bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy
Authors: Guvench Olgun , Weiser Jörg , Shenkin Peter , Kolossváry István , Still W. Clark 
Published: October 2002

AbstractThe generalized Born/surface area (GB/SA) continuum model for solvation free energy is a fast and accurate alternative to using discrete water molecules in molecular simulations of solvated systems. However, computational studies of large solvated molecular systems such as enzyme–ligand complexes can still be computationally expensive even with continuum solvation methods simply because of the large number of atoms in the solute molecules. Because in such systems often only a relatively small portion of the system such as the ligand binding site is under study, it becomes less attractive to calculate energies and derivatives for all atoms in the system. To curtail computation while still maintaining high energetic accuracy, atoms distant from the site of interest are often frozen; that is, their coordinates are made invariant. Such frozen atoms do not require energetic and derivative updates during the course of a simulation. Herein we describe methodology and results for applying the frozen atom approach to both the generalized Born (GB) and the solvent accessible surface area (SASA) parts of the GB/SA continuum model for solvation free energy. For strictly pairwise energetic terms, such as the Coulombic and van‐der‐Waals energies, contributions from pairs of frozen atoms can be ignored. This leaves energetic differences unaffected for conformations that vary only in the positions of nonfrozen atoms. Due to the nonlocal nature of the GB analytical form, however, excluding such pairs from a GB calculation leads to unacceptable inaccuracies. To apply a frozen‐atom scheme to GB calculations, a buffer region within the frozen‐atom zone is generated based on a user‐definable cutoff distance from the nonfrozen atoms. Certain pairwise interactions between frozen atoms in the buffer region are retained in the GB computation. This allows high accuracy in conformational GB comparisons to be maintained while achieving significant savings in computational time compared to the full (nonfrozen) calculation. A similar approach for using a buffer region of frozen atoms is taken for the SASA calculation. The SASA calculation is local in nature, and thus exact SASA energies are maintained. With a buffer region of 8 Å for the frozen‐atom cases, excellent agreement in differences in energies for three different conformations of cytochrome P450 with a bound camphor ligand are obtained with respect to the nonfrozen cases. For various minimization protocols, simulations run 2 to 10.5 times faster and memory usage is reduced by a factor of 1.5 to 5. Application of the frozen atom method for GB/SA calculations thus can render computationally tractable biologically and medically important simulations such as those used to study ligand–receptor binding conformations and energies in a solvated environment. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 214–221, 2002
Hyperovals in nets of small degree
Authors: Drake David A. 
Published: October 2002

AbstractThe existence of an r‐net of order n with a hyperoval is proved for r = 5 when n ≥ 63; for r = 7 when n ≥ 84; for r = 9 when n ≥ 59,573 and for r = 15 when n ≥ 1, 873,273. © 2002 Wiley Periodicals, Inc. J Combin Designs 10: 322–334, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jcd.10018
Lotto design tables
Authors: Li P. C. , van Rees G. H. J. 
Published: October 2002

AbstractAn LD(n,k,p,t;b) lotto design is a set of b k‐sets (blocks) of an n‐set such that any p‐set intersects at least one k‐set in t or more elements. Let L(n,k,p,t) denote the minimum number of blocks in any LD(n,k,p,t;b) lotto design. We will list the known lower and upper bound theorems for lotto designs. Since many of these bounds are recursive, we will incorporate this information in a set of tables for lower and upper bounds for lotto designs with small parameters. We will also use back‐track algorithms, greedy algorithms, and simulated annealing to improve the tables. © 2002 Wiley Periodicals, Inc. J Combin Designs 10: 335–359, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jcd.10020
Mentoring relationships for youth: Investigation of a process‐oriented model
Authors: Parra Gilbert R. , DuBois David L. , Neville Helen A. , Pugh‐Lilly Aalece O. , Povinelli Nan 
Published: October 2002

AbstractWe investigated a process‐oriented model of mentoring using data on 50 relationships in a Big Brothers/Big Sisters program. Data were collected on a monthly basis from both mentors and youth over a one‐year period; relationship benefits for youth were assessed at the end of the year by each type of informant. The degree to which relationships were continued throughout the one‐year period also was assessed. Path analyses using both youth and mentor report data revealed relations among study variables consistent with the proposed model. Mentors' ratings of their efficacy, obtained prior to the start of relationships, predicted greater amounts of mentor/youth contact as well as more positive experiences in relationships (e.g., fewer obstacles). Feelings of closeness between mentors and youth, in turn, were a final common component in model pathways that linked mentor/youth contact and most other measures to greater perceived benefits and relationship continuation. Implications for the design and evaluation of mentoring programs for youth are discussed. © 2002 Wiley Periodicals, Inc.
Who supports? The providers of social support to dual‐parent families caring for young children
Authors: Miller R. Jeff , Darlington Yvonne 
Published: October 2002

AbstractPrevious research points to the importance of both kin and non‐kin ties within social networks as sources of social support. This study examines the kin and non‐kin providers of specific types of support to dual‐parent low‐income Australian families caring for young children. The study highlights the importance of family and friends as support providers. Study participants tended to rely on family, including parents, siblings and other family members, and friends for emotional and information support. Parents also tended to provide material and practical support. While neighbors and community agencies offered some emotional and information support, overall, these sources were minimal.© 2002 Wiley Periodicals, Inc.
Insights into electromagnetic interaction mechanisms
Authors: Goodman Reba , Blank Martin 
Published: October 2002

AbstractLow frequency (< 300 Hz) electromagnetic (EM) fields induce biological changes that include effects ranging from increased enzyme reaction rates to increased transcript levels for specific genes. The induction of stress gene HSP70 expression by exposure to EM fields provides insight into how EM fields interact with cells and tissues. Insights into the mechanism(s) are also provided by examination of the interaction of EM fields with moving charges and their influence on enzyme reaction rates in cell‐free systems. Biological studies with in vitro model systems have focused, in general, on the nature of the signal transduction pathways involved in response to EM fields. It is likely, however, that EM fields also interact directly with electrons in DNA to stimulate biosynthesis. Identification of an EM field‐sensitive DNA sequence in the heat shock 70 (HSP70) promoter, points to the application of EM fields in two biomedical applications: cytoprotection and gene therapy. EM field induction of the stress protein hsp70 may also provide a useful biomarker for establishing a science‐based safety standard for the design of cell phones and their transmission towers. © 2002 Wiley‐Liss, Inc.
Color doppler sonographic finding of retrograde jugular venous flow as a sign of innominate vein occlusion
Authors: Conkbayir Işik , Men Süleyman , Yanik Bahar , Hekimoğlu Baki 
Published: October 2002

AbstractOcclusion or stenosis of the superior vena cava, the innominate vein, or both is an important clinical problem that requires prompt diagnosis. To confirm a suspected occlusion, imaging studies revealing the obstruction and the presence of collateral venous routes are needed. Color Doppler sonography (CDUS) is widely used to evaluate suspected venous thrombosis and collateral pathways. We present the CDUS findings in 2 cases of innominate vein occlusion. In case 1, CDUS of the neck and left upper arm, which harbored a permanent hemodialysis access, showed engorged veins in the upper arm, a patent dialysis access, and some collateral veins in the axilla. The subclavian and internal jugular veins were patent, but the flow in the left internal jugular vein was reversed. The left innominate vein was occluded. In case 2, CDUS of the upper arms showed that the veins, the dialysis access in the left upper arm, and the subclavian and jugular veins were patent, but the flow in the left internal jugular vein and in the right subclavian vein was reversed. Collateral veins were seen in the right axillary region. Both innominate veins were occluded. The resulting collateral pathways, ie, retrograde flow in the ipsilateral jugular vein crossing to the contralateral jugular vein through dural sinuses, were confirmed by venography in both cases. © 2002 Wiley Periodicals, Inc. J Clin Ultrasound 30:392–398, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/jcu.10081
Expression and regulatory role of receptors for vasoactive intestinal peptide in bone cells
Authors: Lundberg Pernilla , Lerner Ulf H. 
Published: October 2002

AbstractAn intense network of nerve fibers can be demonstrated in skeletal tissues, not only in the periosteum but also within cortical bone, growth plate, and bone marrow. This neuro‐osteogenic network expresses a restricted number of signalling molecules, including neuropeptides, neurotransmitters, and neurotrophins. Several lines of evidence indicate that receptors for these molecules are present on bone cells and that activation of these receptors leads to changes in bone cell activities. In addition, deletion of signalling molecules has been shown to alter bone metabolism. In the present review, these studies are summarized with a focus on distribution and effects of vasoactive intestinal peptide. Microsc. Res. Tech. 58:98–103, 2002. © 2002 Wiley‐Liss, Inc.
Cell and molecular biology of human olfaction
Authors: Rawson Nancy E. , Gomez George 
Published: October 2002

AbstractProgress in our understanding of olfactory receptor physiology has progressed greatly over the past 10 years. It has become clear that many anatomical and molecular features of the peripheral aspect of the olfactory system have remained highly conserved across diverse species. Yet, this structure is responsible for conveying a wide variety of information about the environment that is necessary to the successful location of food, mates, and avoidance of danger, and it is thus not surprising that specializations have also evolved to suit the differing needs of different species. While the basic anatomical features reflect those of other mammals, functional studies of human olfactory receptor neurons have revealed physiological features both similar to and differing from those of other mammalian species. This review presents an overview of both the anatomical and physiological data describing the cell and molecular biology of the peripheral human olfactory system and how it functions in health and disease. Microsc. Res. Tech. 58:142–151, 2002. © 2002 Wiley‐Liss, Inc.
Shh‐Bmp2 signaling module and the evolutionary origin and diversification of feathers
Authors: Harris Matthew P. , Fallon John F. , Prum Richard O. 
Published: October 2002

AbstractTo examine the role of development in the origin of evolutionary novelties, we investigated the developmental mechanisms involved in the formation of a complex morphological novelty—branched feathers. We demonstrate that the anterior‐posterior expression polarity of Sonic hedgehog (Shh) and Bone morphogenetic protein 2 (Bmp2) in the primordia of feathers, avian scales, and alligator scales is conserved and phylogenetically primitive to archosaurian integumentary appendages. In feather development, derived patterns of Shh‐Bmp2 signaling are associated with the development of evolutionarily novel feather structures. Longitudinal Shh‐Bmp2 expression domains in the marginal plate epithelium between barb ridges provide a prepattern of the barbs and rachis. Thus, control of Shh‐Bmp2 signaling is a fundamental component of the mechanism determining feather form (i.e., plumulaceous vs. pennaceous structure). We show that Shh signaling is necessary for the formation and proper differentiation of a barb ridge and that it is mediated by Bmp signaling. BMP signaling is necessary and sufficient to negatively regulate Shh expression within forming feather germs and this epistatic relationship is conserved in scale morphogenesis. Ectopic SHH and BMP2 signaling leads to opposing effects on proliferation and differentiation within the feather germ, suggesting that the integrative signaling between Shh and Bmp2 is a means to regulate controlled growth and differentiation of forming skin appendages. We conclude that Shh and Bmp signaling is necessary for the formation of barb ridges in feathers and that Shh and Bmp2 signaling constitutes a functionally conserved developmental signaling module in archosaur epidermal appendage development. We propose a model in which branched feather form evolved by repeated, evolutionary re‐utilization of a Shh‐Bmp2 signaling module in new developmental contexts. Feather animation Quicktime movies can be viewed at http://fallon.anatomy.wisc.edu/feather.html. J. Exp. Zool. (Mol. Dev. Evol.) 294:160–176, 2002. © 2002 Wiley‐Liss, Inc.
Generation of stable retrovirus packaging cell lines after transduction with herpes simplex virus hybrid amplicon vectors‡
Authors: Sena‐Esteves Miguel , Hampl Jürgen A. , Camp Sara M. , Breakefield Xandra O. 
Published: October 2002

AbstractBackgroundA number of properties have relegated the use of Moloney murine leukemia virus (Mo‐MLV)‐based retrovirus vectors primarily to ex vivo protocols. Direct implantation of retrovirus producer cells can bypass some of the limitations, and in situ vector production may result in a large number of gene transfer events. However, the fibroblast nature of most retrovirus packaging cells does not provide for an effective distribution of vector producing foci in vivo, especially in the brain. Effective development of new retrovirus producer cells with enhanced biologic properties may require the testing of a large number of different cell types, and a quick and efficient method to generate them is needed.MethodsMoloney murine leukemia virus (Mo‐MLV) gag‐pol and env genes and retrovirus vector sequences carrying lacZ were cloned into different minimal HSV/AAV hybrid amplicons. Helper virus‐free amplicon vectors were used to co‐infect glioma cells in culture. Titers and stability of retrovirus vector production were assessed.ResultsSimultaneous infection of two glioma lines, Gli‐36 (human) and J3T (dog), with both types of amplicon vectors, generated stable packaging populations that produced retrovirus titers of 0.5–1.2×105 and 3.1–7.1×103 tu/ml, respectively. Alternatively, when cells were first infected with retrovirus vectors followed by infection with HyRMOVAmpho amplicon vector, stable retrovirus packaging populations were obtained from Gli‐36 and J3T cells producing retrovirus titers comparable to those obtained with a traditional retrovirus packaging cell line, ΨCRIPlacZ.ConclusionsThis amplicon vector system should facilitate generation of new types of retrovirus producer cells. Conversion of cells with migratory or tumor/tissue homing properties could result in expansion of the spatial distribution or targeting capacity, respectively, of gene delivery by retrovirus vectors in vivo. Copyright © 2002 John Wiley & Sons, Ltd.
Social funds, sustainability and institutional development impacts: findings from an OED Review
Authors: Carvalho Soniya , Perkins Gillian , White Howard 
Published: October 2002

AbstractThis paper, based on a recent OED review of World Bank social fund projects, presents findings relating to two aspects of social fund performance that have been relatively under‐researched in the social funds literature—the sustainability of benefits and the institutional development impacts. On sustainability, the review found that social fund facilities generally had staffing and equipment levels better or equal to those in comparator facilities although both types of facilities suffered from shortages. While there has been a learning curve, deficiencies were found in the requirements for ongoing operations and maintenance over the operational life of the investments. On institutional development impact, the review found that social fund agencies have developed capacity as effective and innovative organizations. Wider impacts on existing institutions, both positive and negative, need greater attention. Copyright © 2002 John Wiley & Sons, Ltd.
The impact of market reforms on the Senegalese peanut economy
Authors: Hathie Ibrahima , Lopez Rigoberto A. 
Published: October 2002

AbstractThis article assesses the welfare impacts of structural adjustment‐induced peanut market reforms in Senegal. In the pre‐reform period, by keeping peanut prices low, price regulation favoured urban dwellers and processors to the detriment of farmers, although the latter benefited from subsidized credit and inputs. With the reforms, peanut prices increased but the ensuing benefits to farmers were outweighed by higher production costs. Consumers gained due to access to cheaper, imported vegetable oil and processors lost due to excess capacity from lower peanut production. Overall, social welfare decreased illustrating that unfettered market reforms can be detrimental when supportive market institutions are eliminated without addressing alternatives. Copyright © 2002 John Wiley & Sons, Ltd.
Synthesis of 15N and 13C selectively labeled anandamide
Authors: Xie Xiang‐Qun , Yang Hongqin , Choi Greg , Lin Sunyuan , Makriyannis Alexandros 
Published: October 2002

AbstractAnandamide (Figure 1a) (arachidonyl ethanolamide, AEA), (5Z,8Z,11Z,14Z)‐N‐(2‐hydroxyethyl)‐5,8,11,14‐Eicosatetraenamide, is an endogenous cannabinoid ligand possessing important biological activity. The conformation of AEA in its native receptor binding environment is particularly of interest for pharmaceutical research and biochemistry in general. Here we report a novel synthetic pathway, which selectively introduces 15N and 13C isotopes into the anandamide molecule. This isotopically labeled AEA can be studied conformationally in its native binding condition via solid state NMR. These synthetic procedures can also be adapted to produce radioactive ligands for receptor binding assays and other structural studies. Copyright © 2002 John Wiley & Sons, Ltd.
Spoiled gradient‐echo as an arterial spin tagging technique for quick evaluation of local perfusion
Authors: Chai Jyh‐Wen , Chen Jeon‐Hor , Kao Yi‐Hsuan , Liao Jan‐Ray , Chen Clayton Chi‐Chang , Lee San‐Kan , Chu Woei Chyn 
Published: October 2002

AbstractPurposeTo introduce a simple gradient‐echo arterial spin tagging (GREAST) technique available for most commercial magnetic resonance (MR) systems, for a quick evaluation of tissue perfusion.Materials and MethodsThe GREAST technique uses a combination of a short TR spoiled gradient‐echo (SPGR) sequence with a selective presaturation radio frequency (RF) pulse that allows acquiring each tagged and control image within 10–20 seconds. The phantom and human studies were performed for evaluating the feasibility in measurement of local perfusion and the efficacy in alleviation of the asymmetric magnetization transfer (MT) and slice profile effects.ResultsResults show a good linear relationship between the signal attenuation caused by the presaturation pulse and flow rates in the phantom experiment and effective alleviation of the asymmetric MT and slice profile effects for various orientations of imaging slices. Human studies showed good perfusion results in brain imaging. Perfusion imaging on the liver and kidney were also conducted. The results could be significantly improved by effectively lessening motion‐related artifacts.ConclusionThe GREAST technique is simple, easy to use, and applicable to examine local perfusion of the brain and other organs in the trunk. J. Magn. Reson. Imaging 2002;16:51–59. © 2002 Wiley‐Liss, Inc.
MR imaging of the forefoot under weight‐bearing conditions: Position‐related changes of the neurovascular bundles and the metatarsal heads in asymptomatic volunteers
Authors: Weishaupt Dominik , Treiber Karl , Jacob Hilaire A.C. , Kundert Hans‐Peter , Hodler Juerg , Marincek Borut , Zanetti Marco 
Published: October 2002

AbstractPurposeTo assess practicability of weight‐bearing magnetic resonance (MR) imaging of the forefoot, and to demonstrate position‐related changes of the neurovascular bundles and the metatarsal heads in asymptomatic volunteers.Materials and MethodsWith an open‐configuration MR system, 32 feet of 32 asymptomatic individuals aged 20–60 years were studied in supine and weight‐bearing body positions. Transverse T1‐weighted spin‐echo MR images were performed. MR images were evaluated qualitatively with regard to image quality, visibility, and position‐dependent changes of the neurovascular bundle. In addition, the position of the metatarsal heads was analyzed quantitatively.ResultsWeight‐bearing MR imaging was feasible in all 32 feet. Quality of MR images obtained in the weight‐bearing position was superior to that obtained in the supine position (P < 0.05). A change in the position of the neurovascular bundle from below a virtual line paralleling the plantar cortical line to above this line was present in 50 of 61 instances (82%) between the supine and the weight‐bearing positions. When changing from the supine to the weight‐bearing position, there was a significant decrease in the distance between the plantar skin and the metatarsal heads for the second (mean 4.5 mm), third (mean 4.4 mm), and fourth metatarsal heads (mean 3.7 mm) (P < 0.0001). However, the difference for the first (mean 0.5 mm) and fifth (mean 0.9 mm) metatarsal heads was not significant.ConclusionWeight‐bearing MR imaging of the forefoot is feasible using an open‐configuration MR system and demonstrates position‐related changes of the neurovascular bundles relative to the metatarsal heads, as well as position‐related changes of the metatarsal heads themselves. J. Magn. Reson. Imaging 2002;16:75–84. © 2002 Wiley‐Liss, Inc.