The use of foundational ontologies in biomedical research

BACKGROUND

The FAIR principles recommend the use of controlled vocabularies, such as ontologies, to define data and metadata concepts. Ontologies are currently modelled following different approaches, sometimes describing conflicting definitions of the same concepts, which can affect interoperability. To cope with that, prior literature suggests organising ontologies in levels, where domain specific (low-level) ontologies are grounded in domain independent high-level ontologies (i.e., foundational ontologies). In this level-based organisation, foundational ontologies work as translators of intended meaning, thus improving interoperability. Despite their considerable acceptance in biomedical research, there are very few studies testing foundational ontologies. This paper describes a systematic literature mapping that was conducted to understand how foundational ontologies are used in biomedical research and to find empirical evidence supporting their claimed (dis)advantages.

RESULTS

From a set of 79 selected papers, we identified that foundational ontologies are used for several purposes: ontology construction, repair, mapping, and ontology-based data analysis. Foundational ontologies are claimed to improve interoperability, enhance reasoning, speed up ontology development and facilitate maintainability. The complexity of using foundational ontologies is the most commonly cited downside. Despite being used for several purposes, there were hardly any experiments (1 paper) testing the claims for or against the use of foundational ontologies. In the subset of 49 papers that describe the development of an ontology, it was observed a low adherence to ontology construction (16 papers) and ontology evaluation formal methods (4 papers).

CONCLUSION

Our findings have two main implications. First, the lack of empirical evidence about the use of foundational ontologies indicates a need for evaluating the use of such artefacts in biomedical research. Second, the low adherence to formal methods illustrates how the field could benefit from a more systematic approach when dealing with the development and evaluation of ontologies. The understanding of how foundational ontologies are used in the biomedical field can drive future research towards the improvement of ontologies and, consequently, data FAIRness. The adoption of formal methods can impact the quality and sustainability of ontologies, and reusing these methods from other fields is encouraged.

Towards FAIRification of sensitive and fragmented rare disease patient data: challenges and solutions in European reference network registries

INTRODUCTION

Rare disease patient data are typically sensitive, present in multiple registries controlled by different custodians, and non-interoperable. Making these data Findable, Accessible, Interoperable, and Reusable (FAIR) for humans and machines at source enables federated discovery and analysis across data custodians. This facilitates accurate diagnosis, optimal clinical management, and personalised treatments. In Europe, twenty-four European Reference Networks (ERNs) work on rare disease registries in different clinical domains. The process and the implementation choices for making data FAIR ('FAIRification') differ among ERN registries. For example, registries use different software systems and are subject to different legal regulations. To support the ERNs in making informed decisions and to harmonise FAIRification, the FAIRification steward team was established to work as liaisons between ERNs and researchers from the European Joint Programme on Rare Diseases.

RESULTS

The FAIRification steward team inventoried the FAIRification challenges of the ERN registries and proposed solutions collectively with involved stakeholders to address them. Ninety-eight FAIRification challenges from 24 ERNs' registries were collected and categorised into "training" (31), "community" (9), "modelling" (12), "implementation" (26), and "legal" (20). After curating and aggregating highly similar challenges, 41 unique FAIRification challenges remained. The two categories with the most challenges were "training" (15) and "implementation" (9), followed by "community" (7), and then "modelling" (5) and "legal" (5). To address all challenges, eleven types of solutions were proposed. Among them, the provision of guidelines and the organisation of training activities resolved the "training" challenges, which ranged from less-technical "coffee-rounds" to technical workshops, from informal FAIR Games to formal hackathons. Obtaining implementation support from technical experts was the solution type for tackling the "implementation" challenges.

CONCLUSION

This work shows that a dedicated team of FAIR data stewards is an asset for harmonising the various processes of making data FAIR in a large organisation with multiple stakeholders. Additionally, multi-levelled training activities are required to accommodate the diverse needs of the ERNs. Finally, the lessons learned from the experience of the FAIRification steward team described in this paper may help to increase FAIR awareness and provide insights into FAIRification challenges and solutions of rare disease registries.

Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic

BACKGROUND

The COVID-19 pandemic has challenged healthcare systems and research worldwide. Data is collected all over the world and needs to be integrated and made available to other researchers quickly. However, the various heterogeneous information systems that are used in hospitals can result in fragmentation of health data over multiple data 'silos' that are not interoperable for analysis. Consequently, clinical observations in hospitalised patients are not prepared to be reused efficiently and timely. There is a need to adapt the research data management in hospitals to make COVID-19 observational patient data machine actionable, i.e. more Findable, Accessible, Interoperable and Reusable (FAIR) for humans and machines. We therefore applied the FAIR principles in the hospital to make patient data more FAIR.

RESULTS

In this paper, we present our FAIR approach to transform COVID-19 observational patient data collected in the hospital into machine actionable digital objects to answer medical doctors' research questions. With this objective, we conducted a coordinated FAIRification among stakeholders based on ontological models for data and metadata, and a FAIR based architecture that complements the existing data management. We applied FAIR Data Points for metadata exposure, turning investigational parameters into a FAIR dataset. We demonstrated that this dataset is machine actionable by means of three different computational activities: federated query of patient data along open existing knowledge sources across the world through the Semantic Web, implementing Web APIs for data query interoperability, and building applications on top of these FAIR patient data for FAIR data analytics in the hospital.

CONCLUSIONS

Our work demonstrates that a FAIR research data management plan based on ontological models for data and metadata, open Science, Semantic Web technologies, and FAIR Data Points is providing data infrastructure in the hospital for machine actionable FAIR Digital Objects. This FAIR data is prepared to be reused for federated analysis, linkable to other FAIR data such as Linked Open Data, and reusable to develop software applications on top of them for hypothesis generation and knowledge discovery.

Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data

BACKGROUND

The European Platform on Rare Disease Registration (EU RD Platform) aims to address the fragmentation of European rare disease (RD) patient data, scattered among hundreds of independent and non-coordinating registries, by establishing standards for integration and interoperability. The first practical output of this effort was a set of 16 Common Data Elements (CDEs) that should be implemented by all RD registries. Interoperability, however, requires decisions beyond data elements - including data models, formats, and semantics. Within the European Joint Programme on Rare Diseases (EJP RD), we aim to further the goals of the EU RD Platform by generating reusable RD semantic model templates that follow the FAIR Data Principles.

RESULTS

Through a team-based iterative approach, we created semantically grounded models to represent each of the CDEs, using the SemanticScience Integrated Ontology as the core framework for representing the entities and their relationships. Within that framework, we mapped the concepts represented in the CDEs, and their possible values, into domain ontologies such as the Orphanet Rare Disease Ontology, Human Phenotype Ontology and National Cancer Institute Thesaurus. Finally, we created an exemplar, reusable ETL pipeline that we will be deploying over these non-coordinating data repositories to assist them in creating model-compliant FAIR data without requiring site-specific coding nor expertise in Linked Data or FAIR.

CONCLUSIONS

Within the EJP RD project, we determined that creating reusable, expert-designed templates reduced or eliminated the requirement for our participating biomedical domain experts and rare disease data hosts to understand OWL semantics. This enabled them to publish highly expressive FAIR data using tools and approaches that were already familiar to them.

The de novo FAIRification process of a registry for vascular anomalies

BACKGROUND

Patient data registries that are FAIR-Findable, Accessible, Interoperable, and Reusable for humans and computers-facilitate research across multiple resources. This is particularly relevant to rare diseases, where data often are scarce and scattered. Specific research questions can be asked across FAIR rare disease registries and other FAIR resources without physically combining the data. Further, FAIR implies well-defined, transparent access conditions, which supports making sensitive data as open as possible and as closed as necessary.

RESULTS

We successfully developed and implemented a process of making a rare disease registry for vascular anomalies FAIR from its conception-de novo. Here, we describe the five phases of this process in detail: (i) pre-FAIRification, (ii) facilitating FAIRification, (iii) data collection, (iv) generating FAIR data in real-time, and (v) using FAIR data. This includes the creation of an electronic case report form and a semantic data model of the elements to be collected (in this case: the "Set of Common Data Elements for Rare Disease Registration" released by the European Commission), and the technical implementation of automatic, real-time data FAIRification in an Electronic Data Capture system. Further, we describe how we contribute to the four facets of FAIR, and how our FAIRification process can be reused by other registries.

CONCLUSIONS

In conclusion, a detailed de novo FAIRification process of a registry for vascular anomalies is described. To a large extent, the process may be reused by other rare disease registries, and we envision this work to be a substantial contribution to an ecosystem of FAIR rare disease resources.

De-novo FAIRification via an Electronic Data Capture system by automated transformation of filled electronic Case Report Forms into machine-readable data

INTRODUCTION

Existing methods to make data Findable, Accessible, Interoperable, and Reusable (FAIR) are usually carried out in a post hoc manner: after the research project is conducted and data are collected. De-novo FAIRification, on the other hand, incorporates the FAIRification steps in the process of a research project. In medical research, data is often collected and stored via electronic Case Report Forms (eCRFs) in Electronic Data Capture (EDC) systems. By implementing a de novo FAIRification process in such a system, the reusability and, thus, scalability of FAIRification across research projects can be greatly improved. In this study, we developed and implemented a novel method for de novo FAIRification via an EDC system. We evaluated our method by applying it to the Registry of Vascular Anomalies (VASCA).

METHODS

Our EDC and research project independent method ensures that eCRF data entered into an EDC system can be transformed into machine-readable, FAIR data using a semantic data model (a canonical representation of the data, based on ontology concepts and semantic web standards) and mappings from the model to questions on the eCRF. The FAIRified data are stored in a triple store and can, together with associated metadata, be accessed and queried through a FAIR Data Point. The method was implemented in Castor EDC, an EDC system, through a data transformation application. The FAIRness of the output of the method, the FAIRified data and metadata, was evaluated using the FAIR Evaluation Services.

RESULTS

We successfully applied our FAIRification method to the VASCA registry. Data entered on eCRFs is automatically transformed into machine-readable data and can be accessed and queried using SPARQL queries in the FAIR Data Point. Twenty-one FAIR Evaluator tests pass and one test regarding the metadata persistence policy fails, since this policy is not in place yet.

CONCLUSION

In this study, we developed a novel method for de novo FAIRification via an EDC system. Its application in the VASCA registry and the automated FAIR evaluation show that the method can be used to make clinical research data FAIR when they are entered in an eCRF without any intervention from data management and data entry personnel. Due to the generic approach and developed tooling, we believe that our method can be used in other registries and clinical trials as well.

A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration

Rett syndrome (RTT) is a rare neurological disorder mostly caused by a genetic variation in MECP2. Making new MECP2 variants and the related phenotypes available provides data for better understanding of disease mechanisms and faster identification of variants for diagnosis. This is, however, currently hampered by the lack of interoperability between genotype-phenotype databases. Here, we demonstrate on the example of MECP2 in RTT that by making the genotype-phenotype data more Findable, Accessible, Interoperable, and Reusable (FAIR), we can facilitate prioritization and analysis of variants. In total, 10,968 MECP2 variants were successfully integrated. Among these variants 863 unique confirmed RTT causing and 209 unique confirmed benign variants were found. This dataset was used for comparison of pathogenicity predicting tools, protein consequences, and identification of ambiguous variants. Prediction tools generally recognised the RTT causing and benign variants, however, there was a broad range of overlap Nineteen variants were identified that were annotated as both disease-causing and benign, suggesting that there are additional factors in these cases contributing to disease development.

Measurement(s)	Rett syndrome • phenotype • MECP2 Gene
Technology Type(s)	digital curation • network analysis
Sample Characteristic - Organism	Homo sapiens

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13359476

Applying the FAIR Data Principles to the Registry of Vascular Anomalies (VASCA)

BACKGROUND

Connecting currently existing, heterogeneous rare disease (RD) registries would greatly facilitate epidemiological and clinical research. To increase their interoperability, the European Union developed a set of Common Data Elements (CDEs) for RD registries.

OBJECTIVES

To implement the CDEs and the FAIR data principles in the Registry of Vascular Anomalies (VASCA).

METHODS

We created a semantic model for the CDE and transformed this into a Resource Description Framework (RDF) template. The electronic case report forms (eCRF) were mapped to the RDF template and published in a FAIR Data Point (FDP).

RESULTS

The FAIR VASCA registry was successfully implemented using Castor EDC (Electronic Data Capture) software.

CONCLUSION

FAIR technology allows researchers to query and combine data from different registries in real-time.

A framework for exhaustive modelling of genetic interaction patterns using Petri nets

MOTIVATION

Genetic interaction (GI) patterns are characterized by the phenotypes of interacting single and double mutated gene pairs. Uncovering the regulatory mechanisms of GIs would provide a better understanding of their role in biological processes, diseases and drug response. Computational analyses can provide insights into the underpinning mechanisms of GIs.

RESULTS

In this study, we present a framework for exhaustive modelling of GI patterns using Petri nets (PN). Four-node models were defined and generated on three levels with restrictions, to enable an exhaustive approach. Simulations suggest ∼5 million models of GIs. Generalizing these we propose putative mechanisms for the GI patterns, inversion and suppression. We demonstrate that exhaustive PN modelling enables reasoning about mechanisms of GIs when only the phenotypes of gene pairs are known. The framework can be applied to other GI or genetic regulatory datasets.

AVAILABILITY AND IMPLEMENTATION

The framework is available at http://www.ibi.vu.nl/programs/ExhMod.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

FAIR Convergence Matrix: Optimizing the Reuse of Existing FAIR-Related Resources

The FAIR principles articulate the behaviors expected from digital artifacts that are Findable, Accessible, Interoperable and Reusable by machines and by people. Although by now widely accepted, the FAIR Principles by design do not explicitly consider actual implementation choices enabling FAIR behaviors. As different communities have their own, often well-established implementation preferences and priorities for data reuse, coordinating a broadly accepted, widely used FAIR implementation approach remains a global challenge. In an effort to accelerate broad community convergence on FAIR implementation options, the GO FAIR community has launched the development of the FAIR Convergence Matrix. The Matrix is a platform that compiles for any community of practice, an inventory of their self-declared FAIR implementation choices and challenges. The Convergence Matrix is itself a FAIR resource, openly available, and encourages voluntary participation by any self-identified community of practice (not only the GO FAIR Implementation Networks). Based on patterns of use and reuse of existing resources, the Convergence Matrix supports the transparent derivation of strategies that optimally coordinate convergence on standards and technologies in the emerging Internet of FAIR Data and Services.

A Generic Workflow for the Data FAIRification Process

The FAIR guiding principles aim to enhance the Findability, Accessibility, Interoperability and Reusability of digital resources such as data, for both humans and machines. The process of making data FAIR (“FAIRification”) can be described in multiple steps. In this paper, we describe a generic step-by-step FAIRification workflow to be performed in a multidisciplinary team guided by FAIR data stewards. The FAIRification workflow should be applicable to any type of data and has been developed and used for “Bring Your Own Data” (BYOD) workshops, as well as for the FAIRification of e.g., rare diseases resources. The steps are: 1) identify the FAIRification objective, 2) analyze data, 3) analyze metadata, 4) define semantic model for data (4a) and metadata (4b), 5) make data (5a) and metadata (5b) linkable, 6) host FAIR data, and 7) assess FAIR data. For each step we describe how the data are processed, what expertise is required, which procedures and tools can be used, and which FAIR principles they relate to.

FAIR Principles: Interpretations and Implementation Considerations

The FAIR principles have been widely cited, endorsed and adopted by a broad range of stakeholders since their publication in 2016. By intention, the 15 FAIR guiding principles do not dictate specific technological implementations, but provide guidance for improving Findability, Accessibility, Interoperability and Reusability of digital resources. This has likely contributed to the broad adoption of the FAIR principles, because individual stakeholder communities can implement their own FAIR solutions. However, it has also resulted in inconsistent interpretations that carry the risk of leading to incompatible implementations. Thus, while the FAIR principles are formulated on a high level and may be interpreted and implemented in different ways, for true interoperability we need to support convergence in implementation choices that are widely accessible and (re)-usable. We introduce the concept of FAIR implementation considerations to assist accelerated global participation and convergence towards accessible, robust, widespread and consistent FAIR implementations. Any self-identified stakeholder community may either choose to reuse solutions from existing implementations, or when they spot a gap, accept the challenge to create the needed solution, which, ideally, can be used again by other communities in the future. Here, we provide interpretations and implementation considerations (choices and challenges) for each FAIR principle.

The ability of transcription factors to differentially regulate gene expression is a crucial component of the mechanism underlying inversion, a frequently observed genetic interaction pattern

Genetic interactions, a phenomenon whereby combinations of mutations lead to unexpected effects, reflect how cellular processes are wired and play an important role in complex genetic diseases. Understanding the molecular basis of genetic interactions is crucial for deciphering pathway organization as well as understanding the relationship between genetic variation and disease. Several hypothetical molecular mechanisms have been linked to different genetic interaction types. However, differences in genetic interaction patterns and their underlying mechanisms have not yet been compared systematically between different functional gene classes. Here, differences in the occurrence and types of genetic interactions are compared for two classes, gene-specific transcription factors (GSTFs) and signaling genes (kinases and phosphatases). Genome-wide gene expression data for 63 single and double deletion mutants in baker's yeast reveals that the two most common genetic interaction patterns are buffering and inversion. Buffering is typically associated with redundancy and is well understood. In inversion, genes show opposite behavior in the double mutant compared to the corresponding single mutants. The underlying mechanism is poorly understood. Although both classes show buffering and inversion patterns, the prevalence of inversion is much stronger in GSTFs. To decipher potential mechanisms, a Petri Net modeling approach was employed, where genes are represented as nodes and relationships between genes as edges. This allowed over 9 million possible three and four node models to be exhaustively enumerated. The models show that a quantitative difference in interaction strength is a strict requirement for obtaining inversion. In addition, this difference is frequently accompanied with a second gene that shows buffering. Taken together, these results provide a mechanistic explanation for inversion. Furthermore, the ability of transcription factors to differentially regulate expression of their targets provides a likely explanation why inversion is more prevalent for GSTFs compared to kinases and phosphatases.

Recommendations for Improving the Quality of Rare Disease Registries

Rare diseases (RD) patient registries are powerful instruments that help develop clinical research, facilitate the planning of appropriate clinical trials, improve patient care, and support healthcare management. They constitute a key information system that supports the activities of European Reference Networks (ERNs) on rare diseases. A rapid proliferation of RD registries has occurred during the last years and there is a need to develop guidance for the minimum requirements, recommendations and standards necessary to maintain a high-quality registry. In response to these heterogeneities, in the framework of RD-Connect, a European platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research, we report on a list of recommendations, developed by a group of experts, including members of patient organizations, to be used as a framework for improving the quality of RD registries. This list includes aspects of governance, Findable, Accessible, Interoperable and Reusable (FAIR) data and information, infrastructure, documentation, training, and quality audit. The list is intended to be used by established as well as new RD registries. Further work includes the development of a toolkit to enable continuous assessment and improvement of their organizational and data quality.

MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases

Rett syndrome (RTT) is a monogenic rare disorder that causes severe neurological problems. In most cases, it results from a loss-of-function mutation in the gene encoding methyl-CPG-binding protein 2 (MECP2). Currently, about 900 unique MECP2 variations (benign and pathogenic) have been identified and it is suspected that the different mutations contribute to different levels of disease severity. For researchers and clinicians, it is important that genotype-phenotype information is available to identify disease-causing mutations for diagnosis, to aid in clinical management of the disorder, and to provide counseling for parents. In this study, 13 genotype-phenotype databases were surveyed for their general functionality and availability of RTT-specific MECP2 variation data. For each database, we investigated findability and interoperability alongside practical user functionality, and type and amount of genetic and phenotype data. The main conclusions are that, as well as being challenging to find these databases and specific MECP2 variants held within, interoperability is as yet poorly developed and requires effort to search across databases. Nevertheless, we found several thousand online database entries for MECP2 variations and their associated phenotypes, diagnosis, or predicted variant effects, which is a good starting point for researchers and clinicians who want to provide, annotate, and use the data.

BioASF: a framework for automatically generating executable pathway models specified in BioPAX

Motivation: Biological pathways play a key role in most cellular functions. To better understand these functions, diverse computational and cell biology researchers use biological pathway data for various analysis and modeling purposes. For specifying these biological pathways, a community of researchers has defined BioPAX and provided various tools for creating, validating and visualizing BioPAX models. However, a generic software framework for simulating BioPAX models is missing. Here, we attempt to fill this gap by introducing a generic simulation framework for BioPAX. The framework explicitly separates the execution model from the model structure as provided by BioPAX, with the advantage that the modelling process becomes more reproducible and intrinsically more modular; this ensures natural biological constraints are satisfied upon execution. The framework is based on the principles of discrete event systems and multi-agent systems, and is capable of automatically generating a hierarchical multi-agent system for a given BioPAX model.

Results: To demonstrate the applicability of the framework, we simulated two types of biological network models: a gene regulatory network modeling the haematopoietic stem cell regulators and a signal transduction network modeling the Wnt/β-catenin signaling pathway. We observed that the results of the simulations performed using our framework were entirely consistent with the simulation results reported by the researchers who developed the original models in a proprietary language.

Availability and Implementation: The framework, implemented in Java, is open source and its source code, documentation and tutorial are available at http://www.ibi.vu.nl/programs/BioASF.

Contact:j.heringa@vu.nl

Highlights from the ISCB Student Council Symposia in 2016

This editorial provides a brief overview of the 12th International Society for Computational Biology (ISCB) Student Council Symposium and the 4th European Student Council Symposium held in Florida, USA and The Hague, Netherlands, respectively. Further, the role of the ISCB Student Council in promoting education and networking in the field of computational biology is also highlighted.

Highlights from the tenth ISCB Student Council Symposium 2014

This report summarizes the scientific content and activities of the annual symposium organized by the Student Council of the International Society for Computational Biology (ISCB), held in conjunction with the Intelligent Systems for Molecular Biology (ISMB) conference in Boston, USA, on July 11th, 2014.

Bedside diagnosis of mitochondrial dysfunction in aneurysmal subarachnoid hemorrhage

OBJECTIVES

Aneurysmal subarachnoid hemorrhage (SAH) is frequently associated with delayed neurological deterioration (DND). Several studies have shown that DND is not always related to vasospasm and ischemia. Experimental and clinical studies have recently documented that it is possible to diagnose and separate cerebral ischemia and mitochondrial dysfunction bedside. The study explores whether cerebral biochemical variables in SAH patients most frequently exhibit a pattern indicating ischemia or mitochondrial dysfunction.

METHODS

In 55 patients with severe SAH, intracerebral microdialysis was performed during neurocritical care with bedside analysis and display of glucose, pyruvate, lactate, glutamate, and glycerol. The biochemical patterns observed were compared to those previously described in animal studies of induced mitochondrial dysfunction as well as the pattern obtained in patients with recirculated cerebral infarcts.

RESULTS

In 29 patients, the biochemical pattern indicated mitochondrial dysfunction while 10 patients showed a pattern of cerebral ischemia, six of which also exhibited periods of mitochondrial dysfunction. Mitochondrial dysfunction was observed during 5162 h. An ischemic pattern was obtained during 688 h. Four of the patients (40%) with biochemical signs of ischemia died at the neurosurgical department as compared with three patients (10%) in the group of mitochondrial dysfunction.

CONCLUSIONS

The study documents that mitochondrial dysfunction is a common cause of disturbed cerebral energy metabolism in patients with SAH. Mitochondrial dysfunction may increase tissue sensitivity to secondary adverse events such as vasospasm and decreased cerebral blood flow. The separation of ischemia and mitochondrial dysfunction bedside by utilizing microdialysis offers a possibility to evaluate new therapies.

Transport through graphene quantum dots

We review transport experiments on graphene quantum dots and narrow graphene constrictions. In a quantum dot, electrons are confined in all lateral dimensions, offering the possibility for detailed investigation and controlled manipulation of individual quantum systems. The recently isolated two-dimensional carbon allotrope graphene is an interesting host to study quantum phenomena, due to its novel electronic properties and the expected weak interaction of the electron spin with the material. Graphene quantum dots are fabricated by etching mono-layer flakes into small islands (diameter 60-350 nm) with narrow connections to contacts (width 20-75 nm), serving as tunneling barriers for transport spectroscopy. Electron confinement in graphene quantum dots is observed by measuring Coulomb blockade and transport through excited states, a manifestation of quantum confinement. Measurements in a magnetic field perpendicular to the sample plane allowed to identify the regime with only a few charge carriers in the dot (electron-hole transition), and the crossover to the formation of the graphene specific zero-energy Landau level at high fields. After rotation of the sample into parallel magnetic field orientation, Zeeman spin splitting with a g-factor of g ≈ 2 is measured. The filling sequence of subsequent spin states is similar to what was found in GaAs and related to the non-negligible influence of exchange interactions among the electrons.

The Salmonella enterica pan-genome

Salmonella enterica is divided into four subspecies containing a large number of different serovars, several of which are important zoonotic pathogens and some show a high degree of host specificity or host preference. We compare 45 sequenced S. enterica genomes that are publicly available (22 complete and 23 draft genome sequences). Of these, 35 were found to be of sufficiently good quality to allow a detailed analysis, along with two Escherichia coli strains (K-12 substr. DH10B and the avian pathogenic E. coli (APEC O1) strain). All genomes were subjected to standardized gene finding, and the core and pan-genome of Salmonella were estimated to be around 2,800 and 10,000 gene families, respectively. The constructed pan-genomic dendrograms suggest that gene content is often, but not uniformly correlated to serotype. Any given Salmonella strain has a large stable core, whilst there is an abundance of accessory genes, including the Salmonella pathogenicity islands (SPIs), transposable elements, phages, and plasmid DNA. We visualize conservation in the genomes in relation to chromosomal location and DNA structural features and find that variation in gene content is localized in a selection of variable genomic regions or islands. These include the SPIs but also encompass phage insertion sites and transposable elements. The islands were typically well conserved in several, but not all, isolates--a difference which may have implications in, e.g., host specificity.

Electronic properties of graphene nanostructures

In this review, recent developments in the fabrication and understanding of the electronic properties of graphene nanostructures are discussed. After a brief overview of the structure of graphene and the two-dimensional transport properties, the focus is put on graphene constrictions, quantum dots and double quantum dots. For constrictions with a width below 100 nm, the current through the constriction is strongly suppressed for a certain back gate voltage range, related to the so-called transport gap. This transport gap is due to the formation of localized puddles in the constriction, and its size depends strongly on the constriction width. Such constrictions can be used to confine charge carriers in quantum dots, leading to Coulomb blockade effects.

An experimental helical-tubular photobioreactor for continuous production of Nannochloropsis sp

An experimental helical-tubular photobioreactor has been designed for controlled, continuous production of Nannochloropsis sp. Its main advantages are: (1) combination of large ratio of culture volume to surface area along with the optimised light penetration depth, (2) easy control of temperature and contaminants, (3) effective spatial distribution of fresh air and CO(2), (4) better CO(2) transfer through extensive interface surface between fresh air and culture-liquid medium and (5) novel automated flow-through sensor providing continuous cell concentration monitoring. Nannochloropsis sp. population density reached maximum value under rather high temperatures and combined natural and artificial light conditions. An average daily increase of 30 x 10(6)cells ml(-1) was obtained at population densities above 350 x 10(6)cells ml(-1) allowing daily harvesting rates of at least 10% the total volume. Measured cellular density productivity data and estimated volumetric productivity range of 1.10-3.03 g l(-1)day(-1), are among the highest Nannochloropsis sp. productivities reported in the literature.

Effects of Left Bundle-Branch Block on Cardiac Structure, Function, Perfusion, and Perfusion Reserve

Background— We aimed to investigate the cardiac effects of left bundle-branch block (LBBB) using myocardial contrast echocardiography (MCE) to ascertain the value of MCE for detecting coronary artery disease (CAD) and to uncover the mechanism that affects the accuracy of single-photon emission computed tomography (SPECT) in these patients.

Methods and Results— Sixty-three symptomatic LBBB patients (group A), 10 left ventricular ejection fraction–matched control subjects without LBBB and no CAD (group B), and 10 normal control subjects (group C) underwent resting echocardiography. Rest and vasodilator MCE and SPECT were undertaken in LBBB patients. Septal (SW) and posterior wall (PW) thickness, thickening, quantitative myocardial blood flow (MBF), and MBF reserve were measured. SW/PW thickness and percentage thickening ratios were lower ( P <0.01 and P <0.05, respectively) in group A compared with both groups B and C, but resting SW/PW MBF and MBF reserve ratios were similar in all 3 groups. MBF reserve but not MBF was reduced in groups A and B (2.2±0.7 versus 2.2±0.2; P =0.98) compared with group C (3.1±0.5; P <0.01). SW thickness was an independent predictor ( P =0.006) of SPECT perfusion defects in LBBB patients without CAD. MCE (92%) had a sensitivity similar to SPECT (92%); however, the specificity of MCE (95%) was superior ( P <0.0001) to SPECT (47%) for the detection of CAD.

Conclusions— Despite asymmetrical reduction in SW thickness and function, MBF is preserved and MBF reserve is homogeneously reduced in LBBB patients with left ventricular systolic dysfunction. Because of partial volume effects, the accuracy of SPECT for detecting CAD was significantly compromised compared with MCE in this patient cohort.

Carbon dioxide laser circumcisions for children

The carbon dioxide laser for circumcision was introduced by our department in 1989. This study aims to review our experience with laser circumcision for children and to evaluate its cost effectiveness as compared to conventional methods. A retrospective study of 30 patients who underwent conventional circumcision in 1985 and another 30 patients who underwent laser circumcision in 1995 was undertaken. The operating times in both groups were compared. The total cost of use of the laser machine was calculated, taking into account maintenance costs, estimated life span of laser machines (10 years) and costs of disposables used during each circumcision. This was weighed against the cost savings from shorter operating times and reduced operating theatre facility charges. Also, morbidity data from 2781 laser circumcisions done between May 1997 and April 2000 was collected. There was a significant decrease of 5 minutes in operating time for the group of patients who underwent laser circumcision. Calculated cost savings per laser circumcision from the reduced operating theatre time was S dollars 31/-. Of the 2781 cases of laser circumcision performed, there was an overall complication rate of 1.15%. Twenty-nine cases (1.04%) had post circumcision bleeding, of which 10 cases (0.36%) required unplanned return to operating theatre for hemostasis. Three cases (0.11%) had wound infection, requiring admission to hospital. Laser circumcision is a simple method with reduced operative time translating into cost effectiveness. Morbidity rates of laser circumcision compare favourably to those of conventional circumcision based on reports from other institutions.

The influence of fluid shear on the structure and material properties of sulphate-reducing bacterial biofilms

Biofilms of sulphate-reducing Desulfovibrio sp. EX265 were grown in square section glass capillary flow cells under a range of fluid flow velocities from 0.01 to 0.4 m/s (wall shear stress, tau(w), from 0.027 to 1.0 N/m(2)). In situ image analysis and confocal scanning laser microscopy revealed biofilm characteristics similar to those reported for aerobic biofilms. Biofilms in both flow cells were patchy and consisted of cell clusters separated by voids. Length-to-width ratio measurements (l(c):w(c)) of biofilm clusters demonstrated the formation of more "streamlined" biofilm clusters (l(c):w(c)=3.03) at high-flow velocity (Reynolds number, Re, 1200), whereas at low-flow velocity (Re 120), the l(c):w(c) of the clusters was approximately 1 (l(c):w(c) of 1 indicates no elongation in the flow direction). Cell clusters grown under high flow were more rigid and had a higher yield point (the point at which the biofilm began to flow like a fluid) than those established at low flow and some biofilm cell aggregates were able to relocate within a cluster, by travelling in the direction of flow, before attaching more firmly downstream.

Highly comprehensive karyotype analysis by a combination of spectral karyotyping (SKY), microdissection, and reverse painting (SKY-MD)

A technique disclosing most information about chromosome modifications is the technique of choice for the analysis of chromosome alterations. The newly developed method for microdissection of fluorescence-labeled chromosomes (FISH-MD) can improve upon this expectation in combination with 24-color spectral karyotyping (SKY). The highly efficient way to detect chromosome modifications by SKY and the detailed specification of aberrant chromosomes by FISH-MD prompted us to use both techniques in a combined approach called SKY-MD. First, an overview of chromosomal aberrations is obtained by spectral karyotyping and subsequently the derivative chromosomes recognized are characterized in a highly specific manner by microdissection and reverse painting. A small quantity of isolated material dissected directly from a 24-color metaphase is sufficient to obtain very detailed information about the chromosome regions and the breakpoints involved in the derivative chromosomes. Therefore, the combination of spectral karyotyping and microdissection in one procedure, and reverse painting can characterize chromosomal aberrations with a degree of specificity hitherto unknown from individual karyotyping experiments. In this article we compare the efficiency of both the SKY technique and that of classical microdissection with the efficiency obtained by SKY-MD.

Comparative genomic hybridization detects genetic imbalances in primary ovarian carcinomas as correlated with grade of differentiation

BACKGROUND

In the current study the authors attempted to evaluate genetic alterations in a large set of primary ovarian carcinomas and to compare the genetic findings with clinical parameters such as grade of tumor differentiation. This strategy was applied to identify chromosomal regions containing genes associated with tumor progression.

METHODS

Genetic imbalances were assessed in 106 primary ovarian carcinomas using comparative genomic hybridization (CGH). CGH was applied because it is a powerful tool with which to screen the entire genome of a tumor for genetic changes by highlighting regions of altered DNA sequence copy numbers (deletions and amplifications). Multivariate statistical standard procedures were used to determine an association between tumor grading and genetic alterations.

RESULTS

One hundred three carcinomas showed aberrant CGH profiles. The most frequent alterations were amplifications of 8q, 1q, 20q, 3q, and 19p, which occurred in 69-53% of tumors, and underrepresentations of 13q, 4q, and 18q, which occurred in 54-50% of tumors. Undifferentiated ovarian carcinomas (World Health Organization Grade 3) were found to be correlated significantly with underrepresentation of 11p and 13q as well as with overrepresentation of 8q and 7p (P = 0.001, 0.001, 0.01, and 0.027, respectively). However, 12p underrepresentation and 18p overrepresentation were significantly more frequent in well and moderately differentiated tumors (P = 0.01 and 0.004, respectively). To facilitate the interpretation and clinical application of the results of the current study, the significant aberrations were translated into a score system. This score system can be used easily for the prediction of an undifferentiated phenotype with a specificity and sensitivity of 79% and 86%, respectively.

CONCLUSIONS

The current study data show that primary ovarian carcinomas are based on consistent genetic alterations that most likely are important for the development of this tumor entity. The correlation between certain aberrations and undifferentiated carcinomas may help to discriminate between primary and secondary genetic events and may indicate the location of those genes involved in cellular functions associated with tumor progression and the development of anaplastic and aggressive phenotypes.

The influence of fluid shear and AICI3 on the material properties of Pseudomonas aeruginosa PAO1 and Desulfovibrio sp. EX265 biofilms

An understanding of the material properties of biofilms is important when describing how biofilms physically interact with their environment. In this study, aerobic biofilms of Pseudomonas aeruginosa PAO1 and anaerobic sulfate-reducing bacteria (SRB) biofilms of Desulfovibrio sp. EX265 were grown under different fluid shear stresses (tau g) in a chemostat recycle loop. Individual biofilm microcolonies were deformed by varying the fluid wall shear stress (tau w). The deformation was quantified in terms of strain (epsilon), and the relative strength of the biofilms was assessed using an apparent elastic coefficient (Eapp) and residual strain (epsilon r) after three cycles of deformation. Aluminium chloride (AlCl3) was then added to both sets of biofilm and the tests repeated. Biofilms grown under higher shear were more rigid and had a greater yield shear stress than those grown under lower shear. The addition of AlCl3 resulted in a significant increase in Eapp and also increased the yield point. We conclude that the strength of the biofilm is in part dependent on the shear under which the biofilm was grown and that the material properties of the biofilm may be manipulated through cation cross-linking of the extracellular polysaccharide (EPS) slime matrix.

Comparison of comparative genomic hybridization and interphase fluorescence in situ hybridization in ovarian carcinomas: possibilities and limitations of both techniques

Comparative genomic hybridization (CGH) is a valuable technique for cytogenetic analysis of solid tumors. To evaluate the reliability of CGH, we examined DNA of 10 ovarian carcinomas after CGH analysis with single- and double-locus fluorescence in situ hybridization (FISH). The FISH experiments, involving 5 chromosomes (chromosomes 3, 6, 8, 12, and 18) with different FISH probes, confirmed the CGH results in 66.2% of cases (92 of 139 investigated loci). In 4 patients, inconsistent results (41 loci) were related to polyploidy, because CGH cannot detect polyploid karyotypes. The remaining 6 discordant loci can be referred to limitations in both techniques. Re-evaluation of FISH and CGH results by one other is therefore recommended to overcome these technical artifacts. Nevertheless, CGH is of potential value in characterizing chromosomal alterations and might help in generating tumor-specific sets of FISH probes to obtain genetic information of prognostic value within a few days.

Genetic imbalances in precursor lesions of endometrial cancer detected by comparative genomic hybridization

Endometrial hyperplasia is regarded as a precursor lesion of endometrioid adenocarcinomas of the endometrium. The genetic events involved in the multistep process from normal endometrial glandular tissue to invasive endometrial carcinomas are primarily unknown. We chose endometrial hyperplasia as a model for identifying chromosomal aberrations occurring during carcinogenesis. Comparative genomic hybridization (CGH) was performed on 47 formalin-fixed, paraffin-embedded specimens of endometrial hyperplasia using the microdissection technique to increase the number of tumor cells in the samples and reduce contamination from normal cells. CGH analysis revealed that 24 out of 47 (51%) samples had detectable chromosomal imbalances, whereas 23 (49%) were in a genetically balanced state. The incidence of aberrant CGH profiles tended to parallel dysplasia grade, ranging from 22% aberrant profiles in simple hyperplasia to 67% in complex hyperplasia with atypia. The most frequent imbalances were 1p, 16p, and 20q underrepresentations and 4q overrepresentations. Copy number changes in 1p were more frequent in atypical complex hyperplasia than in complex lesions without atypical cells or simple lesions (42% versus 20% and 0%). Our results show that endometrial hyperplasia reveals recurrent chromosomal imbalances which tend to increase with the presence of atypical cells. The most frequent aberrations in endometrial cancer, 1q and 8q overrepresentations, are not present or are rare in its precursor lesions. This analysis provides evidence that tumorigenesis proceeds through the accumulation of a series of genetic alterations and suggests a stepwise mode of tumorigenesis.

Long-term results from a phase II study of single agent paclitaxel (Taxol) in previously platinum treated patients with advanced ovarian cancer: the Nordic experience

BACKGROUND

Owing to the wide spread perception of a possible benefit from paclitaxel in the second-line situation the Nordic Gynecologic Oncology Group (NGOG) conducted two prospective phase II studies of paclitaxel single agent treatment (175 mg/m2, three-hour i.v. infusion with standard pre-medication every third week) in patients with relapsing or progressing epithelial ovarian cancer following platinum.

PATIENTS AND METHODS

Between 1992-1994 138 patients in total were enrolled of whom 136 received paclitaxel and were included in the toxicity and survival analysis, while 112 were evaluable for response.

RESULTS

The overall response rate (CR + PR) was 28% with 16 patients achieving a CR (14%). The estimated median (range) time to progression was 4.1 (0.7-60.7) months. The projected four-year overall survival was 7%, with a median (range) of 9.6 (0.3-60.7) months. A multivariate logistic regression analysis showed that platinum resistance, and WHO performance status at baseline, independently correlated with survival at all three time points (median survival time 9.6, 18, and 24 months). Patients with platinum sensitive tumors and WHO performance status 0 had a median survival of 25.6 months compared to 7.0 months for the rest of the patients (P < or = 0.0001). No serious toxicity was registered.

CONCLUSION

Paclitaxel could safely be administered in an outpatient setting using this schedule. Patients with platinum sensitive tumors and a good performance status were most likely to survive. However, these patients are also most likely to respond to re-treatment with a platinum compound. With reference to the reasonably good tumor control and limited toxicity observed in this study, we conclude that paclitaxel single agent therapy is a viable option in the salvage situation, which in some patients can give long-lasting responses. However, although responses can be induced in a significant number of patients, the survival figures remain poor.

A phase 2 study with epirubicin as second-line treatment of patients with advanced epithelial ovarian cancer

Thirty-six patients with advanced epithelial ovarian cancer received epirubicin as second-line therapy after primary treatment with carboplatin and cyclophosphamide. Thirty-four patients were evaluatable for response, 36 for toxicity. There were 9 responses (response rate 26.4%, 95% CI = 12.9-44.4), 2 complete and 7 partial. Median duration of response was 149 days (range 42-183); 4 patients with partial remission are still on study. Toxicity consisted of fatal cardiac failure and paravenous injection (1 patient), fatal leukopenia and sepsis (1 patient), and severe loss of appetite, nausea and vomiting, fatigue, and general malaise in 3 patients. Platelet nadir grade 4 (WHO) was observed in 2 patients while leukocyte nadir grade 4 was seen in 3 patients. The present study showed a high response rate from standard-dose epirubicin. Toxicity was acceptable in most patients, but 2 patients died from treatment complications which gives a treatment-related mortality rate of 6%. Response was primarily seen in patients with minor tumor load and in good general condition.

Suppression of ventricular arrhythmias during ischemia-reperfusion by agents inhibiting Ins(1,4,5)P3 release

BACKGROUND

Reperfusion following myocardial ischemia causes a rapid and transient release of inositol (1,4,5)triphosphate [Ins(1,4,5)P3]. The aim of this study was to test whether this increased Ins(1,4,5)P3 release was important for the development of ventricular arrhythmias and whether agents that inhibit this signal transduction pathway, such as aminoglycoside antibiotics, suppress arrhythmias.

METHODS AND RESULTS

In perfused rat hearts, ventricular tachycardia (VT), ventricular fibrillation (VF), and accumulation of Ins(1,4,5)P3 were measured during early reperfusion. A number of different compounds, including neomycin, gentamicin, streptomycin, spermine, reserpine, and prazosin, were effective in inhibiting the reperfusion-induced Ins(1,4,5)P3 release and the onset of VT and VF in parallel. A strong correlation existed between Ins(1,4,5)P3 content, measured at 2 minutes of reperfusion, and the incidence of reperfusion VT and VF. In addition, intravenous gentamicin suppressed the onset of arrhythmias under ischemic and reperfusion conditions in vivo.

CONCLUSIONS

Our results are consistent with the view that Ins(1,4,5)P3 release plays a pivotal role in mediating arrhythmias during early reperfusion. Agents inhibiting Ins(1,4,5)P3 release are antiarrhythmic and may have potential use clinically.

Structure, expression, and phylogenetic relationships of a family of ypt genes encoding small G-proteins in the green alga Volvox carteri

In addition to the previously described gene yptV1 encoding a small G-protein we have now identified and sequenced four more ras-related ypt genes (yptV2-yptV5) from the green alga Volvox carteri. The four new genes encode polypeptides consisting of 203 to 217 amino-acid residues that contain the typical sequence elements (GTP-binding domains, effector domain) of the ypt/rab subgroup of the Ras superfamily. Comparison of the derived amino-acid sequences from the V. carteri ypt gene products and their Ypt homologs from other species revealed similarity values ranging from 60% to 85%, whereas intraspecies similarities were found to approach only 55%. The coding sequences are interrupted by 5-7 introns of variable size (70-1000 nucleotides) occupying different positions in the genes. Reverse-transcribed samples of stage-specific RNAs were PCR-amplified with primers specific to yptV1, yptV3, yptV4, and yptV5 to determine if yptV transcription might be restricted to either cell type or to a specific stage of the life cycle. These experiments demonstrated that each of these genes is expressed throughout the entire Volvox life cycle and in both the somatic and the reproductive cells of the alga. The transcription start sites of yptV1 and yptV5 were mapped by primer extension. Expression of recombinant yptV cDNA in E. coli yielded recombinant proteins that bound GTP specifically, demonstrating a property which is typical for small G-proteins. The derived YptV polypeptide sequences were used to group them into four distinct classes of Ras-like proteins. These are the first proteins of the Ras superfamily to be identified in a green alga. We discuss the possible role of the YptV-proteins in the intracellular vesicle transport of Volvox.

Adjuvant radiotherapy and risk of contralateral breast cancer

BACKGROUND

The risk of contralateral breast cancer is increased twofold to fivefold for breast cancer patients. A registry-based cohort study in Denmark suggested that radiation treatment of the first breast cancer might increase the risk for contralateral breast cancer among 10-year survivors.

PURPOSE

Our goal was to assess the role of radiation in the development of contralateral breast cancer.

METHODS

A nested case-control study was conducted in a cohort of 56,540 women in Denmark diagnosed with invasive breast cancer from 1943 through 1978. Case patients were 529 women who developed contralateral breast cancer 8 or more years after first diagnosis. Controls were women with breast cancer who did not develop contralateral breast cancer. One control was matched to each case patient on the basis of age, calendar year of initial breast cancer diagnosis, and survival time. Radiation dose to the contralateral breast was estimated for each patient on the basis of radiation measurements and abstracted treatment information. The anatomical position of each breast cancer was also abstracted from medical records.

RESULTS

Radiotherapy had been administered to 82.4% of case patients and controls, and the mean radiation dose to the contralateral breast was estimated to be 2.51 Gy. Radiotherapy did not increase the overall risk of contralateral breast cancer (relative risk = 1.04; 95% confidence interval = 0.74-1.46), and there was no evidence that risk varied with radiation dose, time since exposure, or age at exposure. The second tumors in case patients were evenly distributed in the medial, lateral, and central portions of the breast, a finding that argues against a causal role of radiotherapy in tumorigenesis.

CONCLUSIONS

The majority of women in our series were perimenopausal or postmenopausal (53% total versus 38% premenopausal and 9% of unknown status) and received radiotherapy at an age when the breast tissue appears least susceptible to the carcinogenic effects of radiation. Based on a dose of 2.51 Gy and estimates of radiation risk from other studies, a relative risk of only 1.18 would have been expected for a population of women exposed at an average age of 51 years. Thus, our data provide additional evidence that there is little if any risk of radiation-induced breast cancer associated with exposure of breast tissue to low-dose radiation (e.g., from mammographic x rays or adjuvant radiotherapy) in later life.