bluuebunny/crossref_metadata_2025_split huggingface dataset:
BioNet: an R-Package for the functional analysis of biological networks
Authors: Beisser Daniela , Klau Gunnar W. , Dandekar Thomas , Müller Tobias , Dittrich Marcus T. 
Published: February 2010

Abstract
Motivation: Increasing quantity and quality of data in transcriptomics and interactomics create the need for integrative approaches to network analysis. Here, we present a comprehensive R-package for the analysis of biological networks including an exact and a heuristic approach to identify functional modules.
Results: The BioNet package provides an extensive framework for integrated network analysis in R. This includes the statistics for the integration of transcriptomic and functional data with biological networks, the scoring of nodes as well as methods for network search and visualization.
Availability: The BioNet package and a tutorial are available from http://bionet.bioapps.biozentrum.uni-wuerzburg.de
Contact: marcus.dittrich@biozentrum.uni-wuerzburg.de; tobias.mueller@biozentrum.uni-wuerzburg.de
The PedsQL™ in Pediatric Patients with Duchenne Muscular Dystrophy: Feasibility, Reliability, and Validity of the Pediatric Quality of Life Inventory Neuromuscular Module and Generic Core Scales
Authors: Davis Sarah E , Hynan Linda S , Limbers Christine A , Andersen C Mariam , Greene Medrith C , Varni James W , Iannaccone Susan T 
Published: February 2010

Objective:
To evaluate the reliability and validity of the PedsQL™ 3.0 Neuromuscular Module (NMM) in assessing health-related quality of life in the Duchenne muscular dystrophy (DMD) population for use as a secondary outcome measure in phase III clinical trials.

Background:
DMD is the most common genetic form of muscular dystrophy in childhood. Clinical trials are underway to evaluate modalities of treatment. The NMM was developed based on interviews of patients with DMD and spinal muscular atrophy. To determine the PedsQL™ reliability and validity, we administered the NMM to patients with DMD and their caregivers.

Design/Methods:
Boys 8 to 18 years old with DMD were recruited from a neuromuscular disease clinic. At baseline, the child and caregiver completed the NMM and the PedsQL™ 4.0 Generic Core Scales (GC). The NMM was repeated 2 to 6 weeks later. Reliability was assessed using Cronbach's coefficient alpha (internal consistency) and intraclass correlation (ICC) (test-retest consistency). Construct validity was assessed by comparing baseline child and caregiver NMM total scores with the GC Total Score, forced vital capacity, cardiac ejection fraction, and ambulatory status.

Results:
Forty-four children and their caregivers completed the study. Internal consistency reliability of the total scale score of the NMM was demonstrated (Child α = 0.85; Caregiver α = 0.87). Test-retest reliability of the NMM was also demonstrated (Child ICC = 0.75, P = 0.001; Caregiver ICC = 0.85, P < 0.001). Validity of the total scale score of the NMM when compared with the GC Total Scale Score was supported (Child r (41) = 0.63, P < 0.001; Caregiver r (42) = 0.64, P < 0.001). Validity of the NMM compared with forced vital capacity was also supported (Child r (38) = 0.35, P = 0.032; Caregiver r (39) = 0.41, P = 0.01). The NMM parent-proxy-report and child self-report “About My Child's Neuromuscular Disease” scale was significantly related to wheelchair use (P < 0.008 and 0.016, respectively); the GC "Child Self-Report “Physical Health” scale was also significantly related to wheelchair use (P < 0.001). We were unable to conduct any analysis with ejection fraction because of the small number of children across all categories.

Conclusions:
The PedsQL™ NMM is a reliable measure of disease-specific health-related quality of life in the DMD population and may be used as an outcome measure in clinical trials.
Asymmetric Phenotype Associated With Rare Myelin Protein Zero Mutation
Authors: Souayah Nizar , Tick Chong Peter Siao 
Published: February 2010

ABSTRACT

Myelin protein zero (MPZ) mutations cause demyelinating neuropathies that range from severe neonatal to milder adult forms. We report a 36-year-old man who developed weakness of his left little finger adduction 3 years earlier. The weakness progressed to his other limbs. Examination revealed mildly high-arched feet with asymmetric weakness of ulnar-innervated muscles (left > right) and asymmetric weakness of peroneal-innervated muscles (right > left). Motor nerve conduction velocities ranged from 18.4 to 24.4 m/s in the upper extremities and from 14.8 to 22.7 in the lower extremities. Left median partial motor conduction block was noted at the forearm segment. Genetic testing demonstrated MPZ mutation with ARG98HIS amino acid change. The patient's father is a 68-year-old man who was asymptomatic and who was noticed to have high-arched feet and asymmetric leg muscle atrophy and weakness (right > left). The patient's 2-year-old son is “clumsy” with history of neonatal laryngomalacia. He has flat feet, areflexia, and difficulty standing on individual right versus left leg. The patient's paternal grandfather had high-arched feet and hearing loss. We conclude that ARG98HIS MPZ mutation may cause hereditary and relatively mild and asymmetric demyelinating sensorimotor polyneuropathy.
Superficial Siderosis Mimicking Amyotrophic Lateral Sclerosis
Authors: Driver-Dunckley Erika D , Hoxworth Joseph M , Patel Naresh P , Bosch E Peter , Goodman Brent P 
Published: February 2010

ABSTRACT

We report a case of superficial siderosis erroneously diagnosed as amyotrophic lateral sclerosis. The patient's symptoms began 18 years prior with unilateral upper extremity weakness, fasciculations, and hyperreflexia. The patient then developed ataxia and hearing loss 15 years after his original symptoms. The magnetic resonance images revealed superficial siderosis involving the spinal cord and brain. We want to attract attention to superficial siderosis as a rare amyotrophic lateral sclerosis mimic disorder.
GD1a-Associated Pure Motor Guillain-Barré Syndrome With Hyperreflexia and Bilateral Papillitis
Authors: Neuwirth Christoph , Mojon Daniel , Weber Markus 
Published: February 2010

ABSTRACT

A patient with acute purely motor polyneuropathy with positive GD1a ganglioside antibodies who presented with paresis in combination with hyperreflexia is reported. Neurophysiological tests revealed features compatible with acute motor axonal neuropathy. Therapy with intravenous immunoglobulin led to rapid clinical improvement. However, at the time when signs of active denervation appeared on electromyographic testing, the patient developed bilateral papillitis. The pathogenesis of pure motor Guillain-Barré syndrome with hyperreflexia and papillitis is discussed.
The Neuromuscular Manifestations of Amyloidosis
Authors: Simmons Zachary , Specht Charles S 
Published: February 2010

Abstract

Amyloidosis is a systemic disease that may be acquired or hereditary and which results in the deposition of amyloid fibrils in a variety of tissues causing their progressive dysfunction. Although the clinical presentation often is dominated by cardiac or renal failure, peripheral neuropathy may be a significant or the initial manifestation, resulting in presentation to the neurologist. Diagnosis often is challenging and may require multiple diagnostic procedures, including more than one biopsy. Acquired and hereditary amyloidosis can be definitively distinguished from one another only by immunohistochemical staining or molecular genetic testing. Treatment remains a challenge, although chemotherapy and autologous stem cell transplantation offer hope for those with primary systemic amyloidosis, whereas liver transplantation is effective for some forms of hereditary amyloid neuropathy. Much less commonly, myopathy may be a clinically significant manifestation of amyloidosis.
Using WebGBrowse to Visualize Genome Annotation on GBrowse
Authors: Podicheti Ram , Dong Qunfeng 
Published: March 2010

INTRODUCTIONAlthough GBrowse is popular for visualizing genomic features along a reference sequence, its installation and configuration are difficult for many biologists. WebGBrowse is a web server that takes a user-supplied annotation file, guides users to configure the display of each genomic feature, and allows users to visualize the genome annotation with integrated GBrowse software. This protocol guides the user through each step of using WebGBrowse.
Determination of Recombinant Baculovirus Display Viral Titer
Authors: Mäkelä Anna R. , Ernst Wolfgang , Grabherr Reingard , Oker-Blom Christian 
Published: March 2010

INTRODUCTIONThe baculovirus expression vector system has been used extensively to produce numerous proteins originating from both prokaryotic and eukaryotic sources. In addition to easy cloning techniques and abundant viral propagation, the system’s insect cell environment provides eukaryotic post-translational modification machinery. The baculovirus display vector system provides a number of advantages over prokaryotic systems, allowing the combination of genotype with phenotype, enabling presentation of foreign peptides or even complex proteins on the baculoviral envelope or capsid. Baculoviruses permit larger gene insertions, are easily propagated, and can be grown to high titers. Furthermore, surface modifications of the viral capsid enable specific targeting. This strategy can be used to enhance viral binding and entry to a wide variety of both dividing and nondividing mammalian cells, as well as to produce antibodies against the displayed antigen. In addition, the technology should enable modifications of intracellular behavior, i.e., trafficking of recombinant “nanoparticles,” a highly relevant feature for studies of targeted gene or protein delivery. Although baculovirus titer can be determined by standard methods such as classical plaque assays or end-point dilution assays, such methods often are tedious and time-consuming. The protocol described here is rapid and can be performed directly using marker genes such as green fluorescent protein or β-galactosidase regulated by baculovirus-specific promoters, or indirectly as an immunoassay with baculovirus-specific antibodies (e.g., anti-gp64).
Combined Transcript and Metabolite Profiling of Arabidopsis Grown under Widely Variant Growth Conditions Facilitates the Identification of Novel Metabolite-Mediated Regulation of Gene Expression
Authors: Hannah Matthew A. , Caldana Camila , Steinhauser Dirk , Balbo Ilse , Fernie Alisdair R. , Willmitzer Lothar 
Published: February 2010

Abstract
Regulation of metabolism at the level of transcription and its corollary metabolite-mediated regulation of transcription are well-documented mechanisms by which plants adapt to circumstance. That said the function of only a minority of transcription factor networks are fully understood and it seems likely that we have only identified a subset of the metabolites that play a mediator function in the regulation of transcription. Here we describe an integrated genomics approach in which we perform combined transcript and metabolite profiling on Arabidopsis (Arabidopsis thaliana) plants challenged by various environmental extremes. We chose this approach to generate a large variance in the levels of all parameters recorded. The data was then statistically evaluated to identify metabolites whose level robustly correlated with those of a particularly large number of transcripts. Since correlation alone provides no proof of causality we subsequently attempted to validate these putative mediators of gene expression via a combination of statistical analysis of data available in publicly available databases and iterative experimental evaluation. Data presented here suggest that, on adoption of appropriate caution, the approach can be used for the identification of metabolite mediators of gene expression. As an exemplary case study we document that in plants, as in yeast (Saccharomyces cerevisiae) and mammals, leucine plays an important role as a regulator of gene expression and provide a leucine response gene regulatory network.
RNA PROCESSING FACTOR2 Is Required for 5′ End Processing of nad9 and cox3 mRNAs in Mitochondria of Arabidopsis thaliana
Authors: Jonietz Christian , Forner Joachim , Hölzle Angela , Thuss Sabine , Binder Stefan 
Published: February 2010

Abstract
In mitochondria of higher plants, the majority of 5′ termini of mature mRNAs are generated posttranscriptionally. To gain insight into this process, we analyzed a natural 5′ end polymorphism in the species Arabidopsis thaliana. This genetic approach identified the nuclear gene At1g62670, encoding a pentatricopeptide repeat protein. The functional importance of this mitochondrial restorer of fertility-like protein, designated RNA PROCESSING FACTOR2 (RPF2), is confirmed by the analysis of a respective T-DNA knockout mutant and its functional restoration by in vivo complementation. RPF2 fulfills two functions: it is required for the generation of a distinct 5′ terminus of transcripts of subunit 9 of the NADH DEHYDROGENASE complex (nad9) and it determines the efficiency of 5′ end formation of the mRNAs for subunit 3 of the CYTOCHROME C OXIDASE (cox3), the latter also being influenced by mitochondrial DNA sequences. Accordingly, recombinant RPF2 protein directly binds to a nad9 mRNA fragment in vitro. Two-dimensional gel electrophoresis and immunodetection analyses reveal that altered 5′ processing does not influence accumulation of the nad9 and cox3 polypeptides. In accessions C24, Oystese-1, and Yosemite-0, different inactive RPF2 alleles exist, demonstrating the variability of this gene in Arabidopsis. The identification of RPF2 is a major step toward the characterization of 5′ mRNA processing in mitochondria of higher plants.
Cell Cycle–Mediated Regulation of Plant Infection by the Rice Blast Fungus
Authors: Saunders Diane G.O. , Aves Stephen J. , Talbot Nicholas J. 
Published: February 2010

AbstractTo gain entry to plants, many pathogenic fungi develop specialized infection structures called appressoria. Here, we demonstrate that appressorium morphogenesis in the rice blast fungus Magnaporthe oryzae is tightly regulated by the cell cycle. Shortly after a fungus spore lands on the rice (Oryza sativa) leaf surface, a single round of mitosis always occurs in the germ tube. We found that initiation of infection structure development is regulated by a DNA replication-dependent checkpoint. Genetic intervention in DNA synthesis, by conditional mutation of the Never-in-Mitosis 1 gene, prevented germ tubes from developing nascent infection structures. Cellular differentiation of appressoria, however, required entry into mitosis because nimA temperature-sensitive mutants, blocked at mitotic entry, were unable to develop functional appressoria. Arresting the cell cycle after mitotic entry, by conditional inactivation of the Blocked-in-Mitosis 1 gene or expression of stabilized cyclinB-encoding alleles, did not impair appressorium differentiation, but instead prevented these cells from invading plant tissue. When considered together, these data suggest that appressorium-mediated plant infection is coordinated by three distinct cell cycle checkpoints that are necessary for establishment of plant disease.
Knowledge creation and business format franchising
Authors: Lindblom Arto , Tikkanen Henrikki 
Published: February 2010

PurposeThis article aims to contribute to the study of knowledge creation and management in business format franchising by focusing on the question of how franchisors can convert the tacit knowledge held by franchisees (such as insights, ideas, and hunches) to explicit knowledge.Design/methodology/approachThe article is conceptual and is largely anchored on the assumptions of the knowledge management, theories of organisational learning and organisational knowledge creation theory.FindingsThe findings emphasise that the conversion of franchisees' tacit knowledge to new explicit knowledge is one of the key knowledge management practices required for successful business format franchising. Proposes that the concept of ba has much to offer in considering knowledge management in a business format franchise system.Research limitations/implicationsWith regard to future research avenues, conceptual and empirical studies are both needed to obtain a clearer understanding of the dynamic process of knowledge creation under business format franchising.Practical implicationsThe article sensitises franchisors to think how knowledge is created under business format franchising, and in particular how the tacit knowledge that franchisees provide can be converted into the form of explicit knowledge. Underlines that franchisors can never control and direct dynamic process of knowledge creation among franchisees, but a franchisor can provide certain conditions that lead franchisees and other members of franchise system to create and disseminate knowledge.Originality/valueThe article proposes that both tacit and explicit knowledge under business format franchising are created in formal or informal groups encompassing bas that may span both horizontally and vertically throughout the business format franchise system.
Purchasing professional services: which decision criteria?
Authors: Sonmez Mahmut , Moorhouse Andy 
Published: February 2010

PurposeThe aim of this paper is to report the findings of a global survey on decision criteria used and the importance attached to these criteria when purchasing professional services for skills training in sales and negotiations.Design/methodology/approachThe research is based on 24 face‐to‐face and telephone interviews with global learning and development managers plus 309 usable responses to an online survey. The respondents are asked to evaluate the importance of six “high level” criteria and 37 sub‐criteria (identified from the interviews and academic literature review) when purchasing professional services. Descriptive statistics and exploratory factor analysis are used to analyse the survey data.FindingsDescriptive statistics reveal that the main criteria split into two distinct groups: pre‐qualifiers and final stage differentiators. Exploratory factor analysis results in a reduced set of 11 factors that explain the underlying structure of decision criteria used for the selection of professional service providers.Practical implicationsThe findings of this research are especially suited for those managing the learning function or directing learning and development strategy at a corporate level, including human resources and executive management. They will also be of interest to professional service firms wanting to gain an insight into the selection process and academic researchers, as this paper helps address the paucity of empirical research into the purchasing criteria for professional services.Originality/valueThe supply chain literature heavily reports on decision criteria and decision making techniques used for supplier selection mainly in the manufacturing industry. This paper draws attention to the need for more research on the services sector.
Optimal decision making on urban renewal projects
Authors: Juan Yi‐Kai , Roper Kathy O. , Castro‐Lacouture Daniel , Ha Kim Jun 
Published: February 2010

PurposeThe aim of this paper is to present a systematic approach to provide decision makers in the Taipei City Government and private developers with an opportunity to review their decisions on urban renewal project selections, and to provide a model which could be adapted for other locations.Design/methodology/approachPorter's diamond model of competitive advantage is applied to establish evaluating criteria on urban competitiveness quality, and a fuzzy set theory combining the PROMETHEE method is used to determine the priority of projects. In assigning scores for urban sustainability, the expected return for each project is calculated for the economic dimension and a subjective scale has been used for the social and environmental dimensions. Genetic algorithms (GA) are introduced to search optimal solutions considering cost‐score tradeoffs for decisions on investment ratio determination and renewal type selection. The proposed approach is tested by evaluating 13 urban renewal projects in Taipei City.FindingsThe three‐stage model proposed by this study has established a comprehensive and systematic approach that considers key factors in urban renewal, assesses renewal projects from the standpoint of urban competitiveness and sustainability, and provides decision makers with helpful guidelines for investment.Research limitations/implicationsThere is difficulty in re‐examining social and environmental issues of the city government's earlier decisions became decision makers did not fully consider these two issues at the beginning of the planning stage, which is a limitation of this research.Originality/valueThe results documented in the paper provide many other cities facing similar renewal decision problems with insightful strategies and useful implications.
Improved capital budgeting decision making: evidence from Canada
Authors: Bennouna Karim , Meredith Geoffrey G. , Marchant Teresa 
Published: February 2010

PurposeThe purpose of this article is to evaluate current techniques in capital budget decision making in Canada, including real options, and to integrate the results with similar previous studies.Design/methodology/approachA mail survey was conducted, which included 88 large firms in Canada.FindingsTrends towards sophisticated techniques have continued; however, even in large firms, 17 percent did not use discounted cash flow (DCF). Of those which did, the majority favoured net present value (NPV) and internal rate of return (IRR). Overall between one in ten to one in three were not correctly applying certain aspects of DCF. Only 8 percent used real options.Research limitations/implicationsOne limitation is that the survey does not indicate why managers continue using less advanced capital budgeting decision techniques. A second is that choice of population may bias results to large firms in Canada.Practical implicationsThe main area for management focus is real options. Other areas for improvement are administrative procedures, using the weighted average cost of capital (WACC), adjusting the WACC for different projects or divisions, employing target or market values for weights, and not including interest expenses in project cash flows. A small proportion of managers also need to start using DCF.Originality/valueThe evaluation shows there still remains a theory‐practice gap in the detailed elements of DCF capital budgeting decision techniques, and in real options. Further, it is valuable to take stock of a concept that has been developed over a number of years. What this paper offers is a fine‐grained analysis of investment decision making, a synthesis and integration of several studies on DCF where new comparisons are made, advice to managers and thus opportunities to improve investment decision making.