bluuebunny/crossref_metadata_2025_split huggingface dataset:
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
Authors: Jones David T. , Buchan Daniel W. A. , Cozzetto Domenico , Pontil Massimiliano 
Published: November 2011

Abstract
Motivation: The accurate prediction of residue–residue contacts, critical for maintaining the native fold of a protein, remains an open problem in the field of structural bioinformatics. Interest in this long-standing problem has increased recently with algorithmic improvements and the rapid growth in the sizes of sequence families. Progress could have major impacts in both structure and function prediction to name but two benefits. Sequence-based contact predictions are usually made by identifying correlated mutations within multiple sequence alignments (MSAs), most commonly through the information-theoretic approach of calculating mutual information between pairs of sites in proteins. These predictions are often inaccurate because the true covariation signal in the MSA is often masked by biases from many ancillary indirect-coupling or phylogenetic effects. Here we present a novel method, PSICOV, which introduces the use of sparse inverse covariance estimation to the problem of protein contact prediction. Our method builds on work which had previously demonstrated corrections for phylogenetic and entropic correlation noise and allows accurate discrimination of direct from indirectly coupled mutation correlations in the MSA.
Results: PSICOV displays a mean precision substantially better than the best performing normalized mutual information approach and Bayesian networks. For 118 out of 150 targets, the L/5 (i.e. top-L/5 predictions for a protein of length L) precision for long-range contacts (sequence separation &gt;23) was ≥0.5, which represents an improvement sufficient to be of significant benefit in protein structure prediction or model quality assessment.
Availability: The PSICOV source code can be downloaded from http://bioinf.cs.ucl.ac.uk/downloads/PSICOV
Contact: d.jones@cs.ucl.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
An Allosteric Coagonist Model for Propofol Effects on α1β2γ2L γ-Aminobutyric Acid Type A Receptors
Authors: Ruesch Dirk , Neumann Elena , Wulf Hinnerk , Forman Stuart A. 
Published: November 2011

Background
Propofol produces its major actions via γ-aminobutyric acid type A (GABA(A)) receptors. At low concentrations, propofol enhances agonist-stimulated GABA(A) receptor activity, and high propofol concentrations directly activate receptors. Etomidate produces similar effects, and there is convincing evidence that a single class of etomidate sites mediate both agonist modulation and direct GABA(A) receptor activation. It is unknown if the propofol binding site(s) on GABA(A) receptors that modulate agonist-induced activity also mediate direct activation.

Methods
GABA(A) α1β2γ2L receptors were heterologously expressed in Xenopus oocytes and activity was quantified using voltage clamp electrophysiology. We tested whether propofol and etomidate display the same linkage between agonist modulation and direct activation of GABA(A) receptors by identifying equiefficacious drug solutions for direct activation. We then determined whether these drug solutions produce equal modulation of GABA-induced receptor activity. We also measured propofol-dependent direct activation and modulation of low GABA responses. Allosteric coagonist models similar to that established for etomidate, but with variable numbers of propofol sites, were fitted to combined data.

Results
Solutions of 19 μM propofol and 10 μM etomidate were found to equally activate GABA(A) receptors. These two drug solutions also produced indistinguishable modulation of GABA-induced receptor activity. Combined electrophysiological data behaved in a manner consistent with allosteric coagonist models with more than one propofol site. The best fit was observed when the model assumed three equivalent propofol sites.

Conclusions
Our results support the hypothesis that propofol, like etomidate, acts at GABA(A) receptor sites mediating both GABA modulation and direct activation.
Musculotendinous Infraspinatus Rupture and Shoulder Weakness
Authors: Lipford Melissa C , Bond Jeffrey R , Steinmann Scott P , Kumar Neeraj 
Published: November 2011

Abstract

We report a patient with bilateral simultaneous onset of weakness of shoulder lateral rotation due to musculotendinous infraspinatus rupture that occurred after shoulder steroid injections. Disruption of the musculotendinous junction of the infraspinatus is a rare recently described entity. Electromyography is normal, and magnetic resonance image findings are characteristic.
Neuromuscular Manifestations of HIV/AIDS
Authors: Harrison Taylor B , Smith Bryan 
Published: November 2011

Abstract

The human immunodeficiency virus (HIV) epidemic, now entering its fourth decade, affects approximately 33 million people living in both developed and resource-limited countries. Neurological complications of the peripheral nervous system are common in HIV-infected patients, and neuromuscular pathology is associated with significant morbidity. Peripheral neuropathy is the most common neuromuscular manifestation observed in HIV/AIDS, and in the antiretroviral era, its prevalence has increased. The purpose of this review was to describe the clinical spectrum of neuromuscular disorders in the setting of HIV infection and to provide an approach to diagnosis and management.
Rituximab and Mycophenolate Combination Therapy in Refractory Dermatomyositis With Multiple Autoimmune Disorders
Authors: Parziale Nicholas , Kovacs Susan C , Thomas Christine B , Srinivasan Jayashri 
Published: November 2011

Abstract

We report a case of dermatomyositis associated with rheumatoid arthritis, Hashimoto thyroiditis, and diabetes mellitus responsive only to combination of rituximab with mycophenolate. A 42-year-old woman presented with proximal muscle weakness, myalgias, fever, night sweats, and shortness of breath. Creatinine kinase was 8155 IU/L, and muscle biopsy was diagnostic of dermatomyositis. She was started on glucocorticoids; her systemic symptoms improved, but her muscle weakness persisted. She was serially treated with intravenous immunoglobulin, azathioprine, and mycophenolate mofetil without improvement in her weakness. She responded dramatically to combination therapy with rituximab and mycophenolate, with improvement in strength and normalization of creatinine kinase. She has been well controlled on rituximab infusion every 6 months and maintenance mycophenolate mofetil.
The Phosphoglucan Phosphatase Like Sex Four2 Dephosphorylates Starch at the C3-Position in Arabidopsis
Authors: Santelia Diana , Kötting Oliver , Seung David , Schubert Mario , Thalmann Matthias , Bischof Sylvain , Meekins David A. , Lutz Andy , Patron Nicola , Gentry Matthew S. , Allain Frédéric H.-T. , Zeeman Samuel C. 
Published: November 2011

Abstract
Starch contains phosphate covalently bound to the C6-position (70 to 80% of total bound phosphate) and the C3-position (20 to 30%) of the glucosyl residues of the amylopectin fraction. In plants, the transient phosphorylation of starch renders the granule surface more accessible to glucan hydrolyzing enzymes and is required for proper starch degradation. Phosphate also confers desired properties to starch-derived pastes for industrial applications. In Arabidopsis thaliana, the removal of phosphate by the glucan phosphatase Starch Excess4 (SEX4) is essential for starch breakdown. We identified a homolog of SEX4, LSF2 (Like Sex Four2), as a novel enzyme involved in starch metabolism in Arabidopsis chloroplasts. Unlike SEX4, LSF2 does not have a carbohydrate binding module. Nevertheless, it binds to starch and specifically hydrolyzes phosphate from the C3-position. As a consequence, lsf2 mutant starch has elevated levels of C3-bound phosphate. SEX4 can release phosphate from both the C6- and the C3-positions, resulting in partial functional overlap with LSF2. However, compared with sex4 single mutants, the lsf2 sex4 double mutants have a more severe starch-excess phenotype, impaired growth, and a further change in the proportion of C3- and C6-bound phosphate. These findings significantly advance our understanding of the metabolism of phosphate in starch and provide innovative options for tailoring novel starches with improved functionality for industry.
Ag lending: the next generation
Authors: Gunderson Michael A. , Detre Joshua D. , Briggeman Brian C. , Wilson Christine A. 
Published: November 2011

PurposeThe purpose of this paper is to identify relevant financial concepts and skills that are being taught and/or should be taught, as part of the financial management curriculum in undergraduate agricultural economics and agribusiness programs.Design/methodology/approachThe skill gap analysis uses survey respondents' rankings of the importance and competence scores of recent graduates' skills. The scores help to identify opportunities for improvement in the most critical areas of importance. The skill gap is calculated as (Average importance–Average competence)*Average importance.FindingsGenerally, employers in the agricultural financial services sector saw greater opportunities for improvement in finance skills relative to non‐finance skills. The results also indicated a greater focus on business and financial risk might be helpful in increasing the competence of new hires. Finally, respondents strongly endorsed maintaining a focus on the problem‐solving skills in undergraduate agribusiness programs.Originality/valueThe value of the study would be that departments of agricultural and applied economics would use the results of this survey to enhance their financial management curriculum and their undergraduate program. By responding to the desires of employers, agricultural economics and agribusiness programs cannot only remain relevant as a source of employees for the industry but the first choice of agricultural financial services sector when they are searching for new hires. This should also help inform students of the desirability of the skills they acquire in their degree programs. This information will also benefit the agricultural finance services sector by assisting college and university instructors in developing and/or enhancing their agricultural finance course(s) so that the may provide their students with the requisite financial and non‐financial skills that they require.
Joint measurement of farm size and farm performance: a confirmatory factor analysis
Authors: Hadrich Joleen C. , Olson Frayne 
Published: November 2011

PurposeThe purpose of this paper is to determine if a single dominant measure defines farm size and farm performance consistently over a ten‐year time period, or if alternative measures are needed. The paper also seeks to determine the correlation between farm size and farm performance and how this correlation may change over time.Design/methodology/approachA confirmatory factor analysis was used to test the relative strength of farm size and performance indicator variables and estimate the relationship between farm size and performance latent variables. Data were collected from the North Dakota Farm and Ranch Business Management Association (NDFRBA) Annual Summaries for 2000‐2009.FindingsResults demonstrated that a single indicator, such as acres or rate of return on assets, may not capture the array of farm size and farm performance concepts and multiple indicators should be used to jointly determine farm size and farm performance measures. Results also found a sequential decrease in correlation between farm size and performance for seven of the ten years.Originality/valueThis paper addresses the issue regarding multiple measures for farm size and farm performance which helps provide the framework to begin developing a systematic classification of farms for use in strategic farm planning and guide future government policies, federal farm programs, and environmental regulations.
A triple hurdle model of US commercial bank use of guaranteed operating loans and interest assistance
Authors: Ahrendsen Bruce L. , Dixon Bruce L. , Settlage Latisha A. , Koenig Steven R. , Dodson Charles B. 
Published: November 2011

PurposeThe purpose of this paper is to estimate a three‐equation model of US commercial bank usage of the Farm Service Agency's (FSA) guaranteed operating loan and interest assistance programs. Also, to identify the key farm and banking variables that affect the decision to use loan guarantees and the volume of loans with interest assistance.Design/methodology/approachA triple hurdle, three‐equation system is estimated to model three decisions: to participate in the FSA operating loan program; whether to use interest assistance given the decision to participate in the operating loan program; and then the degree of participation in the interest assistance program. Statistical selection is modeled. Data on almost all commercial banks in the USA from 1995 to 2003 are used in the estimation sample.FindingsStatistical selection is statistically significant so selection must be included in the models. Variables reflecting state‐level characteristics such as farm debt servicing ratio, individual bank loan‐to‐asset ratio, bank size and the general guaranteed loan and interest assistance environment are significant in all three equations. Intensity of interest assistance use varies markedly across states.Originality/valueThe interest assistance program has high subsidy costs and is an important source of support for financially marginal farmers. Scant prior research has investigated this program. The present study also shows that modeling interest assistance usage must be embedded in a larger model to give a complete specification.
The effects of direct payments on liquidity and repayment capacity of beginning farmers
Authors: Kropp Jaclyn D. , Katchova Ani L. 
Published: November 2011

PurposeUS decoupled direct payments, paid to farm operators based on historic yields and base acreage under the 2002 Farm Bill, may alter a farmer's access to credit or his ability to meet debt servicing obligations. More specifically, direct payments might improve the farmer's liquidity position or repayment capacity enabling the farmer to obtain more favorable credit terms. In turn, more favorable credit terms might allow a farm to remain in business or expand production, leading to current production distortions. Since direct payments are based on historic production, beginning farmers tend to receive lower levels of direct payments and hence these payments might impact beginning farmers differently than more experienced farmers. The purpose of this paper is to investigate the effects of direct payments on liquidity and repayment capacity for experienced and beginning farmers.Design/methodology/approachGiven the manner in which direct payments are calculated and administered, it is likely that direct payments affect beginning farmers and more experienced farmers differently; hence the authors analyze the impacts of direct payments on the current and term debt coverage ratios for these two groups separately. In the analysis, the authors control for farm financial characteristics, farm operator characteristics, and other factors. Data from the US Department of Agriculture (USDA) Agricultural Resource Management Survey (ARMS) for the years 2005, 2006, and 2007 were used in the weighted regression analysis and jackknifed standard errors computed.FindingsA positive significant relationship was found between the level of direct payments (in dollars) and the term debt coverage ratio for experienced farmers, suggesting that direct payments improve repayment capacity. However, this relationship is not significant for beginning farmers. Also, a negative significant relationship was found between the number of base acres and the current ratio for experienced farmers, while this relationship lacks significance for beginning farmers.Originality/valueThe paper provides evidence that decoupled direct payments impact a farmer's liquidity and repayment capacity. Furthermore, direct payments impact beginning and experienced farmers differently. This paper also contributes to the growing body of research investigating the mechanisms by which decoupled payments have the potential to distort current production.
Study on prolonging the working time of silane solution during the silylation process on carbon steel
Authors: Ran Changrong , Lu Wenli , Song Guo , Ran Chao , Zhao Shuo 
Published: November 2011

PurposeIn the industrial silylation process, the cost of production can be greatly reduced by reducing the frequency of the replacement of the silane solution. The purpose of this paper is to describe how a method of discontinuous addition of concentrated solution into the KH560 treatment bath was developed, to improve further the effective availability of the silane solution and reduce cost of production.Design/methodology/approachThe preparation and addition of each incremental amount of concentrated KH560 was studied in detail.FindingsThe results indicate that adding concentrated silane solution is an effective method of maintaining the target bath concentration.Originality/valueThe paper describes how a method of adding concentrated KH560 was developed to prolong the working time of KH560 solution for silane coating production, and to improve the availability of the KH560 in solution. The results indicated that adding concentrated solution was an effective method of prolonging the working time of the silane solution. The mixture ratio of the concentrated solution, and the volume of each incremental amount, both affected the performance of the KH560 solution.
Use of AES in corrosion of copper connectors of electronic devices and equipments in arid and marine environments
Authors: Lopez Gustavo , Tiznado Hugo , Soto Herrera Gerardo , De la Cruz Wencel , Valdez Benjamin , Schorr Miguel , Roumen Zlatev 
Published: November 2011

PurposeThe electronics industry has grown over the past 50 years, mostly in developed countries, contributing to their economic progress. Particularly in the Baja California State located in the northwest of Mexico, these companies have prospered in the industrial parks of Mexicali considered as an arid zone and Ensenada, a port and city on the Pacific Ocean considered as a marine region. In both environments, during winter and summer, the climate impacts on indoor conditions, affecting humidity and temperature, and generating corrosion which decreases the yields of the electronic devices and industrial machines. The purpose of this paper is to investigate the effects of corrosion on electronic devices in these arid and marine environments.Design/methodology/approachThe paper determines the corrosivity levels inside industrial plants of desertic and coast regions in Mexico, to evaluate the deterioration of electronic metals.FindingsRelative humidity, temperature, time of wetness, are recorded and related to the corrosion process in arid and marine environments.Research limitations/implicationsSome missing information about air pollution in Ensenada from some Environmental Monitoring Stations was a limitation, and the need to use complex atmospheric techniques.Originality/valueThe paper shows that it is very important to control metallic corrosion generated by climate factors and air pollution in indoor industrial plants: the corrosion of electronic devices and equipments depletes their yield and can lead to loss‐making failures.
The missing component in MBA programs
Authors: Almog‐Bareket Granit 
Published: November 2011

PurposeThe aim of this paper is to illuminate a crucial component missing in the education of MBA students. This component involves awareness translated into skills that would enable leaders to narrow the gap between vision and practice.Design/methodology/approachAn analysis of MBA curricula shows that the ability to exploit intangible assets has not been explored sufficiently as well as why this ability is instrumental for leadership.FindingsThis study emphasises how crucially important it is for leaders to be able to consolidate a vision and lead change derived from that vision as reflected in their daily managerial practice, and argues that current MBA students need to develop additional unique skills that will enable them to diagnose problems related to the assimilation of change and to measure the effectiveness of this process.Originality/valueThis paper offers an original approach to the link between theory and practice and to the importance of developing a vision that challenges the way this topic is generally taught in MBA programs.
Internal and external antecedents of SMEs' innovation ambidexterity outcomes
Authors: Chang Yi‐Ying , Hughes Mathew , Hotho Sabine 
Published: November 2011

PurposePrior studies have suggested that organizational and environmental antecedents are influential to the development of a balance dimension of innovation ambidexterity, which are proposed to be central to superior firm performance. However, little is known about how such antecedents affect the shaping of innovation ambidexterity in small to medium‐sized enterprises (SMEs) and how these innovations go on to shape firm performance. This paper aims to examine internal and external antecedents of SMEs' innovation ambidexterity outcomes.Design/methodology/approachThe research used a survey method to investigate the 1,000 small‐and medium sized enterprises in Scotland. Firms were randomly selected from the FAME database. Of this sample, 265 firms (26.5 percent) responded to the survey.FindingsThe data analysis reveals that internal organizational structures in a highly dynamic environment stimulate the appearance of innovation ambidexterity. Moreover, it is found that the relationship between organizational and environmental forces and firm performance is partially mediated by a balance dimension of innovation ambidexterity.Practical implicationsThe results show how dangerous the lack of adequate research of these issues at the SME level is. By contrast to larger firms, the results show how internal organizational structures and external environmental conditions affect SMEs to pursue a balance dimension of innovation ambidexterity.Originality/valuePrior studies have paid little attention to the effects of internal organizational structures and external environmental conditions on the appearance of a balance dimension of innovation ambidexterity within SMEs. This paper fills some of the gaps.
Value proposition as a catalyst for a customer focused innovation
Authors: Lindič Jaka , Marques da Silva Carlos 
Published: November 2011

PurposeThis paper seeks to advance the theory on value proposition and innovation by offering a framework for identifying value proposition elements.Design/methodology/approachA single embedded case study is conducted based on Amazon.com's innovations.FindingsBy identifying and systematically analysing innovations by Amazon.com, the concept of value proposition was decomposed into five components: performance, ease of use, reliability, flexibility and affectivity (PERFA).Research limitations/implicationsThe research did not focus on the relationships between the value proposition elements and their relevance in different contexts such as product, industry or customer life cycle.Practical implicationsManagers should support their decision to innovate the value proposition based on customers' perceived value. The findings provide guidance to managers on how to uncover innovative value propositions and potentially create new demand in an uncontested market space.Originality/valueThe paper is an original attempt to correlate value proposition and innovation. It provides researchers and practitioners with a better understanding of the structure of a value proposition and how innovation can influence it.