Unveiling the signaling network of FLT3-ITD AML improves drug sensitivity prediction

Currently, the identification of patient-specific therapies in cancer is mainly informed by personalized genomic analysis. In the setting of acute myeloid leukemia (AML), patient-drug treatment matching fails in a subset of patients harboring atypical internal tandem duplications (ITDs) in the tyrosine kinase domain of the FLT3 gene. To address this unmet medical need, here we develop a systems-based strategy that integrates multiparametric analysis of crucial signaling pathways, and patient-specific genomic and transcriptomic data with a prior knowledge signaling network using a Boolean-based formalism. By this approach, we derive personalized predictive models describing the signaling landscape of AML FLT3-ITD positive cell lines and patients. These models enable us to derive mechanistic insight into drug resistance mechanisms and suggest novel opportunities for combinatorial treatments. Interestingly, our analysis reveals that the JNK kinase pathway plays a crucial role in the tyrosine kinase inhibitor response of FLT3-ITD cells through cell cycle regulation. Finally, our work shows that patient-specific logic models have the potential to inform precision medicine approaches.

Curation of causal interactions mediated by genes associated with autism accelerates the understanding of gene-phenotype relationships underlying neurodevelopmental disorders

Autism spectrum disorder (ASD) comprises a large group of neurodevelopmental conditions featuring, over a wide range of severity and combinations, a core set of manifestations (restricted sociality, stereotyped behavior and language impairment) alongside various comorbidities. Common and rare variants in several hundreds of genes and regulatory regions have been implicated in the molecular pathogenesis of ASD along a range of causation evidence strength. Despite significant progress in elucidating the impact of few paradigmatic individual loci, such sheer complexity in the genetic architecture underlying ASD as a whole has hampered the identification of convergent actionable hubs hypothesized to relay between the vastness of risk alleles and the core phenotypes. In turn this has limited the development of strategies that can revert or ameliorate this condition, calling for a systems-level approach to probe the cross-talk of cooperating genes in terms of causal interaction networks in order to make convergences experimentally tractable and reveal their clinical actionability. As a first step in this direction, we have captured from the scientific literature information on the causal links between the genes whose variants have been associated with ASD and the whole human proteome. This information has been annotated in a computer readable format in the SIGNOR database and is made freely available in the resource website. To link this information to cell functions and phenotypes, we have developed graph algorithms that estimate the functional distance of any protein in the SIGNOR causal interactome to phenotypes and pathways. The main novelty of our approach resides in the possibility to explore the mechanistic links connecting the suggested gene-phenotype relations.

SIGNOR 3.0, the SIGnaling network open resource 3.0: 2022 update

The SIGnaling Network Open Resource (SIGNOR 3.0, https://signor.uniroma2.it) is a public repository that captures causal information and represents it according to an 'activity-flow' model. SIGNOR provides freely-accessible static maps of causal interactions that can be tailored, pruned and refined to build dynamic and predictive models. Each signaling relationship is annotated with an effect (up/down-regulation) and with the mechanism (e.g. binding, phosphorylation, transcriptional activation, etc.) causing the regulation of the target entity. Since its latest release, SIGNOR has undergone a significant upgrade including: (i) a new website that offers an improved user experience and novel advanced search and graph tools; (ii) a significant content growth adding up to a total of approx. 33,000 manually-annotated causal relationships between more than 8900 biological entities; (iii) an increase in the number of manually annotated pathways, currently including pathways deregulated by SARS-CoV-2 infection or involved in neurodevelopment synaptic transmission and metabolism, among others; (iv) additional features such as new model to represent metabolic reactions and a new confidence score assigned to each interaction.

A Resource to Infer Molecular Paths Linking Cancer Mutations to Perturbation of Cell Metabolism

Some inherited or somatically-acquired gene variants are observed significantly more frequently in the genome of cancer cells. Although many of these cannot be confidently classified as driver mutations, they may contribute to shaping a cell environment that favours cancer onset and development. Understanding how these gene variants causally affect cancer phenotypes may help developing strategies for reverting the disease phenotype. Here we focus on variants of genes whose products have the potential to modulate metabolism to support uncontrolled cell growth. Over recent months our team of expert curators has undertaken an effort to annotate in the database SIGNOR 1) metabolic pathways that are deregulated in cancer and 2) interactions connecting oncogenes and tumour suppressors to metabolic enzymes. In addition, we refined a recently developed graph analysis tool that permits users to infer causal paths leading from any human gene to modulation of metabolic pathways. The tool grounds on a human signed and directed network that connects ∼8400 biological entities such as proteins and protein complexes via causal relationships. The network, which is based on more than 30,000 published causal links, can be downloaded from the SIGNOR website. In addition, as SIGNOR stores information on drugs or other chemicals targeting the activity of many of the genes in the network, the identification of likely functional paths offers a rational framework for exploring new therapeutic strategies that revert the disease phenotype.

The Intricacy of the Viral-Human Protein Interaction Networks: Resources, Data, and Analyses

Viral infections are one of the major causes of human diseases that cause yearly millions of deaths and seriously threaten global health, as we have experienced with the COVID-19 pandemic. Numerous approaches have been adopted to understand viral diseases and develop pharmacological treatments. Among them, the study of virus-host protein-protein interactions is a powerful strategy to comprehend the molecular mechanisms employed by the virus to infect the host cells and to interact with their components. Experimental protein-protein interactions described in the scientific literature have been systematically captured into several molecular interaction databases. These data are organized in structured formats and can be easily downloaded by users to perform further bioinformatic and network studies. Network analysis of available virus-host interactomes allow us to understand how the host interactome is perturbed upon viral infection and what are the key host proteins targeted by the virus and the main cellular pathways that are subverted. In this review, we give an overview of publicly available viral-human protein-protein interactions resources and the community standards, curation rules and adopted ontologies. A description of the main virus-human interactome available is provided, together with the main network analyses that have been performed. We finally discuss the main limitations and future challenges to assess the quality and reliability of protein-protein interaction datasets and resources.

The IntAct database: efficient access to fine-grained molecular interaction data

The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of molecular interactions, derived from the scientific literature and from direct data depositions. As of August 2021, IntAct provides more than one million binary interactions, curated by twelve global partners of the International Molecular Exchange consortium, for which the IntAct database provides a shared curation and dissemination platform. The IMEx curation policy has always emphasised a fine-grained data and curation model, aiming to capture the relevant experimental detail essential for the interpretation of the provided molecular interaction data. Here, we present recent curation focus and progress, as well as a completely redeveloped website which presents IntAct data in a much more user-friendly and detailed way.

COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

Phosphomatics: interactive interrogation of substrate-kinase networks in global phosphoproteomics datasets

MOTIVATION

Mass spectrometry-based phosphoproteomics can routinely identify and quantify thousands of phosphorylated peptides from a single experiment. However interrogating possible upstream kinases and identifying key literature for phosphorylation sites is laborious and time-consuming.

RESULTS

Here, we present Phosphomatics-a publicly available web resource for interrogating phosphoproteomics data. Phosphomatics allows researchers to upload phosphoproteomics data and interrogate possible relationships from a substrate-, kinase- or pathway-centric viewpoint.

AVAILABILITY AND IMPLEMENTATION

Phosphomatics is freely available via the internet at: https://phosphomatics.com.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Using the MINT Database to Search Protein Interactions

The Molecular INTeractions Database (MINT) is a public database designed to store information about protein interactions. Protein interactions are extracted from scientific literature and annotated in the database by expert curators. Currently (October 2019), MINT contains information on more than 26,000 proteins and more than 131,600 interactions in over 30 model organisms. This article provides protocols for searching MINT over the Internet, using the new MINT Web Page. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Searching MINT over the internet Alternate Protocol: MINT visualizer Basic Protocol 2: Submitting interaction data.

A Resource for the Network Representation of Cell Perturbations Caused by SARS-CoV-2 Infection

The coronavirus disease 2019 (COVID-19) pandemic has caused more than 2.3 million casualties worldwide and the lack of effective treatments is a major health concern. The development of targeted drugs is held back due to a limited understanding of the molecular mechanisms underlying the perturbation of cell physiology observed after viral infection. Recently, several approaches, aimed at identifying cellular proteins that may contribute to COVID-19 pathology, have been reported. Albeit valuable, this information offers limited mechanistic insight as these efforts have produced long lists of cellular proteins, the majority of which are not annotated to any cellular pathway. We have embarked in a project aimed at bridging this mechanistic gap by developing a new bioinformatic approach to estimate the functional distance between a subset of proteins and a list of pathways. A comprehensive literature search allowed us to annotate, in the SIGNOR 2.0 resource, causal information underlying the main molecular mechanisms through which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and related coronaviruses affect the host-cell physiology. Next, we developed a new strategy that enabled us to link SARS-CoV-2 interacting proteins to cellular phenotypes via paths of causal relationships. Remarkably, the extensive information about inhibitors of signaling proteins annotated in SIGNOR 2.0 makes it possible to formulate new potential therapeutic strategies. The proposed approach, which is generally applicable, generated a literature-based causal network that can be used as a framework to formulate informed mechanistic hypotheses on COVID-19 etiology and pathology.

Towards a unified open access dataset of molecular interactions

The International Molecular Exchange (IMEx) Consortium provides scientists with a single body of experimentally verified protein interactions curated in rich contextual detail to an internationally agreed standard. In this update to the work of the IMEx Consortium, we discuss how this initiative has been working in practice, how it has ensured database sustainability, and how it is meeting emerging annotation challenges through the introduction of new interactor types and data formats. Additionally, we provide examples of how IMEx data are being used by biomedical researchers and integrated in other bioinformatic tools and resources.

The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions

The current Coronavirus Disease 2019 (COVID-19) pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions enables studying fine-grained resolution of the mechanisms behind the virus biology and the human organism response. Here we present a curated dataset of physical molecular interactions, manually extracted by IMEx Consortium curators focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family. Currently, the dataset comprises over 2,200 binarized interactions extracted from 86 publications. The dataset can be accessed in the standard formats recommended by the Proteomics Standards Initiative (HUPO-PSI) at the IntAct database website ( www.ebi.ac.uk/intact ), and will be continuously updated as research on COVID-19 progresses.

SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update

The SIGnaling Network Open Resource 2.0 (SIGNOR 2.0) is a public repository that stores signaling information as binary causal relationships between biological entities. The captured information is represented graphically as a signed directed graph. Each signaling relationship is associated to an effect (up/down-regulation) and to the mechanism (e.g. binding, phosphorylation, transcriptional activation, etc.) causing the up/down-regulation of the target entity. Since its first release, SIGNOR has undergone a significant content increase and the number of annotated causal interactions have almost doubled. SIGNOR 2.0 now stores almost 23 000 manually-annotated causal relationships between proteins and other biologically relevant entities: chemicals, phenotypes, complexes, etc. We describe here significant changes in curation policy and a new confidence score, which is assigned to each interaction. We have also improved the compliance to the FAIR data principles by providing (i) SIGNOR stable identifiers, (ii) programmatic access through REST APIs, (iii) bioschemas and (iv) downloadable data in standard-compliant formats, such as PSI-MI CausalTAB and GMT. The data are freely accessible and downloadable at https://signor.uniroma2.it/.

CancerGeneNet: linking driver genes to cancer hallmarks

CancerGeneNet (https://signor.uniroma2.it/CancerGeneNet/) is a resource that links genes that are frequently mutated in cancers to cancer phenotypes. The resource takes advantage of a curation effort aimed at embedding a large fraction of the gene products that are found altered in cancer cells into a network of causal protein relationships. Graph algorithms, in turn, allow to infer likely paths of causal interactions linking cancer associated genes to cancer phenotypes thus offering a rational framework for the design of strategies to revert disease phenotypes. CancerGeneNet bridges two interaction layers by connecting proteins whose activities are affected by cancer drivers to proteins that impact on the 'hallmarks of cancer'. In addition, CancerGeneNet annotates curated pathways that are relevant to rationalize the pathological consequences of cancer driver mutations in selected common cancers and 'MiniPathways' illustrating regulatory circuits that are frequently altered in different cancers.

The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions

The current coronavirus disease of 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV)-2, has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions can provide fine-grained resolution of the mechanisms behind the virus biology and the human organism response. We present a curated dataset of physical molecular interactions focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family that has been manually extracted by International Molecular Exchange (IMEx) Consortium curators. Currently, the dataset comprises over 4400 binarized interactions extracted from 151 publications. The dataset can be accessed in the standard formats recommended by the Proteomics Standards Initiative (HUPO-PSI) at the IntAct database website (https://www.ebi.ac.uk/intact) and will be continuously updated as research on COVID-19 progresses.

Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration

Muscle regeneration is a complex process governed by the interplay between several muscle-resident mononuclear cell populations. Following acute or chronic damage these cell populations are activated, communicate via cell-cell interactions and/or paracrine signals, influencing fate decisions via the activation or repression of internal signaling cascades. These are highly dynamic processes, occurring with distinct temporal and spatial kinetics. The main challenge toward a system level description of the muscle regeneration process is the integration of this plethora of inter- and intra-cellular interactions. We integrated the information on muscle regeneration in a web portal. The scientific content annotated in this portal is organized into two information layers representing relationships between different cell types and intracellular signaling-interactions, respectively. The annotation of the pathways governing the response of each cell type to a variety of stimuli/perturbations occurring during muscle regeneration takes advantage of the information stored in the SIGNOR database. Additional curation efforts have been carried out to increase the coverage of molecular interactions underlying muscle regeneration and to annotate cell-cell interactions. To facilitate the access to information on cell and molecular interactions in the context of muscle regeneration, we have developed Myo-REG, a web portal that captures and integrates published information on skeletal muscle regeneration. The muscle-centered resource we provide is one of a kind in the myology field. A friendly interface allows users to explore, approximately 100 cell interactions or to analyze intracellular pathways related to muscle regeneration. Finally, we discuss how data can be extracted from this portal to support in silico modeling experiments.

DISNOR: a disease network open resource

DISNOR is a new resource that aims at exploiting the explosion of data on the identification of disease-associated genes to assemble inferred disease pathways. This may help dissecting the signaling events whose disruption causes the pathological phenotypes and may contribute to build a platform for precision medicine. To this end we combine the gene-disease association (GDA) data annotated in the DisGeNET resource with a new curation effort aimed at populating the SIGNOR database with causal interactions related to disease genes with the highest possible coverage. DISNOR can be freely accessed at http://DISNOR.uniroma2.it/ where >3700 disease-networks, linking ∼2600 disease genes, can be explored. For each disease curated in DisGeNET, DISNOR links disease genes by manually annotated causal relationships and offers an intuitive visualization of the inferred ‘patho-pathways’ at different complexity levels. User-defined gene lists are also accepted in the query pipeline. In addition, for each list of query genes—either annotated in DisGeNET or user-defined—DISNOR performs a gene set enrichment analysis on KEGG-defined pathways or on the lists of proteins associated with the inferred disease pathways. This function offers additional information on disease-associated cellular pathways and disease similarity.

Selectivity of the CUBAN domain in the recognition of ubiquitin and NEDD8

Among the members of the ubiquitin-like (Ubl) protein family, neural precursor cell expressed developmentally down-regulated protein 8 (NEDD8) is the closest in sequence to ubiquitin (57% identity). The two modification mechanisms and their functions, however, are highly distinct and the two Ubls are not interchangeable. A complex network of interactions between modifying enzymes and adaptors, most of which are specific while others are promiscuous, ensures selectivity. Many domains that bind the ubiquitin hydrophobic patch also bind NEDD8 while no domain that specifically binds NEDD8 has yet been described. Here, we report an unbiased selection of domains that bind ubiquitin and/or NEDD8 and we characterize their specificity/promiscuity. Many ubiquitin-binding domains bind ubiquitin preferentially and, to a lesser extent, NEDD8. In a few cases, the affinity of these domains for NEDD8 can be increased by substituting the alanine at position 72 with arginine, as in ubiquitin. We have also identified a unique domain, mapping to the carboxyl end of the protein KHNYN, which has a stark preference for NEDD8. Given its ability to bind neddylated cullins, we have named this domain CUBAN (Cullin-Binding domain Associating with NEDD8). We present here the solution structure of the CUBAN domain both in the isolated form and in complex with NEDD8. The results contribute to the understanding of the discrimination mechanism between ubiquitin and the Ubl. They also provide new insights on the biological role of a ill-defined protein, whose function is hitherto only predicted.

SIGNOR: a database of causal relationships between biological entities

Assembly of large biochemical networks can be achieved by confronting new cell-specific experimental data with an interaction subspace constrained by prior literature evidence. The SIGnaling Network Open Resource, SIGNOR (available on line at http://signor.uniroma2.it), was developed to support such a strategy by providing a scaffold of prior experimental evidence of causal relationships between biological entities. The core of SIGNOR is a collection of approximately 12,000 manually-annotated causal relationships between over 2800 human proteins participating in signal transduction. Other entities annotated in SIGNOR are complexes, chemicals, phenotypes and stimuli. The information captured in SIGNOR can be represented as a signed directed graph illustrating the activation/inactivation relationships between signalling entities. Each entry is associated to the post-translational modifications that cause the activation/inactivation of the target proteins. More than 4900 modified residues causing a change in protein concentration or activity have been curated and linked to the modifying enzymes (about 351 human kinases and 94 phosphatases). Additional modifications such as ubiquitinations, sumoylations, acetylations and their effect on the modified target proteins are also annotated. This wealth of structured information can support experimental approaches based on multi-parametric analysis of cell systems after physiological or pathological perturbations and to assemble large logic models.

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases

IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate levels of training, perform quality control on entries and take responsibility for long-term data maintenance. Recently, the MINT and IntAct databases decided to merge their separate efforts to make optimal use of limited developer resources and maximize the curation output. All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset. Both IntAct and MINT are active contributors to the IMEx consortium (http://www.imexconsortium.org).

MINT, the molecular interaction database: 2012 update

The Molecular INTeraction Database (MINT, http://mint.bio.uniroma2.it/mint/) is a public repository for protein-protein interactions (PPI) reported in peer-reviewed journals. The database grows steadily over the years and at September 2011 contains approximately 235,000 binary interactions captured from over 4750 publications. The web interface allows the users to search, visualize and download interactions data. MINT is one of the members of the International Molecular Exchange consortium (IMEx) and adopts the Molecular Interaction Ontology of the Proteomics Standard Initiative (PSI-MI) standards for curation and data exchange. MINT data are freely accessible and downloadable at http://mint.bio.uniroma2.it/mint/download.do. We report here the growth of the database, the major changes in curation policy and a new algorithm to assign a confidence to each interaction.

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

BACKGROUND

Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional metrics. The BioCreative III Protein-Protein Interaction (PPI) tasks were motivated by such considerations, trying to address aspects including how the end user would oversee the generated output, for instance by providing ranked results, textual evidence for human interpretation or measuring time savings by using automated systems. Detecting articles describing complex biological events like PPIs was addressed in the Article Classification Task (ACT), where participants were asked to implement tools for detecting PPI-describing abstracts. Therefore the BCIII-ACT corpus was provided, which includes a training, development and test set of over 12,000 PPI relevant and non-relevant PubMed abstracts labeled manually by domain experts and recording also the human classification times. The Interaction Method Task (IMT) went beyond abstracts and required mining for associations between more than 3,500 full text articles and interaction detection method ontology concepts that had been applied to detect the PPIs reported in them.

RESULTS

A total of 11 teams participated in at least one of the two PPI tasks (10 in ACT and 8 in the IMT) and a total of 62 persons were involved either as participants or in preparing data sets/evaluating these tasks. Per task, each team was allowed to submit five runs offline and another five online via the BioCreative Meta-Server. From the 52 runs submitted for the ACT, the highest Matthew's Correlation Coefficient (MCC) score measured was 0.55 at an accuracy of 89% and the best AUC iP/R was 68%. Most ACT teams explored machine learning methods, some of them also used lexical resources like MeSH terms, PSI-MI concepts or particular lists of verbs and nouns, some integrated NER approaches. For the IMT, a total of 42 runs were evaluated by comparing systems against manually generated annotations done by curators from the BioGRID and MINT databases. The highest AUC iP/R achieved by any run was 53%, the best MCC score 0.55. In case of competitive systems with an acceptable recall (above 35%) the macro-averaged precision ranged between 50% and 80%, with a maximum F-Score of 55%.

CONCLUSIONS

The results of the ACT task of BioCreative III indicate that classification of large unbalanced article collections reflecting the real class imbalance is still challenging. Nevertheless, text-mining tools that report ranked lists of relevant articles for manual selection can potentially reduce the time needed to identify half of the relevant articles to less than 1/4 of the time when compared to unranked results. Detecting associations between full text articles and interaction detection method PSI-MI terms (IMT) is more difficult than might be anticipated. This is due to the variability of method term mentions, errors resulting from pre-processing of articles provided as PDF files, and the heterogeneity and different granularity of method term concepts encountered in the ontology. However, combining the sophisticated techniques developed by the participants with supporting evidence strings derived from the articles for human interpretation could result in practical modules for biological annotation workflows.

Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases

Background

The vast amount of data published in the primary biomedical literature represents a challenge for the automated extraction and codification of individual data elements. Biological databases that rely solely on manual extraction by expert curators are unable to comprehensively annotate the information dispersed across the entire biomedical literature. The development of efficient tools based on natural language processing (NLP) systems is essential for the selection of relevant publications, identification of data attributes and partially automated annotation. One of the tasks of the Biocreative 2010 Challenge III was devoted to the evaluation of NLP systems developed to identify articles for curation and extraction of protein-protein interaction (PPI) data.

Results

The Biocreative 2010 competition addressed three tasks: gene normalization, article classification and interaction method identification. The BioGRID and MINT protein interaction databases both participated in the generation of the test publication set for gene normalization, annotated the development and test sets for article classification, and curated the test set for interaction method classification. These test datasets served as a gold standard for the evaluation of data extraction algorithms.

Conclusion

The development of efficient tools for extraction of PPI data is a necessary step to achieve full curation of the biomedical literature. NLP systems can in the first instance facilitate expert curation by refining the list of candidate publications that contain PPI data; more ambitiously, NLP approaches may be able to directly extract relevant information from full-text articles for rapid inspection by expert curators. Close collaboration between biological databases and NLP systems developers will continue to facilitate the long-term objectives of both disciplines.

Laparoscopic relief of obstructing folded muscular cuff after transanal pull-through for aganglionosis

Transanal endorectal resection and colonic pull-through (TERPT) is a good technique for the management of Hirschsprungs disease. This procedure is feasible in the vast majority of patients and is associated with excellent results, early postoperative recovery, and no visible scars. We report the case of a patient who developed early postoperative severe constipation after TERPT due to unusual folding of the muscular cuff rim, which tightly narrowed the pulled-through colon. This complication was diagnosed and treated by laparoscopy. To prevent it, we recommend splitting of the aganglionic muscular cuff during TERPT.

Laparoscopic relief of obstructing folded muscular cuff after transanal pull-through for aganglionosis

Transanal endorectal resection and colonic pull-through (TERPT) is a good technique for the management of Hirschsprung's disease. This procedure is feasible in the vast majority of patients and is associated with excellent results, early postoperative recovery, and no visible scars. We report the case of a patient who developed early postoperative severe constipation after TERPT due to unusual folding of the muscular cuff rim, which tightly narrowed the pulled-through colon. This complication was diagnosed and treated by laparoscopy. To prevent it, we recommend splitting of the aganglionic muscular cuff during TERPT.

Retroperitoneal abscess and omphalitis in young infants

AIM

To evaluate the aetiopathogenetic factors in cases of retroperitoneal abscess in young infants, particularly the correlation with omphalitis.

METHODS

We describe the cases of two infants, aged 8 and 3 wk, respectively, with a history of omphalitis during the first weeks of life and subsequent development of a retroperitoneal abscess. Both infants underwent surgical drainage of the abscess.

RESULTS

In case 1, Staphylococcus aureus was found in cultures from abscess pus, and in case 2 from umbilical pus, abscess purulent material and blood. Both infants are in good health after a follow-up of 6 mo and 8 y, respectively.

CONCLUSION

Retroperitoneal abscesses in young infants are usually considered to be idiopathic. A correlation with omphalitis was found in both of the reported cases and it is thought that this could have been due to an aetiopathogenetic factor. Furthermore, we stress the importance of suspicion of retroperitoneal abscesses for early diagnosis and treatment, and discuss the therapeutic strategies.

Pyloric atresia: an attempt at anatomic pyloric sphincter reconstruction

BACKGROUND

The standard method of surgical correction of pyloric atresia is gastro-duodenostomy. The authors report a case of pyloric atresia associated with junctional epidermolysis bullosa, treated with a new technique of pyloric sphincter reconstruction by gastric and duodenal mucosa cul-de-sacs advancement and end-to-end anastomosis.

METHODS

The patient was a premature 2,100-g baby girl. X-ray showed gastric dilatation suggesting a congenital gastric obstruction. At surgery a pyloric atresia was found, with the appearance of a well-vascularized solid cord about 1.5 cm long. By longitudinal pyloromyotomy the cul-de-sacs of gastric and duodenal mucosa were reached and then isolated in the respective gastric and duodenal sides to obtain better mobilization. The mucosal cul-de-sacs, thus mobilized, were advanced easily into the pyloric canal, opened longitudinally, and were sutured together using end-to-end anastomosis. The longitudinal pyloromyotomy then was closed diagonally above the reconstructed pyloric neocanal.

RESULTS

The postoperative course was uneventful: oral feeding was started on the 11th postoperative day. At 4 year follow-up the child was well; no gastrointestinal disorders were present, confirmed by x-ray barium meal and by HIDA technetium Tc 99m hepatic scintiscan, which excluded any bilious duodeno-gastric reflux.

CONCLUSION

This technique of pyloric sphincter reconstruction allows preservation of the pyloric sphincter, whose sphincter muscular layer, although hypoplastic, is present in cases of pyloric atresia.

Use of "Gore-Tex surgical membrane" to minimize surgical adhesions in multistaged extrathoracic esophageal elongation for esophageal atresia

The procedure of choice in the surgical correction of "long gap" esophageal atresia should, when possible, preserve the native esophagus. We present a modification of "the multistaged extrathoracic esophageal elongation method," designed to facilitate esophageal elongation and use of a Gore-Tex (W.L. Gore and Associates, Flagstaff, AZ) surgical membrane to minimize surgical adhesions. We used this technique to successfully treat a 1-kg infant, with type A esophageal atresia, associated aortic coartation, and severe necrotizing enterocolitis with multiple perforations. Multistaged extrathoracic esophageal elongation was begun at the age of 9 months and concluded at 17 months.

A case of relapsing polychondritis presenting as mediastinal syndrome, diagnosed by CT scans of the trachea and head

OBJECTIVE

The aim of this study is to evaluate the significance of CT scans of the trachea and head in the diagnosis of Relapsing Polychondritis (RP).

DESIGN

Relapsing polychondritis is a disease involving cartilaginous structures, particularly those of the ears, nose and trachea. Diagnosis is based on specific clinical features and immuno-histopathological evaluation of the cartilages involved.

SETTING AND PATIENTS

We describe a case of RP in which the most evident clinical signs (cough, dyspnoea, vertigo, tinnitus, headache, oedema of the face and shoulders and fever), led us first to suspect a mediastinal compression syndrome.

INTERVENTION

A CT scan of the trachea and head revealed details which established the correct diagnosis, supported by other typical RP symptoms and by histopathological examination of the cartilage.

MAIN OUTCOME MEASURES

Evaluation by CT scan of the chest, the mediastinum, the head and the pinnae.

RESULTS

CT scanning revealed thickening and calcification of the anterolateral tracheal wall and main bronchi besides marked narrowing of the trachea. CT of the head showed calcification also of the external auditory meatus and part of the pinnae.

CONCLUSION

We consider that CT scan of the trachea and head is helpful in evaluating the bronchial tree, the auditory meatus and pinnae as well as being a valid tool for the final diagnosis and in following the course of the disease.

Simultaneous ileal intussusception and volvulus after jejunoileal bypass for morbid obesity

OBJECTIVE

The aim of this work is to consider the mechanical complications of jejunoileal bypass for morbid obesity which can have a serious outcome because of the occult nature of the symptoms.

DESIGN

The mechanical complications of jejunoileal bypass are mainly intussusception of the bypassed ileal segment, internal herniation of the ileal loops through the mesenteric defects and laparocele.

SETTING AND PATIENTS

A recent case is reported in which, most unusually, intussusception and volvulus were both present, with ischaemia and necrosis of the bypassed segment. Moreover, the general health of the patient remains normal despite the severity of the complication.

MAIN OUTCOME MEASURES

Examination of blind loop with CT scan which showed an abdominal mass of uncertain interpretation.

INTERVENTION

A laparotomy revealed a volvulus of bypassed ileal loops, probably caused by a simultaneous ileal intussusception and an adhesion. On account of the extensive nature of the process and the degree of advanced ischaemia and gangrene patches in the folds of the ileum, resection of the entire bypassed segment as far as the previous jejunoileal anastomosis was necessary.

CONCLUSION

The authors point out the occult nature of the manifestations of this type of complication: aspecific abdominal pains in all quadrants, fever, non vomiting, normal passing of faeces and gas and suggested that simultaneous diverticulitis of the colon (frequently found in the obese) can further complicate and delay diagnosis.

Biliopancreatic diversion with pylorus-preserving technique: a new method for the surgical control of hypercholesterolaemia and diabetes II?

OBJECTIVE

The aim of this study was to evaluate the efficacy of biliopancreatic diversion by Scopinaro's method, with a pylorus-preserving modification, in correcting hypercholesterolaemia and diabetes II not controllable by diet or medical treatment.

DESIGN

Besides weight loss, Scopinaro's operation produces a correction of hypercholesterolaemia and diabetes. These results encouraged us to perform BPD without gastric resection, thus preserving the functions of the stomach and pylorus in moderately overweight patients with hypercholesterolaemia and diabetes.

SETTING AND PATIENTS

The pylorus-preserving technique has been performed on two patients suffering from severe hypercholesterolaemia and hyperglycaemia and who were not more than 30% overweight, at Clinica Chirurgica and Chirurgia d'Urgenza Department, University of Sassari, Italy. Both patients had a six-month follow-up assessment. MAIN OUTCOME MEASURES. Examination of cholesterol and glycaemia levels after the operation, and the moderate weight loss.

INTERVENTION

The operation is the same as Scopinaro's with regard to the length of intestine forming the alimentary loop and the common tract. The difference lies in the fact that instead of resecting the stomach and creating a gastroileostomy, we resect the duodenum, and perform a duodenoileostomy. RESULTS. In both patients the cholesterol and glycaemia levels had returned to normal 1 month after the operation and are stable after six months. Weight loss was only moderate.

CONCLUSION

By the preliminary data on two patients treated with our modified technique this method seems to be as effective in controlling lipidic metabolism and diabetes II as the original version of biliopancreatic diversion.

Mental impairment in Parkinson's disease. The role of anticholinergic drugs

The trial has been carried out on 33 treated Parkinsonian patients and 14 healthy controls. A series of psychometric tests were employed in order to show a possible intellectual deterioration in Parkinsonian patients. Bender's test showed greater motor-perceptive deterioration in Parkinsonian patients respect to control, the Wechsler-Bellevue Intelligence Scale evidenced in patients significant deterioration of mnesic and psychomotor capacity. When considering drug treatments patients undergoing combined treatment or anti-cholinergics alone obtained worse results in all tests made whilst patients on L-Dopa alone obtained the best results.

[Treatment of essential headache in developmental age with L-5-HTP (cross over double-blind study versus placebo)]

Thirty patients (mean age: 10.38 years) affected by primary headache were selected for a double-blind cross-over clinical trial. The patients were randomized into 2 homogeneous groups of 15 and treated for 12 weeks with L-5-HTP (100 mg/day) and placebo as per the following design: placebo - L-5-HTP (group A) and L-5-HTP - placebo (group B). Evaluation was carried out every 3 weeks by the Migraine Index supplying a general assessment of the attacks, i.e. severity, duration and frequency. The decrease in mean score values was directly proportional to L-5-HTP treatment, and statistical significance (Wilcoxon's test) was observed only for L-5-HTP in both groups, from 0.05 to 0.01. Improvement, as evaluated by CGI on percentage distribution of the patients, was homogeneous in both groups.

Changed plasma prolactin levels after etoperidone and placebo

A neuroendocrinological study was carried out by evaluating plasma prolactin levels after etoperidone i.m. (100 mg) and placebo. Fourteen male inpatients (mean age: 35.36 +/- 11.7 years) with chronic schizophrenia were selected for the study, whose aim was to improve interpretation of the pharmacological activity of etoperidone. The results suggest that etoperidone plays the role of an atypical psychotropic drug since it does not affect prolactin levels. In addition, the drug is devoid of anticholinergic effects, which facilitates its prospective clinical use for medium-term and long-term therapy.