bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural search and retrieval using a tableau representation of protein folding patterns
Authors: Konagurthu Arun S. , Stuckey Peter J. , Lesk Arthur M. 
Published: January 2008

Abstract
Comparison and classification of folding patterns from a database of protein structures is crucial to understand the principles of protein architecture, evolution and function. Current search methods for proteins with similar folding patterns are slow and computationally intensive. The sharp growth in the number of known protein structures poses severe challenges for methods of structural comparison. There is a need for methods that can search the database of structures accurately and rapidly.
We provide several methods to search for similar folding patterns using a concise tableau representation of proteins that encodes the relative geometry of secondary structural elements. Our first approach allows the extraction of identical and very closely-related protein folding patterns in constant-time (per hit). Next, we address the hard computational problem of extraction of maximally-similar subtableaux, when comparing two tableaux. We solve the problem using Quadratic and Linear integer programming formulations and demonstrate their power to identify subtle structural similarities, especially when protein structures significantly diverge. Finally, we describe a rapid and accurate method for comparing a query structure against a database of protein domains, TableauSearch. TableauSearch is rapid enough to search the entire structural database in seconds on a standard desktop computer. Our analysis of TableauSearch on many queries shows that the method is very accurate in identifying similarities of folding patterns, even between distantly related proteins.
Availability: A web server implementing the TableauSearch is available from http://hollywood.bx.psu.edu/TabSearch
Contact: arun@bx.psu.edu, aml25@psu.edu
Supplementary information: Supplementary Data are available at Bioinformatics online.
First Detection of Virulence to Genes Lr9 and Lr25 Conferring Resistance to Leaf Rust of Wheat Caused by Puccinia triticina in Mexico
Authors: Huerta-Espino J. , Singh R. P. , Reyna-Martinez J. 
Published: January 2008

Leaf rust resistance gene Lr9 was transferred to wheat from Triticum umbellulatum (1). In 1971, 4 years after cultivars with this gene were released in the United States, leaf rust races with virulence to Lr9 were detected. In Mexico, cultivars with Lr9 have not been released and leaf rust races with Lr9 virulence have not been detected. Resistance gene Lr25 was transferred to wheat from Rosen rye (1) and has been effective worldwide, but this gene has not been used commercially because of possible negative effects on yield (1). Rust samples collected at different locations in Nuevo Leon State of Mexico during the 2004–2005 and 2005–2006 wheat crop seasons were analyzed on seedlings of wheat leaf rust differentials in the greenhouse from single pustule isolates. The race nomenclature used is described in Singh (2). Among the races identified from this area, seven, MLJ/SP, TNM/JP, TLB/JP, TNM/KP, TNR/JP, TNB/JN, and TMB/JP, were virulent to both of these genes. Virulence to Lr9 and Lr25 were confirmed by repeating tests using Lr9 differentials ‘RL6010’ and ‘McNair 701’ and Transec and three other Lr25 wheat lines developed at CIMMYT, which carry Lr25. To our knowledge, this is the first confirmed report of virulence to Lr9 in Mexico and virulence to Lr25 in the world. These isolates are conserved at CIMMYT for future reference. References: (1) R. A. McIntosh et al. Wheat Rusts: An Atlas of Resistance Genes. CSIRO Publishing, Melbourne, Australia, 1995. (2) R. P. Singh. Plant Dis. 75:790, 1991.
First Report of ‘Candidatus Liberibacter asiaticus’ from Atalantia buxifolia in Guangdong, China
Authors: Deng X. , Lou Z. , Feng Z. , Li H. , Chen J. , Civerolo E. L. 
Published: January 2008

Atalantia buxifolia (Poir.) Oliv., synonym Severinia buxifolia (Poir.) Ten. as commonly found in literature, is a common landscape plant and a popular Chinese medicinal herb known as Jiubingle or Dongfengjie. It remains unclear if this rutaceous plant could host ‘Candidatus Liberibacter asiaticus’, the pathogen of citrus Huanglongbing (HLB) in Guangdong, P. R. China. This information is important for HLB control in citrus because infected A. buxifolia could serve as a source of inoculum. In August of 1994, three A. buxifolia plants adjacent to a citrus experimental orchard of the South China Agricultural University at Guangzhou were found showing leaf mottle/yellowing symptoms. Two buds from each plant were grafted onto three mandarin trees (Citrus reticulata cv. Pongan) in a psyllid-proof screenhouse for indexing. By October of 1995, typical leaf mottle symptoms were observed in all three grafted trees compared with a healthy control. In March of 1996, one of the A. buxifolia plants was transferred to a screenhouse and has been maintained there. The leaf mottle/yellowing symptoms persisted but did not significantly affect plant growth. DNA was extracted from leaf samples in October 2006 by using the CTAB (cetyltrimethylammoniumbromide) method and assayed by nested-PCR using the general bacterial 16S rDNA primer set fDl/rD1 as the first round of amplification and primer set OI1/OI2c as second round amplification (1,3). After agarose gel electrophoresis and staining with ethidium bromide, an approximate 1.1-kb DNA band was detected in symptomatic samples but not healthy leaf samples of A. buxifolia and C. reticulata. XbaI digestion of the amplicons yielded approximate 500- and 600-bp fragments, characteristic of ‘Ca. L. asiaticus’. Similarly, a standard PCR with primer set A5/J2 (3) yielded an approximate 700-bp DNA band characteristic of ‘Ca. L. asiaticus’ from symptomatic samples only. To our knowledge, this is the first report of graft transmission and PCR detection of ‘Ca. L. asiaticus’ from A. buxifolia in Guangdong, P. R. China. This work also confirms the findings from Taiwan (2) that A. buxifolia could serve as a source of ‘Ca. L. asiaticus’. References: (1) X. Deng et al. Online publication. doi:10.1094/PHP-2007-0419-01-BR. Plant Health Progress, 2007. (2) T.-H. Hung et al. Eur. J. Plant Pathol. 107:183, 2001. (3) S. Jagoueix et al. Mol. Cell. Probes 10:43, 1996.
Severe and Widespread Clubroot Epidemics in Nepal
Authors: Timila R. D. , Correll J. C. , Duwadi V. R. 
Published: January 2008

Cultivation of brassica vegetables has the highest potential for generating income among more traditional rice and maize farmers in Nepal. Among brassica vegetables, the most important are cauliflower (Brassica oleracea var. botrytis L.) and cabbage (B. oleracea var. capitata L.). Although clubroot disease, caused by Plasmodiophora brassicae Woronin, has been observed in Nepal since 1993, severe and widespread epidemics have been observed since 2004 in the Bhaktapur, Kathmandu, Lalitpur, and Palung Valley production areas. Typical disease symptoms (1) are widespread, and disease severity has been particularly severe in the Kathmandu Valley and Palung/Daman area of the Makwanpur District. Many cauliflower fields in these areas have had as much as 100% yield loss between 2004 and 2006 with an estimated 40% overall loss from clubroot. Estimates from interviews with growers in the Palung production area during an intensive farmers' interaction program indicated that cauliflower production was reduced from 5 to 6 metric tons per household (1,500 m2) prior to 2004 to <300 kg per household in 2004 and beyond. The economic loss in this area alone was estimated at $1.4 million in 2004 and 2005. Examination of transplant nurseries indicated that frequently >80% of the seedlings have symptoms of clubroot at the time of transplanting. Soil samples from throughout the production areas indicated that the sandy loam soils were predominately acidic (pH range of 4.2 to 7.2 with >90% below 6.0). Several management practices are being employed to reduce disease severity, including the use of clubroot resistant cultivars, raising the soil pH to >7.0 by using dolomitic lime, testing of the fungicide flusulfamide (Nebijin) and biopesticide Sanjeevani (Trichoderma viride), and biofumigation and solarization of the nursery beds in an effort to reduce disease pressure on transplant material. References: (1) G. R. Dixon. Compendium of Brassica Diseases. S. R. Rimmer et al., eds. American Phytopathological Society, St. Paul, 2007.
First Report of a Leaf Spot on Snow Lotus Caused by Alternaria carthami in China
Authors: Zhao S. , Xie G. , Zhao H. , Li H. , Li C. 
Published: January 2008

Snow lotus (Saussurea involucrata Karel. & Kir. ex Sch. Bip.) is an economically important medicinal herb increasingly grown in China in recent years. In June of 2005, a leaf spot disease on commercially grown plants was found in the QiTai Region, south of the Tianshan Mountain area of Xinjiang, China at 2,100 m above sea level. Disease incidence was approximately 60 to 70% of the plants during the 2006 and 2007 growing seasons. Initial symptoms appeared on older leaves as irregularly shaped, minute, dark brown-to-black spots, with yellow borders on the edge of the leaflet blade by July. As the disease progressed, the lesions expanded, causing the leaflets to turn brown, shrivel, and die. A fungus was consistently isolated from the margins of these lesions on potato dextrose agar. Fifty-eight isolates were obtained that produced abundant conidia in the dark. Conidia were usually solitary, rarely in chains of two, ellipsoid to obclavate, with 6 to 11 transverse and one longitudinal or oblique septum. Conidia measured 60 to 80 × 20 to 30 μm, including a filamentous beak (13 to 47 × 3.5 to 6 μm). According to the morphology, and when compared with the standard reference strains, the causal organism of leaf spot of snow lotus was identified as Alternaria carthami (1,4). Pathogenicity of the strains was tested on snow lotus seedlings at the six-leaf stage. The lower leaves of 20 plants were sprayed until runoff with conidial suspensions of 1 × 104 spores mL–1, and five plants sprayed with sterile distilled water served as controls. All plants were covered with a polyethylene bag, incubated at 25°C for 2 days, and subsequently transferred to a growth chamber at 25°C with a 16-h photoperiod. Light brown lesions developed within 10 days on leaflet margins in all inoculated plants. The pathogen was reisolated from inoculated leaves, and isolates were deposited at the Key Oasis Eco-agriculture Laboratory of Xinjiang Production and Construction Group, Xinjiang and the Institute of Biotechnology, Zhejiang University. No reports of a spot disease caused by A. carthami on snow lotus leaves have been found, although this pathogen has been reported on safflower in western Canada (3), Australia (2), India (1), and China (4). To our knowledge, this is the first report of a leaf spot caused by A. carthami on snow lotus in China. References: (1) S. Chowdhury. J. Indian Bot. Soc. 23:59, 1944. (2) J. A. G. Irwin. Aust. J. Exp. Agric. Anim. Husb. 16:921, 1976. (3) G. A. Petrie. Can. Plant Dis. Surv. 54:155, 1974. (4) T. Y. Zhang. J. Yunnan Agric. Univ.17:320, 2002.
SEUSSandAINTEGUMENTAMediate Patterning and Ovule Initiation during Gynoecium Medial Domain Development
Authors: Azhakanandam Sridevi , Nole-Wilson Staci , Bao Fang , Franks Robert G. 
Published: January 2008

AbstractThe Arabidopsis (Arabidopsis thaliana) gynoecium, the female floral reproductive structure, requires the action of genes that specify positional identities during its development to generate an organ competent for seed development and dispersal. Early in gynoecial development, patterning events divide the primordium into distinct domains that will give rise to specific tissues and organs. The medial domain of the gynoecium gives rise to the ovules, and several other structures critical for reproductive competence. Here we report a synergistic genetic interaction between seuss and aintegumenta mutants resulting in a complete loss of ovule initiation and a reduction of the structures derived from the medial domain. We show that patterning events are disrupted early in the development of the seuss aintegumenta gynoecia and we identify PHABULOSA (PHB), REVOLUTA, and CRABS CLAW (CRC) as potential downstream targets of SEUSS (SEU) and AINTEGUMENTA (ANT) regulation. Our genetic data suggest that SEU additionally functions in pathways that are partially redundant and parallel to PHB, CRC, and ANT. Thus, SEU and ANT are part of a complex and robust molecular system that coordinates patterning cues and cellular proliferation along the three positional axes of the developing gynoecium.
Identification of the structure and origin of a thioacidolysis marker compound for ferulic acid incorporation into angiosperm lignins (and an indicator for cinnamoyl CoA reductase deficiency)
Authors: Ralph John , Kim Hoon , Lu Fachuang , Grabber John H. , Leplé Jean‐Charles , Berrio‐Sierra Jimmy , Derikvand Mohammad Mir , Jouanin Lise , Boerjan Wout , Lapierre Catherine 
Published: January 2008

SummaryA molecular marker compound, derived from lignin by the thioacidolysis degradative method, for structures produced when ferulic acid is incorporated into lignin in angiosperms (poplar, Arabidopsis, tobacco), has been structurally identified as 1,2,2‐trithioethyl ethylguaiacol [1‐(4‐hydroxy‐3‐methoxyphenyl)‐1,2,2‐tris(ethylthio)ethane]. Its truncated side chain and distinctive oxidation state suggest that it derives from ferulic acid that has undergone bis‐8‐O‐4 (cross) coupling during lignification, as validated by model studies. A diagnostic contour for such structures is found in two‐dimensional 13C–1H correlated (HSQC) NMR spectra of lignins isolated from cinnamoyl CoA reductase (CCR)‐deficient poplar. As low levels of the marker are also released from normal (i.e. non‐transgenic) plants in which ferulic acid may be present during lignification, notably in grasses, the marker is only an indicator for CCR deficiency in general, but is a reliable marker in woody angiosperms such as poplar. Its derivation, together with evidence for 4‐O‐etherified ferulic acid, strongly implies that ferulic acid is incorporated into angiosperm lignins. Its endwise radical coupling reactions suggest that ferulic acid should be considered an authentic lignin precursor. Moreover, ferulic acid incorporation provides a new mechanism for producing branch points in the polymer. The findings sharply contradict those reported in a recent study on CCR‐deficient Arabidopsis.
Management education for tomorrow's society†
Authors: Debanné J. G. 
Published: January 2008

Abstract. This paper attempts to anticipate the evolution of several key aspects of the modern life as these will shape the environment in which tomorrow's managers will have to manage. Some attributes of this milieu, in particular, would affect the talent and skill profile of tomorrow's manager, and these are: (i) society and the environment, (ii) information systems, (iii) man, (iv) organizations.A threefold methodology will be used in this ‘futures’ exercise, consisting of (a) extrapolation ‐ mostly implicit, coupled with (b) limit information, and (c) analogy with other evolutionary phenomena. These three techniques will be described within the context of their application.The managerial attributes considered desirable and perhaps essential in the future will be discussed when dealing with the evolution of society, information systems, man and organizations. Conversely, those special attributes, considered important in bygone days or even today but which are expected to be non‐essential in the future, will be touched upon briefly.Sommaire. Cette communication essaie d'anticiper l'évolution de différents aspects de la vie moderne dans la mesure où ils façonnent le milieu que les cadres de l'avenir devront gérer. Certains éléments de ce milieu détermineront les talents et la compétence des cadres de l'avenir, et ce sont (i) la société et le milieu, (ii) les systèmes d'information, (iii) l'homme, (iv) les organisations.Nous utiliserons une médiodologie tripartite pour les exercices de projection qui consistera (a) en une interpolation ‐ surtout implicite ‐ combinée avec une information limite et (c) l'analogie avec d'autres phénomènes d'évolution. Nous décrirons ces trois techniques dans le contexte de leur application.Nous parlerons des qualités considérées comme désirables et peut‐être essentielles chez les cadres de l'avenir lorsque nou traiterons de l'évolution de la société, des systèmes d'information, de l'homme et des organisations. Par contre, nous ne mentionnerons que brievement les qualités particulières qui étaient considérées comme importantes autrefois ou même aujourd'hui mais qui ne semblent pas essentielles pour l'avenir.
National versus regional growth: some issues
Authors: Husband D. D. 
Published: January 2008

Sommaire. Les programmes de développement régional du gouvernement fédéral ont suscité toutes sortes de controverses. Bien que l'on s'accorde généralement pour reconnaître la nécessité de réduire les disparités régionales au Canada, du point de vue revenu et possibilités d'emploi, il semble difficile d'arriver à un accord sur les façons dont on pourrait réduire ces disparités. Le gouvernement fédéral a tendance maintenant à considérer que c'est en encourageant les possibilités d'emploi dans les régions défavorisées que l'on a les meilleures chances de succès, au lieu de ← siphoner → le surplus de main d'æuvre. C'est cette attitude fondamentale et les moyens envisagés qui sont disputés.L'auteur de cette communication fait abstraction des opinions passionnées et des interprétations possibles auxquelles peut donner lieu l'examen des measures prises par le gouvernement fédéral dans le domaine du développement régional. Il s'attache, au contraire, à présenter les arguments qui déterminent la proportion optimale de programmes de migration et de développement régional. Les objectifs de maximisation de l'essor national et de réduction des disparités régionales étant établis, il considère, du point de vue de la pleine utilisation de la main d'œuvre, l'allocation optionnelle des ressources et l'application des principes économiques keynésiens.
From systems analysis to policy analysis
Authors: Sayeed Khalid B. 
Published: January 2008

How Much is Enough?By alain c. enthoven and k. wayne smith. New York: Harper and RowSystematic Thinking for Social Action. By alice rivlin. Washington: The Brookings InstitutionEighth Annual Review: Design for Decision‐Making. An Application to Human Resources Policies. By economic council of Canada. Ottawa: Information Canada
Political factors in the fall of RolIs‐Royce
Authors: Davis Morris , Finerty James , Oliver James 
Published: January 2008

Abstract. While economic and technological difficulties greatly reduced Rolls‐Royce's viability, its passing into receivership can be adequately explained only by invoking additional (and largely political) factors. In the absence of any automatic criteria for aborting a losing project, the Conservative government of the day responded to an abundance of consistently negative politioal implications. Unfortunately for its continued survival, the Rolls‐Royce development of an RB‐211 engine for Lockheed was civilian, not military; prosaic, not meta‐phoric; ostensibly private, not openly governmental; internationally fluctuating, not domestically controllable; a weak coalition, not a strong partnership; profit oriented, not ideologically based; and narrowly subsidized, not internally fund‐able. The Conservative response was probably not unique; and a Labour government wodd Iikely have reacted to these implications in roughly the same way. It is to the circumambient political factors rather than to determinative economic considerations, however, that the decisions reached by either party would be primarily traceable.Sommaire. Des difficultés économiques et technologiques réduisirent de beau‐coup la viabilité de Rolls‐Royce, mais sa mise en faillité ne peut vraiment s'expIi‐quer qu'en invoquant d'autres facteurs complémentaires, surtout politiques. En I'absence de tout critère automatique pour faire avorter un projet non rentable, le gouvernement conservateur du moment réagit à une multitude d'implications politiques, toutes négatives. Malheureusement pour Rolls‐Royce, la création d'un moteur RB‐211 pour Lockheed était une entreprise civile et non pas militaire; prosaïque et non pas métaphorique; manifestement privée et non pas ouverte‐ment gouvernementale; sujette à des fluctuations internationales et non pas contrôlable à I'échelle nationale; dirigée par une coalition faible et non pas par une association forte; à buts lucratifs et non pas idéologiques; subventionnée de facon limitée et non pas financée de I'intérieur. La réaction des conservateurs n'a sans doute rien de très étonnant et un gouvernement travailliste aurait sans doute, en gros, réagi de la même façon à ces données. Ce sont à des facteurs politiques ambiants plutòt qu'à des considérations économiques déterminantes qu'il faudrait attribuer avant tout les décisions prises par l'un ou I'autre parti.
Administrative reform in the federal public service: the first faltering steps
Authors: Baker Walter 
Published: January 2008

Abstract. This paper is complementary to one by H. L. Laframboise published previously in Canadian Public Administration (14, no. 3, fall 1971, pp. 305–25), ‘Administrative reform in the federal public service: signs of a saturation psychosis.’ Where Laframboise stresses the serious concerns that have arisen on the part of many managers over an accumulation of initiatives in administrative reform and seems generally to be advocating that we slow down the pace of such reform, the position taken here is that in our managerial practices we are very seriously below the level required to handle the enormous and complex demands facing the federal public service and therefore must attend far more energetically to administrative reform, albeit more expertly.The paper identifies four key needs to be met in managing public organizations effectively, and treats each of these in some detail: placing men and women of appropriate managerial mind and bent in managerial positions; identifying, developing and using appropriately the growing range of managerial support specialties; facing up to and countering the insularity that seems to afflict even the best of managers; and assuming a managerial approach suited to the dynamic nature of what Warren Bennis has termed ‘the temporary society.’ The paper concludes with a discussion of managing as a set of paradoxes.Sommaire. Cet article traite du même sujet qu'un autre article que publiait dans I'ADMINISTRATION PUBLIQUE DU CANADA (14, no 3, automne 1971, pp. 303–25) par H. L. Laframboise, intitulé“Administrative reform in the federal public service: signs of a saturation psychosis”. Alors que Laframboise soulignait les préscupations sérieuses de plusieurs administrateus devant le grand nombre d'initiatives en matière de réforme administrative et semblait préconiser de façon générale le ralentissement du rythme de cette réforme, l'on soutient ici que nos méthodes de estion sont bien loin de pouvoir répondre aux exigences nombreuses et compexes de la fonction publique féérale, et que partant, nous devons poursuivre la réforme administrative de façon beaucoup plus dynamique et plus experte.L'article détermine quatre exigences primordiales de la gestion efficace des administrations publiques et traite chacune d'elles en détail:affecter à des postes de gestion des hommes et femmes d'esprit et de tendance idoines; déterminer, établir et employer à bon escient l'éventail de plus en plus vaste des spécialités du soutien administratif; combattre la tendance que semblent avoir les meilleurs de nos gestionnaires de se renfermer dans leur coquille; adopter une méthode de gestion adaptée à la nature dynamique de ce que Warren Bennis appelle “la société temporaire”.L'article se termine en assimilant le processus de gestion à une série de paradoxes.