bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Fluency Curriculum in the New Millennium: Building “Skills” Into “Knowledge” Classes
Authors: Quesal Bob , Murphy Bill 
Published: March 2008

Abstract
Recent changes in the standards for the Certificate of Clinical Competence in Speech-Language Pathology (CCC-SLP) have led to changes in the way in which information is presented to students in communication sciences and disorders classes. One of the primary changes is the focus on knowledge and skills outcomes that result from students’ education. Another change is the degree to which those skills and knowledge are specified by the standards. Educators cannot always be assured that all students will obtain “skills” in all areas specified by the standards during their practicum experiences. For that reason, it becomes necessary to add “skills” components to what may have previously been “knowledge” classes. This article presents a number of ideas for adding these “skills” experiences to “knowledge” classes.
Discerning the Division of Cognitive Labor: An Emerging Understanding of How Knowledge Is Clustered in Other Minds
Authors: Keil Frank C. , Stein Courtney , Webb Lisa , Billings Van Dyke , Rozenblit Leonid 
Published: March 2008

AbstractThe division of cognitive labor is fundamental to all cultures. Adults have a strong sense of how knowledge is clustered in the world around them and use that sense to access additional information, defer to relevant experts, and ground their own incomplete understandings. One prominent way of clustering knowledge is by disciplines similar to those that comprise the natural and social sciences. Seven studies explored an emerging sense of these discipline‐based ways of clustering of knowledge. Even 5‐year‐olds could cluster knowledge in a manner roughly corresponding to the departments of natural and social sciences in a university, doing so without any explicit awareness of those academic disciplines. But this awareness is fragile early on and competes with other ways of clustering knowledge. Over the next few years, children come to see discipline‐based clusters as having a privileged status, one that may be linked to increasingly sophisticated assumptions about essences for natural kinds. Possible mechanisms for this developmental shift are examined.
Understanding and Using Principles of Arithmetic: Operations Involving Negative Numbers
Authors: Prather Richard W. , Alibali Martha W. 
Published: March 2008

AbstractPrevious work has investigated adults' knowledge of principles for arithmetic with positive numbers (). The current study extends this past work to address adults' knowledge of principles of arithmetic with a negative number, and also investigates links between knowledge of principles and problem representation. Participants (N = 44) completed two tasks. In the Evaluation task, participants rated how well sets of equations were solved. Some sets violated principles of arithmetic and others did not. Participants rated non‐violation sets higher than violation sets for two different principles for subtraction with a negative number. In the Word Problem task, participants read word problems and set up equations that could be used to solve them. Participants who displayed greater knowledge of principles of arithmetic with a negative number were more likely to set up equations that involved negative numbers. Thus, participants' knowledge of arithmetic principles was related to their problem representations.
Protein for adaptations to exercise training
Authors: Tipton Kevin D. 
Published: March 2008

AbstractNutrient intake before, during, and after training will influence the adaptations that occur in response to the training stimulus. The influence of protein on training adaptations is receiving increasing attention from researchers. Methodological issues should be carefully considered when evaluating evidence of nutritional influence on training adaptations. Evidence suggests that adaptations to training are due to changes in the types and activities of various proteins in response to each exercise bout. Thus, study of the acute metabolic and molecular responses to exercise plus nutrition may provide valuable information about the expected influence on training adaptations. The type of protein, timing of protein ingestion relative to exercise, concurrent ingestion of other nutrients with protein, as well as the type of exercise training performed will impact the adaptations to training with the intake of protein. Protein is an important nutrient for muscle hypertrophy with training, but there is little support for the need for very high (e.g. >2.5–3.0 grams of protein per kilogram of body weight) intakes. Traditionally, endurance athletes have focused on carbohydrate intake, but recently protein has been touted to be critical during and after endurance exercise. There is evidence for and against the importance of protein for endurance exercise and more, well‐controlled studies are required to delineate the importance of protein for endurance exercise adaptations. Whereas nutritional manipulations have customarily been focused on preventing protein degradation, muscle damage, and oxidative stress, recent evidence suggests that these processes may be critical for the optimal adaptive response to training.
Technology/Ideology: How Ideological Fields Influence Consumers' Technology Narratives
Authors: Kozinets Robert V. 
Published: March 2008

Abstract
Through a systematic study of consumer narratives, this article models how technology ideologies influence consumer-level thought, speech, and action. Applying critical discourse analysis and articulation theory approaches, a semiotic square model represents the relations between Techtopian, Green Luddite, Work Machine, and Techspressive ideological elements in an ideological field. The narratives of individual consumers move between ideological elements in ways suggested by the model's semantic relations. The results reveal novel aspects of consumers' dynamic relations to technology ideology and invite further investigations of technology and consumption ideology.
Scaffolding and validation of bacterial genome assemblies using optical restriction maps
Authors: Nagarajan Niranjan , Read Timothy D. , Pop Mihai 
Published: March 2008

Abstract
Motivation: New, high-throughput sequencing technologies have made it feasible to cheaply generate vast amounts of sequence information from a genome of interest. The computational reconstruction of the complete sequence of a genome is complicated by specific features of these new sequencing technologies, such as the short length of the sequencing reads and absence of mate-pair information. In this article we propose methods to overcome such limitations by incorporating information from optical restriction maps.
Results: We demonstrate the robustness of our methods to sequencing and assembly errors using extensive experiments on simulated datasets. We then present the results obtained by applying our algorithms to data generated from two bacterial genomes Yersinia aldovae and Yersinia kristensenii. The resulting assemblies contain a single scaffold covering a large fraction of the respective genomes, suggesting that the careful use of optical maps can provide a cost-effective framework for the assembly of genomes.
Availability: The tools described here are available as an open-source package at ftp://ftp.cbcb.umd.edu/pub/software/soma
Contact: mpop@umiacs.umd.edu
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

AbstractRossi-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.
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

AbstractProgranulin 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

AbstractHIV 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

AbstractThe 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

AbstractRenilla 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

AbstractWe 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.
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.
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

AbstractAim  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.