bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial clustering of protein binding sites for template based protein docking
Authors: Ghoorah Anisah W. , Devignes Marie-Dominique , Smaïl-Tabbone Malika , Ritchie David W. 
Published: August 2011

Abstract
Motivation: In recent years, much structural information on protein domains and their pair-wise interactions has been made available in public databases. However, it is not yet clear how best to use this information to discover general rules or interaction patterns about structural protein–protein interactions. Improving our ability to detect and exploit structural interaction patterns will help to provide a better 3D picture of the known protein interactome, and will help to guide docking-based predictions of the 3D structures of unsolved protein complexes.
Results: This article presents KBDOCK, a 3D database approach for spatially clustering protein binding sites and for performing template-based (knowledge-based) protein docking. KBDOCK combines residue contact information from the 3DID database with the Pfam protein domain family classification together with coordinate data from the Protein Data Bank. This allows the 3D configurations of all known hetero domain–domain interactions to be superposed and clustered for each Pfam family. We find that most Pfam domain families have up to four hetero binding sites, and over 60% of all domain families have just one hetero binding site. The utility of this approach for template-based docking is demonstrated using 73 complexes from the Protein Docking Benchmark. Overall, up to 45 out of 73 complexes may be modelled by direct homology to existing domain interfaces, and key binding site information is found for 24 of the 28 remaining complexes. These results show that KBDOCK can often provide useful information for predicting the structures of unknown protein complexes.
Availability: http://kbdock.loria.fr/
Contact: Dave.Ritchie@inria.fr
Supplementary Information: Supplementary data are available at Bioinformatics online.
iMod: multipurpose normal mode analysis in internal coordinates
Authors: Lopéz-Blanco José Ramón , Garzón José Ignacio , Chacón Pablo 
Published: August 2011

AbstractMotivation: Dynamic simulations of systems with biologically relevant sizes and time scales are critical for understanding macromolecular functioning. Coarse-grained representations combined with normal mode analysis (NMA) have been established as an alternative to atomistic simulations. The versatility and efficiency of current approaches normally based on Cartesian coordinates can be greatly enhanced with internal coordinates (IC).Results: Here, we present a new versatile tool chest to explore conformational flexibility of both protein and nucleic acid structures using NMA in IC. Consideration of dihedral angles as variables reduces the computational cost and non-physical distortions of classical Cartesian NMA methods. Our proposed framework operates at different coarse-grained levels and offers an efficient framework to conduct NMA-based conformational studies, including standard vibrational analysis, Monte-Carlo simulations or pathway exploration. Examples of these approaches are shown to demonstrate its applicability, robustness and efficiency.Contact: pablo@chaconlab.orgSupplementary Information: Supplementary data are available at Bioinformatics online.
Golden Perspective: Application of Laser‐Generated Gold Nanoparticle Conjugates in Reproductive Biology
Authors: Barchanski A , Taylor U , Klein S , Petersen S , Rath D , Barcikowski S 
Published: August 2011

ContentsThe current demand for female calves has grown rapidly and controlling the sex of offspring provides an economically flexible management for the livestock producer. The only functioning method of efficiently producing separate populations of X and Y sperm in mammals is based on relative DNA differentiation by high‐speed flow cytometry. In this context, gold nanoparticles conjugated to sex chromosome‐specific moieties display promising application as novel fluorophor‐alternative for the high‐throughput screening, since they feature no photo bleaching, high quantum yield, good biocompatibility and the possibility of non‐destructive membrane penetration. Especially, gold nanoparticles fabricated by pulsed laser ablation are in the recent focus of interest, due to excellent biocompatibility, fabrication‐dependent, tuneable particle size as well as surface charge and ease of (bio)‐functionalization with a remarkably strong ligand binding. For the purpose of our studies functionalized gold nanoparticles may be used as novel markers for sex‐sorting of mammalian sperm and, depending on the selected probe, also for the selection of sperm with heritable DNA‐sequences interesting for animal breeding.
Complications and postoperative events after cryosurgery for prostate cancer
Authors: Caso Jorge R. , Tsivian Matvey , Mouraviev Vladimir , Kimura Masaki , Polascik Thomas J. 
Published: August 2011

Study Type – Harm (case series)Level of Evidence 4What's known on the subject? and What does the study add?There is limited data available to determine the rate of complications following prostate cryosurgery. This is particularly true when limiting the experience to third generation cryoprobes. Herein we thoroughly report all complications and postoperative events, defined as any deviation from an ideal postoperative course, with extended follow up.OBJECTIVES
There has been a call in the urological literature for standardized reporting of complications.
To use strict criteria aiming to report our complications and other postoperative events in a cohort of men undergoing third‐generation prostate cryosurgery.
PATIENTS AND METHODS
Demographic, clinical and pathological data were collected on men undergoing primary cryosurgery from 2002–2010, excluding those who had received neoadjuvant or adjuvant radiotherapy.
Complications and events were broadly defined as any deviation from the expected postoperative course and any subjective complaint expressed during a follow‐up visit.
Descriptive statistics were generated and compared between groups using chi‐squared and rank sum tests as appropriate.
Logistic regression analyses were performed to assess the potential predictors of any complication or event.
RESULTS
In total, 106 consecutive patients were identified.
There were no intra‐operative complications or instances of equipment failure. We observed 42 early complications, with 48 delayed and 10 late postoperative events.
A total of five (4.7%) patients had persistent urge and/or stress incontinence.
Thirty‐one patients had International Prostate Symptom Score (IPSS) and bother index scores available before and after surgery; median scores decreased from 7 and 2 to 6 and 1, for IPSS and bother index, respectively. Twenty‐four patients had Sexual Health Inventory for Men scores available before surgery and at 2‐year follow‐up; median scores decreased from 11 to 2.
On multivariate analysis, there were no significant associations.
CONCLUSIONS
Modern cryosurgery is safe, and most of the complications and postoperative events are transient.
Erectile function, however, has marked deterioration.
We were unable to identify significant risk factors for complications or postoperative events.
Evolution of the clinical presentation of men undergoing radical prostatectomy for high‐risk prostate cancer
Authors: Pierorazio Phillip M. , Ross Ashley E. , Han Misop , Epstein Jonathan I. , Partin Alan W. , Schaeffer Edward M. 
Published: August 2011

Study Type – Prognosis cohort series (multi‐centre)Level of Evidence 4What's known on the subject? and What does the study add?Men with high‐risk prostate cancer experience recurrence, metastases and death at a higher rate in the prostate cancer population. This study adds greater than 20‐year data regarding the continued evolution of high‐risk prostate cancer toward high‐Gleason disease as the sole determinant of high‐risk status prior to radical prostatectomy. It validates the accumulation of multiple‐risk factors as a poor prognostic indicator in a radical prostatectomy population and demonstrates long‐term cancer specific outcomes, extending the findings demonstrated by previous publications.OBJECTIVE
To investigate the outcomes and potential effect of improved longitudinal screening in men presenting with high‐risk (advanced clinical stage [>T2b], Gleason score 8–10 or prostate‐specific antigen [PSA] level >20 ng/mL) prostate cancer (PC).
PATIENTS AND METHODS
The Institutional Review Board approved, Institutional Radical Prostatectomy Database (1992–2010) was queried for men with high‐risk PC based on D'Amico criteria.
Year of surgery was divided into two cohorts: the Early PSA Era (EPE, 1992–2000) and the Contemporary PSA Era (CPE, 2001–2010).
PC features and outcomes were evaluated using appropriate comparative tests.
RESULTS
In total, 667 men had high‐risk PC in the EPE and 764 in the CPE.
In the EPE, 598 (89.7%) men presented with one high‐risk feature; 173 (29.0%) men had a Gleason score of 8–10 on biopsy. In the CPE, 717 (93.9%) men presented with one high‐risk feature (P= 0.004) and 494 (68.9%) men had a Gleason score of 8–10.
At 10 years, biochemical‐free survival (BFS) was 44.1% and 36.4% in the EPE and CPE, respectively (P= 0.04); metastases‐free survival (MFS) was 77.1% and 85.1% (P= 0.6); and PC‐specific survival (CSS) was 83.3% and 96.2% (P= 0.5).
BFS, MFS and CSS were worse for men with more than one high‐risk feature in both eras.
CONCLUSIONS
Over the PSA era, an increasing percentage of men with high‐risk PC were categorized by a biopsy Gleason score of 8–10.
The accumulation of multiple high‐risk features increases the risk of biochemical recurrence, the development of metastases and death from PC.
BFS, MFS and CSS are stable over the PSA era for these men. The balance between a greater proportion of men having high Gleason disease and a greater proportion with small, less advanced tumours may explain the stability in MFS and CSS over time.
Assessing generalisability through the use of disease registers: findings from a diabetes cohort study
Authors: David Michael , Ware Robert , Donald Maria , Alati Rosa 
Published: August 2011

ObjectivesKnowledge of a study population's similarity to the target population allows researchers to assess the generalisability of their results. Often generalisability is assessed through a comparison of baseline characteristics between individuals who did and did not respond to an invitation to participate in a study. In this prospective population-based cohort, we broadened this assessment by comparing participants with all individuals from a chronic disease register who satisfied the study eligibility criteria but for a number of reasons, such as the absence of consent to be approached for research purposes, did not participate.MethodsData are from the Living with Diabetes Study, a population-based cohort of individuals diagnosed with diabetes mellitus, which commenced in Queensland, Australia in 2008. Individuals were sampled from a federally-funded diabetes register. We compared the characteristics of 3951 study participants with 10 488 non-participants (individuals who were invited to participate but declined) and with 129 900 non-study individuals on the register who did not participate in the study.ResultsStudy participants were more likely than non-study registrants to be male, aged 50–69, have type 2 diabetes non-insulin requiring, be recently registered and be non-indigenous Australians. Study participants were more likely than non-participants to be aged 50–69, have type 1 diabetes and be non-indigenous Australians.ConclusionsThe interpretation of a study's generalisability can alter depending on which non-participating group is compared with participants. When assessing generalisability, participants should be compared with the largest possible group of non-participating individuals. When sampling from a disease register, researchers should be wary of the influence of research consent procedures on the register's coverage.
Interaction of early environment, gender and genes of monoamine neurotransmission in the aetiology of depression in a large population-based Finnish birth cohort
Authors: Nyman Emma S , Sulkava Sonja , Soronen Pia , Miettunen Jouko , Loukola Anu , Leppä Virpi , Joukamaa Matti , Mäki Pirjo , Järvelin Marjo-Riitta , Freimer Nelson , Peltonen Leena , Veijola Juha , Paunio Tiina 
Published: August 2011

ObjectivesDepression is a worldwide leading cause of morbidity and disability. Genetic studies have recently begun to elucidate its molecular aetiology. The authors investigated candidate genes of monoamine neurotransmission and early environmental risk factors for depressiveness in the genetically isolated population-based Northern Finland Birth Cohort 1966 (12 058 live births).DesignThe authors ascertained and subdivided the study sample (n=5225) based on measures of early development and of social environment, and examined candidate genes of monoamine neurotransmission, many of which have shown prior evidence of a gene–environment interaction for affective disorders, namelySLC6A4,TPH2,COMT,MAOAand the dopamine receptor genesDRD1–DRD5.Results and conclusionThe authors observed no major genetic effects of the analysed variants on depressiveness. However, when measures of early development and of social environment were considered, some evidence of interaction was observed. Allelic variants ofCOMTinteracted with high early developmental risk (p=0.005 for rs2239393 and p=0.02 for rs4680) so that the association with depression was detected only in individuals at high developmental risk group (p=0.0046 and β=0.056 for rs5993883–rs2239393–rs4680 risk haplotype CGG including Val158), particularly in males (p=0.0053 and β=0.083 for the haplotype CGG). Rs4274224 fromDRD2interacted with gender (p=0.017) showing a significant association with depressiveness in males (p=0.0006 and β=0.0023; p=0.00005 and β=0.069 for rs4648318–rs4274224 haplotype GG). The results support the role of genes of monoamine neurotransmission in the aetiology of depression conditional on environmental risk and sex, but not direct major effects of monoaminergic genes in this unselected population.
Changes in the quality of doctor–patient communication between 1982 and 2001: an observational study on hypertension care as perceived by patients and general practitioners
Authors: Butalid Ligaya , Verhaak Peter F M , Tromp Fred , Bensing Jozien M 
Published: August 2011

BackgroundThe rise of evidence-based medicine may have implications for the doctor–patient interaction. In recent decades, a shift towards a more task-oriented approach in general practice indicates a development towards more standardised healthcare.ObjectiveTo examine whether this shift is accompanied by changes in perceived quality of doctor–patient communication.DesignGP observers and patient observers performed quality assessments of Dutch General Practice consultations on hypertension videotaped in 1982–1984 and 2000–2001. In the first cohort (1982–1984) 81 patients were recorded by 23 GPs and in the second cohort (2000–2001) 108 patients were recorded by 108 GPs. The GP observers and patient observers rated the consultations on a scale from 1 to 10 on three quality dimensions: medical technical quality, psychosocial quality and quality of interpersonal behaviour. Multilevel regression analyses were used to test whether a change occurred over time.ResultsThe findings showed a significant improvement over time on all three dimensions. There was no difference between the quality assessments of GP observers and patient observers. The three different dimensions were moderately to highly correlated and the assessments of GP observers showed less variability in the second cohort.ConclusionsHypertension consultations in general practice in the Netherlands received higher quality assessments by general practitioners and patients on medical technical quality, psychosocial quality and the quality of interpersonal behaviour in 2000–2001 as compared with the 1980s. The shift towards a more task-oriented approach in hypertension consultations does not seem to detract from individual attention for the patient. In addition, there is less variation between general practitioners in the quality assessments of more recent consultations. The next step in this line of research is to unravel the factors that determine patients' quality assessments of doctor–patient communication.
Examination of nocturnal activity and behaviour in resident white-crowned sparrows (Zonotrichia leucophrys nuttalli)
Authors: Wingfield John C. , Coverdill Alexander J. , Clark Aaron D. , Ramenofsky Marilyn 
Published: August 2011

AbstractObservations of nocturnal activity in resident species held in captivity are often attributed to migratory restlessness (MR). Previous publications investigating migratory white-crowned sparrows (Zonotrichia leucophrys gambelii) provided a distinct set of traits characteristic of MR, which we used to test the expression of activity and behaviour in the resident subspecies (Z. l. nuttalli). Under a winter photocycle, the 24-h activity profile of Z. l. nuttalli closely resembled that of migrant relatives. Following photostimulation, most birds expressed some activity during the dark phase; however, the diel pattern differed greatly from that of migrants. Unlike Z. l. gambelii, peak activity levels during the light phase remained greater than those expressed during the dark phase. Furthermore, birds did not express a quiescent phase prior to the initiation of the dark phase, nor did photostimulation result in increases in body mass or fat deposits. However, two birds did exhibit migration-specific behaviours (beak-up and beak-up flight) coupled with intense dark phase locomotor activity, which is consistent with MR expression. The suite of contrasts between conspecifics however, may suggest a different context of nocturnal behaviour, perhaps representing an underlying ancestral migratory phenotype that may now be associated with territorial or reproductive activities.
The information content of odour, colour and tactile cues in the mate choice of minnows
Authors: Valkama Hannele , Huuskonen Hannu , Taskinen Jouni , Lai Yi-Te , Kekäläinen Jukka , Leppänen Henna-Riikka 
Published: August 2011

AbstractSexual displays often involve many different signal components, which may give information about the same or different mate qualities. We studied the information content of different signals in male minnows (Phoxinus phoxinus) and tested whether females are able to discriminate between males when only olfactory cues are present. We found that females preferred the odour of males with a more saturated (i.e., redder) belly, but only when the females had been in physical contact with the males before the experiments. Instead, when unfamiliar males were used, females did not discriminate between male odours and also the overall swimming activity (mate choice intensity) of the females was significantly lower. More ornamented males had lower number of Philometra ovata parasites (indicated by belly saturation) and Neoechinorhynchus rutili parasites (indicated by belly hue) than their less ornamented counterparts. We did not find experimental evidence for female odour preference being linked to belly hue and breeding tubercle number, but in the nature these traits were associated with the condition factor of the males. Taken together, our results suggest that belly colouration and breeding tubercles give honest information on several aspects of male quality. In addition females may learn the association between male colouration and their olfactory signals and utilize this information when visual signals are not present.
The presence and number of male competitor's scent marks and female reproductive state affect the response of male meadow voles to female conspecifics' odours
Authors: Vaughn Ashlee A. , Ferkin Michael H. 
Published: August 2011

AbstractMale mammals are attracted to the scent marks of sexually receptive female conspecifics. Male voles spend more time investigating the scent marks of female voles in postpartum oestrus (PPE), a heightened state of sexual receptivity that occurs following the delivery of a litter, compared to those of female voles that are not in PPE, but in a moderate state of sexual receptivity. However, both types of females will attract male conspecifics to deposit their scent marks near those deposited by these females. The scent marks deposited by these males may indicate how many males have visited this female, which may affect how attractive she is to other males. In the present study, we exposed male meadow voles, Microtus pennsylvanicus, to the scent mark of a PPE female and a female that was not in PPE, a reference female (REF female); the scent marks of 0, 1 or 5 males were placed adjacent to the scent marks of these two female scent donors. In doing so, we tested three hypotheses. The first hypothesis is males will spend less time investigating the scent mark of a female that has more scent marks of male conspecifics adjacent to it compared to that of a female that has fewer scent marks of male conspecifics adjacent to it. The second hypothesis is the converse of the first hypothesis. The third hypothesis is males will spend more time investigating the scent mark of a PPE female than that of a REF female, independent of the number of scent marks of other males adjacent to them. Overall, our data suggests that a combination of factors may influence a male's preference for the scent marks of potential mates. Most tests suggest that males will respond preferentially to a female if she has more male suitors than another female, independent of the reproductive state of either female. If however, the number of male suitors is the same for each female, males tend to prefer the scent mark of the female that is in a more heightened state of sexual receptivity.
Singing, allogrooming, and allomarking behaviour during inter- and intra-sexual encounters in the Neotropical short-tailed singing mouse (Scotinomys teguina)
Authors: Phelps S.M. , Tang-Martínez Z. , Fernández-Vargas M. 
Published: August 2011

AbstractIn this study we determine whether brief interactions with unfamiliar conspecifics stimulate audible singing behaviour in the Neotropical short-tailed singing mouse (Scotinomys teguina). Specifically, we examine whether intra- or inter-sexual interactions elicit singing in males in a neutral-arena design. We conducted two experiments. In experiment 1, we recorded singing behaviour of male subjects both before and after a brief exposure to a female mouse. Males significantly increased their singing behaviour after the exposure to the female, as compared to prior to the exposure. In experiment 2, we compared the singing behaviour of male test subjects after a brief exposure with one of three different treatment animals: a male, a non-oestrous female and an oestrous female. We found that males are most likely to sing after an interaction with a female, regardless of her reproductive condition. Male subjects sang significantly less following an interaction with another male. Although spontaneous singing is known to occur in males and females, opposite sex elicited-singing behaviour was found to be sexually dimorphic. An interaction with a male was not effective in eliciting singing in females. In experiment 2, we also recorded incidences of allogrooming and allomarking by males during the interactions with males, non-oestrous females, and oestrous females. Male allogrooming and allomarking behaviours using the mid-ventral sebaceous gland tend to occur more frequently during interactions with females as compared to males, but were significantly different only in the case of allogrooming. Thus, this study clearly suggests sex differences in singing, allogrooming and allomarking, and a likely relationship between these behaviours and courtship in this Neotropical rodent.