bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer
Authors: Król Marcin 
Published: March 2003

AbstractThe present study tests performance of different solvation models applied to molecular dynamics simulation of a large, dimeric protein molecule. Analytical Continuum Electrostatics (ACE) with two different parameter sets, older V98 and new V01, and Effective Energy Function (EEF) are employed in molecular dynamics simulation of immunoglobulin G (IgG) light chain dimer and variable domain of IgG light chain. Results are compared with explicit solvent and distance dependent dielectric constant (DDE) calculations. The overall analysis shows that the EEF method yields results comparable to explicit solvent simulations; however, the stability of simulations is lower. On the other hand, the ACE_V98 model does not seem to achieve the accuracy or stability expected in nanosecond timescale MD simulation for the studied systems. The ACE_V01 model greatly improves stability of the calculation; nonetheless, changes in radius of gyration and solvent accessible surface of the studied systems may indicate that the parameter set still needs to be improved if the method is supposed to be used for simulations of large, polymeric proteins. Additionally, electrostatic contribution to the solvation free energy calculated in the ACE model is compared with a numerical treatment of the dielectric continuum model. Wall clock time of all simulations is compared. It shows that EEF calculation is six times faster than corresponding ACE and 50 times faster than explicit solvent simulations. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 531–546, 2003
Dual‐level direct dynamics studies for the reactions of dimethyl ether with hydrogen atom and methyl radical
Authors: Wu Jia‐Yan , Liu Jing‐Yao , Li Ze‐Sheng , Huang Xu‐Ri , Sun Chia‐Chung 
Published: March 2003

AbstractThe dual‐level direct dynamics approach is employed to study the dynamics of the CH3OCH3 + H (R1) and CH3OCH3 + CH3 (R2) reactions. Low‐level calculations of the potential energy surface are carried out at the MP2/6‐311+G(d,p) level of theory. High‐level energetic information is obtained at the QCISD(T) level of theory with the 6‐311+G(3df,3pd) basis set. The dynamics calculations are performed using variational transition state theory (VTST) with the interpolated single‐point energies (ISPE) method, and small‐curvature tunneling (SCT) is included. It is shown that the reaction of CH3OCH3 with H (R1) may proceed much easier and with a lower barrier height than the reaction with CH3 radical (R2). The calculated rate constants and activation energies are in good agreement with the experimental values. The calculated rate constants are fitted to kR1 = 1.16 × 10−19 T3 exp(−1922/T) and kR2 = 1.66 × 10−28 T5 exp(−3086/T) cm3 mol−1 s−1 over a temperature range 207–2100 K. Furthermore, a small variational effect and large tunneling effect in the lower temperature range are found for the two reactions. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 593–600, 2003
Systematic errors in DFT calculations of haloalkane heats of formation
Authors: Cloud C. F. , Schwartz M. 
Published: March 2003

AbstractThe B3LYP and B3PW91 density functionals were employed with a large [BS1 = 6‐311+G(3df,2p)] and small [BS2 = 6‐311G(d,p)] basis set to compute enthalpies of formation (at optimized MP2/6‐31G(d) geometries and with scaled HF/6‐31G(d) frequencies) in the following series of haloalkanes: (1) the 15 fluoro‐, chloro‐, and chlorofluoromethanes, (2) the 18 fluorinated and chlorinated ethanes. Similar to earlier higher level calculations on haloalkanes, the computed enthalpies exhibited very large, systematic deviations from experiment. It was found that these errors could be largely eliminated using a very simple Bond Additivity Correction (BAC) formula, ΔfH°(BAC) = ΔfH°(calc) − nCX · ΔCX [X = F, Cl], in which the BAC parameters, ΔCF and ΔCCl were determined by fitting the equation to experimental data on the four fluoroethanes and chloroethanes, respectively. The resultant BAC corrected enthalpies of formation are in excellent agreement with experiment, with RMS deviations in the same range as quoted RMS errors in measured enthalpies. Therefore, this simple BAC procedure may be utilized to provide reliable semiquantitative estimates of enthalpies of formation in larger haloalkanes, for which higher level ab initio calculations are not feasible. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 640–646, 2003
Use of the Coping Inventory for Stressful Situations in a clinically depressed sample: Factor structure, personality correlates, and prediction of distress
Authors: McWilliams Lachlan A. , Cox Brian J. , Enns Murray W. 
Published: March 2003

AbstractThe Coping Inventory for Stressful Situations (CISS; Endler & Parker, 1990) is a self‐report measure of Emotion‐, Task‐, and Avoidance‐oriented coping. The psychometric properties of the CISS were evaluated in a large sample of outpatients with major depressive disorder (N = 298). The CISS scales demonstrated good reliability and support for their factorial validity was obtained. Relationships between the CISS scales and the broad personality domains from the five‐factor model of personality, as well as two measures of emotional distress, were examined. Less‐adaptive coping strategies (i.e., Emotion‐oriented coping) were associated with less‐adaptive personality traits (i.e., Neuroticism) and with psychological distress (i.e., Depression), whereas the reverse was found regarding adaptive coping strategies (i.e., Task‐orientated coping). The incremental validity of the CISS was demonstrated by multiple‐regression analyses that found two CISS scales accounted for significant variance in psychological distress beyond that contributed by the demographic and personality variables. © 2003 Wiley Periodicals, Inc. J Clin Psychol 59: 423–437, 2003.
Marlowe–Crowne Social Desirability Scale and short Form C: Forensic norms
Authors: Andrews Paul , Meyer Robert G. 
Published: March 2003

AbstractMarlowe–Crowne Social Desirability Scale (MC) (Crowne & Marlowe, 1960) scores were collected on 1096 individuals involved in forensic evaluations. No prior publication of forensic norms was found for this instrument, which provides a measure of biased self‐presentation (dissimulation). MC mean score was 19.42 for the sample. Also calculated was the score on Form C (MC‐C) (Reynolds, 1982), and the mean for this 13‐item scale was 7.61. The scores for the current sample generally are higher than those published for non‐forensic groups, and statistical analysis indicated the difference was significant for both the MC and MC‐C (d = .75 and .70, respectively, p < .001). Neither gender nor educational level proved to be significant factors in accounting for variance, and age did not appear to be correlated with scores. Group membership of subjects based on referral reason (family violence, abuse, neglect, competency, disability) was significant for both the MC and MC‐C scores. Results suggest the MC or MC‐C can be useful as part of a forensic‐assessment battery to measure biased self‐presentation. © 2003 Wiley Periodicals, Inc. J Clin Psychol 59: 483–492, 2003.
Prospects for tooth regeneration in the 21st century: A perspective
Authors: Chai Yang , Slavkin Harold C. 
Published: March 2003

AbstractThe prospects for tooth regeneration in the 21st century are compelling. Using the foundations of experimental embryology, developmental and molecular biology, the principles of biomimetics (the mimicking of biological processes), tooth regeneration is becoming a realistic possibility within the next few decades. The cellular, molecular, and developmental “rules” for tooth morphogenesis are rapidly being discovered. The knowledge gained from adult stem cell biology, especially associated with dentin, cartilage, and bone tissue regeneration, provides additional opportunities for eventual tooth organogenesis. The centuries of tooth development using xenotransplantation, allotransplantation, and autotransplantation have resulted in many important insights that can enhance tooth regeneration. In considering the future, several lines of evidence need to be considered: (1) enamel organ epithelia and dental papilla mesenchyme tissues contain stem cells during postnatal stages of life; (2) late cap stage and bell stage tooth organs contain stem cells; (3) odontogenic adult stem cells respond to mechanical as well as chemical “signals”; (4) presumably adult bone marrow as well as dental pulp tissues contain “odontogenic” stem cells; and (5) epithelial‐mesenchymal interactions are pre‐requisite for tooth regeneration. The authors express “guarded enthusiasm,” yet there should be little doubt that adult stem cell–mediated tooth regeneration will be realized in the not too distant future. The prospects for tooth regeneration could be realized in the next few decades and could be rapidly utilized to improve the quality of human life in many nations around the world. Microsc. Res. Tech. 60:469–479, 2003. © 2003 Wiley‐Liss, Inc.
Regeneration of periodontal Ruffini endings in adults and neonates
Authors: Wakisaka Satoshi , Atsumi Yukako 
Published: March 2003

AbstractWe reviewed the regeneration of periodontal Ruffini endings, primary mechanoreceptors in the periodontal ligament, following injury to the inferior alveolar nerve (IAN) in adult and neonatal rats. Morphologically, mature Ruffini endings are characterized by an extensive arborization of axonal terminals and association with specialized Schwann cells, called lamellar or terminal Schwann cells. Following injury to IAN in the adult, the periodontal Ruffini endings of the rat lower incisor ligament regenerate more rapidly than Ruffini endings in other tissues. During regeneration, terminal Schwann cells migrate into regions where they are never found under normal conditions. The development of periodontal Ruffini endings of the rat incisor is closely associated with the eruption of the teeth; the morphology and distribution of the terminal Schwann cells became almost identical to those in adults during postnatal days 15–18 (PN 15–18d) when the first molars appear in the oral cavity, while the axonal elements showed extensive ramification around PN 28d when the functional occlusion commences. When the IAN was injured in neonates, the regeneration of periodontal Ruffini endings was delayed compared with the adults. The migration of terminal Schwann cells is also observed following IAN injury, after which the distribution of terminal Schwann cells became almost identical to that of the adults, i.e., PN 14d. Since the interaction between axon and Schwann cell is important during regeneration and development, further studies are required to elucidate its molecular mechanism during the regeneration as well as the development of the periodontal Ruffini endings. Microsc. Res. Tech. 60:516–527, 2003. © 2003 Wiley‐Liss, Inc.
Keratinization of the epidermis of the Australian lungfish Neoceratodus forsteri (dipnoi)
Authors: Alibardi Lorenzo , Joss Jean M.P. 
Published: March 2003

AbstractThe differentiation of the epidermis in sarcopterigian fish may reveal some trend of keratinization followed by amphibian ancestors to adapt their epidermis to land. Therefore, the process of keratinization of the epidermis of the Australian lungfish Neoceratodus forsteri was studied by histochemistry, electron microscopy, and keratin immunocytochemistry. The epidermis is tri‐stratified in a 2–3‐month‐old tadpole but becomes 6–8 stratified in young adults. Keratin filaments increase from basal to external cells where loose tonofilament bundles are present. This is shown also by the comparison of positivity to sulfhydryl groups and increasing immunoreactivity to alpha‐keratins in more external layers of the epidermis. Two broad‐spectrum anti alpha‐keratin monoclonal antibodies (AE1 and AE3) stain all epidermal layers as they do in actinopterigian fish. In the adult epidermis, but not in that of the larva, the AE2 antibody (a marker of keratinization in mammalian epidermis) often immunolabels more heavily the external keratinized layers where sulfhydryl groups are more abundant. Mucous granules are numerous and concentrate on the external surface of the epidermis to be discharged and contribute to cuticle formation. Keratin is therefore embedded in a mucus matrix, but neither compact keratin masses nor cell corneous envelope were seen in external cells. It is not known whether specific matrix proteins are associated with mucus. There was no immunolocalization of the keratin‐associated proteins, filaggrin and loricrin, which suggests that the epidermis of this species lacks the matrix and cell corneus envelope proteins characteristic of that of amniotes. In conclusion, while specific keratins (AE2 positive) are probably produced in the uppermost layers as in amphibian epidermis, no interkeratin, matrix proteins seem to be present in external keratinocytes of the lungfish other than mucus. J. Morphol. 256:13–22, 2003. © 2003 Wiley‐Liss, Inc.
Inter‐ and intraspecific variation in the distribution and number of pit organs (free neuromasts) of sharks and rays
Authors: Peach Meredith B. 
Published: March 2003

AbstractThe distribution of pit organs (free neuromasts) has previously been documented for several species of pelagic sharks, but is relatively poorly known for rays and bottom‐dwelling (demersal) sharks. In the present study, the complete distribution of pit organs was mapped in the demersal sharks Heterodontus portusjacksoni, Orectolobus maculatus, Hemiscyllium ocellatum, Chiloscyllium punctatum, and Asymbolus analis, and the rays Rhinobatos typus, Aptychotrema rostrata, Trygonorrhina sp. A, Raja sp. A, and Myliobatis australis. All of these species had pit organs scattered over the dorsolateral surface. The sharks also had “mandibular” pit organs (and “umbilical” pit organs in C. punctatum and A. analis) on the ventral surface, while pit organs were sparse or absent on the ventral surface of rays. All of the species examined here, except for M. australis, also had a “spiracular” group of pit organs adjacent to the eye and/or spiracle. Spiracular pit organs were also recorded for the sawshark Pristiophorus sp. A and the skate Pavoraja nitida, although the remainder of pit organs were not mapped in these species. The distribution and number of pit organs varied both within and among species. Pit organ distribution was asymmetrical in each individual examined, but no particular trend towards left or right “handedness” was observed in any species. Although rays have been thought to have fewer pit organs than sharks in general, this was not the case in the present study. All of the species examined here had few pit organs compared to the pelagic sharks previously documented, but it is not clear whether this is due to ecological or phylogenetic causes. J. Morphol. 256:89–102, 2003. © 2003 Wiley‐Liss, Inc.
Placentation in garter snakes. II. Transmission EM of the chorioallantoic placenta of Thamnophis radix and T. sirtalis
Authors: Blackburn Daniel G. , Lorenz Rachel L. 
Published: March 2003

AbstractTransmission electron microscopy was used to examine the ultrastructure of the allantoplacenta of garter snakes during the last half of gestation. This placenta occupies the dorsal hemisphere of the egg and is formed through apposition of the chorioallantois to the inner lining of the uterus. The uterine epithelium consists of flattened cells with short, irregular microvilli and others that bear cilia. The lamina propria is vascularized and its capillaries lie at the base of the uterine epithelial cells. The chorionic epithelium consists of a bilayer of squamous cells that are particularly thin superficial to the allantoic capillaries. Neither the chorionic epithelium nor the uterine epithelium undergoes erosion during development. Although a thin remnant of the shell membrane intervenes between fetal and maternal tissue at mid‐gestation, it undergoes fragmentation by the end of gestation. Thus, uterine and chorionic epithelial are directly apposed in some regions of the allantoplacenta, forming continuous cellular boundaries at the placental interface. During development, capillaries proliferate in both the uterine and chorioallantoic tissues. By late gestation, the interhemal diffusion distance has thinned in some areas to less than 2 μm through attenuation of the uterine and chorionic epithelia. Morphologically, the allantoplacenta is well adapted for its function in gas exchange. However, the presence of cytoplasmic vesicles, ribosomal ER, and mitochondria in the chorionic and uterine epithelial cells are consistent with the possibility of additional forms of placental exchange. J. Morphol. 256:171–186, 2003. © 2003 Wiley‐Liss, Inc.
Placentation in garter snakes. III. Transmission EM of the omphalallantoic placenta of Thamnophis radix and T. sirtalis
Authors: Blackburn Daniel G. , Lorenz Rachel L. 
Published: March 2003

AbstractThe omphalallantoic placenta is a complex organ that is unique to viviparous squamates. Using transmission EM and light microscopy, we examined this placenta in garter snakes in order to understand its structural organization and functional capabilities. The omphalallantoic placenta is formed from the uterine lining and the bilaminar omphalopleure, the latter of which is associated with the isolated yolk mass and allantois. A thin shell membrane separates the fetal and maternal tissues throughout gestation. The uterine epithelium contains cuboidal cells with large droplets or granules and appears to be secretory. Epithelium of the omphalopleure is specialized for absorption and contains cells with prominent microvilli and others with large cytoplasmic droplets or granules. The brush‐border cells are rich in mitochondria and Golgi bodies and interdigitate extensively with adjacent cells, forming elaborate intercellular canaliculi. Their morphology is consistent with their proposed role in sodium‐coupled water movement. During development, the isolated yolk mass becomes depleted as yolk droplets are digested by cells of the omphalopleure and allantois. However, the allantois does not fuse to or vascularize the inner face of the omphalopleure. Consequently, the distance between fetal and maternal circulatory systems remains large (about 250–300 μm), precluding efficient gas exchange and hemotrophic transfer. The morphology of the omphalallantoic placenta strongly suggests that it functions in nutrient transfer through uterine secretion and fetal absorption. J. Morphol. 256:187–204, 2003. © 2003 Wiley‐Liss, Inc.
Analysis of the CD8‐positive T cell response in Japanese patients with chronic hepatitis C using HLA‐A*2402 peptide tetramers
Authors: Nakamoto Yasunari , Kaneko Shuichi , Takizawa Hisao , Kikumoto Yoshikazu , Takano Masaaki , Himeda Yoshiko , Kobayashi Kenichi 
Published: March 2003

AbstractHepatitis C virus (HCV)‐specific CD8+ cytotoxic T lymphocytes (CTL) contribute to viral clearance in acute, self‐limited hepatitis C as well as to liver cell injury in the more frequent cases with chronic hepatitis C. Although HLA class I‐peptide tetramers have been used to detect circulating HCV epitope‐specific CTL with a high sensitivity and specificity, this technique has been targeted exclusively to the most frequent HLA haplotypes in the Caucasian population and the large number of HCV‐infected Asian patients, most of whom are HLA‐A24 positive, have not been studied. The current study determines the frequency, phenotype, and clinical significance of HCV‐specific CD8+ T lymphocytes with five different HLA‐A*2402 tetramers in 43 HCV infected Japanese patients and 32 controls. Overall, tetramer+ cells were detected in the blood of 33 of 43 patients at frequencies of 0.064–0.75% CD8+CD4−CD14−CD19− T lymphocytes. Interestingly, although the T cell response was always targeted multispecifically against epitopes in different HCV proteins, the relative frequency of cells stained with individual tetramers differed between patients. Furthermore, tetramer+CD8+ T lymphocytes were highly activated, but the phenotypes of different tetramer+ cells varied in each patient. In conclusion, HLA‐A24 restricted, HCV‐specific CD8+ T lymphocytes are found at similar frequencies in Asian patients as HLA‐A2 restricted, HCV‐specific CD8+ T lymphocytes in Caucasian patients. Differences in the frequency and activation status of individual tetramer+ cell populations suggest that CD8+ T lymphocytes with different HCV epitope specificity may mediate differential pathogenetic effects in chronic hepatitis C. J. Med. Virol. 70: 51–61, 2003. © 2003 Wiley‐Liss, Inc.
Enhancement of humoral immune responses to a human cytomegalovirus DNA vaccine: Adjuvant effects of aluminum phosphate and CpG oligodeoxynucleotides
Authors: Temperton Nigel J. , Quenelle Debra C. , Lawson Keirissa M. , Zuckerman Jane N. , Kern Earl R. , Griffiths Paul D. , Emery Vincent C. 
Published: March 2003

AbstractA human cytomegalovirus (HCMV) glycoprotein B (gpUL55) DNA vaccine has been evaluated in BALB/c mice. Intramuscular immunization of these mice with pRc/CMV2‐gB resulted in the generation of high levels of gpUL55‐specific antibody (geometric mean titer [GMT] 1:8900) and neutralizing antibody (GMT 1:74) after 2 booster doses given 5 and 10 weeks after primary inoculation. Emulsifying the construct with the aluminum phosphate gel adjuvant Adju‐Phos before immunization enhanced gpUL55‐specific antibody responses (GMT 1:17800, P = 0.04). Co‐immunization with CpG oligodeoxynucleotides was shown to enhance levels of neutralizing antibodies generated by immunization of mice with a pRc/CMV2‐gB/Adju‐Phos emulsion (P = 0.04). The results provide a rationale for evaluating combinations of other HCMV proteins for incorporation into a multi‐target DNA vaccine, and for the optimization of adjuvant usage, to elicit enhanced levels of neutralizing antibodies. J. Med. Virol. 70:86–90, 2003. © 2003 Wiley‐Liss, Inc.
Absence of SLAM mutations in EBV‐associated lymphoproliferative disease patients
Authors: Ferrand Véronique , Li Cuiling , Romeo Giovanni , Yin Luo 
Published: March 2003

AbstractX‐linked lymphoproliferative disease is a rare inherited immunodeficiency in which affected males present abnormal responses to Epstein‐Barr virus (EBV) infection. The gene defective in X‐linked lymphoproliferative disease, SH2D1A (also named SAP or DSHP), has been identified and shown to code for an adapter protein that interacts with signaling lymphocytic activation molecule (SLAM) and several other members of the CD2 superfamily. SH2D1A is mutated in no more than 60% of X‐linked lymphoproliferative disease patients. It could be postulated that a certain percentage of patients without apparent maternal transmission might be caused by other gene(s) in SH2D1A‐related signal transduction pathways. Being a partner of SH2D1A and having a key role in proliferation and differentiation of the T‐ and B‐lymphocytes, SLAM was considered as a candidate gene for patients who manifest symptoms of X‐linked lymphoproliferative disease but who have no mutations in SH2D1A. As a first step, SLAM mutations were screened for from cDNA of the lymphoblastoid cell line of all available patients. Then conditions for PCR, single‐strand conformational polymorphism (SSCP), heteroduplex analysis, and sequencing were established in all eight exons of SLAM. A total of 31 typical and atypical patients were analysed, from which six novel nucleotide variants were identified; however, none of these variants seems to cause abnormal function of the SLAM gene. Therefore, mutations in coding regions or splicing sites of SLAM are unlikely to play a major role in the mechanism of EBV‐associated lymphoproliferation. J. Med. Virol. 70:131–136, 2003. © 2003 Wiley‐Liss, Inc.