bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of oral ethanol on end‐tidal CO2 tension in patients misusing alcohol
Authors: WOLFF C. B. , GARDNER W. N. , PETERS T. J. 
Published: July 2002

AbstractThis study examines the effect of oral ethanol ingestion on PetCO2 and other respiratory variables in alcohol‐misusing subjects. Twelve patients were given a loading dose of alcohol (0.270 g/kg) followed by a second dose (0.135 g/kg) half an hour later, increasing blood alcohol to a mean of 82.0 ± 10.3 (SEM) mg/100 ml at 1 hour. Five patients were classified as hazardous drinkers with evidence of mild alcohol dependence but no toxicity (Severity of Alcohol Dependency (SADQ) score < 15/60; serum carbohydrate‐deficient transferrin < 6%). These patients showed a significant fall in mean end‐tidal PCO2 (PetCO2) on alcohol (2.08 ± 0.61 mm Hg; p = 0.027) with slightly increased ventilation (1.76 ± 0.94 1 min−1, p = 0.14); responses similar to those previously reported for normal subjects. Seven patients had evidence of moderate alcohol dependency and/or recent use (SADQ > 15/60; CDT > 6%). In these patients P et CO 2 did not fall after alcohol challenge (mean change + 0.61 mm Hg; p > 0.30). There were significant correlations between the changes in P et CO 2 and CDT (n = 12; rs= 0.66, p = 0.019) and SADQ (n = 11; rs= 0.688, p = 0.019). The results show that PetCO2 control is abnormal in the alcohol dependency syndrome.
Phagocytosis of the protozoon Tetrahymena pyriformis as an endpoint in the estimation of cocaine salt and cocaine freebase toxicity
Authors: STEFANIDOU M. , ALEVISOPOULOS G. , MARAVELIAS C. , LOUTSIDIS C. , KOUTSELINIS A. 
Published: July 2002

AbstractCells of the ciliated protozoon Tetrahymena pyriformis strain W, grown in a peptone‐yeast medium, usually contain many phagocytic vacuoles. The phagocytic activity of this protozoon was studied in vivo using heat‐inactivated yeast stained with carmine after exposing the cultures for 1 hour to different doses of cocaine hydrochloride or cocaine freebase (crack) (0.5, 1 or 2 mg/100 ml of protozoan culture).The number of vacuoles formed indicated the phagocytic activity. Cocaine hydrochloride and crack caused a decrease of the phagocytic activity of the protozoon (p < 0.05) when compared to the control cultures. Furthermore, the two chemical forms of cocaine, salt and free‐base respectively, caused quantitatively different effects on the phagocytic activity. Crack produced an extensive decrease in phagocytosis, compared to equal concentrations of cocaine hydrochloride. These results suggest a possible relationship between cocaine abuse and the suppression of phagocytosis that may contribute to the impairment of immunity in drug misusers.
Book and Media Reviews
Authors: COOK CHRIS 
Published: July 2002

Book reviewed in this article:Book reviews in this column will primar ily be of titles focusing completely, or in part, on biolog ical aspects of addiction. However, significant titles of general relevance to the addictions field will also be included, even if they are not “biological”, as will titles of general methodological and clinical relevance, even if they are not on “addictions”. Similar considerations will apply to other media (software, audio tapes and CDs, videos, etc). However, specific “addictions” software applications seem to be relatively uncommon and, as these items are rarely reviewed elsewhere, we will endeavour to include reviews of some of the older programmes that are still useful, as well as new titles that appear. I would appreciate suggestions of any items suitable for reviews, but especially software and other media of specific relevance to the addictions. Please contact: Professor Chris Cook, Kent Institute of Medicine and Health Sciences, University of Kent at Canterbur y, Kent CT2 7NR, UK. Email: c.c.h.cook@ukc.ac.uk Problem Drinking 3rd Edition NICK HEATHER & IAN ROBERTSON Preventing Drunk Driving E. R. SHORE & J. R. FERRARI (Eds) IRMA Addictions ‐ cannabis and cognitive functioning NADIA SOLIWIJ Opium and the People. Opiate use and drug control policy in nineteenth and early twentieth century England Revised edition VIRGINIA BERRIDGE Oxidative Stress in Skeletal Muscle A. Z. REZNICK (Ed.) Laboratory Methods for the Detection of Mutations and Polymorphisms in DNA GRAHAM R. TAYLOR (Ed.) The Scientist as Consultant—building new career opportunities C. J. SINDERMANN & T. K. SAWYER Software Atlas of the Human Brain (Deluxe Edition) JURGEN K. MAI, JOSEPH ASSHEUER & GEORGE PAXINOS The Human Brain—an introduction to the human nervous system MARION HALL & DAVID ROBINSON
Active versus passive cleft‐type speech characteristics
Authors: Harding Anne , Grunwell Pamela 
Published: July 2002

AbstractCleft palate speech is generally described in terms of nasal resonance, nasal emission and compensatory articulations. A longitudinal study of children at different stages of surgical treatment revealed a distinction between passive and active cleft‐type speech characteristics whereby passive characteristics were thought to be the product of structural abnormality or dysfunction and active characteristics were specific articulatory gestures replacing intended consonants. Passive and active patterns of articulation are described and defined in the context of three longitudinal studies of subjects who were at various stages of two different surgical regimes: five bilateral cleft lip and palate (BCLP) subjects aged 1;6‐4;6, 12 mixed unilateral cleft lip and palate (UCLP) and BCLP subjects aged 4;6‐7;6 and nine mixed UCLP and BCLP subjects aged 9;0‐11;0. Reference is also made to data from 12 mixed cleft‐type subjects aged 13;0 who had been treated with different surgical timing regimes. Comparison is made between the incidence of active versus passive processes in relation to oral structure. At age 4;6 speech samples taken from BCLP subjects who had been treated with 1‐stage versus 2‐stage palate repair all evidenced both active and passive processes. The lack of differentiation in speech results irrespective of their current surgical status, i.e. completely repaired palates versus residual cleft of the hard palate, was unexpected. Cleft‐type processes in completely repaired subjects might be accounted for by the inevitable anterior defect following repair of a bilateral cleft. Older subjects with structural defects also evidenced more clefttype processes. The relevance of distinguishing between active and passive processes is underlined by consideration of the effects of structural changes following surgery. The effect of surgery on seven subjects' speech is discussed using the active/passive distinction. Active cleft‐type characteristics did not change as a direct result of surgery, whereas passive characteristics were largely eliminated following surgery. A specific distinction is made between active and passive nasal fricatives, with the implication that active nasal fricatives may not be affected by surgical intervention, whereas passive nasal fricatives may be eliminated by surgery. Accurate distinction between active and passive patterns of articulation may serve to identify those cleft‐type speech error patterns most likely to respond to surgical intervention. Indications from this study are that active cleft‐type characteristics require destabilization in a course of speech and lan guage therapy before the potential benefits of surgery can be properly assessed. An analytical protocol for the interpretation of speech samples is presented and some therapy strategies are proposed for active and passive processes.
Scavenger Receptors and Modified Lipoproteins: Fatal Attractions?
Authors: Zingg Jean‐Marc , Ricciarelli Roberta , Azzi Angelo 
Published: July 2002

AbstractLipoproteins modified by oxidation, glycation, alkylation, and nitration are generated by oxidative stress during inflammation, diabetes, and inadequate supply of dietary antioxidants. A family of genes, the scavenger receptors, recognizes and internalizes modified lipoproteins, making them susceptible to degradation. Clearance of modified lipoproteins by scavenger receptors occurs mainly in macrophages, dendritic cells, and Kupffer cells of the liver. However, scavenger receptor expression also occurs in other cells, such as endothelial cells, aortic smooth muscle cells, neuronal cells, and keratinocytes. Thus, the local clearance of oxidized low‐density lipoprotein and the resolution of inflammatory processes may rely in part on the expression of scavenger receptors in “nonprofessional” phagocytes. Uptake of oxidized low‐density lipoprotein, without an efficient machinery to degrade them and uncontrolled expression of scavenger receptors, may lead to cellular deregulation, apoptosis, and formation of foam cells. Diseases accompanied by oxidation of lipoproteins, such as atherosclerosis, Alzheimer disease, glomerulosclerosis, ataxia with vitamin E deficiency, and possibly age‐dependent lipofuscin deposition, may share a common pathogenetic feature. This review will focus on foam cell formation, mainly within the atherosclerotic lesion, and the possible involvement of aberrant regulation of the scavenger receptor genes. To date, the regulatory mechanisms at the basis of scavenger receptor gene expression and their roles in atherosclerosis and other diseases are not well established. Knowledge on this subject could lead to a better understanding of the pathogenesis, prevention, and therapy of these diseases.
Genomic Organization of the Serine Protease Light Chain of Mouse Complement Factor I Gene
Authors: Jiang Ning , Molina Hector 
Published: July 2002

AbstractA portion of the mouse complement factor I (mCFI) gene encoding for the mCFI light chain was cloned from a mouse 129/SVJ1 bacterial artificial chromosome library. It contains five exons and four introns. The intron sizes are remarkably different from the human homolog. Several polymorphisms were found in exon 13. One polymorphism was in the coding region, which causes a threonine in the Balb/c mCFI to be replaced by an isoleucine in the 129/SVJ1 mCFI. The other two polymorphisms are located in the 3′ untranslated region. The organization of the serine protease domain in mCFI is similar to that of trypsin but very different from that of the other complement serine proteases.
Enzymes Are Open Systems
Authors: Zahradník Frantisek Jan 
Published: July 2002

AbstractThe exchange of mass, energy, and information with the environment typical of open systems can also be found in enzymes. An enzyme is able to receive information on substrate concentration in an arbitrary concentration range. This actually follows from the elementary solution of Michaelis‐Menten kinetics. The Michaelis constant can be seen as a relation between the decreasing parameter of a zero‐order reaction and the increasing parameter of a first‐order reaction over a certain time interval. This excludes the state of zero‐order kinetics and consequently the state of zero content of concentration information.
The Nitrogen Source‐Dependent 126‐kDa Protein From Synechococcus PCC 7942 Plasmalemma: A Trimer of the NrtA Nitrate‐Binding Protein
Authors: Fresneau Chantal , Zinovieva Maria , Blanot Didier , Batelier GÉrard , Arrio Bernard 
Published: July 2002

AbstractExpression of a 126‐kDa protein in the plasmalemma (cytoplasmic membrane) from Synechococcus PCC 7942 is dependent on the nitrogen source. Polyclonal antibody raised against the NrtA protein reacted with the 126‐kDa protein. Two peptide sequences from the 126‐kDa protein were retrieved in NrtA. FPLC purification of plasmalemma solubilised in Triton X‐100 gave a fraction consisting mainly of a 126‐kDa component (72.6%), as shown by sedimentation velocity. Equilibrium sedimentation of the same fraction gave evidence of the existence of an oligomeric structure (Ka = 2×10³ and 2.9 subunits). Thus, the 126‐kDa protein is considered as a trimeric arrangement of the 45‐kDa protein in the plasmalemma.
Conservation of the Centromere/Kinetochore Protein ZW10
Authors: Starr Daniel A. , Williams Byron C. , Li Zexiao , Etemad-Moghadam Bijan , Dawe R. Kelly , Goldberg Michael L. 
Published: July 2002

Mutations in the essential Drosophila melanogaster gene zw10 disrupt chromosome segregation, producing chromosomes that lag at the metaphase plate during anaphase of mitosis and both meiotic divisions. Recent evidence suggests that the product of this gene, DmZW10, acts at the kinetochore as part of a tension-sensing checkpoint at anaphase onset. DmZW10 displays an intriguing cell cycle–dependent intracellular distribution, apparently moving from the centromere/kinetochore at prometaphase to kinetochore microtubules at metaphase, and back to the centromere/kinetochore at anaphase (Williams, B.C., M. Gatti, and M.L. Goldberg. 1996. J. Cell Biol. 134:1127-1140).
We have identified ZW10-related proteins from widely diverse species with divergent centromere structures, including several Drosophilids, Caenorhabditis elegans, Arabidopsis thaliana, Mus musculus, and humans. Antibodies against the human ZW10 protein display a cell cycle–dependent staining pattern in HeLa cells strikingly similar to that previously observed for DmZW10 in dividing Drosophila cells. Injections of C. elegans ZW10 antisense RNA phenocopies important aspects of the mutant phenotype in Drosophila: these include a strong decrease in brood size, suggesting defects in meiosis or germline mitosis, a high percentage of lethality among the embryos that are produced, and the appearance of chromatin bridges at anaphase. These results indicate that at least some aspects of the functional role of the ZW10 protein in ensuring proper chromosome segregation are conserved across large evolutionary distances.
Reduced space hidden Markov model training.
Authors: Tarnas C , Hughey R 
Published: July 2002

Abstract
MOTIVATION: Complete forward-backward (Baum-Welch) hidden Markov model training cannot take advantage of the linear space, divide-and-conquer sequence alignment algorithms because of the examination of all possible paths rather than the single best path. RESULTS: This paper discusses the implementation and performance of checkpoint-based reduced space sequence alignment in the SAM hidden Markov modeling package. Implementation of the checkpoint algorithm reduced memory usage from O(mn) to O (m square root n) with only a 10% slowdown for small m and n, and vast speed-up for the larger values, such as m = n = 2000, that cause excessive paging on a 96 Mbyte workstation. The results are applicable to other types of dynamic programming. AVAILABILITY: A World-Wide Web server, as well as information on obtaining the Sequence Alignment and Modeling (SAM) software suite, can be found at http://www.cse.ucsc. edu/research/compbio/sam.html. CONTACT: rph@cse.ucsc.edu
Frequency-domain analysis of biomolecular sequences
Authors: Anastassiou Dimitris 
Published: July 2002

Abstract
Motivation: Frequency-domain analysis of biomolecular sequences is hindered by their representation as strings of characters. If numerical values are assigned to each of these characters, then the resulting numerical sequences are readily amenable to digital signal processing.
Results: We introduce new computational and visual tools for biomolecular sequences analysis. In particular, we provide an optimization procedure improving upon traditional Fourier analysis performance in distinguishing coding from noncoding regions in DNA sequences. We also show that the phase of a properly defined Fourier transform is a powerful predictor of the reading frame of protein coding regions. Resulting color maps help in visually identifying not only the existence of protein coding areas for both DNA strands, but also the coding direction and the reading frame for each of the exons. Furthermore, we demonstrate that color spectrograms can visually provide, in the form of local ‘texture’, significant information about biomolecular sequences, thus facilitating understanding of local nature, structure and function.
Availability: All software for techniques described in this paper is available from the author upon request.
Contact: anastas@ee.columbia.edu
Gene recognition in eukaryotic DNA by comparison of genomic
sequences
Authors: Novichkov P. S. , Gelfand M. S. , Mironov A. A. 
Published: July 2002

Abstract
Motivation: Sequencing of complete eukaryotic genomes and large syntenic fragments of genomes makes it possible to apply genomic comparison for gene recognition.
Results: This paper describes a spliced alignment algorithm that aligns candidate exon chains of two homologous genomic sequence fragments from different species. The algorithm is implemented in Pro-Gen software. Unlike other algorithms, Pro-Gen does not assume conservation of the exon–intron structure. Amino acid sequences obtained by the formal translation of candidate exons are aligned instead of nucleotide sequences, which allows for distant comparisons. The algorithm was tested on a sample of human–mammal (mouse), human–vertebrate (Xenopus ) and human–invertebrate (Drosophila ) gene pairs. Surprisingly, the best results, 97–98% correlation between the actual and predicted genes, were obtained for more distant comparisons, whereas the correlation on the human–mouse sample was only 93%. The latter value increases to 95% if conservation of the exon–intron structure is assumed. This is caused by a large amount of sequence conservation in non-coding regions of the human and mouse genes probably due to regulatory elements.
Availaility: Pro-Gen v. 3.0 is available to academic researchers free of charge at http://www.anchorgen.com/pro_gen/pro_gen.html.
Contact: misha@imb.imb.ac.ru
* To whom correspondence should be addressed.
MRBAYES: Bayesian inference of phylogenetic trees
Authors: Huelsenbeck John P. , Ronquist Fredrik 
Published: July 2002

Abstract
Summary: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo.
Availability: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
Contact: johnh@brahms.biology.rochester.edu
Fruits, foliage and the evolution of primate colour vision
Authors: Regan B. C. , Julliot C. , Simmen B. , Viénot F. , Charles–Dominique P. , Mollon J. D. 
Published: July 2002

Primates are apparently unique amongst the mammals in possessing trichromatic colour vision. However, not all primates are trichromatic. Amongst the haplorhine (higher) primates, the catarrhines possess uniformly trichromatic colour vision, whereas most of the platyrrhine species exhibit polymorphic colour vision, with a variety of dichromatic and trichromatic phenotypes within the population.It has been suggested that trichromacy in primates and the reflectance functions of certain tropical fruits are aspects of a coevolved seed–dispersal system: primate colour vision has been shaped by the need to find coloured fruits amongst foliage, and the fruits themselves have evolved to be salient to primates and so secure dissemination of their seeds. We review the evidence for and against this hypothesis and we report an empirical test: we show that the spectral positioning of the cone pigments found in trichromatic South American primates is well matched to the task of detecting fruits against a background of leaves. We further report that particular trichromatic platyrrhine phenotypes may be better suited than others to foraging for particular fruits under particular conditions of illumination; and we discuss possible explanations for the maintenance of polymorphic colour vision amongst the platyrrhines.
Polyproline II helical structure in protein unfolded states: Lysine peptides revisited
Authors: Rucker Adam L. , Creamer Trevor P. 
Published: July 2002

AbstractThe left‐handed polyproline II (PPII) helix gives rise to a circular dichroism spectrum that is remarkably similar to that of unfolded proteins. This similarity has been used as the basis for the hypothesis that unfolded proteins possess considerable PPII helical content. It has long been known that homopolymers of lysine adopt the PPII helical conformation at neutral pH, presumably a result of electrostatic repulsion between side chains. It is shown here that a seven‐residue lysine peptide also adopts the PPII conformation. In contrast with homopolymers of lysine, this short peptide is shown to retain PPII helical character under conditions in which side‐chain charges are heavily screened or even neutralized. The most plausible explanation for these observations is that the peptide backbone favors the PPII conformation to maximize favorable interactions with solvent. These data are evidence that unfolded proteins do indeed possess PPII content, indicating that the ensemble of unfolded states is significantly smaller than is commonly assumed.
Mercurial sensitivity of aquaporin 1 endofacial loop B residues
Authors: Kuang Kunyan , Haller Jorge F. , Shi Guangpu , Kang Fengying , Cheung Min , Iserovich Pavel , Fischbarg Jorge 
Published: July 2002

AbstractThe water channel protein aquaporin‐1 (AQP1) has two asparagine‐proline‐alanine (NPA) repeats on loops B and E. From recent structural information, these loops are on opposite sides of the membrane and meet to form a pore. We replaced the mercury‐sensitive residue cysteine 189 in AQP1 by serine to obtain a mercury‐insensitive template (C189S). Subsequently, we substituted three consecutive cysteines for residues 71–73 near the first NPA repeat (76–78) in intracellular loop B, and investigated whether they were accessible to extracellular mercurials. AQP1 and its mutants were expressed in Xenopus laevis oocytes, and the osmotic permeability (Pf) of the oocytes was determined. C189S had wild‐type Pf but was not sensitive to HgCl2. Expression of all three C189S cysteine mutants resulted in increased Pf, and all three mutants regained mercurial sensitivity. These results, especially the inhibitions by the large mercurial p‐chloromercunbenzene‐sulfonic acid (pCMBS) (∼6Å wide), suggest that residues 71–73 at the pore are accessible to extracellular mercurials. A 30‐ps molecular dynamics simulation (at 300 K) starting with crystallographic coordinates of AQP1 showed that the width of the pore bottleneck (between Connolly surfaces) can vary (wavg = 3.9 Å, σ = 0.75; hydrated AQP1). Thus, although the pore width would be ≥ 6 Å only for 0.0026 of the time, this might suffice for pCMBS to reach residues 71–73. Alternative explanations such as passage of pCMBS across the AQP1 tetramer center or other unspecified transmembrane pathways cannot be excluded.
How common is the funnel‐like energy landscape in protein‐protein interactions?
Authors: Tovchigrechko Andrei , Vakser Ilya A. 
Published: July 2002

AbstractThe goal of this study is to verify the concept of the funnel‐like intermolecular energy landscape in protein–protein interactions by use of a series of computational experiments. Our preliminary analysis revealed the existence of the funnel in many protein–protein interactions. However, because of the uncertainties in the modeling of these interactions and the ambiguity of the analysis procedures, the detection of the funnels requires detailed quantitative approaches to the energy landscape analysis. A number of such approaches are presented in this study. We show that the funnel detection problem is equivalent to a problem of distinguishing between distributions of low‐energy intermolecular matches in the funnel and in the low‐frequency landscape fluctuations. If the fluctuations are random, the decision about whether the minimum is the funnel is equivalent to determining whether this minimum is significantly different from a would‐be random one. A database of 475 nonredundant cocrystallized protein–protein complexes was used to re‐dock the proteins by use of smoothed potentials. To detect the funnel, we developed a set of sophisticated models of random matches. The funnel was considered detected if the binding area was more populated by the low‐energy docking predictions than by the matches generated in the random models. The number of funnels detected by use of different random models varied significantly. However, the results confirmed that the funnel may be the general feature in protein–protein association.