bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variability and abundance of the epiphytic bacterial community associated with a green marine Ulvacean alga
Authors: Tujula Niina A , Crocetti Gregory R , Burke Catherine , Thomas Torsten , Holmström Carola , Kjelleberg Staffan 
Published: October 2009

Abstract
Marine Ulvacean algae are colonized by dense microbial communities predicted to have an important role in the development, defense and metabolic activities of the plant. Here we assess the diversity and seasonal dynamics of the bacterial community of the model alga Ulva australis to identify key groups within this epiphytic community. A total of 48 algal samples of U. australis that were collected as 12 individuals at 3 monthly intervals, were processed by applying denaturing gradient gel electrophoresis (DGGE), and three samples from each season were subjected to catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). CARD-FISH revealed that the epiphytic microbial community was comprised mainly of bacterial cells (90%) and was dominated by the groups Alphaproteobacteria (70%) and Bacteroidetes (13%). A large portion (47%) of sequences from the Alphaproteobacteria fall within the Roseobacter clade throughout the different seasons, and an average relative proportion of 19% was observed using CARD-FISH. DGGE based spatial (between tidal pools) and temporal (between season) comparisons of bacterial community composition demonstrated that variation occurs. Between individuals from both the same and different tidal pools, the variation was highest during winter (30%) and between seasons a 40% variation was observed. The community also includes a sub-population of bacteria that is consistently present. Sequences from excised DGGE bands indicate that members of the Alphaproteobacteria and the Bacteroidetes are part of this stable sub-population, and are likely to have an important role in the function of this marine epiphytic microbial community.
Adrenomedullin is expressed during rodent dental tissue development and promotes cell growth and mineralization
Authors: Musson David S. , McLachlan Julia L. , Sloan Alastair J. , Smith Anthony J. , Cooper Paul R. 
Published: October 2009

Background information. ADM (adrenomedullin) has pleiotropic effects, including regulation of inflammation, infection, angiogenesis, mineralized‐tissue formation and development. Recently, we demonstrated up‐regulation of the ADM transcript in diseased pulpal tissue while the protein is sequestered within the dentine extracellular matrix during dentinogenesis. The present study aimed to characterize ADM localization during rodent dental tissue development and determine its potential effects on dental cells. Finally, we sought to profile ADM transcript levels in adult organs and tissues to compare its expression in teeth relative to other tissues.Results. Immunohistochemical analysis of developmental rat oral tissues indicated that, at E16 (embryonic day 16), ADM was present in dental epithelium and, by E18, ADM localized to the dental papilla and inner and outer dental epithelia. By E20, ADM was detected in secretory odontoblasts and ameloblasts and exhibited a similar expression profile to that of the key dentinogenesis signalling molecule, TGF‐β1 (transforming growth factor‐β1). Cell growth analysis in the dental MDPC‐23, OD‐21 and control 3T3 cell lines exposed to ADM (range 10−15–10−7 M) together with EDTA‐extracted DMPs (dentine matrix proteins) (range 0.00001–1000 mg/ml) containing comparable concentrations of ADM demonstrated that ADM stimulated a biphasic response in dental cell growth, comparable with that of DMPs, with peak stimulation observed at ∼10−11 M. For mineralization analysis, cell lines were exposed to combinations of 50 μg/ml ascorbic acid, 10 mM β‐G (β‐glycerophosphate), 10−8 M DEX (dexamethasone) and ADM (range 10−15–10−7 M). The results demonstrated that ADM could substitute for DEX to stimulate mineralization. Postnatally, multiple tissue expression profiling indicated abundant ADM levels in tongue and pulpal tissues.Conclusions. During oral and dental tissue development ADM initially localizes to epithelial tissue, whereas during later stages it is present in mineralized secreting cells, including odontoblasts. ADM may regulate proliferation and mineralization processes during development, whereas, in adulthood, it may be important for maintaining dental tissue homoeostasis.
Undergraduate Research: A Cognitive Apprenticeship Model
Authors: Hagstrom Fran , Baker Kimberly F. , Agan Joseph P. 
Published: October 2009

AbstractThis article presents a cognitive apprenticeship model that can be used to organize undergraduate research. The purpose is to encourage students and faculty to become involved in undergraduate research by providing an outline of the undergraduate research program at the University of Arkansas-Fayetteville. Theoretical articles and empirical studies are used to describe the relevance of this approach to undergraduate research. Procedural descriptions and student comments are included to demystifying the research process.
Administration of a Literacy-Based Curriculum by Teacher and SLP Teams
Authors: Loeb Diane Frome , Daniels Debora Burns 
Published: October 2009

Abstract
A literacy-based language curriculum for Native American and Hispanic American children was jointly administered by four speech-language pathologist (SLP) and teacher teams. Analyses indicated that teachers, when trained and provided with structured lessons, were able to co-administer a curriculum designed to improve language and literacy skills in the classroom.
Academic Preparation for the School-Based SLP: A National Survey
Authors: Means Jennifer 
Published: October 2009

Abstract
The purpose of this study was to ascertain the number of ASHA accredited graduate Communication Sciences and Disorders (CSD) programs offering specific course work addressing school-based issues for the speech-language pathologist. This research was conducted through e-mail survey distribution to 250 universities and colleges across the United States. The results are presented with pedagogy development and program planning suggestions.
On 50 Years of Giving Psychology Away: An Interview with Philip Zimbardo
Authors: Slavich George M. 
Published: October 2009

Philip G. Zimbardo, emeritus professor of psychology at Stanford University, is internationally recognized as the voice and face of contemporary American psychology. He earned his PhD in social psychology from Yale University in 1959 and has since received seven honorary doctorates for his contributions to psychology and society. The author of more than 300 publications and 50 books, Zimbardo's research spans 20 topics, including shyness, evil, teaching, persuasion, hypnosis, dissonance, time perspective, and heroism. He is best known for his landmark study, the Stanford Prison Experiment; his widely seen TV series, Discovering Psychology; and his best-selling textbook, Psychology and Life. He is past president of the Western Psychological Association (WPA) and the American Psychological Association (APA), and has received distinguished teaching awards from WPA, APA, Stanford University, Phi Beta Kappa, and the Society for the Teaching of Psychology. His aim to “give psychology away” is evident in all he does. George M. Slavich is a Beck Institute Scholar, Society in Science: Branco Weiss Fellow, and National Institute of Mental Health Postdoctoral Fellow in Psychology and Medicine at the University of California, San Francisco. He completed undergraduate and graduate coursework at Stanford University, received his PhD in clinical psychology from the University of Oregon, and completed clinical training at McLean Hospital/Harvard Medical School. His research investigates the characteristics, causes, and consequences of life stress in major depression. He is also deeply devoted to teaching and mentoring. He founded the Stanford Undergraduate Psychology Conference and WPA Student Council; he also cofounded the Society of Clinical Psychology's Section on Graduate Student and Early Career Psychologists. For these contributions and others, he received the 2004 Albert Bandura Graduate Research Award, the 2005 Edwin B. Newman Graduate Research Award, and the 2005 Wilbert J. McKeachie Teaching Excellence Award.
Significant speedup of database searches with HMMs by search space reduction with PSSM family models
Authors: Beckstette Michael , Homann Robert , Giegerich Robert , Kurtz Stefan 
Published: October 2009

Abstract
Motivation: Profile hidden Markov models (pHMMs) are currently the most popular modeling concept for protein families. They provide sensitive family descriptors, and sequence database searching with pHMMs has become a standard task in today's genome annotation pipelines. On the downside, searching with pHMMs is computationally expensive.
Results: We propose a new method for efficient protein family classification and for speeding up database searches with pHMMs as is necessary for large-scale analysis scenarios. We employ simpler models of protein families called position-specific scoring matrices family models (PSSM-FMs). For fast database search, we combine full-text indexing, efficient exact p-value computation of PSSM match scores and fast fragment chaining. The resulting method is well suited to prefilter the set of sequences to be searched for subsequent database searches with pHMMs. We achieved a classification performance only marginally inferior to hmmsearch, yet, results could be obtained in a fraction of runtime with a speedup of &gt;64-fold. In experiments addressing the method's ability to prefilter the sequence space for subsequent database searches with pHMMs, our method reduces the number of sequences to be searched with hmmsearch to only 0.80% of all sequences. The filter is very fast and leads to a total speedup of factor 43 over the unfiltered search, while retaining &gt;99.5% of the original results. In a lossless filter setup for hmmsearch on UniProtKB/Swiss-Prot, we observed a speedup of factor 92.
Availability: The presented algorithms are implemented in the program PoSSuMsearch2, available for download at http://bibiserv.techfak.uni-bielefeld.de/possumsearch2/.
Contact: beckstette@zbh.uni-hamburg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Bethesda Hospitals' Emergency Preparedness Partnership: A Model for Transinstitutional Collaboration of Emergency Responses
Authors: Henderson David K. , Malanoski Michael P. , Corapi Gene , Passamani Eugene , Notobartolo Cynthia , Gillette Chris , Hawes Patricia , Lee Laura M. 
Published: October 2009

ABSTRACTThe events of September 11, 2001 identified a need for health care institutions to develop flexible, creative, and adaptive response mechanisms in the event of a local, regional, or national disaster. The 3 major health care institutions in Bethesda, MD—the National Naval Medical Center (NNMC), the Suburban Hospital Healthcare System (SHHS), and the National Institutes of Health Clinical Center (NIHCC)—have created a preparedness partnership that outstrips what any of the institutions could provide independently by pooling complementary resources. The creation of the partnership initially was driven by geographic proximity and by remarkably complementary resources. This article describes the creation of the partnership, the drivers and obstacles to creation, and the functioning and initial accomplishments of the partnership. The article argues that similar proximity and resource relationships exist among institutions at academic centers throughout the United States and suggests that this partnership may serve as a template for other similarly situated institutions. (Disaster Med Public Health Preparedness. 2009;3:168–173)
The ArabidopsisDCREncoding a Soluble BAHD Acyltransferase Is Required for Cutin Polyester Formation and Seed Hydration Properties
Authors: Panikashvili David , Shi Jian Xin , Schreiber Lukas , Aharoni Asaph 
Published: October 2009

AbstractThe cuticle covering every plant aerial organ is largely made of cutin that consists of fatty acids, glycerol, and aromatic monomers. Despite the huge importance of the cuticle to plant development and fitness, our knowledge regarding the assembly of the cutin polymer and its integration in the complete cuticle structure is limited. Cutin composition implies the action of acyltransferase-type enzymes that mediate polymer construction through ester bond formation. Here, we show that a member of the BAHD family of acyltransferases (DEFECTIVE IN CUTICULAR RIDGES [DCR]) is required for incorporation of the most abundant monomer into the polymeric structure of the Arabidopsis (Arabidopsis thaliana) flower cutin. DCR-deficient plants display phenotypes that are typically associated with a defective cuticle, including altered epidermal cell differentiation and postgenital organ fusion. Moreover, levels of the major cutin monomer in flowers, 9(10),16-dihydroxy-hexadecanoic acid, decreased to an almost undetectable amount in the mutants. Interestingly, dcr mutants exhibit changes in the decoration of petal conical cells and mucilage extrusion in the seed coat, both phenotypes formerly not associated with cutin polymer assembly. Excessive root branching displayed by dcr mutants and the DCR expression pattern in roots pointed to the function of DCR belowground, in shaping root architecture by influencing lateral root emergence and growth. In addition, the dcr mutants were more susceptible to salinity, osmotic, and water deprivation stress conditions. Finally, the analysis of DCR protein localization suggested that cutin polymerization, possibly the oligomerization step, is partially carried out in the cytoplasmic space. Therefore, this study extends our knowledge regarding the functionality of the cuticular layer and the formation of its major constituent the polymer cutin.
Naloxone‐responsive acute dystonia and parkinsonism following general anaesthesia
Authors: Iselin‐Chaves I. A. , Grötzsch H. , Besson M. , Burkhard P. R. , Savoldelli G. L. 
Published: October 2009

SummaryVarious movement disorders such as dystonia may acutely develop during or at emergence from general anaesthesia in patients with or without pre‐existing Parkinson disease. These movements are triggered by a variety of drugs including propofol, sevoflurane, anti‐emetics, antipsychotics and opioids. The postulated mechanism involves an imbalance between dopaminergic and cholinergic neurotransmitters in the basal ganglia. We report an acute, severe and generalised dystonic reaction in an otherwise healthy woman at emergence from general anaesthesia, dramatically reversed by the administration of naloxone, pointing to a potential role of the fentanyl and morphine that the patient had received. Recent literature on the mechanisms of abnormal movements induced by opioids are discussed. The severity of the reaction with usual doses of opioids, in a patient with no prior history of parkinsonism, led to further investigation that demonstrated the possibility of an enhanced susceptibility to opioids, involving a genetically determined abnormal function of glycoproteine‐P and catechol‐O‐methyltransferase.
The effect of teriparatide on serum Dickkopf‐1 levels in postmenopausal women with established osteoporosis
Authors: Anastasilakis Athanasios D. , Polyzos Stergios A. , Avramidis Avraam , Toulis Konstantinos A. , Papatheodorou Athanasios , Terpos Evangelos 
Published: October 2009

SummaryObjective  Parathyroid hormone increases the differentiation of osteoblast precursors through canonical wingless (Wnt) signalling, resulting in an osteoanabolic effect. We aimed to evaluate serum levels of the Wnt‐inhibitor Dickkopf‐1 (Dkk‐1) in postmenopausal women with established osteoporosis and their changes with teriparatide (TPTD – human recombinant PTH 1–34).Design and patients  A total of 31 postmenopausal Caucasian women with established osteoporosis (mean age 66·3 ± 1·4 years) received daily injections of 20 μg TPTD for 18 months. Follow‐up was continued for another 6 months after treatment discontinuation (total duration of treatment 24 months).Measurements  Serum samples for total calcium (Ca), intact PTH (iPTH), bone‐specific alkaline phosphatase, C‐terminal cross‐linking telopeptide of type 1 collagen (CTx) and Dkk‐1 were obtained at baseline, and at 6, 18 and 24 months after TPTD initiation. Lumbar spine bone mineral density (BMD) was measured before and after 18 months of TPTD treatment. A total of 16 age‐ and gender‐matched healthy controls were also analysed at baseline.Results  Serum Dkk‐1 levels at baseline were significantly higher in osteoporotic women compared with that in controls (P < 0·002). Dkk‐1 increased significantly during TPTD administration (P < 0·044) and decreased to baseline 6 months after TPTD discontinuation. Dkk‐1 change was positively correlated to Ca (r = 0·530, P = 0·004) and negatively correlated to iPTH change (r = −0·398, P = 0·040). There was no correlation between Dkk‐1 and BMD changes.Conclusions  Our data suggest that Dkk‐1 levels are increased in women with postmenopausal osteoporosis. TPTD therapy results in further increase of Dkk‐1 that may be compensative to TPTD‐induced enhanced Wnt signalling.
Long‐term effect of ghrelin on nutritional status and functional capacity in the elderly: a population‐based cohort study
Authors: Serra‐Prat Mateu , Palomera Elisabet , Roca Maria , Puig‐Domingo Manel ,   The Mataró Ageing Study Group
Published: October 2009

SummaryBackground Ghrelin stimulates GH release and hunger at a central level. Ghrelin declines with age, which may be partially responsible for functional impairment and frailty.Objective To describe the evolution of nutritional status and functional capacity of noninstitutionalized old people over a 2‐year period, as well as to evaluate the relationship between ghrelin and long‐term changes in nutritional and functional status in this population.Design A population‐based cohort study was designed in which 313 randomly selected persons, 70 years old or older, were followed for a 2‐year period. Functional (Barthel and Guralnik scores and hand grip) and nutritional (MNA‐SF, weight and BMI) assessments were performed during basal and 2‐year follow‐up visits. Ghrelin and hormonal components of the gonadotrophe and somatotrophe axis were determined.Results During follow‐up, 13% of men and 20% of women showed a >5% weight loss, and the nutritional status of 18% of men and 39% of women deteriorated. Men lost 12·1% and women lost 9·7% of their initial hand grip strength. In men, low basal ghrelin levels were associated with higher weight loss and poorer hand grip but not with the MNA‐SF measure, whereas in women, low basal ghrelin levels were associated with a decline in nutritional status (MNA‐SF) but not with weight loss and hand grip decline.Conclusion Low ghrelin levels have been related to worsening nutritional status in a 2‐year follow‐up period in people 70 years old or older, which suggests this hormone could become a useful therapeutic target in the elderly.
Endoscopic ultrasound‐guided fine needle aspiration (EUS‐FNA): experience of an academic centre in the USA
Authors: Zhang S. , DeFrias D. V. S. , Alasadi R. , Nayar R. 
Published: October 2009

S. Zhang, D. V. S. DeFrias, R. Alasadi and R. Nayar Endoscopic ultrasound‐guided fine needle aspiration (EUS‐FNA): experience of an academic centre in the USAObjectives:  Endoscopic ultrasound‐guided fine needle aspiration (EUS‐FNA) has become widely accepted as an effective modality for obtaining tissue for primary diagnosis and staging. We have been using EUS‐FNA since July 2001 and herein we summarize our experience over a 5‐year period.Methods:  A computer‐based search for in‐house EUS‐FNA was performed in the pathology database from July 2001 to October 2006. To calculate the sensitivity, specificity and accuracy of EUS‐FNA, the cytology diagnosis was compared with the surgical follow‐up.Results:  A total of 951 EUS‐FNAs were performed during the study period and included 279 pancreatic solid lesions, 186 pancreatic cyst lesions, 249 lymph node aspirations, 111 gastrointestinal (GI) tract submucosal lesions, and 126 miscellaneous lesions. EUS‐FNA had a very high sensitivity and accuracy for solid pancreatic lesions (94.7 and 97.7%, respectively), low sensitivity and accuracy but high specificity (47, 64.8 and 95%, respectively) for cystic lesions. Cyst fluid carcinoembryonic (CEA) levels were significantly higher in mucinous neoplasms than non‐neoplastic cysts. EUS‐FNA also had very high sensitivity and specificity for detecting metastatic carcinoma in lymph nodes (95 and 100%, respectively). GI submucosal spindle cell tumours were further classified with immunohistochemical stains performed either on a cell block or a core biopsy obtained via EUS guidance.Conclusions:  EUS‐FNA has a very high sensitivity and accuracy for pancreatic solid lesions, but the sensitivity for cystic lesions is generally low. Cyst fluid chemical analysis for CEA is helpful, but the overlap between mucinous neoplasm and non‐neoplastic cysts is significant. Recognizing GI contamination is important and immunohistochemical stains are useful for GI submucosal spindle cell lesions.
An audit of cervical cytology in HIV‐positive women
Authors: Hotonu O. E. O. , Hussey J. , Basta M. S. T. , Wadehra V. , Cross P. , Schmid M. L. 
Published: October 2009

O. E. O. Hotonu, J. Hussey, M. S. T. Basta, V. Wadehra, P. Cross and M. L. Schmid An audit of cervical cytology in HIV‐positive womenObjective:  To investigate whether a cohort of human immunodeficiency virus‐positive (HIV+) women were having annual cervical cytology as recommended by the English National Health Service cervical screening programme (NHSCSP) guidelines.Methods:  An audit of cervical cytology in an HIV+ cohort of 187 women by obtaining their last cervical cytology result and recall from local cytology services.Results:  Of the 187 women in the audit, two were ineligible, leaving 185 women, 167 (90.3%) of whom were aged 25–64 years and eligible for screening. Of the 185 women, 126 (68.1%) had a cytology history, 50 (27%) had never had cervical cytology and nine (4.9%) had inadequate details to ascertain whether or not they had a cytology history. Of the 126 with a cytology record, 34 (27%) had a current cytological abnormality, which was low grade in 25 (19.8%) and high grade in nine (7.1%). Among women aged 25–64 years attending the clinic, these percentages were significantly higher than expected for England as a whole (P < 0.001). Of 126 women with a cytology record, 29 (23%) were overdue for their recall date and of these the previous test was abnormal in 14 (48.3%). Cytology tests were taken within the community setting in 61 (48.4%), whereas 65 (51.6%) were seen either at an HIV sexual health clinic or were under colposcopy follow‐up. Of 91 women with negative cytology only 50 (54.9%) were recommended for repeat in 12 months.Conclusion:  This audit demonstrates a high rate of cytological abnormalities among HIV+ women compared with the screening population at large. Implementation of NHSCSP guidelines has been difficult and requires improved care pathways between HIV clinics, primary care and laboratories.