bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonpharmacologic group treatment of insomnia: a preliminary study with cancer survivors
Authors: Davidson Judith R. , Waisberg Jodie L. , Brundage Michael D. , MacLean Alistair W. 
Published: August 2002

AbstractThis study describes, and examines the initial efficacy of, a sleep therapy programme developed for cancer patients with insomnia. The six‐session group programme included stimulus control therapy, relaxation training, and other strategies aimed at consolidating sleep and reducing cognitive‐emotional arousal. The 12 final participants were patients of a regional cancer centre; mean age was 54.7 years (S.D. 10.4); median time from cancer diagnosis was 33.6 months; all had high performance status. Participants kept sleep diaries and rated their sleep quality, mood and functioning at baseline, week 4 and week 8. Significant improvement over baseline was observed at weeks 4 and 8 in the number of awakenings, time awake after sleep onset, sleep efficiency, sleep quality ratings, and scores on European Organization for Research and Treatment of Cancer (EORTC) QLQ‐C30 role functioning and insomnia. Total sleep time and fatigue were significantly improved at week 8.The sleep therapy programme was associated with improved sleep, reduced fatigue and enhanced ability to perform activities in relatively well individuals attending a cancer centre. This is preliminary evidence of the efficacy of the programme. Further research is required to examine the programme's effectiveness and suitability for a wider range of people with cancer. Options for providing cancer patients with access to nonpharmacologic treatments for insomnia are discussed. Copyright © 2001 John Wiley & Sons, Ltd.
Frost heave and thaw consolidation of ploughing boulders in a mid‐alpine environment, Finse, Southern Norway
Authors: Berthling Ivar , Eiken Trond , Sollid Johan Ludvig 
Published: August 2002

AbstractThe frost heave and thaw consolidation of five large ploughing boulders were studied at Finse (UTM32VMN185198), southern Norway, by optical levelling from a bedrock benchmark. The boulders heave 3–7 cm, mainly during the early winter. Thaw consolidation starts while the boulders are still completely snow‐covered in spring, but accelerates considerably when a trench in the snow is melted down to the ground surface around the boulders. During four years of measurements, the vertical position of the boulders lowered by a total mean of 5 mm. Boulder heave was well correlated to the square root of the freezing index, although differences in snow cover between subsequent years had marked effects on the heave of some of the boulders. The overburden pressure of the boulders also influenced total heave. An equation was obtained, relating boulder heave to the square root of the freezing index and the average height of the boulder. Copyright © 2001 John Wiley & Sons, Ltd.RÉSUMÉLe soulèvement par le gel et la retombée au dégel de 5 grands blocs labourant ont été observés à Finse (UTM MN185198), au sud de la Norvège, par nivellement optique à partir d'un repère fixé sur la roche en place. Le soulèvement est de 3‐7 cm et se réalise principalement pendant le début de l'hiver. L'affaissement au dégel débute au printemps alors que les blocs sont encore complètement couverts de neige, mais s'accélère beaucoup quand la neige a fondu autour des blocs. Pendant les quatre années de mesures, les blocs se sont affaissés au dégel d'une moyenne totale de 5 mm. Le soulèvement des blocs est bien corrélé avec la racine carrée de l'index de gel, quoique des différences dans la couverture de neige suivant les années ont des effets marqués sur le soulèvement de quelques blocs. La pression des blocs influence aussi le soulèvement total. Une équation a été obtenue mettant en relation le soulèvement des blocs avec la racine carrée de l'index de gel et la hauteur moyenne des blocs. Copyright © 2001 John Wiley & Sons, Ltd.
Contribution of death receptor and mitochondrial pathways to Fas‐mediated apoptosis in the prostatic carcinoma cell line PC3
Authors: Guseva Natalya V. , Taghiyev Agshin F. , Rokhlin Oskar W. , Cohen Michael B. 
Published: August 2002

AbstractBACKGROUNDTwo main pathways of apoptosis in mammalian cells have been described: the death receptor pathway and the mitochondrial pathway. Two different cell types have been identified for Fas‐mediated apoptosis, each using almost exclusively one of two different signaling pathways. Human prostatic carcinoma cell line, PC3 is sensitive to Fas‐mediated apoptosis, but relation of receptor and mitochondrial pathways is not clear.METHODSCell viability was estimated by calcein assay. Apoptosis was determined by preparation of DNA ladder. Expression of Fas‐associated death domain‐dominant negative (FADD‐DN) and Bcl‐2, activation of caspases, PARP, DFF45, Bid cleavage, and cytochrome c release were assessed using Western blotting techniques. [35S] Methionine‐labeled caspase‐3 was transcribed in vitro and translated using the TNT kit (Promega). A vector containing caspase‐3 was prepared by the ligation of EcoR I/BamHI flanked PCR fragment of full size caspase‐3 cDNA into pBlusckript II SK(+/−) (Stratagen).RESULTSOverexpression of both FADD‐DN and Bcl‐2 genes prevent Fas‐mediated apoptosis in PC3. As predicted, overexpression of FADD‐DN prevented activation of caspase‐8 and Bid cleavage and attenuated the release of cytochrome c and activation of caspases ‐2, ‐7, and ‐9. Bcl‐2 overexpression did not affect caspase‐8 activation and cleavage of Bid but blocked the release of cytochrome c and activation of mitochondria localized caspases ‐2, ‐7, and–9. Overexpression of FADD‐DN and Bcl‐2 affected the activation of caspase‐3 and PARP cleavage differently: FADD‐DN attenuated the activation of caspase‐3 and PARP cleavage whereas Bcl‐2 overexpression prevented caspase‐3 activation and completely blocked cleavage of PARP.CONCLUSIONSThese data suggest that activation of caspase‐8 is necessary but not sufficient to complete Fas‐mediated apoptosis in PC3 cells without activation of the mitochondrial pathway. In addition, caspase‐3 activation after Fas‐receptor ligation involves two steps and is dependent on mitochondrial activation. Prostate 51: 231–240, 2002. © 2002 Wiley‐Liss, Inc.
Essential domain motions in barnase revealed by MD simulations
Authors: Nolde Svetlana B. , Arseniev Alexander S. , Orekhov Vladislav Yu , Billeter Martin 
Published: August 2002

AbstractThe wealth of data accumulated on the bacterial ribonuclease barnase is complemented by molecular dynamics trajectories starting from four different experimental structures and covering a total of >10 ns. Using principal component analysis, the simulations are interpreted in view of dynamic domains and hinges promoting relative motions of these domains. Two domains with residues 7–22 and 52–108 for the first domain and residues 25–51 for the second domain were consistently observed. Hinge regions consist primarily of Tyr24, Ser50, Ile51, and Gly52. Earlier mutation studies have demonstrated that the residues of the hinge regions play essential roles for the stability and activity of barnase. The domain motions are correlated to inter‐domain interactions involving functionally important active site residues, such as Lys27 and Glu73. A model is presented that combines the observation of dynamic domains and their motions with the extensive mutation data from the literature. Enthalpic energy contributions originating from specific inter‐domain interactions as well as entropic energy contributions due to the domain motions are discussed in the frame of this model and compared with destabilization energies measured for corresponding mutants. Proteins 2002;46:250–258. © 2002 Wiley‐Liss, Inc.
Identifying proteins of high designability via surface‐exposure patterns
Authors: Emberly Eldon G. , Miller Jonathan , Zeng Chen , Wingreen Ned S. , Tang Chao 
Published: August 2002

AbstractUsing an off‐lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique lowest‐energy conformation. We find that designability is closely correlated with the pattern of surface exposure of the folded structure. For longer chains, complete enumeration of structures is impractical. Instead, structures can be randomly sampled, and relative designability estimated either from designability within the random sample, or directly from surface‐exposure pattern. We compare the surface‐exposure patterns of those structures identified as highly designable to the patterns of naturally occurring proteins. Proteins 2002;47:295–304. © 2002 Wiley‐Liss, Inc.
Expanding the nitrogen regulatory protein superfamily: Homology detection at below random sequence identity
Authors: Kinch Lisa N. , Grishin Nick V. 
Published: August 2002

AbstractNitrogen regulatory (PII) proteins are signal transduction molecules involved in controlling nitrogen metabolism in prokaryots. PII proteins integrate the signals of intracellular nitrogen and carbon status into the control of enzymes involved in nitrogen assimilation. Using elaborate sequence similarity detection schemes, we show that five clusters of orthologs (COGs) and several small divergent protein groups belong to the PII superfamily and predict their structure to be a (βαβ)2 ferredoxin‐like fold. Proteins from the newly emerged PII superfamily are present in all major phylogenetic lineages. The PII homologs are quite diverse, with below random (as low as 1%) pairwise sequence identities between some members of distant groups. Despite this sequence diversity, evidence suggests that the different subfamilies retain the PII trimeric structure important for ligand‐binding site formation and maintain a conservation of conservations at residue positions important for PII function. Because most of the orthologous groups within the PII superfamily are composed entirely of hypothetical proteins, our remote homology‐based structure prediction provides the only information about them. Analogous to structural genomics efforts, such prediction gives clues to the biological roles of these proteins and allows us to hypothesize about locations of functional sites on model structures or rationalize about available experimental information. For instance, conserved residues in one of the families map in close proximity to each other on PII structure, allowing for a possible metal‐binding site in the proteins coded by the locus known to affect sensitivity to divalent metal ions. Presented analysis pushes the limits of sequence similarity searches and exemplifies one of the extreme cases of reliable sequence‐based structure prediction. In conjunction with structural genomics efforts to shed light on protein function, our strategies make it possible to detect homology between highly diverse sequences and are aimed at understanding the most remote evolutionary connections in the protein world. Proteins 2002;48:75–84. © 2002 Wiley‐Liss, Inc.
Free energy barrier estimation of unfolding the α‐helical surfactant‐associated polypeptide C
Authors: Zangi Ronen , Kovacs Helena , van Gunsteren Wilfred F. , Johansson Jan , Mark Alan E. 
Published: August 2002

AbstractMolecular dynamics simulations were conducted to estimate the free energy barrier of unfolding surfactant‐associated polypeptide C (SP‐C) from an α‐helical conformation. Experimental studies indicate that while the helical fold of SP‐C is thermodynamically stable in phospholipid micelles, it is metastable in a mixed organic solvent of CHCl3/CH3OH/0.1 M HCl at 32:64:5 (v/v/v), in which it undergoes an irreversible transformation to an insoluble aggregate that contains β‐sheet. On the basis of experimental observations, the free energy barrier was estimated to be ∼100 kJ/mole by applying Eyring's transition state theory to the experimental rate of unfolding [Protein Sci 1998;7:2533–2540]. These studies prompted us to carry out simulations to investigate the unwinding process of two helical turns encompassing residues 25–32 in water and in methanol. The results give an upper bound estimation for the free energy barrier of unfolding of SP‐C of ∼20 kJ/mole. The results suggest a need to reconsider the applicability of a single‐mode activated process theory to protein unfolding. Proteins 2001;43:395–402. © 2001 Wiley‐Liss, Inc.
Molecular dynamics simulations of a highly charged peptide from an SH3 domain: Possible sequence–function relationship
Authors: Krueger Brent P. , Kollman Peter A. 
Published: August 2002

AbstractA seven‐residue peptide that is highly conserved in SH3 domains despite being far from the active site has been shown by NMR to be stable in solution. This peptide, biologically important because it is a likely folding nucleus for SH3 domains, provides a challenging subject for molecular dynamics because it is highly charged. We present stable, 10‐ns simulations of both the native‐like diverging turn structure and a helical model. Free energies of these two conformations, estimated through MM‐PBSA analysis using several force fields, suggest a comparable free energy (ΔΔG ≤6 kcal/mol) for native and helix conformations. NOE intensities calculated from the native trajectory reproduce experimental data quite well, suggesting that the conformations sampled by the trajectory reasonably represent those observed in the NMR experiment. The molecular dynamics results, as well as sequence analysis of a diverse 690‐member family of SH3 domain proteins, suggest that the presence of two elements is essential for formation of the diverging turn structure: a pair of residues with low helical propensity in the turn region and, as previously recognized, two hydrophobic residues to close the end of the diverging turn. Thus, these two sequence features may form the structural basis for the function of this peptide as a folding nucleus in this family of proteins. Proteins 2001;45:4–15. © 2001 Wiley‐Liss, Inc.
A family of proteins related to Spätzle, the toll receptor ligand, are encoded in the Drosophila genome
Authors: Parker James S. , Mizuguchi Kenji , Gay Nicholas J. 
Published: August 2002

AbstractThe Drosophila gene Spätzle encodes the activating ligand for the Toll receptor. This signaling pathway is required for dorso‐ventral patterning in the early embryo and an antifungal immune response in larvae and adults. The genome sequence of Drosophila shows that there are a total of eight Toll‐like receptors and these may function in other aspects of embryonic development and innate immunity. Here we describe five Drosophila homologues of Spätzle (Spz2‐6) found using an iterative searching method. All five appear to encode proteins containing neurotrophin‐like cystine‐knot domains. In addition, most retain a characteristic intron‐exon structure shared with the prototype Spätzle gene. This provides evidence that the family arose by ancient gene duplication events and indicates that the gene products may represent activating ligands for corresponding Toll receptors. Expression studies show that only Spz4 is expressed strongly in larvae and adults and thus may be involved in an ancillary antifungal response mediated by Toll‐5. By contrast, Spz6 shows a complex spatial and temporally regulated expression pattern in the late embryo. Thus the new Toll/Spätzle families of signaling molecules may have important roles in other aspects of development and immunity. Proteins 2001;45:71–80. © 2001 Wiley‐Liss, Inc.
Crystal packing interaction that blocks crystallization of a site‐specific DNA binding protein–DNA complex
Authors: Littlefield Otis , Nelson Hillary C.M. 
Published: August 2002

AbstractWe present here three high‐resolution crystal structures of complexes between the DNA‐binding domain of the heat‐shock transcription factor (HSF) and DNA oligomers. Although the DNA oligomers contain HSF's specific binding sequence, called a heat‐shock element, the crystal structures do not contain the specific protein–DNA complex. In one crystal structure, the 10 base pair DNA oligomer is statically disordered. In the other two related structures, the 12 base pair DNA oligomers are in unique positions, but the protein–DNA contacts in these two crystals are not sequence specific. In all three structures, the DNA appears to act as a rigid, polyanion scaffold to support columns of proteins in a crystalline lattice. A robust crystal packing interface between protein monomers obscures the true DNA‐binding surface, known from previous genetic and biochemical studies. By redesigning the protein to interfere with the crystal lattice contacts, we were able to obtain physiologically relevant crystals in a specific protein–DNA complex. Thus, a crystal‐packing interface was able to prevent the weak, but physiological relevant interactions between a protein and DNA. Proteins 2001;45:219–228. © 2001 Wiley‐Liss, Inc.
Free energy distributions in proteins
Authors: Poland Douglas 
Published: August 2002

AbstractProtein molecules in solution have a broad distribution of enthalpy states. A good approximation to the distribution function for enthalpy states can be calculated, using the maximum‐entropy method, from the moments of the distribution that, in turn, are obtained from the experimental temperature dependence of the heat capacity. In the present paper, we show that the enthalpy probability distribution can then be formulated in terms of a free energy function that gives the free energy of the protein corresponding to a particular value of the enthalpy. By the location of the minima in this function, the free energy distribution graphically indicates the most probable values of the enthalpy for the protein. We find that the behavior of the free energy functions for proteins falls somewhere between two different cases: a two‐state like function with two minima, the relative levels of the two states changing with temperature; and, a single‐minimum function where the position of the minimum shifts to higher enthalpy values as the temperature is increased. We show that the temperature dependence of the free energy function can be expressed in terms of a central free energy distribution for a given, fixed temperature (which is most conveniently chosen as the temperature of the maximum in the heat capacity). The nature of this central free energy function for a given protein thus yields all of the thermodynamic behavior of that protein over the temperature range of the denaturation process. Proteins 2001;45:325–336. © 2001 Wiley‐Liss, Inc.
Stabilizing nonpolar/polar side‐chain interactions in the α‐helix
Authors: Andrew Charles D. , Penel Simon , Jones Gareth R. , Doig Andrew J. 
Published: August 2002

AbstractA simplistic, yet often used, view of protein stability is that amino acids attract other amino acids with similar polarity, whereas nonpolar and polar side chains repel. Here we show that nonpolar/polar interactions, namely Val or Ile bonding to Lys or Arg in α‐helices, can in fact be stabilizing. Residues spaced i, i + 4 in α‐helices are on the same face of the helix, with potential to favorably interact and stabilize the structure. We observe that the nonpolar/polar pairs Ile‐Lys, Ile‐Arg, and Val‐Lys occur in protein helices more often than expected when spaced i, i + 4. Partially helical peptides containing pairs of nonpolar/polar residues were synthesized. Controls with i, i + 5 spacing have the residues on opposite faces of the helix and are less helical than the test peptides with the i, i + 4 interactions. Experimental circular dichroism results were analyzed with helix‐coil theory to calculate the free energy for the interactions. All three stabilize the helix with ΔG between −0.14 and −0.32 kcal · mol−1. The interactions are hydrophobic with contacts between Val or Ile and the alkyl groups in Arg or Lys. Side chains such as Lys and Arg can thus interact favorably with both polar and nonpolar residues. Proteins 2001;45:449–455. © 2001 Wiley‐Liss, Inc.
A review of in situ measurement of organic compound transformation in groundwater
Authors: Papiernik Sharon K 
Published: August 2002

AbstractLaboratory assessments of the rate of degradation of organic compounds in groundwater have been criticized for producing unrepresentative results. The potential for organic compounds to be transformed in groundwater has been measured using in situ methods, which avoid problems of attempting to duplicate aquifer conditions in the laboratory. In situ assessments of transformation rates have been accomplished using transport studies and in situ microcosms (ISMs); a review of these methods is given here. In transport studies, organic solutes are injected into an aquifer and the concentrations are monitored as they are transported downgradient. The change in mass of a solute is determined by the area contained under the breakthrough curve (plot of concentration versus time). ISMs isolate a portion of the aquifer from advective flow and act as in situ batch reactors. Experiments using ISMs involve removing water from the ISM, amending it with the solutes of interest, re‐injecting the amended water, and monitoring the solute concentrations with time. In both transport and ISM studies, the loss of organic solutes from solution does not allow a distinction to be made between sorptive, abiotic and biotic transformation losses. Biological activity can be chemically suppressed in ISMs and the results from those experiments used to indicate sorption and abiotic loss. Transformation products may be monitored to provide additional information on transformation mechanisms and rates.Published in 2001 for SCI by John Wiley & Sons, Ltd
Activity of the botanical aphicides 1,5‐diphenyl‐1‐pentanone and 1,5‐diphenyl‐2‐penten‐1‐one on two species of Aphididnae
Authors: Ping Gao , Taiping Hou , Rong Gao , Qiu Cui , Shigui Liu 
Published: August 2002

Abstract1,5‐Diphenyl‐1‐pentanone (A) and 1,5‐diphenyl‐2‐penten‐1‐one (B) are natural products extracted for the first time from Stellera chamaejasme. Laboratory bioassay showed that the two products have strong contact activity and very good anti‐feedant activity against Aphis gossypii and Schizaphis graminum. Both products showed dose‐dependent relationships for both forms of activity against the two aphids, the contact activity of B being about twice that of A. Both products were inferior to methomyl in contact activity but superior in anti‐feedant activity against the two aphids. This is the first report of aphicidal activity in these two compounds, which may represent a new class of aphicide.© 2001 Society of Chemical Industry
Quantitative structure–activity studies of insect growth regulators: XVIII. Effects of substituents on the aromatic moiety of dibenzoylhydrazines on larvicidal activity against the Colorado potato beetle Leptinotarsa decemlineata
Authors: Nakagawa Yoshiaki , Smagghe Guy , Van Paemel Marleen , Tirry Luc , Fujita Toshio 
Published: August 2002

AbstractLarvicidal activity against the Colorado potato beetle Leptinotarsa decemlineata (Say) was measured for a series of N‐tert‐butyl‐dibenzoylhydrazines having various substituents on the benzoyl (A‐ring) moiety nearer to the tert‐butyl group, with the other benzoyl (B‐ring) moiety being unsubstituted. The effects of these substituent on the larvicidal activity were analyzed using classical quantitative structure‐activity relationship (QSAR) procedures. The effects of substituents on the A‐ring moiety on larvicidal activity were entirely different from those against the lepidopteran rice stem borer Chilo suppressalis (Walker) previously reported. Position‐specific steric and hydrophobic effects, as well as certain substitution patterns, were likely to participate in modifying the larvicidal activity. The activity of para‐substituted compounds was generally lower than that of un‐, ortho‐ and meta‐substituted compounds. Most multi‐substituted compounds showed an activity equivalent to or lower than that of the unsubstituted compound. Among 46 compounds tested, the 2‐sec‐butoxy analogue was most potent against L decemlineata, although this compound had previously been shown to be only weakly active against C suppressalis.© 2001 Society of Chemical Industry