bluuebunny/crossref_metadata_2025 huggingface dataset:
They Read, but How Well Do They Understand?
Authors: Alonzo Julie , Basaraba Deni , Tindal Gerald , Carriveau Ronald S.
Published: May 2009

Much of the literature on reading development focuses on measures of early literacy skills (e.g., phonological awareness, phonics, fluency). Elementary educators interested in improving students’ skills in these areas can draw on a wealth of research studies. However, many studies of early literacy skills have not addressed comprehension, obviously an important feature of literacy. The authors used a one-parameter Rasch model to examine the relative difficulty of different multiple-choice reading comprehension items assessing students’ literal, inferential, and evaluative comprehension of fictional narratives. They also examined the difficulty of questions derived from concepts identified by state content standards as important components of reading comprehension, such as character, prediction, and plot sequence. The findings suggest a curvilinear relationship between literal, inferential, and evaluative comprehension, with literal comprehension being the easiest and inferential and evaluative comprehension more challenging. The findings also indicate that assessment objectives differ on the basis of difficulty. Implications of these findings for practice are discussed.
The Epidemiologic Transition: Changing Patterns of Mortality and Population Dynamics
Authors: McKeown Robert E.
Published: May 2009

The epidemiologic transition describes changing patterns of population age distributions, mortality, fertility, life expectancy, and causes of death. A number of critiques of the theory have revealed limitations, including an insufficient account of the role of poverty in determining disease risk and mortality, a failure to distinguish adequately the risk of dying from a given cause or set of causes from the relative contributions of various causes of death to overall mortality, and oversimplification of the transition patterns, which do not fit neatly into either historical periods or geographic locations. Recent developments in epidemiologic methods reveal other limitations. A life course perspective prompts examination of changes in causal pathways across the life span when considering shifts in the age distribution of a population, as described by the epidemiologic transition theory. The ecological model assumes multiple levels of determinants acting in complex and interrelated ways, with higher level determinants exhibiting emergent properties. Development, testing, and implementation of innovative approaches to reduce the risks associated with the sedentary lifestyle and hypernutrition in developed countries should not overshadow the continuing threat from infectious diseases, especially resistant strains or newly encountered agents. Interventions must fit populations and the threats to health they experience while anticipating changes that will emerge with success in some areas. This will require new ways of thinking that go beyond the epidemiologic transition theory.
Where Do Eggs Fit in a Heart-Healthy Diet?
Authors: Curran Celentano Joanne
Published: May 2009

Eggs make up a relatively small contribution to the energy consumption of the average American, in part because of the perception that the cholesterol content makes them a forbidden food for a heart-healthy diet. The relationship between egg cholesterol, blood cholesterol, and cardiovascular disease risk is complex and not clearly understood. In addition, eggs provide many valuable and bioavailable nutrients. Thus, the place of eggs in meal planning should be reconsidered while keeping in mind the diet and lifestyle recommendations of the American Heart Association.
Media as Social Accountability
Authors: Bonner Michelle D.
Published: May 2009

This article examines the role of the media as a mechanism of social accountability. Adding to the work of Enrique Peruzzotti and Catalina Smulovitz, the article argues that the media act as a mechanism of social accountability by providing a forum for debate for a plurality of actors to establish who should be held accountable, what they should be held accountable for, and how they should be held accountable. An analysis of this role of the media is applied to the newspaper coverage of an incident of police violence against social protest in Argentina. The debate in this case contributes to the reframing of excessive police violence against social protest in Argentina as unacceptable, thus acting as a form of preventive accountability.
The Disenchanted Voter
Authors: Hughes Sallie , Guerrero Manuel Alejandro
Published: May 2009

This study of micro-level political decision making responds to an initially perplexing phenomenon that appeared in the 2006 Mexican presidential election, what the authors call the disenchanted voter. The authors found that participants in their longitudinal, qualitative study expressed extreme dissatisfaction with politics, politicians, and the outcomes of a young democracy yet voiced enthusiasm for voting. Checks after the ballot revealed they actually did vote. In this article, the authors argue that this unlikely constellation is explained by participants' emotional appraisals of mediated campaign messages about a polarizing presidential candidate. Grounded in an individual's class position, emotional appraisal of this candidate generated fear in wealthy participants and hope in poorer participants. The coping mechanism, or “secondary assessment” of the candidate, was the firm decision to vote. Based on these findings, the authors propose a model of disenchanted voting that integrates research on emotional appraisal and the social construction of emotions with election salience and personal political efficacy. These findings may be of use in economically polarized democracies beyond Mexico. However, the authors question whether long-term polarizing political discourse is a viable antidote to disenchantment with the uneven economic and social justice outcomes of Latin American democracy.
Mediated Deliberation
Authors: Maia Rousiley C. M.
Published: May 2009

This article investigates the role of the news media in constructing mediated deliberation, focusing on how instrumental politics intertwines with critical argument exchanges in public debates. In the context of Brazil's recent democratization process, the author analyzes mediated deliberation in the national referendum for banning firearm and ammunition sales in 2005. The following indicators are explored: (1) participant accessibility and characterization, (2) use of arguments, (3) reciprocity and responsiveness, and (4) reflexivity and reversibility of opinions. The article argues that normative deliberation principles add to controversy frame studies by helping understand how contending interlocutors increase the quality and the complexity of reasons in dispute in situations where no consensus or general agreement is expected.
β-Arrestin 2 is required for the induction and strengthening of integrin-mediated leukocyte adhesion during CXCR2-driven extravasation
Authors: Molteni Raffaella , Crespo Carolina Lage , Feigelson Sara , Moser Christian , Fabbri Monica , Grabovsky Valentin , Krombach Fritz , Laudanna Carlo , Alon Ronen , Pardi Ruggero
Published: May 2009

Leukocyte extravasation involves interdependent signaling pathways underlying the complex dynamics of firm adhesion, crawling, and diapedesis. While signal transduction by agonist-bound chemokine receptors plays a central role in the above responses, it is unclear how it contributes to the sustained and concurrent nature of such responses, given the rapid kinetics of chemokine-induced trimeric G protein coupling and homologous desensitization. Our findings unveil a novel role of β-arrestins in regulating the activation of signaling pathways underlying discrete integrin-mediated steps in CXCR2-driven leukocyte extravasation. By combining in vivo approaches in β-arrestin knockout mice with in vitro studies in engineered cellular models, we show that membrane-recruited β-arrestin 2 is required for the onset and maintenance of shear stress-resistant leukocyte adhesion mediated by both β1 and β2 integrins. While both β-arrestin isoforms are required for rapid keratinocyte-derived chemokine (KC)–induced arrest onto limiting amounts of vascular cell adhesion molecule-1 (VCAM-1), adhesion strengthening under shear is selectively dependent on β-arrestin 2. The latter synergizes with phospholipase C in promoting activation of Rap1A and B, both of which co-operatively control subsecond adhesion as well as postarrest adhesion stabilization. Thus, receptor-induced Gαi and β-arrestins act sequentially and in spatially distinct compartments to promote optimal KC-induced integrin-dependent adhesion during leukocyte extravasation.
AML with mutated NPM1 carrying a normal or aberrant karyotype show overlapping biologic, pathologic, immunophenotypic, and prognostic features
Authors: Haferlach Claudia , Mecucci Cristina , Schnittger Susanne , Kohlmann Alexander , Mancini Marco , Cuneo Antonio , Testoni Nicoletta , Rege-Cambrin Giovanna , Santucci Antonella , Vignetti Marco , Fazi Paola , Martelli Maria Paola , Haferlach Torsten , Falini Brunangelo
Published: May 2009

Acute myeloid leukemia (AML) with mutated NPM1 usually carries normal karyotype (NK), but it may harbor chromosomal aberrations whose significance remains unclear. We addressed this question in 631 AML patients with mutated/cytoplasmic NPM1. An abnormal karyotype (AK) was present in 93 of 631 cases (14.7%), the most frequent abnormalities being +8, +4, −Y, del(9q), +21. Chromosome aberrations in NPM1-mutated AML were similar to, but occurred less frequently than additional chromosome changes found in other AML with recurrent cytogenetic abnormalities according to WHO classification. Four of the 31 NPM1-mutated AML patients karyotyped at different time points had NK at diagnosis but AK at relapse: del(9q) (n = 2), t(2;11) (n = 1), inv(12) (n = 1). NPM1-mutated AML with NK or AK showed overlapping morphologic, immunophenotypic (CD34 negativity), and gene expression profile (down-regulation of CD34 and up-regulation of HOX genes). No difference in survival was observed among NPM1-mutated AML patients independently of whether they carried a NK or an AK, the NPM1-mutated/FLT3-ITD negative cases showing the better prognosis. Findings in our patients point to chromosomal aberrations as secondary events, reinforce the concept that NPM1 mutation is a founder genetic lesion, and indicate that NPM1-mutated AML should be clinically handled as one entity, irrespective of the karyotype.
A functional genomics approach reveals novel quantitative trait loci associated with platelet signaling pathways
Authors: Jones Chris I. , Bray Sarah , Garner Stephen F. , Stephens Jonathan , de Bono Bernard , Angenent Will G. J. , Bentley David , Burns Philippa , Coffey Alison , Deloukas Panos , Earthrowl Mark , Farndale Richard W. , Hoylaerts Marc F. , Koch Kerstin , Rankin Angela , Rice Catherine M. , Rogers Jane , Samani Nilesh J. , Steward Michael , Walker Adam , Watkins Nicholas A. , Akkerman Jan-Willem , Dudbridge Frank , Goodall Alison H. , Ouwehand Willem H.
Published: May 2009

Platelet response to activation varies widely between individuals but shows interindividual consistency and strong heritability. The genetic basis of this variation has not been properly explored. We therefore systematically measured the effect on function of sequence variation in 97 candidate genes in the collagen and adenosine-diphosphate (ADP) signaling pathways. Resequencing of the genes in 48 European DNA samples nearly doubled the number of known single nucleotide polymorphisms (SNPs) and informed the selection of 1327 SNPs for genotyping in 500 healthy Northern European subjects with known platelet responses to collagen-related peptide (CRP-XL) and ADP. This identified 17 novel associations with platelet function (P < .005) accounting for approximately 46% of the variation in response. Further investigations with platelets of known genotype explored the mechanisms behind some of the associations. SNPs in PEAR1 associated with increased platelet response to CRP-XL and increased PEAR1 protein expression after platelet degranulation. The minor allele of a 3′ untranslated region (UTR) SNP (rs2769668) in VAV3 was associated with higher protein expression (P = .03) and increased P-selectin exposure after ADP activation (P = .004). Furthermore the minor allele of the intronic SNP rs17786144 in ITPR1 modified Ca2+ levels after activation with ADP (P < .004). These data provide novel insights into key hubs within platelet signaling networks.
Abundant c-Fas–associated death domain–like interleukin-1–converting enzyme inhibitory protein expression determines resistance of T helper 17 cells to activation-induced cell death
Authors: Yu Yu , Iclozan Cristina , Yamazaki Tomohide , Yang Xuexian , Anasetti Claudio , Dong Chen , Yu Xue-Zhong
Published: May 2009

Activation-induced cell death (AICD) plays an important role in peripheral T-cell tolerance. AICD in CD4 T helper (Th) cells, including Th1 and Th2 effectors, has been extensively studied. Recently, interleukin-17–producing CD4+ T cells (Th17 cells) have been identified as a unique Th subset, but their susceptibility to AICD and the underlying molecular mechanisms have not been defined. In this study, we found that Th17 cells were significantly less susceptible to AICD than Th1 cells, and Th17 cell resistance to AICD is due to the high levels of c-Fas–associated death domain–like interleukin-1–converting enzyme inhibitory protein preventing Fas-mediated apoptosis. The resistance of Th17 cells to AICD reveals a novel mechanism to explain the high pathogenicity of Th17 cells in autoimmune diseases, and may also provide a rationale to generate tumor-specific Th17 cells for adoptive immunotherapy.
PCOPGene-Net: Holistic Characterisation of cellular states from microarray data based on continuous and non-continuous analysis of gene-expression relationships
Authors: Huerta Mario , Cedano Juan , Peña Dario , Rodriguez Antonio , Querol Enrique
Published: May 2009

Background

Microarray technology is so expensive and powerful that it is essential to extract maximum value from microarray data, specially from large-sample-series microarrays. Our web tools attempt to respond to these researchers' needs by facilitating the possibility to test and formulate from a hypothesis to entire models under a holistic point of view.

Results

PCOPGene-Net is a web application for facilitating the study of the relationships among gene expressions under microarray conditions, to classify these conditions and to study their effect on expression relationships. Furthermore, the system guides the researcher in the navigation through the microarray data by providing the most suitable genes and information for the researcher's interests at each moment. We achieve all of these by means of the zoom-out operation, the zoom-in operation, the non-continuous analysis and crossing the PCOPGene results with external data-servers.

Conclusion

PCOPGene-Net helps to identify cellular states and the genes involved in these. All of that is accomplished in a flexible way, guided by the researcher's interests and taking advantage of the ability of our system to relate gene expressions, even when these relationships are non-continuous and cannot be found using linear or non-linear analytical methods. Currently, our tools are used for tumour-progression study from a holistic point of view.
Upregulation of Toll-like receptor (TLR) expression and release of cytokines from P815 mast cells by GM-CSF
Authors: Yang Haiwei , Wei Jifu , Zhang Huiyun , Lin Liyan , Zhang Wei , He Shaoheng
Published: May 2009

Backgroud

Recently, mast cells have been recognized to express several Toll-like receptors (TLRs) on their membrane surfaces, and granulocyte-macrophage colony-stimulating factor (GM-CSF) was reported to be able to alter expression of TLRs and cytokine production in neutrophils. However, whether GM-CSF modulates the expression of TLR and cytokine production in mast cells is not clear.

Results

Using flow cytometry and real time PCR techniques, we found that GM-CSF upregulated expression of TLR3 and TLR7 in P815 cells in a concentration dependent manner. GM-CSF also provoked approximately up to 2.4 and 2.3 fold increase in IL-13 and IL-6 release from P815 cells, respectively following 16 h incubation. GM-CSF induced IL-13 secretion, TLR3 and TLR7 expression appeared to be through activation of mitogen-activated protein kinase (MAPK) and phosphotidylinositol 3-kinase (PI3K)/Akt signaling pathways, whereas GM-CSF elicited IL-6 release seemed via Akt signaling pathway. At 10 ng/ml, GM-CSF significantly enhanced R-848-induced IL-6 release from P815 cells.

Conclusion

The ability of GM-CSF in modulation of expression of TLR3 and TLR7 in P815 mast cells and in stimulation of IL-13 and IL-6 release from P815 mast cells in vitro suggests that GM-CSF might play an important role in enhancing the innate immune responses of mast cell to viral infection
Insights into the evolution of the snail superfamily from metazoan wide molecular phylogenies and expression data in annelids
Authors: Kerner Pierre , Hung Johanne , Béhague Julien , Le Gouar Martine , Balavoine Guillaume , Vervoort Michel
Published: May 2009

Background

An important issue concerning the evolution of duplicated genes is to understand why paralogous genes are retained in a genome even though the most likely fate for a redundant duplicated gene is nonfunctionalization and thereby its elimination. Here we study a complex superfamily generated by gene duplications, the snail related genes that play key roles during animal development. We investigate the evolutionary history of these genes by genomic, phylogenetic, and expression data studies.

Results

We systematically retrieved the full complement of snail related genes in several sequenced genomes. Through phylogenetic analysis, we found that the snail superfamily is composed of three ancestral families, snail, scratchA and scratchB. Analyses of the organization of the encoded proteins point out specific molecular signatures, indicative of functional specificities for Snail, ScratchA and ScratchB proteins. We also report the presence of two snail genes in the annelid Platynereis dumerilii, which have distinct expression patterns in the developing mesoderm, nervous system, and foregut. The combined expression of these two genes is identical to that of two independently duplicated snail genes in another annelid, Capitella spI, but different aspects of the expression patterns are differentially shared among paralogs of Platynereis and Capitella.

Conclusion

Our study indicates that the snail and scratchB families have expanded through multiple independent gene duplications in the different bilaterian lineages, and highlights potential functional diversifications of Snail and ScratchB proteins following duplications, as, in several instances, paralogous proteins in a given species show different domain organizations. Comparisons of the expression pattern domains of the two Platynereis and Capitella snail paralogs provide evidence for independent subfunctionalization events which have occurred in these two species. We propose that the snail related genes may be especially prone to subfunctionalization, and this would explain why the snail superfamily underwent so many independent duplications leading to maintenance of functional paralogs.
Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE
Authors: Wang Xin , Zhao Yongjun , Wong Kim , Ehlers Peter , Kohara Yuji , Jones Steven J , Marra Marco A , Holt Robert A , Moerman Donald G , Hansen Dave
Published: May 2009

Background

Germ cells must progress through elaborate developmental stages from an undifferentiated germ cell to a fully differentiated gamete. Some of these stages include exiting mitosis and entering meiosis, progressing through the various stages of meiotic prophase, adopting either a male (sperm) or female (oocyte) fate, and completing meiosis. Additionally, many of the factors needed to drive embryogenesis are synthesized in the germ line. To increase our understanding of the genes that might be necessary for the formation and function of the germ line, we have constructed a SAGE library from hand dissected C. elegans hermaphrodite gonads.

Results

We found that 4699 genes, roughly 21% of all known C. elegans genes, are expressed in the adult hermaphrodite germ line. Ribosomal genes are highly expressed in the germ line; roughly four fold above their expression levels in the soma. We further found that 1063 of the germline-expressed genes have enriched expression in the germ line as compared to the soma. A comparison of these 1063 germline-enriched genes with a similar list of genes prepared using microarrays revealed an overlap of 460 genes, mutually reinforcing the two lists. Additionally, we identified 603 germline-enriched genes, supported by in situ expression data, which were not previously identified. We also found >4 fold enrichment for RNA binding proteins in the germ line as compared to the soma.

Conclusion

Using multiple technological platforms provides a more complete picture of global gene expression patterns. Genes involved in RNA metabolism are expressed at a significantly higher level in the germ line than the soma, suggesting a stronger reliance on RNA metabolism for control of the expression of genes in the germ line. Additionally, the number and expression level of germ line expressed genes on the X chromosome is lower than expected based on a random distribution.
Identification and target prediction of miRNAs specifically expressed in rat neural tissue
Authors: Hua You-Jia , Tang Zhong-Yi , Tu Kang , Zhu Li , Li Yi-Xue , Xie Lu , Xiao Hua-Sheng
Published: May 2009

Background

MicroRNAs (miRNAs) are a large group of RNAs that play important roles in regulating gene expression and protein translation. Several studies have indicated that some miRNAs are specifically expressed in human, mouse and zebrafish tissues. For example, miR-1 and miR-133 are specifically expressed in muscles. Tissue-specific miRNAs may have particular functions. Although previous studies have reported the presence of human, mouse and zebrafish tissue-specific miRNAs, there have been no detailed reports of rat tissue-specific miRNAs. In this study, Home-made rat miRNA microarrays which established in our previous study were used to investigate rat neural tissue-specific miRNAs, and mapped their target genes in rat tissues. This study will provide information for the functional analysis of these miRNAs.

Results

In order to obtain as complete a picture of specific miRNA expression in rat neural tissues as possible, customized miRNA microarrays with 152 selected miRNAs from miRBase were used to detect miRNA expression in 14 rat tissues. After a general clustering analysis, 14 rat tissues could be clearly classified into neural and non-neural tissues based on the obtained expression profiles with p values < 0.05. The results indicated that the miRNA profiles were different in neural and non-neural tissues. In total, we found 30 miRNAs that were specifically expressed in neural tissues. For example, miR-199a was specifically expressed in neural tissues. Of these, the expression patterns of four miRNAs were comparable with those of Landgraf et al., Bak et al., and Kapsimani et al. Thirty neural tissue-specific miRNAs were chosen to predict target genes. A total of 1,475 target mRNA were predicted based on the intersection of three public databases, and target mRNA's pathway, function, and regulatory network analysis were performed. We focused on target enrichments of the dorsal root ganglion (DRG) and olfactory bulb. There were four Gene Ontology (GO) functions and five KEGG pathways significantly enriched in DRG. Only one GO function was significantly enriched in the olfactory bulb. These targets are all predictions and have not been experimentally validated.

Conclusion

Our work provides a global view of rat neural tissue-specific miRNA profiles and a target map of miRNAs, which is expected to contribute to future investigations of miRNA regulatory mechanisms in neural systems.
A probable aculeacin A acylase from the Ralstonia solanacearum GMI1000 is N-acyl-homoserine lactone acylase with quorum-quenching activity
Authors: Chen Chin-Nung , Chen Chii-Jaan , Liao Chen-Ting , Lee Chia-Yin
Published: May 2009

Background

The infection and virulence functions of diverse plant and animal pathogens that possess quorum sensing systems are regulated by N-acylhomoserine lactones (AHLs) acting as signal molecules. AHL-acylase is a quorum quenching enzyme and degrades AHLs by removing the fatty acid side chain from the homoserine lactone ring of AHLs. This blocks AHL accumulation and pathogenic phenotypes in quorum sensing bacteria.

Results

An aac gene of undemonstrated function from Ralstonia solanacearum GMI1000 was cloned, expressed in Escherichia coli; it inactivated four AHLs that were tested. The sequence of the 795 amino acid polypeptide was considerably similar to the AHL-acylase from Ralstonia sp. XJ12B with 83% identity match and shared 39% identity with an aculeacin A acylase precursor from the gram-positive actinomycete Actinoplanes utahensis. Aculeacin A is a neutral lipopeptide antibiotic and an antifungal drug. An electrospray ionisation mass spectrometry (ESI-MS) analysis verified that Aac hydrolysed the amide bond of AHL, releasing homoserine lactone and the corresponding fatty acids. However, ESI-MS analysis demonstrated that the Aac could not catalyze the hydrolysis of the palmitoyl moiety of the aculeacin A. Moreover, the results of MIC test of aculeacin A suggest that Aac could not deacylate aculeacin A. The specificity of Aac for AHLs showed a greater preference for long acyl chains than for short acyl chains. Heterologous expression of the aac gene in Chromobacterium violaceum CV026 effectively inhibited violacein and chitinase activity, both of which were regulated by the quorum-sensing mechanism. These results indicated that Aac could control AHL-dependent pathogenicity.

Conclusion

This is the first study to find an AHL-acylase in a phytopathogen. Our data provide direct evidence that the functioning of the aac gene (NP520668) of R. solanacearum GMI1000 is via AHL-acylase and not via aculeacin A acylase. Since Aac is a therapeutic potential quorum-quenching agent, its further biotechnological applications in agriculture, clinical and bio-industrial fields should be evaluated in the near future.
Expression patterns of Neil3 during embryonic brain development and neoplasia
Authors: Hildrestrand Gunn A , Neurauter Christine G , Diep Dzung B , Castellanos Cesilie G , Krauss Stefan , Bjørås Magnar , Luna Luisa
Published: May 2009

Background

The base excision repair pathway is responsible for repairing small DNA base lesions caused by endogenous and exogenous damaging agents. Repair is initiated by DNA glycosylases that recognize and remove the lesions. NEIL3 is one of 11 mammalian DNA glycosylases identified to date and it was discovered on the basis of sequence homology to the E. coli Fpg and Nei glycosylases. Difficulties in purifying the protein have limited its biochemical characterization and in contrast to the other glycosylases, its function remains unclear.

Results

In this study we describe the expression pattern of Neil3 during mouse embryonic development with special focus on brain development. We have also looked at the expression of NEIL3 in several normal and tumor tissues. Quantitative real-time PCR and in situ hybridization revealed that Neil3 was highly expressed at embryonic days 12–13, when neurogenesis starts. The expression decreased during development and in the adult brain,Neil3 could not be detected in any of the brain areas examined by quantitative real-time PCR. During embryogenesis and in newborn mice specific expression was observed in areas known to harbour neural stem and progenitor cells such as the subventricular zone and the dentate gyrus. Finally, NEIL3 expression was higher in tumors compared to normal tissues, except for testis and pancreas.

Conclusion

Our findings indicate that mammalian NEIL3 is specifically expressed in brain areas where neurogenesis takes place during development and that its expression is tightly regulated both temporally and spatially. In addition, NEIL3 seems to be upregulated in tumor tissues compared to normal tissues. Altogether, mammalian NEIL3 seems to be highly expressed in cells with high proliferative potential.
Seroprevalence of Immunoglobulin G antibodies against pertussis toxin among asymptomatic medical students in the west of Iran: a cross sectional study
Authors: Hashemi Seyyed Hamid , Ranjbar Mitra , Hajilooi Mehrdad , Seif-Rabiei Mohammad-Ali , Bolandi Mahnaz , Moghimi Javad
Published: May 2009

Background

Pertussis is a highly communicable, vaccine-preventable respiratory infection. Immune response against this disease can be induced by infection or vaccination. Protection after childhood vaccination is minimal after ten years. Our aim was to assess pertussis immunity state in a population of healthy young medical students.

Methods

In this seroepidemiological survey, blood samples were obtained from 163 first-year medical students in Hamedan University, Iran. Serum level of IgG against pertussis toxin (IgG-PT) was measured by Enzyme-Linked Immunosorbent Assay (ELISA) method. For qualitative assessment, IgG-PT levels more than 24 unit (U)/ml were considered positive. Data was analysed qualitatively and quantitatively considering gender and age groups.

Results

There were 83 males and 80 females, with a mean age of 19.48 years, Prevalence of IgG-PT was 47.6% with mean level of 71.7 u/ml (95% confidence interval: 68.1–75.3). No statistically significant difference was observed with respect to sero-positivity of IgG-PT between males and females (45 cases (54%) vs. 34 cases (42%); P = 0.06). Mean IgG-PT levels in males and females were 84 U/ml and 58.8 U/ml, respectively (P = 0.91).

Conclusion

A considerable proportion of our study population with a positive history of childhood vaccination for pertussis was not serologically immune to pertussis. A booster dose of acellular pertussis vaccine may be indicated in Iranian, medical students regarding their serologic conditions and outstanding role in health care systems.
Caesarean section in four South East Asian countries: reasons for, rates, associated care practices and health outcomes
Authors: Festin Mario R , Laopaiboon Malinee , Pattanittum Porjai , Ewens Melissa R , Henderson-Smart David J , Crowther Caroline A ,   The SEA-ORCHID Study Group
Published: May 2009

Background

Caesarean section is a commonly performed operation on women that is globally increasing in prevalence each year. There is a large variation in the rates of caesarean, both in high and low income countries, as well as between different institutions within these countries. This audit aimed to report rates and reasons for caesarean and associated clinical care practices amongst nine hospitals in the four South East Asian countries participating in the South East Asia-Optimising Reproductive and Child Health in Developing countries (SEA-ORCHID) project.

Methods

Data on caesarean rates, care practices and health outcomes were collected from the medical records of the 9550 women and their 9665 infants admitted to the nine participating hospitals across South East Asia between January and December 2005.

Results

Overall 27% of women had a caesarean section, with rates varying from 19% to 35% between countries and 12% to 39% between hospitals within countries. The most common indications for caesarean were previous caesarean (7.0%), cephalopelvic disproportion (6.3%), malpresentation (4.7%) and fetal distress (3.3%). Neonatal resuscitation rates ranged from 7% to 60% between countries. Prophylactic antibiotics were almost universally given but variations in timing occurred between countries and between hospitals within countries.

Conclusion

Rates and reasons for caesarean section and associated clinical care practices and health outcomes varied widely between the four South East Asian countries.
Rasch model analysis of the Depression, Anxiety and Stress Scales (DASS)
Authors: Shea Tracey L , Tennant Alan , Pallant Julie F
Published: May 2009

Background

There is a growing awareness of the need for easily administered, psychometrically sound screening tools to identify individuals with elevated levels of psychological distress. Although support has been found for the psychometric properties of the Depression, Anxiety and Stress Scales (DASS) using classical test theory approaches it has not been subjected to Rasch analysis. The aim of this study was to use Rasch analysis to assess the psychometric properties of the DASS-21 scales, using two different administration modes.

Methods

The DASS-21 was administered to 420 participants with half the sample responding to a web-based version and the other half completing a traditional pencil-and-paper version. Conformity of DASS-21 scales to a Rasch partial credit model was assessed using the RUMM2020 software.

Results

To achieve adequate model fit it was necessary to remove one item from each of the DASS-21 subscales. The reduced scales showed adequate internal consistency reliability, unidimensionality and freedom from differential item functioning for sex, age and mode of administration. Analysis of all DASS-21 items combined did not support its use as a measure of general psychological distress. A scale combining the anxiety and stress items showed satisfactory fit to the Rasch model after removal of three items.

Conclusion

The results provide support for the measurement properties, internal consistency reliability, and unidimensionality of three slightly modified DASS-21 scales, across two different administration methods. The further use of Rasch analysis on the DASS-21 in larger and broader samples is recommended to confirm the findings of the current study.
Evaluation of uptake and attitude to voluntary counseling and testing among health care professional students in Kilimanjaro region, Tanzania
Authors: Charles Mgosha P , Kweka Eliningaya J , Mahande Aneth M , Barongo Longin R , Shekalaghe Seif , Nkya Hassan M , Lowassa Asanterabi , Mahande Michael J
Published: May 2009

Background

Voluntary counseling and testing (VCT) is a corner stone for successful implementation of prevention, care and support services among HIV negative and positive individuals. VCT is also perceived to be an effective strategy in risk reduction among sexually active young people.. This study aimed to assess the acceptability of VCT and its actual uptake among young health care professional students at KCM College of Tumaini University and Allied health schools.

Methods

This was a cross-sectional study. A structured questionnaire was used among health care professional students aged 18–25 years who were enrolled in degrees, diplomas and certificates courses at Kilimanjaro Christian Medical College and all other Allied health schools

Results

A total of 309 students were recruited, among these 197 (63.8%) were females. All respondents were aware of the benefits of VCT. Only 107 (34.6%) of students have had VCT done previously. About 59 (19.1%) of the students had negative for health care professional to attend VCT. Risk perception among the students was low (37.2%) even though they were found to have higher risk behaviors that predispose them to get HIV infection.

Conclusion

Awareness of VCT services and willingness to test is high among students; however its uptake is low. In order to promote these services, a comprehensive training module on VCT needs to be included in their training curricula. In particular, more emphasis should focus on the benefits of VCT and to help the students to internalize the risk of HIV so that they can take preventive measures.
Education level and physical functional limitations among Japanese community residents-gender difference in prognosis from stroke
Authors: Honjo Kaori , Iso Hiroyasu , Ikeda Ai , Inoue Manami , Tsugane Shoichiro ,   The JPHC Study Group
Published: May 2009

Background

Little research has been conducted to examine the relationship between education level and functional limitations among Japanese community residents. We sought to examine the association between education level and physical functional limitations among Japanese men and women, and whether that association was modified by gender and history of stroke.

Methods

We examined prevalence of physical functional limitation by educational level using the data from a total of 29,134 Japanese men and women aged 50–69 years living in communities in 2000. The information of educational level (junior high school graduates, senior high school graduates, college and/or higher education) and physical functional limitations (no need for assistance, need for assistance when going outdoors, and need for assistance to carry out indoor activities) were obtained by self-administrated questionnaire.

Results

The proportions of the subjects reported their highest level of schooling were 48% for junior high school, 39% for high school, and 13% for college. Three hundred and twenty eight subjects (1% of total subjects) reported having some physical functional limitations. Multinomial logistic regression analyses showed that the odds ratio of needing assistance to carry out indoor activities were 4.84(95%CI:3.61,6.50) for lowest education level group and 2.21(95%CI:1.00,4.86) for middle education level group compared to highest education level group. The corresponding odds ratios of needing assistance when going outdoors were 2.36(95%CI: 2.03,2.72) and 1.08(95%CI:0.73,1.60), respectively. Further, the significant excess prevalence of having functional limitations associated with the low education level was identified for men regardless of history of stroke and for women without history of stroke.

Conclusion

Low education level was associated with the higher prevalence of physical functional limitations for both genders. That association among persons with history of stroke was observed for men but not for women probably due to gender differences in stroke subtypes and social support.
Negative pressure wound therapy for soft tissue injuries around the foot and ankle
Authors: Lee Hyun-Joo , Kim Joon-Woo , Oh Chang-Wug , Min Woo-Kie , Shon Oog-Jin , Oh Jong-Keon , Park Byung-Chul , Ihn Joo-Chul
Published: May 2009

Background

This study was performed to evaluate the results of negative pressure wound therapy (NPWT) in patients with open wounds in the foot and ankle region.

Materials and methods

Using a NPWT device, 16 patients were prospectively treated for soft tissue injuries around the foot and ankle. Mean patient age was 32.8 years (range, 3–67 years). All patients had suffered an acute trauma, due to a traffic accident, a fall, or a crush injury, and all had wounds with underlying tendon or bone exposure. Necrotic tissues were debrided before applying NPWT. Dressings were changed every 3 or 4 days and treatment was continued for 18.4 days on average (range, 11–29 days).

Results

Exposed tendons and bone were successfully covered with healthy granulation tissue in all cases except one. The sizes of soft tissue defects reduced from 56.4 cm2 to 42.9 cm2 after NPWT (mean decrease of 24%). In 15 of the 16 cases, coverage with granulation tissue was achieved and followed by a skin graft. A free flap was needed to cover exposed bone and tendon in one case. No major complication occurred that was directly attributable to treatment. In terms of minor complications, two patients suffered scar contracture of grafted skin.

Conclusion

NPWT was found to facilitate the rapid formation of healthy granulation tissue on open wounds in the foot and ankle region, and thus, to shorten healing time and minimize secondary soft tissue defect coverage procedures.
Systematic identifiability testing for unambiguous mechanistic modeling – application to JAK-STAT, MAP kinase, and NF-κ B signaling pathway models
Authors: Quaiser Tom , Mönnigmann Martin
Published: May 2009

Background

When creating mechanistic mathematical models for biological signaling processes it is tempting to include as many known biochemical interactions into one large model as possible. For the JAK-STAT, MAP kinase, and NF-κ B pathways a lot of biological insight is available, and as a consequence, large mathematical models have emerged. For large models the question arises whether unknown model parameters can uniquely be determined by parameter estimation from measured data. Systematic approaches to answering this question are indispensable since the uniqueness of model parameter values is essential for predictive mechanistic modeling.

Results

We propose an eigenvalue based method for efficiently testing identifiability of large ordinary differential models and compare this approach to three existing ones. The methods are benchmarked by applying them to models of the signaling pathways mentioned above. In all cases the eigenvalue method proposed here and the orthogonal method find the largest set of identifiable parameters, thus clearly outperforming the other approaches. The identifiability analysis shows that the pathway models are not identifiable, even under the strong assumption that all system state variables are measurable. We demonstrate how the results of the identifiability analysis can be used for model simplification.

Conclusion

While it has undoubtedly contributed to recent advances in systems biology, mechanistic modeling by itself does not guarantee unambiguous descriptions of biological processes. We show that some recent signal transduction pathway models have reached a level of detail that is not warranted. Rigorous identifiability tests reveal that even if highly idealized experiments could be carried out to measure all state variables of these signaling pathways, some unknown parameters could still not be estimated. The identifiability tests therefore show that the level of detail of the investigated models is too high in principle, not just because too little experimental information is available. We demonstrate how the proposed method can be combined with biological insight, however, to simplify these models.
Microarray analysis of RNA extracted from formalin-fixed, paraffin-embedded and matched fresh-frozen ovarian adenocarcinomas
Authors: Fedorowicz Grazyna , Guerrero Steve , Wu Thomas D , Modrusan Zora
Published: May 2009

Background

Gene expression profiling of formalin-fixed, paraffin-embedded (FFPE) samples represents a valuable approach for advancing oncology diagnostics and enhancing retrospective clinical studies; however, at present, this methodology still requires optimization and thus has not been extensively used. Here, we utilized thorough quality control methods to assess RNA extracted from FFPE samples and then compared it to RNA extracted from matched fresh-frozen (FF) counterparts. We preformed genome-wide expression profiling of FF and FFPE ovarian serous adenocarcinoma sample pairs and compared their gene signatures to normal ovary samples.

Methods

RNA from FFPE samples was extracted using two different methods, Ambion and Agencourt, and its quality was determined by profiling starting total RNA on Bioanalyzer and by amplifying increasing size fragments of beta actin (ACTB) and claudin 3 (CLDN3) by reverse-transcriptase polymerase chain reaction. Five matched FF and FFPE ovarian serous adenocarcinoma samples, as well as a set of normal ovary samples, were profiled using whole genome Agilent microarrays. Reproducibility of the FF and FFPE replicates was measured using Pearson correlation, whereas comparison between the FF and FFPE samples was done using a Z-score analysis.

Results

Data analysis showed high reproducibility of expression within each FF and FFPE method, whereas matched FF and FFPE pairs demonstrated lower similarity, emphasizing an inherent difference between the two sample types. Z-score analysis of matched FF and FFPE samples revealed good concordance of top 100 differentially expressed genes with the highest correlation of 0.84. Genes characteristic of ovarian serous adenocarcinoma, including a well known marker CLDN3, as well as potentially some novel markers, were identified by comparing gene expression profiles of ovarian adenocarcinoma to those of normal ovary.

Conclusion

Conclusively, we showed that systematic assessment of FFPE samples at the RNA level is essential for obtaining good quality gene expression microarray data. We also demonstrated that profiling of not only FF but also of FFPE samples can be successfully used to identify differentially expressed genes characteristic of ovarian carcinoma.
Application of linear preview control to modelling human steering control
Authors: Odhams A M C , Cole D J
Published: May 2009

A well-known linear optimal preview controller has been investigated for potential application to modelling human steering control. The controller was modified to account for some characteristics of human control: limited understanding of the system being controlled, time delay in the control action, and a neuromuscular system with a finite bandwidth. The standard and modified controllers were compared in terms of their state and preview gains, and also in terms of their response during a lane-change manoeuvre. A technique for dealing with target paths that turn through more than 90° within the preview distance is introduced that overcomes a limitation of previous time domain implementations of linear optimal preview steering control. The results suggest some conditions necessary to identify models of human steering control. Identification of human time delay is likely to require non-previewed disturbances to the system. Identification of a driver's limited understanding of vehicle dynamics is likely to require the controlled vehicle to have non-simple dynamics. Work to identify the steering control models described in this paper from driving simulator experiments has been completed and will be reported in a later paper.
Investigation of the interaction between a vehicle and the road using the second road excitation on the vehicle
Authors: Li S-H , Yang S-P , Lu Y-J
Published: May 2009

A two-degrees-of-freedom quarter-vehicle suspension model is used in this work. The road is modelled as a Bernoulli—Euler beam with simply supported ends on a linear viscoelastic Kelvin foundation. Thus a two-dimensional vehicle—road system is built. Analytical solutions of the vehicle body, wheel, and road's dynamic response are derived by the mode superposition method. The solutions are directed to analyse the distribution of road displacement and the concept of second road excitation on the vehicle is proposed. Influences of the second road excitation on the vehicle suspension displacement, vehicle body acceleration, and tyre force are investigated. It is found that second road excitation should be considered in vehicle dynamic analysis when a heavy vehicle runs on a smooth highway road.
Computational pregnant occupant model, ‘Expecting’, for crash simulations
Authors: Serpil Acar B , van Lopik D
Published: May 2009

A computational model of the pregnant occupant, which is capable of simulating the dynamic response to acceleration impacts, is introduced. The occupant model represents a 5th percentile female at around the 38th week of pregnancy. A finite element uterus and multi-body fetus is integrated into an existing female model to incorporate pregnant female anthropometry.

The complete model, ‘Expecting’, is used to simulate a range of frontal impacts of increasing severity from 15km/h to 45km/h. Three levels of occupant restraint, completely unrestrained, three-point seat belt, and three-point seat belt with an airbag, are investigated. The strains developed in the uterus because of loading from the seat belt and steering-wheel unit are presented, together with an analysis of stress distribution due to inertial loading of the fetus on the uterus.

The unrestrained cases are shown to be the most dangerous to the fetus, owing to the large interaction with the vehicle steering wheel at the level of the placenta. The use of a three-point seat belt together with a driver airbag appears to offer the greatest protection to the fetus.