bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of irrigation uniformity on evapotranspiration and onion yield
Authors: JIMÉNEZ M. , DE JUAN J. A. , TARJUELO J. M. , ORTEGA J. F. 
Published: January 2010

SUMMARYThe main objective of the current study was to analyse how water application through a sprinkler irrigation system influences yield of onion (Allium cepaL.), taking into account water application heterogeneity and the effects on theoretical crop evapotranspiration (ETc). Field experiments were conducted on commercial onion plots, irrigated with a permanent sprinkler irrigation system, located in Albacete, Spain, over two irrigation seasons. Two experimental plots were selected each study year: plot A (PA), in which water was applied heterogeneously by using sprinklers with different nozzle combinations, and plot B (PB, used as the reference plot) in which the four sprinklers were maintained with the same nozzle combinations. Both experimental plots were divided into 25 subplots with the aim of studying the water distribution (measured as Christiansen uniformity coefficient (CU)), the impact on the actual evapotranspiration (ETa) and the yield obtained. Irrigation was scheduled using a daily simplified water balance method within the root area following the approach of the Food and Agriculture Organization. In the present study, sprinkler irrigation in PAresulted in lower CU (65–82% lower in 2002 and 59–79% lower in 2005) compared with PB(78–92% lower in 2002 and 79–93% lower in 2005). Between 30 May and 18 August 2002, the estimated crop water requirements in PAin the absence of water deficit was 22 mm over the accumulated value of ETc (491v.469 mm), while estimated crop water requirements under water deficit were 187 mm below ETc (282v.469 mm). In 2005, between 29 May and 25 August, ETa without water deficit was more similar to ETc (458v.444 mm) but Eta under water deficit was 242 mm. The greater uniformity of water distribution in PBwas translated into a greater uniformity of yield distribution. A smaller range in yield was observed in PBwhen compared with PA. No statistically significant differences were observed between PAand PBin the crop quality parameters bulb moisture content, total soluble solids, pH and total acidity.
DIFFERENTIALS IN SEX RATIO AT BIRTH AMONG NATIVES AND IMMIGRANTS IN GREECE: AN ANALYSIS EMPLOYING NATIONWIDE MICRO-DATA
Authors: VERROPOULOU GEORGIA , TSIMBOS CLEON 
Published: January 2010

SummaryThis study uses micro-level information on the live births registered in Greece for 2006 to assess differentials in the propensity to have a male offspring between natives and immigrants. The sex ratio at birth for the whole population is 106.3 but it is considerably higher among immigrants (110.9) than among natives (105.4). Relatively high sex ratios at birth are observed for several migrant groups; differentials between natives, on the one hand, and Albanians (109.5) and Asians (129.0), on the other, are significant. The high sex ratio at birth for Albanians seems typical of that population. For Asians, the result is consistent with international findings though it may also be partly related to the small number of observations.
Housing Wealth and Inheritance
Authors: Munro Moira 
Published: January 2010

ABSTRACTOwner-occupation is now an important source of wealth for many people. Housing has experienced price appreciation much in excess of most other assets over the last 20 years and, at the same time, owner-occupation has expanded dramatically. This paper first discusses the impact that this growth in popular wealth holding has had on the overall distribution of income and points to its great importance for all groups except the very wealthy. The importance of housing wealth to the individual is also discussed. Despite the importance of housing wealth, both at an individual and at the broader level, there is virtually no evidence on the transmission of wealth between generations for the mass of people with moderate wealth. This paper rectifies this by analysing the patterns of inheritance of housing wealth for a sample of estates in Glasgow. The evidence shows that wealth left by owner-occupiers is typically passed to a very small group in the close family. The amount of money received can be quite substantial, but tends to go to those in the same or the following generation, that is, people already in middle or old age themselves. Thus, housing inheritance is not likely to be passed directly to young, first time buyers, but to people who already have an established housing career.
The Netherlands: A Passive Social Democratic Welfare State in a Christian Democratic Ruled Society
Authors: Van Kersbergen Kees , Becker Uwe 
Published: January 2010

ABSTRACTThe Netherlands are of considerable interest to students of comparative social policy, because Christian democracy and not social democracy is the leading political force. This article analyses the history of the Dutch system of social security in terms of political forces and their power resources. In particular, it considers the reasons for the comparatively high level of social security development in the Netherlands. The various approaches which have been adopted in much current research in comparative social policy are critically discussed in the context of the Dutch experience.
Delusions and misbeliefs
Authors: Coltheart Max 
Published: January 2010

AbstractBeliefs may be true or false, and grounded or ungrounded. McKay & Dennett (M&D) treat these properties of belief as independent. What, then, do they mean by misbelief? They state that misbeliefs are “simply false beliefs.” So would they consider a very well-grounded belief that is false a misbelief? And why can't beliefs that are very poorly grounded be considered delusions, even when they are true?
Lamarck, Artificial Intelligence (AI), and belief
Authors: Wilks Yorick 
Published: January 2010

AbstractNothing in McKay & Dennett's (M&D's) target article deals with the issue of how the adaptivity, or some other aspect, of beliefs might become a biological adaptation; which is to say, how the functions discussed might be coded in such a way in the brain that their development was also coded in gametes or sex transmission cells.
Adaptive diversity and misbelief
Authors: Cokely Edward T. , Feltz Adam 
Published: January 2010

AbstractAlthough it makes some progress, McKay & Dennett's (M&D's) proposal is limited because (1) the argument for adaptive misbelief is not new, (2) arguments overextend the evidence provided, and (3) the alleged sufficient conditions are not as prohibitive as suggested. We offer alternative perspectives and evidence, including individual differences research, indicating that adaptive misbeliefs are likely much more widespread than implied.
Breeding biology of the Critically Endangered Galapagos Petrel Pterodroma phaeopygia on San Cristóbal Island: conservation and management implications
Authors: CRUZ-DELGADO FRANCISCO , GONZÁLEZ JOSÉ A. , WIEDENFELD DAVID A. 
Published: January 2010

SummaryThe Galapagos Petrel Pterodroma phaeopygia is endemic to the Galapagos Archipelago, where it nests on only five islands. The species is considered ‘Critically Endangered’, mostly due to the effects of alien invasive species, which impair its reproductive success. During 2002–2003 we studied the breeding biology of the petrels nesting on San Cristóbal island. The study revealed particular characteristics of the San Cristóbal petrel population and differences compared to those of other islands, mostly related to nesting habitat, phenology, reproductive success and causes of mortality. On San Cristóbal, petrel nests were primarily located along ravines, in areas of dense vegetation cover formed by the endemic shrub Miconia robinsoniana and a wide variety of native ferns. Over 90% of the nests on the island were located on private agricultural land. The petrel population has a prolonged reproductive period covering 10 months. Laying dates occurred mostly from May to October, with a peak during August, although eggs may be occasionally laid between November and March. The incubation period averaged 50.8 days (range: 46–53), and parental care 103.7 days (range: 98–108). Overall reproductive success was 23.6%; 63.8% for eggs and 37.1% for chicks. Predation by rats was the primary cause (72.2%) of nest failure. Rat control campaigns and clearing of exotic plant species in areas of high density of petrel nests, as well as promoting cooperation agreements between conservation authorities and landowners of the properties where nests are located, are suggested among other critical management measures intended to reduce nest mortality and ensure the survival of the San Cristóbal petrel population.
Abundance of invertebrate prey for birds on organic and conventional arable farms in the Netherlands
Authors: KRAGTEN S. , TAMIS W. L. M. , GERTENAAR E. , MIDCAP RAMIRO S. M. , VAN DER POLL R. J. , WANG J. , DE SNOO G. R. 
Published: January 2010

SummaryAs a result of agricultural intensification, populations of farmland birds have been in steep decline for several decades. Reduction in food abundance has been mentioned as one factor behind these declines. Extensive farm management, such as use of organic methods, is expected to provide more food for birds. In this study we compared invertebrate prey abundance for birds during the breeding season between organic and conventional arable farms. We made comparisons for three different groups of birds: (1) birds feeding on soil-living invertebrates (earthworms), (2) birds feeding on ground-dwelling invertebrates and (3) birds feeding on aerial invertebrates. Invertebrate abundance was compared between organic and conventional farms, crop and non-crop habitats, and between crop and non-crop habitats under the same farm management. On organic sites, earthworm abundance was 2–4 times higher than on conventional sites, but no differences were found between crop types. Total abundance of ground-dwelling invertebrates did not differ between organic and conventional sites, but positive effects were found for several individual taxonomic groups, such as carabid beetles and spiders. On organic farms, invertebrate abundance was higher in carrots, cereals and onions compared to other crops; on conventional farms this was true for onions. When compared with most crops, ground-dwelling invertebrate abundance was low in uncropped field margins and on ditch banks. On organic farms, aerial invertebrate abundance was approximately 70% higher than on conventional farms. On cereal fields, aerial invertebrates were especially abundant.
Predicting biodegradation products and pathways: a hybrid knowledge- and machine learning-based approach
Authors: Wicker Jörg , Fenner Kathrin , Ellis Lynda , Wackett Larry , Kramer Stefan 
Published: January 2010

Abstract
Motivation: Current methods for the prediction of biodegradation products and pathways of organic environmental pollutants either do not take into account domain knowledge or do not provide probability estimates. In this article, we propose a hybrid knowledge- and machine learning-based approach to overcome these limitations in the context of the University of Minnesota Pathway Prediction System (UM-PPS). The proposed solution performs relative reasoning in a machine learning framework, and obtains one probability estimate for each biotransformation rule of the system. As the application of a rule then depends on a threshold for the probability estimate, the trade-off between recall (sensitivity) and precision (selectivity) can be addressed and leveraged in practice.
Results: Results from leave-one-out cross-validation show that a recall and precision of ∼0.8 can be achieved for a subset of 13 transformation rules. Therefore, it is possible to optimize precision without compromising recall. We are currently integrating the results into an experimental version of the UM-PPS server.
Availability: The program is freely available on the web at http://wwwkramer.in.tum.de/research/applications/biodegradation/data.
Contact: kramer@in.tum.de
iMotifs: an integrated sequence motif visualization and analysis environment
Authors: Piipari Matias , Down Thomas A. , Saini Harpreet , Enright Anton , Hubbard Tim J.P. 
Published: January 2010

Abstract
Motivation: Short sequence motifs are an important class of models in molecular biology, used most commonly for describing transcription factor binding site specificity patterns. High-throughput methods have been recently developed for detecting regulatory factor binding sites in vivo and in vitro and consequently high-quality binding site motif data are becoming available for increasing number of organisms and regulatory factors. Development of intuitive tools for the study of sequence motifs is therefore important.
iMotifs is a graphical motif analysis environment that allows visualization of annotated sequence motifs and scored motif hits in sequences. It also offers motif inference with the sensitive NestedMICA algorithm, as well as overrepresentation and pairwise motif matching capabilities. All of the analysis functionality is provided without the need to convert between file formats or learn different command line interfaces.
The application includes a bundled and graphically integrated version of the NestedMICA motif inference suite that has no outside dependencies. Problems associated with local deployment of software are therefore avoided.
Availability: iMotifs is licensed with the GNU Lesser General Public License v2.0 (LGPL 2.0). The software and its source is available at http://wiki.github.com/mz2/imotifs and can be run on Mac OS X Leopard (Intel/PowerPC). We also provide a cross-platform (Linux, OS X, Windows) LGPL 2.0 licensed library libxms for the Perl, Ruby, R and Objective-C programming languages for input and output of XMS formatted annotated sequence motif set files.
Contact: matias.piipari@gmail.com; imotifs@googlegroups.com
invertFREGENE: software for simulating inversions in population genetic data
Authors: O'Reilly Paul F. , Coin Lachlan J. M. , Hoggart Clive J. 
Published: January 2010

Abstract
Summary: Inversions are a common form of structural variation, which may have a marked effect on the genome and methods to infer quantities of interest such as those relating to population structure and natural selection. However, due to the challenge in detecting inversions, little is presently known about their impact. Software to simulate inversions could be used to provide a better understanding of how to detect and account for them; but while there are several software packages for simulating population genetic data, none incorporate inversion polymorphisms. Here, we describe a software package, modified from the forward-in-time simulator FREGENE, which simulates the evolution of an inversion polymorphism, of specified length, location, frequency and age, in a population of sequences. We describe previously unreported signatures of inversions in SNP data observed in invertFREGENE results and a known inversion in humans.
Availability: C++ source code and user manual are available for download from http://www.ebi.ac.uk/projects/BARGEN/ under the GPL licence.
Contact: l.coin@ic.ac.uk; c.hoggart@ic.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
XDIA: improving on the label-free data-independent analysis
Authors: Carvalho Paulo C. , Han Xuemei , Xu Tao , Cociorva Daniel , Carvalho Maria da Gloria , Barbosa Valmir C. , Yates John R. 
Published: January 2010

Abstract
Summary: XDIA is a computational strategy for analyzing multiplexed spectra acquired using electron transfer dissociation and collision-activated dissociation; it significantly increases identified spectra (∼250%) and unique peptides (∼30%) when compared with the data-dependent ETCaD analysis on middle-down, single-phase shotgun proteomic analysis. Increasing identified spectra and peptides improves quantitation statistics confidence and protein coverage, respectively.
Availability: The software and data produced in this work are freely available for academic use at http://fields.scripps.edu/XDIA
Contact: paulo@pcarvalho.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Cell Wall-Degrading Enzymes Enlarge the Pore Size of Intervessel Pit Membranes in Healthy andXylella fastidiosa-Infected Grapevines
Authors: Pérez-Donoso Alonso G. , Sun Qiang , Roper M. Caroline , Greve L. Carl , Kirkpatrick Bruce , Labavitch John M. 
Published: January 2010

AbstractThe pit membrane (PM) is a primary cell wall barrier that separates adjacent xylem water conduits, limiting the spread of xylem-localized pathogens and air embolisms from one conduit to the next. This paper provides a characterization of the size of the pores in the PMs of grapevine (Vitis vinifera). The PM porosity (PMP) of stems infected with the bacterium Xylella fastidiosa was compared with the PMP of healthy stems. Stems were infused with pressurized water and flow rates were determined; gold particles of known size were introduced with the water to assist in determining the size of PM pores. The effect of introducing trans-1,2-diaminocyclohexane-N,N,N′,N′-tetraacetic acid (CDTA), oligogalacturonides, and polygalacturonic acid into stems on water flux via the xylem was also measured. The possibility that cell wall-degrading enzymes could alter the pore sizes, thus facilitating the ability of X. fastidiosa to cross the PMs, was tested. Two cell wall-degrading enzymes likely to be produced by X. fastidiosa (polygalactuoronase and endo-1,4- β -glucanase) were infused into stems, and particle passage tests were performed to check for changes in PMP. Scanning electron microscopy of control and enzyme-infused stem segments revealed that the combination of enzymes opened holes in PMs, probably explaining enzyme impacts on PMP and how a small X. fastidiosa population, introduced into grapevines by insect vectors, can multiply and spread throughout the vine and cause Pierce's disease.
Analysis of Arabidopsis with Highly Reduced Levels of Malate and Fumarate Sheds Light on the Role of These Organic Acids as Storage Carbon Molecules
Authors: Zell Martina B. , Fahnenstich Holger , Maier Alexandra , Saigo Mariana , Voznesenskaya Elena V. , Edwards Gerald E. , Andreo Carlos , Schleifenbaum Frank , Zell Christiane , Drincovich María F. , Maurino Verónica G. 
Published: January 2010

Abstract
While malate and fumarate participate in a multiplicity of pathways in plant metabolism, the function of these organic acids as carbon stores in C3 plants has not been deeply addressed. Here, Arabidopsis (Arabidopsis thaliana) plants overexpressing a maize (Zea mays) plastidic NADP-malic enzyme (MEm plants) were used to analyze the consequences of sustained low malate and fumarate levels on the physiology of this C3 plant. When grown in short days (sd), MEm plants developed a pale-green phenotype with decreased biomass and increased specific leaf area, with thin leaves having lower photosynthetic performance. These features were absent in plants growing in long days. The analysis of metabolite levels of rosettes from transgenic plants indicated similar disturbances in both sd and long days, with very low levels of malate and fumarate. Determinations of the respiratory quotient by the end of the night indicated a shift from carbohydrates to organic acids as the main substrates for respiration in the wild type, while MEm plants use more reduced compounds, like fatty acids and proteins, to fuel respiration. It is concluded that the alterations observed in sd MEm plants are a consequence of impairment in the supply of carbon skeletons during a long dark period. This carbon starvation phenotype observed at the end of the night demonstrates a physiological role of the C4 acids, which may be a constitutive function in plants.
Lentiviral shRNA silencing of BDNF inhibits in vivo multiple myeloma growth and angiogenesis via down‐regulated stroma‐derived VEGF expression in the bone marrow milieu
Authors: Zhang Lu , Hu Yu , Sun Chun‐yan , Li Jiang , Guo Tao , Huang Jing , Chu Zhang‐bo 
Published: January 2010

Bone marrow (BM) neovascularization and vascular endothelial growth factor (VEGF) expression in multiple myeloma (MM) correlate with disease progression. Brain derived neurotrophic factor (BDNF) is highly expressed by malignant plasma cells isolated from the majority of MM patients. Recently, BDNF was identified as a potential proangiogenic factor for the promotion of endothelial cell survival, induction of neoangiogenesis in ischemic tissues, and increase of VEGF expression in neuroblastoma. Since tropomyosin receptor kinase B (TrkB), the receptor of BDNF, is expressed by stromal cells within the BM milieu, here we sought to evaluate the involvement of BDNF/TrkB in myeloma–marrow stroma interaction and its effects on BM angiogenesis. TrkB was abundantly expressed by bone marrow stromal cells (BMSCs) isolated from healthy donors. Stimulation of BMSCs with BDNF induced a time‐ and dose‐ dependent increase in VEGF secretion, which was completely abolished by K252α, an inhibitor of TrkB. BDNF triggered activation of signal transducer and activator of transcription 3 (STAT3) and activator protein‐1 (AP‐1), whereas STAT3 was involved in mediating VEGF expression. We further delineated the biological significance of BDNF in MM by using lentiviral short‐interfering RNA (shRNA). When myeloma cells were cocultured with BMSCs in a noncontact Transwell system, VEGF levels in supernatants were significantly decreased when BDNF expression was knocked down. Furthermore, silencing of BDNF expression significantly inhibited xenograft tumor growth and angiogenesis, and prolonged survival in mouse model. Our studies demonstrate that BDNF, as a potential stimulator of angiogenesis, contributes to MM tumorgenesis; it mediates stromal–MM cell interactions via selective activation of specific receptor TrkB and downstream signal transducer STAT3, regulating VEGF secretion.(Cancer Sci 2010; 101: 1117–1124)