it and train support system partners to use it is under‐researched. This article bridges this gap by offering a case example of the planning, development, and use of a synthesis and translation product called Promoting Science‐based Approaches to Teen Pregnancy Prevention using Getting To Outcomes. The case presented documents the process used for developing the synthesis and translation product, reports on efforts to engage the Prevention Support system to use the product, and how we approached building interaction between the Synthesis and Translation System and the Support System partners. Practice‐oriented evaluation data are also presented. Implications for practice, policy and research are discussed.Special Issue: Advances in Bridging Research and Practice Using the Interactive System Framework for Dissemination and Implementation; Guest Editors: Abraham Wandersman, Paul Flaspohler, Catherine A. Lesesne, Richard Puddy; Action Editor: Emilie Phillips Smith