bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning based prediction for peptide drift times in ion mobility spectrometry
Authors: Shah Anuj R. , Agarwal Khushbu , Baker Erin S. , Singhal Mudita , Mayampurath Anoop M. , Ibrahim Yehia M. , Kangas Lars J. , Monroe Matthew E. , Zhao Rui , Belov Mikhail E. , Anderson Gordon A. , Smith Richard D. 
Published: May 2010

Abstract
Motivation: Ion mobility spectrometry (IMS) has gained significant traction over the past few years for rapid, high-resolution separations of analytes based upon gas-phase ion structure, with significant potential impacts in the field of proteomic analysis. IMS coupled with mass spectrometry (MS) affords multiple improvements over traditional proteomics techniques, such as in the elucidation of secondary structure information, identification of post-translational modifications, as well as higher identification rates with reduced experiment times. The high throughput nature of this technique benefits from accurate calculation of cross sections, mobilities and associated drift times of peptides, thereby enhancing downstream data analysis. Here, we present a model that uses physicochemical properties of peptides to accurately predict a peptide's drift time directly from its amino acid sequence. This model is used in conjunction with two mathematical techniques, a partial least squares regression and a support vector regression setting.
Results: When tested on an experimentally created high confidence database of 8675 peptide sequences with measured drift times, both techniques statistically significantly outperform the intrinsic size parameters-based calculations, the currently held practice in the field, on all charge states (+2, +3 and +4).
Availability: The software executable, imPredict, is available for download from http:/omics.pnl.gov/software/imPredict.php
Contact: rds@pnl.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
FuncBase : a resource for quantitative gene function annotation
Authors: Beaver John E. , Taşan Murat , Gibbons Francis D. , Tian Weidong , Hughes Timothy R. , Roth Frederick P. 
Published: May 2010

Abstract
Summary: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. For example, a custom Cytoscape viewer shows functional linkage graphs relevant to the gene or function of interest. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases.
Availability: FuncBase as well as all underlying data and annotations are freely available via http://func.med.harvard.edu/
Contact: fritz_roth@hms.harvard.edu
Exercise training for systolic heart failure: Cochrane systematic review and meta‐analysis
Authors: Davies Edward J. , Moxham Tiffany , Rees Karen , Singh Sally , Coats Andrew J.S. , Ebrahim Shah , Lough Fiona , Taylor Rod S. 
Published: May 2010

AimsTo determine the effect of exercise training on clinical events and health‐related quality of life (HRQoL) of patients with systolic heart failure.Methods and resultsWe searched electronic databases including Medline, EMBASE, and Cochrane Library up to January 2008 to identify randomized controlled trials (RCTs) comparing exercise training and usual care with a minimum follow‐up of 6 months. Nineteen RCTs were included with a total of 3647 patients, the majority of whom were male, low‐to‐medium risk, and New York Heart Association class II–III with a left ventricular ejection fraction of <40%. There was no significant difference between exercise and control in short‐term (≤12 months) or longer‐term all‐cause mortality or overall hospital admissions. Heart failure‐related hospitalizations were lower [relative risk: 0.72, 95% confidence interval (CI): 0.52–0.99] and HRQoL improved (standardized mean difference: −0.63, 95% CI: −0.80 to −0.37) with exercise therapy. Any effect of cardiac exercise training on total mortality and HRQoL was independent of degree of left ventricular dysfunction, type of cardiac rehabilitation, dose of exercise intervention, length of follow‐up, trial quality, and trial publication date.ConclusionCompared with usual care, in selected heart failure patients, exercise training reduces heart failure‐related hospitalizations and results in clinically important improvements in HRQoL. High‐quality RCT and cost‐effectiveness evidence is needed for the effect of exercise training in community‐based settings and in more severe heart failure patients, elderly people, and women.
Population structure of beaked redfish, Sebastes mentella: evidence of divergence associated with different habitats
Authors: Cadrin Steven X. , Bernreuther Matthias , Daníelsdóttir Anna Kristín , Hjörleifsson Einar , Johansen Torild , Kerr Lisa , Kristinsson Kristjan , Mariani Stefano , Nedreaas Kjell , Pampoulie Christophe , Planque Benjamin , Reinert Jákup , Saborido-Rey Fran , Sigurðsson Thorsteinn , Stransky Christoph 
Published: May 2010

Abstract
Cadrin, S. X., Bernreuther, M., Daníelsdóttir, A. K., Hjörleifsson, E., Johansen, T., Kerr, L., Kristinsson, K., Mariani, S., Nedreaas, K., Pampoulie, C., Planque, B., Reinert, J., Saborido-Rey, F., Sigurðsson, T., and Stransky, C. 2010. Population structure of beaked redfish, Sebastes mentella: evidence of divergence associated with different habitats. – ICES Journal of Marine Science, 67: 1617–1630. Throughout their range, Sebastes spp. are adapted to a diversity of ecological niches, with overlapping spatial distributions of different species that have little or no morphological differences. Divergence of behavioural groups into depth-defined adult habitats has led to reproductive isolation, adaptive radiation, and speciation in the genus Sebastes. Recent genetic research, supported by life-history information, indicates four biological stocks of Sebastes mentella in the Irminger Sea and adjacent waters: a western stock, a deep-pelagic stock, a shallow-pelagic stock, and an Iceland slope stock. Congruent differences in fatty acids and parasites suggest that these genetically distinct populations are adapted to disparate trophic habitats in pelagic waters (shallower and deeper than the deep-scattering layer) and in demersal habitats on the continental slope. Morphology of pelagic forms is also more streamlined than demersal forms. Although genetic differences and evidence for reproductive isolation are clear, these populations appear to share common nursery habitats on the Greenland shelf. We propose a redefinition of practical management units near the Irminger Sea based on geographic proxies for biological stocks and minimizing mixed-stock catches according to the spatial patterns of the recent fishery.
Forms, effects, function: LIS students' attitudes towards portable e‐book readers
Authors: Pattuelli M. Cristina , Rabina Debbie 
Published: May 2010

PurposeThis study aims to investigate the use of a popular portable e‐reader device, the Kindle 2, among library and information science (LIS) students and its effects on individual reading practices and the potential applications for library services.Design/methodology/approachUsing journal logs and diary‐interviews as methods of data collection, the study analyzes the use of the Kindle over a one‐week period by a pool of 20 LIS students at Pratt Institute's School of Information and Library Science.FindingsThe findings reveal four key areas that provide a framework for data interpretation: usage patterns, user interaction, effect on reading habits, and future applications. One major finding is that the portability of the device and its convenience of use anywhere and any time is pivotal for enhancing the students' reading experience and outweighs the limitations of the device's usability.Research limitations/implicationsResults may not be generalizable due to the small size and homogeneity of the sample.Originality/valueThe social and cultural impacts of e‐book readers in everyday life have received little attention so far. In particular, questions about the effects of e‐readers on individual reading practices and the potential applications for library delivery systems have yet to be examined. This study is one of the first to investigate the use of portable e‐book readers.
The attitudes and behaviours of illegal downloaders
Authors: Williams Peter , Nicholas David , Rowlands Ian 
Published: May 2010

PurposeThe purpose of this paper is to summarise and evaluate the literature on digital consumer behaviour and attitudes towards digital piracy.Design/methodology/approachThe paper presents a review and synthesis of the academic literature on the subject, using the authors' unique “pro‐forma” approach to the evaluation of individual papers.FindingsA major limitation in the studies reported became apparent. They are almost exclusively concerned with the behaviours and attitudes of young people. There is a dearth of studies looking at demographic differences, and also a lack of longitudinal work. Given these constraints, the literature strongly suggests that social and situational factors impact on the likelihood of illegally obtaining digital content more than ethical considerations. Anonymity is a strong indicator, “de‐individualising” people and releasing them from traditional societal constraints and making the digital world far different from the physical one. The literature is ambiguous on whether punishment acts as a deterrent.Practical implicationsThe main point that comes out of these studies is that the digital world is not the same as the physical world. It is changing basic assumptions about the idea of ownership, sharing, and copying content. Laws prohibiting all unauthorised downloading potentially criminalise millions of people, so new and creative business models are needed to resolve the problem.Originality/valueThe authors believe this to be the first systematic review of current literature in this area since the issue became topical with the Pirate Bay trial and the Government's Digital Britain report.
Competitive intelligence skills needed to enhance South Africa's competitiveness
Authors: Strauss A.C. , du Toit A.S.A. 
Published: May 2010

PurposeSouth Africa as a country continues to rank low in the world of competitiveness. It is the aim of this paper to focus on the need for South African organisations to perceive competitive intelligence (CI) as one of the most important tools to improve their competitiveness through a systematic, practical approach to make the CI cycle worthwhile, especially through skills development. The paper intends to identify the skills CI professionals in South Africa need in order to conduct the CI process in organisations effectively, thereby improving the country's competitive position.Design/methodology/approachThe research for the paper is based on an extensive review of literature to identify the skills needed by CI professionals. A survey was conducted, by questionnaire, among organisations in South Africa with existing CI units in which the respondents had to identify the skills they deemed necessary for the CI professional to run the CI process effectively.FindingsFindings suggested that the majority of respondents were 40 years and older, in the top structure of larger organisations and had been using CI for longer than five years. The overwhelming result is that there are skills inequalities between what skills respondents view as crucial and those that rated highest in their self‐evaluation. Skills identified as most important include, among others, networking, research skills and analytical abilities.Research limitations/implicationsCI in South Africa is still in its infancy and in 2008 no professional CI groups existed. As a result, there is no recognised list of practising South African CI professionals available in South Africa. For this reason the respondent database consists of attendees of CI courses, workshops and seminars held by the Department of Information and Knowledge Management at the University of Johannesburg.Practical implicationsThe research indicated that where CI had been established in certain organisations for at least five years, it did not reflect positively overall on South Africa's current competitive situation. Where there is a systematic CI approach, however, problem‐solving is easier to address and negatives could be turned around. With this in mind and a proper “buy‐in” into skills development, it will have a very positive outcome for all the organisations that wish to improve their competitiveness.Originality/valueFor a country such as South Africa (and other developing countries) this research is of extreme importance as the country is facing a serious shortage of skills. Skills development of CI professionals can create a strategic advantage for the country and increase South Africa's competitiveness.
LIS as a field of study: socio‐cultural influences on students' decision making
Authors: Moniarou‐Papaconstantinou Valentini , Tsatsaroni Anna , Katsis Athanassios , Koulaidis Vasilis 
Published: May 2010

PurposeUsing Bourdieu‐inspired sociological literature, this paper aims to report on a study that examines the educational choices of new entrants in the three library and information science (LIS) schools operating in Greece at the undergraduate level, with reference to their socio‐cultural characteristics.Design/methodology/approachData were obtained through a questionnaire, distributed to 187 LIS students, aiming to address the question of what attracted them to the LIS field.FindingsAnalysis reveals three distinctive student groups in the sample and shows that these differ in respect to the reasons attracting them to LIS. The first group, with restricted cultural resources at their disposal, is attracted only by extrinsic reasons, namely the prospect of immediate employment. The second group, of middle level parental education, is attracted by intrinsic reasons, most notably the qualitative characteristics of the field as a future profession. This group seems to use these qualities to preserve the belief in an upwards moving and successful educational career. Qualities attracting the students of the third group, when examined with reference to their socio‐cultural characteristics, indicate that the choice of subject made is linked to their socially acquired ability to recognise what may be promising regarding possible future LIS career paths. This is in contrast to students from low socio‐cultural backgrounds, who seem not to have access to the high cultural resources the LIS field requires for “decoding” and understanding its hidden possibilities.Originality/valueThis paper uses socio‐cultural explanations of students' choice of LIS as a field of study, contributing methodologically and substantively to this area of research.
Biography
Authors: Turvey Calum G. 
Published: May 2010

PurposeThe purpose of this paper is to review the life of the famous mathematician Kiyosi Itô and discuss his influence on the study of agricultural finance and agricultural economics.Design/methodology/approachThis paper is a qualitative historical review.FindingsThe paper provides a biographical stretch of Itô's life. It is shown that his influence started to infiltrate the agricultural economics profession at around 1985 and is currently a major influence of a range of economic issues from farm policy to agricultural investments.Research limitations/implicationsThe biography is limited to a review of Itô's academic life and influence.Practical implicationsThe paper offers a historical perspective on how probability emerged as a critical piece of the economic puzzle. For scholars and practitioners of agricultural finance, the paper provides an in depth review of how Itô processes have, and can, be used.Originality/valueThis paper provides a historical perspective on Itô that is of use to students and scholars of rural credit. This is the first “biography” of Itô to discuss his influence on agricultural finance and agricultural economics.
A model of microfinance with adverse selection, loan default, and self‐financing
Authors: Batabyal Amitrajeet A. , Beladi Hamid 
Published: May 2010

PurposeThe purpose of this paper is to analyze a market for microfinance in a region of a developing nation in which all projects are either of high or low quality. There is adverse selection because only borrowers know whether their project is of high or low quality but the microfinance institutions (MFIs) do not. The MFIs are competitive, risk neutral, and they offer loan contracts specifying the amount to be repaid only if a borrower's project makes a profit. Otherwise, this borrower defaults on his contract.Design/methodology/approachA game theoretic model is used that explicitly accounts for adverse selection and then a study is made of the trinity of adverse selection, loan default, and self‐financing.FindingsFirst, in the pooling equilibrium, a borrower with a low‐quality business project will obtain positive expected profit. In contrast, this borrower will obtain zero expected profit in the separating equilibrium. Second, for small enough values of the probability p that a business project is of high quality, MFIs will not finance any business project in the pooling equilibrium. Third, the cost of sending a signal is not too high and hence a separating equilibrium exists. Finally, under some circumstances, self‐financing can be used to mitigate adverse selection related problemsResearch limitations/implicationsThis paper studies a model with only two types of business projects. In addition, no allowance is made for repeated interactions between borrowers and MFIs.Originality/valueThis paper usefully shows that under some circumstances, a credible signaling device such as self‐financing can be used to mitigate adverse selection related problems that routinely plague interactions between poor borrowers in developing countries and MFIs.
Spatial producer heterogeneity in crop insurance product decisions within major corn producing states
Authors: Adhikari Shyam , Belasco Eric J. , Knight Thomas O. 
Published: May 2010

PurposeThe purpose of this paper is to examine the spatial components of producer heterogeneity in crop insurance product selection among US corn producers and identifies neighborhood spillover or agent marketing effects in these decisions.Design/methodology/approachCounty‐level insurance and yield data are used to demonstrate that a gradual shift from yield‐based insurance to revenue‐based insurance has spatial patterns. Conventional risk variables such as yield variability, price variability, prevalence of irrigation, other crops, and yield‐price relationships play an important role in this shift and are consistently estimated only when spatial components are included. A spatial random effects model is used to also identify the impact of spatial lag effects, which include neighborhood spillover and agent marketing effects, on the share of corn acres insured with revenue‐based plans vs yield‐based plans.FindingsTheoretically consistent variables associated with risk are found to significantly influence the choice between crop revenue and yield insurance. Non‐linear parameters identify the region‐specific effects from changes in irrigation, yield price correlation, and the prevalence of corn production on insurance decisions. In addition, spatial components such as the decisions made by nearby producers and marketing drives are also found to influence decisions. These results may demonstrate the relative influence of trusted sources, such as nearby producers and insurance agents, on insurance decisions.Originality/valueTraditional risk variables are consistently estimated by controlling for spatial heterogeneity. This study also reveals the propensity of producers to rely on the opinions of other producers or agents that they know.
A spatial Bayesian approach to weather derivatives
Authors: Paulson Nicholas D. , Hart Chad E. , Hayes Dermot J. 
Published: May 2010

PurposeWhile the demand for weather‐based agricultural insurance in developed regions is limited, there exists significant potential for the use of weather indexes in developing areas. The purpose of this paper is to address the issue of historical data availability in designing actuarially sound weather‐based instruments.Design/methodology/approachA Bayesian rainfall model utilizing spatial kriging and Markov chain Monte Carlo techniques is proposed to estimate rainfall histories from observed historical data. An example drought insurance policy is presented where the fair rates are calculated using Monte Carlo methods and a historical analysis is carried out to assess potential policy performance.FindingsThe applicability of the estimation method is validated using a rich data set from Iowa. Results from the historical analysis indicate that the systemic nature of weather risk can vary greatly over time, even in the relatively homogenous region of Iowa.Originality/valueThe paper shows that while the kriging method may be more complex than competing models, it also provides a richer set of results. Furthermore, while the application is specific to forage production in Iowa, the rainfall model could be generalized to other regions by incorporating additional climatic factors.
Assessing the potential value for an automated dairy cattle body condition scoring system through stochastic simulation
Authors: Bewley J.M. , Boehlje  , Gray A.W. , Hogeveen H. , Kenyon S.J. , Eicher S.D. , Schutz M.M. 
Published: May 2010

PurposeAutomated body condition scoring (BCS) through extraction of information from digital images has been demonstrated to be feasible; and commercial technologies are being developed. The primary objective of this research was to identify the factors that influence the potential profitability of investing in an automated BCS system.Design/methodology/approachAn expert opinion survey was conducted to provide estimates for potential improvements associated with technology adoption. A stochastic simulation model of a dairy system, designed to assist dairy producers with investment decisions for precision dairy farming technologies was utilized to perform a net present value (NPV) analysis. Benefits of technology adoption were estimated through assessment of the impact of BCS on the incidence of ketosis, milk fever, and metritis, conception rate at first service, and energy efficiency.FindingsImprovements in reproductive performance had the largest influence on revenues followed by energy efficiency and then by disease reduction. The impact of disease reduction was less than anticipated because the ideal BCS indicated by experts resulted in a simulated increase in the proportion of cows with BCS at calving 3.50. The estimates for disease risks and conception rates, obtained from literature, however, suggested that this increase would result in increased disease incidence. Stochastic variables that had the most influence on NPV were: variable cost increases after technology adoption; the odds ratios for ketosis and milk fever incidence and conception rates at first service associated with varying BCS ranges; uncertainty of the impact of ketosis, milk fever, and metritis on days open, unrealized milk, veterinary costs, labor, and discarded milk; and the change in the percentage of cows with BCS at calving 3.25 before and after technology adoption. The deterministic inputs impacting NPV were herd size, management level, and level of milk production. Investment in this technology may be profitable but results were very herd‐specific. A simulation modeling a deterministic 25 percent decrease in the percentage of cows with BCS at calving ≤3.25 demonstrated a positive NPV in 86.6 percent of 1,000 iterations.Originality/valueThis investment decision can be analyzed with input of herd‐specific values using this model.