bluuebunny/crossref_metadata_2025 huggingface dataset:
Occurrence and distribution of humpback whales (Megaptera novaeangliae) on the north coast of the State of Bahia, Brazil, 2000–2006
Authors: Rossi-Santos Marcos R. , Neto Elitieri S. , Baracho Clarêncio G. , Cipolotti Sérgio R. , Marcovaldi Enrico , Engel Marcia H.
Published: March 2008

Rossi-Santos, M. R., Neto, E. S., Baracho, C. G., Cipolotti, S. R., Marcovaldi, E., and Engel, M. H. 2008. Occurrence and distribution of humpback whales (Megaptera novaeangliae) on the north coast of the State of Bahia, Brazil, 2000–2006. – ICES Journal of Marine Science, 65: 667–673. The Abrolhos Bank off Brazil is considered the main breeding ground for the humpback whale (Megaptera novaeangliae) in the Southwest Atlantic. However, owing to an increase in the occurrence of the species along the north coast of the State of Bahia, it has been suggested that the species is reoccupying that region, which was probably utilized by the whales before commercial whaling. Information is presented on the occurrence and distribution of humpback whales along the north coast of the State of Bahia, with a comparative overview, for the period 2000–2006. Daily research cruises were conducted from July to October, departing from Praia do Forte (13°40′S 38°10′W) and lasting ∼9 h. Data on sampling and sighting effort, and geographical position and composition of groups of humpback whales, were collected on standardized field sheets. In all, 230 surveys were performed, covering some 9740 nautical miles in 1645 h of sampling effort, during which 1626 humpback whales were sighted, including 118 calves. Humpback whales were sighted throughout the study area. Solitary individuals and pairs were the most frequent group composition, 26% and 37% of the observed groups (n = 723), respectively. Depth of water varied from 15 to 1657 m (mean = 62.4; s.d. = 99). The sightings values were grouped into depth classes to ascertain the highest frequencies (∼30%) for the two classes, i.e. between 35.1 and 55 m of water. There was an increase in the encounter rates of humpback whales on the north coast of the State of Bahia between 2000 and 2006, identifying a difference in SPUE [sightings per unit (h) of effort] among years (Kruskal–Wallis H = 30.155, d.f. = 6, p < 0.05). The results support the hypothesis that humpback whales are reoccupying former breeding areas along the Brazilian coast.
Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias
Authors: Brandström Mikael , Ellegren Hans
Published: March 2008

Studies of microsatellites evolution based on marker data almost inherently suffer from an ascertainment bias because there is selection for the most mutable and polymorphic loci during marker development. To circumvent this bias we took advantage of whole-genome shotgun sequence data from three unrelated chicken individuals that, when aligned to the genome reference sequence, give sequence information on two chromosomes from about one-fourth (375,000) of all microsatellite loci containing di- through pentanucleotide repeat motifs in the chicken genome. Polymorphism is seen at loci with as few as five repeat units, and the proportion of dimorphic loci then increases to 50% for sequences with ∼10 repeat units, to reach a maximum of 75%–80% for sequences with 15 or more repeat units. For any given repeat length, polymorphism increases with decreasing GC content of repeat motifs for dinucleotides, nonhairpin-forming trinucleotides, and tetranucleotides. For trinucleotide repeats which are likely to form hairpin structures, polymorphism increases with increasing GC content, indicating that the relative stability of hairpins affects the rate of replication slippage. For any given repeat length, polymorphism is significantly lower for imperfect compared to perfect repeats and repeat interruptions occur in >15% of loci. However, interruptions are not randomly distributed within repeat arrays but are preferentially located toward the ends. There is negative correlation between microsatellite abundance and single nucleotide polymorphism (SNP) density, providing large-scale genomic support for the hypothesis that equilibrium microsatellite distributions are governed by a balance between rate of replication slippage and rate of point mutation.
Structure dissection of human progranulin identifies well‐folded granulin/epithelin modules with unique functional activities
Authors: Tolkatchev Dmitri , Malik Suneil , Vinogradova Anna , Wang Ping , Chen Zhigang , Xu Ping , Bennett Hugh P.J. , Bateman Andrew , Ni Feng
Published: March 2008

Progranulin is a secreted protein with important functions in several physiological and pathological processes, such as embryonic development, host defense, and wound repair. Autosomal dominant mutations in the progranulin gene cause frontotemporal dementia, while overexpression of progranulin promotes the invasive progression of a range of tumors, including those of the breast and the brain. Structurally, progranulin consists of seven‐and‐a‐half tandem repeats of the granulin/epithelin module (GEM), several of which have been isolated as discrete 6‐kDa GEM peptides. We have expressed all seven human GEMs using recombinant DNA in Escherichia coli. High‐resolution NMR showed that only the three GEMs, hGrnA, hGrnC, and hGrnF, contain relatively well‐defined three‐dimensional structures in solution, while others are mainly mixtures of poorly structured disulfide isomers. The three‐dimensional structures of hGrnA, hGrnC, and hGrnF contain a stable stack of two β‐hairpins in their N‐terminal subdomains, but showed a more flexible C‐terminal subdomain. Interestingly, of the well‐structured GEMs, hGrnA demonstrated potent growth inhibition of a breast cancer cell line, while hGrnF was stimulatory. Poorly folded peptides were either weakly inhibitory or without activity. The functionally active and structurally well‐characterized human hGrnA offers a unique opportunity for detailed structure–function studies of these important GEM proteins as novel members of mammalian growth factors.
Design of an engineered N‐terminal HIV‐1 gp41 trimer with enhanced stability and potency
Authors: Dwyer John J. , Wilson Karen L. , Martin Kimberly , Seedorff Jennifer E. , Hasan Aisha , Medinas Robyn J. , Davison Donna K. , Feese Michael D. , Richter Hans‐Thomas , Kim Hidong , Matthews Thomas J. , Delmedico Mary K.
Published: March 2008

HIV fusion is mediated by a conformational transition in which the C‐terminal region (HR2) of gp41 interacts with the N‐terminal region (HR1) to form a six‐helix bundle. Peptides derived from the HR1 form a well‐characterized, trimeric coiled‐coil bundle in the presence of HR2 peptides, but there is little structural information on the isolated HR1 trimer. Using protein design, we have designed synthetic HR1 peptides that form soluble, thermostable HR1 trimers. In vitro binding of HR2 peptides to the engineered trimer suggests that the design strategy has not significantly impacted the ability to form the six‐helix bundle. The peptides have enhanced antiviral activity compared to wild type, with up to 30‐fold greater potency against certain viral isolates. In vitro passaging was used to generate HR1‐resistant virus and the observed resistance mutations map to the HR2 region of gp41, demonstrating that the peptides block the fusion process by binding to the viral HR2 domain. Interestingly, the activity of the HR2 fusion inhibitor, enfuvirtide (ENF), against these resistant viruses is maintained or improved up to fivefold. The 1.5 Å crystal structure of one of these designs has been determined, and we show that the isolated HR1 is very similar to the conformation of the HR1 in the six‐helix bundle. These results provide an initial model of the pre‐fusogenic state, are attractive starting points for identifying novel fusion inhibitors, and offer new opportunities for developing HIV therapeutics based on HR1 peptides.
Substrate specificity of human kallikreins 1 and 6 determined by phage display
Authors: Li Hai‐Xin , Hwang Bum‐Yeol , Laxmikanthan Gurunathan , Blaber Sachiko I. , Blaber Michael , Golubkov Pavel A. , Ren Pengyu , Iverson Brent L. , Georgiou George
Published: March 2008

The human tissue kallikrein (KLK) family contains 15 secreted serine proteases that are expressed in a wide range of tissues and have been implicated in different physiological functions and disease states. Of these, KLK1 has been shown to be involved in the regulation of multiple physiological processes such as blood pressure, smooth muscle contraction, and vascular cell growth. KLK6 is overexpressed in breast and ovarian cancer tissues and has been shown to cleave peptide derived from human myelin protein and Aβ amyloid peptide in vitro. Here we analyzed the substrate specificity of KLK1 and KLK6, by substrate phage display using a random octapeptide library. Consistent with earlier biochemical data, KLK1 was shown to exhibit both trypsin‐ and chymotrypsin‐like selectivities with Tyr/Arg preferred at site P1, Ser/Arg strongly preferred at P1′, and Phe/Leu at P2. KLK6 displayed trypsin‐like activity, with the P1 position occupied only by Arg and a strong preference for Ser in P1′. Docking simulations of consensus peptide provide information on the identity of the enzyme residues that are responsible for substrate binding. Bioinformatic analysis suggested several putative KLK6 protein substrates, such as ionotropic glutamate receptor (GluR) and synphilin.
Structure–function studies on the active site of the coelenterazine‐dependent luciferase from Renilla
Authors: Woo Jongchan , Howell Matthew H. , von Arnim Albrecht G.
Published: March 2008

Renilla luciferase (RLUC) is a versatile tool for gene expression assays and in vivo biosensor applications, but its catalytic mechanism remains to be elucidated. RLUC is evolutionarily related to the α/β hydrolase family. Its closest known homologs are bacterial dehalogenases, raising the question of how a protein with a hydrolase fold can function as a decarboxylating oxygenase. Molecular docking simulations with the coelenterazine substrate against an RLUC homology model as well as a recently determined RLUC crystal structure were used to build hypotheses to identify functionally important residues, which were subsequently tested by site‐directed mutagenesis, heterologous expression, and bioluminescence emission spectroscopy. The data highlighted two triads of residues that are critical for catalysis. The putative catalytic triad residues D120, E144, and H285 bear only limited resemblance to those found in the active site of aequorin, a coelenterazine‐utilizing photoprotein, suggesting that the reaction scheme employed by RLUC differs substantially from the one established for aequorin. The role of H285 in catalysis was further supported by inhibition using diethylpyrocarbonate. Multiple substitutions of N53, W121, and P220—three other residues implicated in product binding in the homologous dehalogenase Sphingomonas LinB—also supported their involvement in catalysis. Together with luminescence spectra, our data lead us to propose that the conserved catalytic triad of RLUC is directly involved in the decarboxylation reaction of coelenterazine to produce bioluminescence, while the other active‐site residues are used for binding of the substrate.
Zn2+ binding to human calbindin D28k and the role of histidine residues
Authors: Bauer Mikael C. , Nilsson Hanna , Thulin Eva , Frohm Birgitta , Malm Johan , Linse Sara
Published: March 2008

We have studied the binding of Zn2+ to the hexa EF‐hand protein, calbindin D28k—a strong Ca2+‐binder involved in apoptosis regulation—which is highly expressed in brain tissue. By use of radioblots, isothermal titration calorimetry, and competition with a fluorescent Zn2+ chelator, we find that calbindin D28k binds Zn2+ to three rather strong sites with dissociation constants in the low micromolar range. Furthermore, we conclude based on spectroscopic investigations that the Zn2+‐bound state is structurally distinct from the Ca2+‐bound state and that the two forms are incompatible, yielding negative allosteric interaction between the zinc‐ and calcium‐binding events. ANS titrations reveal a change in hydrophobicity upon binding Zn2+. The binding of Zn2+ is compatible with the ability of calbindin to activate myo‐inositol monophosphatase, one of the known targets of calbindin. Through site‐directed mutagenesis, we address the role of cysteine and histidine residues in the binding of Zn2+. Mutation of all five cysteines into serines has no effect on Zn2+‐binding affinity or stoichiometry. However, mutating histidine 80 into a glutamine reduces the binding affinity of the strongest Zn2+ site, indicating that this residue is involved in coordinating the Zn2+ ion in this site. Mutating histidines 5, 22, or 114 has significantly smaller effects on Zn2+‐binding affinity.
Towards a consensus for calculating dendrogram‐based functional diversity indices
Authors: Mouchet Maud , Guilhaumon François , Villéger Sébastien , Mason Norman W. H. , Tomasini Jean‐Antoine , Mouillot David
Published: March 2008

The widely used FD index of functional diversity is based on the construction of a dendrogram. This index has been the subject of a strong debate concerning the choice of the distance and the clustering method to be used, since the method chosen may greatly affect the FD values obtained. Much of this debate has been centred around which method of dendrogram construction gives a faithful representation of species distribution in multidimensional functional trait space. From artificially generated datasets varying in species richness and correlations between traits, we test whether any single combination of clustering method(s) and distance consistently produces a dendrogram that most closely corresponds to the matrix of functional distances between pairs of species studied. We also test the ability of consensus trees, which incorporate features common to a range of different dendrograms, to summarize distance matrices. Our results show that no combination of clustering method(s) and distance constantly outperforms the others due to the complexity of interactions between correlations of traits, species richness, distance measures and clustering methods. Furthermore, the construction of a consensus tree from a range of dendrograms is often the best solution. Consequently, we recommend testing all combinations of distances and clustering methods (including consensus trees), then selecting the most reliable tree (with the lowest dissimilarity) to estimate FD value. Furthermore we suggest that any index that requires the construction of functional dendrograms potentially benefits from this new approach.
GDNF‐mediated signaling via RET tyrosine 1062 is essential for maintenance of spermatogonial stem cells
Authors: Jijiwa Mayumi , Kawai Kumi , Fukihara Jun , Nakamura Akari , Hasegawa Masaki , Suzuki Chikage , Sato Tomoko , Enomoto Atsushi , Asai Naoya , Murakumo Yoshiki , Takahashi Masahide
Published: March 2008

Well‐organized spermatogenesis, including the maintenance of spermatogonial stem cells (SSCs), is indispensable for continuous male fertility. Signaling by glial cell line‐derived neurotrophic factor (GDNF) via the RET/GDNF family receptor α1 (GFRα1) receptor complex is essential for self‐renewal of murine SSCs and may also regulate their differentiation. When phosphorylated, tyrosine 1062 in RET presents a binding site for the phosphotyrosine‐binding domains of several adaptor and effector proteins that are important for activation of a variety of intracellular signaling pathways. In this study, we investigated the role of signaling via RET tyrosine 1062 in spermatogenesis using RET Y1062F knockin mice (Y1062F mice), in which tyrosine 1062 was replaced with phenylalanine. Homozygous Y1062F mice showed marked atrophy of testes due to reduced production of germ cells. RET‐expressing spermatogonia in seminiferous tubules of homozygous Y1062F mice decreased after postnatal day (P) 7 and germ cells were almost undetectable by P21. These phenomena appeared to be due to a lack of SSC self‐renewal and inability to maintain the undifferentiated state. Our findings suggest that RET signaling via tyrosine 1062 is essential for self‐renewal of SSCs and regulation of their differentiation.
Essential role of C/EBPα in G‐CSF‐induced transcriptional activation and chromatin modification of myeloid‐specific genes
Authors: Iida Satoshi , Watanabe‐Fukunaga Rie , Nagata Shigekazu , Fukunaga Rikiro
Published: March 2008

Granulocyte colony‐stimulating factor (G‐CSF) regulates the proliferation and differentiation of neutrophilic progenitor cells. Here, we investigated the roles of CCAAT/enhancer‐binding protein (C/EBP)α in the G‐CSF‐induced transcriptional activation and chromatin modification of the CCR2 and myeloperoxidase (MPO) genes in IL‐3‐dependent myeloid FDN1.1 cells. Chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assays revealed that G‐CSF activates C/EBPα to bind target promoters. ChIP mapping experiments across the CCR2 and MPO genes showed that G‐CSF induces histone H3 modifications: the acetylation of Lys9, trimethylation of Lys4 and trimethylation of Lys9. The distribution profile of the trimethylated Lys9 was distinct from that of the two other modifications. All the G‐CSF‐induced C/EBPα recruitment, transcriptional activation and histone modifications were reversed by re‐stimulation with IL‐3, and were abolished by short hairpin RNA (shRNA)‐mediated knockdown of C/EBPα. These results indicate that C/EBPα is activated by G‐CSF to bind target promoters, and plays critical roles in the transcriptional activation and dynamic chromatin modification of target genes during neutrophil differentiation.
Recognition of forked and single‐stranded DNA structures by human RAD18 complexed with RAD6B protein triggers its recruitment to stalled replication forks
Authors: Tsuji Yuri , Watanabe Kenji , Araki Kimi , Shinohara Masanori , Yamagata Yuriko , Tsurimoto Toshiki , Hanaoka Fumio , Yamamura Ken‐ichi , Yamaizumi Masaru , Tateishi Satoshi
Published: March 2008

Post‐replication DNA repair facilitates the resumption of DNA synthesis upon replication fork stalling at DNA damage sites. Despite the importance of RAD18 and polymerase η (Polη) for post‐replication repair (PRR), the molecular mechanisms by which these factors are recruited to stalled replication forks are not well understood. We present evidence that human RAD18 complexed with RAD6B protein preferentially binds to forked and single‐stranded DNA (ssDNA) structures, which are known to be localized at stalled replication forks. The SAP domain of RAD18 (residues 248–282) is crucial for binding of RAD18 complexed with RAD6B to DNA substrates. RAD18 mutated in the SAP domain fails to accumulate at DNA damage sites in vivo and does not guide DNA Polη to stalled replication forks. The SAP domain is also required for the efficient mono‐ubiquitination of PCNA. The SAP domain mutant fails to suppress the ultraviolet (UV)‐sensitivity of Rad18‐knockout cells. These results suggest that RAD18 complexed with RAD6B is recruited to stalled replication forks via interactions with forked DNA or long ssDNA structures, a process that is required for initiating PRR.
The effectiveness of office information systems: a social action perspective
Authors: Lyytinen K. , Klein H. , Hirschheim R.
Published: March 2008

Abstract. The purpose of this paper is to show that a number of basic issues have not been adequately addressed in existing office information systems research. Prominent among these are the nature and role of offices, the goals of office information systems development, and the nature of its organizational and managerial consequences. It is proposed that office information systems should be analysed as social action systems the behaviour of which is strongly affected by socially determined forces and constraints such as the behaviour‐channelling influences of authority, norms, customs, habits and precedence. Four types of social action are discussed: instrumental, strategic, communicative and discursive. Three contexts for perceiving and analysing the effects of social action in offices are introduced: technology, language and organization. Office information systems changes affect elements and relationships in these three contexts in different ways. By cross‐relating social action types and contexts, nine classes of object systems are identified. Each object system class implies a different category of effectiveness concerns which in turn implies different office information system design requirements. The paper notes that the existing research literature has primarily been concerned with only three of the nine object systems. For more effective office information systems development, however, the other systems also need to be considered. The paper concludes by exploring how this may be done.
Information systems management and strategy formulation: the ‘stages of growth’ model revisited
Authors: Galliers R D , Sutherland A R
Published: March 2008

Abstract. The original ‘stages of growth’ model, as applied to the field of Information Systems (Gibson & Nolan, 1974), may be viewed as seminal, given the influence it has had on both theory and practice (Nolan, 1984; Sullivan, 1985; Ward, et al., 1990). This is so, despite the model's lack of substantiation based on empirical evidence, the overly simplistic assumptions on which it is based, and the limited focus of the original concept (Benbasat, et al., 1984; King & Kraemer, 1984).

Since its first appearance, the model has been refined following many applications (Nolan, 1979, 1984). In addition, others have developed ‘stages of growth’ models of their own. For example, Somogyi & Galliers, (1987a, b)provide a model depicting the move from basic data processing systems to strategic information systems, tracing the early days of commercial applications of computing through to the present day (Ward et al. 1990). Earl (1983, 1986, 1988, 1989) proposes a stages‐model for information systems planning, as does Bhabuta (1988), while Hirschheim, et al. (1988) have developed a more broadly focused model associated with the development of the information‐systems management function.

As a result of a review of the above and of a case study research undertaken in Perth, Western Australia, a revised model was developed, which takes account of current thinking and past experience in the application of the various ‘stages of growth’ models (Sutherland & Galliers, 1989).

This paper sets out to review some of these models and proceeds to describe the process of developing, testing and applying the revised ‘stages of growth’ model. The model is more broadly focused than the original concept, incorporating strategic, organizational, human resource and management considerations. As a result, it is argued that this model has greater utility than its predecessors.
A method to help end‐users validate the functional specification for a computer system
Authors: Moynihan T. , O'Connor N.
Published: March 2008

Abstract. Described is a method to help users for a proposed computer system validate the functional specification for that system. Users construct an objectoriented model of the proposed functionality from the specification. The process of building the model improves users' understanding of the system and helps them identify any deficiencies in the specification. The method is applied to a real specification and a number of serious anomalies are found which would probably have been missed by a traditional review or walk‐through. It is concluded that the method is probably helpful, robust and reproducible for ‘transformational’ computer systems of low or moderate complexity.
Information retrieval and hypertext: competing technologies or complementary access methods
Authors: Smeaton Alan F
Published: March 2008

Abstract. Information retrieval typically involves accessing textual information from a database in response to a user's vague information need. Hypertext or hypermedia, on the other hand, involves a user browsing through a database of textual or multimedia information in response to a variety of types of information need. Thus information retrieval can be said to have a searching metaphor while hypertext has a browsing analogy. Initially, these two technologies for information access appear to be very different, almost competitive in nature. In this paper information retrieval systems are briefly reviewed and hypertext systems are also examined. These two techniques for accessing information have been integrated into a prototype system which is described. The system dynamically generates guided tours in response to a user's query and the tour guides the user through the hypertext. Some experiments reporting on the effectiveness of this as an information access strategy are given.
Information systems effectiveness: research designs for causal inference
Authors: Haga W. J. , Zviran M.
Published: March 2008

Abstract.This paper examines the capacity of the research designs of 37 empirical studies of information systems (IS) effectiveness to provide a basis for the development of theories about behaviour related to IS effectiveness. The power of each study to support causal inference was evaluated in terms of (a) its handling of the time dimension, (b) its ability to weigh differences and (c) its resistance to internal validity threats that pose alternative explanations for its reported findings. Of the reviewed studies, 29.7% could account for the time dimension, 32.4% employed a comparison group and 16.2% were not susceptible to any internal validity threats. Only 13.5% of the studies combined an accounting for the time dimension with the use of a comparison group. Of these, however, only 5.4% were also invulnerable to internal validity threats. The research designs of nearly 95% of these published studies were deficient in supporting causal inference. In those studies, suggestions that one variable was causally related to another variable could not be substantiated. Encouragement for the future capacity of IS effectiveness research to support causal inference was found in a trend towards the use of quasiexperimental designs. Recommendations are made regarding ways to increase the inferential capacity of research designs employed in the study of IS effectiveness.
The nature of research: qualitative or quantitative, narrative or paradigmatic?
Authors: Remenyi Dan , Williams Brian
Published: March 2008

Abstract. This paper explores the role of qualitative and quantitative approaches in information systems research. The importance of qualitative data and the construction of narratives as a key procedure in the development of theoretical conjectures and empirical generalizations or hypotheses are discussed. This paper also puts the importance of paradigmatic thinking and research into perspective by contrasting this approach with narrative thinking and qualitative research.

A recent PhD dissertation on strategic information systems is used to illustrate some of the concepts discussed in the paper.

Although the paper advocates the importance of qualitative research and argues that in some respects it may be regarded as more creative than quantitative research, it clearly recognizes that the distinguishing feature of modern science is the formulation of laws, very often mathematical, that capture the essential features of a problem and allow us to make predictions both into the future and about other current situations.
Residual bacteria in root apices removed by a diagonal root‐end resection: a histopathological evaluation
Authors: Lin S. , Platner O. , Metzger Z. , Tsesis I.
Published: March 2008

Aim  To assess bacteria in the apical portion of the root end after 45° root‐end resection in teeth with persistent periapical lesions.

Methodology  The study included 27 apical root segments from patients with persistent periapical lesions. Histological sections of the coronal part of the amputated root segment were stained with Brown and Brenn to detect the presence of bacteria in the main root canal and/or in irregular root spaces and dentinal tubules. The quality of each root canal filling was evaluated using preoperative radiographs of filling, length of root filling as assessed from the distance between its apical end and the radiographic apex, diameter of apical preparation, and presence of apical perforations or deviations from the root canal. Two endodontists, blinded to the bacteriological results, independently evaluated the radiographs.

Results  Bacteria were present in 23 (85.2%) specimens: five in only the main canal (21.7%), 10 in only the dentinal tubules and irregular spaces (43.5%), and eight in both irregular spaces and dentinal tubules and in the main root canal (34.8%). No correlation was found between the technical quality of the root filling assessed radiographically and bacterial presence in the central canal or irregular areas.

Conclusions  Infected irregular areas were found in the root tips of teeth with persistent periapical lesions. This was found regardless of the radiographic quality of the root filling. Diagonal, 45° root‐end resection may expose such contaminated irregularities to the periapical tissue.
Ex vivo evaluation of the ability of the ROOT ZX II to locate the apical foramen and to control the apical extent of rotary canal instrumentation
Authors: Felippe W. T. , Felippe M. C. S. , Reyes Carmona J. , Crozoé F. C. I. , Alvisi B. B.
Published: March 2008

Aim  To evaluate the capacity of the ROOT ZX II to locate the apical foramen and to control the apical extent of rotary instrumentation.

Methodology  Sixty‐five extracted human single rooted teeth were selected and measured directly using a size 15 K‐Flexofile introduced in the canal until the tip was visible at the major foramen (direct length, DL). The teeth were then measured electronically (EL1) with the ROOT ZX II when used passively, that is without rotation. To test the auto reverse function, the root canals were instrumented with nickel titanium rotary instruments. Instrumentation was carried out apically until rotation was reversed by the automatic apical reverse (AAR) function at different levels (2, 1 and 0.5). The instrumented length at each level was measured and registered as AAR2, AAR1 and AAR0.5, respectively. After instrumentation, a second passive electronic measurement was conducted and noted as electronic length 2 (EL2). All measurements were expressed in millimetres with accuracy set to 0.5 mm. Percentages of acceptable measurements for each electronic reading were calculated and compared using the proportions test. The Wilcoxon’s signed rank test was used to compare the differences between DL/EL1 and DL/EL2, and to compare EL2 with the different AAR measurements. The critical value of statistical significance was 5%.

Results  EL1 and EL2 measurements were coincident to DL in 56 (86%) and 54 (83%) of the cases, respectively. The proportions test showed no statistically significant difference between these percentages (P > 0.05). The Wilcoxon’s signed rank test did not show any differences (P > 0.05) when comparing the mean difference between DL with EL1 (0.03) and DL with EL2 (0.10). Statistically significant differences were observed when comparing EL2 with AAR2 and with AAR1.

Conclusions  The ROOT ZX II reliably located the major apical foramen, but was not an accurate method for controlling the apical extent of rotary instrumentation. Rotary instrumentation with the automatic apical reverse feature was always closer to the foramen than expected.
Extraoral endodontic treatment, odontotomy and intentional replantation of a double maxillary lateral permanent incisor: case report and 6‐year follow‐up
Authors: Sivolella S. , Bressan E. , Mirabal V. , Stellini E. , Berengo M.
Published: March 2008

Aim  To describe combined endodontic, surgical and orthodontic treatment of a maxillary lateral incisor fused with a supernumerary.

Summary  Double tooth is a dental irregularity consequent to fusion of two or more teeth or dental gemination. The teeth most commonly involved are deciduous, but in 0.1% of cases permanent teeth are affected, in which case aesthetic, functional and periodontal problems can result. This paper reports a clinical case of a double tooth in the position of the maxillary right lateral permanent incisor. Combined orthodontic, endodontic and surgical treatment (intentional replantation) allowed the tooth to be retained without periodontal compromise and with a positive orthodontic result both immediately and 6 years following intervention.

Key learning points

A conservative approach that addresses periodontal, pulpal and tooth tissues, can result in the retention of a double tooth.

Maintenance of the root and alveolar bone in young adults at least until full skeletal maturation should be the main treatment objective.
Ridge preservation in cases requiring tooth extraction during endodontic surgery: a case report
Authors: Lin S. , Cohenca N. , Muska E. A. , Front E.
Published: March 2008

Aim  To provide a treatment option to endodontists performing surgery that will enhance ridge preservation when tooth extraction is required.

Summary  A 47‐year‐old woman was referred to an endodontic practice for apical root‐end resection of tooth 22 because of refractory periradicular disease. Radiographic examination revealed a large periradicular lesion, 5 mm in diameter and a root‐end filling at the root apex. The treatment plan included exploratory surgery and apical root‐end resection. A vertical root fracture was diagnosed and the decision was made to extract the tooth. The socket was grafted with a cancellous bovine bone and covered with a resorbable collagen membrane. Follow‐up examination revealed favourable bone healing with formation of a new cortical plate and the preservation of soft tissue width and height in the aesthetic area.

Key learning points

The principles of guided bone regeneration.

Preserving or reconstructing the extraction socket.

Enhances the ability to restore function and provide aesthetically pleasing restorations to patients without violating the predictability and function of the prostheses.
Quality factors and grades for the classification and standardisation of complex ready pasta meals
Authors: Kindt Maddalena , Mazzaracchio Palmira , Barbiroli Giancarlo
Published: March 2008

The aim of this study is to arrive at a new classification of ready pasta meals, through the evaluation of their global quality, since their growing number, present in the market, often may be cause of confusion to consumers, because the parameters that contribute to the quality level are not clearly identifiable and measurable. After having explored several possible quality factors, we arrived at the conclusion that at least five must be taken into consideration: degree of pulping of the pasta, capacity to hold the sauce, weight constancy, wholeness and defects. Then, three quality grades are here proposed and discussed. Particular emphasis should be given to the sauce, because it highly influences on the global quality of these foodstuffs.
Menopausal symptom experience: an online forum study
Authors: Im Eun‐Ok , Liu Yi , Dormire Sharon , Chee Wonshik
Published: March 2008

Title.  Menopausal symptom experience: an online forum study

Aim.  The aim of the study was to explore the menopausal symptom experience of White midlife women.

Background.  Recent cross‐cultural investigations have indicated important ethnic differences in menopausal symptoms and have challenged the universality of these symptoms. Currently available cultural knowledge on menopausal experience, however, is inadequate to guide appropriate and adequate care even for White women in the menopausal transition.

Method.  A cross‐sectional qualitative online forum study was conducted in 2007 with 23 midlife women who self‐identified as non‐Hispanic Whites using convenience sampling. Seven topics related to menopausal symptom experience were used to guide the online forum for 6 months. The data were analysed using thematic analysis.

Results.  The experiences of menopause caused women to redefine themselves within their busy daily life schedules. They were optimistic about their symptoms, and tried to laugh at the experience to boost their inner strength and motivate themselves to persevere. Many thought that both generational and life‐style differences were much more important than ethnic differences in menopausal symptom experiences. In seeking assistance with the symptoms of menopause, women were not satisfied with the guidance of their physicians.

Conclusion.  Nurses need to listen carefully to what women themselves say about their own experiences with menopausal symptoms and avoid imposing predetermined symptom management strategies. Further studies of women’s perceptions of life‐style influences are needed to guide symptom management. In addition, studies of generational changes in menopausal symptom experience are needed.
Glycan microarray analysis of Candida glabrata adhesin ligand specificity
Authors: Zupancic Margaret L. , Frieman Matthew , Smith David , Alvarez Richard A. , Cummings Richard D. , Cormack Brendan P.
Published: March 2008

The Candida glabrata genome encodes at least 23 members of the EPA (epithelial adhesin) family responsible for mediating adherence to host cells. To better understand the mechanism by which the Epa proteins contribute to pathogenesis, we have used glycan microarray analysis to characterize their carbohydrate‐binding specificities. Using Saccharomyces cerevisiae strains surface‐expressing the N‐terminal ligand‐binding domain of the Epa proteins, we found that the three Epa family members functionally identified as adhesins in Candida glabrata (Epa1, Epa6 and Epa7) bind to ligands containing a terminal galactose residue. However, the specificity of the three proteins for glycans within this class varies, with Epa6 having a broader specificity range than Epa1 or Epa7. This result is intriguing given the close homology between Epa6 and Epa7, which are 92% identical at the amino acid level. We have mapped a five‐amino‐acid region within the N‐terminal ligand‐binding domain that accounts for the difference in specificity of Epa6 and Epa7 and show that these residues contribute to adherence to both epithelial and endothelial cell lines in vitro.
Peroxidases in the early responses of different potato cultivars to infection by Potato virus YNTN
Authors: Milavec M. , Gruden K. , Ravnikar M. , Kovač M.
Published: March 2008

Peroxidases (POXs) were investigated in three cultivars of potato (Solanum tuberosum) with different susceptibilities to infection by Potato virus YNTN (PVYNTN). Soluble, ionically‐bound and covalently‐bound POXs were analysed over 24 h post inoculation (hpi) in bottom inoculated leaves, upper intact leaves, and in roots. The first changes were observed at 3 hpi when the activity of ionically‐bound POXs increased significantly in the inoculated leaves of tolerant cv. Pentland Squire and of resistant cv. Santé. The most pronounced changes were found in the resistant variety, where the increase was twice that in control plants. In contrast, in the inoculated leaves of susceptible cv. Igor, there was a decrease in ionically‐bound POXs, accompanied by a two fold increase in the activity of covalently‐bound POXs. Also at 3 hpi, cv. Santé showed increased activity of all three types of POXs in the upper intact leaves. Over the period of the experiment, enhanced activity of soluble POXs, correlated with the virus infection, was observed in both types of leaves of the susceptible cv. Igor. However, in resistant cv. Santé, the upper intact leaves of virus‐inoculated plants showed a more intense but transient early response of soluble POXs. Part of a new POX gene was isolated from leaves of potato cv. Igor. A nucleotide sequence of 394 bp was determined and the abundance of the POX transcript was analysed by real‐time PCR. There was no correlation between PVYNTN infection and the abundance of the transcript.
Quantification of within‐season focal spread of wheat take‐all in relation to pathogen genotype and host spatial distribution
Authors: Willocquet L. , Lebreton L. , Sarniguet A. , Lucas P.
Published: March 2008

Within season gradient of wheat take‐all was measured in field experiments according to line or random sowing host spatial distribution, and two Gaeumannomyces graminis var. tritici (Ggt) isolates (G1i and G2i), representative of the G1 and G2 genotype groups in terms of aggressiveness. Root disease incidence and severity were assessed at six dates from early March to late June on plants located at regular distances from the inoculum sources. Simple models relating disease intensity at different levels of hierarchy fitted observed data well, and indicated a strong disease aggregation both within and among plants. Disease severity on source plants placed nearby the inoculum source increased over time, ranging from 5 to 46% at the first assessment, and from 55 to 98% at the last assessment, being in general larger for G2i than G1i. In line‐sown plots, disease progressed steadily along the line but did not extend beyond 20 cm, seldom reaching the neighbour line. Disease rarely reached 25 cm in the direct‐seeded crop stands. These results indicate that Ggt intensifies but does not spread to a large extent during a cropping season. Distance from the source, pathogen genotype and assessment date had a significant effect on disease severity according to mixed model analyses, disease spread being larger for G2i than G1i. However, no significant effect of host spatial distribution could be detected. Yield loss within 20 cm of the source plant ranged between 20 and 40%, and was not significantly affected by pathogen genotype or host spatial distribution.
Dimensions and architecture of late Pleistocene submarine lobes off the northern margin of East Corsica
Authors: DEPTUCK MARK E. , PIPER DAVID J. W. , SAVOYE BRUNO , GERVAIS ANNE
Published: March 2008

Sandy lobe deposits on submarine fans are sensitive recorders of the types of sediment gravity flows supplied to a basin and are economically important as hydrocarbon reservoirs. This study investigates the causes of variability in 20 lobes in small late Pleistocene submarine fans off East Corsica. These lobes were imaged using ultra‐high resolution boomer seismic profiles (<1 m vertical resolution) and sediment type was ground truthed using piston cores published in previous studies. Repeated crossings of the same depositional bodies were used to measure spatial changes in their dimensions and architecture. Most lobes increase abruptly down‐slope to a peak thickness of 8 to 42 m, beyond which they show a progressive, typically more gradual, decrease in thickness until they thin to below seismic resolution or pass into draping facies of the basin plain. Lobe areas range from 3 to 70 km2 and total lengths from 2 to 14 km, with the locus of maximum sediment accumulation from 3 to 28 km from the shelf‐break. Based on their location, dimensions, internal architecture and nature of the feeder channel, the lobes are divided into two end‐member types. The first are small depositional bodies located in proximal settings, clustered near the toe‐of‐slope and fed by slope gullies or erosive channels lacking or with poorly developed levées (referred to as ‘proximal isolated lobes’). The second are larger architecturally more complex depositional bodies deposited in more distal settings, outboard more stable and longer‐lived levéed fan valleys (referred to as ‘composite mid‐fan lobes’). Hybrid lobe types are also observed. At least three hierarchical levels of compensation stacking are recognized. Individual beds and bed‐sets stack to form lobe‐elements; lobe‐elements stack to form composite lobes; and composite lobes stack to form lobe complexes. Differences in the size, shape and architectural complexity of lobe deposits reflect several inter‐related factors including: (i) flow properties (volume, duration, grain‐size, concentration and velocity); (ii) the number and frequency of flows, and their degree of variation through time; (iii) gradient change and sea floor morphology at the mouth of the feeder conduit; (iv) lobe lifespan prior to avulsion or abandonment; and (v) feeder channel geometry and stability. In general, lobes outboard stable fan valleys that are connected to shelf‐incised canyons are wider, longer and thicker, accumulate in more basinal locations and are architecturally more complex.
The Lower Permian Wasp Head Formation, Sydney Basin: high‐latitude, shallow marine sedimentation following the late Asselian to early Sakmarian glacial event in eastern Australia
Authors: RYGEL MICHAEL C. , FIELDING CHRISTOPHER R. , BANN KERRIE L. , FRANK TRACY D. , BIRGENHEIER LAUREN , TYE STUART C.
Published: March 2008

The Lower Permian Wasp Head Formation (early to middle Sakmarian) is a ∼95 m thick unit that was deposited during the transition to a non‐glacial period following the late Asselian to early Sakmarian glacial event in eastern Australia. This shallow marine, sandstone‐dominated unit can be subdivided into six facies associations. (i) The marine sediment gravity flow facies association consists of breccias and conglomerates deposited in upper shoreface water depths. (ii) Upper shoreface deposits consist of cross‐stratified, conglomeratic sandstones with an impoverished expression of the Skolithos Ichnofacies. (iii) Middle shoreface deposits consist of hummocky cross‐stratified sandstones with a trace fossil assemblage that represents the Skolithos Ichnofacies. (iv) Lower shoreface deposits are similar to middle shoreface deposits, but contain more pervasive bioturbation and a distal expression of the Skolithos Ichnofacies to a proximal expression of the Cruziana Ichnofacies. (v) Delta‐influenced, lower shoreface‐offshore transition deposits are distinguished by sparsely bioturbated carbonaceous mudstone drapes within a variety of shoreface and offshore deposits. Trace fossil assemblages represent distal expressions of the Skolithos Ichnofacies to stressed, proximal expressions of the Cruziana Ichnofacies. Impoverished trace fossil assemblages record variable and episodic environmental stresses possibly caused by fluctuations in sedimentation rates, substrate consistencies, salinity, oxygen levels, turbidity and other physio‐chemical stresses characteristic of deltaic conditions. (vi) The offshore transition‐offshore facies association consists of mudstone and admixed sandstone and mudstone with pervasive bioturbation and an archetypal to distal expression of the Cruziana Ichnofacies. The lowermost ∼50 m of the formation consists of a single deepening upward cycle formed as the basin transitioned from glacioisostatic rebound following the Asselian to early Sakmarian glacial to a regime dominated by regional extensional subsidence without significant glacial influence. The upper ∼45 m of the formation can be subdivided into three shallowing upward cycles (parasequences) that formed in the aftermath of rapid, possibly glacioeustatic, rises in relative sea‐level or due to autocyclic progradation patterns. The shift to a parasequence‐dominated architecture and progressive decrease in ice‐rafted debris upwards through the succession records the release from glacioisostatic rebound and amelioration of climate that accompanied the transition to broadly non‐glacial conditions.