bluuebunny/crossref_metadata_2025 huggingface dataset:
Training Teachers to Follow a Task Analysis to Engage Middle School Students With Moderate and Severe Developmental Disabilities in Grade-Appropriate Literature
Authors: Browder Diane M. , Trela Katherine , Jimenez Bree
Published: June 2008

The purpose of this study Was to train teachers to folloW a task analysis to teach a story-based literacy lesson using adapted, grade-appropriate middle school literature to students With moderate and severe developmental disabilities. A multiple-probe-across-participants design Was used to examine the effects of training teachers to folloW a literacy lesson plan task analysis on the number of steps completed by teachers on the literacy lesson plan template and changes made by students in response to teachers' use of the literacy lesson plan. Results indicated a functional relationship betWeen teacher training and the number of lesson plan steps folloWed, With a corresponding student increase in both overall and independent correct responses. Implications for practice and future research are discussed.
Comparison of the Acquisition and Maintenance of Teaching Functional and Core Content Sight Words in Special and General Education Settings
Authors: Collins Belva C. , Evans Abby , Creech-Galloway Carey , Karl Jennifer , Miller Angela
Published: June 2008

In this investigation, the acquisition of both functional and core content sight Words Was compared as replicated across three formats: direct massed trial instruction in a special education resource room, direct distributed trial instruction in a general education classroom, and embedded distributed trial instruction in a general education classroom. Four students With moderate disabilities across three age groups participated. During direct instructional trials, both functional and core content sight Words Were presented using a constant time delay procedure. During embedded trials, the students received instruction in the same manner as their peers Without disabilities (e.g., teacher lecture, Worksheets, activities). Although the results varied slightly across participants, there Were minimal differences in the acquisition and maintenance of both functional and core content sight Words across the three presentation formats.
Components of Visual Literacy: Teaching Logos
Authors: Alberto Paul A. , Fredrick Laura , Hughes Melissa , McIntosh Laura , Cihak David
Published: June 2008

Definitions of literacy that focus solely on reading words provide too narrow a framework for many students with severe disabilities. Obtaining information from the environment may be accomplished in a variety of modes, such as visual literacy, which is the ability to discern meaning conveyed through images. A component of visual literacy is picture reading. This study demonstrates the teaching of logo reading through time delay as an additional component of visual literacy. Visual literacy is discussed as a primary means of obtaining information for some students and as an additional means of literacy for students who can also learn to read Words.
Effectiveness of Direct Instruction for Teaching Statement Inference, Use of Facts, and Analogies to Students With Developmental Disabilities and Reading Delays
Authors: Flores Margaret Munro , Ganz Jennifer B.
Published: June 2008

This study investigated the effects of a Direct Instruction (DI) reading comprehension program implemented With students Who had developmental disabilities, including autism spectrum disorders (ASD) and reading delays. There is little research in the area of reading comprehension for students With ASD and no research as to the effectiveness of reading comprehension DI. A multiple-probe-across-behaviors design Was employed. A functional relationship betWeen Direct Instruction and reading comprehension skills and behaviors Was demonstrated across all behavioral conditions and across students. Results and their implications are discussed.
Integrated Word Identification and Communication Instruction for Students With Complex Communication Needs
Authors: Hanser Gretchen A. , Erickson Karen A.
Published: June 2008

The current study investigated the effectiveness of an integrated word identification and communication intervention for children with complex communication needs. Using a nonconcurrent, multiple baseline design, the study involved three participants who completed 75 lessons across 4 to 6 weeks of instruction. All three participants improved their skills of word identification, developmental spelling, icon sequencing, and expressive communication. Generalization was documented through increases in the frequency of communication using icon sequencing and spelling outside of the instructional program. Implications for the development of integrated word study programs that combine systematic, sequential phonics instruction with instruction in the use of augmentative communication are discussed, along with directions for future research.
Structural Equation Modeling of Student Involvement in Transition-Related Actions
Authors: Sands Deanna J. , Spencer Karen C. , Gliner Jeff , Swaim Randall
Published: June 2008

Structural equation modeling was used to examine the relative influence of, and interaction between, three exogenous latent factors (student skills, family climate, educational opportunities) and two endogenous factors (student self-determination, student action taking). Data were collected from 237 middle school and high school students with disabilities from three different school districts representing rural, suburban, and urban settings. The hypothesized relationships among five latent factors were partially supported by findings. When nonsignificant paths were eliminated, a final model revealed a number of significant paths between latent factors and the residuals of individual variables. The latent factor Educational Opportunities was significantly related to student self-determination. Residuals from the latent factors Student Skills and Family Climate were significantly related to student self-determination and action taking. An unexpected finding was the apparent lack of significant relationships between student skills and family climate, and student self-determination and student action taking. Findings and proposed direction for future research are discussed.
Freedom, Support, Authority, and Responsibility
Authors: Shumway Donald L.
Published: June 2008

The professional direction of the lives of individuals with developmental disabilities is giving way to self-determination. This values-based movement relies on philosophical, managerial, and personal commitment to inclusive policy making, independent support brokerage, and the shifting of resource control to individually managed budgets. The Robert Wood Johnson Foundation (RWJF) National Program in Self-Determination is facilitating change through the support of "learning community" grants to self-advocacy organizations, to Arc, and to others (e.g., University Affiliated Programs). Multiyear implementation grants have been made to 29 states, and a longitudinal evaluation is underway. Local implementation is demonstrating creativity in establishing new tools for self-directed management of resources, listening to people, and reinvesting in communities.
The Importance of Family Involvement for Promoting Self-Determination in Adolescents with Autism and Other Developmental Disabilities
Authors: Field Sharon , Hoffman Alan
Published: June 2008

Self-determination has recently become an important concept in special education and disability services. The concept of self-determination is defined and component skills delineated. Some of the component skills of self-determination may pose particular challenges to people with autism and other developmental disabilities due to the difficulties in communication skills and social relationships experienced by many people in this population. Family involvement is an important variable affecting the development and expression of self-determination in people with autism and other developmental disabilities. Strategies to promote and support parental involvement in self-determination instruction are discussed.
Autism and Section 504
Authors: Katsiyannis Antonis , Reid Robert
Published: June 2008

Although Section 504 of the Rehabilitation Act of 1973 has been in effect for more than 20 years, it has had little direct impact on educational practice until fairly recently. Moreover, the primary thrust has been directed toward children with mild disabilities. In this article, we focus on Section 504 as it pertains to children with autism. We describe eligibility requirements for Section 504, and rights and protections afforded. We also discuss trends in litigation for students with autism. Finally, we discuss potential issues pertaining to children with autism served under Section 504.
The Use of Priming to Introduce Toilet Training to a Child with Autism
Authors: Bainbridge Nicole , Smith Myles Brenda
Published: June 2008

The purpose of this investigation was to analyze the effects of priming in introducing toilet training to a 3-year-old boy with autism. Using an ABAB design, the number of wet and dry diapers was analyzed in relation to the initiation of toilet use. The data, which were collected throughout the child's day, showed an increase in initiation of toilet use and a decrease in wet diapers when priming was used.
Use of Self-Operated Auditory Prompts to Decrease Off-Task Behavior for a Student with Autism and Moderate Mental Retardation
Authors: Taber Teresa A. , Seltzer Allison , Juane Heflin L. , Alberto Paul A.
Published: June 2008

The use of a self-operated auditory prompting system by a 12-year-old student with autism and moderate mental retardation to decrease inappropriate and off-task behavior was examined in two settings. The effectiveness of the prompting system was assessed using a multiple probe across settings design with an embedded withdrawal in each setting. An analysis of the data indicated a significant decrease in the number of teacher-delivered prompts required by the student to engage in appropriate behavior and remain on task. In this investigation, the self-operated auditory prompting system served as the stimulus control for the student's appropriate and on-task behavior, its use generalized across settings without additional training, and it was successfully used by a student with autism and moderate mental retardation.
Workplace Supports
Authors: Unger Darlene D.
Published: June 2008

This article describes employers' assessment of the types of workplace supports available within their businesses, the workplace accommodations provided to supported employees, and the role of human service providers in facilitating those accommodations. Employee support needs in the areas of employee training and benefits, career advancement, and work culture were addressed by the 53 employers who participated in the study. The results indicated that employers are quite capable of providing workplace accommodations for workers with significant disabilities, drawing on existing employer resources. The data indicated that employers are going beyond mere compliance with the Americans with Disabilities Act of 1990 "reasonable accommodations" provisions; employers reported responding to employee needs in such areas as career advancement, changing something about one's job, and social integration. Often, supervisors and co-workers played instrumental roles in providing support to co-workers with disabilities.
Evaluating Effects of a Social Story Intervention on a Young Girl with Autism
Authors: Norris Christine , Dattilo John
Published: June 2008

There has been little evaluation of the effectiveness of social stories. The purpose of this study was to examine the effects of a social story intervention on the social behaviors of an 8-year-old girl with autism who attended an inclusive second-grade classroom. Several observations were used to establish a baseline level on her inappropriate social interactions that occurred during lunch (e.g., talking or singing to herself, making noises). Following baseline, individualized social stories that addressed her inappropriate social interactions, as well as appropriate alternative behaviors, were introduced to the girl. Although data were somewhat variable, her inappropriate social interactions during lunch decreased by approximately 50% from the first day to the last day of the social story intervention. This study provides insights into the relationship between a social story intervention and social behaviors occurring between a student with autism and her peers.
The Precarious Safety Net
Authors: Auxter David , Halloran William , Berry Hugh G. , O'Mara Susan
Published: June 2008

The Personal Responsibility and Work Opportunity Reconciliation Act (PRWORA) of 1996 substantially changed the Supplemental Security Income (SSI) program, and the implementation of these changes has important implications for children and youth with disabilities. SSI is a federal program administered by the Social Security Administration that provides cash assistance and increased access to Medicaid health insurance and vocational rehabilitation for low-income persons with disabilities. PRWORA required redeterminations for all youth receiving SSI benefits within 1 year after reaching age 18 using stricter adult disability criteria. As a result, the majority of age 18 SSI participants were recommended for cessation nationally. These changes have critical implications for transition planning, employment, and quality of life for young SSI participants and those removed from the program. This article examines the background of the SSI program, age 18 redetermination procedures, current implementation data, and issues focusing on the involvement of teachers and rehabilitation professionals involved in the transition planning process. Recommendations for practice and future research are also discussed.
Educators' Assessment Accommodation Preferences for Students with Autism
Authors: Simpson Richard L. , Griswold Deborah E. , Myles Brenda Smith
Published: June 2008

This study reports the results of a survey of teachers and related-services professionals experienced in working with students with autism. The survey focused on identifying students with autism spectrum disorders who were perceived to be appropriate for participation in a large-scale group assessment. Respondents identified minimally necessary testing accommodations or children considered appropriate to participate in districtwide testing.
Defining Managed Care and Its Application to Individuals with Disabilities
Authors: Shoaf Lisa Donegan
Published: June 2008

Managed health care was originally targeted toward healthy populations, but recently, managed care has moved into less traditional markets, including managing health care for individuals with disabilities. An understanding of managed care concepts and their application to individuals with disabilities is important, as these models are applied to this population. The purpose of this article is to define managed care from the perspective of each stakeholder and describe how managed care is currently affecting community services and outpatient care for individuals with disabilities. Broad definitions of managed care and the roles and considerations for the various stakeholders in managed care are presented. Various types of managed care models are discussed. Trends in the application of managed care to individuals with disabilities are also presented.
Engagement with print: Low-income families and Head Start children
Authors: Lynch Jacqueline
Published: June 2008

This research examined the types of print literacy activities low-income parents reported engaging in with their four-year-old children. There were 38 parents of children involved in Head Start, a pre-school program for children from low-income families living in the USA, who participated in this study. Children were assessed on their knowledge about print. Geographical backgrounds of families accounted for some differences in the types and frequency of print literacy activities parents reported to engage in with their children. However, there were no significant differences in children's print knowledge based on geographical factors. This research may suggest the important role of pre-school and particular parent—child activities in developing children's early print concepts.
Interpretation Programs at a Historic Preservation Site
Authors: Farmer James , Knapp Doug
Published: June 2008

The focus of the current study is to better comprehend the long-term impacts of interpretation programs at a historical site. The authors used a mixed methods research approach to uncover and explore both the immediate impacts of the experience as well as the long-term information that was retained 6 months following attendance of the short duration program. The findings support previous research in interpretation and suggest that a direct connection to the resource promotes long-term retention of tour topics. This study uses pre- and postquestionnaires, in-depth and informal interviewing, observations, and the synthesis of qualitative and quantitative data to investigate the phenomenon.
Life after the thymus: CD31+ and CD31− human naive CD4+ T-cell subsets
Authors: Kohler Siegfried , Thiel Andreas
Published: June 2008

Early in life, thymic export establishes the size and the diversity of the human naive T-cell pool. Yet, on puberty thymic activity drastically decreases. Because the overall size of the naive T-cell pool decreases only marginally during ageing, peripheral postthymic expansion of naive T cells has been postulated to account partly for the maintenance of T-cell immunity in adults. So far, the analysis of these processes had been hampered by the inability to distinguish recent thymic emigrants from proliferated, peripheral, naive T cells. However, recently, CD31 has been introduced as a marker to distinguish 2 subsets of naive CD4+ T cells with distinct T-cell receptor excision circle (TREC) content in the peripheral blood of healthy humans. Here, we review studies that have characterized TREChi CD31+ thymicnaive CD4+ T cells and have accordingly used the assessment of this distinct subset of naive CD4+ T cells as a correlate of thymic activity. We will discuss further potential clinical applications and how more research on CD31+ thymicnaive and CD31− centralnaive CD4+ T cells may foster our knowledge of the impact of thymic involution on immune competence.
Measuring the prevalence of regional mutation rates: an analysis of silent substitutions in mammals, fungi, and insects
Authors: Fox Aleah K , Tuch Brian B , Chuang Jeffrey H
Published: June 2008

Background

The patterns of mutation vary both within and across genomes. It has been shown for a few mammals that mutation rates vary within the genome, while for unknown reasons, the sensu stricto yeasts have uniform rates instead. The generality of these observations has been unknown. Here we examine silent site substitutions in a more expansive set (20 mammals, 27 fungi, 4 insects) to determine why some genomes demonstrate this mosaic distribution and why others are uniform.

Results

We applied several intragene and intergene correlation tests to measure regional substitution patterns. Assuming that silent sites are a reasonable approximation to neutrally mutating sequence, our results show that all multicellular eukaryotes exhibit mutational heterogeneity. In striking contrast, all fungi are mutationally uniform – with the exception of three Candida species: C. albicans, C. dubliniensis, and C. tropicalis. We speculate that aspects of replication timing may be responsible for distinguishing these species. Our analysis also reveals classes of genes whose silent sites behave anomalously with respect to the mutational background in many species, indicating prevalent selective pressures. Genes associated with nucleotide binding or gene regulation have consistently low silent substitution rates in every mammalian species, as well as multiple fungi. On the other hand, receptor genes repeatedly exhibit high silent substitution rates, suggesting they have been influenced by diversifying selection.

Conclusion

Our findings provide a framework for understanding the regional mutational properties of eukaryotes, revealing a sharp difference between fungi and multicellular species. They also elucidate common selective pressures acting on eukaryotic silent sites, with frequent evidence for both purifying and diversifying selection.
RAWUL: A new ubiquitin-like domain in PRC1 Ring finger proteins that unveils putative plant and worm PRC1 orthologs
Authors: Sanchez-Pulido Luis , Devos Damien , Sung Zinmay R , Calonje Myriam
Published: June 2008

Background

Polycomb group (PcG) proteins are a set of chromatin-modifying proteins that play a key role in epigenetic gene regulation. The PcG proteins form large multiprotein complexes with different activities. The two best-characterized PcG complexes are the PcG repressive complex 1 (PRC1) and 2 (PRC2) that respectively possess histone 2A lysine 119 E3 ubiquitin ligase and histone 3 lysine 27 methyltransferase activities. While PRC2-like complexes are conserved throughout the eukaryotic kingdoms, PRC1-like complexes have only been described in Drosophila and vertebrates. Since both complexes are required for the gene silencing mechanism in Drosophila and vertebrates, how PRC1 function is realized in organisms that apparently lack PRC1 such as plants, is so far unknown. In vertebrates, PRC1 includes three proteins, Ring1B, Ring1A, and Bmi-1 that form an E3 ubiquitin ligase complex. These PRC1 proteins have an N-terminally located Ring finger domain associated to a poorly characterized conserved C-terminal region.

Results

We obtained statistically significant evidences of sequence similarity between the C-terminal region of the PRC1 Ring finger proteins and the ubiquitin (Ubq)-like family proteins, thus defining a new Ubq-like domain, the RAWUL domain. In addition, our analysis revealed the existence of plant and worm proteins that display the conserved combination of a Ring finger domain at the N-terminus and a RAWUL domain at the C-terminus.

Conclusion

Analysis of the conserved domain architecture among PRC1 Ring finger proteins revealed the existence of long sought PRC1 protein orthologs in these organisms, suggesting the functional conservation of PRC1 throughout higher eukaryotes.
Ex vivo recovery and activation of dysfunctional, anergic, monocyte-derived dendritic cells from patients with operable breast cancer: critical role of IFN-alpha
Authors: Satthaporn Sukchai , Aloysius Mark M , Robins Richard A , Verma Chandan , Chuthapisith Suebwong , Mckechnie Alasdair J , El-Sheemy Mohamad , Vassanasiri Wichai , Valerio David , Clark David , Jibril Jibril A , Eremin Oleg
Published: June 2008

Background

Dendritic cells (DCs) play a crucial role in initiating effective cell-mediated immune responses, but are dysfunctional and anergic in breast cancer. Reversal of this dysfunction and establishment of optimal DC function is a key prerequisite for the induction of effective anti-cancer immune responses.

Results

Peripheral blood DCs (PBDCs) and lymph node DCs (LNDCs) generatedin vitrofrom adherent cultures of peripheral blood monocytes (PBMs) and lymph node monocytes (LNMs), respectively, using the 4 cytokine conditioned medium (CCM) (GM-CSF+IL-4+TNF-α+IFN-α) or 3 CCM (GM-CSF+IL-4+TNF-α) demonstrated a significantly higher degree of recovery and functional capacity in a mixed lymphocyte DC reaction (MLDCR, p < 0.001), expressed significantly higher levels of HLA-DR, CD86, compared with 2 CCM (GM-CSF+IL-4) or medium alone generated DCs from PBMs and LNMs (p < 0.001). The PBDCs generated with 3 CCM or 4 CCM showed a significantly (p < 0.001) enhanced macropinocytotic capability (dextran particles) and induced increased production and secretion of interleukin-12p40 (IL-12p40)in vitro(p < 0.001), compared with PBDCs generated from monocytes using 2 CCM or medium alone. Lipopolysaccharide (LPS) stimulation of PBDCs generated with 4 CCM demonstrated enhanced secretion of IL-6 but not IL-12p70, compared with control DCs unstimulated with LPS (p < 0.001).

Conclusion

Dysfunctional and anergic PBDCs and LNDCs from patients with operable breast cancer can be optimally reversed byex vivoculturing of precursor adherent monocytes using a 4 CCM containing IFN-α. Maximal immunophenotypic recovery and functional reactivation of DCs is seen in the presence of IFN-α. However, 4 CCM containing IFN-α generated-PBDCs, do not produce and secrete IL-12p70in vitro.
Bacteria of the Burkholderia cepacia complex are cyanogenic under biofilm and colonial growth conditions
Authors: Ryall Ben , Lee Xiaoyun , Zlosnik James EA , Hoshino Saiko , Williams Huw D
Published: June 2008

Background

The Burkholderia cepacia complex (Bcc) is a collection of nine genotypically distinct but phenotypically similar species. They show wide ecological diversity and include species that are used for promoting plant growth and bio-control as well species that are opportunistic pathogens of vulnerable patients. Over recent years the Bcc have emerged as problematic pathogens of the CF lung. Pseudomonas aeruginosa is another important CF pathogen. It is able to synthesise hydrogen cyanide (HCN), a potent inhibitor of cellular respiration. We have recently shown that HCN production by P. aeruginosa may have a role in CF pathogenesis. This paper describes an investigation of the ability of bacteria of the Bcc to make HCN.

Results

The genome of Burkholderia cenocepacia has 3 putative HCN synthase encoding (hcnABC) gene clusters. B. cenocepacia and all 9 species of the Bcc complex tested were able to make cyanide at comparable levels to P. aeruginosa, but only when grown surface attached as colonies or during biofilm growth on glass beads. In contrast to P. aeruginosa and other cyanogenic bacteria, cyanide was not detected during planktonic growth of Bcc strains.

Conclusion

All species in the Bcc are cyanogenic when grown as surface attached colonies or as biofilms.
Evidence of platelet activation in multiple sclerosis
Authors: Sheremata William A , Jy Wenche , Horstman Lawrence L , Ahn Yeon S , Alexander J Steven , Minagar Alireza
Published: June 2008

Objective

A fatality in one multiple sclerosis (MS) patient due to acute idiopathic thrombocytopenic purpura (ITP) and a near fatality in another stimulated our interest in platelet function abnormalities in MS. Previously, we presented evidence of platelet activation in a small cohort of treatment-naive MS patients.

Methods

In this report, 92 normal controls and 33 stable, untreated MS patients were studied. Platelet counts, measures of platelet activation [plasma platelet microparticles (PMP), P-selectin expression (CD62p), circulating platelet microaggragtes (PAg)], as well as platelet-associated IgG/IgM, were carried out. In addition, plasma protein S activity was measured.

Results

Compared to controls, PMP were significantly elevated in MS (p < 0.001) and CD62p expression was also markedly elevated (p < 0.001). Both are markers of platelet activation. Platelet-associated IgM, but not IgG, was marginally elevated in MS (p = 0.01). Protein S in MS patients did not differ significantly from normal values.

Conclusion

Platelets are significantly activated in MS patients. The mechanisms underlying this activation and its significance to MS are unknown. Additional study of platelet activation and function in MS patients is warranted.
Effect of prolonging radiation delivery time on retention of gammaH2AX
Authors: Moiseenko Vitali , Banáth Judit P , Duzenli Cheryl , Olive Peggy L
Published: June 2008

Background and purpose

Compared to conventional external beam radiotherapy, IMRT requires significantly more time to deliver the dose. Prolonging dose delivery potentially increases DNA repair which would reduce the biological effect. We questioned whether retention of γH2AX, a measure of lack of repair of DNA damage, would decrease when dose delivery was protracted.

Materials and methods

Exponentially growing SiHa cervical carinoma cells were irradiated with 6 MV photons in a water tank using a VarianEX linear accelerator. Cells held at 37°C received 2 Gy in 0.5 min and 4 Gy in 1 min. To evaluate effect of dose delivery prolongation, 2 and 4 Gy were delivered in 30 and 60 min. After 24 h recovery, cells were analyzed for clonogenic survival and for residual γH2AX as measured using flow cytometry.

Results

Increasing the dose delivery time from 0.5 or 1 min to 30 or 60 min produced a signficant increase in cell survival from 0.45 to 0.48 after 2 Gy, and from 0.17 to 0.20 after 4 Gy. Expression of residual γH2AX decreased from 1.27 to 1.22 relative to background after 2 Gy and 1.46 to 1.39 relative to background after 4 Gy, but differences were not statistically significant. The relative differences in the slopes of residual γH2AX versus dose for acute versus prolonged irradiation bordered on significant (p = 0.055), and the magnitude of the change was consistent with the observed increase in surviving fraction.

Conclusion

These results support the concept that DNA repair underlies the increase in survival observed when dose delivery is prolonged. They also help to establish the limits of sensitivity of residual γH2AX, as measured using flow cytometry, for detecting differences in response to irradiation.
Pathway analysis reveals functional convergence of gene expression profiles in breast cancer
Authors: Shen Ronglai , Chinnaiyan Arul M , Ghosh Debashis
Published: June 2008

Background

A recent study has shown high concordance of several breast-cancer gene signatures in predicting disease recurrence despite minimal overlap of the gene lists. It raises the question if there are common themes underlying such prediction concordance that are not apparent on the individual gene-level. We therefore studied the similarity of these gene-signatures on the basis of their functional annotations.

Results

We found the signatures did not identify the same set of genes but converged on the activation of a similar set of oncogenic and clinically-relevant pathways. A clear and consistent pattern across the four breast cancer signatures is the activation of the estrogen-signaling pathway. Other common features include BRCA1-regulated pathway, reck pathways, and insulin signaling associated with the ER-positive disease signatures, all providing possible explanations for the prediction concordance.

Conclusion

This work explains why independent breast cancer signatures that appear to perform equally well at predicting patient prognosis show minimal overlap in gene membership.
Fibroepithelioma of pinkus in a 9-year-old boy: a case report
Authors: Pan Zenggang , Huynh Nhi , Sarma Deba P
Published: June 2008

Fibroepithelioma of Pinkus (FEP) is a rare indolent variety of basal cell carcinoma that is typically polypoid and located on the trunk of adult males aged 40–60 years. Basal cell carcinoma (including FEP) is very rare in the pediatric population. We are reporting such a case occurring in a 9-year-old boy.
Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy
Authors: Kim Wan Kyu , Krumpelman Chase , Marcotte Edward M
Published: June 2008

The complete set of mouse genes, as with the set of human genes, is still largely uncharacterized, with many pieces of experimental evidence accumulating regarding the activities and expression of the genes, but the majority of genes as yet still of unknown function. Within the context of the MouseFunc competition, we developed and applied two distinct large-scale data mining approaches to infer the functions (Gene Ontology annotations) of mouse genes from experimental observations from available functional genomics, proteomics, comparative genomics, and phenotypic data. The two strategies — the first using classifiers to map features to annotations, the second propagating annotations from characterized genes to uncharacterized genes along edges in a network constructed from the features — offer alternative and possibly complementary approaches to providing functional annotations. Here, we re-implement and evaluate these approaches and their combination for their ability to predict the proper functional annotations of genes in the MouseFunc data set. We show that, when controlling for the same set of input features, the network approach generally outperformed a naïve Bayesian classifier approach, while their combination offers some improvement over either independently. We make our observations of predictive performance on the MouseFunc competition hold-out set, as well as on a ten-fold cross-validation of the MouseFunc data. Across all 1,339 annotated genes in the MouseFunc test set, the median predictive power was quite strong (median area under a receiver operating characteristic plot of 0.865 and average precision of 0.195), indicating that a mining-based strategy with existing data is a promising path towards discovering mammalian gene functions. As one product of this work, a high-confidence subset of the functional mouse gene network was produced — spanning >70% of mouse genes with >1.6 million associations — that is predictive of mouse (and therefore often human) gene function and functional associations. The network should be generally useful for mammalian gene functional analyses, such as for predicting interactions, inferring functional connections between genes and pathways, and prioritizing candidate genes. The network and all predictions are available on the worldwide web.
Consistent probabilistic outputs for protein function prediction
Authors: Obozinski Guillaume , Lanckriet Gert , Grant Charles , Jordan Michael I , Noble William Stafford
Published: June 2008

In predicting hierarchical protein function annotations, such as terms in the Gene Ontology (GO), the simplest approach makes predictions for each term independently. However, this approach has the unfortunate consequence that the predictor may assign to a single protein a set of terms that are inconsistent with one another; for example, the predictor may assign a specific GO term to a given protein ('purine nucleotide binding') but not assign the parent term ('nucleotide binding'). Such predictions are difficult to interpret. In this work, we focus on methods for calibrating and combining independent predictions to obtain a set of probabilistic predictions that are consistent with the topology of the ontology. We call this procedure 'reconciliation'. We begin with a baseline method for predicting GO terms from a collection of data types using an ensemble of discriminative classifiers. We apply the method to a previously described benchmark data set, and we demonstrate that the resulting predictions are frequently inconsistent with the topology of the GO. We then consider 11 distinct reconciliation methods: three heuristic methods; four variants of a Bayesian network; an extension of logistic regression to the structured case; and three novel projection methods - isotonic regression and two variants of a Kullback-Leibler projection method. We evaluate each method in three different modes - per term, per protein and joint - corresponding to three types of prediction tasks. Although the principal goal of reconciliation is interpretability, it is important to assess whether interpretability comes at a cost in terms of precision and recall. Indeed, we find that many apparently reasonable reconciliation methods yield reconciled probabilities with significantly lower precision than the original, unreconciled estimates. On the other hand, we find that isotonic regression usually performs better than the underlying, unreconciled method, and almost never performs worse; isotonic regression appears to be able to use the constraints from the GO network to its advantage. An exception to this rule is the high precision regime for joint evaluation, where Kullback-Leibler projection yields the best performance.
Joint inversion of crosshole radar and seismic traveltimes acquired at the South Oyster Bacterial Transport Site
Authors: Linde Niklas , Tryggvason Ari , Peterson John E. , Hubbard Susan S.
Published: June 2008

The structural approach to joint inversion, entailing common boundaries or gradients, offers a flexible and effective way to invert diverse types of surface-based and/or crosshole geophysical data. The cross-gradients function has been introduced as a means to construct models in which spatial changes in two distinct physical-property models are parallel or antiparallel. Inversion methods that use such structural constraints also provide estimates of nonlinear and nonunique field-scale relationships between model parameters. Here, we jointly invert crosshole radar and seismic traveltimes for structurally similar models using an iterative nonlinear traveltime tomography algorithm. Application of the inversion scheme to synthetic data demonstrates that it better resolves lithologic boundaries than the individual inversions alone. Tests of the scheme on GPR and seismic data acquired within a shallow aquifer illustrate that the resultant models have improved correlations with flowmeter data in comparison with models based on individual inversions. The highest correlation with the flowmeter data is obtained when the joint inversion is combined with a stochastic regularization operator and the vertical integral scale is estimated from the flowmeter data. Point-spread functions show that the most significant resolution improvements offered by the joint inversion are in the horizontal direction.
Regulation of Angiotensin Type 2 Receptor in Bovine Granulosa Cells
Authors: Portela Valério M. , Gonçalves Paulo B. D. , Veiga Angela M. , Nicola Edmir , Buratini José , Price Christopher A.
Published: June 2008

Angiotensin II (AngII) is best known for its role in blood pressure regulation, but it also has documented actions in the reproductive system. There are two AngII receptors, type 1 (AGTR1) and type 2 (AGTR2). AGTR2 mediates the noncardiovascular effects of AngII and is expressed in the granulosa cell layer in rodents and is associated with follicle atresia. In contrast, expression of AGTR2 is reported to occur only in theca cells in cattle. The objective of the present study was to determine whether AngII also plays a role in follicle atresia in cattle. RT-PCR demonstrated AGTR2 mRNA in both granulosa and theca cells of bovine follicles. The presence of AGTR2 protein was confirmed by immunofluorescence. Abundance of AGTR2 mRNA in granulosa cells was higher in healthy compared with atretic follicles, whereas in theca cells, it did not change. Granulosa cells were cultured in serum-free medium, and treatment with hormones that increase estradiol secretion (FSH, IGF-I, and bone morphogenetic protein-7) increased AGTR2 mRNA and protein levels, whereas fibroblast growth factors inhibited estradiol secretion and AGTR2 protein levels. The addition of AngII or an AGTR2-specific agonist to granulosa cells in culture did not affect estradiol secretion or cell proliferation but inhibited abundance of mRNA encoding serine protease inhibitor E2, a protein involved in tissue remodeling. Because estradiol secretion is a major marker of nonatretic granulosa cells, these data suggest that AngII is not associated with follicle atresia in cattle but may have other specific roles during follicle growth.
Molecular and Morphological Changes in Placenta and Embryo Development Associated with the Inhibition of Polyamine Synthesis during Midpregnancy in Mice
Authors: López-García Carlos , López-Contreras Andrés Joaquín , Cremades Asunción , Castells Maria Teresa , Marín Faustino , Schreiber Fernanda , Peñafiel Rafael
Published: June 2008

Polyamines play an essential role in murine development, as demonstrated by both gene ablation in ornithine decarboxylase (ODC)-deficient embryos and pharmacological treatments of pregnant mice. However, the molecular and cellular mechanisms by which ODC inhibition affects embryonic development during critical periods of pregnancy are mostly unknown. Our present results demonstrate that the contragestational effect of α-difluoromethylornithine (DFMO), a suicide inhibitor of ODC, when given at d 7–9 of pregnancy, is associated with embryo growth arrest and marked alterations in the development of yolk sac and placenta. Blood island formation as well as the transcript levels of embryonary globins α-like x chain and β-like y-chain was markedly decreased in the yolk sac. At the placental level, abnormal chorioallantoic attachment, absence of the spongiotrophoblast layer and a deficient development of the labyrinthine zone were evident. Real-time RT-PCR analysis showed that transcript levels of the steroidogenic genes steroidogenic acute regulatory protein, 3β-hydroxysteroid dehydrogenase VI, and 17α-hydroxylase were markedly decreased by DFMO treatment in the developing placenta at d 9 and 10 of pregnancy. Plasma values of progesterone and androstenedione were also decreased by DFMO treatment. Transcriptomic analysis also detected changes in the expression of several genes involved in placentation and the differentiation of trophoblastic lineages. In conclusion, our results indicate that ODC inhibition at d 8 of pregnancy is related to alterations in yolk sac formation and trophoblast differentiation, affecting processes such as vasculogenesis and steroidogenesis.
Patients’ Knowledge and Understanding of the Implications of Wearing Dentures. Report of a Survey Conducted at a Dental Institute in the South of India
Authors: Shigli Kamal , Angadi Gangadhar Shivappa , Hegde Pradnya , Hebbal Mamata
Published: June 2008

Aim

The aim of this survey was to assess the knowledge and perceptions of denture treatment among a group of patients who attended the Karnataka Lingayat Education Society's (KLES) Institute of Dental Sciences, Belgaum, Karnataka State, India.

Method

A questionnaire with four general questions and 14 statements/questions about denture construction and wearing was developed and piloted. Ethical approval was sought and granted. After some revisions, the questionnaire was given to all patients attending KLES over a two-month period.

Results

All 423 patients who attended KLES in the two-month period completed the questionnaire. Five questionnaires were not analysed because of ambiguity in the answers. The final patient sample was 418 (207 females and 211 males, mean age 40 ± 15.3 years) of whom 140 (33.5%) were dentate and 278 (66.5%) edentulous in either one or both jaws. Among the 278 edentulous patients, 143 (51.4%) had not worn any kind of denture and 135 (48.6%) wore dentures. There was a wide variation in the accuracy of the patients’ knowledge of denture treatment. In particular, more than 20% did not know that complete denture treatment requires five or more visits, that denture wearers may experience oral pain, whether or not dentures may cause more problems than natural teeth, or that dentures may make audible clicks and cause problems when speaking.

Conclusion

Patient education is an essential element in successful denture treatment. It should begin prior to the treatment, to ensure that the technical capability of the clinician matches the expectations of the patient. The initial appointment needs to be used as an educational tool to raise patients’ level of understanding of prosthetic rehabilitation and how the proposed treatment will meet their needs.
The Emerging Dental Workforce: Short-Term Expectations of, and Influences on Dental Students Graduating from a London Dental School in 2005
Authors: Gallagher Jennifer E , Clarke Wendy , Wilson Nairn HF
Published: June 2008

Aim

The aim of this research was to identify short-term career aspirations and goals of final-year dental students at a London dental school and the perceived factors that influenced these aspirations.

Methods

Two methods were used to collect data on final-year students’ short-term career plans and influences. Qualitative data were collected through focus groups and analysed using ‘framework methodology’. These findings informed a questionnaire survey of all students at the end of their final undergraduate year. Data were entered into and analysed using a statistical software package.

Results

Thirty-five students participated in focus groups, with recruitment continuing until data were saturated. Ninety per cent (n=126) of the total population (140) responded to the questionnaire survey; the majority were Asian (70%), female (58%), and aged 23 years (59%). Short-term professional expectations focused around ‘achieving professional status within a social context’, ‘gaining professional experience’, ‘developing independence’ and ‘achieving financial stability’. ‘Achieving financial stability’ was ranked as the most important influence in decision-making about their career in the short term (77%), followed by ‘balance of work and other aspects of life’ (75%) and ‘good lifestyle’ (75%). Four out of ten intended to work towards membership of a Royal College and/or becoming a specialist. Proximity to family (81%) and friends (79%) was an important or very important influence on location in the short term. Asian students were significantly more likely to rate ‘proximity to family’ ( p=0.042), working in an ‘urban area’ ( p=0.001) and ‘opportunities for private care’ ( p=0.043) of greater importance than their White counterparts.

Conclusions

Short-term aspirations involve ‘achieving professional status within a social context’, and personal, social, professional and financial goals. Location of future practice was significantly associated with ethnicity.
Developing, Enabling and Facilitating Practice-Based Research in Primary Dental Care
Authors: Eaton Kenneth A , Narain Amrita , Batchelor Paul
Published: June 2008

As part of the Faculty of General Dental Practice (UK)'s strategy to develop a research base for primary dental care, a one-day seminar was held at The Royal College of Surgeons of England on Friday, 1st February 2008. The aims for the day were to bring together the Divisional Research Contacts (DRCs), Faculty members with an interest in research, and regional and national leaders in primary care research; to update DRCs and Faculty members on developments and opportunities in primary care research; and to raise awareness of the Faculty's work among the leaders of primary care research. Of the 33 who attended the seminar, 12 were DRCs.
Incidence of mastoid surgery in england: implications for training
Authors: Phillips JS , Yung MW
Published: June 2008

Mastoid surgery is one of the benchmark procedures in ear, nose and throat (ENT) SpR training. All SpRs must demonstrate competency in this surgery before they are awarded the Certificate of Completion of Training. ENT, as in all surgical specialties, is currently going through changes in training. There is pressure to reduce the number of years while maintaining the same standard of surgical training. National and European policy has also meant that opportunities in the UK will be impaired. Training is often limited by the opportunities available to each training region and the number of SpRs competing for these opportunities.
Assessing laparoscopic skills in the novice
Authors: Fielding DE , Ferguson E , Baxendale B , Mannion A , Maxwell-Armstrong CA
Published: June 2008

Graduate-entry degrees are common in the US and Australia and are offered by 14 universities in the UK. The University of Nottingham has recently seen the integration of its graduate-entry medicine (GEM) students with its traditional medical undergraduates (BMedSci) on their first clinical attachment. Those pursuing a surgical career will be subject to shortened training as part of Modernising Medical Careers. Furthermore, the increase in minimally invasive techniques will lead to simulator training being utilised as this is a method to which laparoscopic skills acquisition lends itself. A number of validated curricula have been developed since the use of simulators was first suggested as a tool for endoscopic surgical training. Indeed, recent work has shown that simulation may improve psychomotor skills within the context of a surgical procedure.