bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discrimination of outer membrane proteins using support vector machines
Authors: Park Keun-Joon , Gromiha M. Michael , Horton Paul , Suwa Makiko 
Published: October 2005

Abstract
Motivation: Discriminating outer membrane proteins from other folding types of globular and membrane proteins is an important task both for dissecting outer membrane proteins (OMPs) from genomic sequences and for the successful prediction of their secondary and tertiary structures.
Results: We have developed a method based on support vector machines using amino acid composition and residue pair information. Our approach with amino acid composition has correctly predicted the OMPs with a cross-validated accuracy of 94% in a set of 208 proteins. Further, this method has successfully excluded 633 of 673 globular proteins and 191 of 206 α-helical membrane proteins. We obtained an overall accuracy of 92% for correctly picking up the OMPs from a dataset of 1087 proteins belonging to all different types of globular and membrane proteins. Furthermore, residue pair information improved the accuracy from 92 to 94%. This accuracy of discriminating OMPs is higher than that of other methods in the literature, which could be used for dissecting OMPs from genomic sequences.
Availability: Discrimination results are available at
Contact: michael-gromiha@aist.go.jp
Evolution and diversification of a sexually dimorphic luminescent system in ponyfishes (Teleostei: Leiognathidae), including diagnoses for two new genera
Authors: Sparks John S. , Dunlap Paul V. , Smith W. Leo 
Published: October 2005

AbstractA phylogeny was generated for Leiognathidae, an assemblage of bioluminescent, Indo‐Pacific schooling fishes, using 6175 characters derived from seven mitochondrial genes (16S,COI,ND4,ND5,tRNA‐His,tRNA‐Ser,tRNA‐Leu), two nuclear genes (28S,histone H3), and 15 morphological transformations corresponding to features of the fishes' sexually dimorphic light‐organ system (LOS; e.g., circumesophageal light organ, lateral lining of the gas bladder, transparent flank and opercular patches). Leiognathidae comprises three genera,Gazza,Leiognathus, andSecutor. Our results demonstrate that Leiognathidae,Gazza, andSecutorare monophyletic, whereasLeiognathusis not. The recovered pattern of relationships reveals that a structurally complex, strongly sexually dimorphic and highly variable species‐specific light organ is derived from a comparatively simple non‐dimorphic structure, and that evolution of other sexually dimorphic internal and external features of the male LOS are closely linked with these light‐organ modifications. Our results demonstrate the utility of LOS features, both for recovering phylogeny and resolving taxonomic issues in a clade whose members otherwise exhibit little morphological variation. We diagnose two new leiognathid genera,PhotopectoralisandPhotoplagios, on the basis of these apomorphic LOS features and also present derived features of the LOS to diagnose several additional leiognathid clades, includingGazzaandSecutor. Furthermore, we show that five distinct and highly specialized morphologies for male‐specific lateral luminescence signaling, which exhibit species‐specific variation in structure, have evolved in these otherwise outwardly conservative fishes. Leiognathids inhabit turbid coastal waters with poor visibility and are often captured in mixed assemblages of several species. We hypothesize that the species‐specific, sexually dimorphic internal and external modifications of the leiognathid LOS provide compelling evidence for an assortative mating scheme in which males use species‐specific patterns of lateral luminescence signaling to attract mates, and that this system functions to maintain reproductive isolation in these turbid coastal environments.© The Willi Hennig Society 2005.
Generating implied alignments under direct optimization using POY
Authors: Giribet Gonzalo 
Published: October 2005

AbstractThe concept of implied alignments, as used in modern systematics literature, is discussed. Basic notions about how to generate implied alignments are given together with explicit examples. The objective of this article is to guide researchers on how to produce implied alignments for validating purposes in an efficient manner using POY.© The Willi Hennig Society 2005.
Targeting optimal introns for phylogenetic analyses in non‐model taxa: experimental results in Asian pitvipers
Authors: Creer Simon , Malhotra Anita , Thorpe Roger S. , Pook Catharine E. 
Published: October 2005

AbstractNuclear introns are increasingly used as phylogenetic markers. Here, we present a multidisciplinary approach towards optimal locus selection and amplification using Asian pitvipers as an example of a non‐model taxon, and raise the profile of length variant heterozygotes (LVHs) in intron loci. Taxon‐specific primers were identified using a bioinformatic approach, and also designed from existing exon primed, intron crossing (EPIC) primer amplifications. Eleven further universal EPIC primer pairs were assayed using a range of PCR optimization strategies. Taxon‐specific primers yielded the most consistent amplifications, but assaying a large number of universal EPIC primers yielded another appropriate locus for phylogenetic purposes. Modified Taq DNA polymerases such as JumpStart™Taq either significantly improved the specificity and yield of EPIC PCR amplifications (of low copy number nuclear targets), or resulted in amplifications that were not significantly worse than those derived from a generic Taq DNA polymerase. Finally, LVHs were detected in all loci that were sequenced suggesting that they are relatively common in introns. This study provides an efficient and cost effective template for the successful identification of intron markers for molecular systematics which is universally applicable to other non‐model taxon groups.© The Willi Hennig Society 2005.
Survey of paediatric case management practices in Australia for children and young people with acquired brain injury (ABI)
Authors: Scheinberg A. M. , Gibson W. , Hughes D. , Miles A. , Murphy P. , Noronha J. 
Published: October 2005

AbstractAim  To investigate the characteristics of paediatric acquired brain injury (ABI) case managers and their organizations in Australia, and to determine the ways in which case managers deliver their service, maintain professional development and evaluate outcomes.Methods  Postal survey of 57 known paediatric ABI case managers working at 24 separate organizations in Australia.Results  Out of 40 questionnaires returned (70%), the majority of respondents had been providing case management for over 5 years (55%). Co‐ordination of services was ranked the most important component of case management, with services most frequently delivered by telephone. Evaluation of case management outcomes was reported by only 52% of the case managers. Whilst the majority of case managers had received some form of training (83%), this varied widely from informal in‐house training, to workshops run by insurance companies and government agencies.Discussion  This survey provides information about current case management practices for children with ABI in Australia. Detailing what case managers do is a first step towards developing controlled research designs which are required to demonstrate whether case management is effective in terms of clinical outcomes and cost–benefit.
Audit of local performance compared with standards recommended by the national guidelines for aetiologic investigation of permanent childhood hearing impairment
Authors: Yoong S. , Spencer N. 
Published: October 2005

AbstractBackground  National guidelines for aetiologic investigation of childhood deafness were developed as the Newborn Hearing Screening Program (NHSP) was being implemented in the United Kingdom. This guidance document was expected to be incorporated into the operational procedure of the NHSP.Method  This criterion‐based audit compared local care set against developed guidelines that can be used to assess the appropriateness of specific investigations, services and outcomes. Data on children diagnosed to have sensorineural deafness from March 2002–2004 were extracted from an established computerized database for analysis.Results  Forty‐seven children were included; 17 have bilateral severe to profound hearing loss, 25 have bilateral mild to moderate loss and 5 with unilateral loss. A high proportion of Pakistani children were from consanguineous marriages with a family history of deafness. Total 29.8% of children were diagnosed through newborn screening and 70.2% detected through hearing surveillance programmes. For children with bilateral severe to profound deafness, 53.0% accepted, 5.9% declined and 41.2% were not offered imaging of their inner ears. A total of 47.1% accepted and 52.9% declined electrocardiograph (ECG) evaluation. Total 70.6% accepted and 29.4% declined connexin mutations testing. Parental requests were required for those with lesser degree of hearing loss. Total 24% accepted, 28% declined and 48% were not offered connexin testing. None were offered ECG and imaging. Testing for congenital infections was inappropriate for children over 1 year old. Ten subjects accepted and five declined this investigation. In the total group, 63.8% accepted, 17.0% declined and 19.1% were not offered referral to the ophthalmic service. Total 46.8% accepted, 44.7% declined and 8.5% were not offered referral to genetics service. Investigations resulted in two connexin‐positive children with moderate loss.Conclusion  Our study identified key areas where guidelines were not followed. These were related to lack of funding and parental choice. This sample has a higher connexin ‘hit’ rate for lesser degree deafness.
Parental reported bullying among Nordic children: a population‐based study
Authors: Nordhagen R. , Nielsen A. , Stigum H. , Köhler L. 
Published: October 2005

AbstractBackground  Bullying has been shown to be a serious problem amongst school children, but few studies have been population‐based and included pre‐school children.Methods  The study is part of a cross‐sectional comparative study in 1984 and 1996, focusing on children's and their families’ health and welfare in the Nordic countries. At each point of time parents of 3000 randomly selected children aged 2–17 years in each of five Nordic countries received a postal questionnaire. Altogether approximately 20 000 questionnaires were completed. The prevalence of bullying, risk factors for bullying and possible effect factors were analysed.Results  Parents reported bullying of their child in 15.1% of the cases. Bullying varied from 7.2% in Sweden to about 20% in Denmark and Finland. There was a small increase in bullying from 13.7% in 1984 to 16.4% in 1996. Bullying was most frequent in boys (OR: 1.4) and in children 2–6 and 7–12 years old (OR: 2.0 and 2.2 compared with older children). Children of single parents and of parents with low education had increased risks (OR: 1.4 and 1.4). Children with chronic conditions had higher risks for being bullied (OR: 2.3). In 1996 children with psychiatric/nervous problems and hyperactivity had high risks for being bullied (OR: 8.8 and 10.5) and for bullying others (3.9 and 3.5). Being bullied was associated with poor thriving and psychosomatic and psychological problems. No countries had national interventions before 1984, but Sweden had early focused on the problem and implemented a strong national policy before 1996. After 1996 national anti‐bullying policies were strengthened in the Nordic countries, most in Sweden and Norway.Conclusion  Bullying is common among Nordic children, including pre‐school children. Bullying is a threat to children's health, and augments problems in children with chronic conditions. The low prevalence of bullying in Sweden may be a result from sustained, strong anti‐bullying policies. There is still a need for continuing interventions.
Symptoms of inattention and hyperactivity in children with habitual snoring: evidence from a community‐based study in Istanbul
Authors: Arman A. R. , Ersu R. , Save D. , Karadag B. , Karaman G. , Karabekiroglu K. , Karakoc F. , Dagli E. , Berkem M. 
Published: October 2005

AbstractBackground  Neurobehavioural symptoms of inattention and hyperactivity are common in children with sleep‐disordered breathing (SDB). Prevalence rates of habitual snoring and attention deficit hyperactivity disorder (ADHD) are very similar and both have a substantial negative effect on children's behavioural health.Objective  We examined the differences for subjective attentional and hyperactivity measures reported by parents and teachers among primary school children with habitual snoring and age‐ and sex‐matched controls in a community‐based case‐control study in Istanbul.Methods  In 2002, a survey was carried out to determine the prevalence of snoring in 2147 primary school children. After one year, in 2003, 151 children with habitual snoring and 302 controls from this survey were studied with parental SDB questionnaire, Conners’ Parent (Conners‐P) and Teacher Scales, and an inattention hyperactivity scale (IHS). Exclusion criteria included history of ADHD diagnosis, controls who started to snore and habitual snorers (HS) who no longer snored in this follow‐up study.Results  Ninety‐six HS and 190 control subjects (mean age: 9.4 ± 1.3) were evaluated. HS had significantly more symptoms of hyperactivity (Conners‐ADHD index) (P: 0.033), attentional (P: 0.019), and conduct and oppositional defiant in subscales (P: 0.001) of Conners‐P and IHS‐Parents. A pooled score of Conners‐P ADHD Index > 60 and IHS‐Parent score > 1.25 showed considerable difference in HS when compared with controls (5.1% vs. 1.4%) (P < 0.0001). Daytime hyperactivity and excessive daytime sleepiness reported by parents correlated with scores of Conners‐P and IHS‐P (P < 0.01). Teachers’ observations showed significant correlations with learning disability and the level of academic performance in HS (P < 0.01). Other behavioural parameters related to SDB were not significantly correlated with teachers’ ADHD ratings in HS.Conclusion  Increased rates of moderate hyperactivity as well as conduct and oppositional defiant symptoms in HS reported by the parents might reflect a negative impact on overall neurobehavioural health. The teachers’ scores yielded no significant results among HS and controls. This may be caused by the limitation due to shared method variance. The negative effect of crowded classes on teachers’ evaluations must be also taken into consideration. After exclusion of a diagnosis of ADHD in children presenting with hyperactivity and inattention, children with habitual snoring with prominent scores of behavioural measures should be considered as candidates for further assessment by a sleep specialist.
Not by bread alone project: a 2‐year follow‐up report
Authors: Taneja V. , Aggarwal R. , Beri R. S. , Puliyel J. M. 
Published: October 2005

AbstractBackground  We have previously reported the developmental gains achieved, after introducing a simple programme of structured play to stimulate children in an orphanage. It was envisaged that the caregivers could continue the programme. However, the enthusiasm of the caregivers waned over the year the programme was entrusted to them. After 1 year, a full time play therapist was recruited to rejuvenate the play programme.Methods  Children's development was assessed using the Indian adaptation of the Bayley Scales of Infant Development. The first assessment was done when the play therapist joined. Subsequently, three‐monthly assessments were done and the scores achieved were recorded.Results  The initial mean motor and mental scores, when the play therapist joined, were 66.14 and 56.95, respectively (similar to the pre‐intervention scores of the pilot study reported in an earlier paper). The scores improved to 81.84 and 78.25 within 3 months of restarting the play programme.Conclusion  The schedule of the ‘Not by Bread Alone’ project can accelerate the motor and mental development of children in orphanages. However, it requires a highly motivated and dedicated person to sustain this programme over long periods.
Maternal responsiveness and infant intentional communication: implications for the early communicative and linguistic development
Authors: Paavola L. , Kunnari S. , Moilanen I. 
Published: October 2005

AbstractBackground  Maternal responsiveness has been found to have an important role in early language acquisition. From early on, children can also be regarded as active participants in interaction who demonstrate increasing competence in conveying messages to their interactive partners. Hence, in order to demonstrate consistent effects of maternal responses, it is important to take into account individual differences among children. In the present study, the relation between the frequencies of maternal responses and infant intentional communicative acts as well as their predictive validity to subsequent early communicative and linguistic skills was examined.Methods  The participants were 27 Finnish‐speaking mothers and their healthy firstborn infants. Maternal and infant interactive behaviour was analysed from 20‐min samples of free play collected during home visits at the infants’ age of 10 months. At 12 months the children were assessed for their communicative and linguistic skills by using the Finnish version of the MacArthur Communicative Development Inventories and the Communication and Symbolic Behaviour Scales.Results  The frequencies of maternal responses and infant intentional communicative acts were not intercorrelated. As for subsequent communicative and linguistic skills, the results of regression analyses indicated that both maternal responsiveness and infant intentional communication predict early comprehensive skills, whereas expressive skills – the use of both verbal and gestural communicative means – are predicted only by infant intentional communication.Conclusion  The results of the present study suggest that maternal responsiveness during the prelinguistic stage is not necessarily dependent on children's communicative competence. As predictors of early communicative and linguistic skills, both maternal responsiveness and infant intentional communication make a distinctive contribution.
Relation between the changes in physical activity and body‐mass index during adolescence: a multicentre longitudinal study
Authors: Reading Richard 
Published: October 2005

.

Kimm S.Y.S.,
Glynn N.W.,
Obarzanek E.,
Kriska A.M.,
Daniels S.R.,
Barton B.A.,
Liu K.
(
2005
)

,
366
,
301
–
307
.
Background  The role of physical activity in preventing obesity during adolescence remains unknown. We examined changes in activity in relation to changes in body‐mass index (BMI) and adiposity in a cohort of 1152 black and 1135 white girls from the USA, who were followed up prospectively from ages 9–19 years.Methods  Body‐mass index and sum of skinfold thickness were assessed annually, whereas habitual activity was assessed at years 1 (baseline), 3, 5, and 7–10. Each girls’ overall activity status was categorized as active, moderately active, or inactive. Longitudinal regression models examined associations between changes in activity and in overall activity status with changes in BMI and in sum of skinfold thickness.Findings  Each decline in activity of 10 metabolic equivalent [MET]‐times per week was associated with an increase in BMI of 0.14 kg/m2 (SE 0.03) and in sum of skinfold thickness of 0.62 mm (0.17) for black girls, and of 0.09 kg/m2 (0.02) and 0.63 mm (0.13) for white girls. At ages 18 or 19 years, BMI differences between active and inactive girls were 2.98 kg/m2 (P < 0.0001) for black girls and 2.10 kg/m2 (P < 0.0001) for white girls. Similar results were apparent for sum of skinfold thickness. For moderately active girls, changes in BMI and sum of skinfold thickness were about midway between those for active and inactive girls.Interpretation  Changes in activity levels of US girls during adolescence significantly affected changes in BMI and adiposity. Thus, preventing the steep decline in activity during adolescence is an important method to reduce obesity.
Changing patterns of childhood mortality in Wolverhampton
Authors: Reading Richard 
Published: October 2005

.

Moore A.
(
2005
)

,
90
,
687
–
691
.
Objectives  To review the incidence and characteristics of preventable childhood deaths in an urban population in the UK and to determine whether the excess of preventable deaths seen previously in Asian girls still exists.Design  A retrospective survey of childhood deaths from 1996 to 2002 classified in terms of preventability and compared with a previous study conducted 20 years earlier from 1976 to 1982.Setting  The city of Wolverhampton in the UK.Main outcome measures  Deaths from all causes in children under the age of 5 years.Results  There has been a reduction in the number of deaths in all age groups and from all causes. The post‐neonatal mortality rate fell from 6.5/1000 in 1976 to 3.1/1000 live births in 2002 largely because of the fall in the numbers of deaths caused by sudden infant death syndrome. Preventable deaths are still associated with low birth weight (P < 0.001) and poverty (unemployment and overcrowding in the earlier study (P < 0.05) and with the Townsend score in this study (P < 0.02). There were fewer deaths among Asians and no female excess. There was a new category not seen in the previous study, deaths caused by homicide. The death rate for homicide in the first year of life was much higher in Wolverhampton (18.7/100 000) than in England and Wales (4.6/100 000).Conclusions  Low birth weight and adverse socio‐economic conditions remain important factors associated with preventable deaths. There is no longer an increased risk of preventable death in Asian girls. The number of non‐accidental deaths is a major cause for concern.
Surgical Approaches to Recipient Vessels of the Fore‐ and HindLimbs for Microvascular Free Tissue Transfer in Dogs
Authors: Degner Daniel A. , Walshaw Richard , David Fowler J. , Lanz Otto I. , Ocello Peter , Maier Jackie , Blaezer Loren , Smith Rick J. 
Published: October 2005

Objective—To develop and evaluate surgical approaches to the arteries and veins of the fore‐ and hindlimbs for use as potential recipient vessels for free tissue transfer.Study Design—Experimental anatomic study.Sample Population—Canine cadavers (11): 2 preserved and 9 fresh cadavers.Methods—Fore‐ and hindlimbs from 1 preserved cadaver injected with a pigmented silicone/barium mixture, through the common carotid artery and external jugular vein, were cut in 1 cm cross‐sections. Tissue sections were used to identify the location of vessels >1 mm that could be used as recipient vessels for free tissue transfer. The other preserved cadaver was used to develop surgical approaches to these vessels. Three surgeons evaluated the written descriptions and illustrations for these approaches using fresh cadavers. Modifications to the surgical approaches were made based on recommendations from these surgeons.Results—Six approaches were developed to isolate forelimb recipient vessels: palmar access, distal medial antebrachial, mid‐antebrachial, proximal antebrachial, distal humeral, and mid‐humeral vascular access. Twelve approaches were developed to isolate recipient vessels of the hindlimb: plantar access, dorsal tarsal, cranial distal tibial, craniomedial distal tibial, lateral distal tibial, medial distal tibial, medial femorotibial, lateral distal femoral, medial femoral, proximal medial femoral, groin, and proximal lateral femoral vascular access.Conclusions—Six forelimb and 12 hindlimb sites were identified for surgical access to recipient vessels (>1 mm diameter) suitable for use in free tissue transfer for wound reconstruction.Clinical Relevance—For reconstruction of complex wounds of the extremities of dogs, surgeons should consider use of readily accessible recipient vessels that would allow for free tissue transfer to the fore‐ and hindlimbs.