bluuebunny/crossref_metadata_2025_split huggingface dataset:
Porcine Parvovirus VP1/VP2 on a Time Series Epitope Mapping: exploring the effects of high hydrostatic pressure on the immune recognition of antigens
Authors: de Souza Ancelmo Rabelo , Yamin Marriam , Gava Danielle , Ciacci Zanella Janice Reis , Viccari Gatti Maria Sílvia , Sampaio Bonafe Carlos Francisco , Lima Neto Daniel Ferreira de 
Published: May 2018

ABSTRACTPorcine parvovirus (PPV) is a DNA virus that causes reproductive failure in gilts and sows, resulting in embryonic and fetal losses worldwide. Epitope mapping of PPV is important for developing new vaccines. In this study, we used spot synthesis analysis for epitope mapping of the capsid proteins of PPV (NADL-2 strain) and correlated the findings with predictive data from immunoinformatics. The virus was exposed to three conditions prior to inoculation in pigs: native (untreated), high hydrostatic pressure (350 MPa for 1 h) at room temperature and high hydrostatic pressure (350 MPa for 1h) at −18 °C, compared with a commercial vaccine produced using inactivated PPV. The screening of serum samples detected 44 positive spots corresponding to 20 antigenic sites. Each type of inoculated antigen elicited a distinct epitope set.In silicoprediction located linear and discontinuous epitopes in B cells that coincided with several epitopes detected in spot synthesis of sera from pigs that received different preparations of inoculum. The approach used here provided important information on the antibody/antigen interactions required to improve B cell responses to PPV and may be useful in developing novel strategies for producing new vaccines.Abbreviations3D, three dimensional; HHP, high hydrostatic pressure; ID, identification; IEDB, Immune Epitope Database; ORFs, open reading frames; p.i., post-infection; PPV, porcine parvovirus; RMSD, root-mean-square deviation of atomic positions; R(g), radius of gyration. RMSF, root-mean-square fluctuation; SK6, Swine kidney cell; SPF, specific pathogen free; TCID50/mL, Median Tissue Culture Infectious Dose; HI, Hemagglutination Inhibition.
Quasi-neutral molecular evolution — When positive and negative selection cancel out
Authors: Chen Bingjie , Shi Zongkun , Chen Qingjian , Shibata Darryl , Wen Haijun , Wu Chung-I 
Published: May 2018

AbstractIn the absence of both positive and negative selection, DNA sequences evolve at the neutral rate, R = 1. Due to the prevalence of negative selection, R∼1 is rarely achieved in organismal evolution. However, when R ∼ 1 is observed, it does not necessarily indicate neutral evolution because positive and negative selection could be equally strong but in opposite directions - hereby referred to as quasi-neutrality. We now show that somatic-cell evolution could be the paradigm of quasi-neutral evolution for these reasons: 1) Quasi-neutrality is much more likely in small populations (size N < 50) than in large ones; 2) Stem cell population sizes in single niches of normal tissues, from which tumors likely emerges, have small N’s (usually < 50); 3) the genome-wide evolutionary rate across tissue types is close to R = 1; 4) Relative to the average of R ∼ 1, many genes evolve at a much higher or lower rate, thus hinting both positive and negative selection; 5) When N < 50, selection efficacy decreases rapidly as N decreases even when the selection intensity stays constant; 6) Notably, N is smaller in the small intestine (SmI) than in the colon (CO); hence, the ∼ 70 fold higher rate of phenotypic evolution (observed as cancer risk) in the latter can be explained by the greater efficacy of selection, which then leads to the fixation of more advantageous mutations and fewer deleterious ones in the CO. Under quasineutrality, positive and negative selection can be measured in the same system as the two forces are simultaneously present or absent.
iSEE: Interface Structure, Evolution and Energy-based machine learning predictor of binding affinity changes upon mutations
Authors: Geng Cunliang , Vangone Anna , Folkers Gert E. , Xue Li C. , Bonvina Alexandre M.J.J. 
Published: May 2018

AbstractQuantitative evaluation of binding affinity changes upon mutations is crucial for protein engineering and drug design. Machine learning-based methods are gaining increasing momentum in this field. Due to the limited number of experimental data, using a small number of sensitive predictive features is vital to the generalization and robustness of such machine learning methods. Here we introduce a fast and reliable predictor of binding affinity changes upon single point mutation, based on a random forest approach. Our method, iSEE, uses a limited number of interface Structure, Evolution and Energy-based features for the prediction. iSEE achieves, using only 31 features, a high prediction performance with a Pearson correlation coefficient (PCC) of 0.80 and a root mean square error of 1.41 kcal mol-1 on a diverse training dataset consisting of 1102 mutations in 57 protein-protein complexes. It competes with existing state-of-the-art methods on two blind test datasets. Predictions for a new dataset of 540 mutations in 58 protein complexes from the recently published SKEMPI 2.0 database reveals that none of the current methods perform well (PCC<0.4), although their combination does improve the predictions. Feature analysis for iSEE underlines the significance of evolutionary conservations for quantitative prediction of mutation effects.
Integrating genotype and weather variables for soybean yield prediction using deep learning
Authors: Shook Johnathon , Wu Linjiang , Gangopadhyay Tryambak , Ganapathysubramanian Baskar , Sarkar Soumik , Singh Asheesh K. 
Published: May 2018

AbstractRealized performance of complex traits is dependent on both genetic and environmental factors, which can be difficult to dissect due to the requirement for multiple replications of many genotypes in diverse environmental conditions. To mediate these problems, we present a machine learning framework in soybean (Glycine max (L.) Merr.) to analyze historical performance records from Uniform Soybean Tests (UST) in North America, with an aim to dissect and predict genotype response in multiple envrionments leveraging pedigree and genomic relatedness measures along with weekly weather parameters. The ML framework of Long Short Term Memory - Recurrent Neural Networks works by isolating key weather events and genetic interactions which affect yield, seed oil, seed protein and maturity enabling prediction of genotypic responses in unseen environments. This approach presents an exciting avenue for genotype x environment studies and enables prediction based systems. Our approaches can be applied in plant breeding programs with multi-environment and multi-genotype data, to identify superior genotypes through selection for commercial release as well as for determining ideal locations for efficient performance testing.
Mind the gap – Assessing maturity of demand planning, a cornerstone of S&OP
Authors: Vereecke Ann , Vanderheyden Karlien , Baecke Philippe , Van Steendam Tom 
Published: May 2018

Purpose
The purpose of this paper is to develop and empirically validate a model for assessing demand planning maturity in organisations.

Design/methodology/approach
The authors developed a maturity assessment model for demand planning through iterations of theoretical and empirical work, combining insights from literature and practitioners. An online survey is developed to validate the model using data from different industries.

Findings
The authors identify six dimensions of demand planning maturity: data management, the use of forecasting methods, the forecasting system, performance management, the organisation and people management. The empirical study indicates that demand data are well managed and organisation readiness is high, yet improvements in the forecasting system and the management of forecast performance are needed. The results show a positive relationship between the size of an organisation and its demand planning maturity.

Practical implications
The contribution of this work is to propose an assessment model and survey instrument for demand planning maturity. This will help the practitioner to understand the current level of maturity of the demand planning process, reflect on the desired level and develop action plans to close the gap.

Originality/value
There is broad literature on process maturity assessment in general and on sales and operations planning (S&OP) maturity in particular. However, there is no comprehensive model for assessing the maturity of demand planning, which is a specific and critical process within the overall S&OP process. The authors fill this gap by offering a demand planning maturity model.
Learning analytics to improve writing skills for young children – an holistic approach
Authors: Steinhauer Nina , Gros Michael , Ebner Martin , Ebner Markus , Huppertz Anneliese , Cormann Mike , Biermeier Susanne , Burk Lena , Edtstadler Konstanze , Gabriel Sonja , Wintschnig Martina , Aspalter Christian , Martich Susanne 
Published: May 2018

Purpose
Due to the important role of orthography in society, the project called IDeRBlog presented in this paper created a web-based tool to motivate pupils to write text as well as to read and to comment on texts written by fellow students. In addition, IDeRBlog aims to improve student’s German orthography skills and supports teachers and parents with training materials for their students. The paper aims to discuss these issues.

Design/methodology/approach
With the aid of learning analytics, the submitted text is analyzed and special feedback is given to the students so that they can try to correct the misspelled words themselves. The teachers as well as the parents are benefiting from the analysis and exercises suggested by the system.

Findings
A recent study showed the efficiency of the system in form of an improvement of the students’ orthographic skills. Over a period of four months 70 percent of the students achieved a significant reduction of their spelling mistakes.

Originality/value
IDeRBlog is an innovative approach to improving orthography skills combining blogging and new media with writing and practice.
To quit or not to quit
Authors: Joe Sheng-Wuu , Hung Wei-Ting , Chiu Chou-Kang , Lin Chieh-Peng , Hsu Ya-Chu 
Published: May 2018

Purpose
To deepen our understanding about the development of turnover intention, the purpose of this paper is to develop a model that explains how ethical climate influences turnover intention based on the ethical climate theory and social identity theory.

Design/methodology/approach
The hypotheses of this study were statistically tested using a survey of working professionals from Taiwan’s high-tech industry. Of the 400 questionnaires distributed to the working professionals from five large high-tech firms in a well-known science park in Northern Taiwan, 352 usable questionnaires were returned for a questionnaire response rate of 88 percent.

Findings
The test results of this study first show that all three dimensions of ethical climate (i.e. instrumental, benevolent, and principled) are indirectly related to turnover intention via the mediation of firm attractiveness. Moreover, instrumental and benevolent climate directly relate to turnover intention, whereas benevolent climate negatively moderates the relationship between principled climate and firm attractiveness.

Originality/value
This study finds that benevolent climate plays a dual role as an antecedent and a moderator in the formation of turnover intention, complementing prior studies that merely concentrate on the single role of benevolent climate as either an antecedent or a moderator. The effect of principled climate on organizational identification complements the theoretical discussion by Victor and Cullen (1987) about deontology in which an ethical workplace climate (such as legitimacy) drives employees to invest in identity attachments to the organization and influences their future career decision (e.g. turnover).
Landscape context and farm uptake limit effects of bird conservation in the Swedish Volunteer & Farmer Alliance
Authors: Josefsson Jonas , Pärt Tomas , Berg Åke , Lokhorst Anne Marike , Eggers Sönke 
Published: May 2018

Abstract

In Europe, agri‐environmental schemes (AES) have been unsuccessful in halting biodiversity declines to any great extent. Two shortcomings of AES include the low farm uptake and the modest efficacy of many AES options. Partly in response to these shortcomings, initiatives encouraging farmers to take an active role in biodiversity conservation have gained in popularity. However, almost no evaluations of such initiatives exist.

We evaluated uptake of conservation advice on farms in the Swedish Volunteer & Farmer Alliance, a BirdLife Sweden‐coordinated project aimed at farmland bird conservation, and the response of farmland birds to those actions using farm‐level survey data, in a before‐after implementation assessment.

Uptake was higher for unsubsidised (i.e. non‐AES) measures than for AES options, and depended mainly on farmers’ interest in nature, with farm size and production type having less importance.

In general, abundances of non‐crop nesting and field‐nesting bird species declined between inventory years (median interval 3 years). Decreases were more marked in agriculturally marginal regions than in more arable‐dominated regions, and declines were stronger on organic than on conventional farms.

Negative abundance trends among non‐crop nesting species were reduced by an increasing number of conservation measures at the farm, but only in the more arable‐dominated landscapes. Changes in field‐nesting species, or at species level, did not significantly relate to implemented measures, but the power to detect such effects was generally small due to the small sample size of high‐uptake farms as well as high inter‐farm variability.

Synthesis and applications. Our results suggest that volunteer farmer alliances and the addition of unsubsidised measures may be successful in changing the local number of non‐crop nesting farmland birds, at the farm level, particularly in intensively managed agricultural landscapes. Thus, unsubsidised measures can be a useful addition to the set of agri‐environment tools, although their effects on breeding bird numbers are (as with agri‐environmental schemes) dependent on landscape context, as well as on ensuring high on‐farm uptake of different interventions.
Pathogen dynamics under both bottom‐up host resistance and top‐down hyperparasite attack
Authors: Parratt Steven R. , Laine Anna‐Liisa 
Published: May 2018

Abstract

The relative importance of bottom‐up versus top‐down control of population dynamics has been the focus of much debate. In infectious disease biology, research is typically focused on the bottom‐up process of host resistance, wherein the direction of control flows from the lower to the higher trophic level to impact on pathogen population size and epidemiology. However, the importance of top‐down control by a pathogen's natural enemies has been mostly overlooked.

Here, we explore the effects of, and interaction between, host genotype (i.e., genetic susceptibility to pathogen infection) and infection by a hyperparasitic fungus, Ampelomyces spp., on the establishment and early epidemic growth and transmission of a powdery mildew plant pathogen (Podosphaera plantaginis). We used a semi‐natural field experiment to contrast the impacts of hyperparasite infection, host‐plant resistance and spatial structure to reveal the key factors that determine pathogen spread. We then used a laboratory‐based inoculation approach to test whether the field experiment results hold across multiple pathogen–host genetic combinations and to explore hyperparasite effects on the pathogen's later life‐history stages.

We found that hyperparasite infection had a negligible effect on within‐host infection development and between‐host spread of the pathogen during the onset of epidemics. In contrast, host‐plant resistance was the major determinant of whether plants became infected, and host genotype and proximity to an infection source determined infection severity.

Our laboratory study showed that, while the interaction between host and pathogen genotypes was the key determinant of infection outcome, hyperparasitism did, on average, reduce the severity of infection. Moreover, hyperparasite infection negatively influenced the production of the pathogen's overwintering structures.

Synthesis and applications. Our results suggest that bottom‐up host resistance affects pathogen spread, but top‐down control of powdery mildew pathogens is likely more effective against later life‐history stages. Further, while hyperparasitism in this system can reduce early pathogen growth under stable laboratory conditions, this effect is not detectable in a semi‐natural environment. Considering the effects of hyperparasites at multiple points in pathogen's life history will be important when considering hyperparasite‐derived biocontrol measures in other natural and agricultural systems.
Banding age ratios reveal prairie waterfowl fecundity is affected by climate, density dependence and predator–prey dynamics
Authors: Specht Hannah M. , Arnold Todd W. 
Published: May 2018

Abstract

Fecundity estimates for demographic modelling are difficult to acquire at the regional spatial scales that correspond to climate shifts, land use impacts or habitat management programmes. Yet they are important for evaluating such effects. While waterfowl managers have historically used harvest‐based age ratios to assess fecundity at continental scales, widely available age ratios from late summer banding (ringing) data present an underutilized opportunity to examine a regional fecundity index with broad temporal replication.

We used age ratios from banding data and hierarchical mixed‐effect models to examine how fecundity of five North American dabbling duck species was affected by temporal variation in hydrological cycles, intra‐ and interspecific density dependence and alternate prey availability, and whether those relationships were consistent across a broad geographic area.

Model‐estimated fecundity was within the range of traditional harvest‐based fecundity estimates for each species. Ecological covariates explained between 16% and 53% of the temporal variation in fecundity, dependent on species. Increasing wetland inundation and an indicator of vole population irruptions were consistent predictors of increasing fecundity across all species. Species exhibited mixed positive and negative responses to interspecific and intraspecific breeding pair densities hypothesized to affect nest and brood survival respectively, highlighting the importance of integrating brood survival into fecundity metrics for precocial species.

Declines in fecundity over time and across space at more northern latitudes may reflect stronger policies for grassland and wetland protection in the U.S. versus Canadian portions of the prairies over the time period of our study. Maintaining the capacity of less permanent basins to rehydrate in wetter periods through easement protection benefits fecundity, particularly for late‐nesting species that acquire a greater proportion of their reproductive energy on the breeding grounds.

Synthesis and applications. Age ratios derived from postbreeding banding operations allowed us to attribute variation in waterfowl fecundity to temporal ecological variables. Effects of habitat management for waterfowl may be masked unless analysts account for this temporal variation. Postbreeding‐pulse age ratios at capture could be useful as fecundity metrics in integrated population models and for evaluating population dynamics of extensively banded nongame species, especially if adjusted for capture vulnerability using within‐season recapture data.
The Benefits of Farm Animal Welfare Legislation: The Case of the EU Broiler Directive and Truthful Reporting
Authors: Bennett Richard , Balcombe Kelvin , Jones Philip , Butterworth Andrew 
Published: May 2018

AbstractThe EU Broiler Directive came into force in the UK in June 2010 with the aim of setting new minimum standards, monitoring broiler welfare and addressing any welfare problems. A survey questionnaire was used to elicit information from a stratified sample of citizens in England and Wales regarding their willingness to pay for the provisions of the Directive, as an estimate of the consumer surplus associated with the legislation. We also explore the usefulness of Prelec's () Bayesian Truth Serum (BTS) in promoting respondents’ truthful reporting. A median willingness to pay of £21.50 per household per year (corrected for sample bias and possible ‘yea saying’) was estimated from 665 responses. This provides an estimated benefit of the legislation to citizens of over £503 million per year, equivalent to 5.3% of current consumer expenditure on chicken. This compares to an estimated £22 million per year cost of producers’ compliance and government enforcement associated with the legislation. No statistically significant differences in responses between respondents that did and did not have a BTS incentive to answer questions truthfully were found, which might reflect apparently truthful answers in this case, an insufficiently strong financial incentive or a weakened effect due to an element of disbelief in the BTS amongst the sample. The analysis suggests that the benefits of the Broiler Directive to citizens greatly outweigh the additional costs to producers, making a case for the legislation to be retained.
Agricultural Trade Liberalisation in the 21st Century: Has It Done the Business?
Authors: Bureau Jean‐Christophe , Guimbard Houssein , Jean Sébastien 
Published: May 2018

AbstractBased on a novel, detailed, time‐consistent tariff database taking account of import protection developments in the agricultural sector since 2001, we propose a statistical decomposition of the changes in the various types of tariffs. The results show that the multilateral system has played a limited role in trade liberalisation over the period. Many countries have continued to apply much lower tariffs on agricultural products than their WTO ceilings. Moreover, there has been substantial unilateral dismantling of tariffs over the period, so that much of the liberalisation took place outside WTO and regional agreements. The number of regional trade agreements has surged, but their impact on applied agricultural tariffs has been limited. Finally, we investigate the tariffs, trade and production implications for food and agricultural products of two extreme scenarios in the future development of trade negotiations: an ambitious surge of regional agreements and a trade war within the WTO context.
DNA Profiles from Fingerprint Lifts—Enhancing the Evidential Value of Fingermarks Through Successful DNA Typing
Authors: Subhani Zuhaib , Daniel Barbara , Frascione Nunzianda 
Published: May 2018

AbstractThis study evaluated the compatibility of the most common enhancement methods and lifting techniques with DNA profiling. Emphasis is placed on modern lifting techniques (i.e., gelatin lifters and Isomark™) and historical fingerprint lifts for which limited research has been previously conducted. A total of 180 fingerprints were deposited on a glass surface, enhanced, lifted, and processed for DNA typing. DNA could be extracted and profiled for all the powders and lifts tested and from both groomed fingerprints and natural prints with no significant difference in the percentage of profile recovered. DNA profiles could also be obtained from historical fingerprint lifts (79.2% of 72 lifts) with one or more alleles detected. These results demonstrate the compatibility between different powder/lift combinations and DNA profiling therefore augmenting the evidential value of fingerprints in forensic casework.