bluuebunny/crossref_metadata_2025_split huggingface dataset:
Policy prospects for the hills and uplands
Authors: Harvey D. R. 
Published: September 2010

AbstractThe arguments presented in this paper strongly support the stated intention of the European Commission that farm product prices must be set more competitively with the world market. Indeed, they go further. The only long-term sustainable agricultural policy for the European Community is to let farm products compete unsupported on a free-trade world market (the ultimate objective of the GATT negotiations). This does not deny either justification or need for some form of compensation to the present industry for the loss of support. However, the argument does clearly require that such compensation should be ‘neutral’ — that it should not distort or alter production and allocation decisions from those which would be taken in the absence of such compensation. The only genuinely neutral compensation would be single lump sum capital transfer through a government bond issue. However, failing this, definitely limited annual support payments independent of current production decisions and relating to past production quantities less than those which would be produced under uncompensated free-trade would be ‘quasi neutral’, and might as a result be acceptable as non-distorting under GATT. In this sense, the price reduction proposals currently being discussed are a definite step in the right direction, especially for cereals.Nevertheless, agriculture faces a continued period of difficult adjustment, especially difficult in the hill and upland areas. As far as conventional agriculture is concerned, there is little prospect of these areas being able to compete directly in the final consumer markets at world price competitive levels. Their comparative advantage will lie with the production of breeding and store animals, to be finished on grass or grain in more productive locations. Fewer people will be able to earn a full-time living from agriculture in these areas and other things being equal, hill and upland farms seem likely to become even more extensive ranching operations than is the case at present. However, other things are not equal. It seems likely that society will continue to value the non-productive elements of hill and upland agriculture, which in many cases are seen as adding to the amenity and landscape qualities of these regions. Since the demand for these features will grow, ways will be found to supplement farming incomes in these areas (especially) in order to conserve the landscape, wildlife and amenity characteristics.
Practical pasture management in hill and upland systems
Authors: Johnson J. , Merrell B. G. 
Published: September 2010

AbstractThe imbalance in area of conservation to grazing has resulted in systems which attempt to maximize grazing and minimize winter feeding. This is rendered more difficult by the short growing season and generally poorer quality of indigenous vegetation when compared with, for example, perennial ryegrass and white clover. Recent changes in government policy discourage land improvement and emphasis nowadays concentrates on maximizing use of, for example, moorland whilst at the same time maintaining its longer-term production and environmental quality. Sward height guidelines can be used to optimize production and utilization of sown grassland for sheep and cattle. Information is also available to integrate heather moorland into farming systems, as a result of an increased understanding of grazing preferences. It remains as important as ever to maintain production from the limited area of improved ground, and improvements in perennial ryegrass and white clover varieties can be introduced successfully into hill and upland systems. Change in such systems however is often constrained by both social and economic factors and this needs to be acknowledged if the agricultural emphasis in the hills and uplands is to have proper direction.
Future of animal production in hill and upland areas
Authors: Maxwell T. J. 
Published: September 2010

AbstractTogether hill and upland agriculture (LFA) currently utilizes from 44% of the land area of the UK and employs directly some 126,000 people. An estimate of gross output from these sectors in 1990 was around £1.3 billion. These data indicate that there can be little doubt about the significance of agriculture and livestock production in hill and upland areas. Since the Second World War output has increased substantially by virtue of a better control of sheep diseases, improved grazing management, sheep and cattle husbandry and the financial incentives offered by successive governments for land improvement, fencing and buildings. However, these incentives have not in themselves led to an economically viable agriculture for most hill and upland areas.It is questionable if it was ever the intention of any UK government that financial support for the hill and upland livestock industries to improve productivity was the sole objective of their policies for hill and upland areas. While it has always been the case that Agricultural Departments have had the major responsibility for administering the major financial support, the reason for doing so has been as much to do with a social policy of making it possible for people to live in the remoter countryside as it has been to do with improving the output and viability of agriculture.It is therefore inconceivable that support for hill and upland economies will be withdrawn. It may be, however, that the amount of support will become less as the Common Agriculture Policy is reformed and that element of support which is currently attached to product price is progressively removed. For the future, the indications are that support is much more likely to continue on the basis of headage payments related to breeding livestock quotas and linked to specific management protocols to meet conservation and wider environmental objectives.Even with the levels of financial support that can be reasonably expected over the next decade, the financial constraints upon, or the opportunities that may arise for individual land owners will inevitably lead to land being removed from agriculture.However, it is likely that livestock production will continue to dominate much of the hill and upland areas within a management context which will reflect the size of the business, the need to meet specific environmental objectives and the range of other activities and employment opportunities with which the farm household is involved.Although we must expect that the economics of animal production in the hill and upland areas of the UK will no longer justify a continuation of farming in some areas, the great majority of farms will continue to adopt more efficient technologies, improve their breeding programme and adapt their land management rôle to meet the needs of conservation and the maintenance and enhancement of landscape quality.
A life-course approach to co-residence in the Netherlands, 1850–1940
Authors: KOK JAN , MANDEMAKERS KEES 
Published: September 2010

ABSTRACTIn this article, we study variations in co-residence with kin in the Netherlands in the late nineteenth and early twentieth centuries. We use the reconstructed life courses of 17,527 individuals derived from the Historical Sample of the Netherlands (HSN) database. The life-course approach allows us to look at co-residence from the perspectives of both the receiving households and the co-resident kin. What made households take in relatives and do we find a preference for one type of relative over another? What was the background of people who decided to co-reside in another household? How important were family-related ‘altruistic’ motives compared with economic ones? The outcomes suggest the predominance of altruistic motives for co-residence, apart from persistent inheritance customs in the eastern part of the country.
Nun apothecaries and the impact of the Secularization in Southwest Germany
Authors: MAEGRAITH JANINE CHRISTINA 
Published: September 2010

ABSTRACTThis article examines the interplay of the Secularization of 1803, the ‘professionalisation’ of pharmacy, and increasing state control in Württemberg after 1806 by looking at convent pharmacies and their destiny after the secularization of the convents in 1803. This interplay consequently led to the temporary abolition of convent pharmacies and with them an important occupational niche for female apothecaries was thus lost. The research is based on a detailed case study of the convent pharmacy in Gutenzell in Upper Swabia, 50 kilometres south of Ulm.
Maximum likelihood estimation of locus-specific mutation rates in Y-chromosome short tandem repeats
Authors: Ravid-Amir Osnat , Rosset Saharon 
Published: September 2010

AbstractMotivation: Y-chromosome short tandem repeats (Y-STRs) are widely used for population studies, forensic purposes and, potentially, the study of disease, therefore knowledge of their mutation rate is valuable. Here we show a novel method for estimation of site-specific Y-STR mutation rates from partial phylogenetic information, via the maximum likelihood framework.Results: Given Y-STR data classified into haplogroups, we de-scribe the likelihood of observed data, and develop optimization strategies for deriving maximum likelihood estimates of mutation rates. We apply our method to Y-STR data from two recent papers. We show that our estimates are comparable, often more accurate than those obtained in familial studies, although our data sample is much smaller, and was not collected specifically for our study. Furthermore, we obtain mutation rate estimates for DYS388, DYS426, DYS457, three STRs for which there were no mutation rate measures until now.Contact: saharon@post.tau.ac.il
Parsimony and likelihood reconstruction of human segmental duplications
Authors: Kahn Crystal L. , Hristov Borislav H. , Raphael Benjamin J. 
Published: September 2010

Abstract
Motivation: Segmental duplications &gt; 1 kb in length with ≥ 90% sequence identity between copies comprise nearly 5% of the human genome. They are frequently found in large, contiguous regions known as duplication blocks that can contain mosaic patterns of thousands of segmental duplications. Reconstructing the evolutionary history of these complex genomic regions is a non-trivial, but important task.
Results: We introduce parsimony and likelihood techniques to analyze the evolutionary relationships between duplication blocks. Both techniques rely on a generic model of duplication in which long, contiguous substrings are copied and reinserted over large physical distances, allowing for a duplication block to be constructed by aggregating substrings of other blocks. For the likelihood method, we give an efficient dynamic programming algorithm to compute the weighted ensemble of all duplication scenarios that account for the construction of a duplication block. Using this ensemble, we derive the probabilities of various duplication scenarios. We formalize the task of reconstructing the evolutionary history of segmental duplications as an optimization problem on the space of directed acyclic graphs. We use a simulated annealing heuristic to solve the problem for a set of segmental duplications in the human genome in both parsimony and likelihood settings.
Availability: Supplementary information is available at http://www.cs.brown.edu/people/braphael/supplements/.
Contact: clkahn@cs.brown.edu; braphael@cs.brown.edu.
Solenoid and non-solenoid protein recognition using stationary wavelet packet transform
Authors: Vo An , Nguyen Nha , Huang Heng 
Published: September 2010

Abstract
Motivation: Solenoid proteins are emerging as a protein class with properties intermediate between structured and intrinsically unstructured proteins. Containing repeating structural units, solenoid proteins are expected to share sequence similarities. However, in many cases, the sequence similarities are weak and non-detectable. Moreover, solenoids can be degenerated and widely vary in the number of units. So that it is difficult to detect them. Recently, several solenoid repeats detection methods have been proposed, such as self-alignment of the sequence, spectral analysis and discrete Fourier transform of sequence. Although these methods have shown good performance on certain data sets, they often fail to detect repeats with weak similarities. In this article, we propose a new approach to recognize solenoid repeats and non-solenoid proteins using stationary wavelet packet transform (SWPT). Our method associates with three advantages: (i) naturally representing five main factors of protein structure and properties by wavelet analysis technique; (ii) extracting novel wavelet features that can capture hidden components from solenoid sequence similarities and distinguish them from global proteins; (iii) obtaining statistics features that capture repeating motifs of solenoid proteins.
Results: Our method analyzes the characteristics of amino acid sequence in both spectral and temporal domains using SWPT. Both global and local information of proteins are captured by SWPT coefficients. We obtain and integrate wavelet-based features and statistics-based features of amino acid sequence to improve the classification task. Our proposed method is evaluated by comparing to state-of-the-art methods such as HHrepID and REPETITA. The experimental results show that our algorithm consistently outperforms them in areas under ROC curve. At the same false positive rate, the sensitivity of our WAVELET method is higher than other methods.
Availability: http://www.naaan.org/anvo/Software/Software.htm
Contact: anphuocnhu.vo@mavs.uta.edu
Prototypes of elementary functional loops unravel evolutionary connections between protein functions
Authors: Goncearenco Alexander , Berezovsky Igor N. 
Published: September 2010

Abstract
Motivation: Earlier studies of protein structure revealed closed loops with a characteristic size 25–30 residues and ring-like shape as a basic universal structural element of globular proteins. Elementary functional loops (EFLs) have specific signatures and provide functional residues important for binding/activation and principal chemical transformation steps of the enzymatic reaction. The goal of this work is to show how these functional loops evolved from pre-domain peptides and to find a set of prototypes from which the EFLs of contemporary proteins originated.
Results: This article describes a computational method for deriving prototypes of EFLs based on the sequences of complete genomes. The procedure comprises the iterative derivation of sequence profiles followed by their hierarchical clustering. The scoring function takes into account information content on profile positions, thus preserving the signature. The statistical significance of scores is evaluated from the empirical distribution of scores of the background model. A set of prototypes of EFLs from archaeal proteomes is derived. This set delineates evolutionary connections between major functions and illuminates how folds and functions emerged in pre-domain evolution as a combination of prototypes.
Contact: Igor.Berezovsky@uni.no
A graphical method for reducing and relating models in systems biology
Authors: Gay Steven , Soliman Sylvain , Fages François 
Published: September 2010

Abstract
Motivation: In Systems Biology, an increasing collection of models of various biological processes is currently developed and made available in publicly accessible repositories, such as biomodels.net for instance, through common exchange formats such as SBML. To date, however, there is no general method to relate different models to each other by abstraction or reduction relationships, and this task is left to the modeler for re-using and coupling models. In mathematical biology, model reduction techniques have been studied for a long time, mainly in the case where a model exhibits different time scales, or different spatial phases, which can be analyzed separately. These techniques are however far too restrictive to be applied on a large scale in systems biology, and do not take into account abstractions other than time or phase decompositions. Our purpose here is to propose a general computational method for relating models together, by considering primarily the structure of the interactions and abstracting from their dynamics in a first step.
Results: We present a graph-theoretic formalism with node merge and delete operations, in which model reductions can be studied as graph matching problems. From this setting, we derive an algorithm for deciding whether there exists a reduction from one model to another, and evaluate it on the computation of the reduction relations between all SBML models of the biomodels.net repository. In particular, in the case of the numerous models of MAPK signalling, and of the circadian clock, biologically meaningful mappings between models of each class are automatically inferred from the structure of the interactions. We conclude on the generality of our graphical method, on its limits with respect to the representation of the structure of the interactions in SBML, and on some perspectives for dealing with the dynamics.
Availability: The algorithms described in this article are implemented in the open-source software modeling platform BIOCHAM available at http://contraintes.inria.fr/biocham The models used in the experiments are available from http://www.biomodels.net/
Contact: francois.fages@inria.fr
Temporal waves of coherent gene expression during Drosophila embryogenesis
Authors: Papatsenko Ilya , Levine Mike , Papatsenko Dmitri 
Published: September 2010

Abstract
Motivation: Animal development depends on localized patterns of gene expression. Whole-genome methods permit the global identification of differential expression patterns. However, most gene-expression-clustering methods focus on the analysis of entire expression profiles, rather than temporal segments or time windows.
Results: In the current study, local clustering of temporal time windows was applied to developing embryos of the fruitfly, Drosophila melanogaster. Large-scale developmental events, involving temporal activation of hundreds of genes, were identified as discrete gene clusters. The time-duration analysis revealed six temporal waves of coherent gene expression during Drosophila embryogenesis. The most powerful expression waves preceded major morphogenetic movements, such as germ band elongation and dorsal closure. These waves of gene expression coincide with the inhibition of maternal transcripts during early development, the specification of ectoderm, differentiation of the nervous system, differentiation of the digestive tract, deposition of the larval cuticle and the reorganization of the cytoskeleton during global morphogenetic events. We discuss the implications of these findings with respect to the gene regulatory networks governing Drosophila development.
Availability: Data and software are available from the UC Berkeley web resource http://flydev.berkeley.edu/cgi-bin/GTEM/dmap_dm-ag/index_dmap.htm
Contact: dimitri.papatsenko@mssm.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Retinoic acids exhibit anti‐fibrotic activity through the inhibition of 5‐lipoxygenase expression in scleroderma fibroblasts
Authors: XIAO Rong , YOSHIDA Nobuyo , HIGASHI Yuko , LU Qian‐Jin , FUKUSHIGE Tomoko , KANZAKI Tamotsu , KANEKURA Takuro 
Published: September 2010

AbstractThe pathogenesis of systemic sclerosis (SSc) is not fully understood and there is no effective treatment for this disease. Retinoic acid (RA) can modulate connective tissue metabolism, exhibit anti‐fibrotic activity, and improve the clinical symptoms of SSc. However, the mechanisms by which RA elicits its anti‐fibrotic actions remain to be determined. The aim of this study was to elucidate the underlying mechanisms by which RA exerts beneficial effects on scleroderma. Cultured skin fibroblasts from patients with scleroderma were treated with RA and their effect on the expression of 5‐lipoxygenase (LOX), transforming growth factor (TGF)‐β1, connective tissue growth factor (CTGF), type I and type III collagen was tested by reverse transcription polymerase chain reaction (RT–PCR) and western immunoblotting. The effect of MK886, a 5‐LOX‐specific inhibitor, on the expression of TGF‐β1, CTGF, type I and type III collagen was also examined by RT–PCR. In cultured scleroderma fibroblasts, the expression of 5‐LOX was elevated compared with normal human dermal fibroblasts. RA significantly inhibited the expression of 5‐LOX and of TGF‐β1, CTGF, type I and type III collagen. We further found that the expression of TGF‐β1, CTGF and type I and type III collagen mRNA was inhibited by MK886 in scleroderma fibroblasts. In vitro, RA reduced 5‐LOX expression in scleroderma fibroblasts and downregulated TGF‐β1 and CTGF expression, leading to the inhibition of type I and type III collagen synthesis. Our results indicate that the clinical effects of RA on scleroderma are, at least in part, attributable to the reduction of 5‐LOX expression and the subsequent suppression of TGF‐β1 and CTGF expression that results in the blockade of collagenogenesis.
Variation in inflorescence characters and inflorescence development in ecotypes and cultivars of Lolium perenne L.
Authors: McGrath S. , Hodkinson T. R. , Charles T. M. , Zen D. G. , Barth S. 
Published: September 2010

AbstractA sufficient database of seed yield components is the prerequisite to predict which component contributes most to the seed yield complex and to dissect the biology of the complex quantitative trait seed yield. Phenotypic variation of eleven vegetative and reproductive traits was characterized for 2481 individuals from fifty Lolium perenne L. (perennial ryegrass) ecotypes and cultivars. Considerable levels of among‐ and within‐population variation were found across several inflorescence characters. Principal component and canonical variate analysis separated ecotypes from cultivars, and cultivars generally had later dates of ear emergence, better spring and summer growth, longer rachis length and more spikelets per spike than ecotypes. Strong positive relationships were seen between inflorescence characters using both correlation and regression analyses. The strong relationship between rachis length and other inflorescence characters suggested that rachis length could be used as a performance predictor for several other characters of the spike. This phenotypic study has helped to determine basic patterns of morphological diversity and correlations between characters. It is discussed in which way further developmental genetic studies can be directed.