bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering transcriptional interactions via an adaptive fuzzy logic approach
Authors: Chuang Cheng-Long , Hung Kenneth , Chen Chung-Ming , Shieh Grace S 
Published: December 2009

AbstractBackgroundTo date, only a limited number of transcriptional regulatory interactions have been uncovered. In a pilot study integrating sequence data with microarray data, a position weight matrix (PWM) performed poorly in inferring transcriptional interactions (TIs), which represent physical interactions between transcription factors (TF) and upstream sequences of target genes. Inferring a TI means that the promoter sequence of a target is inferred to match the consensus sequence motifs of a potential TF, and their interaction type such as AT or RT is also predicted. Thus, a robust PWM (rPWM) was developed to search for consensus sequence motifs. In addition to rPWM, one feature extracted from ChIP-chip data was incorporated to identify potential TIs under specific conditions. An interaction type classifier was assembled to predict activation/repression of potential TIs using microarray data. This approach, combining an adaptive (learning) fuzzy inference system and an interaction type classifier to predicttranscriptionalregulatorynetworks, was named AdaFuzzy.ResultsAdaFuzzy was applied to predict TIs using real genomics data fromSaccharomyces cerevisiae. Following one of the latest advances in predicting TIs, constrained probabilistic sparse matrix factorization (cPSMF), and using 19 transcription factors (TFs), we compared AdaFuzzy to four well-known approaches using over-representation analysis and gene set enrichment analysis. AdaFuzzy outperformed these four algorithms. Furthermore, AdaFuzzy was shown to perform comparably to 'ChIP-experimental method' in inferring TIs identified by two sets of large scale ChIP-chip data, respectively. AdaFuzzy was also able to classify all predicted TIs into one or more of the four promoter architectures. The results coincided with known promoter architectures in yeast and provided insights into transcriptional regulatory mechanisms.ConclusionAdaFuzzy successfully integrates multiple types of data (sequence, ChIP, and microarray) to predict transcriptional regulatory networks. The validated success in the prediction results implies that AdaFuzzy can be applied to uncover TIs in yeast.
A pooling-based genome-wide analysis identifies new potential candidate genes for atopy in the European Community Respiratory Health Survey (ECRHS)
Authors: Castro-Giner Francesc , Bustamante Mariona , Ramon González Juan , Kogevinas Manolis , Jarvis Deborah , Heinrich Joachim , Antó Josep-Maria , Wjst Matthias , Estivill Xavier , de Cid Rafael 
Published: December 2009

Abstract

Background
Asthma and atopy are complex phenotypes with shared genetic component. In this study we attempt to identify genes related to these traits performing a two-stage DNA pooling genome-wide analysis in order to reduce costs. First, we assessed all markers in a subset of subjects using DNA pooling, and in a second stage we evaluated the most promising markers at an individual level.

Methods
For the genome-wide analysis, we constructed DNA pools from 75 subjects with atopy and asthma, 75 subjects with atopy and without asthma and 75 control subjects without atopy or asthma. In a second stage, the most promising regions surrounding significant markers after correction for false discovery rate were replicated with individual genotyping of samples included in the pools and an additional set of 429 atopic subjects and 222 controls from the same study centres.

Results

Homo sapiens protein kinase-like protein SgK493 (SGK493) was found to be associated with atopy. To lesser extent mitogen-activated protein kinase 5 (MAP3K5), collagen type XVIII alpha 1 (COL18A1) and collagen type XXIX alpha 1 (COL29A1) were also found to be associated with atopy. Functional evidences points out a role for MAP3K5, COL18A1 and COL29A1 but the function of SGK493 is unknown.

Conclusion
In this analysis we have identified new candidate regions related to atopy and suggest SGK493 as an atopy locus, although these results need further replication.
Helping someone with problem drinking: Mental health first aid guidelines - a Delphi expert consensus study
Authors: Kingston Anna H , Jorm Anthony F , Kitchener Betty A , Hides Leanne , Kelly Claire M , Morgan Amy J , Hart Laura M , Lubman Dan I 
Published: December 2009

Abstract

Background
Alcohol is a leading risk factor for avoidable disease burden. Research suggests that a drinker's social network can play an integral role in addressing hazardous (i.e., high-risk) or problem drinking. Often however, social networks do not have adequate mental health literacy (i.e., knowledge about mental health problems, like problem drinking, or how to treat them). This is a concern as the response that a drinker receives from their social network can have a substantial impact on their willingness to seek help. This paper describes the development of mental health first aid guidelines that inform community members on how to help someone who may have, or may be developing, a drinking problem (i.e., alcohol abuse or dependence).

Methods
A systematic review of the research and lay literature was conducted to develop a 285-item survey containing strategies on how to help someone who may have, or may be developing, a drinking problem. Two panels of experts (consumers/carers and clinicians) individually rated survey items, using a Delphi process. Surveys were completed online or via postal mail. Participants were 99 consumers, carers and clinicians with experience or expertise in problem drinking from Australia, Canada, Ireland, New Zealand, the United Kingdom, and the United States. Items that reached consensus on importance were retained and written into guidelines.

Results
The overall response rate across all three rounds was 68.7% (67.6% consumers/carers, 69.2% clinicians), with 184 first aid strategies rated as essential or important by ≥80% of panel members. The endorsed guidelines provide guidance on how to: recognize problem drinking; approach someone if there is concern about their drinking; support the person to change their drinking; respond if they are unwilling to change their drinking; facilitate professional help seeking and respond if professional help is refused; and manage an alcohol-related medical emergency.

Conclusion
The guidelines provide a consensus-based resource for community members seeking to help someone with a drinking problem. Improving community awareness and understanding of how to identify and support someone with a drinking problem may lead to earlier recognition of problem drinking and greater facilitation of professional help seeking.
Interventions for promoting physical activity among European teenagers: a systematic review
Authors: De Meester Femke , van Lenthe Frank J , Spittaels Heleen , Lien Nanna , De Bourdeaudhuij Ilse 
Published: December 2009

Abstract

Background
Although physical activity is considered to yield substantial health benefits, the level of physical activity among European teenagers is not sufficient. Adolescence is characterized by a decline in physical activity level. Many studies investigated the effectiveness of interventions promoting physical activity among young people, but none dealt with the available evidence specific for Europe. This review was conducted to summarize the effectiveness of interventions to promote physical activity among European teenagers.

Methods
A systematic review was conducted to identify European intervention studies published in the scientific literature since 1995. Four databases were searched, reference lists were scanned and the publication lists of the authors of the retrieved articles were checked. The ANGELO framework was used to categorise the included studies by setting and by intervention components.

Results
The literature search identified 20 relevant studies. Fifteen interventions were delivered through the school setting, of which three included a family component and another three a family and community component. One intervention was conducted within a community setting, three were delivered in primary care and one was delivered through the internet. Ten interventions included only an individual component, whereas the other ten used a multi-component approach. None of the interventions included only an environmental component.
Main findings of the review were: (1) school-based interventions generally lead to short term improvements in physical activity levels; (2) improvements in physical activity levels by school-based interventions were limited to school related physical activity with no conclusive transfer to leisure time physical activity; (3) including parents appeared to enhance school-based interventions; (4) the support of peers and the influence of direct environmental changes increased the physical activity level of secondary school children; (5) the assumption that a multi-component approach should produce synergistic results can not be confirmed; (6) when interventions aimed to affect more than one health behaviour the intervention appeared to be less effective in favour of physical activity.

Conclusion
Overall, the current European literature supports the short-term effectiveness of school-based physical activity promotion programmes. The available evidence for the effectiveness in other settings is rather limited and underscores the need for further research.
A MIF haplotype is associated with the outcome of patients with severe sepsis: a case control study
Authors: Lehmann Lutz E , Book Malte , Hartmann Wolfgang , Weber Stefan U , Schewe Jens-Christian , Klaschik Sven , Hoeft Andreas , Stüber Frank 
Published: December 2009

Abstract

Background
Macrophage migration inhibitory factor (MIF) plays an important regulatory role in sepsis. In the promoter region a C/G single nucleotide polymorphism (SNP) at position -173 (rs755622) and a CATT5-8 microsatellite at position -794 are related to modified promoter activity. The purpose of the study was to analyze their association with the incidence and outcome of severe sepsis.

Methods
Genotype distributions and allele frequencies in 169 patients with severe sepsis, 94 healthy blood donors and 183 postoperative patients without signs of infection or inflammation were analyzed by real time PCR and Sequence analysis. All included individuals were Caucasians.

Results
Genotype distribution and allele frequencies of severe sepsis patients were comparable to both control groups. However, the genotype and allele frequencies of both polymorphisms were associated significantly with the outcome of severe sepsis. The highest risk of dying from severe sepsis was detectable in patients carrying a haplotype with the alleles -173 C and CATT7 (p = 0.0005, fisher exact test, RR = 1,806, CI: 1.337 to 2.439).

Conclusion
The haplotype with the combination of the -173 C allele and the -794 CATT7 allele may not serve as a marker for susceptibility to sepsis, but may help identify septic patients at risk of dying.
Primary plasmacytoma of the cranial vault: a case report
Authors: Zigouris Anrdeas , Drosos Dimitrios , Alexiou George A , Fotakopoulos George , Mihos Evaggelos , Pahatouridis Dimitrios , Tsiouris Spyridon , Fotopoulos Andreas D , Voulgaris Spyridon 
Published: December 2009

Abstract
We report one case of a 78-year-old woman who referred to our hospital because of a progressive right hemiparesis. On clinical examination a painless large soft mass in the left parietal region was observed. CT and MRI revealed an extra-axial mass in the in the left fronto-temporo-parietal region. The lesion was totally excised despite the bleeding tendency. Histology disclosed the presence of a plasmacytoma. Postoperative, the patient developed an epidural hematoma that required immediate evacuation. On further investigation active tuberculosis was detected. On follow up examination 1 year later no tumor recurrence or evidence of multiple myeloma was detected.
Association of BRCA1 Mutations With Occult Primary Ovarian Insufficiency: A Possible Explanation for the Link Between Infertility and Breast/Ovarian Cancer Risks
Authors: Oktay Kutluk , Kim Ja Yeon , Barad David , Babayev Samir N. 
Published: December 2009

Purpose Germline mutations in BRCA genes are associated with breast and ovarian cancer susceptibility. Because infertility is associated with breast and ovarian cancer risks, we hypothesized that the mutations in the BRCA gene may be associated with low response to fertility treatments. Methods We performed ovarian stimulation in 126 women with breast cancer by using letrozole and gonadotropins for the purpose of fertility preservation by embryo or oocyte cryopreservation. As surrogates of ovarian reserve, the oocyte yield and the incidence of low response were compared with ovarian stimulation according to BRCA mutation status. Results Of the 82 women who met the inclusion criteria, 47 women (57%) had undergone BRCA testing, and 14 had a mutation in BRCA genes, of which two were of clinically undetermined significance. In BRCA mutation–positive patients, low ovarian response rate was significantly higher compared with BRCA mutation–negative patients (33.3 v 3.3%; P = .014) and with BRCA-untested women (2.9%; P = .012). All BRCA mutation–positive low responders had BRCA1 mutations, but low response was not encountered in women who were only BRCA2 mutation positive. Compared with controls, BRCA1 mutation– but not BRCA2 mutation–positive women produced lower numbers of eggs (7.4 [95% CI, 3.1 to 17.7] v 12.4 [95% CI, 10.8 to 14.2]; P = .025) and had as many as 38.3 times the odds ratio of low response (95% CI, 4.1 to 353.4; P = .001). Conclusion BRCA1 mutations are associated with occult primary ovarian insufficiency. This finding may, at least in part, explain the link between infertility and breast/ovarian cancer risks.
The Effect of Agitation and Quenchant Temperature on the Heat Transfer Coefficients for 6061 Aluminum Alloy Quenched in Distilled Water
Authors: Maniruzzaman Mohammed , Fontecchio Marco , Sisson Richard D. 
Published: December 2009

Abstract
A 6061 aluminum alloy probe was quenched using a Center for Heat Treating Excellence probe-quenching system in distilled water while varying bath temperature and the agitation level. Time versus temperature data were collected during the quench using a thermocouple embedded inside the probe. The surface heat transfer coefficients as a function of temperature were calculated using the Newtonian cooling approximation. The maximum heat transfer coefficient values ranged from 1054 W/m2⋅K for 100°C water with no agitation to 3822 W/m2⋅K for 5°C water with the agitation of 1850 r/min. The data also showed that at higher levels of agitation and lower bath temperatures, the maximum heat transfer coefficient increased.
Stress Field Evolution in a Ball Bearing Raceway Fatigue Spall
Authors: Branch Nathan A. , Arakere Nagaraj K. , Svendsen Vaughn , Forster Nelson H. 
Published: December 2009

Abstract
The governing mechanisms of fatigue spall propagation in ball bearing inner raceways are investigated through the use of elastic-plastic finite element modeling, X-ray diffraction, and the visual inspection of fatigue spall cracks. The model simulates multiple ball impacts with a fatigue spall’s edge in a 208 size ball bearing operating at 10,000 rpm. Ball impacts are shown to cause severe plastic deformation within the spall edge and induce tensile residual stresses. The finite element results are supported by X-ray diffraction measurements and the locations of cracks observed around the edge of a spall.
Preterm Birth, Social Disadvantage, and Cognitive Competence in Swedish 18- to 19-Year-Old Men
Authors: Ekeus Cecilia , Lindström Karolina , Lindblad Frank , Rasmussen Finn , Hjern Anders 
Published: December 2009

OBJECTIVE: The aim was to study the impact of a range of gestational ages (GAs) on cognitive competence in late adolescence and how this effect is modified by contextual social adversity in childhood.METHODS: This was a register study based on a national cohort of 119664 men born in Sweden from 1973 to 1976. Data on GA and other perinatal factors were obtained from the Medical Birth Register, and information on cognitive test scores was extracted from military conscription at the ages of 18 to 19 years. Test scores were analyzed as z scores on a 9-point stanine scale, whereby each unit is equivalent to 0.5 SD. Socioeconomic indicators of the childhood household were obtained from the Population and Housing Census of 1990. The data were analyzed by multivariate linear regression.RESULTS: The mean cognitive test scores decreased in a stepwise manner with GA. In unadjusted analysis, the test scores were 0.63 stanine unit lower in men who were born after 24 to 32 gestational weeks than in those who were born at term. The difference in global scores between the lowest and highest category of socioeconomic status was 1.57. Adjusting the analysis for the childhood socioeconomic indicators decreased the effect of GA on cognitive test scores by 26% to 33%. There was also a multiplicative interaction effect of social adversity and moderately preterm birth on cognitive test scores.CONCLUSIONS: This study confirms previous claims of an incremental association of cognitive competence with GA. Socioeconomic indicators in childhood modified this effect at all levels of preterm birth.
Timing of Parent and Child Communication About Sexuality Relative to Children's Sexual Behaviors
Authors: Beckett Megan K. , Elliott Marc N. , Martino Steven , Kanouse David E. , Corona Rosalie , Klein David J. , Schuster Mark A. 
Published: December 2009

OBJECTIVE: To examine timing of parent–child discussions about sexual topics relative to child-reported sexual behavior.METHODS: Longitudinal study of employed parents and their children, with an initial survey followed by subsequent surveys 3, 6, and 12 months later. Participants were 141 parents, along with their children (13–17 years), who were control participants in a randomized, controlled trial to evaluate a worksite-based intervention to improve parent–adolescent communication. Main outcomes were parent and child reports of discussion of up to 24 sexual topics and presexual and sexual acts (ranging from handholding to vaginal intercourse) that occurred before the first survey and in the intervals between subsequent pairs of surveys.RESULTS: Sexual topics tend to group into 3 sets. The first set includes topics such as girls' bodies and menstruation and typically coincides with children's presexual stage (handholding, kissing). The second set includes topics such as birth control efficacy and refusing sex and typically coincides with the precoital stage (genital touching and oral sex). The third set typically occurs when children have initiated intercourse. Over half of children engage in genital touching before discussing birth control efficacy, resisting partner pressure for sex, sexually transmitted disease symptoms, condom use, choosing birth control, or partner condom refusal; &gt;40% of children have intercourse before any discussion about sexually transmitted disease symptoms, condom use, choosing birth control, or partner condom refusal.CONCLUSIONS: Many parents and adolescents do not talk about important sexual topics before adolescents' sexual debut. Clinicians can facilitate this communication by providing parents with information about sexual behavior of adolescents.
Food Allergy Knowledge, Attitudes, and Beliefs of Primary Care Physicians
Authors: Gupta Ruchi S. , Springston Elizabeth E. , Kim Jennifer S. , Smith Bridget , Pongracic Jacqueline A. , Wang Xiaobin , Holl Jane 
Published: December 2009

OBJECTIVE: To provide insight into food allergy knowledge and perceptions among pediatricians and family physicians in the United States.
METHODS: A national sample of pediatricians and family physicians was recruited between April and July 2008 to complete the validated, Web-based Chicago Food Allergy Research Survey for Primary Care Physicians. Findings were analyzed to provide composite/itemized knowledge scores, describe attitudes and beliefs, and examine the effects of participant characteristics on response.
RESULTS: The sample included 407 primary care physicians; 99% of the respondents reported providing care for food-allergic patients. Participants answered 61% of knowledge-based items correctly. Strengths and weaknesses were identified in each content domain evaluated by the survey. For example, 80% of physicians surveyed knew that the flu vaccine is unsafe for egg-allergic children, 90% recognized that the number of food-allergic children is increasing in the United States, and 80% were aware that there is no cure for food allergy. However, only 24% knew that oral food challenges may be used in the diagnosis of food allergy, 12% correctly rejected that chronic nasal problems are not symptom of food allergy, and 23% recognized that yogurts/cheeses from milk are unsafe for children with immunoglobulin E–mediated milk allergies. Fewer than 30% of the participants felt comfortable interpreting laboratory tests to diagnose food allergy or felt adequately prepared by their medical training to care for food-allergic children.
CONCLUSIONS: Knowledge of food allergy among primary care physicians was fair. Opportunities for improvement exist, as acknowledged by participants' own perceptions of their clinical abilities in the management of food allergy.
Children on the Homefront: The Experience of Children From Military Families
Authors: Chandra Anita , Lara-Cinisomo Sandraluz , Jaycox Lisa H. , Tanielian Terri , Burns Rachel M. , Ruder Teague , Han Bing 
Published: December 2009

OBJECTIVE: Although studies have begun to explore the impact of the current wars on child well-being, none have examined how children are doing across social, emotional, and academic domains. In this study, we describe the health and well-being of children from military families from the perspectives of the child and nondeployed parent. We also assessed the experience of deployment for children and how it varies according to deployment length and military service component.
PARTICIPANTS AND METHODS. Data from a computer-assisted telephone interview with military children, aged 11 to 17 years, and nondeployed caregivers (n = 1507) were used to assess child well-being and difficulties with deployment. Multivariate regression analyses assessed the association between family characteristics, deployment histories, and child outcomes.
RESULTS: After controlling for family and service-member characteristics, children in this study had more emotional difficulties compared with national samples. Older youth and girls of all ages reported significantly more school-, family-, and peer-related difficulties with parental deployment (P &lt; .01). Length of parental deployment and poorer nondeployed caregiver mental health were significantly associated with a greater number of challenges for children both during deployment and deployed-parent reintegration (P &lt; .01). Family characteristics (eg, living in rented housing) were also associated with difficulties with deployment.
CONCLUSIONS: Families that experienced more total months of parental deployment may benefit from targeted support to deal with stressors that emerge over time. Also, families in which caregivers experience poorer mental health may benefit from programs that support the caregiver and child.