bluuebunny/crossref_metadata_2025_split huggingface dataset:
In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists
Authors: Saeys Yvan , Rouzé Pierre , Van de Peer Yves 
Published: January 2007

AbstractMotivation: Prediction of the coding potential for stretches of DNA is crucial in gene calling and genome annotation, where it is used to identify potential exons and to position their boundaries in conjunction with functional sites, such as splice sites and translation initiation sites. The ability to discriminate between coding and non-coding sequences relates to the structure of coding sequences, which are organized in codons, and by their biased usage. For statistical reasons, the longer the sequences, the easier it is to detect this codon bias. However, in many eukaryotic genomes, where genes harbour many introns, both introns and exons might be small and hard to distinguish based on coding potential.Results: Here, we present novel approaches that specifically aim at a better detection of coding potential in short sequences. The methods use complementary sequence features, combined with identification of which features are relevant in discriminating between coding and non-coding sequences. These newly developed methods are evaluated on different species, representative of four major eukaryotic kingdoms, and extensively compared to state-of-the-art Markov models, which are often used for predicting coding potential. The main conclusions drawn from our analyses are that (1) combining complementary sequence features clearly outperforms current Markov models for coding potential prediction in short sequence fragments, (2) coding potential prediction benefits from length-specific models, and these models are not necessarily the same for different sequence lengths and (3) comparing the results across several species indicates that, although our combined method consistently performs extremely well, there are important differences across genomes.Supplementary data: Contact: yvan.saeys@psb.ugent.be
THE ELECTROSTATIC FIELD OF TWO EQUAL CIRCULAR CO-AXIAL CONDUCTING DISKS
Authors: LOVE E. R. 
Published: January 2007

Abstract
In the earliest discussion of this problem Nicholson (1) expressed the potential as a series of spheroidal harmonics with coefficients satisfying an infinite system of linear equations, and gave a formula for an explicit solution; but this formula appears to be meaningless and its derivation to contain serious errors.
In the present paper, starting tentatively from Nicholson's infinite system of linear equations, a much simpler, though still implicit, specification of the potential is developed; this involves a Fredholm integral equation the existence and uniqueness of whose solution are deducible from standard theory. The specification so obtained for the potential is shown rigorously to satisfy the differential equation and boundary conditions of the electrostatic problem.
The Neumann series of the integral equation is shown to converge to its solution, so that the potential, and other aspects of the field, can be explicitly formulated and thus computed.
The errors in Nicholson's process of solving his system of equations are exhibited in detail, and it is concluded that attempts to carry through that process without error cannot lead to an explicit solution.
Further analysis of gene‐for‐gene disease resistance specificity in flax
Authors: ELLIS JEFFREY G. , LAWRENCE GREGORY J. , DODDS PETER N. 
Published: January 2007

SUMMARYThe flax rust resistance gene L, a nucleotide binding site, leucine‐rich repeat (NBS‐LRR) class of plant resistance gene, has 12 characterized alleles with different gene‐for‐gene resistance specificities. Here the specificities of presumptive L1, L5, L8 and L11 genomic clones are confirmed by transgenic expression. L6 and L11 differ by 33 amino acids, 32 in the LRR region and one in the C‐terminal non‐LRR region, and recognize unrelated avirulence proteins, AvrL567 and AvrL11, respectively. To analyse the specificity differences, 13 L6L11 recombinant genes were constructed in vitro and tested in transgenic flax for resistance to F2 progeny of rust strain CH5, in which the unlinked avirulence genes AvrL567 and AvrL11 segregate. The data show that the single C‐terminal non‐LRR region polymorphism is not involved in L6–L11 specificity differences, that polymorphisms necessary for specificity are spread throughout the LRR region and that some polymorphisms essential for L11 are not essential for L6. Seven ‘null’ recombinants expressed no resistance when tested with CH5‐derived rusts. These were tested for new resistance specificities by inoculation with a strain of rust, Bs‐1, which is distantly related to CH5 and which potentially carries a different range of avirulence specificities. The ‘null’ recombinant L6L11RV, which differs from L6 and L11 by its susceptibility to CH5, was resistant to strain Bs‐1. The specificity difference is due to a reduction in the number of AvrL567 variants recognized by L6L11RV compared with L6 and not due to recognition of an unrelated Avr gene product in strain Bs‐1.
Negative bending in seismic reflection associated with time‐advanced and time‐retarded fields
Authors: Ikelle Luc T. , Gangi Anthony F. 
Published: January 2007

ABSTRACTWe present an analysis of scattering diagrams (i.e., Feynman‐like diagrams for wave scattering) of the correlation‐type representation theorem for ordinary inhomogeneous media with both positive stiffnesses and positive Poisson's ratios. This analysis reveals scattering events whose scattering diagrams include “negative” bending (i.e., bending in the opposite direction of that of scattering diagrams in ordinary inhomogeneous media). Unlike common scattering events, these events are inconsistent with the current interpretation of some of the basic physical laws, such as Snell's law, just like the so‐called “negative refraction” in optics. Yet we find them very useful, for instance, in suppressing some undesired events from scattering data.
Paraxial ray methods for anisotropic inhomogeneous media
Authors: Jan Moser Tijmen , Červený Vlastislav 
Published: January 2007

ABSTRACTA new formalism of surface‐to‐surface paraxial matrices allows a very general and flexible formulation of the paraxial ray theory, equally valid in anisotropic and isotropic inhomogeneous layered media. The formalism is based on conventional dynamic ray tracing in Cartesian coordinates along a reference ray. At any user‐selected pair of points of the reference ray, a pair of surfaces may be defined. These surfaces may be arbitrarily curved and oriented, and may represent structural interfaces, data recording surfaces, or merely formal surfaces. A newly obtained factorization of the interface propagator matrix allows to transform the conventional 6 × 6 propagator matrix in Cartesian coordinates into a 6 × 6 surface‐to‐surface paraxial matrix. This matrix defines the transformation of paraxial ray quantities from one surface to another. The redundant non‐eikonal and ray‐tangent solutions of the dynamic ray‐tracing system in Cartesian coordinates can be easily eliminated from the 6 × 6 surface‐to‐surface paraxial matrix, and it can be reduced to 4 × 4 form. Both the 6 × 6 and 4 × 4 surface‐to‐surface paraxial matrices satisfy useful properties, particularly the symplecticity. In their 4 × 4 reduced form, they can be used to solve important boundary‐value problems of a four‐parametric system of paraxial rays, connecting the two surfaces, similarly as the well‐known surface‐to‐surface matrices in isotropic media in ray‐centred coordinates. Applications of such boundary‐value problems include the two‐point eikonal, relative geometrical spreading, Fresnel zones, the design of migration operators, and more.
FACTOR RINGS OF PSEUDO-FROBENIUS RINGS
Authors: FAITH CARL 
Published: January 2007

If R is right pseudo-Frobenius (= PF), and A is an ideal, when is R/A right PF? Our main result, Theorem 3.7, states that this happens iff the ideal A′ of the basic ring B of R corresponding to A has left annihilator F in B generated by a single element on both sides. Moreover, in this case B/A′ ≈ F in mod-B, (see Theorem 3.5), a property that does not extend to R, that is, in general R/A is not isomorphic to the left annihilator of A. (See Example 4.3(2) and Theorem 4.5.) Theorem 4.6 characterizes Frobenius rings among quasi-Frobenius (QF) rings. As an application of the main theorem, in Theorem 3.9 we prove that if A is generated as a right or left ideal by an idempotent e, then e is central (and R/A is then trivially right PF along with R). This generalizes the result of F. W. Anderson for quasi-Frobenius rings. (See Theorem 2.2 for a new proof.). In Proposition 1.6, we prove that a generalization of this result holds for finite products R of full matrix rings over local rings; namely, an ideal A is finitely generated as a right or left ideal iff A is generated by a central idempotent. We also note a theorem going back to Nakayama, Goursaud, and the author that every factor ring of R is right PF iff R is a uniserial ring. (See Theorem 5.1.).
Emergency Death Meditations for Internal Alchemists
Authors: Eskildsen Stephen 
Published: January 2007

AbstractAn "emergency death meditation" is a psychic technique performed by a religious adept who has yet to attain the desired level of perfection but faces imminent death. This essay examines a few Daoist examples of such techniques endorsed in late Tang or early Song internal alchemical texts, such as the Taibai huandan pian, Zhen longhu jiuxian jing, and Dongyuanzi neidan jue. These texts describe emergency death meditation methods whereby the practitioner hopes to "enter the womb", "change the dwelling", "repel the killer demons" or "flee the numbers". The intended result is that the Spirit either transfers to another womb or body (in the cases of "entering a womb" and "changing the dwelling") or manages to stay on in its accustomed body (in the cases of "expelling the killer demons" and "fleeing the numbers"). In either case, the adept hopes subsequently to resume training and persevere in it until the Spirit is rendered pure yang and the loftiest mode of immortality is attained. The essay also discusses the intriguing parallels and possible connections between these emergency death meditations (especially "entering the womb") and those taught and practiced in Tantric Buddhist circles. Une "méditation d'urgence au moment de la mort" est une technique psychique utilisée par un adepte n'ayant pas encore atteint le niveau désiré de perfection mais confronté à une mort imminente. Cet article examine quelques exemples taoïstes de telles techniques approuvées par des textes d' alchimie interne datant de la fin des Tang ou du début des Song, tels le Taibai huandan pian, le Zhen long – hu jiuxian jing et le Dongyuanzi neidan jue. Ces texts décrivent des méthodes de méditation d' urgence face à la mort grace auxquelles l'adepte espère "entrer dans l'utérus", "changer de résidence", "repousserles démons tueurs" ou "fuir les nombres". Le résultat attendu est soit que l'Esprit émigre vers un autre utérus ou un autre corps, soit (dans les cas "repousser les démons tueurs" et "fuir les nombres") qu'il réussisse à rester dans son corps habituel. Dans un cas comme dans l'autre l'adepte espère reprendre par la suite sa preparation et persévérer jusqu'à ce que son Esprit devienne pur yang et atteigne le niveau suprême d'immortalité. L'article aborde également les parallèles intéressants et les connexions possibles entre ces techniques de méditation d'urgence (en particulier "entrer dans l'utérus") et celles qui étaient enseignées et pratiquées dans les milieux du bouddhisme tantrique.
Sociocultural Problem-Solving Skills in Preschoolers of High Intellectual Ability
Authors: Nellis Leah M. , Gridley Betty E. 
Published: January 2007

This study investigated the ability-related differences in planning skill on a sociocultural task, as well as the performance impact of working with a peer. Shopping routes through a model grocery store were planned by 30 average-ability and 20 high-ability preschool children. All subjects planned a total of five shopping trips. The first and last trips were completed alone, while the three middle trips were either completed alone, with a sane-ability peer, or with a peer of different ability. Data were analyzed With a series of multivariate analyses of variance (MANOVA) with a within-subjects factor representing the measure of planning skill across Lists 2, 3, and 4. Results indicated that preschool-aged children did not differ in planning skill on the basis of cognitive ability. In addition, high-ability preschoolers performed equally we1l when working alone, with a peer of One ability, or with a peer of less ability.
Intraosseous Innervation of the Human Patella
Authors: Barton R. Shane , Ostrowski Mary L. , Anderson Terrence D. , Ilahi Omer A. , Heggeness Michael H. 
Published: January 2007

Background The soft tissue structures surrounding the human knee joint have been the subject of extensive anatomic study. The detailed histologic findings within the bone of the human patella, however, have not been systematically studied. While the nerves supplied to the periarticular soft tissues have been very well documented, the nerves supplied to the interior of the bony patella have never been described. Hypothesis This study tests the hypothesis that the patella contains an intraosseous nerve network. Further, the authors investigate the anatomic location of these intraosseous nerves to better understand their possible clinical relevance. Study Design Descriptive laboratory study. Methods Ten matched pairs of cadaveric patellae (left and right patellae from the same individual; 20 total) were prepared for evaluation by hematoxylin and eosin staining using a technique that allows the creation of complete, large histologic sections of individual patellae. The matched specimens were dissected free of soft tissue and then sectioned using a diamond-wafering saw into 3-mm sagittal (left patella) and transverse (right patella) sections. Sections were then decalcified and whole-mounted into paraffin blocks for further sectioning using a large-format microtome. All 20 specimens were prepared for evaluation. Age at death averaged 80 years (range, 64-91). All specimens demonstrated at least grade II chondromalacia. Results Nineteen of 20 (95%) specimens demonstrated intraosseous nerves. Of 248 sections studied, 116 (47%) demonstrated intraosseous nerves, with 227 individual nerves identified. The density of intraosseous nerves was greatest in the medial and central portions of the patella, with a significant paucity identified laterally. Conclusion The primary intraosseous innervation of the patella derives from a medially based neurovascular bundle. Clinical Relevance A better understanding of the nerves within the human bony patella may improve understanding the patho-physiology of anterior knee pain syndromes.
Topical buparvaquone formulations for the treatment of cutaneous leishmaniasis
Authors: Garnier Tracy , Mäntylä Antti , Järvinen Tomi , Lawrence M Jayne , Brown Marc B , Croft Simon L 
Published: January 2007

Abstract
As the part of a study to develop buparvaquone (BPQ) formulations for the treatment of cutaneous leishmaniasis, the topical delivery of BPQ and one of its prodrugs from a range of formulations was evaluated. In previous studies, BPQ and its prodrugs were shown to be potent antileishmanials in-vitro, with ED50 values in the nanomolar range. 3-Phosphono-oxymethyl-buparvaquone (3-POM-BPQ) was the most potent antileishmanial and was chosen, together with the parent drug, for further investigation. The ability of the parent and prodrug formulations to cross human and murine skin was tested in-vitro using the Franz diffusion cells. Formulations intended for topical application containing either BPQ or 3-POM-BPQ were developed using excipients that were either acceptable for topical use (GRAS or FDA inactive ingredients) or currently going through the regulatory process. BPQ was shown to penetrate both human epidermal membranes and full thickness BALB/c skin from a range of formulations (gels, emulsions). Similarly, 3-POM-BPQ penetrated full-thickness BALB/c skin from several gel formulations. In-vitro binding studies showed that BPQ bound melanin in a dose-dependent manner and preferably bound to delipidized skin over untreated BALB/c skin (on a weight to weight basis). The results confirm that BPQ and its prodrug 3-POM-BPQ can penetrate the skin from several formulations, making them potentially interesting candidates for further investigation of topical formulations using in-vivo models of cutaneous leishmaniasis.
Efflux of baicalin, a flavone glucuronide of Scutellariae Radix, on Caco-2 cells through multidrug resistance-associated protein 2
Authors: Akao Teruaki , Hanada Masato , Sakashita Yoko , Sato Keisuke , Morita Masashi , Imanaka Tsuneo 
Published: January 2007

Abstract
Baicalin and its aglycone, baicalein, being are strong antioxidants and have various pharmacological actions. Baicalein has shown a unique metabolic fate in rat intestine, being excreted into the intestinal lumen from mucosal (epithelial) cells following glucuronidation of baicalein absorbed after oral administration. The purpose of this study was to examine the absorption and excretion of baicalin and baicalein in a Caco-2 cell monolayer model to evaluate the disposition of baicalin and baicalein in the human intestine. When baicalein at 5μM was loaded on the apical side of the Caco-2 cell monolayer, baicalein was not transferred to the basolateral side, but more baicalin was excreted onto the apical side than was being absorbed onto the basolateral side. The amount of baicalin recovered on both sides accounted for more than 90% of the baicalein absorbed from the apical surface. This was supported by the fact that Caco-2 cell microsomes showed UDP-glucuronate glucuronosyl-transferase activity towards baicalein to form baicalin. On the other hand, when baicalein was loaded at higher concentrations, baicalin excretion became saturated, and then baicalein was transferred to the basolateral side. Furthermore, baicalin efflux was not inhibited by MDR1/P-glycoprotein substrates such as ciclosporin and vinblastine, but significantly inhibited by multidrug resistance-associated protein 2 (MRP2, ABCC2) substrates such as probenecid and genistein. MRP2 was also detected in Caco-2 cells by Western blotting using specific antibodies. In addition, baicalin, but not baicalein, enhanced dose-dependently the vanadate-sensitive ATPase activity of human MRP2. These results indicated that, in Caco-2 cells, any baicalein absorbed after loading at low concentrations of baicalein was not transferred to the basolateral side, but was first transformed into baicalin in the cells and excreted through the action of MRP2, mainly to the apical side.
The War of “Who Is Who”: Autochthony, Nationalism, and Citizenship in the Ivoirian Crisis
Authors: Marshall-Fratani Ruth 
Published: January 2007

Abstract:Over the past four years the Ivoirian crisis has seen as its central dynamic the mobilization of the categories of autochthony and territorialized belonging in an ultranationalist discourse vehicled by the party in power. More than just a struggle to the death for state power, the conflict involves the redefinition of the content of citizenship and the conditions of sovereignty. The explosion of violence and counterviolence provoked and legitimated by the mobilization of these categories does not necessarily signify either the triumph of those monolithic identities “engineered” during the colonial occupation, nor the disintegration of the nation-state in the context of globalization. The Ivoirian case shows the continued vitality of the nation-state: not only as the principal space in terms of which discourses of authochtony are constructed, but also in terms of the techniques and categories that the political practice of autochthony puts into play. While in some senses the Ivoirian conflict appears to be a war without borders—in particular with the “spillover” of the Liberian war in the west during 2003—it is above all a waraboutborders, crystallizing in liminal spaces and social categories and on emerging practices and ways of life.
Deciding on Institutionalization for a Relative with Dementia: The Most Difficult Decision for Caregivers
Authors: Caron Chantal D. , Ducharme Francine , Griffith Jennifer 
Published: January 2007

ABSTRACTThe decision to move a family member with dementia to a nursing home is a difficult experience for caregivers. Complex psychosocial factors are involved and knowledge of predictive factors alone is insufficient. Using grounded theory, this study explores the decision-making process with regards to institutionalization, from the perspective of family caregivers. Fourteen people who moved a relative to long-term care in the preceding 6 months were interviewed. Data analysis using comparative analysis and line-by-line dimensional analysis was used to develop a theoretical model of the decision-making process. Three factors within the model were central to the process: (a) caregivers' perceptions of their ability to provide care, (b) caregivers' evaluations of their relatives' ability to make care decisions, and (c) the evolving influence of contextual factors and interactions with healthcare professionals. The contribution of these findings to new conceptualizations of institutionalization is discussed.
Accessible Support for Family Caregivers of Seniors with Chronic Conditions: From Isolation to Inclusion
Authors: Stewart Miriam , Barnfather Alison , Neufeld Anne , Warren Sharon , Letourneau Nicole , Liu Lili 
Published: January 2007

ABSTRACTAccessible support programs can improve health outcomes for family caregivers of older relatives with a chronic condition. Over the course of 6 months, 27 experienced family caregivers provided weekly support via the telephone to 66 individuals, either new family caregivers of seniors recently diagnosed with stroke or newly vulnerable family caregivers (i.e., facing increasing demands from the deterioration of their senior relative's condition) of seniors with Alzheimer's disease. Qualitative data documented the perceived impact of the intervention, including increased satisfaction with support, coping skills, caregiving competence and confidence, and decreased caregiver burden and loneliness. Caregivers identified varied support processes that overcame support deficits in their social networks. These processes can facilitate replication in future research and inform practice, programs, and policies.
Age at first sexual intercourse, genes, and social context: Evidence from twins and the dopamine D4 receptor gene
Authors: Guo Guang , Tong Yuying 
Published: January 2007

AbstractWe carried out two distinct types of genetic analysis with data from the National Longitudinal Study of Adolescent Health. The first was a non-DNA twin analysis using monozygotic (identical) and same-sex dizygotic (fraternal) twins. The second analysis investigates the association between age at first sexual intercourse and the 48-bp repeat polymorphism in the dopamine receptor D4 gene (DRD4). The twin analysis shows that MZ twins correlate their timing of first sex to a much greater extent than do the same-sex DZ twins. Our analysis of the polymorphisms in DRD4 indicates that those with an any-3R genotype experienced a risk of first sexual intercourse 23% (p=.016), 233% (p=.0001), 28% (p=.012), and 69% (p=.006) higher than those with an other/other (or any-4R) genotype in the all-ethnicities (n=2,552), Asian, white, and Hispanic samples, respectively. The risk of first sex does not differ between the two genotypes in the African American sample. These results were obtained after adjusting the standard socioeconomic covariates, including gender, parental education, family structure, and community poverty in the regression model. Evidence from both twin and genetic-variant analyses points to a role of genes in the timing of first sexual intercourse.