bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feature subset selection for splice site prediction
Authors: Degroeve Sven , De Baets Bernard , Van de Peer Yves , Rouzé Pierre 
Published: May 2011

Abstract
Motivation: The large amount of available annotated Arabidopsis thaliana sequences allows the induction of splice site prediction models with supervised learning algorithms (see Haussler (1998) for a review and references). These algorithms need information sources or features from which the models can be computed. For splice site prediction, the features we consider in this study are the presence or absence of certain nucleotides in close proximity to the splice site. Since it is not known how many and which nucleotides are relevant for splice site prediction, the set of features is chosen large enough such that the probability that all relevant information sources are in the set is very high. Using only those features that are relevant for constructing a splice site prediction system might improve the system and might also provide us with useful biological knowledge. Using fewer features will of course also improve the prediction speed of the system.
Results: A wrapper-based feature subset selection algorithm using a support vector machine or a naive Bayes prediction method was evaluated against the traditional method for selecting features relevant for splice site prediction. Our results show that this wrapper approach selects features that improve the performance against the use of all features and against the use of the features selected by the traditional method.
Availability: The data and additional interactive graphs on the selected feature subsets are available at http://www.psb.rug.ac.be/gps
Contact: svgro@gengenp.rug.ac.beyvdp@gengenp.rug.ac.be
First Report of Beet severe curly top virus in Jalapeño Pepper in Chihuahua, Mexico
Authors: Robles-Hernandez L. , Gonzalez-Franco A. C. , Gill-Langarica E. M. , Sago C. , Nikolaeva O. V. , Karasev A. V. 
Published: May 2011

Curly top is a serious problem in many irrigated crops in the semiarid areas in the western United States. The disease is caused by a complex of leafhopper-transmitted curtoviruses, one of which, Beet mild curly top virus (BMCTV), was previously found in chili pepper in Zacatecas and Aguascalientes, Mexico (3). During the past few years, sporadic symptoms similar to curly top disease were observed in jalapeño pepper in the south-central area of Chihuahua State. Symptomatic plants were scattered in otherwise healthy looking pepper stands and displayed stunting and yellowing. Affected leaves were brittle, showed upward curling, and a distinct green vein pattern with interveinal yellowing. In June and August of 2010, field surveys were conducted in Cordillera-Escuadra, Meoqui-Estacion Consuelo, Meoqui-Lomas del Consuelo, and Delicias-Presa Francisco I Madero. Ninety-four leaf samples were collected from symptomatic jalapeño pepper plants and subjected to ELISA and PCR testing for curly top. Of the 94 samples, 11 were found to be positive by triple-antibody sandwich-ELISA with polyclonal antibodies against curly top (2). To confirm the identification of curly top and type the specific curtovirus identified, four ELISA-positive samples were subjected to a PCR analysis using a virus-specific primer set for curtovirus typing designed by Chen et al. (1). All four samples tested produced a single 720-bp band with primers BSCTVv2688 and BGc396 (1) characteristic of the Beet severe curly top virus (BSCTV). These curly top-specific PCR amplicons were sequenced and found to be 99% similar to the BSCTV nucleotide sequence in the C1 gene region (GenBank Accession No. X97203); corresponding sequences were deposited in GenBank under Accession Nos. JF437870 to JF437873. To our knowledge, this is the first report of the curly top virus in the State of Chihuahua, demonstrating that curly top is established and common in jalapeño pepper here and will need surveillance in other vegetable crops under irrigation. References: (1) L. F. Chen et al. Plant Dis. 94:99, 2010. (2) J. Durrin et al. Plant Dis. 94:972, 2010. (3) R. Velásquez-Valle et al. Plant Dis. 92:650, 2008.
Is There Division of Labor in Cooperative Pseudoscorpions? An Analysis of the Behavioral Repertoire of a Tropical Species
Authors: Tizo‐Pedroso Everton , Del‐Claro Kleber 
Published: May 2011

AbstractDivision of labor is a strategy that maximizes the foraging and reproductive success of eusocial insects. Although some arachnids exhibit colony structure and social organization similar to that of hymenopterans, temporal polyethism has only been demonstrated in few species. The social organization of cooperative pseudoscorpions Paratemnoides nidificator is similar to that of social spiders, but it involves a clear division of labor. Work allocation was experimentally investigated in colonies composed of only one developmental stage (young or adults) or by one sex (males or females), through laboratory manipulation. During 44 h of observation, more than 14 000 behavioral repetitions were quantified, distributed in 95 different types of behavioral acts, and grouped in 10 behavioral categories. The results showed that reproductive colonies of P. nidificator are maintained by gender‐ and age‐based activities. Males and non‐reproductive females performed the external cleaning of the colony and prey capture. Reproductive females take care of the juveniles and build reproductive silk chambers. Nymphs build most of the molt chambers and perform internal cleaning. In the absence of nymphs, male colonies survived 1–2 mo, while female colonies survived 3–4 mo. In nymph colonies, work is readjusted so that all maintenance tasks are executed. This is the first study clearly demonstrating division of tasks in arachnids. It suggests that specialization is an adaptative and evolutionarily old trait in this species. Unlike cooperative spiders, P. nidificator possesses physiological (e.g. reproduction, ecdysis, lifespan) and behavioral (e.g. behavioral synchrony or self‐organization) characteristics that allow task specialization.
Lack of Evidence for the Prior Residence Effect in the Allegheny Mountain Dusky Salamander (Desmognathus ochrophaeus)
Authors: Plenderleith T. Lynette , Forester Don C. 
Published: May 2011

AbstractTerritorial disputes are frequently settled by an advantage afforded to one of the contestants by asymmetries such as size difference, strength and motivation. Allegheny Mountain Dusky Salamanders (Desmognathus ochrophaeus) are reported to defend cover objects, a form of territorial behaviour. We conducted an experiment to determine whether or not adult salamanders of this species exhibit prior residence effect during staged encounters involving size‐matched, same sex conspecifics (i.e. does familiarity with a territory predict successful defence?). We tested 154 adult salamanders (72 female, 82 male) in reciprocal trials in which each animal acted as a resident and as an intruder. We recorded multiple agonistic behaviours including: front‐trunk raised, all‐trunk raised, nudge, bite, bite‐and‐hold and jaw‐lock. We assigned these behaviours scaled point values and calculated an index of aggression for each animal as a resident and as an intruder. We found that in same sex trials, males were significantly more aggressive than females. Although D. ochrophaeus exhibited stereotypical, agonistic behaviours similar to those reported for Plethodon, unlike Plethodon the outcomes of symmetrical social encounters were not influenced by residential status. Prior residence is documented to be a major determinant of territorial disputes among diverse animal taxa, including salamanders. However, our research suggests that the phenomenon is not universal and may depend on qualities of the microhabitat in which a species has evolved.
Effects of dietary supplementation of Chinese medicinal herbs on polymorphonuclear neutrophil immune activity and small intestinal morphology in weanling pigs
Authors: Huang C. W. , Lee T. T. , Shih Y. C. , Yu B. 
Published: May 2011

SummaryThe purpose of this study was to evaluate the effects of dietary Chinese medicinal herbs (CMH) supplementation composed of Panax ginseng, Dioscoreaceae opposite, Atractylodes macrocephala, Glycyrrhiza uralensis, Ziziphus jujube and Platycodon grandiflorum, on the performance, intestinal tract morphology and immune activity in weanling pigs. Two hundred and forty weaned pigs were assigned randomly to four dietary groups including the negative control (basal diet), 0.1% CMH, 0.3% CMH and 0.114% antibiotic (Chlortetracycline calcium Complex, Sulfathiazole and Procaine Penicillin G) supplementation groups for a 28‐day feeding trial. Results indicated that both CMH supplementation groups had a better gain and feed/gain than control group (CT) during the first 2 weeks of the experimental period. The 0.3% CMH had a significant decrease in the diarrhoea score in first 10 days of experimental period when compared with other groups. The CMH supplementation groups had a higher villous height, increased lactobacilli counts in digesta of ileum and decreased coliform counts in colon compared with CT. The immune activities of polymorphonuclear leucocytes (PMNs), including the respiratory burst and Salmonella‐killing ability, were significantly enhanced in CMH supplementation groups at day 7 of experiment period. The CMH and antibiotic supplementations increased the nutrient digestibility such as dietary dry matter, crude protein and gross energy in weanling pigs. In conclusion, the dietary CMH supplementation improved intestinal morphology and immune activities of PMNs, thus giving rise to nutrient digestibility and reduce diarrhoea frequency in weanling pigs.
EUTHYPHRO AND THE GOODNESS OF GOD INCARNATE
Authors: Le Poidevin Robin 
Published: May 2011

AbstractA familiar problem is here viewed from an unfamiliar angle. The familiar problem is the Euthyphro dilemma: if God wills something because it is good, then goodness is independent of God, so God becomes, morally speaking, de trop. On the other hand, if something is good because God wills it, then, given the absence of constraint on what God may will, moral truths are – counterintuitively – contingent. An examination of the kinds of necessity and possibility at work in this conundrum leads us to the most promising solution: there is a metaphysical connection between God and goodness. What he wills is an expression of his nature. But (and this is the unfamiliar angle), that solution now poses an acute problem for an understanding of the Incarnation. For if God is constitutive of goodness, and Christ is God incarnate, then Christ is constitutive of goodness. But Christ, as a human, is subject to external moral evaluation and obligation, which entails that he is not constitutive of goodness. This metaethical difficulty is not easily met by the usual strategies by which Christ is understood to have two natures. Reflection on our moral relations to our past selves, however, suggests a way forward.
Combining the Intensity and Sequencing of the Poverty Experience: A Class of Longitudinal Poverty Indices
Authors: Mendola Daria , Busetta Annalisa , Milito Anna Maria 
Published: May 2011

SummaryTraditional measures of the persistence of poverty do not devote enough attention to the sequence of spells of poverty. We propose a new class of indices which measures the severity of chronic poverty, taking into account the way in which spells of poverty and non-poverty follow one another along individual life courses. All the years spent in poverty concur with the measurement of the persistency of poverty, albeit with a decreasing contribution provided that the distance between two consecutive spells of poverty becomes longer. Moreover, the distance from the poverty line and the poverty persistence probabilities are explicitly taken into account. A macrolevel index, which allows comparisons across nations and accounts for the mobility in the national income distributions, is also provided and it is used to explain the differentials of persistence of poverty among young European adults.
Evaluation of a portable glucose meter for use in cattle and sheep
Authors: Katsoulos Panagiotis D. , Minas Anastasios , Karatzia Maria A. , Pourliotis Konstantinos , Christodoulopoulos Georgios 
Published: May 2011

Background: In farm animal practice, determination of blood glucose concentration under field conditions is often necessary.Objective: As there is no portable glucose meter device developed for use in farm animals, the analytical accuracy of a portable glucometer designed for people was evaluated for its use in cattle and sheep.Methods: Blood samples from 90 cattle and 101 sheep were used in the study. Glucose concentration was determined in whole blood immediately after blood collection from the jugular vein with the One Touch Vita portable glucometer and in serum with an enzymatic colorimetric method. The agreement between methods was assessed by Passing and Bablok regression analysis. The precision and the accuracy of the measurements were determined using the concordance correlation coefficient.Results: There was a strong linear relationship between the glucose values obtained using the portable glucometer and those obtained by the bench method in both cattle and sheep. Precision was 95% for cattle and 88% for sheep, whereas accuracy was 92% and 99%, respectively. The mean glucose values obtained using the portable glucometer were significantly lower by 8.3% in cattle and 3.2% in sheep than those determined by the bench method.Conclusion: The One Touch Vita portable glucometer can be used in clinical practice to determine blood glucose concentrations in cattle and sheep, but reference intervals (RI) must be corrected to allow for negative bias. Based on these equations the RI for blood glucose in cattle and sheep using the portable glucometer were corrected to 1.84–4.17 and 2.41–4.35 mmol/L, respectively.
Frequency of dog erythrocyte antigen 1.1 expression in dogs from Portugal
Authors: Ferreira Rui R. F. , Gopegui Rafael R. , Matos Augusto J. F. 
Published: May 2011

Background:Dog erythrocyte antigen (DEA) 1.1 is the antigen considered most responsible for severe hemolysis owing to incompatible blood transfusions in previously sensitized dogs. Few reports describe the frequency of DEA 1.1 expression in European dogs, and there are no reports in dogs from Portugal.Objective:The aims of this study were to identify the frequency of DEA 1.1 expression in Portuguese dogs, to examine the relationship between phenotypic traits and expression of this blood group, and to assess the risk of transfusing blood that is not typed or cross‐matched.Methods:Expression of DEA 1.1 was determined in 274 dogs using a migration gel test. Weight, sex, breed, and hair length and color were recorded for each dog. Results were analyzed by descriptive statistical analysis, probabilistic analysis, and χ2‐tests.Results:Of 274 dogs, 56.9% were DEA 1.1‐positive and 43.1% were DEA 1.1‐negative. All Boxers, German Shepherds, and Dobermans were DEA 1.1‐negative, whereas all Saint Bernards, 88.9% of Golden Retrievers, 88.2% of Rottweilers, and 61.4% of mixed breed dogs were DEA 1.1‐positive. A significant relationship between DEA 1.1 expression and phenotypic traits was not found. The probability of sensitization of recipient dogs following first‐time transfusion with blood that was not typed or cross‐matched was 24.5%; the probability of an acute hemolytic reaction following a second transfusion with blood from any other donor in the absence of pretransfusion compatibility testing was 6%.Conclusion:The frequency of DEA 1.1 expression in dogs in Portugal is high, and there is a potential risk of sensitization following transfusion with blood that is not typed or cross‐matched. Breed‐related frequencies may help predict DEA 1.1‐positivity, but the best practice is to type and cross‐match blood before transfusion.
States of Citizenship: Contexts and Cultures of Public Engagement and Citizen Action
Authors: Cornwall Andrea , Robins Steven , Von Lieres Bettina 
Published: May 2011

SummaryDrawing on case studies from the Citizenship Development Research Centre, this paper contends that mechanisms aimed at enhancing citizen engagement need to be contextualised in the states of citizenship in which they are applied. It calls for more attention to be focused on understanding trajectories of citizenship experience and practice in particular kinds of states. It suggests that whilst efforts have been made by donors to get to grips with history and context – such as DFID's Drivers of Change analyses or Sida's Power Studies – less attention has been given to exploring the implications of the dissonance between the normative dimensions of global narratives of participation and accountability, and the lived experience of civic engagement and the empirical realities of ‘civil society’ in diverse kinds of states. By exploring instantiations of citizenship in different kinds of states, the paper reflects on what citizen engagement comes to imply in these contexts. In doing so, it draws attention to the diverse ways in which particular subject‐positions and forms of identification are articulated in the pursuit of concrete social and political projects.
Global petroleum systems in space and time
Authors: May S. , Kleist R. , Kneller E. , Johnson C. , Creaney S. 
Published: May 2011

Abstract
Each of the Earth's approximately 900 sedimentary basins is a unique result of geologic, hydrologic, atmospheric and biologic processes. The interaction of these processes results in complex histories that are palaeogeographically linked within tectonic provinces. Process-based genetic analysis provides the fundamental framework for predicting the distribution and character of petroleum systems. New technologies enable the exploitation of this predictability and are themselves the origin of new ideas and improved systems understanding. Petroleum geoscience embraces both forward modelling of processes as well as observation, calibration and inverse modelling. This approach of forward and inverse modelling promotes a general scientific methodology of simulation, prediction, testing and learning that allows us to describe the genetics of sedimentary basins. Genetic analysis can be applied to the spectrum of resource types from hydrocarbon to groundwater to mineral systems and across the range of scales from regional to play to prospect. Like the study of evolution through the fossil record, fundamental characteristics of petroleum systems can be recovered from the patterns of their distribution within the framework provided by plate motion, palaeogeography and palaeoclimate. These fundamental drivers control regional tectonics, subsidence, fill history and deformation that result in the phenotypic expression of individual basins and their fluid systems. Genetic analysis results in a taxonomic hierarchy that facilitates prediction and guides resource exploration. Although genetic analysis provides a framework for understanding the distribution and nature of petroleum systems, that framework itself is insufficient to address the challenges now facing the petroleum industry. New technologies are required to enable exploration in frontier settings, to identify new opportunities in mature basins, to maximize recovery from existing fields, and to unlock the potential of unconventional resources. Future success in all of these areas is fundamentally dependent on our ability to conceptualize new ideas.
From thrust-and-fold belt to foreland: hydrocarbon occurrences in Italy
Authors: Bertello F. , Fantoni R. , Franciosi R. , Gatti V. , Ghielmi M. , Pugliese A. 
Published: May 2011

Abstract

Italy is the most hydrocarbon endowed country of southern Europe, with total discovered reserves (produced+remaining) of 1840 million barrels of oil and 30 trillion ft
3
of gas. The production of oil amounts to 43.2 million barrels per year, about 75% of which comes from the Val d'Agri Field in the southern Apennines. The production of gas is 340 billion ft
3
per year, most of it coming from the northern Adriatic Sea. Hydrocarbon occurrences derive from a variety of petroleum systems which are the result of a complex geological history. At least five important source rocks have been recognized which are distributed in age from Mesozoic through Pleistocene. Three of them were deposited during Mesozoic crustal extension and are mainly oil-prone. Hydrocarbon occurrences associated with these sources are usually found in complex carbonate structures along the Apennines thrust-and-fold belt and in the foreland. Villafortuna–Trecate (Po Plain), Val d'Agri/Tempa Rossa (southern Apennines) and Gela (Sicily) fields represent the largest oil accumulations pertaining to these systems. Two other important sources rocks were deposited in the foredeep terrigenous units of the foreland basins which formed during the Cenozoic orogenesis. The older source is thermogenic gas-prone and is found in the highly tectonized Oligo-Miocene foredeep wedges: gas occurrences associated with this source are mainly concentrated along the northern Apennines margin (e.g. Cortemaggiore Field), in Calabria (e.g. Luna Field) and Sicily (e.g. Gagliano Field). The younger source is biogenic gas-prone and is situated in the outer Plio-Pleistocene foredeeps. The most important gas fields of Italy, located in the eastern Po Plain and northern Adriatic sea (Barbara and other gas fields), have originated from this source. Hydrocarbon exploration in Italy is overall mature, especially for gas, whose residual potential is estimated to be 6.0 trillion ft
3
of reserves. The remaining potential of oil is estimated to be 800 million barrels.
Upper Jurassic reservoir sandstones in the Danish Central Graben: new insights on distribution and depositional environments
Authors: Johannessen P. N. , Dybkjær K. , Andersen C. , Kristensen L. , Hovikoski J. , Vosgerau H. 
Published: May 2011

Abstract
Recently available well data from the northern part of the Danish Central Graben have been analysed to further understand the basin development, biostratigraphy, depositional models and palaeogeography of Upper Jurassic reservoir sandstones, which are the primary exploration targets in this basin. Notably, the discovery of the Hejre accumulation in 2001, where oil has been encountered in Upper Jurassic good reservoir quality sandstones at a depth of more than 5000 m, triggered renewed interest in the Upper Jurassic High Temperature–High Pressure sandstone play in the area.
Overall the Danish Central Graben was transgressed from east to west during the Late Jurassic. During the Late Kimmeridgian, marginal and shallow marine sandstones assigned to the Heno Formation were deposited at the margin of the Feda Graben, and on the Gertrud and Heno Plateaus and constitute the reservoirs in the Freja and Hejre discoveries. The sandstones are analogues to the UK Fulmar and Norwegian Ula Formations encountered in several hydrocarbon fields.
During the Early Volgian, the transgression continued westwards across the Outer Rough Basin along the margin of the Mid North Sea High, where shoreface sandstones with excellent porosities and permeabilities were deposited close to similar sandstones of the Fulmar Formation in the British Fergus, Fife and Angus fields.

During this overall westward transgression, the eastern and central parts of the Danish Central Graben continued to subside and offshore mudstones accumulated, locally intercalated with gravity-flow sandstones. In the easternmost Danish Central Graben, in the Tail End Graben, Upper Kimmeridgian gravity-flow sandstones of the Svane-1 well have proved the presence of gas at
c
. 6 km depth.

Hydrocarbon-bearing Upper Jurassic sandstone reservoirs at significant depths (deeper than 5 km) may form the future exploration targets in the northern part of the Danish Central Graben.