bluuebunny/crossref_metadata_2025 huggingface dataset:
New concepts for expressing forced expiratory volume in 1 s arising from survival analysis
Authors: Miller M. R. , Pedersen O. F.
Published: September 2009

Spirometric lung function is partly determined by sex, age and height (Ht). Commonly, lung function is expressed as a percentage of the predicted value (PP) in order to account for these effects.

Since the PP method retains sex, age and Ht bias, forced expiratory volume in 1 s (FEV1) standardised by powers of Ht and by a new sex-specific lower limit (FEV1quotient (FEV1Q)) were investigated to determine which method best predicted all-cause mortality in >26,967 patients and normal subjects.

On multivariate analysis, FEV1Q was the best predictor, with a hazard ratio for the worst decile of 6.9 compared to 4.1 for FEV1PP. On univariate analysis, the hazard ratios were 18.8 compared to 6.1, respectively; FEV1·Ht−3was the next-best predictor of survival. Median survival was calculated for simple cut-off values of FEV1Q and FEV1·Ht−3. These survival curves were accurately fitted (r2 = 1.0) by both FEV1Q and FEV1·Ht−3values expressed polynomially, and so an individual's test result could be used to estimate survival (withsdfor median survival of 0.22 and 0.61 yrs, respectively).

It is concluded that lung function impairment should be expressed in a new way, here termed the FEV1Q, or, alternatively, as FEV1·Ht−3, since these indices best relate spirometric lung function to all-cause mortality and survival.
Study of prone positioning to reduce ventilator-associated pneumonia in hypoxaemic patients
Authors: Mounier R. , Adrie C. , Français A. , Garrouste-Orgeas M. , Cheval C. , Allaouchiche B. , Jamali S. , Dinh-Xuan A. T. , Goldgran-Toledano D. , Cohen Y. , Azoulay E. , Timsit J-F. , Ricard J-D.
Published: September 2009

The aim of the present study was to examine whether prone positioning (PP) affects ventilator associated-pneumonia (VAP) and mortality in patients with acute lung injury/adult respiratory distress syndrome.

2,409 prospectively included patients were admitted over 9 yrs (2000–2008) to 12 French intensive care units (ICUs) (OUTCOMEREA). The patients required invasive mechanical ventilation (MV) and had arterial oxygen tension/inspiratory oxygen fraction ratios <300 during the first 48 h. Controls were matched to PP patients on the PP propensity score (±10%), MV duration longer than that in PP patients before the first turn prone, and centre.

VAP incidence was similar in the PP and control groups (24versus13 episodes·1,000 patient-days MV−1respectively, p = 0.14). After adjustment, PP did not decrease VAP occurrence (HR 1.64 (95% CI 0.70–3.84); p = 0.25) but significantly delayed hospital mortality (HR 0.56 (95% CI 0.39–0.79); p = 0.001), without decreasing 28-day mortality (37% in both groups).Post hocanalyses indicated that PP did not protect against VAP but, when used for >1 day, might decrease mortality and benefit the sickest patients (Simplified Acute Physiology Score >50).

In ICU patients with hypoxaemic acute respiratory failure, PP had no effect on the risk of VAP. PP delayed mortality without decreasing 28-day mortality. PP >1 day might decrease mortality, particularly in the sickest patients.
Prevention of panic attacks and panic disorder in COPD
Authors: Livermore N. , Sharpe L. , McKenzie D.
Published: September 2009

This study examined whether cognitive behavioural therapy (CBT) could prevent the development or worsening of panic-spectrum psychopathology and anxiety symptoms in chronic obstructive pulmonary disease (COPD).

41 patients with COPD, who had undergone pulmonary rehabilitation, were randomised to either a four-session CBT intervention condition (n = 21) or a routine care condition (n = 20). Assessments were at baseline, post-intervention, and at 6-, 12- and 18-month follow-ups. Primary outcomes were the rates of panic attacks, panic disorder and anxiety symptoms. Secondary outcomes were depressive symptoms, catastrophic cognitions about breathing difficulties, disease-specific quality of life and hospital admission rates.

There were no significant differences between the groups on outcome measures at baseline. By the 18-month follow-up assessment, 12 (60%) routine care group participants had experienced at least one panic attack in the previous 6 months, with two (17%) of these being diagnosed with panic disorder, while no CBT group participants experienced any panic attacks during the follow-up phase. There were also significant reductions in anxiety symptoms and catastrophic cognitions in the CBT group at all three follow-ups and a lower number of hospital admissions between the 6- and 12-month follow-ups.

The study provides evidence that a brief, specifically targeted CBT intervention can treat panic attacks in COPD patients and prevent the development and worsening of panic-spectrum psychopathology and anxiety symptoms.
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

Background

Ascidians 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.

Results

In 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.

Conclusion

Integration 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

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

Background

The 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.

Results

We 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.

Conclusion

Severe 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

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

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

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

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

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

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

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.
Increased NO bioavailability in aging male rats by genistein and exercise training: using 4, 5-diaminofluorescein diacetate
Authors: Eksakulkla Sukanya , Suksom Daroonwan , Siriviriyakul Prasong , Patumraj Suthiluk
Published: September 2009

Background

Several kinds of anti-oxidants have drawn a lot of intension for their benefits on vascular protection. In addition, it has been demonstrated that exercise training could improve endothelial function by up-regulating endothelial nitric oxide synthase (eNOS) protein. Therefore, the present study aims to investigate the effects of genistein, a potent phyto-antioxidant, and exercise training on age-induced endothelial dysfunction in relation to NO bioavailability using in situ NO-sensitive fluorescent dye detection.

Methods

Male Wistar rats (20-22-month old) were divided into four groups: aged rats treated with corn oil, (Aged+Veh, n = 5), aged rats treated with genistein (Aged+Gen, n = 5, (0.25 mg/kg BW/day, s.c.)), aged rats with and without exercise training (Aged+Ex, n = 5, swimming 40 min/day, 5 days/week for 8 weeks) (Aged+Without-Ex, n = 5). Cremaster arterioles (15-35 micrometer) were visualized by fluorescein isothiocyanate labeled dextran (5 microgram/ml). The vascular response to acetylcholine (Ach; 10-5M, 5 ml/5 min) was accessed after 1-min norepinephrine preconstriction (10 micro molar). To determine NO bioavailability, the Krebs-Ringer buffer with 4, 5-diaminofluorescein-diacetate (3 micro molar DAF-2DA), and 10 micro- molar Ach saturated with 95%N2 and 5%CO2 were used. Changes of DAF-2T-intensities along the cremaster arterioles were analyzed by the Image Pro-Plus Software (Media Cybernatics, Inc, USA). Liver malondialdehyde (MDA) level was measured by thiobarbituric acid reaction and used as an indicator for oxidative stress.

Results

The results showed that means arterial blood pressure for both Aged+Gen and Aged+Ex groups were significantly reduced when compared to the Aged groups, Aged+Veh and Aged+Without-Ex (P < 0.05). Among the treated groups, Ach-induced vasodilatation were significantly increased (P < 0.05) and was associated with increased NO-associated fluorescent intensities (P < 0.05). On the other hand, MDA levels were significantly reduced (P < 0.05) when Aged+Veh was compared to Aged+Without-Ex.

Conclusion

These findings showed that genistein and exercise training could improve age-induced endothelial dysfunction and is related to the increased NO bioavailability.
A cross-study gene set enrichment analysis identifies critical pathways in endometriosis
Authors: Zhao Hongbo , Wang Qishan , Bai Chunyan , He Kan , Pan Yuchun
Published: September 2009

Background

Endometriosis is an enigmatic disease. Gene expression profiling of endometriosis has been used in several studies, but few studies went further to classify subtypes of endometriosis based on expression patterns and to identify possible pathways involved in endometriosis. Some of the observed pathways are more inconsistent between the studies, and these candidate pathways presumably only represent a fraction of the pathways involved in endometriosis.

Methods

We applied a standardised microarray preprocessing and gene set enrichment analysis to six independent studies, and demonstrated increased concordance between these gene datasets.

Results

We find 16 up-regulated and 19 down-regulated pathways common in ovarian endometriosis data sets, 22 up-regulated and one down-regulated pathway common in peritoneal endometriosis data sets. Among them, 12 up-regulated and 1 down-regulated were found consistent between ovarian and peritoneal endometriosis. The main canonical pathways identified are related to immunological and inflammatory disease. Early secretory phase has the most over-represented pathways in the three uterine cycle phases. There are no overlapping significant pathways between the dataset from human endometrial endothelial cells and the datasets from ovarian endometriosis which used whole tissues.

Conclusion

The study of complex diseases through pathway analysis is able to highlight genes weakly connected to the phenotype which may be difficult to detect by using classical univariate statistics. By standardised microarray preprocessing and GSEA, we have increased the concordance in identifying many biological mechanisms involved in endometriosis. The identified gene pathways will shed light on the understanding of endometriosis and promote the development of novel therapies.
Receptor oligomerization and beyond: a case study in bone morphogenetic proteins
Authors: Heinecke Kai , Seher Axel , Schmitz Werner , Mueller Thomas D , Sebald Walter , Nickel Joachim
Published: September 2009

Background

Transforming growth factor (TGF)β superfamily members transduce signals by oligomerizing two classes of serine/threonine kinase receptors, termed type I and type II. In contrast to the large number of ligands only seven type I and five type II receptors have been identified in mammals, implicating a prominent promiscuity in ligand-receptor interaction. Since a given ligand can usually interact with more than one receptor of either subtype, differences in binding affinities and specificities are likely important for the generation of distinct ligand-receptor complexes with different signaling properties.

Results

In vitro interaction analyses showed two different prototypes of binding kinetics, 'slow on/slow off' and 'fast on/fast off'. Surprisingly, the binding specificity of ligands to the receptors of one subtype is only moderate. As suggested from the dimeric nature of the ligands, binding to immobilized receptors shows avidity due to cooperative binding caused by bivalent ligand-receptor interactions. To compare these in vitro observations to the situation in vivo, binding studies on whole cells employing homodimeric as well as heterodimeric bone morphogenetic protein 2 (BMP2) mutants were performed. Interestingly, low and high affinity binding sites were identified, as defined by the presence of either one or two BMP receptor (BMPR)-IA receptor chains, respectively. Both sites contribute to different cellular responses in that the high affinity sites allow a rapid transient response at low ligand concentrations whereas the low affinity sites facilitate sustained signaling but higher ligand concentrations are required.

Conclusion

Binding of a ligand to a single high affinity receptor chain functioning as anchoring molecule and providing sufficient complex stability allows the subsequent formation of signaling competent complexes. Another receptor of the same subtype, and up to two receptors of the other subtype, can then be recruited. Thus, the resulting receptor arrangement can principally consist of four different receptors, which is consistent with our interaction analysis showing low ligand-receptor specificity within one subtype class. For BMP2, further complexity is added by the fact that heterooligomeric signaling complexes containing only one type I receptor chain can also be found. This indicates that despite prominent ligand receptor promiscuity a manifold of diverse signals might be generated in this receptor limited system.
Pathophysiology of age-related diseases
Authors: Campisi Giuseppina , Chiappelli Martina , De Martinis Massimo , Franco Vito , Ginaldi Lia , Guiglia Rosario , Licastro Federico , Lio Domenico
Published: September 2009

A Symposium regarding the Pathophysiology of Successful and Unsuccessful Ageing was held in Palermo, Italy on 7-8 April 2009. Three lectures from that Symposium by G. Campisi, L. Ginaldi and F. Licastro are here summarized. Ageing is a complex process which negatively impacts on the development of various bodily systems and its ability to function. A long life in a healthy, vigorous, youthful body has always been one of humanity's greatest dreams. Thus, a better understanding of the pathophysiology of age-related diseases is urgently required to improve our understanding of maintaining good health in the elderly and to program possible therapeutic intervention.
Torque Teno Virus (TTV) distribution in healthy Russian population
Authors: Vasilyev Evgeny V , Trofimov Dmitry Y , Tonevitsky Alexander G , Ilinsky Valery V , Korostin Dmitriy O , Rebrikov Denis V
Published: September 2009

Background

Torque teno virus (TTV) is a circular, single-stranded DNA virus that chronically infects healthy individuals of all ages worldwide. There is a lot of data on the prevalence and genetic heterogeneity of TTV in healthy populations and in patients with various diseases now available. However, little is known about TTV load among healthy human population. In this study we analyzed TTV load in the group of 512 Russian elite athletes, who are supposed to be, by some standards, the healthiest part of the human population.

Results

The prevalence rate of TTV among the Russian Olympic Reserve members was 94% (for test sensitivity about 1000 genome equivalents per 1 ml of blood). Quantities varied from 103 (which corresponded to detection limit) to 1010 copies per 1 ml of blood, with median at 2.7 × 106 copies.

Conclusion

About 94% of healthy individuals in Russian population have more than 1000 TTV genome copies per 1 ml of blood. This result exceeds the previously published data, and can be explained by either more sensitive PCR test system or by higher TTV distribution in Russian population or both. TTV viral load neither depends on gender, nor age.
Cysteine protease activation and apoptosis in Murine norovirus infection
Authors: Furman Linnzi M , Maaty Walid S , Petersen Lena K , Ettayebi Khalil , Hardy Michele E , Bothner Brian
Published: September 2009

Background

Noroviruses are the leading cause of viral gastroenteritis. Because a suitablein vitroculture system for the human virus has yet to be developed, many basic details of the infection process are unknown. Murine norovirus (MNV) serves as a model system for the study of norovirus infection. Recently it was shown that infection of RAW 264.7 cells involved a novel apoptotic pathway involving survivin.

Results

Using a different set of approaches, the up-regulation of caspases, DNA condensation/fragmentation, and membrane blebbing, all of which are markers of apoptosis, were confirmed. Live cell imaging and activity-based protein profiling showed that activation of caspase-like proteases occurred within two hours of infection, followed by morphological changes to the cells. MNV infection in the presence of caspase inhibitors proceeded via a distinct pathway of rapid cellular necrosis and reduced viral production. Affinity purification of activity-based protein profiling targets and identification by peptide mass fingerprinting showed that the cysteine protease cathepsin B was activated early in infection, establishing this protein as an upstream activator of the intrinsic apoptotic pathway.

Conclusion

This work adds cathepsin B to the noncanonical programmed cell death induced by MNV, and provides data suggesting that the virus may induce apoptosis to expand the window of time for viral replication. This work also highlights the significant power of activity-based protein profiling in the study of viral pathogenesis.
Hybrid stochastic simplifications for multiscale gene networks
Authors: Crudu Alina , Debussche Arnaud , Radulescu Ovidiu
Published: September 2009

Background

Stochastic simulation of gene networks by Markov processes has important applications in molecular biology. The complexity of exact simulation algorithms scales with the number of discrete jumps to be performed. Approximate schemes reduce the computational time by reducing the number of simulated discrete events. Also, answering important questions about the relation between network topology and intrinsic noise generation and propagation should be based on general mathematical results. These general results are difficult to obtain for exact models.

Results

We propose a unified framework for hybrid simplifications of Markov models of multiscale stochastic gene networks dynamics. We discuss several possible hybrid simplifications, and provide algorithms to obtain them from pure jump processes. In hybrid simplifications, some components are discrete and evolve by jumps, while other components are continuous. Hybrid simplifications are obtained by partial Kramers-Moyal expansion [1–3] which is equivalent to the application of the central limit theorem to a sub-model. By averaging and variable aggregation we drastically reduce simulation time and eliminate non-critical reactions. Hybrid and averaged simplifications can be used for more effective simulation algorithms and for obtaining general design principles relating noise to topology and time scales. The simplified models reproduce with good accuracy the stochastic properties of the gene networks, including waiting times in intermittence phenomena, fluctuation amplitudes and stationary distributions. The methods are illustrated on several gene network examples.

Conclusion

Hybrid simplifications can be used for onion-like (multi-layered) approaches to multi-scale biochemical systems, in which various descriptions are used at various scales. Sets of discrete and continuous variables are treated with different methods and are coupled together in a physically justified approach.
As the bell tolls: a foundation study on pancreatic cancer consumer's research priorities
Authors: Saunders Carla , Gooden Helen , Robotin Monica , Mumford Jan
Published: September 2009

Background

This is the first investigation of its kind to explore the views of people affected by pancreatic cancer with regard to research priorities. Pancreatic cancer has an extremely poor outlook in terms of early diagnosis, effective treatment and survival. Those affected by the disease generally lack opportunities to voice their needs or concerns in an organised manner, link with others affected by the condition and take part in research.

Methods

This qualitative study adopts a self-selected telephone focussed discussion group approach. Information was obtained from distinct carer and patient groups after adequate controls such as the 'safe space' technique (repeatedly enquiring on and respecting the emotional needs) were implemented to protect participants from undue physical and psychological distress.

Results

Five themes emerged overall, with three themes being common between the patients and carers groups. Early detection, clinician communication and public awareness were areas of recurring discussion and consensus for both groups. The fourth theme to emerge for the patient group centred on quality of care, while the fourth theme of the carer group focused on the need for more and improved treatment options.

Conclusion

Research priorities for pancreatic cancer consumers have been identified via an investigation that was tailored to meet exceptional needs. This research gives us a primary understanding of the role that pancreatic cancer patients can play in identifying areas of research that are responsive to their needs and priorities when suitably planned. Importantly it also provides a much greater understanding of the grim realities of the disease for those affected. This work is likely to be of value to anyone planning to work with those with a time limited, challenging condition.
Nonopportunistic Neurologic Manifestations of the Human Immunodeficiency Virus: An Indian Study
Authors: Deshpande Alaka K , Patnaik Mrinal M
Published: September 2009

Context

HIV‐1 is a neurotropic virus. In a resource‐limited country such as India, large populations of affected patients now have access to adequate chemoprophylaxis for opportunistic infections (OIs), allowing them to live longer. Unfortunately the poor availability of highly active antiretroviral therapy (HAART) has allowed viral replication to proceed unchecked. This has resulted in an increase in the debilitating neurologic manifestations directly mediated by the virus.

Objective

The main objective of this study was to identify and describe in detail the direct neurologic manifestations of HIV‐1 in antiretroviral treatment (ART)‐naive, HIV‐infected patients (excluding the neurologic manifestations produced by opportunistic pathogens).

Design

Three hundred successive cases of HIV‐1 infected, ART‐naive patients with neurologic manifestations were studied over a 3‐year period. Each case was studied in detail to identify and then exclude manifestations due to opportunistic pathogens. The remaining cases were then analyzed specially in regard to their occurrence and the degree of immune suppression (CD4+ cell counts).

Setting and Patients

The study was carried out in an apex, tertiary, referral care center for HIV/AIDS in India. All patients were admitted for a detailed analysis.

No interventions were carried out, as this was an observational study.

Results

Of the 300 cases, 67 (22.3%) had neurologic manifestations due to the direct effects of HIV‐1. The HIV infection involved the neuroaxis at all levels. The distribution of cases showed that the region most commonly involved was the brain (50.7%). The manifestations included stroke syndromes (29.8%), demyelinating illnesses (5.9%), AIDS dementia complex (5.9%), and venous sinus thrombosis (4.4%). The other manifestations seen were peripheral neuropathies (35.8% of cases), spinal cord pathologies (5.9% of cases), radiculopathies (4.4% of cases), and a single case of myopathy. The onset of occurrence of these diseases and their progression were then correlated with the CD4+ cell counts.

Conclusion

HIV infection is responsible for a large number of nonopportunistic neurologic manifestations that occur across a large immune spectrum. During the early course of the disease, the polyclonal hypergammaglobulinemia induced by the virus results in demyelinating diseases of the central‐ and peripheral nervous systems (CNS and PNS). As the HIV infection progresses, the direct toxic effects of the virus unfold, directly damaging the CNS and PNS, resulting in protean clinical manifestations.
Characterization of Cdk9 T-loop phosphorylation in resting and activated CD4+ T lymphocytes
Authors: Ramakrishnan Rajesh , Dow Eugene C , Rice Andrew P
Published: September 2009

Low levels of Cdk9 T-loop autophosphorylation in quiescent CD4+ T lymphocytes may limit RNA polymerase II elongation.

The cellular kinase complex P-TEFb is composed of Cdk9 and cyclin T, and it is required for expression of most protein-coding genes by RNAP II. Cdk9 has been shown recently to be activated in cis by autophosphorylation of Thr186 in its T-loop. Using a phosphospecific Cdk9 antibody, we examined the level of Cdk9 T-loop phosphorylation in resting and activated CD4+ T lymphocytes. Cdk9 T-loop phosphorylation was found to be low-to-undetectable in resting CD4+ T lymphocytes, and upon activation by distinct stimuli, there is a rapid (<1 h) increase in pCdk9 that does not require protein synthesis. The low level of Cdk9 T-loop phosphorylation was not to be a result of the absence of an associated regulatory cyclin partner. These observations suggest that autophosphorylation of the Cdk9 T-loop is repressed in resting CD4+ T lymphocytes. The low level of T-loop phosphorylation in resting cells is also reflected in a low level of phosphorylation of Ser2 in the carboxyl terminal domain of RNAP II, suggesting that lack of Cdk9 T-loop autophosphorylation may limit RNAP II elongation in quiescent CD4+ T lymphocytes.