bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classification of scientific networks using aggregated journal‐journal citation relations in the Journal Citation Reports
Authors: Chen C.‐M. 
Published: August 2008

AbstractI propose an approach to classifying scientific networks in terms of aggregated journal‐journal citation relations of the ISI Journal Citation Reports using the affinity propagation method. This algorithm is applied to obtain the classification of SCI and SSCI journals by minimizing intracategory journal‐journal (J‐J) distances in the database, where distance between journals is calculated from the similarity of their annual citation patterns with a cutoff parameter, t, to restrain the maximal J‐J distance. As demonstrated in the classification of SCI journals, classification of scientific networks with different resolution is possible by choosing proper values of t. Twenty journal categories in SCI are found to be stable despite a difference of an order of magnitude in t. In our classifications, the level of specificity of a category can be found by looking at its value of $\overline D $RJ (the average distance of members of a category to its representative journal), and relatedness of category members is implied by the value of $\overline D $J‐J (the average J‐J distance within a category). Our results are consistent with the ISI classification scheme, and the level of relatedness for most categories in our classification is higher than their counterpart in the ISI classification scheme.
Net energy and strategic decision‐making
Authors: Poldy Franzi 
Published: August 2008

AbstractRecent calls for the dismissal of net energy are based on an inadequate understanding of the concept and are profoundly mistaken. Net energy captures one of the most important characteristics of an energy resource, and is central to strategic thinking about long‐term energy futures. Net energy relates the economy's need for energy to the energy expenditure required to meet that need. It determines the relative size of the energy sector in the economy. With high‐net‐energy fossil resources under threat, the strategic challenge is to find alternatives with comparable net energies. The calls for the dismissal of net energy are based on a number of misunderstandings about the treatment of primary and fossil resources in the calculation. Underlying them is a concern with the introduction of alternative fuels in the current economy rather than with the nature of energy supply in a post‐fossil world. This is a legitimate concern that may well require other metrics, but it is not a reason to dismiss net energy. © 2008 Society of Chemical Industry and John Wiley & Sons, Ltd
Role of non‐coding RNAs in neurodegeneration and stress response in Drosophila
Authors: Savvateeva‐Popova Elena , Medvedeva Anna , Popov Andrei , Evgen'ev Michael 
Published: August 2008

AbstractThe inherent limitations of genetic analysis in humans and other mammals as well as striking conservation of most genes controlling nervous system functioning in flies and mammals made Drosophila an attractive model to investigate various aspects of brain diseases. Since RNA research has made great progress in recent years here we present an overview of studies demonstrating the role of various non‐coding RNAs in neurodegeneration and stress response in Drosophila as a model organism. We put special emphasis on the role of non‐coding micro RNAs, hsr‐omega transcripts, and artificial small highly structured RNAs as triggers of neuropathology including aggregates formation, cognitive abnormalities and other symptoms. Cellular stress is a conspicuous feature of many neurodegenerative diseases and the production of specialized proteins protects the nerve cells against aggregates formation. Therefore, herein we describe some data implicating various classes of non‐coding RNAs in stress response in Drosophila. All these findings highlight Drosophila as an important model system to investigate various brain diseases potentially mediated by some non‐coding RNAs including polyglutamine diseases, Alzheimer's disease, Huntigton's disease, and many others.
Microanatomical study on the functional origin and direction of the thoracodorsal nerve from the trunks of brachial plexus
Authors: Lu Wei , Xu Jian‐Guang , Wang Da‐Ping , Gu Yu‐Dong 
Published: August 2008

AbstractIpsilateral C7 nerve root transfer or neurotization has been used for the repair of brachial plexus avulsions. In this procedure, the ipsilateral C7 nerve root is used as a donor nerve and is implanted into the damaged nerve of the brachial plexus in order to reinnervate distal muscles. However, this procedure may result in unintended injury to the thoracodorsal nerve, which receives motor fascicles form the cervical nerves of C6, C7, and C8, but mainly from C7. Damage to the thoracodorsal nerve ultimately results in weakness or paralysis of the latissimus dorsi muscle, which it innervates. In the present study, 20 adult cadaveric brachial plexus specimens and 3 fresh specimens were dissected using microscopy. The origin and direction of motor fascicles from the three trunks of the brachial plexus to the thoracodorsal nerve were investigated. Motor fiber counts of C7 and the thoracodorsal nerve were also performed. Several observations can be made: (1) The origin of the thoracodorsal nerve can be divided into three types: Type A, the thoracodorsal nerve originated from the superior and middle trunks; Type B, the thoracodorsal nerve originated from the inferior and middle trunks; and Type C, the thoracodorsal nerve originated from all three trunks. (2) More than 52% of the motor fibers in the thoracodorsal nerve originated in the C7 nerve root. (3) Motor fascicles from C7 to the thoracodorsal nerve were mostly localized in the posterior‐interanl part of C7 at the trunk‐division boundary. In conclusion, we suggest that: (1) Because of variation in the origin of the thoracodorsal nerve, electromyography should be routinely performed intraoperatively during C7 nerve root transfer to determine the origin type and avoid thoracodorsal fascicle injury. (2) Preservation of the posterior‐internal part of C7 (selective C7 transfer) can protect thoracodorsal nerve fascicles from damage and prevent postoperative dysfunction of the latissimus dorsi muscle. Clin. Anat. 21:509–513, 2008. © 2008 Wiley‐Liss, Inc.
Tracheobronchial variations in Turkish population
Authors: Beder Sumru , Küpeli̇ Eli̇f , Karnak Demet , Kayacan Oya 
Published: August 2008

AbstractThe tracheobronchial tree exhibits highly individualistic features and many variations. As the anatomic variations among Turkish population have not been studied previously, we aimed to evaluate the type and frequency of tracheobronchial variations (TBVs) in our bronchoscopy population. In a 3‐year period, 1,114 patients underwent flexible bronchoscopy (FB). Among these, 780 (70%) were male. The mean age of the patients was 51.3 ± 15.1 (range: 17–84) years. In 639 cases, no TBV were detected. A total of 999 TBV were observed in 475 patients. Of all, 71.3% (713) of the total TBV were detected in males. Forty‐nine and six‐tenths percent (49.6%) of the TBV were observed on the right bronchial system, 49.2% on the left, and 1.2% in the trachea. The five most frequently observed TBV were right lower lobe basal orifice with two subsegments, left lower lobe basal orifice with two subsegments, left upper lobe with three segments, right upper lobe with two segments, and right lower lobe with a subapical segment. In the same lobe bronchus, single variation and two different TBV were seen in 85% and 15% of patients, respectively. Number of TBV increased linearly with the number of lobes involved. The availability and popularity of FB in recent years has led to the increase in identification and reporting of TBV. TBV should be correctly identified and documented. This information is invaluable during follow‐up bronchoscopies as well as lung resection. Clin. Anat. 21:531–538, 2008. © 2008 Wiley‐Liss, Inc.
Membrane protein analysis of human breast cancer cell line MCF‐7 by different membrane washing methods
Authors: Ruan Yusong , Pei Weijing , Wan Mingxi 
Published: August 2008

AbstractMembrane and membrane‐associated proteins are rich in known or potential pharmaceutical drug targets for carcinogenesis. In order to systemically analyze membrane proteins of human breast cancer, we isolated membrane from MCF‐7 cells by sequential extraction by washing with three different buffers, namely, phosphate buffer (5 mM, pH 8.0), Tris (40 mM, pH 9.5), and sodium carbonate (100 mM pH 11). The extracted proteins were separated by two‐dimensional gel electrophoresis (2‐DE) using cup‐loading and were then analyzed by peptide mass fingerprinting (PMF). A total of 137 spots from the gels of the three procedures were successfully identified. They corresponded to 79 distinct proteins. Among them, 22 exclusive proteins belonging to each washing procedure were also found, including P‐glycoprotein, endoplasmin, Stress‐70 protein, ADAM 10, protein disulfide isomerase, and glutamate receptor. These results indicate phosphate buffer to be the most beneficial for enrichment of peripheral membrane proteins, and sodium carbonate is beneficial for the presentation of integral membrane proteins but usually with poor resolution. The reference maps and identified proteins will serve as a basis for the further investigation of breast cancer, especially the proteomic comparison among different cell types of breast cancer, or among the different stages in the drug interfering process of the MCF‐7 cell line. Copyright © 2008 John Wiley & Sons, Ltd.
Analysis of CRE‐mediated recombination driven by myosin light chain 1/3 regulatory elements in embryonic and adult skeletal muscle: A tool to study fiber specification
Authors: Mourkioti Foteini , Slonimsky Esfir , Huth Marion , Berno Valeria , Rosenthal Nadia 
Published: August 2008

AbstractAn increasing number of genes have been implicated in skeletal muscle fiber diversity. To study the contribution of diverse genetic elements to the regulation of fiber‐type composition, we generated a transgenic mouse in which CRE recombinase expression is driven by muscle‐specific regulatory sequences of the myosin light chain 1/3 locus (MLC). Using ROSA26 conditional reporter mice, we detected expression of the MLC‐Cre transgene starting from embryonic day 12.5 (E12.5). By E15, recombination was detected in all muscle‐derived structures. Immunohistochemical analysis revealed CRE activity was restricted to fast‐twitch (type II) and excluded from slow‐twitch (type I) fibers of skeletal muscle. The MLC‐Cre transgenic mouse can be used in conjunction with conditional alleles to study both developmental patterning and maintenance of fast fiber‐type phenotypes. genesis 46:424–430, 2008. © 2008 Wiley‐Liss, Inc.
Anisotropic mesh adaption for time‐dependent problems
Authors: Micheletti S. , Perotto S. 
Published: August 2008

AbstractWe propose a space–time adaptive procedure for a model parabolic problem based on a theoretically sound anisotropic a posteriori error analysis. A space–time finite element scheme (continuous in space but discontinuous in time) is employed to discretize this problem, thus allowing for non‐matching meshes at different time levels. Copyright © 2008 John Wiley & Sons, Ltd.
A convective weakly viscoelastic rotating flow with pressure Neumann condition
Authors: Claeyssen Julio R. , Asenjo Elba Bravo , Rubio Obidio 
Published: August 2008

AbstractThe objective of this work is to investigate through the numeric simulation, the effects of the weakly viscoelastic flow within a rotating rectangular duct subject to a buoyancy force due to the heating of one of the walls of the duct. A direct velocity–pressure algorithm in primitive variables with a Neumann condition for the pressure is employed. The spatial discretization is made with finite central differences on a staggered grid. The pressure field is directly updated without any iteration. Numerical simulations were done for several Weissemberg numbers (We) and Grashof numbers (Gr) . The numerical results show that for high Weissemberg numbers (We>7.4 × 10−5) and for ducts with aspect ratio 2:1 and 8:1, the secondary flow is restabilized with a stretched double vortex configuration. It is also observed that when the Grashof number is increased (Gr>17 × 10−4) , the buoyancy force neutralizes the effects of the Coriolis force for ducts with aspect ratio 8:1. Copyright © 2008 John Wiley & Sons, Ltd.
A high‐resolution wetting and drying algorithm for free‐surface hydrodynamics
Authors: Casulli Vincenzo 
Published: August 2008

AbstractA new wetting and drying algorithm for numerical modeling free‐surface flows is proposed and analyzed. A well structured, mildly nonlinear system for the discrete water surface elevation is derived from the governing differential equations by requiring a correct mass balance in wet areas as well as in the region of transition from wet to dry and from dry to wet. Existence and uniqueness of the numerical solution, along with a convergence analysis of an iterative scheme for the mildly nonlinear system, is provided. The present algorithm is devised to use high‐resolution bathymetric data at subgrid level. The resulting model is quite efficient, does not require a threshold value for minimal water depth, does not produce un‐physical negative water depths and generates accurate results with relatively coarse mesh and large time step size. These features are illustrated on a severe test‐case with known analytical solution. Copyright © 2008 John Wiley & Sons, Ltd.
The measurement of efficiency and productivity of health care delivery
Authors: Hollingsworth Bruce 
Published: August 2008

AbstractThe measurement of efficiency and productivity of health service delivery has become a small industry. This is a review of 317 published papers on frontier efficiency measurement. The techniques used are mainly based on non‐parametric data envelopment analysis, but there is increasing use of parametric techniques, such as stochastic frontier analysis. Applications to hospitals and other health care organizations and areas are reviewed and summarised, and some meta‐type analysis undertaken. Cautious conclusions are that public provision may be potentially more efficient than private, in certain settings. The paper also considers conceptualizations of efficiency, and points to dangers and opportunities in generating such information. Finally, some criteria for assessing the use and usefulness of efficiency studies are established, with a view to helping both researchers and those assessing whether or not to act upon published results. Copyright © 2008 John Wiley & Sons, Ltd.
Fluorescence lifetime optical projection tomography
Authors: McGinty James , Tahir Khadija B. , Laine Romain , Talbot Clifford B. , Dunsby Christopher , Neil Mark A. A. , Quintana Laura , Swoger James , Sharpe James , French Paul M. W. 
Published: August 2008

AbstractWe describe a quantitative fluorescence projection tomography technique which measures the 3‐D fluorescence lifetime distribution in optically cleared specimens up 1 cm in diameter. This is achieved by acquiring a series of wide‐field time‐gated images at different relative time delays with respect to a train of excitation pulses, at a number of projection angles. For each time delay, the 3‐D time‐gated intensity distribution is reconstructed using a filtered back projection algorithm and the fluorescence lifetime subsequently determined for each reconstructed horizontal plane by iterative fitting to a mono‐exponential decay. Due to its inherently ratiometric nature, fluorescence lifetime is robust against intensity based artefacts as well as producing a quantitative measure of the fluorescence signal. We present a 3‐D fluorescence lifetime reconstruction of a mouse embryo labelled with an alexa‐488 conjugated antibody targeted to the neurofilament, which clearly differentiates between the extrinsic label and the autofluorescence, particularly from the heart and dorsal aorta. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Expression of Sox and fibrillar collagen genes in lamprey larval chondrogenesis with implications for the evolution of vertebrate cartilage
Authors: Ohtani Kaoru , Yao Tuoya , Kobayashi Mari , Kusakabe Rie , Kuratani Shigeru , Wada Hiroshi 
Published: August 2008

AbstractLampreys possess unique types of cartilage in which elastin‐like proteins are the dominant matrix component, whereas gnathostome cartilage is mainly composed of fibrillar collagen. Despite the differences in protein composition, the Sox–col2a1 genetic cascade was suggested to be conserved between lamprey pharyngeal cartilage and gnathostome cartilage. We examined whether the cascade is conserved in another type of lamprey cartilage, the trabecular cartilage. We found that SoxD and SoxE are expressed in both trabecular and pharyngeal cartilages. However, trabecular cartilage shows no clade A fibrillar collagen gene expression, including genes expressed in pharyngeal cartilage of this animal. On the basis of these observations, we propose that lampreys possess an ancestral type of cartilage that is similar to amphioxus gill cartilage, and in this respect, gnathostome cartilage can be regarded as derived for the loss of elastin‐like protein as a cartilage component and recruitment of fibrillar collagen, which is included as a minor component in the ancestral cartilage, as the main component. J. Exp. Zool. (Mol. Dev. Evol.) 310B:596–607, 2008. © 2008 Wiley‐Liss, Inc.
An innovative approach to supporting hospitalist physicians towards academic success
Authors: Howell Eric , Kravet Steven , Kisuule Flora , Wright Scott M. 
Published: August 2008

AbstractBACKGROUND:Academic hospitalist physicians face significant challenges that may threaten their chances for successful and timely promotions, such as heavy clinical workloads, limited training in research, and relatively few experienced mentors in their field. The appreciable growth of hospital medicine groups in recent years, as has occurred at our institution, compounds the predicament by diluting the limited resources that are available to support these physicians.METHODS:A needs assessment was followed by the development of specific objectives for the division and for individual members of the division related to academic success. The resulting 3‐pronged strategy to support the academic success of our group was based on securing strong mentorship, investing requisite resources, and committing to recruit fellowship‐trained new faculty.RESULTS:To date, the initiative has resulted in an increased number of peer‐reviewed publication and grants, as well as national leadership roles for division members. Journal of Hospital Medicine 2008;3:314–318. © 2008 Society of Hospital Medicine.
Approach to and management of the acute stroke patient with atrial fibrillation: A literature review
Authors: Marmagkiolis Konstantinos , Nikolaidis Ioannis G. , Politis Themos , Goldstein Lawrence 
Published: August 2008

AbstractStroke remains an increasing worldwide cause of disability and mortality, and it is the second leading cause of death in industrialized countries.1 Patients with atrial fibrillation form a unique group with increased risk of cardioembolic stroke. Despite the widespread application of the National Institutes of Health stroke scale and guidelines,2, 3 patients with atrial fibrillation represent a clinically challenging group that deserves a special approach during the acute stroke phase.The mechanism of stroke in these patients is either cardioembolic [especially with an international normalized ratio (INR) < 2.0] or hemorrhagic (especially with INR > 5.0)4, 5 (Figure 1). Atrial fibrillation with valvular heart disease significantly increases the risk for ischemic stroke. Specifically, patients with mitral stenosis who develop atrial fibrillation increase their risk of cardioembolism by 3 to 7 times.6 Many patients with atrial fibrillation still develop ischemic or hemorrhagic stroke despite appropriate use of anticoagulation. Prior stroke, transient ischemic attacks, congestive heart failure, hypertension, age > 75, and diabetes mellitus are all well‐established risk factors for the development of stroke in patients with atrial fibrillation.7, 8 The CHADS‐2 score is the most widely studied and clinically used method for stratifying patients with nonrheumatic atrial fibrillation.8 In our review, we present the most recent clinical guidelines and trends for the approach to and management of this patient group. Journal of Hospital Medicine 2008;3:326–332. © 2008 Society of Hospital Medicine.
Mode of action of antimicrobial peptide P45 on Listeria monocytogenes
Authors: Sirtori Lisana Reginini , Motta Amanda de Souza da , Brandelli Adriano 
Published: August 2008

AbstractThe mode of action of an antimicrobial peptide produced by Bacillus sp. P45 isolated from the intestine of the Amazonian basin fish Piaractus mesopotamicus was investigated. The antimicrobial peptide was purified from culture supernatants by precipitation with ammonium sulfate and gel filtration chromatography. The peptide has an EC50 of 300 AU (activity units) ml–1 and kills all viable cells of Listeria monocytogenes with a concentration of 800 AU ml–1. A decrease in OD was observed when L. monocytogenes cultures were treated with the peptide, suggesting that cells were lysed. Transmission electron microscopy showed damage of the cell envelope and loss of protoplasmic material. The peptide P45 was bactericidal and bacteriolytic to L. monocytogenes. There is evidence that the mode of action is interefering at cell membranes and the cell wall. The knowledge of the mode of action of antimicrobial peptides is an essential step to consider their utilization in food or clinic. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Archaeal diversity in acid mine drainage from Dabaoshan Mine, China
Authors: Qiu Guan‐zhou , Wan Min‐xi , Qian Lin , Huang Zhi‐ying , Liu Kai , Liu Xue‐duan , Shi Wu‐yang , Yang Yu 
Published: August 2008

AbstractThree acid mine drainage (AMD) samples collected from Dabaoshan Mine (Guangdong Province, China) were studied. In addition to physicochemical analyses, the diversity and community structures of the archaeal communities in these samples were described at the genetic level by amplified ribosomal DNA restriction analysis (ARDRA). Nine different ARDRA patterns were obtained from 146 clones and were studied as operational taxonomic units (OTUs), which were re‐amplified and sequenced. Sequence data and phylogenetic analysis showed that most of the clones belonged to the Thermoplasmatales, and that archaea belonging to the Sulfolobales were absent. Only 1 OTU attributed to Ferroplasma was found and was observed to be abundant in all 3 samples. Eight OTUs were related to 2 new undefined groups in the Thermoplasmatales. Of the 8 OTUs, the clones in 2 similar units were isolated from samples collected from an abandoned sulfide mine (Huelva, Spain) and those in 5 similar units were isolated from samples collected from a closed copper mine (Tonglushan, China). These diversities were characterized by the reciprocal of Simpson's index (1/D) and correlated with the concentrations of ferrous ions and toxic ions in the AMD samples. The high temperature of the sampling sites was one of the factors that could explain why archaea belonging to the Thermoplasmatales were abundant in the analyzed AMD samples while those belonging to the Sulfolobales were absent. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)