bluuebunny/crossref_metadata_2025_split huggingface dataset:
CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
Authors: Patel Sandeep , Mackerell Alexander D. , Brooks Charles L. 
Published: June 2004

AbstractA fluctuating charge (FQ) force field is applied to molecular dynamics simulations for six small proteins in explicit polarizable solvent represented by the TIP4P‐FQ potential. The proteins include 1FSV, 1ENH, 1PGB, 1VII, 1H8K, and 1CRN, representing both helical and β‐sheet secondary structural elements. Constant pressure and temperature (NPT) molecular dynamics simulations are performed on time scales of several nanoseconds, the longest simulations yet reported using explicitly polarizable all‐atom empirical potentials (for both solvent and protein) in the condensed phase. In terms of structure, the FQ force field allows deviations from native structure up to 2.5 Å (with a range of 1.0 to 2.5 Å). This is commensurate to the performance of the CHARMM22 nonpolarizable model and other currently existing polarizable models. Importantly, secondary structural elements maintain native structure in general to within 1 Å (both helix and β‐strands), again in good agreement with the nonpolarizable case. In qualitative agreement with QM/MM ab initio dynamics on crambin (Liu et al. Proteins 2001, 44, 484), there is a sequence dependence of average condensed phase atomic charge for all proteins, a dependence one would anticipate considering the differing chemical environments around individual atoms; this is a subtle quantum mechanical feature captured in the FQ model but absent in current state‐of‐the‐art nonpolarizable models. Furthermore, there is a mutual polarization of solvent and protein in the condensed phase. Solvent dipole moment distributions within the first and second solvation shells around the protein display a shift towards higher dipole moments (increases on the order of 0.2–0.3 Debye) relative to the bulk; protein polarization is manifested via the enhanced condensed phase charges of typical polar atoms such as backbone carbonyl oxygens, amide nitrogens, and amide hydrogens. Finally, to enlarge the sample set of proteins, gas‐phase minimizations and 1 ps constant temperature simulations are performed on various‐sized proteins to compare to earlier work by Kaminsky et al. (J Comp Chem 2002, 23, 1515). The present work establishes the feasibility of applying a fully polarizable force field for protein simulations and demonstrates the approach employed in extending the CHARMM force field to include these effects. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1504–1514, 2004
Pharmacotherapy for performance anxiety disorders: Occasionally useful but typically contraindicated
Authors: Birk Lee 
Published: June 2004

AbstractPharmacotherapy is an effective part of treatment for most anxiety disorders, but not for specific phobia or performance anxiety. In them it is contraindicated, because it interferes with the effectiveness of exposure therapies and the extinction of fear responses. Interference with exposure–extinction is a drug side effect that should rarely if ever be tolerated in treating them. This article reviews the many indications for pharmacotherapy in treating most anxiety disorders and contrasts its usefulness in treatment of anxiety disorders with its relatively rare usefulness in treating specific phobias and performance anxiety. In both the latter disorders, benzodiazepines interfere with exposure and generally are best avoided, although temporary use, with safeguards, can sometimes be helpful for a specific phobia. The recent discovery that d‐cycloserine (DCS) facilitates exposure and the extinction of anxiety offers promise that it could in the future be usefully and broadly employed to catalyze and enhance exposure therapies. © 2004 Wiley Periodicals, Inc. J Clin Psychol/In Session.
Characterization of adhesion and differentiation markers of osteogenic marrow stromal cells
Authors: Marom R. , Shur I. , Solomon R. , Benayahu Dafna 
Published: June 2004

AbstractMarrow stroma cells (MSC) play a major role in osteogenesis. The potential of the MSC to differentiate to bone‐forming cells relies upon molecular regulation. This study analyzed MBA‐15 cells for the expression of genes and proteins that are key regulators of osteoblast differentiation. These cells express Cbfa1 and c‐fos transcription factors (TF) of osteoprogenitor proliferating cells. RT‐PCR and immunohistochemistry were used to demonstrate the message and protein expression of extracellular matrix proteins that are a prerequisite for matrix formation and mineralization, including alkaline phosphatase (ALP), osteocalcin, osteopontin, biglycan, and bone sialoprotein (BSP). The activity of ALP was correlated at various cell densities with co‐expression of osteocalcin or osteopontin. Adhering cells must attach to the appropriate matrix to enable survival and differentiation. Using attachment assays, we demonstrated that MBA‐15 cells adhered to collagenous matrix and the effect on survival measured by changes in intracellular calcium (Ca) levels. The cells' adhesion to matrix is mediated via cell surface molecules. We quantified the expression of cells surface molecules that are important players in mediating cell–matrix interaction. Flow cytometry analysis (FACS) was used to determine the expression of CD‐31 (36%), and lower levels were identified for CD‐62E and CD11b. In summary, the present study demonstrates the expression of molecular markers that are distinctive for the osteoblastic phenotype in MBA‐15 marrow stroma cells and have crucial role in cell–matrix interaction, in establishing the cellular osteogenic phenotype and their survival. © 2005 Wiley‐Liss, Inc.
High‐dose retinoic acid modulates rat calvarial osteoblast biology
Authors: Song HanJoon M. , Nacamuli Randall P. , Xia Wei , Bari Ali S. , Shi Yun‐Ying , Fang Tony D. , Longaker Michael T. 
Published: June 2004

AbstractRetinoic acid has been shown to adversely affect craniofacial development. Cleft palate and craniosynostosis are two examples of craniofacial defects associated with prenatal exposure to this agent. Although the effects of retinoic acid on cephalic neural crest‐derived tissues have previously been studied, the specific effects of retinoic acid on the cellular biology of osteoblasts remain unclear. The purpose of this study was to analyze in detail the effects of pharmacologic doses of retinoic acid on the differentiation and proliferation of osteoblasts derived from an intramembranous source. Primary rat calvarial osteoblasts were established in culture and treated with 1 or 10 μM all‐trans‐retinoic acid. Retinoic acid treatment markedly increased expression of osteopontin up to 48 h after stimulation. Consistent with this early stage of differentiation, both mRNA and protein analysis of FGF receptor isoforms demonstrated a switch in predominance from fibroblast growth factor receptor 2 (fgfr2) to fgfr1. Analysis of PCNA protein confirmed inhibition of proliferation by retinoic acid. To determine whether these alterations in osteoblast biology would lead to increased differentiation, we examined short term [alkaline phosphatase (AP) activity] and long term (von Kossa staining) surrogates of bone formation in vitro. These assays confirmed that retinoic acid increased osteogenesis, with a 4‐fold increase in bone nodule formation in cells treated with 10 μM retinoic acid after 28 days. Overall, our results demonstrated that pharmacologic doses of all‐trans‐retinoic acid decreased osteoblast proliferation and increased differentiation, suggesting that retinoic acid may effect craniofacial development by pathologically enhancing osteogenesis. © 2005 Wiley‐Liss, Inc.
Ancient DNA as a multidisciplinary experience
Authors: Cipollaro M. , Galderisi U. , Di Bernardo G. 
Published: June 2004

AbstractInvestigation into DNA from archeological remains offers an inestimable tool for unraveling the history of humankind. However, a series of basic and technical difficulties renders the analysis of ancient DNA (aDNA) molecules troublesome, depending either on their own peculiar characteristics or on the complexity of processes affecting the bone matrix over time, all compromising the preservation of ancient DNA. This review underlines the contribution of many different disciplines, in particular molecular biology and genetics, to overcome these obstacles. The role of each expertise is illustrated to appropriately address the questions arising in aDNA investigations. © 2004 Wiley‐Liss, Inc.
Transvaginal color Doppler sonography for predicting response to concurrent chemoradiotherapy for locally advanced cervical carcinoma
Authors: Alcázar Juan Luis , Castillo Gerardo , Martínez‐Monge Rafael , Jurado Matías 
Published: June 2004

AbstractPurposeThis study was conducted to evaluate the potential role of transvaginal color Doppler sonography (TVCD) in predicting response to concurrent chemoradiotherapy for locally advanced cervical cancer.Methods and MaterialsTumor vascularity was assessed using TVCD before the start of concurrent chemoradiotherapy in 21 patients (median age, 47 years; range, 31–75 years) with histologically proven locally advanced cervical cancer. The lowest resistance index (RI), lowest pulsatility index (PI), and highest peak systolic velocity (PSV) from central vessels within the tumor were recorded and used for analysis. All patients were clinically evaluated by physical examination and CT scanning after completing the chemoradiotherapy protocol. Complete clinical response (CR) was determined when no residual tumor was found. Partial clinical response (PR) was determined when the tumor volume had decreased more than 50%.ResultsCR was achieved in 11 patients (52%), whereas 10 (48%) had PR. The initial median tumor volume was not statistically different between those with CR (26 cm3) and those with PR (28 cm3) (p = 0.71). RI was higher in those tumors with CR (median, 0.47) than in those with PR (median, 0.29) (p < 0.01). Likewise, PI was higher in tumors with CR (median, 0.81) than in those with PR (median, 0.41) (p < 0.01). No differences were found in PSV. The likelihood ratio for CR for tumors with a lowest RI of 0.35 or more was 2.7 (95% confidence interval, 1.8–3.6) and the likelihood ratio for CR for tumors with a lowest PI of 0.45 or more was 3.3 (95% confidence interval, 2.1–4.5).ConclusionsThe results suggest that TVCD may be useful in predicting clinical response to concurrent chemoradiation in patients with locally advanced cervical cancer. © 2004 Wiley Periodicals, Inc. J Clin Ultrasound 32:267–272, 2004
Testicular sonography: Is an echogenic ring a sign of a benign lesion?
Authors: Butteriss David J.A. , Elliott Simon T. 
Published: June 2004

AbstractThe differentiation of benign from malignant testicular lesions is important to avoid unnecessary surgical intervention but is often difficult, particularly in the case of focal hypoechoic lesions. We present the description of 3 cases of an echogenic ring that appeared around a hypoechoic testicular mass on sonograms. The ring proved to be a fibrous capsule around a benign lesion. If these observations are confirmed in larger series, the sonographic pattern described here may help reduce the number of orchiectomies performed for benign lesions. © 2004 Wiley Periodicals, Inc. J Clin Ultrasound 32:306–308, 2004
Hominins do not share a common postnatal facial ontogenetic shape trajectory
Authors: Cobb S.N. , O'Higgins P. 
Published: June 2004

AbstractThis paper examines the hypothesis raised by recent studies that postnatal trajectories of shape change in the facial skeleton are parallel between, at least, chimpanzees, modern humans and also fossil hominins, specifically australopithecines and possibly Neanderthals. In contrast, other studies point to divergences in postnatal shape trajectories within diverse groups of primates. As such there is some debate regarding the relative contributions of pre and postnatal ontogeny to adult morphological differences. This paper presents a series of geometric morphometric studies of the ontogeny of facial shape in hominins with the specific aim of resolving these issues. The results indicate that many differences in facial shape between hominins are established prenatally, however highly significant divergences of postnatal facial ontogeny are found among living hominins. Our studies point to possible differences between the shape ontogeny of theAustralopithecus africanusface and that of African apes on the one hand and humans on the other. However, sampling experiments indicate that the small sample size of available specimens ofA. africanusdoes not permit any conclusions to be drawn regarding comparative shape ontogeny of the face.J. Exp. Zool. (Mol. Dev. Evol.) 302B:302–321, 2004.© 2004 Wiley‐Liss, Inc.
Pressor effects of electrical stimulation of medial prefrontal cortex in unanesthetized rats
Authors: Tavares Rodrigo Fiacadori , Antunes‐Rodrigues José , de Aguiar Corrêa Fernando Morgan 
Published: June 2004

AbstractThe medial prefrontal cortex (MPFC) is involved in central nervous system (CNS)‐mediated cardiovascular modulation. We compared the cardiovascular effects of electrical stimulation (EE) of the MPFC in unanesthetized rats to those observed after stimulation of the same area in urethane‐anesthetized rats. Electrical stimulation (35, 106, 177, 247, 318, and 389 μA rms/10 sec, 60‐Hz sine wave) of the MPFC of urethane‐anesthetized rats caused depressor responses of stimulus‐related intensity. The cardiovascular response to electrical stimulation of the MPFC in unanesthetized rats was characterized by stimulus‐related pressor responses. No significant heart rate changes were observed during the EE period in any case. The pressor response to electrical stimulation (106 μA rms/10 sec, 60‐Hz sine wave) of the MPFC was not affected by intravenous pretreatment with the vasopressin antagonist dTyr(CH2)5(Me)AVP (50 μg/kg, intravenously), by hypophysectomy, or by intravenous pretreatment with the angiotensin II antagonist losartan (1 mg/kg, intravenously). The pressor response was blocked by intravenous pretreatment with the ganglionic blocker mecamylamine (2 mg/kg, intravenously) but was not affected by adrenal demedullation, thus suggesting involvement of the neural component of the sympathetic nervous system without a major involvement of its hormonal component. Our results confirmed the occurrence of depressor responses after electrical stimulation of the MPFC in urethane‐anesthetized rats and evidenced that only pressor responses are observed after its stimulation in unanesthetized rats. The fact that the pressor response to the stimulation of the MPFC was blocked by a ganglioplegic suggests that the MPFC has functional excitatory actions over the sympathetic nervous system. © 2004 Wiley‐Liss, Inc.
Treatment of cerebellar granule cell neurons with the neurotrophic factor pigment epithelium‐derived factor in vitro enhances expression of other neurotrophic factors as well as cytokines and chemokines
Authors: Yabe Takeshi , Herbert J. Taylor , Takanohashi Asako , Schwartz Joan P. 
Published: June 2004

AbstractMicroarray analyses demonstrated that a variety of genes was affected by treatment of cerebellar granule cell neurons with the neurotrophic factor pigment epithelium‐derived factor (PEDF). The genes for neurotrophins, glial cell‐derived neurotrophic factor (GDNF), and their receptors were regulated differentially in immature versus mature neurons; however, nerve growth factor (NGF), neurotrophin (NT)‐3, and GDNF did not contribute to the protective effect of PEDF. Brain‐derived neurotrophic factor (BDNF) seemed capable of inducing apoptosis, because a blocking antibody enhanced the protective effect of PEDF. In addition, PEDF exposure also stimulated expression of several cytokine and chemokine genes. Removal of the less than 1% of microglia in the cultures by treatment with L‐leucine methyl ester, combined with enzyme‐linked immunosorbent assays (ELISAs), demonstrated that the cerebellar granule cells constitutively produce three chemokines, macrophage inflammatory protein (MIP)‐1α, MIP‐2, and MIP‐3α, whose production is enhanced further by treatment with PEDF. Blocking antibodies to each of the chemokines was protective under control conditions, suggesting that they may contribute to the “natural” apoptosis occurring in the cultures, and enhanced the effects of PEDF. Although PEDF enhanced production of all three chemokines, the blocking antibodies did not increase its protective effect against induced apoptosis. These results suggest that although PEDF enhances expression of other neurotrophic factors or chemokines, it does not exert its neuroprotective effect on cerebellar granule cells through their production. © 2004 Wiley‐Liss, Inc.
Luminescence chronology of non‐glacial sediments in Changeable Lake, Russian High Arctic, and implications for limited Eurasian ice‐sheet extent during the LGM
Authors: Berger Glenn W. , Melles Martin , Banerjee Debabrata , Murray Andrew S. , Raab Alexandra 
Published: June 2004

AbstractA 10.5 m core from Changeable Lake in the Severnaya Zemlya Archipelago just north of the Taymyr Peninsula intersects ca. 30 cm of diamicton at its base, interpreted as a basal till. Because the upper 10.13 m of this core consists of non‐glacial sediments, a maximum numeric age for these non‐glacial sediments would provide a clear lower limit to the timing of the last glaciation in the area of Changeable Lake. Radiocarbon (14C) dating of several materials from this core yielded widely scattered results. Consequently we applied photonic dating to sediments above the diamicton. The experimental single‐aliquot‐regenerative (SAR) dose fine‐grain method was applied to two samples, using the ‘double SAR’ approach. With one exception, these fine‐grain SAR results and the results of application of the SAR method to sand‐sized quartz grains from two samples, at ca. 9.95 m and ca. 10.05 m depth, are discrepant with age estimates from the multi‐aliquot infrared‐photon‐stimulated luminescence (IR‐PSL) method applied to fine grains. Multi‐aliquot IR‐PSL dating of 10 samples produces ages increasing monotonically from ca. 4 ka at 2 m to 53 ± 4 ka at 9.97 m. These self‐consistent multi‐aliquot IR‐PSL ages, along with limiting 14C ages of >47 ka at ca. 10 m, provide direct evidence that glacial ice did not advance over this lake basin during the Last Glacial Maximum, and thus delimit the northeastern margin of the Barents–Kara Sea ice‐sheet to somewhere west of this archipelago. The last regional glaciation probably occurred during marine isotope stage (MIS) 4 or earlier. Copyright © 2004 John Wiley & Sons, Ltd.
Pedosedimentary development of part of a Late Quaternary loess‐palaeosol sequence in northwest Argentina
Authors: Kemp Rob A. , King Matthew , Toms Philip , Derbyshire Edward , Sayago José Manuel , Collantes Miriam M. 
Published: June 2004

AbstractThe field properties, magnetic susceptibility, particle size, calcium carbonate content, soil micromorphology and optical luminescence ages of the upper 6.1 m and lowermost 4.7 m of the 45 m loess–palaeosol sequence at El Lambedero in the Tafí del Valle region of Tucumán Province (Sierras Pampeanas, northwest Argentina) have been used to set up a partial stratigraphy and chronology, as well as a basic pedosedimentary model of loess accumulation, palaeosol development, reworking and erosion for the site. The minimum ages derived from the basal part of the section suggest that loess began to accumulate some time before 165 ka. A thick and well‐developed pedocomplex in the upper profile is correlated with at least the latter part of marine isotope stage (MIS) 5, whereas the overlying palaeosol may be attributable to pedogenic activity during MIS 3. The absence of material younger than 33 ka close to the surface of this rounded spur landform is probably the result of either non‐deposition or erosional stripping in response to climatic change, or episodic uplift in this seismically active region. Copyright © 2004 John Wiley & Sons, Ltd.
Characterization of minerals and biogeochemical markers on Mars: A Raman and IR spectroscopic study of montmorillonite
Authors: Bishop Janice L. , Murad Enver 
Published: June 2004

AbstractRaman spectroscopy is likely to be one of a number of instruments deployed to Mars on future landed missions. The goals of these missions will include characterizing the mineralogy of the rocks and soils, in addition to determining if the planet may be or may have been habitable for life. The astrobiology questions are linked to understanding the aqueous and biogeochemical history of Mars. Clay minerals are studied here because if they are found on Mars they may provide information about the geochemistry of the primary rocks and the aqueous history of the planet. This study compares Raman and IR spectra of the SWy‐1, STx‐1 and SAz‐1 montmorillonites. These samples contain admixtures of organic material, carbonate, amorphous silica and fine‐grained quartz, which can all be detected using Raman spectroscopy. Less than 0.1 wt% C as organic material was detected in each of the samples through peaks associated with CC or CH bonds. Carbonate was detected in the Raman spectra for the sample containing 1.65 wt% CO3 but not for 0.15 wt% CO3. Raman spectra exhibit unique bands near 200 and 700 cm−1 that are due to tetrahedral SiO4 in layer silicates and vary depending on the mineral structure. Raman spectra of clay minerals also have unique metal–OH bending vibrations between 840 and 920 cm−1 that provide information about the octahedral cations present. Copyright © 2004 John Wiley & Sons, Ltd.
Morphological, thermal, rheological and retrogradation properties of potato starch fractions varying in granule size
Authors: Singh Narpinder , Kaur Lovedeep 
Published: June 2004

AbstractThe physicochemical properties of small, medium and large starch granules separated from four potato cultivars were investigated to reveal whether functional properties differed among the various size classes of the starches. Large‐size fractions showed higher amylose content and light transmittance and lower swelling power than small‐size fractions. The granules from the three fractions had diameters of 5–20, 25–40 and 40–85 µm respectively. The large and medium granules were ellipsoidal to irregular or cuboidal while the small granules were spherical or ellipsoidal in shape. The transition temperatures and gelatinisation temperature range of the fractionated starches increased while the enthalpy of gelatinisation decreased with decreasing granule size. Rheological parameters such as peak storage (G′) and loss (G″) moduli increased in the order small‐, medium‐ and large‐granule starches when subjected to temperature sweep testing. The breakdown in peak G′ during the heating cycle and retrogradation during storage were found to be highest for large‐ and lowest for small‐size fractions. The differences in functional properties among the different size fractions suggested that the granule size distribution is an important parameter that can influence the behaviour of potato starch during processing. Copyright © 2004 Society of Chemical Industry