bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simple sequence-based kernels do not predict protein–protein interactions
Authors: Yu Jiantao , Guo Maozu , Needham Chris J. , Huang Yangchao , Cai Lu , Westhead David R. 
Published: August 2010

Abstract
Motivation: A number of methods have been reported that predict protein–protein interactions (PPIs) with high accuracy using only simple sequence-based features such as amino acid 3mer content. This is surprising, given that many protein interactions have high specificity that depends on detailed atomic recognition between physiochemically complementary surfaces. Are the reported high accuracies realistic?
Results: We find that the reported accuracies of the predictions are significantly over-estimated, and strongly dependent on the structure of the training and testing datasets used. The choice of which protein pairs are deemed as non-interactions in the training data has a variable impact on the accuracy estimates, and the accuracies can be artificially inflated by a bias towards dominant samples in the positive data which result from the presence of hub proteins in the protein interaction network. To address this bias, we propose a positive set-specific method to create a ‘balanced’ negative set maintaining the degree distribution for each protein, leading to the conclusion that simple sequence-based features contain insufficient information to be useful for predicting PPIs, but that protein domain-based features have some predictive value.
Availability: Our method, named ‘BRS-nonint’, is available at http://www.bioinformatics.leeds.ac.uk/BRS-nonint/. All the datasets used in this study are derived from publicly available data, and are available at http://www.bioinformatics.leeds.ac.uk/BRS-nonint/PPI_RandomBalance.html
Contact: maozuguo@hit.edu.cn; d.r.westhead@leeds.ac.uk
miRNAkey: a software for microRNA deep sequencing analysis
Authors: Ronen Roy , Gan Ido , Modai Shira , Sukacheov Alona , Dror Gideon , Halperin Eran , Shomron Noam 
Published: August 2010

Abstract
Motivation: MicroRNAs (miRNAs) are short abundant non-coding RNAs critical for many cellular processes. Deep sequencing (next-generation sequencing) technologies are being readily used to receive a more accurate depiction of miRNA expression profiles in living cells. This type of analysis is a key step towards improving our understanding of the complexity and mode of miRNA regulation.
Results: miRNAkey is a software package designed to be used as a base-station for the analysis of miRNA deep sequencing data. The package implements common steps taken in the analysis of such data, as well as adds unique features, such as data statistics and multiple read determination, generating a novel platform for the analysis of miRNA expression. A user-friendly graphical interface is applied to determine the analysis steps. The tabular and graphical output contains general and detailed reports on the sequence reads and provides an accurate picture of the differentially expressed miRNAs in paired samples.
Availability and implementation: See http://ibis.tau.ac.il/miRNAkey
Contact: nshomron@post.tau.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
Paraneoplastic Motor Neuron Disease Associated With Purkinje Cell Autoantibody Type 1
Authors: Distad B Jane , Weiss Michael D 
Published: August 2010

Abstract

Motor neuron disease has been reported as a rare result of systemic cancers, likely related to an autoimmune effecter mechanism. These patients have been described as having a more rapid onset of symptoms than typical motor neuron disease. Few of these reports demonstrate an association of a cancer-related autoantibody and with motor neuron disease. We present a 54-year-old woman with infiltrating ductal carcinoma of the breast who later developed lower motor neuron disease and was found to have Purkinje cell autoantibodies type 1. The association of lower motor neuron disease as a consequence of breast cancer with this autoantibody profile has not been described previously. This report emphasizes the importance of considering a paraneoplastic syndrome in a patient with an uncommon presentation of motor neuron disease.
Adult-Onset Acid Maltase Deficiency With Isolated Axial Muscle Involvement
Authors: Salem Bassel , Thaisetthawatkul Pariwat , Fernandes J Americo , McComb Rodney D 
Published: August 2010

Introduction:
We report a patient with acid maltase deficiency who presented with subacute respiratory failure as the first symptom without significant extremity weakness.

Methods and Results:
Electromyography of extremities was normal but showed myopathic changes and myotonic discharges limited to axial muscles only. Muscle biopsy confirmed the diagnosis.

Conclusion:
It is essential to examine axial muscles during electromyography if a patient presents with respiratory failure of unclear etiology even if the clinical examination does not show significant weakness in the extremities and electromyographic findings in the extremities are unremarkable.
Molecular and Physiological Analysis of Drought Stress in Arabidopsis Reveals Early Responses Leading to Acclimation in Plant Growth
Authors: Harb Amal , Krishnan Arjun , Ambavaram Madana M.R. , Pereira Andy 
Published: September 2010

AbstractPlant drought stress response and resistance are complex biological processes that need to be analyzed at a systems level using genomics and physiological approaches to dissect experimental models that address drought stresses encountered by crops in the field. Toward this goal, a controlled, sublethal, moderate drought (mDr) treatment system was developed in Arabidopsis (Arabidopsis thaliana) as a reproducible assay for the dissection of plant responses to drought. The drought assay was validated using Arabidopsis mutants in abscisic acid (ABA) biosynthesis and signaling displaying drought sensitivity and in jasmonate response mutants showing drought resistance, indicating the crucial role of ABA and jasmonate signaling in drought response and acclimation. A comparative transcriptome analysis of soil water deficit drought stress treatments revealed the similarity of early-stage mDr to progressive drought, identifying common and specific stress-responsive genes and their promoter cis-regulatory elements. The dissection of mDr stress responses using a time-course analysis of biochemical, physiological, and molecular processes revealed early accumulation of ABA and induction of associated signaling genes, coinciding with a decrease in stomatal conductance as an early avoidance response to drought stress. This is accompanied by a peak in the expression of expansin genes involved in cell wall expansion, as a preparatory step toward drought acclimation by the adjustment of the cell wall. The time-course analysis of mDr provides a model with three stages of plant responses: an early priming and preconditioning stage, followed by an intermediate stage preparatory for acclimation, and a late stage of new homeostasis with reduced growth.
How can employee engagement be improved at the RRG Group? Part 2
Authors: Evans Cheryl , Redfern David C. 
Published: August 2010

PurposeThis is the second section of a two‐part study of employee engagement. The first part, in the previous issue (Vol. 42, No. 5, 2010), explored the literature that places this study in context. The key aim of the study is to assess the main factors encouraging or preventing employee engagement, focusing specifically on staff employed within nine Toyota branches of the RRG Group.Design/methodology/approachThe main methods used to investigate employee engagement were: assessing the qualitative data through attitudinal surveys, analyzing complete customer satisfaction (CCS) scores and telephone interviews with previous employees who had voluntarily resigned between January and June 2009.FindingsThe business has been called the RRG Group Limited which operates within the UK Motor Retail Industry and was acquired by the Top Fortune 500 Japanese Corporation Marubeni in 2000. The Group employs approximately 650 and consists of 19 dealerships that are located in the North West of England, comprising Lexus, Peugeot, Mazda and Toyota franchises, in addition to two Accident Repair Centres. The Group is now one of the largest Toyota retail groups within Europe. The main conclusions are that engagement levels across the nine RRG Toyota franchises appear fairly high within the majority of the branches. However, there are key factors which appear to be preventing engagement at particular branches which need to be addressed in order to improve engagement such as communication, remuneration, the branch induction process and work/life balance.Practical implicationsThe primary recommendations include leadership development for management in certain skills, a focus on fostering a two‐way conversation with employees and finally to continuously monitor and evaluate practices through annual attitudinal surveys and setting realistic action plans in order to make improvements.Originality/valueThe nature of the challenge for management in securing engagement and improving work performance is explored.
Interdisciplinary collaboration
Authors: Little Jennifer J. , Fallon Moira , Dauenhauer Jason , Balzano Betsy , Halquist Donald 
Published: August 2010

PurposeMany colleges and universities require both undergraduate and graduate students to plan and conduct research as a part of graduation requirements. However, a number of barriers exist for both instructors and students in understanding and conducting research. A small group of, The College at Brockport, instructors who had taught introductory research and research methodology gathered together with librarians as a faculty learning community (FLC) to share information about their instructional methods for teaching research skills. The paper aims to discuss this initiative.Design/methodology/approachFollowing an initiative to foster career‐span faculty development, The College at Brockport made a three‐year commitment to implement a variety of topic‐based FLCs beginning in the fall 2008 semester.FindingsLike librarians across the country Brockport librarians have been creating research guides, or “pathfinders,” for decades. The term “pathfinder” was coined in the early 1970s when MIT librarians developed lists of resources and references pertaining to subject disciplines. When LibGuides are marketed, it is not surprising that libraries are quick to adopt this platform to produce pathfinders. LibGuides are chosen because they provide a convenient and simple way to create and update research guides using a live interface, employ web 2.0 technologies in a user‐friendly format, and encourage collaboration.Originality/valueBased on the evaluative and qualitative feedback the LibGuide has been refined further. It is a guide that will be under modification as more faculty and students use it.
Generation next: recruiting minority students to librarianship
Authors: Love Emily 
Published: August 2010

PurposeConsidering the shortage of minority representation in the library profession, this paper aims to examine minority students' awareness of librarianship and investigates the impact of marketing academic librarianship to students at the campus' cultural centers as a recruitment method.Design/methodology/approachThe paper analyses previous studies and provides results from a survey distributed to minority students at two of the cultural centers and at the Summer Research Opportunities Program, a program that prepares minority students for graduate studies.FindingsResults indicate a connection between presentations to students about academic librarianship and their interest in pursuing the profession. Findings highlight students' lack of awareness of librarian job responsibilities and the findings also highlight students' preferred methods for continued mentorship and support.Research limitations/implicationsMore qualitative research would prove valuable to gain in‐depth feedback from students about their understanding of the library profession and what factors are most and least likely to attract them to the profession. A second paper is planned to investigate the number of students who pursued a library degree that attended one of these sessions.Practical implicationsThe paper highlights a simple, affordable and replicable alternative to time‐intensive and heavily subsidized recruitment programs.Social implicationsAs the population becomes more diverse and patron needs change, the library profession, which is predominantly white, will need to diversify to reflect patrons' increasingly diverse needs.Originality/valueMany large‐scale recruitment initiatives recruit minority students to academic librarianship. This paper describes a small‐scale and effective approach to minority student recruitment.
Principles of employment relations in Islam: a normative view
Authors: Syed Jawad , Ali Abbas J. 
Published: August 2010

PurposeThe purpose of this paper is to describe a normative perspective of employment relations in Islam.Design/methodology/approachThe perspective on employment relations offered in this paper is based on a reading of the principal Islamic texts (the Qur'an and the hadith) and a review of the literature on Islamic economics.FindingsDespite varied interpretations and practices of the economic system in Islam, it is possible to identify a common emphasis on ethical conduct of employers and employees and social justice in Islamic ideology.Originality/valueGiven the paucity of research on employment relations in Islam, the paper offers an original perspective on this topic.
Risk‐return trade‐offs to different educational paths: vocational, academic and mixed
Authors: Tuor Simone N. , Backes‐Gellner Uschi 
Published: August 2010

PurposeThe purpose of this paper is to investigate the rates of return and the risks of different types of educational paths – all leading to a tertiary educational degree. The paper seeks to distinguish a purely academic educational path from a purely vocational path and a mixed path with loops through both systems.Design/methodology/approachThe paper studies the labor market outcome to compare earnings and calculate net return rates as well as risk measures to investigate whether different educational paths are characterized by different risk‐return trade‐offs. Entrepreneurs are separated from employees in order to examine whether for the same combination of education the labour market outcomes differ between the two groups.FindingsThe empirical results are based on the Swiss Labor Force Survey (SLFS) and demonstrate that mixed educational paths are well rewarded in the labor market. However, for entrepreneurs a high return is also associated with a high income variance.Research limitations/implicationsThe findings provide evidence for the existence of complementarities between vocational and academic education. Further research on mixed educational paths might provide more insight into this presumed relationship.Practical implicationsSince the results indicate that mixed educational paths are a worthwhile strategy, the permeability of a national education system is a very important educational policy issue.Originality/valueThe study is innovative in three ways: first, it focuses on complete educational paths and not just the highest educational degree. Second, an alternative measure, the Baldwin rate of return, is used to assess the profitability attached to different educational paths. Third, the income risk associated with each educational path is calculated.
Resources in vocational education and post‐schooling outcomes
Authors: Maliranta Mika , Nurmi Satu , Virtanen Hanna 
Published: August 2010

PurposeThe purpose of this paper is to examine the determinants of labour market outcomes after the initial vocational basic education (ISCED 3).Design/methodology/approachA multinomial logit model is used for examining the effect of school resources and other factors on students' post‐schooling outcomes defined as employment, further studies, non‐employment and dropping out. Analysis has been done by using unique linked register data on students, their parents, teachers, educational organisations and business companies in Finland.FindingsThe results indicate that teaching expenditures do not matter but teachers' characteristics have a role to play. Teachers with a university degree increase the employment probability of the students, whereas the formal competence of the teachers does not have such positive effects. The students' characteristics and performance in comprehensive schools play an important role in determining the outcomes. Local business conditions affect the outcomes of boys but less those of girls. The official quality evaluations adopted in recent years seem to pay attention especially to such aspects of education production that are important for providing capabilities for further studies but less so for employability.Originality/valueEmployability seems to be a great challenge to the initial vocational basic education. The findings for local business conditions give support to the view that measures of education policy do not suffice but need to be complemented with those of regional or employment policy, for example, policies aiming to increase regional mobility of the labour force. Such complementary tools are particularly important for boys.
The facilities manager preparing for climate change related disaster
Authors: Warren Clive M.J. 
Published: August 2010

PurposeClimate change is predicted to have a significant effect on the frequency of extreme weather events and the occurrence of natural disasters. There is a need for facilities managers to mitigate against potential disruption and prepare for future events. Current practice, however, as illustrated by the literature shows that little risk assessment is currently undertaken with few organisations preparing integrated disaster management plans or business continuity plans to help them meet the challenge. This paper aims to describe the current climate change predictions and the likely consequences for building assets in the face of extreme weather events.Design/methodology/approachThe paper was based on literature review of current climate change data and published research and guidance for facilities managers in preparing risk assessment and disaster plans.FindingsThe research reveals that there exists a divergence between current scientific data relating to potential effects of climate change on the built environment and the level of disaster planning and organisational resilience to extreme weather events.Research limitations/implicationsThe paper provides an overview of the recent changes in disaster occurrence and the potential for increasing climate‐related crisis and disasters which have potential to significantly compromise the ongoing use of an organisation's facilities. The paper concludes that facilities managers need to be proactive in their risk assessment and disaster planning.Practical implicationsThe paper highlights the potential for increased climate change‐related natural disasters. Property assets are likely to be significantly impacted and as a consequence facilities disaster plans should address the issue of natural disaster preparedness. Current literature reveals a limited level of disaster planning is occurring.Originality/valueThe paper provides an important link between current climate change predictions, the increasing levels of natural disasters resulting from climate change and the potential for significant disruption to business facilities. The paper builds on earlier research highlighting the potential for climate‐related natural disaster.
Literature review on design terror mitigation for facility managers in public access buildings
Authors: Lavy Sarel , Dixit Manish K. 
Published: August 2010

PurposeThe purpose of this paper is to identify key risks that are posed to the security of a site and building perimeters in the first and second lines of defense against terrorism, and are relevant to facility managers.Design/methodology/approachA qualitative approach to the literature review was applied. This involved an extensive literature search of existing peer‐reviewed research papers, as well as state and federal reports to mark crucial issues relating to the security of a facility. Strategies to deal with the critical issues pertaining to the security of a facility were reviewed, based on the literature.FindingsThe paper identifies major security risks suggested by the literature and lists strategies to address those risks. The paper also proposes recommendations made by the literature; their implementation may provide a higher level of security to key areas located in the first and second lines of building defense.Practical implicationsThe site and building perimeter areas that offer great potential for avoiding and deterring terror attacks are often neglected in terms of security planning, which seriously hampers efforts to provide an enhanced level of security to the facility. The paper points out these areas and major security issues related to them, so they can be taken care of by design professionals as well as facility managers.Originality/valueThe paper provides a comprehensive and detailed review of various aspects tied to the security level of critical areas of the building and site perimeters that could be useful to facility managers of critical facilities.
Proactive orientation and its influence for technology acquisition
Authors: Haro‐Domínguez Carmen , Ortega‐Egea Teresa , Tamayo‐Torres Ignacio 
Published: August 2010

PurposeThe purpose of this paper is to analyse the influence of the manager's strategic orientation concerning technology acquisition and its repercussions for the firm's performance.Design/methodology/approachThese relationships are studied using a sample of Spanish engineering consulting firms, most of them small‐ and medium‐sized enterprises.FindingsThe results obtained show that the proactive character adopted by managers will directly influence the decision‐making process concerning technology acquisitions. Managers with a proactive strategic orientation adopt both internal technological development and the external acquisition of technology, but a slight preference is observed for internal development, even though it achieves considerably less satisfactory results than those achieved with external technology acquisition.Research limitations/implicationsThe paper is exploratory in character, and its goal is to show whether interrelations exist between the variables. The sample refers only to engineering consultancies. Another limitation is the cross‐sectional character of the analysis performed.Practical implicationsTo obtain perfect adaptation of the firm to its environment, it is crucial that the manager be committed on both the tactical and the operating strategic levels. The paper shows the important role of the manager's strategic orientation in his or her decisions on technology acquisition. Success in this kind of decision is of vital importance to the firm. The high costs of internal development prevent immediate profits, and external acquisition brings high risks.Originality/valueThe paper seeks to stimulate new lines of research regarding these two variables (technology acquisition and manager's strategic orientation) and their repercussions for the firm.