Human bronchial epithelial cells exposed in vitro to cigarette smoke at the air-liquid interface resemble bronchial epithelium from human smokers

Organotypic culture of human primary bronchial epithelial cells is a useful in vitro system to study normal biological processes and lung disease mechanisms, to develop new therapies, and to assess the biological perturbations induced by environmental pollutants. Herein, we investigate whether the perturbations induced by cigarette smoke (CS) and observed in the epithelium of smokers' airways are reproducible in this in vitro system (AIR-100 tissue), which has been shown to recapitulate most of the characteristics of the human bronchial epithelium. Human AIR-100 tissues were exposed to mainstream CS for 7, 14, 21, or 28 min at the air-liquid interface, and we investigated various biological endpoints [e.g., gene expression and microRNA profiles, matrix metalloproteinase 1 (MMP-1) release] at multiple postexposure time points (0.5, 2, 4, 24, 48 h). By performing a Gene Set Enrichment Analysis, we observed a significant enrichment of human smokers' bronchial epithelium gene signatures derived from different public transcriptomics datasets in CS-exposed AIR-100 tissue. Comparison of in vitro microRNA profiles with microRNA data from healthy smokers highlighted various highly translatable microRNAs associated with inflammation or with cell cycle processes that are known to be perturbed by CS in lung tissue. We also found a dose-dependent increase of MMP-1 release by AIR-100 tissue 48 h after CS exposure in agreement with the known effect of CS on this collagenase expression in smokers' tissues. In conclusion, a similar biological perturbation than the one observed in vivo in smokers' airway epithelium could be induced after a single CS exposure of a human organotypic bronchial epithelium-like tissue culture.

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems

With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation.

Database URL:http://causalbionet.com

Statistical analysis of predominantly transient protein-protein interfaces

A non-redundant set of 170 protein-protein interfaces of known structure was statistically analyzed for residue and secondary-structure compositions, pairing preferences and side-chain-backbone interaction frequencies. By focussing mainly on transient protein-protein interfaces, the results underline previous findings for protein-protein interfaces but also show some new interesting aspects of transient interfaces. The residue compositions at interfaces found in this study correlate well with the results of other studies. On average, contacts between pairs of hydrophobic and polar residues were unfavorable, and the charged residues tended to pair subject to charge complementarity. Secondary structure composition analysis shows that neither helices nor beta-sheets are dominantly populated at interfaces. Analyzing the pairing preferences of the secondary structure elements revealed a higher affinity within the same elements and alludes to tight packings. In addition, the results for the side-chain and backbone interaction frequencies, which were measured under more stringent conditions, showed a high occurrence of side-chain-backbone interactions. Taking a closer look at the helix and beta-sheet binding frequencies for a given side-chain and backbone interaction underlined the relevance of tight packings. The polarity of interfaces increased with decreasing interface size. These types of information may be useful for scoring complexes in protein-protein docking studies or for prediction of protein-protein interfaces from the sequences alone.

Causes and effects of road traffic accidents in Saudi Arabia

In Saudi Arabia the motor vehicle is the main means of transportation. Between 1971 and 1997; 564,762 people died or were injured in road traffic accidents, a figure equivalent to 3.5% of the total population in Saudi Arabia. During this period 66,914 people have died on the roads in Saudi Arabia due to road accidents, amounting to one person killed and four injured every hour. Over 65% of accidents occur because of vehicles travelling at excess speed and/or drivers disobeying traffic signals. Of deaths in Ministry of Health hospitals, 81% are due to road traffic accidents and 20% of their beds are occupied by traffic accidents victims. Also, 79.2% of patients admitted to Riyadh Armed Forces Hospital with spinal injuries has sustained their injuries as a result of a motor vehicle accident. We recommend compulsory use of safety seat belts in vehicles and the setting up of a new database to collect, store and analyse information relating to the road traffic accidents.

Incidence of fatal pulmonary embolism after 1,390 knee arthroplasties without routine prophylactic anticoagulation, except in high-risk cases

A consecutive series of 1,390 primary total knee arthroplasty (TKA) procedures (1,201 patients, 1,600 arthroplasties) performed between January 1980 and July 1994 were reviewed to establish the incidence of death from pulmonary embolism (PE). Nine hundred twenty-three bi- or tricompartment TKAs and 467 unicompartment TKAs were performed as one-stage procedures. Chemical thromboprophylaxis was used only in high-risk cases in which there was a history of previous thromboembolism or obesity. There were no deaths from PE after unicompartment arthroplasty procedures. Autopsy confirmed PE as the cause of death in 2 patients following bi- and tricompartment TKAs (0.22%; 95% confidence interval [CI], 0.03-0.8%). The incidence was higher for one-stage bilateral TKA as 1 of the autopsy-confirmed deaths occurred in this group 0.7% (95% CI, 0.02-3.78%). Two other deaths were certified without postmortem examination (pneumonia and myocardial infarction in each case). As PE could not be ruled out as the cause of death in the latter 2 cases, these were considered as possible PE deaths to provide the maximum possible death rate that could result. Thus, the maximum possible incidence of fatal PE after TKA without routine use of chemical anticoagulation was 0.4% (95% CI 0.1-1.1%). It is concluded that the risk of fatal PE after unilateral TKA and unicompartment knee arthroplasty is low. The risk of clinical, nonfatal thromboembolic events, which might themselves warrant prophylaxis, was not quantified in this article.

St. Georg sledge for medial compartment knee replacement. 461 arthroplasties followed for 4 (1-17) years

We evaluated the long-term outcome of 461 medial compartment knee arthroplasties operated at one orthopedic center from 1974 to 1993 through survivorship analysis. Prospective assessment was based on clinical examinations using a modified Bristol knee-scoring system and complete radiographical knee survey. 92% had good or excellent results on objective scoring, and range of motion averaged 112 degrees. 3 criteria were applied to indicate failure: 1) revision or recommended revision, 2) severe-to-moderate pain or revision, 3) lost to follow-up. 20 arthroplasties were revised or recommended to be revised at mean 5.5 years. The incidence of failure due to progression of arthrosis in the unreplaced compartment was low (< 2%). Loosening or wear occurred in 6 cases (1.5%), 2 of which developed fracture of implant. With revisions only as end-point to failure, the survival was 87% at 10 years (95% CI 81%-93%, effective number at risk = 133). In addition to revisions, 19 knees were considered to have failed, as moderate-to-severe pain was noted at follow-up and the survival was reduced to 74% at 10 years with pain or revision as endpoint (95% CI 65%-82%, effective number at risk = 105). We conclude that unicompartmental knee arthroplasty gives long-term pain relief in elderly patients with medial compartment arthrosis.

Phase II clinical trial of a vas deferens injectable contraceptive for the male

Following up on an earlier clinical trial demonstrating the safety of an intra-vas deferens injection of a contraceptive drug named Risug, comprised of styrene maleic anhydride (SMA) in a solvent vehicle of dimethylsulphoxide (DMSO), a study to assess the contraceptive effectiveness of a specific dose (60 mg) of SMA bilaterally was planned and implemented. Male subjects and their wives with normal reproductive profiles were the volunteer subjects. The wives were not using any contraceptives. The results reconfirm the safety and show that for a period of at least 1 year, the treatment leads to azoospermia in the male and gives pregnancy protection.

A 28-day rat inhalation study with an integrated molecular toxicology endpoint demonstrates reduced exposure effects for a prototypic modified risk tobacco product compared with conventional cigarettes

Towards a systems toxicology-based risk assessment, we investigated molecular perturbations accompanying histopathological changes in a 28-day rat inhalation study combining transcriptomics with classical histopathology. We demonstrated reduced biological activity of a prototypic modified risk tobacco product (pMRTP) compared with the reference research cigarette 3R4F. Rats were exposed to filtered air or to three concentrations of mainstream smoke (MS) from 3R4F, or to a high concentration of MS from a pMRTP. Histopathology revealed concentration-dependent changes in response to 3R4F that were irritative stress-related in nasal and bronchial epithelium, and inflammation-related in the lung parenchyma. For pMRTP, significant changes were seen in the nasal epithelium only. Transcriptomics data were obtained from nasal and bronchial epithelium and lung parenchyma. Concentration-dependent gene expression changes were observed following 3R4F exposure, with much smaller changes for pMRTP. A computational-modeling approach based on causal models of tissue-specific biological networks identified cell stress, inflammation, proliferation, and senescence as the most perturbed molecular mechanisms. These perturbations correlated with histopathological observations. Only weak perturbations were observed for pMRTP. In conclusion, a correlative evaluation of classical histopathology together with gene expression-based computational network models may facilitate a systems toxicology-based risk assessment, as shown for a pMRTP.

Phase I clinical trial of an injectable contraceptive for the male

Earlier studies on the rat and the monkey had demonstrated that an injection of styrene maleic anhydride (SMA) in a solvent vehicle of dimethyl sulphoxide (DMSO) into the lumen of the vas deferens is toxicologically safe and has contraceptive action. Phase I clinical trial was therefore undertaken on 38 male volunteers giving varying doses of SMA, ranging between 5 mg and 140 mg, into each vas deferens. A dose of 70 mg is the predicted therapeutic dose based on animal data. That the compound is within the vas deferens lumen during the period of the safety assessment is inferred from the effect on the spermatozoa count in ejaculates which reach azoospermic levels in the higher dose ranges. The treatment is well tolerated with only minimal side effects in a few cases and no long-term adverse effects.

Assessment and management of children aged 1-59 months presenting with wheeze, fast breathing, and/or lower chest indrawing; results of a multicentre descriptive study in Pakistan

BACKGROUND AND AIMS

Using current WHO guidelines, children with wheezing are being over prescribed antibiotics and bronchodilators are underutilised. To improve the WHO case management guidelines, more data is needed about the clinical outcome in children with wheezing/pneumonia overlap.

METHODOLOGY

In a multicentre prospective study, children aged 1-59 months with auscultatory/audible wheeze and fast breathing and/or lower chest indrawing were screened. Response to up to three cycles of inhaled salbutamol was recorded. The responders were enrolled and sent home on inhaled bronchodilators, and followed up on days 3 and 5.

RESULTS

A total of 1622 children with wheeze were screened from May 2001 to April 2002, of which 1004 (61.8%) had WHO defined non-severe and 618 (38.2%) severe pneumonia. Wheeze was audible in only 595 (36.7%) of children. Of 1004 non-severe pneumonia children, 621 (61.8%) responded to up to three cycles of bronchodilator. Of 618 severe pneumonia children, only 166 (26.8%) responded. Among responders, 93 (14.9%) in the non-severe and 63 (37.9%) children in the severe pneumonia group showed subsequent deterioration on follow ups. No family history of wheeze, temperature >100 degrees F, and lower chest indrawing were identified as predictors of subsequent deterioration.

CONCLUSIONS

Two third of children with wheeze are not identified by current WHO ARI (acute respiratory infections) guidelines. Antibiotics are over prescribed and bronchodilators under utilised in children with wheeze. Children with wheeze constitute a special ARI group requiring a separate management algorithm. In countries where wheeze is common it would be worthwhile to train health workers in use of the stethoscope to identify wheeze.

Contraception in male monkeys by intra-vas deferens injection of a pH lowering polymer

A new male method of contraception by injecting a polymer, styrene-maleic anhydride (SMA), into the lumen of the vas deferens has been studied on rhesus monkeys. The polymer has the dual feature that it can occlude the vas deferens lumen and also it can inhibit the fertilising ability of spermatozoa by virtue of the pH lowering effect. Matings with females were carried out when the lumen was completely occluded giving azoospermia as well as with partial block and spermatozoa present in the semen. All matings were infertile. Data up to one year is presented. All indications are that the contraceptive effect will last for a considerably long period.

Construction of biological networks from unstructured information based on a semi-automated curation workflow

Capture and representation of scientific knowledge in a structured format are essential to improve the understanding of biological mechanisms involved in complex diseases. Biological knowledge and knowledge about standardized terminologies are difficult to capture from literature in a usable form. A semi-automated knowledge extraction workflow is presented that was developed to allow users to extract causal and correlative relationships from scientific literature and to transcribe them into the computable and human readable Biological Expression Language (BEL). The workflow combines state-of-the-art linguistic tools for recognition of various entities and extraction of knowledge from literature sources. Unlike most other approaches, the workflow outputs the results to a curation interface for manual curation and converts them into BEL documents that can be compiled to form biological networks. We developed a new semi-automated knowledge extraction workflow that was designed to capture and organize scientific knowledge and reduce the required curation skills and effort for this task. The workflow was used to build a network that represents the cellular and molecular mechanisms implicated in atherosclerotic plaque destabilization in an apolipoprotein-E-deficient (ApoE(-/-)) mouse model. The network was generated using knowledge extracted from the primary literature. The resultant atherosclerotic plaque destabilization network contains 304 nodes and 743 edges supported by 33 PubMed referenced articles. A comparison between the semi-automated and conventional curation processes showed similar results, but significantly reduced curation effort for the semi-automated process. Creating structured knowledge from unstructured text is an important step for the mechanistic interpretation and reusability of knowledge. Our new semi-automated knowledge extraction workflow reduced the curation skills and effort required to capture and organize scientific knowledge. The atherosclerotic plaque destabilization network that was generated is a causal network model for vascular disease demonstrating the usefulness of the workflow for knowledge extraction and construction of mechanistically meaningful biological networks.

Polyethylene glycol induces apoptosis in HT-29 cells: potential mechanism for chemoprevention of colon cancer

Recent experimental evidence suggests that polyethylene glycol (PEG) is a highly effective chemopreventive agent against colon cancer; however, the mechanism(s) remain largely unexplored. To further elucidate this issue, we evaluated the effect of PEG on two human colon cancer cell lines. PEG treatment resulted in a dose- and time-dependent reduction in cell number without alteration in markers of cell proliferation. However, there was a dramatic and specific, concentration-dependent induction of apoptosis, with 50 mM PEG rendering approximately half the cells apoptotic. This corresponded with a 17-fold induction in the expression of the pro-apoptotic protein, prostate apoptosis response-4. Our data suggest that induction of apoptosis may be responsible, at least in part, for the ability of PEG to prevent experimental colon cancer.

Management of spontaneous pneumothorax-a Welsh survey

The authors sought to determine to what degree current practice by hospital physicians and accident and emergency (A&E) departments in Wales conformed to the British Thoracic Society's guidelines for the management of spontaneous pneumothorax. Questionnaires were posted to all consultants involved in emergency medical admissions in Wales (149 consultant physicians and 23 A&E consultants) of whom 101 (59%) replied. Only 45% used the classification, "small, moderate, or complete" to describe the size of pneumothorax. Just 44% would do as recommended by the British Thoracic Society and discharge an asymptomatic patient with a primary pneumothorax and 34% would discharge a patient with a primary pneumothorax after successful aspiration. Only 20% were prepared to try aspiration initially for a secondary pneumothorax with a complete lung collapse. Thirty four per cent would follow the recommendation to remove a chest drain without prior clamping of the tube 24 hours after bubbling had stopped. In the event of a persistent air leak 69% would refer patients or seek a specialist opinion. Physicians with an interest in respiratory medicine tolerated persistent air leaks for significantly longer than did non-respiratory physicians (median of 7 v 5 days, p=0.001). The survey indicates that fewer than expected consultant physicians and A&E consultants in Wales manage spontaneous pneumothoraces in the way recommended by the guidelines. Physicians with an interest in respiratory medicine tended to comply with these guidelines more than general physicians with interests other than respiratory medicine or A&E consultants but the trend was not significant at the 5% level. It is felt that the guidelines should be disseminated more widely, ensuring that emergency admissions units and A&E departments have copies on display or easily accessible, and that they could be expanded to cover other aspects such as timing for surgery.

Teratoid Wilms' tumour: a report of two cases

We report two cases of Wilms' tumour in which the degree of heterologous differentiation was sufficient to warrant the diagnosis of teratoid Wilms' tumour. The first description of neural elements in this Wilms' variant and the first cytogenetic analysis of teratoid Wilms' tumour are presented.

Comprehensive systems biology analysis of a 7-month cigarette smoke inhalation study in C57BL/6 mice

Smoking of combustible cigarettes has a major impact on human health. Using a systems toxicology approach in a model of chronic obstructive pulmonary disease (C57BL/6 mice), we assessed the health consequences in mice of an aerosol derived from a prototype modified risk tobacco product (pMRTP) as compared to conventional cigarettes. We investigated physiological and histological endpoints in parallel with transcriptomics, lipidomics, and proteomics profiles in mice exposed to a reference cigarette (3R4F) smoke or a pMRTP aerosol for up to 7 months. We also included a cessation group and a switching-to-pMRTP group (after 2 months of 3R4F exposure) in addition to the control (fresh air-exposed) group, to understand the potential risk reduction of switching to pMRTP compared with continuous 3R4F exposure and cessation. The present manuscript describes the study design, setup, and implementation, as well as the generation, processing, and quality control analysis of the toxicology and ‘omics’ datasets that are accessible in public repositories for further analyses.

On Crowd-verification of Biological Networks

Biological networks with a structured syntax are a powerful way of representing biological information generated from high density data; however, they can become unwieldy to manage as their size and complexity increase. This article presents a crowd-verification approach for the visualization and expansion of biological networks.

Web-based graphical interfaces allow visualization of causal and correlative biological relationships represented using Biological Expression Language (BEL). Crowdsourcing principles enable participants to communally annotate these relationships based on literature evidences. Gamification principles are incorporated to further engage domain experts throughout biology to gather robust peer-reviewed information from which relationships can be identified and verified.

The resulting network models will represent the current status of biological knowledge within the defined boundaries, here processes related to human lung disease. These models are amenable to computational analysis. For some period following conclusion of the challenge, the published models will remain available for continuous use and expansion by the scientific community.

Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL)

Success in extracting biological relationships is mainly dependent on the complexity of the task as well as the availability of high-quality training data. Here, we describe the new corpora in the systems biology modeling language BEL for training and testing biological relationship extraction systems that we prepared for the BioCreative V BEL track. BEL was designed to capture relationships not only between proteins or chemicals, but also complex events such as biological processes or disease states. A BEL nanopub is the smallest unit of information and represents a biological relationship with its provenance. In BEL relationships (called BEL statements), the entities are normalized to defined namespaces mainly derived from public repositories, such as sequence databases, MeSH or publicly available ontologies. In the BEL nanopubs, the BEL statements are associated with citation information and supportive evidence such as a text excerpt. To enable the training of extraction tools, we prepared BEL resources and made them available to the community. We selected a subset of these resources focusing on a reduced set of namespaces, namely, human and mouse genes, ChEBI chemicals, MeSH diseases and GO biological processes, as well as relationship types ‘increases’ and ‘decreases’. The published training corpus contains 11 000 BEL statements from over 6000 supportive text excerpts. For method evaluation, we selected and re-annotated two smaller subcorpora containing 100 text excerpts. For this re-annotation, the inter-annotator agreement was measured by the BEL track evaluation environment and resulted in a maximal F-score of 91.18% for full statement agreement. In addition, for a set of 100 BEL statements, we do not only provide the gold standard expert annotations, but also text excerpts pre-selected by two automated systems. Those text excerpts were evaluated and manually annotated as true or false supportive in the course of the BioCreative V BEL track task.

Database URL:http://wiki.openbel.org/display/BIOC/Datasets

Vagus nerve stimulation: indications and limitations

Vagus nerve stimulation (VNS) is an established treatment for selected patients with medically refractory seizures. Recent studies suggest that VNS could be potentially useful in the treatment of resistant depressive disorder. Although a surgical procedure is required in order to implant the VNS device, the possibility of a long-term benefit largely free of severe side effects could give VNS a privileged place in the management of resistant depression. In addition, VNS appears to affect pain perception in depressed adults; a possible role of VNS in the treatment of severe refractory headache, intractable chronic migraine and cluster headache has also been suggested. VNS is currently investigated in clinical studies, as a potential treatment for essential tremor, cognitive deficits in Alzheimer's disease, anxiety disorders, and bulimia. Finally, other studies explore the potential use of VNS in the treatment of resistant obesity, addictions, sleep disorders, narcolepsy, coma and memory and learning deficits.