bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ab initio crystal structure predictions for flexible hydrogen‐bonded molecules. Part II. Accurate energy minimization
Authors: van Eijck Bouke P. , Mooij Wijnand T. M. , Kroon Jan 
Published: August 2002

AbstractA method is described to perform ab initio energy minimization for crystals of flexible molecules. The intramolecular energies and forces are obtained directly from ab initio calculations, whereas the intermolecular contributions follow from a potential that had been parameterized earlier on highly accurate quantum‐chemical calculations. Glycol and glycerol were studied exhaustively as prototypes. Lists of hypothetical crystal structures were generated using an empirical force field, after which ab initio energy minimizations were performed for a few hundreds of these. The experimental crystal structures were found among the structures with lowest energy, provided that sufficiently large basis sets were used. Moreover, their crystal geometries were well reproduced. This approach enables a systematic comparison between the merits of force fields at various levels of sophistication. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 805–815, 2001
Density functional theory studies on the dissociation energies of metallic salts: relationship between lattice and dissociation energies
Authors: Kim Chang Kon , Won Jongok , Kim Hoon Sik , Kang Yong Soo , Li Hong Guang , Kim Chan Kyung 
Published: August 2002

AbstractThe formation and physicochemical properties of polymer electrolytes strongly depend on the lattice energy of metal salts. An indirect but efficient way to estimate the lattice energy through the relationship between the heterolytic bond dissociation and lattice energies is proposed in this work. The heterolytic bond dissociation energies for alkali metal compounds were calculated theoretically using the Density Functional Theory (DFT) of B3LYP level with 6‐311+G(d,p) and 6‐311+G(2df,p) basis sets. For transition metal compounds, the same method was employed except for using the effective core potential (ECP) of LANL2DZ and SDD on transition metals for 6‐311+G(d,p) and 6‐311+G(2df,p) calculations, respectively. The dissociation energies calculated by 6‐311+G(2df,p) basis set combined with SDD basis set were better correlated with the experimental values with average error of ca. ±1.0% than those by 6‐311+G* combined with the LANL2DZ basis set. The relationship between dissociation and lattice energies was found to be fairly linear (r>0.98). Thus, this method can be used to estimate the lattice energy of an unknown ionic compound with reasonably high accuracy. We also found that the dissociation energies of transition metal salts were relatively larger than those of alkaline metal salts for comparable ionic radii. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 827–834, 2001
Molecular dynamics simulation of the hydrocarbon region of a biomembrane using a reduced representation model
Authors: Whitehead Lewis , Edge Colin M. , Essex Jonathan W. 
Published: August 2002

AbstractThe development of a coarse‐grained reduced‐representation model of the hydrocarbon region of a biological membrane is reported. The potential is based on the popular Gay–Berne model of liquid crystals, and involves the linking of individual Gay–Berne ellipsoids by harmonic springs to form each hydrocarbon chain. Diffusion coefficients and order parameters have been calculated by molecular dynamics computer simulations for a range of parameter sets. The results clearly demonstrate the presence of a phase transition from an ordered low‐temperature solid phase reminiscent of the Lβ′ phase of phospholipids, to a high‐temperature disordered phase reminiscent of the Lα phase. Order parameters calculated for each layer of the model are consistent with the experimental segmental order parameters reported for dipalmitoyl phosphatidylcholine. The application of this model to the study of small molecule diffusion within the membrane core is proposed. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1622–1633, 2001
Polymer collapse, protein folding, and the percolation threshold
Authors: Meirovitch Hagai 
Published: August 2002

AbstractWe study the transition of polymers in the dilute regime from a swollen shape at high temperatures to their low‐temperature structures. The polymers are modeled by a single self‐avoiding walk (SAW) on a lattice for whichlof the monomers (the H monomers) are self‐attracting, i.e., if two nonbonded H monomers become nearest neighbors on the lattice they gain energy of interaction (ϵ=−∣ϵ∣); the second type of monomers, denoted P, are neutral. This HP model was suggested by Lau and Dill (Macromolecules 1989, 22, 3986–3997) to study protein folding, where H and P are the hydrophobic and polar amino acid residues, respectively. The model is simulated on the square and simple cubic (SC) lattices using the scanning method. We show that the ground state and the sharpness of the transition depend on the lattice, the fractiongof the H monomers, as well as on their arrangement along the chain. In particular, if the H monomers are distributed at random andgis larger than the site percolation threshold of the lattice, a collapsed transition is very likely to occur. This conclusion, drawn for the lattice models, is also applicable to proteins where aneffectivelattice with coordination number between that of the SC lattice and the body centered cubic lattice is defined. Thus, the average fraction of hydrophobic amino acid residues in globular proteins is found to be close to the percolation threshold of the effective lattice. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 166–171, 2002
Dynamics of a protein and water molecules surrounding the protein: Hydrogen‐bonding between vibrating water molecules and a fluctuating protein
Authors: Yoshioki Shuzo 
Published: August 2002

AbstractInternal and rigid‐body motions of bovine pancreatic trypsin inhibitor (BPTI) and of water molecules surrounding the BPTI are studied in a vicinity of an energy minimum using a normal mode analysis proposed as the independent molecule model. Water's rigid‐body motion is predominant in comparison to its internal motions. We have derived information about the relationship between the magnitude of a thermal ellipsoid of an H‐bonding atom and the anisotropy of its ellipsoid, and the relationship between the magnitude of the ellipsoid and the H‐bond strength. We see a relationship between vibrational frequencies (assuming rigid‐body motion of the water molecules) and the H‐bond strength of the water taking part in this H‐bonding. Analyzing the H‐bond strength, we found that a hydrogen in water is likely to H‐bond to oxygen in the protein, whereas an oxygen in water has a less strong preference to H‐bond to the protein. For water molecules acting as the hydrogen acceptor, strong H‐bonding has longer lifetimes than weak H‐bonding. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 402–413, 2002
Direct constructions of additive codes
Authors: Bierbrauer Jürgen 
Published: August 2002

AbstractA code isqm‐aryq‐linear if its alphabet forms anm‐dimensional vector space over 𝔽qand the code is linear over 𝔽q. Theseadditive codesform a natural generalization of linear codes. Our main results are direct constructions of certain families of additive codes. These comprise the additive generalization of the Kasami codes, an additive generalization of the Bose‐Bush construction of orthogonal arrays of strength 2 as well as a class of additive codes which are being used for deep space communication. © 2002 Wiley Periodicals, Inc. J Combin Designs 10: 207–216, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jcd.20000
The search for the holy grail: Heart rate variability and Thought Field Therapy
Authors: Herbert James D. , Gaudiano Brandon A. 
Published: August 2002

AbstractThought Field Therapy (TFT) is one of several unusual psychotherapies that have witnessed rapid growth over the past few years, despite the absence of scientific support. Promoters of TFT frequently cite changes in heart rate variability (HRV) as evidence of TFT's effects. Pignotti and Steinberg (2001) present reports of 39 cases in which HRV was assessed prior to and immediately following TFT. Serious methodological shortcomings preclude interpretation of these data with respect to either the efficacy of TFT or the clinical utility of HRV. Ethical concerns are raised about the aggressive promotion of TFT and the misuse of HRV. © 2001 John Wiley & Sons, Inc. J Clin Psychol 57: 1207–1214, 2001.
Depression in chronic medical illness: The case of coronary heart disease
Authors: Burg Matthew M. , Abrams David 
Published: August 2002

AbstractDepression is an important predictor of morbidity and mortality in patients with coronary disease, particularly after myocardial infarction, independent of previous cardiac history or CAD severity. Depression also is associated with poor long‐term psychosocial outcomes. The prevalence of major depression among post‐MI patients is 15 to 20%, with an additional 27% reporting symptoms of minor depression. This article briefly reviews the literature on depression in patients with coronary disease, including previously published efforts to treat the disorder in this group. A case review then is provided, highlighting important aspects of treatment. © 2001 John Wiley & Sons, Inc. J Clin Psychol/In Session 57: 1323–1337, 2001.
Patterns of object relations and reality testing deficits in schizophrenia: Clusters and their symptom and personality correlates
Authors: Bell Morris D. , Greig Tamasine Conway , Bryson Gary , Kaplan Edward 
Published: August 2002

AbstractBell Object Relations Reality Testing Inventory (BORRTI) profile scores were used to cluster 222 outpatients with schizophrenia or schizoaffective disorder. An eight‐cluster solution was subjected to replication analysis, and six clusters were found valid and replicable. These clusters were sorted into three pairs that were interpreted as follows: Residually Impaired consisted of Sealed‐Over Recovery and Integrated Recovery; Socially Withdrawn consisted of Socially Withdrawn and Socially Withdrawn—Autistic; and Psychotically Egocentric consisted of Psychotically Egocentric and Psychotically Egocentric—Severe. Clusters were compared on Positive and Negative Syndrome Scale ratings and on subscales from the Eysenck Personality Questionnaire. MANOVAs indicated significant differences among clusters. These differences provided further interpretations of cluster membership. Implications for the use of BORRTI profiles for treatment and rehabilitation planning are discussed. © 2001 John Wiley & Sons, Inc. J Clin Psychol 57: 1353–1367, 2001.
Regulation of expression and activity of four PKC isozymes in confluent and mechanically stimulated UMR‐108 osteoblastic cells
Authors: Geng W.D. , Boskovic G. , Fultz M.E. , Li C. , Niles R.M. , Ohno S. , Wright G.L. 
Published: August 2002

AbstractThe transcript (mRNA), protein levels, enzyme activity, and cellular localization of four protein kinase C (PKC) isozymes identified in rat osteogenic sarcoma cells (UMR‐108) were studied at confluent density and during mechanical stress (cyclic stretch). Western blot analysis indicated that growth to confluent density significantly increased the protein levels of cPKC‐α (11.6‐fold), nPKC‐δ (5.3‐fold), and nPKC‐ϵ (22.0‐fold) but not aPKC‐ζ. Northern blot analysis indicated a significant (2.3‐fold) increase in the 10 kb transcript of cPKC‐α, a slight (1.3‐fold) increase in that of nPKC‐ϵ but no detectable change in that of the remaining isozymes. Enzyme activity assays of the individually immunoprecipitated isozymes yielded detectable kinase activity only for PKC‐α, PKC‐δ, and PKC‐ϵ and only in confluent cells, corroborating the selective increase of these isozymes at confluent density. The UMR‐108 cells showed a dramatic orientation response to mechanical stress with cell reshaping and alignment of the cell long axis perpendicular to the axis of force, remodeling of the actin cytoskeleton, and the appearance of multiple peripheral sites which stained for actin, vinculin, and PKC in separate experiments. Longer term mechanical stress beyond 24 h, however, resulted in no significant change in the mRNA level, protein level, or enzyme activity of any of the four PKC isozymes investigated. The results indicate that there are isozyme‐selective increases in the protein levels of PKC isozymes of osteoblastic UMR‐108 cells upon growth to confluence which may be regulated at the transcriptional or the post‐transcriptional level. The results from UMR‐108 cells support the earlier proposal (Carvalho RS, Scott JE, Suga DM, Yen EH. 1994. J Bone Miner Res 9(7):999–1011) that PKC could be involved in the early phase of mechanotransduction in osteoblasts through the activation of focal adhesion assembly/disassembly and the remodeling of the actin cytoskeleton. © 2001 Wiley‐Liss, Inc.
Regulation of BMP‐7 expression by retinoic acid and prostaglandin E2
Authors: Paralkar V.M. , Grasser W.A. , Mansolf A.L. , Baumann A.P. , Owen T.A. , Smock S.L. , Martinovic S. , Borovecki F. , Vukicevic S. , Ke H.Z. , Thompson D.D. 
Published: August 2002

AbstractBone morphogenetic proteins (BMPs) are members of the transforming growth factor‐beta (TGF‐β) gene superfamily of growth and differentiation factors. Members of the BMP family were originally cloned and characterized by their ability to induce ectopic bone formation. Of the various BMPs cloned, the bone inductive ability of BMP‐7 (OP‐1) and BMP‐2 has been well characterized. Both BMP‐7 and ‐2 have been shown to have clinical utility in the healing of non‐union fractures. However, in spite of the various advances in BMP research, the physiological regulation of BMPs is not well understood. Here we studied the expression of BMP‐7 by cloning a 4.6‐kB fragment of the human BMP‐7 promoter (hBMP‐7p) and placing it upstream of a luciferase reporter. The promoter reporter construct was stably transfected into different cell backgrounds and its regulation by various factors was investigated. We show that retinoic acid (RA) treatment results in an upregulation of the hBMP‐7p reporter activity. This regulation of the hBMP‐7p was further confirmed by Northern blot, PCR, and Western blot analyses, which showed an increase in both BMP‐7 mRNA and protein expression upon treatment with RA. We further show that RA specifically upregulates expression of osteocalcin via activation of BMP‐7 mRNA and protein in vitro. Similarly, prostaglandin E2 (PGE2) treatment increases BMP‐7 mRNA and protein levels, but does not transcriptionally activate the hBMP‐7p. Additionally, in vivo expression of BMP‐7 in bone was increased upon PGE2 treatment. In conclusion, RA and PGE2 upregulate BMP‐7 protein expression both in vitro and in vivo. J. Cell. Physiol. 190: 207–217, 2002. © 2002 Wiley‐Liss, Inc.
Expression and targeting of the tight junction protein CLDN1 in CLDN1‐negative human breast tumor cells
Authors: Hoevel Thorsten , Macek Robert , Mundigl Olaf , Swisshelm Karen , Kubbies Manfred 
Published: August 2002

AbstractClaudins and occludin constitute the major transmembrane proteins of tight junctions (TJs). We have previously identified the human homologue of the murine Cldn1, CLDN1 (SEMP1) that is expressed in normal, mammary gland‐derived epithelial cells but is absent in most human breast cancer cell lines. To investigate the potential functions of CLDN1 protein in tumor and normal epithelial cells, we developed an I‐NGFR retroviral vector and monoclonal anti‐CLDN1 antibody. In subconfluent and confluent breast cancer cells, MDA‐MB‐435 and MDA‐MB‐361, endogenous CLDN1 expression was not detected by an anti‐CLDN1 monoclonal antibody by Western blot analysis or quantitative RT‐PCR. When CLDN1‐negative breast cancer cell lines were transduced with a CLDN1 retrovirus the cells express CLDN1 mRNA constitutively as shown by quantitative RT‐PCR. Immunofluorescence analyses of the CLDN1 retroviral transduced breast tumor cells using monoclonal antibodies against CLDN1 reveals a subcellular distribution at cell–cell contact sites similar to the CLDN1 homing pattern in T47‐D cells, which express endogenous CLDN1. This cell–cell contact co‐localization of CLDN1 was evident in CLDN1‐transduced breast tumor cells which fail to express occludin protein (MDA‐MB‐361 and MDA‐MB‐435) and express relatively little ZO‐1 protein (MDA‐MB‐435), suggesting that other proteins may be responsible for targeting of CLDN1 to cell–cell contact sites. The re‐expression of CLDN1 decreases the paracellular flux of 3 and 40 kDa dextran despite the absence of occludin in the MDA‐MB‐361 tumor cells. Our findings indicate that in CLDN1‐negative breast tumor cells, the basal protein partner requirements for physiological homing of the CLDN1 protein are intact, and that CLDN1 gene transfer and protein expression itself might be sufficient to exert a TJ‐mediate gate function in metastatic tumor cells even in the absence of other TJ‐associated proteins, such as occludin. J. Cell. Physiol. 191: 60–68, 2002. © 2002 Wiley‐Liss, Inc.
Havep53gene mutations and protein expression a different biological significance in colorectal cancer?*
Authors: Bazan Viviana , Migliavacca Manuela , Tubiolo Carla , Macaluso Marcella , Zanna Ines , Corsale Simona , Amato Antonella , Calò Valentina , Dardanoni Gabriella , Morello Vincenza , Farina Mario La , Albanese Ida , Tomasino Rosa Maria , Gebbia Nicola , Russo Antonio 
Published: August 2002

Abstractp53 alterations are considered the most common genetic events in many types of neoplasms, including colorectal carcinoma (CRC). These alterations include mutations of the gene and/or overexpression of the protein. The aim of our study was to assess whether in 160 patients undergoing resective surgery for primary operable CRC there was an association between p53 mutations and protein overexpression and between these and other biological variables, such as cell DNA content (DNA‐ploidy) and S‐phase fraction (SPF), and the traditional clinicopathological variables. p53 mutations, identified by PCR‐SSCP‐sequencing analysis, were found in 68/160 patients (43%) and positive staining for p53 protein, detected with the monoclonal antibody DO‐7, was present in 48% (77/160) of the cases, with agreement of 57% (91/160). In particular, a significant association was found between increased p53 expression and genetic alterations localized in the conserved regions of the gene or in the L3 DNA‐binding domain and the specific type of mutation. Furthermore, both overexpression of p53 and mutations in the conserved areas of the gene were found more frequently in distal than in proximal CRCs, suggesting that they might be “biologically different diseases.” Although p53 mutations in conserved areas were associated with flow cytometric variables, overexpression of p53 and mutations in its L3 domain were only related respectively to DNA‐aneuploidy and high SPF. These data may reflect the complex involvement of p53 in the different pathways regulating cell‐cycle progression. In conclusion, the combination of the mutational status and immunohistochemistry of p53, and flow cytometric data may provide an important insight into the biological features of CRCs. J. Cell. Physiol. 191: 237–246, 2002. © 2002 Wiley‐Liss, Inc.
Versatile protein tag, SUMO: Its enzymology and biological function
Authors: Kim Keun IL , Baek Sung Hee , Chung Chin Ha 
Published: August 2002

AbstractSmall ubiquitin‐related modifier (SUMO) is a member of a ubiquitin‐like protein family that regulates cellular function of a variety of target proteins. SUMO and ubiquitin are synthesized as precursors that need to be processed prior to conjugation to target proteins, and their mature forms have a similar tertiary structure. The mechanism for SUMO conjugation is also analogous to that of the ubiquitin system, such as the utilization of E1, E2, and E3 cascade enzymes. However, the biological consequence of SUMO modification is quite different from that of the ubiquitin system. Whereas ubiquitination of most proteins is for the degradative pathway, SUMO modification of target proteins is involved in nuclear protein targeting, formation of subnuclear structures, regulation of transcriptional activities or DNA binding abilities of transcription factors, and control of protein stability. This review will summarize the recent progress made in the enzymology of SUMO and its biological significance. © 2002 Wiley‐Liss, Inc.
Growth and characterization of a cell line from a human primary neuroendocrine carcinoma of the skin (Merkel cell carcinoma) in culture and as xenograft
Authors: Krasagakis Konstantin , Almond‐Roesler Brigitte , Geilen Christoph , Fimmel Sabine , Krengel Sven , Chatzaki Ekaterini , Gravanis Achille , Orfanos Constantin E. 
Published: August 2002

AbstractThe primary neuroendocrine carcinoma of the skin or Merkel cell carcinoma (MCC) is a skin tumor with aggressive biological behaviour. Experimental models for investigating the biological properties of the tumor are prerequisite for developing new therapeutic approaches. In this study, we report the establishment and characterisation of a cell line derived from the lymph‐node metastasis of a patient with highly aggressive MCC. Merkel carcinoma cells (MCC‐1) grew as floating aggregates in suspension cultures for more than two years and over 70 subcultures. The proliferation rate in suspension cultures was rather moderate with a population doubling time of 69 h. The immunocytochemical pattern of the cultured MCC‐1 was similar to that of the original tumor with expression of cytokeratin 18, neuron‐specific enolase, neurofilaments, and synaptophysin. In addition, reverse transcriptase polymerase chain reaction (RT‐PCR) revealed presence of chromogranin A mRNA in the MCC‐1 cell line. Furthermore, electron microscopy yielded the rare finding of neuroendocrine granules in the cytoplasm of the cultured cells. The cell line MCC‐1 was able to form colonies in soft agar. Nude mice developed solid tumors with similar histology to the original tumor after subcutaneous and intravenous injections of cultured MCC‐1, and malignant ascites was seen after intraperitoneal injection. Also, two MCC‐1 sublines were established by reculturing cells from the xenografts grown in vivo and immunocytochemistry confirmed their neuroendocrine origin. The MCC‐1 line may thus serve as a model for studying the biology and the metastatic potential of Merkel cell carcinoma. © 2001 Wiley‐Liss, Inc.
Bioaccumulation of palladium by Desulfovibrio desulfuricans
Authors: Yong Ping , Rowson Neil A , Farr J Peter G , Harris I Rex , Macaskie Lynne E 
Published: August 2002

AbstractPalladium uptake by resting cell suspensions of Desulfovibrio desulfuricans NCIMB 8307 was studied without or with electron donor (formate), which gave metal uptake attributable to biosorption of Pd(II) and bioreduction of Pd(II) to Pd(0), respectively. The maximum biosorption capacity of palladium (at pH 2) was up to 196 mg Pd g−1 dry cells (1.85 mmol g−1; approx 20% of the dry weight). Biosorption was to 85% of the maximum in less than 10 min and the biomass was saturated within 30 min. Biosorption of Pd(II) was greater from the chloro‐ than the ammine complex and was inhibited in the presence of excess chloride ion. Bioreductive accumulation of Pd(II) from Pd(NH3)42+ was achieved in the presence of electron donor (formate) but was also inhibited by excess Cl−. Up to 100% of Pd(II) reduction to Pd(0) was achieved within 5 min anaerobically at pH 7 and 30 min at pH 3. Pd(0) was localized on the biomass surface using electron microscopy and was characterized using energy dispersive X‐ray microanalysis (EDAX) and X‐ray diffraction analysis (XRD). Biosorption was Pd‐specific with respect to Pt and Rh using test solutions and acid (aqua regia) leachates from spent automotive catalysts. The total Pd removed from the latter was only 15%, attributable to the inhibitory effect of residual chloride ion from the acidic extractant. Pd biorecovery is limited by the need for an improved extraction technology to minimize the formation of PdCl42− in solution rather than by constraints of the Pd‐accumulating biomass.© 2002 Society of Chemical Industry