bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterisation of cell adhesion in airway epithelial cell types using electric cell–substrate impedance sensing
Authors: Heijink I. H. , Brandenburg S. M. , Noordhoek J. A. , Postma D. S. , Slebos D-J. , van Oosterhout A. J. M. 
Published: September 2009

Research on epithelial cell lines and primary epithelium is required to dissect the mechanisms underlying the structural abnormalities in airway epithelium observed for respiratory diseases, including asthma and chronic obstructive pulmonary disease.The novel electric cell–substrate impedance sensing technique was used to monitor cell adhesion/spreading, barrier function and wound healing. Primary bronchial epithelium was compared with airway epithelial cell lines 16HBE14o-, BEAS-2B, NCI-H292 and A549.BEAS-2B, A549 and primary cells form a confluent monolayer more rapidly than do 16HBE14o- cells. In contrast, 16HBE14o- cells form stronger intercellular contacts, with a 10-fold higher resistance than BEAS-2B, A549 and NCI-H292 cells and a five-fold increase over primary cells. Accordingly, expression of the adhesion molecules zona occludens-1 and E-cadherin was highest in 16HBE14o- cells. These molecules were localised in intercellular junctions in both 16HBE14o- and primary cells. Finally, restoration of barrier function upon injury was impaired in BEAS-2B compared to 16HBE14o- cells.In conclusion, epithelial cell types display remarkable phenotypic differences and should, accordingly, be used to address specific research questions. 16HBE14o- cells appear most suitable for studies on barrier formation, whereas resemblance in attachment of primary and BEAS-2B and A549 cells makes the latter more important for translational research on cell–matrix contact.
Nested PCR in lung tissue for diagnosis of pulmonary tuberculosis
Authors: Park J. S. , Kang Y. A. , Kwon S. Y. , Yoon H. I. , Chung J-H. , Lee C-T. , Lee J. H. 
Published: September 2009

Diagnosis of pulmonary tuberculosis (TB) is difficult in cases with an unusual presentation and often requires a lung biopsy. The goal of this study was to determine the clinical usefulness of nested PCR on lung tissue for the diagnosis of pulmonary TB.Clinical and laboratory data were reviewed from patients who underwent diagnostic lung biopsies, followed by nested TB PCR on formalin-fixed paraffin-embedded lung tissue specimens. The diagnostic yield and clinical impact of nested PCR were investigated.Of the 223 patients studied, 142 were diagnosed with TB. Microbiologically confirmed TB was identified in 71 patients. Compared to culture results, the sensitivity, specificity, positive predictive value and negative predictive value of nested PCR were 85%, 99%, 98% and 88%, respectively. Nested PCR was more sensitive than acid-fast bacilli smear of respiratory specimens and histopathological findings. The PCR results provided an early diagnosis and initiation of treatment for TB. However, negative PCR results did not lead to discontinuation of unnecessary TB treatment in patients on medication.In conclusion, nested PCR on lung tissue specimens is a useful diagnostic test for pulmonary TB in patients with an unusual presentation.
Interleukin-17A activation on bronchial epithelium and basophils: a novel inflammatory mechanism
Authors: Wong C. K. , Cao J. , Yin Y. B. , Lam C. W. K. 
Published: September 2009

Basophils are the accessory cell type for T-helper (Th)2 induction and initiators in immunoglobulin E-mediated chronic allergic inflammation. Basophils and Th17 cells accumulate at the inflammatory sites, such as the airways of allergic asthmatic patients.We investigated the activation of interleukin (IL)-17A on the primary human basophils/KU812 basophilic cells and primary human bronchial epithelial cells/BEAS-2B bronchial epithelial cells. Cytokines, chemokines, adhesion molecules and intracellular signalling molecules were assayed by ELISA or flow cytometry.Co-culture of bronchial epithelial cells and basophils could significantly induce the release of IL-6, an epithelial inflammatory cytokine, and CCL2, a chemokine for basophils, esosinophils and monocytes. Such induction was synergistically enhanced by IL-17A, and direct interaction between these two cells was necessary for IL-17A-induced IL-6 and CCL2 release. Surface expression of intercellular adhesion molecule-1 on bronchial epithelial cells was also upregulated upon their interaction. The interaction of basophils and bronchial epithelial cells under IL-17A stimulation was differentially regulated by extracellular signal-regulated kinase, c-Jun N-terminal protein kinase, p38 mitogen-activated protein kinase and nuclear factor-κB pathways.These findings suggest a novel immunopathological role of Th17 cells and basophils in allergic asthma through the activation of granulocyte-mediated inflammation initiated by the direct interaction between basophils and bronchial epithelial cells.
Muscle differentiation in a colonial ascidian: organisation, gene expression and evolutionary considerations
Authors: Degasperi Valentina , Gasparini Fabio , Shimeld Sebastian M , Sinigaglia Chiara , Burighel Paolo , Manni Lucia 
Published: September 2009

AbstractBackgroundAscidians are tunicates, the taxon recently proposed as sister group to the vertebrates. They possess a chordate-like swimming larva, which metamorphoses into a sessile adult. Several ascidian species form colonies of clonal individuals by asexual reproduction. During their life cycle, ascidians present three muscle types: striated in larval tail, striated in the heart, and unstriated in the adult body-wall.ResultsIn the colonial ascidianBotryllus schlosseri, we investigated organisation, differentiation and gene expression of muscle beginning from early buds to adults and during zooid regression. We characterised transcripts for troponin T (BsTnT-c), adult muscle-type (BsMA2) and cytoplasmic-type (BsCA1) actins, followed byin situhybridisation (ISH) on sections to establish the spatio-temporal expression ofBsTnT-candBsMA2during asexual reproduction and in the larva. Moreover, we characterised actin genomic sequences, which by comparison with other metazoans revealed conserved intron patterns.ConclusionIntegration of data from ISH, phalloidin staining and TEM allowed us to follow the phases of differentiation of the three muscle kinds, which differ in expression pattern of the two transcripts. Moreover, phylogenetic analyses provided evidence for the close relationship between tunicate and vertebrate muscle genes. The characteristics and plasticity of muscles in tunicates are discussed.
Genome-wide analysis of Tol2 transposon reintegration in zebrafish
Authors: Kondrychyn Igor , Garcia-Lecea Marta , Emelyanov Alexander , Parinov Sergey , Korzh Vladimir 
Published: September 2009

Abstract

Background

Tol2, a member of the hAT family of transposons, has become a useful tool for genetic manipulation of model animals, but information about its interactions with vertebrate genomes is still limited. Furthermore, published reports on Tol2 have mainly been based on random integration of the transposon system after co-injection of a plasmid DNA harboring the transposon and a transposase mRNA. It is important to understand how Tol2 would behave upon activation after integration into the genome.

Results
We performed a large-scale enhancer trap (ET) screen and generated 338 insertions of the Tol2 transposon-based ET cassette into the zebrafish genome. These insertions were generated by remobilizing the transposon from two different donor sites in two transgenic lines. We found that 39% of Tol2 insertions occurred in transcription units, mostly into introns. Analysis of the transposon target sites revealed no strict specificity at the DNA sequence level. However, Tol2 was prone to target AT-rich regions with weak palindromic consensus sequences centered at the insertion site.

Conclusion
Our systematic analysis of sequential remobilizations of the Tol2 transposon from two independent sites within a vertebrate genome has revealed properties such as a tendency to integrate into transcription units and into AT-rich palindrome-like sequences. This information will influence the development of various applications involving DNA transposons and Tol2 in particular.
Pherotypes are driving genetic differentiation within Streptococcus pneumoniae
Authors: Carrolo Margarida , Pinto Francisco R , Melo-Cristino Jose , Ramirez Mario 
Published: September 2009

AbstractBackgroundThe boundaries of bacterial species and the mechanisms underlying bacterial speciation are matters of intense debate. Theoretical studies have shown that recombination acts as a strong cohesive force preventing divergence in bacterial populations.Streptococcus pneumoniaepopulations have the telltale signs of high recombination with competence implicated as the major driving force behind gene exchange. Competence inS. pneumoniaeis triggered by a quorum-sensing mechanism controlled by the competence-stimulating peptide pheromone.ResultsWe studied the distribution of the two major pherotypes in the pneumococcal population and their association with serotype, antimicrobial resistance and genetic lineage. Using multilocus sequence data we evaluated pherotype influence on the dynamics of horizontal gene transfer. We show that pherotype is a clonal property of pneumococci. Standard population genetic analysis and multilocus infinite allele model simulations support the hypothesis that two genetically differentiated populations are defined by the major pherotypes.ConclusionSevere limitations to gene flow can therefore occur in bacterial species in the absence of geographical barriers and within highly recombinogenic populations. This departure from panmixia can have important consequences for our understanding of the response of pneumococci to human imposed selective pressures such as vaccination and antibiotic use.
Structural analysis of the full-length gene encoding a fibronectin-binding-like protein (CadF) and its adjacent genetic loci within Campylobacter lari
Authors: Hirayama Junichi , Sekizuka Tsuyoshi , Tazumi Akihiro , Taneike Ikue , Moore John E , Millar B Cherie , Matsuda Motoo 
Published: September 2009

Abstract

Background
The combined sequences encoding a partial and putative rpsI open reading frame (ORF), non-coding (NC) region, a putative ORF for the Campylobacter adhesin to fibronectin-like protein (cadF), a putative Cla_0387 ORF, NC region and a partial and putative Cla_0388 ORF, were identified in 16 Campylobacter lari isolates, using two novel degenerate primer pairs. Probable consensus sequence at the -35 and -10 regions were identified in all C. lari isolates, as a promoter.

Results
Thus, cadF (-like) gene is highly conserved among C. lari organisms. Transcription of the cadF (-like) gene in C. lari cells in vivo was also confirmed and the transcription initiation site was determined. A peptidoglycan-associating alpha-helical motif in the C-terminal regions of some bacterial cell-surface proteins was completely conserved amongst the putative cadF (-like) ORFs from the C. lari isolates.

Conclusion
The putative cadF (-like) ORFs from all C. lari isolates were nine amino acid larger than those from C. jejuni, and showed amino acid residues 137 -140 of FALG (50% identity), instead of the FRLS residues of the maximal fibronectin-binding activity site demonstrated within C. jejuni CadF. A neighbor joining tree constructed based on cadF (-like) gene sequence information formed a major cluster consisting of C. lari isolates, separating from the other three thermophilic campylobacters.
Geographic distribution of methyltransferases of Helicobacter pylori: evidence of human host population isolation and migration
Authors: Vale Filipa F , Mégraud Francis , Vítor Jorge MB 
Published: September 2009

Abstract

Background

Helicobacter pylori colonizes the human stomach and is associated with gastritis, peptic ulcer, and gastric cancer. This ubiquitous association between H. pylori and humans is thought to be present since the origin of modern humans. The H. pylori genome encodes for an exceptional number of restriction and modifications (R-M) systems. To evaluate if R-M systems are an adequate tool to determine the geographic distribution of H. pylori strains, we typed 221 strains from Africa, America, Asia, and Europe, and evaluated the expression of different 29 methyltransferases.

Results
Independence tests and logistic regression models revealed that ten R-M systems correlate with geographical localization. The distribution pattern of these methyltransferases may have been originated by co-divergence of regional H. pylori after its human host migrated out of Africa. The expression of specific methyltransferases in the H. pylori population may also reflect the genetic and cultural background of its human host. Methyltransferases common to all strains, M. HhaI and M. NaeI, are likely conserved in H. pylori, and may have been present in the bacteria genome since the human diaspora out of Africa.

Conclusion
This study indicates that some methyltransferases are useful geomarkers, which allow discrimination of bacterial populations, and that can be added to our tools to investigate human migrations.
Mitochondrial BNIP3 upregulation precedes endonuclease G translocation in hippocampal neuronal death following oxygen-glucose deprivation
Authors: Zhao Shen-Ting , Chen Ming , Li Shu-Ji , Zhang Ming-Hai , Li Bo-Xing , Das Manas , Bean Jonathan C , Kong Ji-Ming , Zhu Xin-Hong , Gao Tian-Ming 
Published: September 2009

Abstract

Background
Caspase-independent apoptotic pathways are suggested as a mechanism for the delayed neuronal death following ischemic insult. However, the underlying signalling mechanisms are largely unknown. Recent studies imply the involvement of several mitochondrial proteins, including endonuclease G (EndoG) and Bcl-2/adenovirus E1B 19 kDa-interacting protein (BNIP3), in the pathway of non-neuronal cells.

Results
In this report, using western blot analysis and immunocytochemistry, we found that EndoG upregulates and translocates from mitochondria to nucleus in a time-dependent manner in cultured hippocampal neurons following oxygen-glucose deprivation (OGD). Moreover, the translocation of EndoG occurs hours before the observable nuclear pyknosis. Importantly, the mitochondrial upregulation of BNIP3 precedes the translocation of EndoG. Forced expression of BNIP3 increases the nuclear translocation of EndoG and neuronal death while knockdown of BNIP3 decreases the OGD-induced nuclear translocation of EndoG and neuronal death.

Conclusion
These results suggest that BNIP3 and EndoG play important roles in hippocampal neuronal apoptosis following ischemia, and mitochondrial BNIP3 is a signal protein upstream of EndoG that can induce neuronal death.
Upper gastrointestinal symptoms, psychosocial co-morbidity and health care seeking in general practice: population based case control study
Authors: Bröker Linda E , Hurenkamp Gerard JB , ter Riet Gerben , Schellevis François G , Grundmeijer Hans G , van Weert Henk C 
Published: September 2009

Abstract

Background
The pathophysiology of upper gastrointestinal (GI) symptoms is still poorly understood. Psychological symptoms were found to be more common in patients with functional gastrointestinal complaints, but it is debated whether they are primarily linked to GI symptoms or rather represent motivations for health-care seeking. Purpose of our study was to compare co-morbidity, in particular psychological and social problems, between patients with and without upper GI symptoms. In addition, we investigated whether the prevalence of psychological and social problems is part of a broader pattern of illness related health care use.

Methods
Population based case control study based on the second Dutch National Survey of general practice (conducted in 2001). Cases (adults visiting their primary care physician (PCP) with upper GI symptoms) and controls (individuals not having any of these complaints), matched for gender, age, PCP-practice and ethnicity were compared. Main outcome measures were contact frequency, prevalence of somatic as well as psychosocial diagnoses, prescription rate of (psycho)pharmacological agents, and referral rates. Data were analyzed using odds ratios, the Chi square test as well as multivariable logistic regression analysis.

Results
Data from 13,389 patients with upper GI symptoms and 13,389 control patients were analyzed. Patients with upper GI symptoms visited their PCP twice as frequently as controls (8.6 vs 4.4 times/year). Patients with upper GI symptoms presented not only more psychological and social problems, but also more other health problems to their PCP (odds ratios (ORs) ranging from 1.37 to 3.45). Patients with upper GI symptoms more frequently used drugs of any ATC-class (ORs ranging from 1.39 to 2.90), including psychotropic agents. The observed differences were less pronounced when we adjusted for non-attending control patients. In multivariate regression analysis, contact frequency and not psychological or social co-morbidity was strongest associated with patients suffering from upper GI symptoms.

Conclusion
Patients with upper GI symptoms visit their PCP more frequently for problems of any organ system, including psychosocial problems. The relationship between upper GI symptoms and psychological problems is equivocal and may reflect increased health care demands in general.
Evaluation of an evidence-based guidance on the reduction of physical restraints in nursing homes: a cluster-randomised controlled trial [ISRCTN34974819]
Authors: Haut Antonie , Köpke Sascha , Gerlach Anja , Mühlhauser Ingrid , Haastert Burkhard , Meyer Gabriele 
Published: September 2009

Abstract

Background
Physical restraints are regularly applied in German nursing homes. Their frequency varies substantially between centres. Beneficial effects of physical restraints have not been proven, however, observational studies and case reports suggest various adverse effects. We developed an evidence-based guidance on this topic. The present study evaluates the clinical efficacy and safety of an intervention programme based on this guidance aimed to reduce physical restraints and minimise centre variations.

Methods/Design
Cluster-randomised controlled trial with nursing homes randomised either to the intervention group or to the control group with standard information. The intervention comprises a structured information programme for nursing staff, information materials for legal guardians and residents' relatives and a one-day training workshop for nominated nurses. A total of 36 nursing home clusters including approximately 3000 residents will be recruited. Each cluster has to fulfil the inclusion criteria of at least 20% prevalence of physical restraints at baseline. The primary endpoint is the number of residents with at least one physical restraint at six months. Secondary outcome measures are the number of falls and fall-related fractures.

Discussion
If successful, the intervention should be implemented throughout Germany. In case the intervention does not succeed, a three-month pre-post-study with an optimised intervention programme within the control group will follow the randomised trial.

Trial registration
ISRCTN34974819
Genome-wide association reveals three SNPs associated with sporadic amyotrophic lateral sclerosis through a two-locus analysis
Authors: Sha Qiuying , Zhang Zhaogong , Schymick Jennifer C , Traynor Bryan J , Zhang Shuanglin 
Published: September 2009

Abstract

Background
Amyotrophic lateral sclerosis (ALS) is a fatal, degenerative neuromuscular disease characterized by a progressive loss of voluntary motor activity. About 95% of ALS patients are in "sporadic form"-meaning their disease is not associated with a family history of the disease. To date, the genetic factors of the sporadic form of ALS are poorly understood.

Methods
We proposed a two-stage approach based on seventeen biological plausible models to search for two-locus combinations that have significant joint effects to the disease in a genome-wide association study (GWAS). We used a two-stage strategy to reduce the computational burden associated with performing an exhaustive two-locus search across the genome. In the first stage, all SNPs were screened using a single-marker test. In the second stage, all pairs made from the 1000 SNPs with the lowest p-values from the first stage were evaluated under each of the 17 two-locus models.

Results
we performed the two-stage approach on a GWAS data set of sporadic ALS from the SNP Database at the NINDS Human Genetics Resource Center DNA and Cell Line Repository http://ccr.coriell.org/ninds/. Our two-locus analysis showed that two two-locus combinations--rs4363506 (SNP1) and rs3733242 (SNP2), and rs4363506 and rs16984239 (SNP3) -- were significantly associated with sporadic ALS. After adjusting for multiple tests and multiple models, the combination of SNP1 and SNP2 had a p-value of 0.032 under the Dom∩Dom epistatic model; SNP1 and SNP3 had a p-value of 0.042 under the Dom × Dom multiplicative model.

Conclusion
The proposed two-stage analytical method can be used to search for joint effects of genes in GWAS. The two-stage strategy decreased the computational time and the multiple testing burdens associated with GWAS. We have also observed that the loci identified by our two-stage strategy can not be detected by single-locus tests.
Biomechanical optimization of different fixation modes for a proximal femoral L-osteotomy
Authors: Tai Ching-Lung , Chen Weng-Pin , Chen Hsih-Hao , Lin Chien-Yu , Lee Mel S 
Published: September 2009

Abstract

Background
Numerous proposed surgical techniques have had minimal success in managing greater trochanter overgrowth secondary to retarded growth of the femoral capital epiphysis. For reconstruction of residual hip deformities, a novel type of proximal femur L-osteotomy was performed with satisfactory results. Although the clinical outcome was good, the biomechanical characteristics of the femur after such an osteotomy have not been clearly elucidated. Therefore, this study presents a three dimensional finite element analysis designed to understand the mechanical characteristics of the femur after the L-osteotomy.

Methods
A patient with left hip dysplasia was recruited as the study model for L-osteotomy. The normal right hip was used as a reference for performing the corrective surgery. Four FEA models were constructed using different numbers of fixation screws but the same osteotomy lengths together with four FEA models with the same number of fixation screws but different osteotomy lengths. The von Mises stress distributions and femoral head displacements were analyzed and compared.

Results
The results revealed the following: 1). The fixation devices (plate and screws) sustained most of the external loading, and the peak value of von Mises stress on the fixation screws decreased with an increasing number of screws. 2). Additional screws are more beneficial on the proximal segment than on the distal segment for improving the stability of the postoperative femur. 3). The extent of osteotomy should be limited because local stress might be concentrated in the femoral neck region with increasing length of the L-osteotomy.

Conclusion
Additional screw placement on the proximal segment improves stability in the postoperative femur. The cobra-type plate with additional screw holes in the proximal area might improve the effectiveness of L-osteotomies.