bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinicopathological significance of circadian rhythm‐related gene expression levels in patients with epithelial ovarian cancer
Authors: TOKUNAGA HIDEKI , TAKEBAYASHI YUJI , UTSUNOMIYA HIROKI , AKAHIRA JUN‐ICHI , HIGASHIMOTO MASASHI , MASHIKO MIYUKI , ITO KIYOSHI , NIIKURA HITOSHI , TAKENOSHITA SEI‐ICHI , YAEGASHI NOBUO
Published: August 2008

Objective. Recent studies implicate circadian genes in the regulation of cell cycle, apoptosis, and cell proliferation at a molecular level. These genesey affect cancer incidence, prognosis, and chemosensitivity. In this study, we measured the expression levels of clock genes and correlated their expression levels with clinicopathological parameters in epithelial ovarian cancer. Methods. The expression levels of core clock genes, per1, per2, per3, cry1, cry2, Bmal1, clock, and CKIɛ were quantified by real‐time quantitative Reverse transcription‐polymerase chain reaction in 83 ovarian cancer tissues and 11 normal ovarian tissues. Results. The expression levels of per1, per2, cry2, clock, CKIɛ in ovarian cancers were significantly lower than those in normal ovaries. In contrast, cry1 expression was highest among the eight examined clock genes, followed by per3 and Bmal1. Cry1 expression was much higher in cancer than that in normal ovaries. Localized circadian gene expression was determined in cancer cells by in situ hybridization analysis. Cry1 expression was significantly reduced in mucinous and grade 3 tumors. Bmal1 expression was also significantly reduced in mucinous adenocarcinomas as compared to other histologies. In a multivariate analysis, the combination of low cry1 expression and low Bmal1 expression was an independent prognostic factor, as well as stage and histological subtype. Conclusions. The antiphase expression of cry1 and Bmal1 may be preserved in ovarian cancers. The combination of cry1 and Bmal1 expression might become a possible prognostic marker in epithelial ovarian cancer.
The effects of the introduction of the no‐smoking policy at HMYOI Warren Hill on bullying behaviour
Authors: Lawrence Sally , Welfare Heather
Published: August 2008

The current research explores the prevalence of bullying behaviour at HMYOI Warren Hill and the Carlford Unit. The introduction of the no‐smoking policy at the establishment was also explored in relation to its effect on bullying behaviour given that tobacco has historically been the main item that young people have been bullied for. The Direct and Indirect Prisoner behaviour Checklist ‐ Revised (DIPC‐R) and a questionnaire designed to identify the effect of the introduction of the no‐smoking policy on bullying behaviour were used within this study to answer the following questions: what is the prevalence of bullying behaviour at Warren Hill and the Carlford Unit, and do young people at Warren Hill and the Carlford Unit think that the rate and nature of bullying has been affected by the introduction of the no‐smoking policy? One hundred and fifteen young people took part in the study. At Warren Hill, Bully/Victims were the most prevalent type identified and this was significantly greater than the number of young people identified as Pure Victims or Not Involved. On the Carlford Unit, Not Involved was the most prevalent type identified, and this finding provides limited support for the theories of bullying behaviour identified within the present study. The study found that the rate of bullying decreased following the introduction of the no‐smoking policy at Warren Hill. The findings from this study are being used in the development of a new Violence Reduction Policy at HMYOI Warren Hill.
Effect Of Nurse-Led Multidisciplinary Rounds On Reducing the Unnecessary Use Of Urinary Catheterization in Hospitalized Patients
Authors: Fakih Mohamad G. , Dueweke Cathleen , Meisner Susan , Berriel-Cass Dorine , Savoy-Moore Ruth , Brach Nicole , Rey Janice , Desantis Laura , Saravolatz Louis D.
Published: August 2008

Objective.

To determine the effect of nurse-led multidisciplinary rounds on reducing the unnecessary use of urinary catheters (UCs).

Design.

Quasi-experimental study with a control group, in 3 phases: preintervention, intervention, and postintervention.

Setting.

Twelve medical-surgical units within a 608-bed teaching hospital, from May 2006 through April 2007.

Intervention.

A nurse trained in the indications for UC utilization participated in daily multidisciplinary rounds on 10 medical-surgical units. If no appropriate indication for a patient's UC was found, the patient's nurse was asked to contact the physician to request discontinuation. Data were collected before the intervention (for 5 days), during the intervention (for 10 days), and 4 weeks after the intervention (for 5 days). Two units served as controls.

Results.

Of 4,963 patient-days observed, a UC was present in 885 (for a total of 885 “UC-days”). There was a significant reduction in the rate of UC utilization from 203 UC-days per 1,000 patient-days in the preintervention phase to 162 UC-days per 1,000 patient-days in the intervention phase (P = .002). The postintervention rate of 187 UC-days per 1,000 patient-days was higher than the rate during the intervention (P = .05) but not significantly different from the preintervention rate (P = .32). The rate of unnecessary use of UCs also decreased from 102 UC-days per 1,000 patient-days in the preintervention phase to 64 UC-days per 1,000 patient-days during the intervention phase (P < .001); and, significantly, the rate rose to 91 UC-days per 1,000 patient-days in the postintervention phase (P = .01). The rate of discontinuation of unnecessary UCs in the intervention phase was 73 (45%) of 162.

Conclusions.

A nurse-led multidisciplinary approach to evaluate the need for UCs was associated with a reduction of unnecessary UC use. Efforts to sustain the intervention-induced reduction may be successful when trained advocates continue this effort with each team.
Cancer outlier detection based on likelihood ratio test
Authors: Hu Jianhua
Published: August 2008

Motivation: Microarray experiments can be used to help study the role of chromosomal translocation in cancer development through cancer outlier detection. The aim is to identify genes that are up- or down-regulated in a subset of cancer samples in comparison to normal samples.

Results: We propose a likelihood-based approach which targets detecting the change of point in mean expression intensity in the group of cancer samples. A desirable property of the proposed approach is the availability of theoretical significance-level results. Simulation studies showed that the performance of the proposed approach is appealing in terms of both detection power and false discovery rate. And the real data example also favored the likelihood-based approach in terms of the biological relevance of the results.

Availability: R code to implement the proposed method in the statistical package R is available at: http://odin.mdacc.tmc.edu/~jhhu/cod-analysis/.

Contact:  jhu@mdanderson.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Protein function prediction and annotation in an integrated environment powered by web services (AFAWE)
Authors: Jöcker Anika , Hoffmann Fabian , Groscurth Andreas , Schoof Heiko
Published: August 2008

Summary: Many sequenced genes are mainly annotated through automatic transfer of annotation from similar sequences. Manual comparison of results or intermediate results from different tools can help avoid wrong annotations and give hints to the function of a gene even if none of the automated tools could return any result.

AFAWE simplifies the task of manual functional annotation by running different tools and workflows for automatic function prediction and displaying the results in a way that facilitates comparison. Because all programs are executed as web services, AFAWE is easily extensible and can directly query primary databases, thereby always using the most up-to-date data sources. Visual filters help to distinguish trustworthy results from non-significant results. Furthermore, an interface to add detailed manual annotation to each gene is provided, which can be displayed to other users.

Availability: AFAWE is available at http://bioinfo.mpiz-koeln.mpg.de/afawe/

Contact:  afawe-admin@mpiz-koeln.mpg.de

Supplementary information: SIFTER pipeline (S1), AFAWE tutorial (S2).
Host manipulation as a parasite transmission strategy when manipulation is exploited by non-host predators
Authors: Seppälä Otto , Jokela Jukka
Published: August 2008

Trophically transmitted parasites often alter their intermediate host's phenotype, thereby predisposing hosts to increased predation. This is generally considered to be a parasite strategy evolved to enhance transmission to the next host. However, the adaptive value of host manipulation is not clear, as it may be associated with costs, such as increased susceptibility to predator species that are unsuitable next hosts for the parasites. Thus, it has been proposed that, to be adaptive, manipulation should be specific by predisposing hosts more strongly to predation by target hosts (next host in the life cycle) than to non-hosts. Here we formally evaluate this prediction, and show that manipulation does not have to be specific to be adaptive. However, when manipulation is nonspecific, it needs to effectively increase the overall predation risk of infected hosts if it is to increase the parasite transmission probability. Thus, when initial predation risk is low, even highly nonspecific manipulation strategies can be adaptive. However, when initial predation risk is high, manipulation needs to be more specific to increase parasite transmission success. Therefore, nonspecific host manipulation may evolve in nature, but the adaptive value of a certain manipulation strategy can vary among different parasite populations depending on the variation in initial predation risk.
Acoustic experience shapes female mate choice in field crickets
Authors: Bailey Nathan W , Zuk Marlene
Published: August 2008

Female choice can drive the evolution of extravagant male traits. In invertebrates, the influence of prior social experience on female choice has only recently been considered. To better understand the evolutionary implications of experience-mediated plasticity in female choice, we investigated the effect of acoustic experience during rearing on female responsiveness to male song in the field cricket
Teleogryllus oceanicus
. Acoustic experience has unique biological relevance in this species: a morphological mutation has rendered over 90 per cent of males on the Hawaiian island of Kauai silent in fewer than 20 generations, impeding females' abilities to locate potential mates. Females reared in silent conditions mimicking Kauai were less discriminating of male calling song and more responsive to playbacks, compared with females that experienced song during rearing. Our results to our knowledge, are the first demonstration of long-term effects of acoustic experience in an arthropod, and suggest that female
T. oceanicus
may be able to compensate for the reduced availability of long-range male sexual signals by increasing their responsiveness to the few remaining signallers. Understanding the adaptive significance of experience-mediated plasticity in female choice provides insight into processes that facilitate rapid evolutionary change and shape sexual selection pressure in natural populations.
African Odyssey project – satellite tracking of black storks Ciconia nigra breeding at a migratory divide
Authors: Bobek Miroslav , Hampl Radek , Peške Lubomír , Pojer František , Šimek Jaroslav , Bureš Stanislav
Published: August 2008

The African Odyssey project focuses on studying the migration of the black stork Ciconia nigra breeding at a migratory divide. In 1995–2001, a total of 18 black storks breeding in the Czech Republic were equipped with satellite (PTT) and VHF transmitters. Of them, 11 birds were tracked during at least one migration season and three birds were tracked repeatedly. The birds migrated either across western or eastern Europe to spend the winter in tropical west or east Africa, respectively. One of the juveniles made an intermediate route through Italy where it was shot during the first autumn migration. The mean distance of autumn migration was 6,227 km. The eastern route was significantly longer than the western one (7,000 km and 5,667 km respectively). Important stopover sites were discovered in Africa and Israel. Wintering areas were found from Mauritania and Sierra Leone in the west to Ethiopia and Central African Republic in the east and south. One of the storks migrating by the eastern migration route surprisingly reached western Africa. Birds that arrived early in the wintering areas stayed longer than those arriving later. On the average, birds migrating via the western route spent 37 d on migration compared to 80 d for birds migrating via the eastern route. The mean migration speed in the autumn was 126 km/d and the fastest stork flew 488 km/d when crossing the Sahara. The repeatedly tracked storks showed high winter site fidelity.
Change in plasma acylation stimulating protein during euglycaemic‐hyperinsulinaemic clamp in overweight and obese postmenopausal women: a MONET study
Authors: St‐Pierre David H. , Cianflone Katherine , Smith Jessica , Coderre Lise , Karelis Antony D. , Imbeault Pascal , Lavoie Jean‐Marc , Rabasa‐Lhoret Rémi
Published: August 2008

Objective  Acylation‐stimulating protein (ASP) has been shown to positively stimulate fatty acid esterification and glucose uptake in adipocytes. In vitro studies demonstrate that insulin stimulates ASP secretion from adipocytes. Individuals with obesity and/or metabolic disturbances (insulin resistance and type 2 diabetes) have increased plasma ASP.

Design  The present study was designed to evaluate whether ASP levels are influenced by the metabolic profiles of overweight and obese postmenopausal women during a euglycaemic/hyperinsulinaemic clamp (EHC).

Patients  The study population consisted of 76 overweight and obese sedentary postmenopausal women.

Measurements  We evaluated insulin sensitivity, plasma ASP levels, body composition including visceral adipose tissue area, blood lipid profiles, liver enzymes, peak aerobic capacity, resting metabolic rate (RMR) and total energy expenditure (TEE).

Results  We observed wide interindividual variations of ASP levels during the EHC. Therefore, subjects were divided into three groups based on ASP changes. Negative ASP Responders (NAR; n = 24) showed a –20% or greater decrease in ASP levels while Positive ASP Responders (PAR; n = 42) displayed ASP fluctuations superior to +20%. Ten subjects had little or no ASP change and were considered as Zero ASP responders (ZAR). PAR women displayed a worse metabolic profile than NAR women, including higher BMI, visceral adipose tissue, fasting insulin levels, lean body mass, and alanine aminotransferase (ALT), a marker of impaired liver function. After adjustment for BMI, only ALT remained significantly different, while lean body mass (P = 0·08) and visceral adipose tissue (P = 0·07) remained marginally higher. Correlation analysis of all subjects demonstrated that fasting ASP levels correlated positively with albumin and VO2 peak and this association remained significant after adjustments for the effect of BMI. In addition, the percentage maximal change in ASP levels during the EHC was positively associated with BMI, lean body mass, visceral adipose tissue, fasting insulin, HOMA, TEE, RMR, ALT and AST.

Conclusion  Overall these results suggest that an elevated ASP response during the EHC is associated with metabolic disturbances in overweight and obese postmenopausal women.
Applying life‐history strategies for freshwater macroinvertebrates to lentic waters
Authors: VERBERK WILCO C. E. P. , SIEPEL HENK , ESSELINK HANS
Published: August 2008

Effective environmental management requires a sound understanding of the causal mechanisms underlying the relationship of species with their environment. Mechanistic explanations linking species and environment are ultimately based on species traits. Many tools for ecological assessment and biomonitoring lack such explanations. Elsewhere, we have defined life‐history strategies, based on the interrelations between species traits and their functional implications.

This study tests the hypothesis that life‐history strategies represent different solutions to particular ecological problems, thus connecting species and their environment through species traits. Data on aquatic macroinvertebrates in a variety of waterbodies were analysed in terms of life‐history strategies. These waterbodies differed in environmental conditions and macroinvertebrate assemblages. Solutions to the ecological problems present in each type of water body were expected to be reflected in the abundance of (species exhibiting) different life‐history strategies.

Results show clear differences in strategy composition between the different water types, which could be related to the prevailing environmental conditions through mechanistic explanations. For example, species with a long period of juvenile development and a synchronized emergence of short‐lived adults were most dominant in large mesotrophic waterbodies with stable and predictable environmental conditions. In contrast, species that have a rapid development and spread successive reproduction attempts over a longer time period were most abundant in waterbodies with fluctuating and less predictable environmental conditions.

Differences in strategy composition provide insight into the prevailing environmental conditions related to temporal predictability, and habitat favourability, from the perspective of the species themselves. By reducing diverse species assemblages to a small number of strategies, representing easily interpretable relationships, this approach may be useful in environmental quality assessment programmes, including those required by the European Water Framework Directive. Based on mechanistic explanations, life‐history strategies may generate testable predictions and guide future research. Further research may focus on expanding life‐history strategies to include other species groups and ecosystems.
Feeding difficulty in older adults with dementia
Authors: Chang Chia‐Chi , Roberts Beverly L
Published: August 2008

Aims and objectives.  To use concept analysis to identify characteristics of feeding difficulty and its antecedents and consequences that provide direction for assessment and management.

Background.  Feeding difficulty is often recognised as a common problem for older adults and is associated with weight loss, poor nutrition and risk for aspiration pneumonia. The cognitive impairment found in persons with dementia impairs the ability of these adults to complete motor and perceptual tasks required for eating and often prevent the older adult from accepting help with feeding from caregivers.

Design.  Systematic review.

Methods.  In 2006, literature searches using keywords (feeding, eating, nutrition, malnutrition, feeding assessment, dementia, ageing and concept analysis, dementia and feeding and excluding enteral feeding, tube feedings, PEG and enteral nutrition) were done in Medline, CINHAL, AGELINE and Social Science Full Text. Seventy relevant articles in English were found. After a review of the relevant articles, concept analysis was used to develop a definition of feeding difficulty, its defining characteristics and to delineate feeding difficulty from its antecedents and consequences.

Results.  Feeding difficulties arise at the interface between the caregiver strategies to assist the older adult with getting food into the mouth and chewing and swallowing food. A model of feeding difficulty delineates the antecedents and consequences of feeding difficulties.

Conclusions.  The conceptual model of feeding difficulties provides a strong and clear organising structure for research that can be used to developed evidence based guidelines for practice.

Relevance to clinical practice.  The conceptual model provides directions for assessment of feeding difficulties and their antecedents. The model can be used to identify interventions that address antecedents of feeding difficulty (risk factors) and different types of feeding difficulties.
Patients’ perceptions of their participation in discharge planning after acute stroke
Authors: Almborg Ann‐Helene , Ulander Kerstin , Thulin Anders , Berg Stig
Published: August 2008

Aims and objectives.  To describe stroke patients’ perceptions of their participation in the discharge planning process and identify correlates of perceived participation.

Background.  Patients have the right to participate in discharge planning, but earlier research has shown that they are often dissatisfied with the information they receive and their involvement in goal‐setting during discharge planning.

Design.  Cross‐sectional study.

Methods.  The sample consisted of 188 persons (mean age 74 years, SD 11·2) with acute stroke who were admitted to a stroke unit at a hospital in southern Sweden during 2003–2005. Data was collected by face‐to‐face interviews 2–3 weeks after discharge using the ‘Patients’ Questionnaire on Participation in Discharge Planning’. This instrument measures perceived participation in discharge planning in three subscales: P‐Information, P‐Medical Treatment, P‐Goals and Needs.

Results.  The percentage of patients who perceived that they had participated in discharge planning was as follows: 72–90% according to P‐Information, 29–38% according to P‐Medical Treatment and 15–47% according to P‐Goals and Needs. Age, education and performance of activities of daily living were significantly related to perceived participation as measured by different subscales.

Conclusions.  Most of the patients perceived that they received information, but fewer perceived participation in the planning of medical treatment and needs of care/service/rehabilitation and goal‐setting. Professionals need to pay more attention to patients in different subgroups to facilitate their participation in discharge planning.

Relevance to clinical practice.  To facilitate and increase patients’ participation in discharge planning, methods should be implemented for goal‐setting and identifying patients’ needs. Methods that foster patient participation may improve goal‐orientated care, services and rehabilitation after discharge.
Evaluation of the performance of using mean absolute amplitude analysis of thoracic and abdominal signals for immediate indication of sleep apnoea events
Authors: Ng Alice SL , Chung Joanne WY , Gohel Mayur DI , Yu Winnie WM , Fan Ka L , Wong Thomas KS
Published: August 2008

Aim.  To evaluate the sensitivity of mean absolute amplitudes of the thoracic and the abdominal signals as a prompt indicator of the occurrence of sleep apnoea events.

Background.  To provide symptomatic management of sleep apnoea, a reliable method of detecting sleep apnoea is essential to ensure that the intervention can be applied only when needed. It is also crucial to identify the threshold for the trigger of an intervention using a deployed sensor.

Design.  Twenty‐six subjects aged between 18–65 years who were diagnosed with obstructive or central sleep apnoea underwent an overnight sleep study.

Method.  Signals of nasal and oral airflow, thoracic and abdominal efforts and pulse oximetry level were recorded using a polysomnography device.

Results.  With a 95% CI, the overall area under the receiver operating characteristic of the thoracic signal, the abdominal signal and the combination of the thoracic and the abdominal signals were 84·56, 87·48 and 90·91%, respectively. Using −20, −25 and −30% as a cut‐off point, the sensitivity values of thoracic signal, abdominal signal and combination of the thoracic and the abdominal signals ranged from 70·29–86·25% and the specificity values ranged from 74·82 to 90·09%.

Conclusions.  Using mean absolute amplitude analysis, the results of this study showed that combination of the thoracic and the abdominal signals achieved the best overall and individual performances compared with thoracic signal and abdominal signal. Overall, thoracic signal, abdominal signal and combination of the thoracic and the abdominal signals have a good performance with an receiver operating characteristic value higher than 80%. The thoracic and the abdominal signals were good parameters for the identification of the occurrence of sleep apnoea, being as quick as the nasal airflow signal.

Relevance to clinical practice.  These results suggested that sleep apnoea events could be identified through constant monitoring of the patient’s thoracic and abdominal signals. Knowledge of these signals could help nurses to manage sleep apnoea in patients.
Cytotoxic chemotherapy for incurable colorectal cancer: living with a PICC‐line
Authors: Molloy Doreen , Smith Lorraine N , Aitchison Tom
Published: August 2008

Aims.  (i) To determine which aspects of living with a peripherally inserted central catheter (PICC) line cause Modified de Gramont (MdG) patients most difficulty. (ii) To explore MdG patients’ views of the PICC‐line experience. (iii) To determine if patients view PICC‐lines as a benefit or a burden when receiving ambulatory MdG chemotherapy.

Design.  A two‐stage, descriptive study.

Methods.  Phase 1 comprised semi‐structured interviews. Phase 2 surveyed the MdG population. Phase 1 interview data informed the Phase 2 questionnaire. The setting was a West of Scotland Cancer Care Centre and the sample was: Phase 1, a convenience sample of 10 MdG patients; Phase 2, 62 consecutive patients.

Results.  A response rate of 93·9% for Phase 2. The majority of PICC‐line patients held favourable views towards having a PICC‐line and adapted well with minimal disruption to daily life. Concerns were evident regarding coping at home with a PICC‐line, chemotherapy spillage, dealing with complex information and the responsibility of patients/carers regarding PICC‐line management. Patients preferred ambulatory chemotherapy to in‐patient treatment.

Conclusions.  PICC‐lines should be considered for more chemotherapy patients but service development is necessary to ensure individual needs are addressed.

Relevance to clinical practice.  Contributes to the PICC‐line literature by providing a national patient perspective on a range of daily living activities (DLAs). PICC‐line patients prefer out‐patient ambulatory chemotherapy rather than in‐patient treatment. The longer a patient has a PICC‐line, the more able they are to manage activities such as dressing. Concerns remain over chemotherapy spillage, partner/carer responsibility for PICC‐line maintenance and the proper balance between required information and what the patient wants to know.
A family caregiver‐oriented discharge planning program for older stroke patients and their family caregivers
Authors: Shyu Yea‐Ing Lotus , Chen Min‐Chi , Chen Sien‐Tsong , Wang Hsiao‐Ping , Shao Jung‐Hua
Published: August 2008

Aims.  To test the effectiveness of a discharge planning program for dyads of older stroke survivors and their family caregivers in Taiwan.

Background.  Family caregivers of stroke survivors often feel inadequately prepared to deal with the physical, cognitive and emotional needs of the stroke survivors. However, little information could be found on discharge planning programs for caregivers of stroke survivors in Asian families.

Design.  A randomised experimental design was used to explore the effects of a discharge planning program for 158 dyads of older stroke patients and their family caregivers.

Methods.  The control group (n = 86 dyads) received only routine hospital discharge planning services and the experimental group (n = 72 dyads) received routine hospital discharge planning services plus the caregiver‐oriented discharge planning program. Outcome variables were measured at baseline, before discharge and one month after hospital discharge. Variables were measured by the Nurse Evaluation of Caregiver Preparation Scale, Preparedness for Caregiving Scale, Caregiver Discharge Needs Satisfaction Scale and Perception of Balance between Competing Needs Scale.

Results.  Caregivers in the experimental group had significantly better nurse evaluation and self‐evaluation of preparation after the program than before, and greater satisfaction of discharge needs one month after discharge than before discharge. Caregivers in the experimental group had significantly better nurse evaluations and self‐evaluations of preparation and better satisfaction of discharge needs after the program compared with the control group. However, no significant difference was found between caregiver groups in perceived balance of competing needs.

Conclusions.  This discharge planning program benefited family caregivers of older stroke patients during the transition from hospitalisation to one month after discharge.

Relevance to clinical practice.  This caregiver‐oriented discharge planning program, with its emphasis on individualised health education and home visits following discharge may improve caregivers’ preparation and the satisfaction of their needs during the discharge transition.
Masticatory dysfunction in persons with Down’s syndrome. Part 1: aetiology and incidence
Authors: FAULKS D. , COLLADO V. , MAZILLE M.‐N. , VEYRUNE J.‐L. , HENNEQUIN M.
Published: August 2008

Summary The functional and anatomical characteristics of Down’s syndrome have direct repercussions on oral health. Orofacial dysfunction is on account of poor neuromotor control, muscle weakness, dental anomalies, dysmorphology and intercurrent illness. In particular, feeding and swallowing are impaired. The aim of this first article was to summarize the orofacial difficulties encountered by persons with Down’s syndrome at all stages of life and to explain their aetiology. Indicators are proposed for the identification of masticatory problems within this population and reduced masticatory efficiency is discussed in relation to repercussions on oral and general health and on the social integration of persons with Down’s syndrome. A second article will describe techniques for preventing, treating and compensating for masticatory dysfunction in this population.
Disentangling the effects of recombination, selection, and demography on the genetic variation at a major histocompatibility complex class II gene in the alpine chamois
Authors: MONA S. , CRESTANELLO B. , BANKHEAD‐DRONNET S. , PECCHIOLI E. , INGROSSO S. , D’AMELIO S. , ROSSI L. , MENEGUZ P. G. , BERTORELLE G.
Published: August 2008

The major histocompatibility complex (MHC) harbours some of the most polymorphic loci in vertebrate genomes. MHC genes are thought to be subject to some form of balancing selection, most likely pathogen‐mediated selection. Hence, MHC genes are excellent candidates for exploring adaptive processes. In this study, we investigated the genetic variation at exon 2 of the DRB class II MHC locus in 191 alpine chamois (Rupicapra rupicapra) from 10 populations in the eastern Alps of Italy. In particular, we were interested in distinguishing and estimating the relative impact of selective and demographic factors, while taking into account the confounding effect of recombination. The extremely highdn/dsratio and the presence of trans‐species polymorphisms suggest that a strong long‐term balancing selection effect has been operating at this locus throughout the evolutionary history of this species. We analysed patterns of genetic variation within and between populations, and the mitochondrial D‐loop polymorphism patterns were analysed to provide a baseline indicator of the effects of demographic processes. These analyses showed that (i) the chamois experienced a demographic decline in the last 5000–30 000 years, most likely related to the postglacial elevation in temperature; (ii) this demographic process can explain the results of neutrality tests applied to MHC variation within populations, but cannot justify the much weaker divergence between populations implied by MHC as opposed to mitochondrial DNA; (iii) similar sets of divergent alleles are probably maintained with similar frequencies by balancing selection in different populations, and this mechanism is also operating in small isolated populations, which are strongly affected by drift.
Cell‐specific localization of Na+ in roots of durum wheat and possible control points for salt exclusion
Authors: LÄUCHLI ANDRÉ , JAMES RICHARD A. , HUANG CHENG X. , McCULLY MARGARET , MUNNS RANA
Published: August 2008

Sodium exclusion from leaves is an important mechanism for salt tolerance in durum wheat. To characterize possible control points for Na+ exclusion, quantitative cryo‐analytical scanning electron microscopy was used to determine cell‐specific ion profiles across roots of two durum wheat genotypes with contrasting rates of Na+ transport from root to shoot grown in 50 mm NaCl. The Na+ concentration in Line 149 (low transport genotype) declined across the cortex, being highest in the epidermal and sub‐epidermal cells (48 mm) and lowest in the inner cortical cells (22 mm). Na+ was high in the pericycle (85 mm) and low in the xylem parenchyma (34 mm). The Na+ profile in Tamaroi (high transport genotype) had a similar trend but with a high concentration (130 mm) in the xylem parenchyma. The K+ profiles were generally inverse to those of Na+. Chloride was only detected in the epidermis. These data suggest that the epidermal and cortical cells removed most of the Na+ and Cl‐ from the transpiration stream before it reached the endodermis, and that the endodermis is not the control point for salt uptake by the plant. The pericycle as well as the xylem parenchyma may be important in the control of net Na+ loading of the xylem.
Plastid genomes in a regenerating tobacco shoot derive from a small number of copies selected through a stochastic process
Authors: Lutz Kerry Ann , Maliga Pal
Published: August 2008

The plastid genome (ptDNA) of higher plants is highly polyploid, and the 1000–10 000 copies are compartmentalized with up to approximately 100 plastids per cell. The problem we address here is whether or not a newly arising genome can be established in a developing tobacco shoot, and be transmitted to the seed progeny. We tested this by generating two unequal ptDNA populations in a cultured tobacco cell. The parental tobacco plants in this study have an aurea (yellowish–golden) leaf color caused by the presence of a barau gene in the ptDNA. In addition, the ptDNA carries an aadA gene flanked with the phiC31 phage site‐specific recombinase (Int) attP/attB target sites. The genetically distinct ptDNA copies were obtained by Int, which either excised only the aadA marker gene (i.e. did not affect the aurea phenotype) or triggered the deletion of both the aadA and barau transgenes, and thereby restored the green color. The ptDNA determining green plastids represented only a small fraction of the population and was not seen in a transient excision assay, and yet three out of the 53 regenerated shoots carried green plastids in all developmental layers. The remaining 49 Int‐expressing plants had either exclusively aurea (24) or variegated (25) leaves with aurea and green sectors. The formation of homoplastomic green shoots with the minor green ptDNA in all developmental layers suggests that the ptDNA population in a regenerating shoot apical meristem derives from a small number of copies selected through a stochastic process.
Interaction of the K+‐channel KAT1 with the coat protein complex II coat component Sec24 depends on a di‐acidic endoplasmic reticulum export motif
Authors: Sieben Christian , Mikosch Melanie , Brandizzi Federica , Homann Ulrike
Published: August 2008

The correct functioning of ion channels depends not only on the control of their activity but also on the regulation of the number of channels in the membrane. For example, it has been proposed that the density of the plant K+‐channel KAT1 may be adjusted by controlling its export from its site of synthesis, the endoplasmic reticulum (ER). Efficient transport of the channel to the plasma membrane was found to depend on a di‐acidic ER export signal in the C‐terminus of the protein. Studies in yeast and mammals indicate that di‐acidic ER export motifs are essential for enrichment of proteins into ER‐derived coat protein complex II (COPII) vesicles and are recognized by Sec24 a component of the COPII coat. To investigate whether similar mechanisms also exist in plants we have analysed the interaction of KAT1 with Sec24 in vivo using fluorescence resonance energy transfer (FRET) measurements in Vicia faba guard cells. These measurements revealed a FRET signal between KAT1 and Sec24 fused to the cyan fluorescent protein and the yellow fluorescent protein, respectively, indicating an interaction between KAT1 and Sec24. The FRET signal only occurred in the perinuclear region of the ER and was dependent on the di‐acidic ER export motif of KAT1. Together, the results point to a highly conserved mechanism for ER export of KAT1 whereby the channel is recruited into COPII vesicles via binding of the di‐acidic motif to Sec24.
Impact of a new invasive ctenophore (Mnemiopsis leidyi) on the zooplankton community of the Southern Caspian sea
Authors: Roohi Abolghasem , Yasin Zulfigar , Kideys Ahmet E. , Hwai Aileen Tan Shau , Khanari Ali Ganjian , Eker‐Develi Elif
Published: August 2008

The invasive ctenophore Mnemiopsis leidyi (Agassiz), which was transported from the Black Sea into the Caspian Sea at the end of the 1990s, has negatively affected the ecosystem of the Caspian Sea. Zooplankton abundance, biomass and species composition were evaluated on the Iranian coast of the Caspian Sea during 2001–2006. A total of 18 merozooplankton (13 species composed of larvae of benthic animals) and holozooplankton (four Copepoda and one Cladocera) species were identified. The total number of zooplankton species found here was 50% less than in a previous investigation performed in the same region in 1996 before the introduction of Mnemiopsis leidyi into the Caspian Sea. Cladocera species seemed to be highly affected by the invasion of Mnemiopsis leidyi; only one species, Podon polyphemoides, remained in the study area, whereas 24 Cladocera species were found in the study carried out in 1996. Whereas among the Copepoda Eurytemora minor, Eurytemora grimmi, Calanipeda aquae dulcis and Acartia tonsa that were abundant before the Mnemiopsis leidyi invasion, only A. tonsa (copepodites and adults) dominated the inshore and offshore waters after the invasion. The maximum in zooplankton abundance (22,088 ± 24,840 ind·m−3) and biomass (64.1 ± 56.8 mg·m−3) were recorded in December 2001 and August 2004, respectively. The annual mean zooplankton abundance during 2001–2006 was in the range of 3361–8940 ind·m−3; this was two‐ to five‐fold less than the zooplankton abundance in 1996. During 2001–2006, the highest abundance and biomass of Mnemiopsis leidyi were observed during summer‐autumn months coincident with warm temperatures and generally when the abundance of other zooplankton organisms was low.
Arrhythmogenic substrates in myocardial infarct
Authors: Takamatsu Tetsuro
Published: August 2008

Life‐threatening ventricular tachyarrhythmias are common clinical complications in ischemic heart diseases, especially infarcted heart. Although electrophysiological mechanisms have been extensively clarified for the genesis of arrhythmias in myocardial infarct, arrhythmogenic substrates in the infarct that eventually lead to electrical derangements are not fully understood. This review focuses on the intracellular calcium ion (Ca2+) dynamics and connexin43 (Cx43) gap junctions that play pivotal roles in excitation/contraction processes and intercellular communication, respectively, in heart muscle cells. Recent development of Ca2+‐sensitive fluorescent dyes as well as microscopy imaging techniques has contributed substantially to a more precise understanding of spatiotemporal aspects in the intra‐ and inter‐cellular dynamics of Ca2+ in cardiomyocytes. Ca2+ waves, heterogeneous wave‐like elevations of the intracellular Ca2+ concentrations ([Ca2+]i) that develop under [Ca2+]i‐overloaded conditions of the injured myocardium, play an essential role in arrhythmias, especially in triggered arrhythmias. Alteration of Cx43‐mediated electrical coupling, that is, gap junction remodeling that arises at myocyte–myocyte and myocyte–myofibroblast interfaces, would also be an important substrate for arrhythmias, especially re‐entrant tachyarrhythmias. Clarification of these substrates would provide not only deeper insights into the upstream events of life‐threatening tachyarrhythmias in the infarcted heart but also bases for new therapeutic strategies for cardiovascular diseases.
Clinical relevance of CD10, BCL‐6 and multiple myeloma‐1 expression in diffuse large B‐cell lymphomas in Malaysia
Authors: Peh Suat‐Cheng , Gan Gin‐Gin , Lee Lin‐Kiat , Eow Geok‐Im
Published: August 2008

Diffuse large B‐cell lymphoma (DLBCL) is the most common subtype of non‐Hodgkin lymphoma, and it is recognized to constitute a heterogenous group of neoplasms. It can be divided into germinal center B‐cell‐like (GCB) and non‐GCB subgroups. The aim of the present study was to evaluate the utility of immunophenotype subgrouping of DLBCL in a cohort of multi‐ethnic Asian patients. A total of 84 reconfirmed de novo DLBCL were immunostained for the expression of CD10, BCL‐2, BCL‐6 and multiple myeloma‐1. Thirty‐three (39.3%) had the GCB phenotype, and the remainder (60.7%), the non‐GCB phenotype. The results concur with most reports using a similar method of stratification. Forty‐five patients had complete demographic and phenotype studies and 42 patients did not have rituximab treatment and had sufficient data for survival rate analysis. Similar to other studies, patients with combined low and low–intermediate International Prognostic Index score had better overall survival (P = 0.006). But patients with GCB phenotype did not have better prognosis, and BCL‐2 expression was not associated with better prognosis. The expression of BCL‐6 was associated with lower overall survival rate (P = 0.038). No apparent difference in overall and disease‐free survival was noted between patients with GCB and non‐GCB disease. BCL‐6 expression by tumor cells appears to be associated with poorer prognosis.
Evaluation of intra‐ and interobserver agreement and its clinical significance for scoring bcl‐2 immunohistochemical expression in diffuse large B‐cell lymphoma
Authors: Borlot Vinicius Freitas , Biasoli Irene , Schaffel Rony , Azambuja Denize , Milito Cristiane , Luiz Ronir Raggio , Scheliga Adriana , Spector Nelson , Morais José Carlos
Published: August 2008

Immunohistochemistry (IHC) has become an essential part of diagnosis and clinical research in lymphomas. There is considerable heterogeneity, however, in IHC findings regarding expression rate and positivity cut‐offs, which creates a degree of uncertainty that has prevented its incorporation for prognostic purposes. The purpose of the present study was to assess intra‐ and interobserver agreement in scoring bcl‐2 expression on IHC. The study materials were 81 diffuse large B‐cell lymphomas. Slides were processed in the same laboratory, and were analyzed independently and in a blinded manner by four pathologists twice, at least 1 month apart. The positivity rates ranged from 31% to 41% in the first evaluation, and from 30% to 43% in the second evaluation. The two analyses by the same pathologist gave concordant results in 88–93% of cases (κ = 0.71–0.83). Complete agreement among all observers varied from 72% to 79%. The experience of the observer did not influence intra‐observer concordance. Cooperative analysis of discordant slides led to consensus in all cases. The variation observed in scoring bcl‐2 expression is acceptable for use in lymphoma diagnosis and classification. The use of IHC stratification, however, for clinical decisions regarding treatment will require standardization and centralized consensus review, and must await the results of ongoing prospective trials.
Dietary fibre and the gut microbiota
Authors: Scott K. P. , Duncan S. H. , Flint H. J.
Published: August 2008

Summary The complex human colonic microbiota plays a key role in gut health, and both the composition and metabolism of the gut microbiota are strongly diet related. Controlled dietary intake studies in obese individuals demonstrated that consumption of low‐carbohydrate diets results in low faecal butyrate concentrations together with a low abundance of the major butyrate‐producing bacteria,Roseburiaspp. andEubacterium rectalegroup.

Resistant dietary carbohydrates, including pre‐biotics, escape digestion in the upper gastrointestinal tract and are fermented to short‐chain fatty acids (SCFAs) by bacteria in the colon. The main SCFAs formed are acetate, propionate and butyrate. Model colonic fermentor systems employed to determine which bacterial groups utilise specific substrates indicated that the bacterial composition and production of SCFAs is substrate dependent. The bacterial colonisers of specific substrates were identified using 16S rRNA sequence analysis. Sequences recovered from bran were most closely related toRoseburiaspp.,E. rectaleandClostridium hathewayi, while on resistant starch, sequences were most closely related toRuminococcus bromiiandBifidobacterium adolescentis.

Differing intakes of dietary carbohydrate also impact on other factors in the colon such as transit and pH. In continuous fermentor systems, a slightly acidic pH (5.5) representative of the proximal colon gave fourfold higher butyrate concentrations than at the higher pH of 6.5, which is more representative of the distal colon.Bacteroidetesdominated the fermentor at pH 6.5, while the major butyrate‐producing bacterial groups competed more effectively for carbohydrate substrates when the pH was mildly acidic (5.5). Inin vitrostudies in which pH values were even lower, pH 5.2, lactate and acetate accumulated. In contrast, lactate was not detected at pH 6.4 although stable isotope studies revealed that lactate was actively produced. Lactate accumulation at low pH appears to be as a result of the loss of lactate‐utilising bacteria includingEubacterium hallii.

It is clear that the composition of the colonic microbiota and the balance of its metabolic products is strongly influenced by diet and, in particular, by the intake of resistant carbohydrates and dietary fibre.
Valuing executive stock options: performance hurdles, early exercise and stochastic volatility
Authors: Brown Philip , Szimayer Alex
Published: August 2008

Accounting standards require companies to assess the fair value of any stock options granted to executives and employees. We develop a model for accurately valuing executive and employee stock options, focusing on performance hurdles, early exercise and uncertain volatility. We apply the model in two case studies and show that properly computed fair values can be significantly lower than traditional Black–Scholes values. We then explore the implications for pay‐for‐performance sensitivity and the design of effective share‐based incentive schemes. We find that performance hurdles can require a much greater fraction of total compensation to be a fixed salary, if pre‐existing incentive levels are to be maintained.
Co‐speech gesture as input in verb learning
Authors: Goodrich Whitney , Hudson Kam Carla L.
Published: August 2008

People gesture a great deal when speaking, and research has shown that listeners can interpret the information contained in gesture. The current research examines whether learners can also use co‐speech gesture to inform language learning. Specifically, we examine whether listeners can use information contained in an iconic gesture to assign meaning to a novel verb form. Two experiments demonstrate that adults and 2‐, 3‐, and 4‐year‐old children can infer the meaning of novel intransitive verbs from gestures when no other source of information is present. The findings support the idea that gesture might be a source of input available to language learners.
Who needs employees?
Authors: Crainer Stuart , Birkinshaw Julian
Published: August 2008

Jack Hughes founded his company on an unusual business model that is uniquely satisfying the needs of software developers and their clients. Stuart Crainer and Julian Birkinshaw say there are some important lessons in business as unusual.