bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for a clustered spatial distribution of clupeid fish schools in the Norwegian Sea and off the coast of southwest Africa
Authors: Haugland Eli Kyrkjebø , Misund Ole Arve 
Published: October 2004

Abstract
To quantify and characterize the spatial distribution of clupeid fish schools, sonar data were collected during surveys off the coast of Namibia in 1994 (pilchard (Sardinops sagax), anchovy (Engraulis capensis), and round herring (Etrumeus whiteheadi)), off Angola in 1995 (sardinella (Sardinella sp.)) and in the Norwegian Sea in 1997 and 1998 (Norwegian spring-spawning herring (Clupea harengus L.)). The two-dimensional distances between clupeid schools were calculated in the order that the different schools were observed along the survey vessels transect lines. In all four surveys, two different modes (frequency distribution maximums) were observed. The first mode, representing the most usual interschool distance, was about 60 m. The second mode, around 1600 m, probably represented the distances between different clusters. The distances between clupeid schools and between different clusters were found to be about the same for separate pelagic clupeid species, locations, and years of observation. The mean diameters of the school clusters were estimated to vary between 450 and 1450 m.
Simulating trawl herding in flatfish: the role of fish length in behaviour and swimming characteristics
Authors: Winger Paul D. , Walsh Stephen J. , He Pingguo , Brown Joseph A. 
Published: October 2004

AbstractTheoretical modeling indicates that the herding efficiency of flatfish by bottom-trawl sweeps is highly sensitive to subtle changes in fish behaviour. Yet the degree of variation in herding behaviour within a species, population, or individual remains poorly understood because of the difficulty observing and measuring fish behaviour in this region of the gear. The purpose of this study was to simulate herding under laboratory conditions in order to examine the behaviour and swimming characteristics of flatfish. Using a large flume equipped with a moving floor, we examined the effect of fish length on gait use, behaviour, and swimming kinematics in American plaice (Hippoglossoides platessoides). While swimming at a speed comparable to the herding speed of trawl sweeps (0.3 m s−1), smaller plaice (<30 cm) spent a large percentage of time using the kick-swim gait, while larger fish (≥30 cm) preferred cruising. In total, 65% of plaice exhibited settling behaviour, analogous to the swim-and-settle behaviour observed in response to trawl sweeps. The frequency of this behaviour and the distance swum between settles were independent of fish length. Only the frequency of gliding changed with the duration of swimming. Like other teleost species, tailbeat frequency decreased with increasing fish length. The results from this study indicate that fish length affects gait use and swimming kinematics in flatfish, but not the frequency of gliding and settling behaviours. These observations support the hypothesis of size-selective herding and provide further insight into the herding efficiency of trawl sweeps.
Multiple cesarean section morbidity
Authors: Makoha F.W. , Felimban H.M. , Fathuddien M.A. , Roomi F. , Ghabra T. 
Published: October 2004

AbstractObjectiveTo quantify maternal risk associated with multiple cesarean sections (CSs) and determine whether the third CS defines a threshold for increased morbidity.MethodsFrom January 1997 to January 2002, the clinical records of 3191 women who were delivered by CS at our referral maternity center were examined for selected indicators of maternal morbidity. The women were assigned to groups based on number of CSs and the frequency of each indicator was determined. A composite score for each indicator among women grouped by number of consecutive CSs was then derived to compare risk between groups and against the third CS.ResultsBy all indicators studied, morbidity increased with successive CSs before and through the third CS. However, compared with the third, the risk of major morbidity was significantly increased with the fifth, and much worse at the sixth CS for placenta previa (odds ratio [OR]=3.8, 95% confidence interval [CI]=1.9–7.4), placenta accreta (OR=6.1, 95% CI=2.0–18.4) and hysterectomy (OR=5.9, 95% CI=1.5–24.4). But the third and fourth CSs had the same risk of major morbidity for placenta previa (OR=1.4, 95% CI=0.8–2.2), placenta accreta (OR=1.0, 95% CI=0.3–2.9) and hysterectomy (OR=0.3, 95% CI=0.0–2.7).ConclusionsThe third CS does not define a threshold for increased risk to the mother. Instead, overall morbidity rises continually with each successive CS. However, specifically for major morbidity from the triad of placenta previa, placenta accreta and hysterectomy during CS, the fourth CS carries the same risk as the third.
Rumination, mood and social problem-solving in major depression
Authors: DONALDSON C. , LAM D. 
Published: October 2004

Background. Ruminating when depressed is thought to lower mood and impair problem-solving, while distraction is thought to alleviate mood and assist problem-solving. The present study investigates each of these proposals using both naturally occurring and experimentally induced rumination and distraction in a sample of patients with major depression.Method. Thirty-six patients with major depression and 36 control participants were randomly allocated to either a rumination or distraction induction condition. Levels of trait rumination and distraction were measured at baseline, mood and problem-solving were measured before and after the inductions.Results. In terms of trait measures, depressed patients with higher levels of trait rumination reported poorer mood and gave less effective problem solutions than those who were less ruminative. Trait distraction was not associated with mood or problem-solving. In terms of induced responses, depressed patients who were made to ruminate experienced a deterioration in their mood and gave poorer problem solutions. For those receiving the distraction induction, mood improved in all patients and problem-solving improved in patients who were not naturally ruminating at a high level. Neither induction had an impact on mood or problem-solving in control participants.Conclusions. Treatment for depression associated with adverse life events may need to target rumination as well as problem-solving deficits if interventions are to be effective. The differential effects of self-applied versus experimentally induced distraction require further investigation. Future research will need to consider that high levels of trait rumination may interfere with the impact of experimental inductions.
High-frequency repetitive transcranial magnetic stimulation in schizophrenia: a combined treatment and neuroimaging study
Authors: HAJAK G. , MARIENHAGEN J. , LANGGUTH B. , WERNER S. , BINDER H. , EICHHAMMER P. 
Published: October 2004

Background. Repetitive transcranial magnetic stimulation (rTMS) of frontal brain regions is under study as a non-invasive method in the treatment of affective disorders. Recent publications provide increasing evidence that rTMS may be useful in treating schizophrenia. Results are most intriguing, demonstrating a reduction of negative symptoms following high-frequency rTMS. In this context, disentangling of negative and depressive symptoms is of the utmost importance when understanding specific rTMS effects on schizophrenic symptoms.Method. Using a sham-controlled parallel design, 20 patients with schizophrenia were included in the study. Patients were treated with high-frequency 10 Hz rTMS over 10 days. Besides clinical ratings, ECD-SPECT (technetium-99 bicisate single photon emission computed tomography) imaging was performed before and after termination of rTMS treatment.Results. High-frequency rTMS leads to a significant reduction of negative symptoms combined with a trend for non-significant improvement of depressive symptoms in the active stimulated group as compared with the sham stimulated group. Additionally, a trend for worsening of positive symptoms was observed in the actively treated schizophrenic patients. In both groups no changes in regional cerebral blood flow could be detected by ECD-SPECT.Conclusions. Beneficial effects of high-frequency rTMS on negative and depressive symptoms were found, together with a trend for worsening positive symptoms in schizophrenic patients.
The incidence and prevalence of pervasive developmental disorders: a Danish population-based study
Authors: LAURITSEN M. B. , PEDERSEN C. B. , MORTENSEN P. B. 
Published: October 2004

Background. Based on prevalence studies and the few incidence studies of pervasive developmental disorders (PDDs) the prevalence and incidence of these disorders have been claimed to be increasing.Method. The annual and age-specific prevalence and incidence rates of childhood autism, atypical autism, Asperger's disorder, and pervasive developmental disorder not otherwise specified (PDD-NOS) in Denmark during the period 1971–2000 in children younger than 10 years were estimated using data from the Danish Psychiatric Central Register.Results. A total of 2·4 million children younger than 10 years were followed and 2061 cases with the PDDs studied were identified. Generally, the prevalence and incidence rates of the PDDs studied were stable until the early 1990s after which an increase in the occurrence of all disorders was seen, until 2000. The annual incidence rate per 10000 children younger than 10 years was 2·0 for childhood autism, 0·7 for atypical autism, 1·4 for Asperger's disorder, and 3·0 for PDD-NOS in 2000. We calculated a ‘corrected’ prevalence of childhood autism at 11·8, atypical autism at 3·3, Asperger's disorder at 4·7, and PDD-NOS at 14·6 per 10000 children younger than 10 years on 1 January 1 2001.Conclusions. We found that the estimated prevalences of the PDDs studied were probably underestimated. Furthermore, the increasing prevalence and incidence rates during the 1990s may well be explained by changes in the registration procedures and more awareness of the disorders, although a true increase in the incidence cannot be ruled out.
A twin study of early cannabis use and subsequent use and abuse/dependence of other illicit drugs
Authors: AGRAWAL ARPANA , NEALE MICHAEL C. , PRESCOTT CAROL A. , KENDLER KENNETH S. 
Published: October 2004

Introduction. Cannabis use is strongly associated with the use and abuse/dependence of other illicit drugs. Gateway and common liabilities models have been employed to explain this relationship. We sought to examine this association using a combination of the discordant twin design and modeling methods.Method. We assess the relationship between early cannabis use and the subsequent use and abuse/dependence of other illicit drugs in a population-based sample of male and female twin pairs using four analyses: (i) analysis of the association between early cannabis use and other illicit drug use and abuse/dependence in the entire sample of twins, (ii) assessment of the influence of early cannabis use in twin 1 on twin 2's use or abuse/dependence of other illicit drugs, (iii) use of twin pairs discordant for early cannabis use in a discordant twin design and (iv) a model-fitting procedure.Results. We found: (i) a strong association between early cannabis use and use and abuse/dependence of other illicit drugs in the sample, (ii) twin 1's early cannabis use is significantly associated with the twin 2's other illicit drug use, (iii) the role of correlated genetic factors with some evidence for a causal influence, and (iv) the correlated liabilities model fits the data well.Conclusions. Early cannabis use is strongly associated with other illicit drug use and abuse/dependence. The relationship arises largely due to correlated genetic and environmental influences with persisting evidence for some causal influences.
Partial PTSD versus full PTSD: an empirical examination of associated impairment
Authors: BRESLAU NAOMI , LUCIA VICTORIA C. , DAVIS GLENN C. 
Published: October 2004

Background. Partial PTSD, employed initially in relation to Vietnam veterans, has been recently extended to civilian victims of trauma. We examined the extent to which partial PTSD is distinguishable from full DSM-PTSD with respect to level of impairment.Method. A representative sample of 2181 persons was interviewed by telephone to record lifetime traumatic events and to assess DSM-IV PTSD criteria. Partial PTSD was defined as [ges ]1 symptom in each of three symptom groups (criteria B, C and D) and duration of [ges ]1 month. Impairment in persons with PTSD and partial PTSD was measured by number of work-related and personal disability days during the 30-day period when the respondent was most upset by the trauma.Results. Compared to exposed persons with neither PTSD nor partial PTSD, increment in work-loss days associated with PTSD was 11·4 (S.E.=0·6) days and with partial PTSD, 3·3 (S.E.=0·4) days (adjusted for sex, education and employment). Similar disparities were found across other impairment indicators. Persons who fell short of PTSD criteria by one symptom of avoidance and numbing reported an increment of 5·0 (S.E.=0·7) work-loss days, 6·0 fewer than full PTSD. PTSD was associated with excess impairment, controlling for number of symptoms. A significantly lower proportion of persons with partial PTSD than full PTSD experienced symptoms for more than 2 years. A lower proportion of persons with partial PTSD than full PTSD had an etiologic event of high magnitude.Conclusions. PTSD identifies the most severe trauma victims, who are markedly distinguishable from victims with subthreshold PTSD.
Poor social integration and suicide: fact or artifact? A case-control study
Authors: DUBERSTEIN P. R. , CONWELL Y. , CONNER K. R. , EBERLY S. , EVINGER J. S. , CAINE E. D. 
Published: October 2004

Background. Sociological studies have shown that poor social integration confers suicide risk. It is not known whether poor integration amplifies risk after adjusting statistically for the effects of mental disorders and employment status.Method. A case-control design was used to compare 86 suicides and 86 living controls 50 years of age and older, matched on age, gender, race, and county of residence. Structured interviews were conducted with proxy respondents for suicides and controls. Social integration was defined in reference to two broad levels of analysis: family (e.g. sibship status, childrearing status) and social/community (e.g. social interaction, religious participation, community involvement).Results. Bivariate analyses showed that suicides were less likely to be married, have children, or live with family. They were less likely to engage in religious practice or community activities and they had lower levels of social interaction. A trimmed logistic regression model showed that marital status, social interaction and religious involvement were all associated with suicide even after statistical adjusting for the effects of affective disorder and employment status. Adding substance abuse to the model eliminated the effects of religious involvement.Conclusions. The association between family and social/community indicators of poor social integration and suicide is robust and largely independent of the presence of mental disorders. Findings could be used to enhance screening instruments and identify problem behaviors, such as low levels of social interaction, which could be targeted for intervention.
Distinct protein interfaces in transmembrane domains suggest an in vivo folding model
Authors: Stevens Timothy J. , Mizuguchi Kenji , Arkin Isaiah T. 
Published: October 2004

AbstractGiven the known high‐resolution structures of α‐helical transmembrane domains, we show that there are statistically distinct classes of transmembrane interfaces which relate to the folding and oligomerization of transmembrane domains. Distinct types of interfaces have been categorized and refer to those between: the same polypeptide chain, different polypeptide chains, helices that are sequential neighbors, and those that are nonsequential. These different interfaces may reflect different phases in the mechanism of transmembrane domain folding and are consistent with the current experimental evidence pertaining to the folding and oligomerization of transmembrane domains. The classes of helix‐helix interfaces have been identified in terms of the numbers and different types of pairwise amino acid interactions. The specific measures used are interaction entropy, the information content of interacting partners compared to a random set of contacts, the amino acid composition of the classes and the abundances of specific amino acid pairs in close contact. Knowledge of the clear differences in the types of helix‐helix contacts helps with the derivation of knowledge‐based constraints which until now have focused on only the interiors of transmembrane domains as compared to the exterior. Taken together, an in vivo model for membrane protein folding is presented, which is distinct from the familiar two‐stage model. The model takes into account the different interfaces of membrane helices defined herein, and the available data regarding folding in the translocation channel.
To be folded or to be unfolded?
Authors: Garbuzynskiy Sergiy O. , Lobanov Michail Yu. , Galzitskaya Oxana V. 
Published: October 2004

AbstractThe lack of ordered structure in “natively unfolded” proteins raises a general question: Are there intrinsic properties of amino acid residues that are responsible for the absence of fixed structure at physiological conditions? In this article, we demonstrate that the competence of a protein to be folded or to be unfolded may be determined by the property of amino acid residues to form a sufficient number of contacts in a globular state. The expected average number of contacts per residue calculated from the amino acid sequence alone (using the average number of contacts for 20 amino acid residues in globular proteins) can be used as one of the simple indicators of natively unfolded proteins. The prediction accuracy for the sets of 80 folded and 90 natively unfolded proteins reaches 89% if the expected average number of contacts is used as a parameter and 83% in the case of hydrophobicity. An optimal set of artificial parameters for 20 amino acid residues obtained by Monte Carlo algorithm to maximally separate the sets of 90 natively unfolded and 80 folded proteins demonstrates the upper limit for prediction accuracy, which is 95%.
Folding of a designed simple ankyrin repeat protein
Authors: Devi V. Sathya , Binz H. Kaspar , Stumpp Michael T. , Plückthun Andreas , Bosshard Hans Rudolf , Jelesarov Ilian 
Published: October 2004

AbstractAnkyrin repeats (AR) are 33‐residue motifs containing a β‐turn, followed by two α‐helices connected by a loop. AR occur in tandem arrangements and stack side‐by‐side to form elongated domains involved in very different cellular tasks. Recently, consensus libraries of AR repeats were constructed. Protein E1_5 represents a member of the shortest library, and consists of only a single consensus repeat flanked by designed N‐ and C‐terminal capping repeats. Here we present a biophysical characterization of this AR domain. The protein is compactly folded, as judged from the heat capacity of the native state and from the specific unfolding enthalpy and entropy. From spectroscopic data, thermal and urea‐induced unfolding can be modeled by a two‐state transition. However, scanning calorimetry experiments reveal a deviation from the two‐state behavior at elevated temperatures. Folding and unfolding at 5°C both follow monoexponential kinetics with kfolding = 28 sec−1 and kunfolding = 0.9 sec−1. Kinetic and equilibrium unfolding parameters at 5°C agree very well. We conclude that E1_5 folds in a simple two‐state manner at low temperatures while equilibrium intermediates become populated at higher temperatures. A chevron‐plot analysis indicates that the protein traverses a very compact transition state along the folding/unfolding pathway. This work demonstrates that a designed minimal ankyrin repeat protein has the thermodynamic and kinetic properties of a compactly folded protein, and explains the favorable properties of the consensus framework.
Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold‐type I, pyridoxal‐5′‐phosphate‐dependent enzymes
Authors: Paiardini Alessandro , Bossa Francesco , Pascarella Stefano 
Published: October 2004

AbstractThe wealth of biological information provided by structural and genomic projects opens new prospects of understanding life and evolution at the molecular level. In this work, it is shown how computational approaches can be exploited to pinpoint protein structural features that remain invariant upon long evolutionary periods in the fold‐type I, PLP‐dependent enzymes. A nonredundant set of 23 superposed crystallographic structures belonging to this superfamily was built. Members of this family typically display high‐structural conservation despite low‐sequence identity. For each structure, a multiple‐sequence alignment of orthologous sequences was obtained, and the 23 alignments were merged using the structural information to obtain a comprehensive multiple alignment of 921 sequences of fold‐type I enzymes. The structurally conserved regions (SCRs), the evolutionarily conserved residues, and the conserved hydrophobic contacts (CHCs) were extracted from this data set, using both sequence and structural information. The results of this study identified a structural pattern of hydrophobic contacts shared by all of the superfamily members of fold‐type I enzymes and involved in native interactions. This profile highlights the presence of a nucleus for this fold, in which residues participating in the most conserved native interactions exhibit preferential evolutionary conservation, that correlates significantly (r = 0.70) with the extent of mean hydrophobic contact value of their apolar fraction.
Predicting enzyme family class in a hybridization space
Authors: Chou Kuo‐Chen , Cai Yu‐Dong 
Published: October 2004

AbstractGiven the sequence of a protein, how can we predict whether it is an enzyme or a non‐enzyme? If it is, what enzyme family class it belongs to? Because these questions are closely relevant to the biological function of a protein and its acting object, their importance is self‐evident. Particularly with the explosion of protein sequences entering into data banks and the relatively much slower progress in using biochemical experiments to determine their functions, it is highly desired to develop an automated method that can be used to give fast answers to these questions. By hybridizing the gene ontology and pseudo‐amino‐acid composition, we have introduced a new method that is called GO‐PseAA predictor and operate it in a hybridization space. To avoid redundancy and bias, demonstrations were performed on a data set in which none of the proteins in an individual class has ≥40% sequence identity to any other. The overall success rate thus obtained by the jackknife cross‐validation test in identifying enzyme and non‐enzyme was 93%, and that in identifying the enzyme family was 94% for the following six main Enzyme Commission (EC) classes: (1) oxidoreductase, (2) transferase, (3) hydrolase, (4) lyase, (5) isomerase, and (6) ligase. The corresponding rates by the independent data set test were 98% and 97%, respectively.