bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate mass comparison coupled with two endopeptidases enables identification of protein termini
Authors: Kishimoto Taro , Kondo Jun , Takai‐Igarashi Takako , Tanaka Hiroshi 
Published: December 2010

AbstractProtein termini play important roles in biological processes, but there have been few methods for comprehensive terminal proteomics. We have developed a new method that can identify both the amino and the carboxyl termini of proteins. The method independently uses two proteases, (lysyl endopeptidase) Lys‐C and peptidyl‐Lys metalloendopeptidase (Lys‐N), to digest proteins, followed by LC‐MS/MS analysis of the two digests. Terminal peptides can be identified by comparing the peptide masses in the two digests as follows: (i) the amino terminal peptide of a protein in Lys‐C digest is one lysine residue mass heavier than that in Lys‐N digest; (ii) the carboxyl terminal peptide in Lys‐N digest is one lysine residue mass heavier than that in Lys‐C digest; and (iii) all internal peptides give exactly the same molecular masses in both the Lys‐C and the Lys‐N digest, although amino acid sequences of Lys‐C and Lys‐N peptides are different (Lys‐C peptides end with lysine, whereas Lys‐N peptides begin with lysine). The identification of terminal peptides was further verified by examining their MS/MS spectra to avoid misidentifying pairs as termini. In this study, we investigated the usefulness of this method using several protein and peptide mixtures. Known protein termini were successfully identified. Acetylation on N‐terminus and protein isoforms, which have different termini, was also determined. These results demonstrate that our new method can confidently identify terminal peptides in protein mixtures.
Adjusting conformational switching behavior of helical polycarbodiimides through substituent induced polarity effects
Authors: Kennemur Justin G. , Kilgore Chris A. , Novak Bruce M. 
Published: December 2010

AbstractRecent discoveries on the improved versatility of helical polycarbodiimides capable of undergoing low energy reversible conformational changes from realignment of their restricted polyarene pendant groups has led to seven new polycarbodiimides that each present unique information in regards to how the electronics and connectivity of the arene π‐system play a crucial role in the behavior of these polymers. In addition to their individual anomalous behavior, this series of functional polymers unlock new answers toward the global understanding of the governing forces behind this complex switching process. Through the incorporation of functional groups covalently attached to the naphthalene pendant, dramatic changes and new application of these systems are realized. Variable temperature polarimetry is used to observe the reversible conformational changes of these chiral polymers. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Development of CBT for chemotherapy‐related cognitive change: results of a waitlist control trial
Authors: Ferguson Robert J. , McDonald Brenna C. , Rocque Michael A. , Furstenberg Charlotte T. , Horrigan Susan , Ahles Tim A. , Saykin Andrew J. 
Published: December 2010

AbstractObjective: To evaluate the efficacy of a brief cognitive‐behavioral therapy (CBT) that is being developed for management of cognitive dysfunction following chemotherapy among breast cancer survivors. Memory and Attention Adaptation Training (MAAT) is a brief CBT designed to improve the quality of life and function among cancer survivors with post‐chemotherapy cognitive complaints.Methods: An initial, two‐group (MAAT versus waitlist, no treatment control), randomized clinical trial (RCT) was conducted. Forty stage I and II female breast cancer survivors (mean age = 50; SD = 6.4) were randomized to conditions and assessed at baseline, post‐treatment (8 weeks) and 2‐month follow‐up assessment points on measures of: (1) self‐reported daily cognitive failures; (2) quality of life; and (3) neuropsychological performance. Participants were also assessed for satisfaction with MAAT.Results: With education and IQ as covariates, MAAT participants made significant improvements relative to controls on the spiritual well‐being subscale of the quality of life measure and on verbal memory, but statistical significance was not achieved on self‐report of daily cognitive complaints. However, moderate‐to‐large effect sizes were observed on these outcomes. Participants gave MAAT high satisfaction ratings.Conclusions: Although this initial RCT is a small study, MAAT participants appear to improve on one measure of quality of life and verbal memory performance relative to no treatment controls and rate MAAT with high satisfaction. These data are encouraging and support the continued development and evaluation of MAAT efficacy.Copyright © 2010 John Wiley & Sons, Ltd.
The impact of social and personal resources on psychological distress in women at risk for hereditary breast cancer
Authors: den Heijer Mariska , Vos Joël , Seynaeve Caroline , Vanheusden Kathleen , Duivenvoorden Hugo J. , Tilanus‐Linthorst Madeleine , Menke‐Pluymers Marian B. E. , Tibben Aad 
Published: December 2010

AbstractObjective: The objectives of the present study were to (1) evaluate whether social and personal resources were independently related to psychological distress and (2) examine the interrelationships of social and personal resources in women at risk for hereditary breast cancer.Methods: General and breast cancer specific distress, family communication regarding hereditary breast cancer, perceived social support, self‐esteem, self‐concept, and demographics were assessed in 222 high‐risk women, having opted either for regular surveillance or prophylactic surgery.Results: Structural equation modeling showed that (1) both personal and social resources were independently associated with psychological distress and (2) the associations between social resources and psychological distress were partially mediated by personal resources. Support from family and friends was associated with a higher level of self‐esteem, which in turn was associated with less general distress. Furthermore, communication regarding cancer within the nuclear family was associated with decreased feelings of stigmatization, which in turn was associated with less general and breast cancer specific distress. Moreover, open communication within the family was associated with a reduced sense of vulnerability.Conclusion: Health workers involved in the care of high‐risk women should carefully monitor women's personal and social resources, and if compromised refer them for appropriate support. Copyright © 2010 John Wiley & Sons, Ltd.
A Heuristic Model of Twin Fluid Internally Mixed Atomization using Distributed Weber Number Criterion
Authors: Kushari Abhijit 
Published: December 2010

AbstractThis paper describes the development and predictions of a model that depicts the two‐phase flow within an internally mixed air‐assisted liquid atomizer using a statistical Weber number criterion. The main objective of this study is to develop an analytical tool that could be used in the design of internally mixed injectors and to predict the injector's flow and spray characteristics under different operating conditions. Basic conservation equations, along with appropriate boundary conditions, are used to model the two‐phase air‐liquid flow inside the injector. A statistically distributed Weber number criterion is used to estimate the sizes of the droplets being produced in the process. The liquid flow rates and mean droplet sizes, predicted by the model, are compared with the experimental data and they are found to be in fair agreement with each other.
Differential expression of red cell proteins in hemoglobinopathy
Authors: Chakrabarti Abhijit , Bhattacharya Dipankar , Basu Avik , Basu Sumanta , Saha Sutapa , Halder Suchismita 
Published: December 2010

AbstractRed blood cell proteome has not been studied well until recently, as the large abundance of hemoglobin posed challenge to the detection of other cytosolic proteins in the linear dynamic range. However, in the last couple of years, due to emergence of various novel hemoglobin depletion strategies and more state‐of‐the‐art detection techniques, a number of works on erythrocyte proteome have appeared in the literature. As a result, we now have much deeper information about both the membrane as well as the cytosolic proteins of erythrocytes. In this review, we have discussed the role of red cell proteome on the two most well‐studied hemoglobin disorders, sickle cell disease and thalassemia, emphasizing on the differential expression of the redox regulator proteins and chaperones, in particular. We have also touched upon the importance of the association of the varying levels of hemoglobin variants, particularly HbE on the clinical manifestation of composite diseases like HbEβ thalassemia.
The dynameomics rotamer library: Amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water
Authors: Scouras Alexander D. , Daggett Valerie 
Published: December 2010

AbstractWe have recently completed systematic molecular dynamics simulations of 807 different proteins representing 95% of the known autonomous protein folds in an effort we refer to as Dynameomics. Here we focus on the analysis of side chain conformations and dynamics to create a dynamic rotamer library. Overall this library is derived from 31,000 occurrences of each of 86,217 different residues, or 2.7 × 109 rotamers. This dynamic library has 74% overlap of rotamer distributions with rotamer libraries derived from static high‐resolution crystal structures. Seventy‐five percent of the residues had an assignable primary conformation, and 68% of the residues had at least one significant alternate conformation. The average correlation time for switching between rotamers ranged from 22 ps for Met to over 8 ns for Cys; this time decreased 20‐fold on the surface of the protein and modestly for dihedral angles further from the main chain. Side chain S2 axis order parameters were calculated and they correlated well with those derived from NMR relaxation experiments (R = 0.9). Relationships relating the S2 axis order parameters to rotamer occupancy were derived. Overall the Dynameomics rotamer library offers a comprehensive depiction of side chain rotamer preferences and dynamics in solution, and more realistic distributions for dynamic proteins in solution at ambient temperature than libraries derived from crystal structures, in particular charged surface residues are better represented. Details of the rotamer library are presented here and the library itself can be downloaded at http://www.dynameomics.org.
Metals affect the structure and activity of human plasminogen activator inhibitor‐1. II. Binding affinity and conformational changes
Authors: Thompson Lawrence C. , Goswami Sumit , Peterson Cynthia B. 
Published: December 2010

AbstractHuman plasminogen activator inhibitor type 1 (PAI‐1) is a serine protease inhibitor with a metastable active conformation. The lifespan of the active form of PAI‐1 is modulated via interaction with the plasma protein, vitronectin, and various metal ions. These metal ions fall into two categories: Type I metals, including calcium, magnesium, and manganese, stabilize PAI‐1 in the absence of vitronectin, whereas Type II metals, including cobalt, copper, and nickel, destabilize PAI‐1 in the absence of vitronectin, but stabilize PAI‐1 in its presence. To provide a mechanistic basis for understanding the unusual modulation of PAI‐1 structure and activity, the binding characteristics and conformational effects of these two types of metals were further evaluated. Steady‐state binding measurements using surface plasmon resonance indicated that both active and latent PAI‐1 exhibit a dissociation constant in the low micromolar range for binding to immobilized nickel. Stopped‐flow measurements of approach‐to‐equilibrium changes in intrinsic protein fluorescence indicated that the Type I and Type II metals bind in different modes that induce distinct conformational effects on PAI‐1. Changes in the observed rate constants with varying concentrations of metal allowed accurate determination of binding affinities for cobalt, nickel, and copper, yielding dissociation constants of ∼40, 30, and 0.09 μM, respectively. Competition experiments that tested effects on PAI‐1 stability were consistent with these measurements of affinity and indicate that copper binds tightly to PAI‐1.
Metals affect the structure and activity of human plasminogen activator inhibitor‐1. I. Modulation of stability and protease inhibition
Authors: Thompson Lawrence C. , Goswami Sumit , Ginsberg David S. , Day Duane E. , Verhamme Ingrid M. , Peterson Cynthia B. 
Published: December 2010

AbstractHuman plasminogen activator inhibitor type 1 (PAI‐1) is a serine protease inhibitor with a metastable active conformation. Under physiological conditions, half of the inhibitor transitions to a latent state within 1–2 h. The interaction between PAI‐1 and the plasma protein vitronectin prolongs this active lifespan by ∼50%. Previously, our group demonstrated that PAI‐1 binds to resins using immobilized metal affinity chromatography (Day, U.S. Pat. 7,015,021 B2, March 21, 2006). In this study, the effect of these metals on function and stability was investigated by measuring the rate of the transition from the active to latent conformation. All metals tested showed effects on stability, with the majority falling into one of two types depending on their effects. The first type of metal, which includes magnesium, calcium and manganese, invoked a slight stabilization of the active conformation of PAI‐1. A second category of metals, including cobalt, nickel and copper, showed the opposite effects and a unique vitronectin‐dependent modulation of PAI‐1 stability. This second group of metals significantly destabilized PAI‐1, although the addition of vitronectin in conjunction with these metals resulted in a marked stabilization and slower conversion to the latent conformation. In the presence of copper and vitronectin, the half‐life of active PAI‐1 was extended to 3 h, compared to a half‐life of only ∼30 min with copper alone. Nickel had the largest effect, reducing the half‐life to ∼5 min. Together, these data demonstrate a heretofore‐unknown role for metals in modulating PAI‐1 stability.
Antiinflammatory activity of Phyllanthus emblica, Plumbago zeylanica and Cyperus rotundus in acute models of inflammation
Authors: Dang G. K. , Parekar R. R. , Kamat S. K. , Scindia A. M. , Rege N. N. 
Published: December 2010

AbstractExperimental studies conducted earlier have proved that Phyllanthus emblica (Pe), Plumbago zeylanica (Pz) and Cyperus rotundus (Cr), plants from the medohara group of Ayurveda possess antiatherosclerotic activity. As inflammation is also one of the pathophysiological factors, it was of interest to evaluate whether these drugs exhibit any antiinflammatory activity. Two models of acute inflammation, namely carrageenan induced rat paw edema and acetic acid induced peritonitis in mice were used. In the model of carrageenan induced paw edema Pe, Pz and Cr showed a trend to reduce the edema while the combination of Pe + Pz (PI: 20.64%) showed results comparable to aspirin (23.74%). Whereas in a model of acetic acid induced peritonitis, all the plant drugs i.e. Pe, Pz, Cr and a combination of Pe + Pz showed a significant decrease in the protein content of the peritoneal exudates compared with the disease control group (p < 0.05), however, only Pe + Pz exhibited activity comparable to aspirin. Copyright © 2010 John Wiley & Sons, Ltd.
Performance bounds and suboptimal policies for linear stochastic control via LMIs
Authors: Wang Yang , Boyd Stephen 
Published: December 2010

AbstractIn a recent paper, the authors showed how to compute performance bounds for infinite‐horizon stochastic control problems with linear system dynamics and arbitrary constraints, objective, and noise distribution. In this paper, we extend these results to the finite‐horizon case, with asymmetric costs and constraint sets. In addition, we derive our bounds using a new method, where we relax the Bellman equation to an inequality. The method is based on bounding the objective with a general quadratic function, and using linear matrix inequalities (LMIs) and semidefinite programming (SDP) to optimize the bound. The resulting LMIs are more complicated than in the previous paper (which only used quadratic forms) but this extension allows us to obtain good bounds for problems with substantial asymmetry, such as supply chain problems. The method also yields very good suboptimal control policies, using control‐Lyapunov methods. Copyright © 2010 John Wiley & Sons, Ltd.
Frequency domain analysis of noise‐induced control chattering in sliding mode controls
Authors: Yeh Yi‐Liang , Chen Min‐Shin 
Published: December 2010

AbstractThe switching sliding mode control is robust with respect to disturbances, but its control signal has the so‐called chattering phenomenon that can damage the actuator and the system. To remove the chattering phenomenon, it has been proposed that one can use a continuous boundary layer design to replace the switching control. This paper shows, via the frequency domain analysis, that even when a boundary layer design is used, stochastic measurement noise can still induce the chattering phenomenon in control signals. Such noise‐induced chattering is almost unavoidable in noisy environments when the control accuracy requirement is high. Copyright © 2010 John Wiley & Sons, Ltd.
Design of UDE‐based controllers from their two‐degree‐of‐freedom nature
Authors: Zhong Qing‐Chang , Kuperman Alon , Stobart R. K. 
Published: December 2010

AbstractThe control algorithm based on the uncertainty and disturbance estimator (UDE) is a robust control strategy and has received wide attention in recent years. In this paper, the two‐degree‐of‐freedom nature of UDE‐based controllers is revealed. The set‐point tracking response is determined by the reference model, whereas the disturbance response and robustness are determined by the error feedback gain and the filter introduced to estimate the uncertainty and disturbances. It is also revealed that the error dynamics of the system is determined by two filters, of which one is determined by the error feedback gain and the other is determined by the filter introduced to estimate the uncertainty and disturbances. The design of these two filters are decoupled in the frequency domain. Moreover, after introducing the UDE‐based control, the Laplace transform can be applied to some time‐varying systems for analysis and design because all the time‐varying parts are lumped into a signal. It has been shown that, in addition to the known advantages over the time‐delay control, the UDE‐based control also brings better performance than the time‐delay control under the same conditions. Design examples and simulation results are given to demonstrate the findings. Copyright © 2010 John Wiley & Sons, Ltd.
Inter‐HAP handoff analysis for multi‐cell short‐endurance HAP communications systems
Authors: Li Shufeng , Grace David , Wei Jibo , Ma Dongtang 
Published: December 2010

AbstractIn this paper, we investigate an inter‐high‐altitude platform (HAP) handoff model for multi‐cell short‐endurance HAP wireless communications systems. Equations are derived to calculate system parameters, such as minimum user beamwidth and handoff opportunity (HO) interval, and system performance, such as handoff success ratio, inter‐HAP HO start rate and handoff load, when the current serving platform is replaced either for maintenance or for periodic replacement. Research results show some directions on how to select the trajectory of the platform, user beamwidth and handoff schemes. It is shown that it is better for the replacing platform to fly above and be as close as possible to the current serving platform. A higher altitude adopted by the current serving platform will allow a narrower user beamwidth. Two cellular handoff schemes are presented. It is shown that in the case of users with a wider antenna beamwidth free selection of any handoff destination cell can result in the handoff load being very high. By restricting the handoff destination cell to the cell with the same cell number within the footprints of the two platforms, the handoff traffic can be reduced to a minimum, but the two platforms are required to maintain the same relative cell layout. Copyright © 2010 John Wiley & Sons, Ltd.
Identifying and utilizing secure paths inad hocassistive medical environments
Authors: Belsis P. , Vassis D. , Skourlas C. 
Published: December 2010

ABSTRACTAs the capabilities of mobile devices continuously improve, a lot of environments that utilize such devices extend their functionalities; as a notable example, assistive environments offer a lot of characteristics that seemed inevitable a few years ago. In the healthcare domain modern systems are able to support advanced characteristics such as those associated with remote treatment facilities. In these environments sensitive medical data are being transmitted; therefore there is a need to ensure the security properties of medical information. A number of strict security requirements often imposed by different international legislation processes emerge due to the sensitivity of data being transmitted. In addition, in the absence of fixed infrastructures and stable topologies there is a need to create secure paths end‐to‐end for secure and efficient communication. In this paper we present an architecture that allows dissemination of medical information in a secure manner in the absence of stable topologies and infrastructures built upon resource efficient devices. The presented architecture utilizes advanced management techniques, achieving secure and privacy‐preserving transmission of sensitive data. We present a combination of different techniques and with a number of initial measurements we show the effective operation of our architecture in the presence of an adequately large number of users participating in the performance test‐bed scenario. Copyright © 2010 John Wiley & Sons, Ltd.
A fingerprint based bio‐cryptographic security protocol designed for client/server authentication in mobile computing environment
Authors: Xi Kai , Ahmad Tohari , Han Fengling , Hu Jiankun 
Published: December 2010

AbstractWith fast evolution of mobile devices and mobile network, the need of protecting user sensitive information locally and performing secure user authentication remotely become evermore increasing. Bio‐cryptography is emerging as a powerful solution which can combine the advantages of conventional cryptography and biometric security. In this paper, we present an efficient bio‐cryptographic security protocol designed for client/server authentication in current mobile computing environment, with a reasonable assumption that server is secure. In this protocol, fingerprint biometric is used in user verification, protected by a computationally efficient Public Key Infrastructure (PKI) scheme, Elliptic Curve Cryptography (ECC). The genuine fingerprint information is hidden in the feature vault which is the mixture of genuine and chaff features. Fingerprint features are not only used for biometric verification but also for cryptographic key generation. Our security analysis shows that the proposed protocol can provide a secure and trustworthy authentication of remote mobile users over insecure network. Experimental results on public domain database show an acceptable verification performance. We also tested the computational costs and efficiency of our protocol on the CLDC emulator using Java ME (previous J2ME) programming technology. The simulation results prove that the proposed protocol suits current mobile environment. Copyright © 2010 John Wiley & Sons, Ltd.