bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA
Authors: Pierstorff Nora , Bergman Casey M. , Wiehe Thomas 
Published: October 2006

Abstract
Motivation: Predicting cis-regulatory modules (CRMs) in higher eukaryotes is a challenging computational task. Commonly used methods to predict CRMs based on the signal of transcription factor binding sites (TFBS) are limited by prior information about transcription factor specificity. More general methods that bypass the reliance on TFBS models are needed for comprehensive CRM prediction.
Results: We have developed a method to predict CRMs called CisPlusFinder that identifies high density regions of perfect local ungapped sequences (PLUSs) based on multiple species conservation. By assuming that PLUSs contain core TFBS motifs that are locally overrepresented, the method attempts to capture the expected features of CRM structure and evolution. Applied to a benchmark dataset of CRMs involved in early Drosophila development, CisPlusFinder predicts more annotated CRMs than all other methods tested. Using the REDfly database, we find that some ‘false positive’ predictions in the benchmark dataset correspond to recently annotated CRMs. Our work demonstrates that CRM prediction methods that combine comparative genomic data with statistical properties of DNA may achieve reasonable performance when applied genome-wide in the absence of an a priori set of known TFBS motifs.
Availability: The program CisPlusFinder can be downloaded at . All software is licensed under the Lesser GNU Public License (LGPL).
Contact: nora.pierstorff@uni-koeln.de.
Supplementary information: Supplementary data are available at Bioinformatics online.
Postnatal changes in the expression of genes located in the callipyge region in sheep skeletal muscle
Authors: Perkins A. C. , Kramer L. N. , Spurlock D. M. , Hadfield T. S. , Cockett N. E. , Bidwell C. A. 
Published: October 2006

SummaryThe expression of five genes surrounding the callipyge (CLPG) mutation was analysed in skeletal muscles from lambs at one prenatal and two postnatal ages that coincide with the onset and establishment of muscle hypertrophy. Genotype‐specific changes in transcript abundance were detected for paternal allele‐specific DLK1 and PEG11 (the official symbol of the latter is RTL1) and the maternal allele‐specific MEG3, PEG11AS and MEG8 when the mutation was inherited in cis. There were differences in the temporal and muscle‐specific effects on expression between the maternal allele‐specific genes and paternal allele‐specific genes. Maternal inheritance of the CLPG allele had a significant effect on the expression of MEG3 and MEG8 at prenatal and postnatal ages, whereas paternal inheritance of DLK1 and PEG11 only affected postnatal expression. Genotype‐specific changes in PEG11AS expression were detected only in prenatal muscle. Maternal inheritance of the mutation caused similar changes in MEG3 and MEG8 expression in the semimembranosus, which undergoes hypertrophy, and the supraspinatus, which does not hypertrophy. Paternal inheritance of the mutation caused changes in PEG11 expression in both muscles, although the magnitude of expression in semimembranosus was more than 100‐fold greater than in supraspinatus. DLK1 expression was upregulated in callipyge animals at both postnatal ages in the semimembranosus, but there was no effect of genotype on DLK1 expression in the supraspinatus at any age. Increased DLK1 expression was likely the primary cause of muscle hypertrophy, but a contribution of PEG11 to the phenotype cannot be ruled out based on gene expression.
Pro‐inflammatory bone marrow milieu in patients with chronic idiopathic neutropenia is associated with impaired local production of interleukin‐10
Authors: Koumaki Vasiliki , Damianaki Athina , Ximeri Maria , Pontikoglou Charis , Axioti Fani , Spanoudakis Michael , Eliopoulos George D. , Papadaki Helen A. 
Published: October 2006

SummaryThe levels of interleukin‐10 (IL‐10) were evaluated in long‐term bone marrow (BM) culture supernatants from 54 patients with chronic idiopathic neutropenia (CIN) and 30 healthy volunteers using enzyme‐linked immunoabsorbent assay. Cytokine levels were significantly reduced in patients, compared with controls, and strongly correlated with peripheral blood neutrophil counts. Low levels of supernatant IL‐10 were associated with increased values of supernatant IL‐1β, tumour necrosis factor‐α, IL‐6 and transforming growth factor‐β1. We suggest that the pro‐inflammatory milieu in the BM of CIN patients may be causatively related to the impaired production of IL‐10, a cytokine normally displaying strong anti‐inflammatory properties.
Change and continuity: childbirth and parenting across three generations of women in the United Arab Emirates
Authors: Green K. E. , Smith D. E. 
Published: October 2006

AbstractBackground  The United Arab Emirates (UAE) is a country that has undergone remarkable physical, economic and social shifts in its short modern history. And while the economic and structural transformations of the society have been well documented and publicized, information about the changes and transformations of family processes is sparse. This study is one of the first steps towards documenting the changes in family processes, namely those related to childbirth and parenting, as described by three generations of Emirati women.Methods  Family triads of Grandmothers, Mothers and married Daughters (n = 216) were interviewed in local Arabic dialect by Emirati female research assistants. Data were analysed using chi square and Analysis of Variance.Results  Generational differences were found between the Grandmothers, Mothers and Daughters in: number of births, maternal age at first birth, location and type of birth attendant, medication during labour and birth, father presence at birth, social support following birth, feeding and weaning of infant, and preventive infant health care. Changes were not found in the proximity to the mother of the infant during sleep.Conclusions  The age of first birth has risen for Emirati women and the birth rate may have dropped. Health care has also significantly improved. These results are discussed in relation to government initiatives and physical and social change within the UAE and the Middle East.
Examining how contexts shape young children’s perspectives of health
Authors: Irwin L. G. , Johnson J. L. , Henderson A. , Dahinten V. S. , Hertzman C. 
Published: October 2006

AbstractBackground We know that the social conditions in which children live exert a strong influence on their health; yet, we do not know how children’s experience of these conditions of daily life shape their perspectives of health.Methods Through ethnographic research methods, the first author spent 1 year with the 14 6‐year‐old children involved in this research and examined how the contexts of daily life influenced the children’s perspectives of health. The children involved in this study all lived in a neighbourhood characterized as having a complex of mid to high range of neighbourhood factors associated with vulnerability.Results The findings demonstrate that the children were able to articulate the health requirements of physical activity and healthy eating that supports their health. However, there was a disparity between the children’s health knowledge, their perceptions and their contextual realities in relation to health. Children spoke of concerns for their physical safety within their schools and neighbourhoods; their lack of free range of play, and that they had few opportunities to play with or get to know neighbourhood friends.Conclusion Professionals in contact with children and families who live in challenging social conditions need to be aware of how these contexts shape children’s understanding of their own health potential.
Listen to me, too! Lessons from involving children with complex healthcare needs in research about multi‐agency services
Authors: Watson D. , Abbott D. , Townsley R. 
Published: October 2006

AbstractBackground  Children with complex healthcare needs are often excluded, both from active involvement in research projects and from direct consultation in services. During a 3‐year research study into multi‐agency services for children with complex healthcare needs, the authors involved children in a number of innovative ways and endeavoured to discover what impact, if any, multi‐agency working made to them.Methods  The researchers ‘spent time’ with 18 children with complex healthcare needs. They used a variety of methods to engage with the children in a meaningful way. More than half of the children had no verbal communication, so it was necessary in some cases to work with an advocate, usually the parent, to aid the process.Results  Children with complex healthcare needs can take part in research as long as the research is set up sensitively and flexibly. In terms of the impact of multi‐agency working, the authors concluded significant advances had been achieved for this group: almost all the children were living at home and attending school. However, there were significant gaps in addressing children’s human rights in relation to communication, independence and relationships. In addition, many of the children had very little effective direct consultation with the multi‐agency services.Conclusions  There are significant advances in involving disabled children in research and in service delivery, but there is still some way to go in involving those with complex healthcare needs. The challenges are considerable, but the benefits far outweigh these, not least being the value that parents, carers and the children themselves place upon being listened to.
Rates and causes of child mortality in an area of high HIV prevalence in rural South Africa
Authors: Garrib Anupam , Jaffar Shabbar , Knight Stephen , Bradshaw Debbie , Bennish Michael L. 
Published: October 2006

SummaryObjective  To determine child mortality rates in a rural area of South Africa with high HIV prevalence.Methods  A community‐based survey was conducted between 1 January 2000 and 31 December 2002 on deaths in children under the age of 15 years. Children were followed up through four monthly home visits. Cause of death was ascertained by verbal autopsy. Rates were calculated using Poisson regression.Results  Mortality ratios were 59.6 deaths per 1000 live births for infants and 97.1 for children under 5 years of age. Infant and under‐5 mortality rates were, respectively, 67.5 and 21.1 deaths per 1000 person‐years. HIV/AIDS was attributed to 41% of deaths in the under‐5 age group, with a mortality rate of 8.6 per 1000 person‐years. Lower respiratory infections caused an estimated 24.9 deaths per 1000 person‐years in children under 1 year of age.Conclusions  In rural South Africa, infant and child mortality levels are high, with HIV/AIDS estimated as the single largest cause of death. Interventions to reduce child mortality are required urgently.
Development of a psychological treatment service for pruritic skin conditions
Authors: Long Dorota , Long Randall A , Grillo Marianne P , Marshman Gillian 
Published: October 2006

SUMMARYThe role of psychological contributions to common dermatological disease is increasingly recognized. It is often a challenge to find suitable psychological services to complement dermatological treatment. This paper describes the development of a psychological treatment service to reduce scratching behaviour found in common pruritic skin conditions. Our Department of Dermatology together with a consultation–liaison psychiatrist designed a four‐session outpatient treatment programme incorporating psychiatric assessment, psychoeducation about the itch–scratch cycle, behavioural analysis, habit reversal techniques and between‐session tasks for the patient to complete. This programme is actively modified in consultation with patients and their therapists to suit each patient’s individual needs. Formal investigation is required to determine if this psychological treatment adds benefit in overall symptom control beyond dermatological treatment alone.
Chondrocutaneous advancement flap for reconstruction of helical rim defects in dermatologic surgery
Authors: Krunic Aleksandar L , Weitzul Sarah , Taylor R Stan 
Published: October 2006

SUMMARYThe helical rim is often affected with cutaneous malignancies and requires special attention in the repair, owing to the complex cartilaginous contour, preservation of the aesthetic contour and restoration of its supportive function for eyeglasses and hearing aids. We review the surgical technique of chondrocutaneous advancement flap described by Antia and Buch as one of the most cosmetically appealing and versatile approaches for the repair of small defects of the ear helix.
Recurrent cutaneous tumour with features of an osteosarcoma: Primary osteosarcoma or cutaneous carcinosarcoma?
Authors: Tran Kayla L. , Karim Rooshdiya Z. , McKenzie Paul R. , Stretch Jonathan 
Published: October 2006

We report the case of a recurrent tumour with histological features of an osteosarcoma, and discuss the differential diagnosis.An 80 year old woman presented with a fungating tumour on the right calf, arising from an area of previous split skin grafting. There was also a new 1–2 cm diameter nodule at the medial ankle of the right leg. The patient had previously had a lesion removed from the same site, reported as a squamous cell carcinoma. The recurrent calf lesion was excised, as well as the skin nodule on the medial ankle of the right leg. Histological examination of both specimens showed similar features, with a malignant neoplasm having features of an osteosarcoma, with osteoid formation. No carcinomatous component was seen in the sections examined. Immunohistochemical studies for cytokeratin, S100, HMB45 and Melan‐A were negative in the malignant cells. Tumour giant cells were CD68 positive.The differential diagnoses included recurrent squamous cell carcinoma presenting as a carcinosarcoma with sarcomatous overgrowth, primary cutaneous osteosarcoma, metastatic osteosarcoma, malignant mixed dermal tumour, malignant peripheral nerve sheath tumour with an osteosarcomatous component and undifferentiated pleomorphic sarcoma with osteosarcoma‐like areas.Primary cutaneous carcinosarcomas, primary cutaneous osteosarcomas and metastatic osteosarcoma to the skin are all rare. Squamous cell carcinomas and basal cell carcinomas are the most common epithelial component of cutaneous carcinosarcomas, with osteosarcomas and undifferentiated pleomorphic sarcomas (malignant fibrous histiocytomas) the most commonly reported sarcomatous component. Extraskeletal osteosarcomas are also uncommon, with the skin a rarely reported primary site. Predisposing factors for extraskeletal osteosarcomas include past trauma, pre‐existing soft tissue calcification, ossification, myositis ossificans and intramuscular injection sites.This is an unusual presentation of what would appear to be a recurrent tumour, previously diagnosed as squamous cell carcinoma. The histological appearance raises a number of possibilities, requiring clinicopathological correlation.
Two‐year interim results from a 5‐year study evaluating clinical recurrence of superficial basal cell carcinoma after treatment with imiquimod 5% cream daily for 6 weeks
Authors: Quirk Chris , Gebauer Kurt , Owens Mary , Stampone Patti 
Published: October 2006

SUMMARYImiquimod 5% cream is approved in the USA, Europe and Australia to treat superficial basal cell carcinoma, using a regimen of once daily, 5 times per week for 6 weeks. Vehicle‐controlled, phase III clinical trials show that imiquimod is safe and effective for treating superficial basal cell carcinoma with dosing 5 or 7 times per week for 6 weeks. This phase III, open‐label study evaluates the long‐term (5 years) clinical efficacy and safety of dosing once daily, for which this manuscript reports the 2‐year time point in the follow‐up period. For the 169 enrolled subjects, the tumour selected for treatment was assessed clinically to determine initial clearance at the 12‐week post‐treatment visit. If clinically clear of superficial basal cell carcinoma, subjects entered a 5‐year, long‐term follow‐up period. Subjects were evaluated for recurrence at the 3‐, 6‐, 12‐ and 24‐month follow‐up visits. The initial clearance rate at 12 weeks post treatment was 94.1%. The proportion of subjects who were clinically clear at the 2‐year follow‐up visit was estimated to be 82.0%. Imiquimod was tolerated when applied daily, with erythema reported for all subjects participating in the study. The recurrence rate observed suggests that once daily dosing and 5×/week dosing yield similar clearance rates, but daily dosing increases local skin reactions.
Surgical management of extensive gnathophyma
Authors: Schintler MV , Arbab E , Aberer W , Spendel S , Scharnagl E 
Published: October 2006

AbstractRhinophyma is an uncommon disease of the nose characterized by irregular skin thickening and nodular deformation. The extensive growth causing ‘whisky nose’ is due to hyperplasia of the sebaceous glands and the surrounding connective tissue. Other facial regions may concomitantly be affected. We present a case of extensive gnathophyma accompanying minor lesions of the nose. Surgical treatment led to an excellent cosmetic result.
A simple and practical method in treatment of ingrown nails: splinting by flexible tube
Authors: Nazari S 
Published: October 2006

AbstractBackground  The ingrown nail (or onychocryptosis) is a common problem that occurs mostly in the big toe and causes high amounts of morbidity in affected patients. Many therapeutic methods have been described, most of them leading to severe damage to the nail or to frequent relapses. The nail splinting technique is a successful, simple and non‐invasive therapeutic method for treating ingrown nails.Objective  To determine efficacy of the plastic tube insertion technique in patients with ingrown toenail and its use as a standard treatment.Materials and Methods  We encountered 32 cases (age range 9–67 years) of ingrown toenails in this clinical trial. All of the patients were treated using the plastic nail tube insertion technique for 7 to 15 days. Patients were examined daily for the first 3 days of treatment and were evaluated 3 and 6 months after treatment. All patients were followed up by a single observer.Results  Recurrence was seen in only two patients after 6 months of treatment (6.25%).Conclusion  The low recurrence rate using the nail splinting technique in the treatment of ingrown toenail, as well as its simple application, shows that this treatment constitutes an effective, non‐invasive method. It appears that this technique can substitute other more invasive surgical methods, particularly in the early stages of this disease.
Age at First Intoxication and Alcohol Use Disorders in Southwest California Indians
Authors: Ehlers Cindy L. , Slutske Wendy S. , Gilder David A. , Lau Philip , Wilhelmsen Kirk C. 
Published: October 2006

Background: In several national surveys, a younger age of onset of first drink and/or regular drinking has been associated with a higher likelihood of the development of alcohol dependence. Some studies have suggested that age at first drink is primarily an environmentally driven variable whereas others suggest that it may be partially mediated by a general vulnerability to exhibit problem behaviors. Although Native Americans, overall, have the highest prevalence of alcohol dependence of any U.S. ethnic group, the relationship of age of onset of intoxication with alcohol dependence in Native American populations is relatively unknown.Methods: Demographic information and DSM‐III‐R diagnoses were obtained from 525 Southwest California (SWC) Indian adults residing on contiguous reservations. Survival analyses and Cox and logistic regression were used to investigate the relationship between age of onset of first intoxication and the development of alcohol dependence. Heritability of the age of onset of first intoxication was also determined using SOLAR.Results: Age at first intoxication was not found to be heritable in this population. Early onset of intoxication, however, was found to be significantly associated with both a shorter time to onset of alcohol dependence and increased prevalence in this population, even on taking into account several other risk factors including externalizing diagnoses.Conclusions: These data suggest that effective environmental prevention efforts at reducing underage drinking may be an important strategy to lower the prevalence of alcohol dependence in this high‐risk population.
Clinical Characteristics of Obstructive Sleep Apnea in Community‐Dwelling Older Adults
Authors: Endeshaw Yohannes 
Published: October 2006

OBJECTIVES: To examine whether traditional risk factors are common in older adults with obstructive sleep apnea (OSA).DESIGN: Cross‐sectional study.SETTING: Atlanta, Georgia.PARTICIPANTS: A convenience sample of 94 community‐dwelling adults aged 62 to 91.MEASUREMENTS: Demographic, medical, and sleep‐related information obtained using questionnaires. Epworth Sleepiness Scale (ESS) and 72‐hour voiding diary were used to determine daytime sleepiness and nocturia frequency, respectively. Overnight ambulatory sleep recording device was used to screen for OSA.RESULTS: Fifteen female and 15 male subjects had an apnea‐hypopnea index (AHI) of 15 or more per hour of sleep (moderate to severe OSA). Traditional risk factors such as snoring, body mass index, and neck circumference were not significantly associated with OSA. An AHI of 15 or more per hour was independently associated with not feeling well rested in the morning, higher ESS score, and greater frequency of nocturia.CONCLUSION: Traditional risk factors for OSA were not common presenting symptoms and signs in study subjects with an AHI of 15 or more per hour of sleep; this may contribute to underdiagnosis of OSA in this population. Subjects with an AHI of 15 or more per hour had more sleep‐related complaints and excessive daytime sleepiness. Although occult, this suggests that OSA may contribute to disease burden in this group of people.
Genetic Ancestry and Risk Factors for Breast Cancer among Latinas in the San Francisco Bay Area
Authors: Ziv Elad , John Esther M. , Choudhry Shweta , Kho Jennifer , Lorizio Wendy , Perez-Stable Eliseo J. , Burchard Esteban Gonzalez 
Published: October 2006

Abstract
Background: Genetic association studies using case-control designs are susceptible to false-positive and false-negative results if there are differences in genetic ancestry between cases and controls. We measured genetic ancestry among Latinas in a population-based case-control study of breast cancer and tested the association between ancestry and known breast cancer risk factors. We reasoned that if genetic ancestry is associated with known breast cancer risk factors, then the results of genetic association studies would be confounded.
Methods: We used 44 ancestry informative markers to estimate individuals' genetic ancestry in 563 Latina participants. To test whether ancestry is a predictor of hormone therapy use, parity, and body mass index (BMI), we used multivariate logistic regression models to estimate odds ratios (OR) and 95% confidence intervals (95% CI) associated with a 25% increase in Indigenous American ancestry, adjusting for age, education, and the participant's and grandparents' place of birth.
Results: Hormone therapy use was significantly less common among women with higher Indigenous American ancestry (OR, 0.78; 95% CI, 0.63-0.96). Higher Indigenous American ancestry was also significantly associated with overweight (BMI, 25-29.9 versus &lt;25) and obesity (BMI, ≥30 versus &lt;25), but only among foreign-born Latina women (OR, 3.44; 95% CI, 1.97-5.99 and OR, 1.95; 95% CI, 1.24-3.06, respectively).
Conclusion: Some breast cancer risk factors are associated with genetic ancestry among Latinas in the San Francisco Bay Area. Therefore, case-control genetic association studies for breast cancer should directly measure genetic ancestry to avoid potential confounding. (Cancer Epidemiol Biomarkers Prev 2006;15(10):1878–85)