bluuebunny/crossref_metadata_2025_split huggingface dataset:
LiveBench‐8: The large‐scale, continuous assessment of automated protein structure prediction
Authors: Rychlewski Leszek , Fischer Daniel 
Published: December 2004

AbstractWe present the results of the evaluation of the latest LiveBench‐8 experiment. These results provide a snapshot view of the state of the art in automated protein structure prediction, just before the 2004 CAFASP‐4/CASP‐6 experiments begin. The last CAFASP/CASP experiments demonstrated that automated meta‐predictors entail a significant advance in the field, already challenging most human expert predictors. LiveBench‐8 corroborates the superior performance of meta‐predictors, which are able to produce useful predictions for over one‐half of the test targets. More importantly, LiveBench‐8 identifies a handful of recently developed autonomous (nonmeta) servers that perform at the very top, suggesting that further progress in the individual methods has recently been obtained.
Release of ADP from the catalytic subunit of protein kinase A: A molecular dynamics simulation study
Authors: Lu Benzhuo , Wong Chung F. , McCammon J. Andrew 
Published: December 2004

AbstractSubstrate phosphorylation by cAMP‐dependent‐protein kinase A (protein kinase A, PKA) has been studied extensively. Phosphoryl transfer was found to be fast, whereas ADP release was found to be the slow, rate‐limiting step. There is also evidence that ADP release may be preceded by a partially rate‐limiting conformational change. However, the atomic details of the conformational change and the mode of ADP release are difficult to obtain experimentally. In this work, we studied ADP release from PKA by carrying out molecular dynamics simulations with different pulling forces applied to the ligand. The detailed ADP release pathway and the associated conformational changes were analyzed. The ADP release process was found to involve a swinging motion with the phosphate of ADP anchored to the Gly‐rich loop, so that the more buried adenine base and ribose ring came out before the phosphate. In contrast to the common belief that a hinge‐bending motion was responsible for the opening of the ligand‐binding cleft, our simulations showed that the small lobe exhibited a large amplitude “rocking” motion when the ligand came out. The largest conformational change of the protein was observed at about the first quarter time point along the release pathway. Two prominent intermediate states were observed in the release process.
Thermodynamic consequences of disrupting a water‐mediated hydrogen bond network in a protein:pheromone complex
Authors: Sharrow Scott D. , Edmonds Katherine A. , Goodman Michael A. , Novotny Milos V. , Stone Martin J. 
Published: December 2004

AbstractThe mouse pheromones (±)‐2‐sec‐butyl‐4,5‐dihydrothiazole (SBT) and 6‐hydroxy‐6‐methyl‐3‐heptanone (HMH) bind into an occluded hydrophobic cavity in the mouse major urinary protein (MUP‐1). Although the ligands are structurally unrelated, in both cases binding is accompanied by formation of a similar buried, water‐mediated hydrogen bond network between the ligand and several backbone and side chain groups on the protein. To investigate the energetic contribution of this hydrogen bond network to ligand binding, we have applied isothermal titration calorimetry to measure the binding thermodynamics using several MUP mutants and ligand analogs. Mutation of Tyr‐120 to Phe, which disrupts a hydrogen bond from the phenolic hydroxyl group of Tyr‐120 to one of the bound water molecules, results in a substantial loss of favorable binding enthalpy, which is partially compensated by a favorable change in binding entropy. A similar thermodynamic effect was observed when the hydrogen bonded nitrogen atom of the heterocyclic ligand was replaced by a methyne group. Several other modifications of the protein or ligand had smaller effects on the binding thermodynamics. The data provide supporting evidence for the role of the hydrogen bond network in stabilizing the complex.
Automatic generation and evaluation of sparse protein signatures for families of protein structural domains
Authors: Blades Matthew J. , Ison Jon C. , Ranasinghe Ranjeeva , Findlay John B.C. 
Published: December 2004

AbstractWe identified key residues from the structural alignment of families of protein domains from SCOP which we represented in the form of sparse protein signatures. A signature‐generating algorithm (SigGen) was developed and used to automatically identify key residues based on several structural and sequence‐based criteria. The capacity of the signatures to detect related sequences from the SWISSPROT database was assessed by receiver operator characteristic (ROC) analysis and jack‐knife testing. Test signatures for families from each of the main SCOP classes are described in relation to the quality of the structural alignments, the SigGen parameters used, and their diagnostic performance. We show that automatically generated signatures are potently diagnostic for their family (ROC50 scores typically >0.8), consistently outperform random signatures, and can identify sequence relationships in the “twilight zone” of protein sequence similarity (<40%). Signatures based on 15%–30% of alignment positions occurred most frequently among the best‐performing signatures. When alignment quality is poor, sparser signatures perform better, whereas signatures generated from higher‐quality alignments of fewer structures require more positions to be diagnostic. Our validation of signatures from the Globin family shows that when sequences from the structural alignment are removed and new signatures generated, the omitted sequences are still detected. The positions highlighted by the signature often correspond (alignment specificity >0.7) to the key positions in the original (non‐jack‐knifed) alignment. We discuss potential applications of sparse signatures in sequence annotation and homology modeling.
Comparison between TRF2 and TRF1 of their telomeric DNA‐bound structures and DNA‐binding activities
Authors: Hanaoka Shingo , Nagadoi Aritaka , Nishimura Yoshifumi 
Published: December 2004

AbstractMammalian telomeres consist of long tandem arrays of double‐stranded telomeric TTAGGG repeats packaged by the telomeric DNA‐binding proteins TRF1 and TRF2. Both contain a similar C‐terminal Myb domain that mediates sequence‐specific binding to telomeric DNA. In a DNA complex of TRF1, only the single Myb‐like domain consisting of three helices can bind specifically to double‐stranded telomeric DNA. TRF2 also binds to double‐stranded telomeric DNA. Although the DNA binding mode of TRF2 is likely identical to that of TRF1, TRF2 plays an important role in the t‐loop formation that protects the ends of telomeres. Here, to clarify the details of the double‐stranded telomeric DNA‐binding modes of TRF1 and TRF2, we determined the solution structure of the DNA‐binding domain of human TRF2 bound to telomeric DNA; it consists of three helices, and like TRF1, the third helix recognizes TAGGG sequence in the major groove of DNA with the N‐terminal arm locating in the minor groove. However, small but significant differences are observed; in contrast to the minor groove recognition of TRF1, in which an arginine residue recognizes the TT sequence, a lysine residue of TRF2 interacts with the TT part. We examined the telomeric DNA‐binding activities of both DNA‐binding domains of TRF1 and TRF2 and found that TRF1 binds more strongly than TRF2. Based on the structural differences of both domains, we created several mutants of the DNA‐binding domain of TRF2 with stronger binding activities compared to the wild‐type TRF2.
Psychological Collectivism as a Moderator of the Impact of Supervisor–Subordinate Personality Similarity on Employees’ Service Quality
Authors: Hui C. Harry , Cheng Kevin , Gan Yiqun 
Published: December 2004

Des chercheurs ont démontré que le collectivisme psychologique joue un rôle modérateur dans la relation entre certains construits. Les caractéristiques situationnelles peuvent avoir différents impacts sur les individualistes et les collectivistes dont les attitudes et valeurs divergent face aux relations interpersonnelles. Les collectivistes accordent beaucoup d’importance aux relations harmonieuses avec autrui, et seraient démoralisés quand ces relations sont menacées ou qu’elles ne se développent pas. Les individualistes voient l’individu comme la base de la survie et sont moins affectés par un manque d’harmonie. Nous avions prévu que l’effet de la similitude de personnalité entre superviseur–subordonné sur la qualité des services qu’un employé offre serait plus grand pour les collectivistes que pour les individualistes. Cette hypothèse a été testée auprès de 605 représentants à la clientèle et 113 superviseurs pour qui la similitude de personnalité a été mesurée par le nombre d’items pour lesquels les deux parties ont donné la même réponse. Bien que le collectivisme psychologique n’a pas d’effet direct sur la qualité du service, une analyse de régression indique que cette variable entre en interaction avec la similitude de personnalité. Ce résultat donne plus de soutien au modèle du rôle modérateur du collectivisme psychologique.Researchers have found psychological collectivism (PC) to play a moderating role in relationships among certain constructs. Situational characteristics may have different impacts on individualists and collectivists, who have discrepant attitudes and values regarding interpersonal relationships. The collectivists strongly value harmonious relationships with others, and would be demoralised when such relationships are threatened or do not materialise at all. The individualists view the self as the basic unit of survival, and are less affected even if harmony is not guaranteed. On the basis of this PC‐as‐moderator perspective, we expected that the effect of supervisor–subordinate personality similarity on the quality of service an employee delivers would be stronger among collectivists than among individualists. This hypothesis was tested with 605 front‐line customer service staff and 113 supervisors, whose personality similarity was indexed by the number of personality items to which both parties gave the same answers. Although psychological collectivism does not have direct effect on service quality, regression analysis shows that it interacts with personality similarity, lending further support to the PC‐as‐moderator model.
Antecedents and Consequences of Employees’ Adjustment to Overseas Assignment: A Meta‐analytic Review
Authors: Hechanova Regina , Beehr Terry A. , Christiansen Neil D. 
Published: December 2004

La recherche sur les antécédents et les conséquences de l’ajustement des expatriés a été revue de façon qualitative et avec la méthode quantitative de méta‐analyse. Les prédicteurs individuels, environnementaux, reliés au travail et reliés à la famille, de l’ajustement général, interactionnel et au travail ont été analysés. L’efficacité personnelle, la fréquence des interactions dans le pays hôte, et le soutien familial ont prédit les trois types d’ajustement. De plus, des compétences élevées en relations interpersonnelles ont été associées à un meilleur ajustement à l’environnement en général. Les résultats ont également démontré que la variable “conflit de rôle”était corrélée négativement avec l’ajustement au travail alors que l’ambiguïté du rôle et la discrétion ont été associés avec l’ajustement au travail. Un modèle d’équations structurelles a été développé avec les corrélations agrégées pour illustrer les relations causales possibles impliquant un facteur général d’ajustement et les résultats des tensions au travail, la satisfaction au travail, l’engagement organisationnel, l’intention de quitter, ainsi que la performance au travail. L’hypothèse était que l’ajustement influencerait les tensions et la satisfaction au travail et que ces deux dernières variables auraient un effet sur l’engagement organisationnel, la performance et l’intention de quitter. Le modèle a bien correspondu aux données.Research on the antecedents and consequences of expatriate adjustment was reviewed using meta‐analytic methods. The antecedents and outcomes of three facets of adjustment were examined. Self‐efficacy, frequency of interaction with host nationals, and family support consistently predicted all three types of adjustment. In addition, better interpersonal skills were associated with greater adjustment to general environment. Greater cultural novelty was associated with less interactional adjustment. Role conflict, ambiguity, and discretion were also strong predictors of work adjustment. A structural equations model that illustrated causal relationships involving expatriate adjustment and outcomes of job strain, job satisfaction, organisational citizenship, intent to turnover, and job performance generated a good fit with the data.
Testing the Impact of Job Search and Recruitment Source on New Hire Turnover in a Maquiladora
Authors: Linnehan Frank , Blau Gary 
Published: December 2004

En faisant appel à un échantillon de 345 travailleurs mexicains d’une maquiladora, cette étude met à l’épreuve l’impact d’échelles de comportement de recherches préliminaires et actives de travail, l’impact de l’orientation des salariés et de mesures des sources de recrutement américaines et mexicaines sur le changement de personnel. Au delà des variables sous contrôle, la recherche active de travail et les mesures des sources de recrutement et d’orientation des salariés entretenaient des relations positives et significatives avec le changement de personnel. Beaucoup des sources de recrutement mexicaines présentaient avec les démissions une liaison négative plus forte que beaucoup des sources de recrutement américaines. Les résultats montrent qu’une prise en considération attentive de la culture mexicaine est indispensable si l’on veut favoriser un développement réussi des multinationales au Mexique.Using a sample of 345 Mexican maquiladora workers, this study tested the impact of preparatory and active job search behavior scales, employee referral, US and Mexican recruitment source measures on new hire turnover. Beyond controlled‐for variables, active job search and employee referral recruitment source measures were found to have significant, positive relationships to new hire turnover. Number of Mexican recruitment sources used had a stronger negative relationship to voluntary turnover than number of US recruitment sources used. These findings suggest that careful consideration of Mexican culture is needed to enhance the successful growth of international firms in Mexico.
Cross‐cultural Variance in Goal Orientations and their Effects
Authors: Lee Cynthia , Tinsley Catherine , Bobko Philip 
Published: December 2004

Nous avons comparé l’orientation des buts d’un échantillon d’étudiants américains (n= 104) et un de Hong Kong (n= 175). Notre résultat principal indique que l’échantillon américain reproduit les résultats de la méta‐analyse de Beaubien et Payne (1999), en indiquant une corrélation très près de zéro entre les orientations d’apprentissage et de performance. Cela suggère que les étudiants des États‐Unis considèrent ces deux orientations comme différentes. Cependant, tel que prévu, dans l’échantillon d’étudiants de Hong Kong, la corrélation entre les orientations d’apprentissage et de performance est très élevée (r= .71, p < .01) suggérant que ces étudiants ne font pas de distinction entre ces deux orientations (ou que ces deux orientations sont fondamentalement les mêmes pour eux). De façon similaire, nous avons trouvé que les deux orientations de but sont associées positivement avec la performance en classe pour l’échantillon de Hong Kong alors que seule l’orientation d’apprentissage est liée à la performance pour les étudiants américains. Enfin, tel que prévu, les étudiants féminins dans l’échantillon chinois ont une orientation de performance plus élevé que les étudiants masculins. Cependant, les résultats ont aussi indiqué que le sexe n’est pas liéà aucune des orientations dans l’échantillon américain. Ce dernier résultat est cohérent avec les résultats de Button et al. (1996) mais non avec ceux de Beaubien et Payne (1999).We compared goal orientations of United States (n= 104) and Hong Kong (n= 175) student samples. Our major finding was that our United States sample replicated Beaubien and Payne's (1999) meta‐analysis, indicating that the correlation between learning and performance goal orientations is near zero. This suggests that United States students embrace learning and performance goal orientations as separate and distinct ideas. However, as hypothesised, in the Hong Kong student sample, the correlation between learning and performance goal orientation was r= .71 (p < .01) suggesting that these students do not readily distinguish the two goal orientations (or that these two goal orientations are fundamentally the same to them). Similarly, we found that both goal orientations showed positive associations with classroom performance in the Hong Kong sample, but only learning goal orientation was related to performance in the US sample. Lastly, as hypothesised, female students in the Hong Kong sample had higher performance goal orientations than male students. However, gender was unrelated to both goal orientations in the United States sample—consistent with Button, Mathiew, and Zajac's (1996) findings but inconsistent with Beaubien and Payne's (1999) findings.
Auctions Versus Beauty Contests: The Allocation of UMTS Licences in Europe
Authors: Cartelier L. 
Published: December 2004

The deployment of the so‐called UMTS 3rd generation mobile networks is a step of vital importance for the promotion of competition in the telecommunications sector. The provision of high‐traffic services presupposes that operators have access to the hertzian spectrum.The hertzian spectrum is a natural resource whose scarcity derives from the fact that only part of it is usable, for both technical and economic reasons. While the resource was sufficient to meet users' needs, the hertzian spectrum was allocated for little or no charge, on the principle of ‘first come, first served’. However, with the explosion of technical progress in transmission technologies, new applications and new forms of use appeared, leading to a drastic increase in potential demand. It is in this context that the idea of charging for use of the spectrum arose, so as to discourage uneconomical use of the resource (e.g. stockpiling, wastage), to ensure a fair allocation between competing users and to forestall congestion.The purpose of this paper is first to examine the procedures for the allocation of hertzian spectrum operating licences, from the points of view of efficiency, transparency and sharing of the surplus. We shall then compare the results from the two approaches that were actually used in Europe: the open ascending auction and the beauty contest, before turning our attention to new forms of public action that result from the process of liberalization.
Does fetal screening affect women's worries about the health of their baby?
Authors: Georgsson Öhman Susanne , Saltvedt Sissel , Grunewald Charlotta , Waldenström Ulla 
Published: December 2004

Background.  Screening for fetal abnormality may increase women's anxiety as attention is directed at the possibility of something being wrong with the baby. The aim of this study was to evaluate the effect of ultrasound screening for Down's syndrome on women's anxiety in mid‐pregnancy and 2 months after delivery.Method.  Two thousand and twenty‐six women were randomly allocated to an ultrasound examination at 12–14 gestational weeks (gws) including risk assessment for Down's syndrome or to a routine scan at 15–20 gws. Questionnaires including the State‐Trait Anxiety Inventory (STAI), the Cambridge Worry Scale (CWS), and the Edinburgh Postnatal Depression Scale (EPDS) were filled in at baseline in early pregnancy, at 24 gws and 2 months after delivery.Results.  No statistically significant differences were found between the trial groups regarding women's worries about the health of the baby, general anxiety and depressive symptoms during pregnancy or 2 months after delivery. Women's worries about something being wrong with the baby in the early ultrasound group and routine group, respectively, decreased from baseline (39.1% versus 36.0%) to mid‐pregnancy (29.2% versus 27.8%), and finally to 2 months after delivery (5.2% versus 6.6%).Conclusion.  Fetal screening for Down's syndrome by an early ultrasound scan did not cause more anxiety or concerns about the health of the baby in mid‐pregnancy or 2 months after birth than in women who had a routine scan.
Review of nonsurgical and surgical treatment and the role of insulin‐sensitizing agents in the management of infertile women with polycystic ovary syndrome
Authors: Saleh Ahmed M. , Khalil Hala S. 
Published: December 2004

Objectives.  To review the nonsurgical and surgical treatment and the role of insulin‐sensitizing agents in the management of anovulatory infertile women with polycystic ovary syndrome (PCOS).Materials and methods.  The search term of subfertile women with anovulation and PCOS was used for identification of randomized controlled trials. Nonrandomized controlled studies were identified through computer MEDLINE and EMBASE searches for the years 1980–2002.Results.  For obese PCOS women weight loss of > 5% of pretreatment weight restores menstrual regularity in 89%, of whom 30% achieved spontaneous pregnancy. It was estimated that 75–80% of anovulatory PCOS women will respond to clomiphene citrate (CC) and 35–50% will achieve pregnancy. For CC‐resistant PCOS women (20–25%), CC + metformin (1.5 g/day) for 3–6 months has a 70% chance of restoration of regular menses and ovulation, and a 23% chance of pregnancy. Laparoscopic ovarian drilling (LOD) can be offered to CC‐resistant PCOS women. There was no statistically significant difference in the ovulation rate following LOD with electrocoagulation and laser [83% vs. 77.5%; odds ratio (OR) 1.4; 95% CI 0.9–2.1], while there was a significantly higher cumulative pregnancy rate at 12 months after surgery (65% vs. 54.5%; OR 1.5; 95% CI 1.1–2.1).Conclusion.  Diet and exercise followed by CC should be used for nonsurgical ovulation induction. For CC‐resistant PCOS women, metformin may be included in a stepwise approach before a surgical approach. LOD with electrocautery is superior to laser drilling and gonadotropin therapy.
Chlamydiae in the ejaculate: their influence on the quality and morphology of sperm
Authors: Veznik Zdenek , Pospisil Leopold , Svecova Drahomira , Zajicova Atanaska , Unzeitig Vit 
Published: December 2004

Background.  Given the lack of information concerning the role of Chlamydia trachomatis in male fertility, the aim of this study was to ascertain and analyze the quality of Chlamydiae‐positive and ‐negative semen.Material and methods.  Sperm count was performed according to the 1999 World Health Organization (WHO) laboratory manual for examination of human semen and sperm–cervical mucus interaction, and sperm survival was assessed by a 120‐min test. The evaluation of the morphological examination of ejaculates was carried out using the sasmo (strict morphological analysis of ejaculates) computer program. Chlamydiae were detected by immunofluorescent reaction using the Progen Biotechnik GmbH diagnostic set. Fisher's exact test and the χ‐quadrate test were used for statistical analysis.Results.  Of the total of 627 sperm samples examined, Chlamydiae were detected in 136 cases (21.7%). Sperm analysis showed significant differences between Chlamydiae‐positive and ‐negative samples. The Chlamydiae‐contaminated group showed normal sperm morphology 14.4% lower, volume 6.4% lower, concentration 8.3% lower, motility 7.8% and velocity 9.3% lower than in Chlamydiae‐negative samples. The average values for normal spermatozoa and motility in the Chlamydiae‐positive group were also significantly reduced.Conclusion.  Chlamydia trachomatis was found to be a possible factor in sperm pathology. These results could help to elucidate the role of Chlamydia trachomatis in male infertility.