BQsupports: systematic assessment of the support and novelty of new biomedical associations

MOTIVATION

Living a Big Data era in Biomedicine, there is an unmet need to systematically assess experimental observations in the context of available information. This assessment would offer a means for a comprehensive and robust validation of biomedical data results and provide an initial estimate of the potential novelty of the findings.

RESULTS

Here we present BQsupports, a web-based tool built upon the Bioteque biomedical descriptors that systematically analyzes and quantifies the current support to a given set of observations. The tool relies on over 1000 distinct types of biomedical descriptors, covering over 11 different biological and chemical entities, including genes, cell lines, diseases, and small molecules. By exploring hundreds of descriptors, BQsupports provide support scores for each observation across a wide variety of biomedical contexts. These scores are then aggregated to summarize the biomedical support of the assessed dataset as a whole. Finally, the BQsupports also suggests predictive features of the given dataset, which can be exploited in downstream machine learning applications.

AVAILABILITY AND IMPLEMENTATION

The web application and underlying data are available online (https://bqsupports.irbbarcelona.org).

Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque

Biomedical data is accumulating at a fast pace and integrating it into a unified framework is a major challenge, so that multiple views of a given biological event can be considered simultaneously. Here we present the Bioteque, a resource of unprecedented size and scope that contains pre-calculated biomedical descriptors derived from a gigantic knowledge graph, displaying more than 450 thousand biological entities and 30 million relationships between them. The Bioteque integrates, harmonizes, and formats data collected from over 150 data sources, including 12 biological entities (e.g., genes, diseases, drugs) linked by 67 types of associations (e.g., ‘drug treats disease’, ‘gene interacts with gene’). We show how Bioteque descriptors facilitate the assessment of high-throughput protein-protein interactome data, the prediction of drug response and new repurposing opportunities, and demonstrate that they can be used off-the-shelf in downstream machine learning tasks without loss of performance with respect to using original data. The Bioteque thus offers a thoroughly processed, tractable, and highly optimized assembly of the biomedical knowledge available in the public domain.

Biomedical data is accumulating at a fast pace and integrating it into a unified framework is a major challenge. Here, the authors present a resource that contains pre-calculated biomedical descriptors derived from a very large knowledge graph.

A community challenge for a pancancer drug mechanism of action inference from perturbational profile data

The Columbia Cancer Target Discovery and Development (CTD2) Center is developing PANACEA, a resource comprising dose-responses and RNA sequencing (RNA-seq) profiles of 25 cell lines perturbed with ∼400 clinical oncology drugs, to study a tumor-specific drug mechanism of action. Here, this resource serves as the basis for a DREAM Challenge assessing the accuracy and sensitivity of computational algorithms for de novo drug polypharmacology predictions. Dose-response and perturbational profiles for 32 kinase inhibitors are provided to 21 teams who are blind to the identity of the compounds. The teams are asked to predict high-affinity binding targets of each compound among ∼1,300 targets cataloged in DrugBank. The best performing methods leverage gene expression profile similarity analysis as well as deep-learning methodologies trained on individual datasets. This study lays the foundation for future integrative analyses of pharmacogenomic data, reconciliation of polypharmacology effects in different tumor contexts, and insights into network-based assessments of drug mechanisms of action.

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Drug-perturbed RNA sequencing data can be used to identify drug targets

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Technology-based drug-target definitions often subsume literature definitions

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Literature and screening datasets provide complementary information on drug mechanisms

Bioactivity descriptors for uncharacterized chemical compounds

Chemical descriptors encode the physicochemical and structural properties of small molecules, and they are at the core of chemoinformatics. The broad release of bioactivity data has prompted enriched representations of compounds, reaching beyond chemical structures and capturing their known biological properties. Unfortunately, bioactivity descriptors are not available for most small molecules, which limits their applicability to a few thousand well characterized compounds. Here we present a collection of deep neural networks able to infer bioactivity signatures for any compound of interest, even when little or no experimental information is available for them. Our signaturizers relate to bioactivities of 25 different types (including target profiles, cellular response and clinical outcomes) and can be used as drop-in replacements for chemical descriptors in day-to-day chemoinformatics tasks. Indeed, we illustrate how inferred bioactivity signatures are useful to navigate the chemical space in a biologically relevant manner, unveiling higher-order organization in natural product collections, and to enrich mostly uncharacterized chemical libraries for activity against the drug-orphan target Snail1. Moreover, we implement a battery of signature-activity relationship (SigAR) models and show a substantial improvement in performance, with respect to chemistry-based classifiers, across a series of biophysics and physiology activity prediction benchmarks.

Multi-center observational study on occurrence and related clinical factors of neurogenic heterotopic ossification in patients with disorders of consciousness

Aims: to assess occurrence and clinical correlates of neurogenic heterotopic ossifications (NHO) in patients with prolonged disorder of consciousness (DoC).Design: multi-center cross-sectional observational study.Setting: 23 intensive neurorehabilitation units.Subjects: 287 patients with prolonged disorder of consciousness (DoC; 150 in vegetative state, VS, and 128 in minimally conscious state, MCS) of different etiology (vascular = 125, traumatic = 83, anoxic = 56, others = 14).Main Measures: clinical evidence of NHO confirmed by standard radiological and/or sonographic evaluation; Coma Recovery Scale-Revised; Disability Rating Scale (DRS); Early Rehabilitation Barthel Index; presence of ventilator support, spasticity, bone fractures and paroxysmal sympathetic hyperactivity.Results: 31 patients (11.2%) presented NHO. Univariate analyses showed that NHO was associated with VS diagnosis, traumatic etiology, high DRS category and total score, and high occurrence of limb spasticity and bone fractures. A cluster-corrected binary logistic regression model (excluding spasticity available in a subset of patients) showed that only lower DRS total score and presence of bone fractures were independently associated with NHO.Conclusions: NHO are relatively frequent in patients with DoC, and are independently associated with functional disability, bone fractures and spasticity. These findings contribute to identifying patients with DoC prone to develop NHO and requiring special interventions to improve functional recovery.

Bioactivity Profile Similarities to Expand the Repertoire of COVID-19 Drugs

Until a vaccine becomes available, the current repertoire of drugs is our only therapeutic asset to fight the SARS-CoV-2 outbreak. Indeed, emergency clinical trials have been launched to assess the effectiveness of many marketed drugs, tackling the decrease of viral load through several mechanisms. Here, we present an online resource, based on small-molecule bioactivity signatures and natural language processing, to expand the portfolio of compounds with potential to treat COVID-19. By comparing the set of drugs reported to be potentially active against SARS-CoV-2 to a universe of 1 million bioactive molecules, we identify compounds that display analogous chemical and functional features to the current COVID-19 candidates. Searches can be filtered by level of evidence and mechanism of action, and results can be restricted to drug molecules or include the much broader space of bioactive compounds. Moreover, we allow users to contribute COVID-19 drug candidates, which are automatically incorporated to the pipeline once per day. The computational platform, as well as the source code, is available at https://sbnb.irbbarcelona.org/covid19.

Multi-center study on overall clinical complexity of patients with prolonged disorders of consciousness of different etiologies

Aim: to assess overall clinical complexity of patients with acquired disorders of consciousness (DoC) in vegetative state/unresponsive wakefulness syndrome (VS/UWS) vs. minimally conscious state- MCS) and in different etiologies..Design: Multi-center cross-sectional observational study.Setting: 23 intensive neurorehabilitation units.Subjects: 264 patients with DoC in the post-acute phase: VS/UWS = 141, and MCS = 123 due to vascular (n = 125), traumatic (n = 83) or anoxic (n = 56) brain injury.Main Measures: Coma Recovery Scale-Revised, and Disability Rating Scale (DRS); presence of medical devices (e.g., for eating or breathing); occurrence and severity of medical complications.Results: patients in DoC, and particularly those in VS/UWS, showed severe overall clinical complexity. Anoxic patients had higher overall clinical complexity, lower level of responsiveness/consciousness, higher functional disability, and higher needs of medical devices. Vascular patients had worse premorbid clinical comorbidities. The two etiologies showed a comparable rate of MC, higher than that observed in traumatic etiology.Conclusion: overall clinical complexity is significantly higher in VS/UWS than in MCS, and in non-traumatic vs. traumatic etiology. These findings could explain the worse clinical evolution reported in anoxic and vascular etiologies and in VS/UWS patients and contribute to plan patient-tailored care and rehabilitation programmes.

Introducing "best single template" models as reference baseline for the Continuous Automated Model Evaluation (CAMEO)

Critical blind assessment of structure prediction techniques is crucial for the scientific community to establish the state of the art, identify bottlenecks, and guide future developments. In Critical Assessment of Techniques in Structure Prediction (CASP), human experts assess the performance of participating methods in relation to the difficulty of the prediction task in a biennial experiment on approximately 100 targets. Yet, the development of automated computational modeling methods requires more frequent evaluation cycles and larger sets of data. The "Continuous Automated Model EvaluatiOn (CAMEO)" platform complements CASP by conducting fully automated blind prediction evaluations based on the weekly pre-release of sequences of those structures, which are going to be published in the next release of the Protein Data Bank (PDB). Each week, CAMEO publishes benchmarking results for predictions corresponding to a set of about 20 targets collected during a 4-day prediction window. CAMEO benchmarking data are generated consistently for all methods at the same point in time, enabling developers to cross-validate their method's performance, and referring to their results in publications. Many successful participants of CASP have used CAMEO-either by directly benchmarking their methods within the system or by comparing their own performance to CAMEO reference data. CAMEO offers a variety of scores reflecting different aspects of structure modeling, for example, binding site accuracy, homo-oligomer interface quality, or accuracy of local model confidence estimates. By introducing the "bestSingleTemplate" method based on structure superpositions as a reference for the accuracy of 3D modeling predictions, CAMEO facilitates objective comparison of techniques and fosters the development of advanced methods.

SWISS-MODEL: homology modelling of protein structures and complexes

Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated workflows and servers simplify and streamline the homology modelling process, also allowing users without a specific computational expertise to generate reliable protein models and have easy access to modelling results, their visualization and interpretation. Here, we present an update to the SWISS-MODEL server, which pioneered the field of automated modelling 25 years ago and been continuously further developed. Recently, its functionality has been extended to the modelling of homo- and heteromeric complexes. Starting from the amino acid sequences of the interacting proteins, both the stoichiometry and the overall structure of the complex are inferred by homology modelling. Other major improvements include the implementation of a new modelling engine, ProMod3 and the introduction a new local model quality estimation method, QMEANDisCo. SWISS-MODEL is freely available at https://swissmodel.expasy.org.

Modeling of Protein Tertiary and Quaternary Structures Based on Evolutionary Information

Proteins are subject to evolutionary forces that shape their three-dimensional structure to meet specific functional demands. The knowledge of the structure of a protein is therefore instrumental to gain information about the molecular basis of its function. However, experimental structure determination is inherently time consuming and expensive, making it impossible to follow the explosion of sequence data deriving from genome-scale projects. As a consequence, computational structural modeling techniques have received much attention and established themselves as a valuable complement to experimental structural biology efforts. Among these, comparative modeling remains the method of choice to model the three-dimensional structure of a protein when homology to a protein of known structure can be detected.The general strategy consists of using experimentally determined structures of proteins as templates for the generation of three-dimensional models of related family members (targets) of which the structure is unknown. This chapter provides a description of the individual steps needed to obtain a comparative model using SWISS-MODEL, one of the most widely used automated servers for protein structure homology modeling.

DynBench3D, a Web-Resource to Dynamically Generate Benchmark Sets of Large Heteromeric Protein Complexes

Multi-protein machines are responsible for most cellular tasks, and many efforts have been invested in the systematic identification and characterization of thousands of these macromolecular assemblies. However, unfortunately, the (quasi) atomic details necessary to understand their function are available only for a tiny fraction of the known complexes. The computational biology community is developing strategies to integrate structural data of different nature, from electron microscopy to X-ray crystallography, to model large molecular machines, as it has been done for individual proteins and interactions with remarkable success. However, unlike for binary interactions, there is no reliable gold-standard set of three-dimensional (3D) complexes to benchmark the performance of these methodologies and detect their limitations. Here, we present a strategy to dynamically generate non-redundant sets of 3D heteromeric complexes with three or more components. By changing the values of sequence identity and component overlap between assemblies required to define complex redundancy, we can create sets of representative complexes with known 3D structure (i.e., target complexes). Using an identity threshold of 20% and imposing a fraction of component overlap of <0.5, we identify 495 unique target complexes, which represent a real non-redundant set of heteromeric assemblies with known 3D structure. Moreover, for each target complex, we also identify a set of assemblies, of varying degrees of identity and component overlap, that can be readily used as input in a complex modeling exercise (i.e., template subcomplexes). We hope that resources like this will significantly help the development and progress assessment of novel methodologies, as docking benchmarks and blind prediction contests did. The interactive resource is accessible at https://DynBench3D.irbbarcelona.org.

SWISS-MODEL: homology modelling of protein structures and complexes

Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated workflows and servers simplify and streamline the homology modelling process, also allowing users without a specific computational expertise to generate reliable protein models and have easy access to modelling results, their visualization and interpretation. Here, we present an update to the SWISS-MODEL server, which pioneered the field of automated modelling 25 years ago and been continuously further developed. Recently, its functionality has been extended to the modelling of homo- and heteromeric complexes. Starting from the amino acid sequences of the interacting proteins, both the stoichiometry and the overall structure of the complex are inferred by homology modelling. Other major improvements include the implementation of a new modelling engine, ProMod3 and the introduction a new local model quality estimation method, QMEANDisCo. SWISS-MODEL is freely available at https://swissmodel.expasy.org.

Biallelic mutations in mitochondrial tryptophanyl-tRNA synthetase cause Levodopa-responsive infantile-onset Parkinsonism

Mitochondrial aminoacyl‐tRNA synthetases (mtARSs) are essential, ubiquitously expressed enzymes that covalently attach amino acids to their corresponding tRNA molecules during translation of mitochondrial genes. Deleterious variants in the mtARS genes cause a diverse array of phenotypes, many of which involve the nervous system. Moreover, distinct mutations in mtARSs often cause different clinical manifestations. Recently, the gene encoding mitochondrial tryptophanyl tRNA synthetase (WARS2) was reported to cause 2 different neurological phenotypes, a form of autosomal recessive intellectual disability and a syndrome of severe infantile‐onset leukoencephalopathy. Here, we report the case of a 17‐year‐old boy with compound heterozygous mutations in WARS2 (p.Trp13Gly, p.Ser228Trp) who presented with infantile‐onset, Levodopa‐responsive Parkinsonism at the age of 2 years. Analysis of patient‐derived dermal fibroblasts revealed decreased steady‐state WARS2 protein and normal OXPHOS content. Muscle mitochondrial studies suggested mitochondrial proliferation without obvious respiratory chain deficiencies at the age of 9 years. This case expands the phenotypic spectrum of WARS2 deficiency and emphasizes the importance of mitochondrial protein synthesis in the pathogenesis of Parkinsonism.

Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12

Every second year, the community experiment "Critical Assessment of Techniques for Structure Prediction" (CASP) is conducting an independent blind assessment of structure prediction methods, providing a framework for comparing the performance of different approaches and discussing the latest developments in the field. Yet, developers of automated computational modeling methods clearly benefit from more frequent evaluations based on larger sets of data. The "Continuous Automated Model EvaluatiOn (CAMEO)" platform complements the CASP experiment by conducting fully automated blind prediction assessments based on the weekly pre-release of sequences of those structures, which are going to be published in the next release of the PDB Protein Data Bank. CAMEO publishes weekly benchmarking results based on models collected during a 4-day prediction window, on average assessing ca. 100 targets during a time frame of 5 weeks. CAMEO benchmarking data is generated consistently for all participating methods at the same point in time, enabling developers to benchmark and cross-validate their method's performance, and directly refer to the benchmarking results in publications. In order to facilitate server development and promote shorter release cycles, CAMEO sends weekly email with submission statistics and low performance warnings. Many participants of CASP have successfully employed CAMEO when preparing their methods for upcoming community experiments. CAMEO offers a variety of scores to allow benchmarking diverse aspects of structure prediction methods. By introducing new scoring schemes, CAMEO facilitates new development in areas of active research, for example, modeling quaternary structure, complexes, or ligand binding sites.

Assessment of protein assembly prediction in CASP12

We present the results of the first independent assessment of protein assemblies in CASP. A total of 1624 oligomeric models were submitted by 108 predictor groups for the 30 oligomeric targets in the CASP12 edition. We evaluated the accuracy of oligomeric predictions by comparison to their reference structures at the interface patch and residue contact levels. We find that interface patches are more reliably predicted than the specific residue contacts. Whereas none of the 15 hard oligomeric targets have successful predictions for the residue contacts at the interface, six have models with resemblance in the interface patch. Successful predictions of interface patch and contacts exist for all targets suitable for homology modeling, with at least one group improving over the best available template for each target. However, the participation in protein assembly prediction is low and uneven. Three human groups are closely ranked at the top by overall performance, but a server outperforms all other predictors for targets suitable for homology modeling. The state of the art of protein assembly prediction methods is in development and has apparent room for improvement, especially for assemblies without templates.

Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology

Cellular processes often depend on interactions between proteins and the formation of macromolecular complexes. The impairment of such interactions can lead to deregulation of pathways resulting in disease states, and it is hence crucial to gain insights into the nature of macromolecular assemblies. Detailed structural knowledge about complexes and protein-protein interactions is growing, but experimentally determined three-dimensional multimeric assemblies are outnumbered by complexes supported by non-structural experimental evidence. Here, we aim to fill this gap by modeling multimeric structures by homology, only using amino acid sequences to infer the stoichiometry and the overall structure of the assembly. We ask which properties of proteins within a family can assist in the prediction of correct quaternary structure. Specifically, we introduce a description of protein-protein interface conservation as a function of evolutionary distance to reduce the noise in deep multiple sequence alignments. We also define a distance measure to structurally compare homologous multimeric protein complexes. This allows us to hierarchically cluster protein structures and quantify the diversity of alternative biological assemblies known today. We find that a combination of conservation scores, structural clustering, and classical interface descriptors, can improve the selection of homologous protein templates leading to reliable models of protein complexes.

Use of robotic colonoscopy in patients with previous incomplete colonoscopy

OBJECTIVE

Conventional colonoscopy (CC) is the gold standard to diagnostic and therapeutic approach to colon. However, in few cases, cecal intubation could fail due to colon anatomy, patient compliance and physician expertise. Endotics robotic colonoscopy is a novel, safe, mini-invasive modality to explore the entire colon. Our aim was to assess, in a retrospective study, Endotics ability of cecal intubation in all cases in which CC failed.

PATIENTS AND METHODS

Between January 2008 and December 2012, 276 Endotics robotic colonscopy examinations were performed at the Gastroenterology and Metabolic Diseases Unit of Pisa University Hospital, Pisa, Italy, in a series of consecutive patients who had undergone CC and failed cecal intubation.

RESULTS

We assessed the cecal intubation rate in 102 patients addressed to Endotics after previous incomplete CC. Overall, endotics system was successful in 93.1% of the incomplete conventional colonoscopy cases (95% performance).

CONCLUSIONS

Whenever the intended exploration of the entire colon with CC failed, the endotics robotic endoscopy represented a useful tool as it helped examine the entire colon in almost all cases.

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces generate reliable models without the need for complex software packages or downloading large databases. Here, we describe the latest version of the SWISS-MODEL expert system for protein structure modelling. The SWISS-MODEL template library provides annotation of quaternary structure and essential ligands and co-factors to allow for building of complete structural models, including their oligomeric structure. The improved SWISS-MODEL pipeline makes extensive use of model quality estimation for selection of the most suitable templates and provides estimates of the expected accuracy of the resulting models. The accuracy of the models generated by SWISS-MODEL is continuously evaluated by the CAMEO system. The new web site allows users to interactively search for templates, cluster them by sequence similarity, structurally compare alternative templates and select the ones to be used for model building. In cases where multiple alternative template structures are available for a protein of interest, a user-guided template selection step allows building models in different functional states. SWISS-MODEL is available at http://swissmodel.expasy.org/.

Extensor hallucis longus transfer as an alternative to split transfer of the tibialis anterior tendon to correct equinovarus foot in hemiplegic patients without overactivity of tibialis anterior

This study assessed if transfer of the extensor hallucis longus is a valid alternative treatment to split transfer of the tibialis anterior tendon in adult hemiplegic patients without overactivity of the tibialis anterior.

One group of 15 patients had overactivity of tibialis anterior in the swing phase, and underwent the split transfer. A further group of 14 patients had no overactivity of tibialis anterior, and underwent transfer of extensor hallucis longus. All patients had lengthening of the tendo Achillis and tenotomies of the toe flexors. All were evaluated clinically and by three-dimensional gait analysis pre- and at one year after surgery. At this time both groups showed significant reduction of disability in walking. Gait speed, stride length and paretic propulsion had improved significantly in both groups. Dorsiflexion in the swing phase, the step length of the healthy limb and the step width improved in both groups, but only reached statistical significance in the patients with transfer of the extensor hallucis longus. There were no differences between the groups at one year after operation.

When combined with lengthening of the tendo Achillis, transfer of the extensor hallucis longus can be a valid alternative to split transfer of the tibialis anterior tendon to correct equinovarus foot deformity in patients without overactivity of tibialis anterior.

Administration of type A botulinum toxin after total hip replacement

Pain after hip replacement is one of the most common problems during rehabilitation and is often the main obstacle in rehabilitation, even though it can often be controlled by localized cryotherapy and/or administration of analgesics. However, patients with positive anamnesis for hip arthritis and long-lasting pain may report persistence of symptoms for months after surgical intervention; often, in these patients, contractures and muscle retraction in the pelvic region are observed. The present study reports the case of a female patient who suffered from complications after total hip replacement (THR) for osteoarthritis. Due to severe pain in the gluteal region not responding to standard treatments the patient was unable to stand in an upright position or walk, so she was forced to stop the rehabilitation program. Treatment by injection of botulinum toxin type A (BTX-A) in the gluteus maximus muscle brought about the complete resolution of pain and functional recovery. The follow-up visits, carried out after 6 and 16 months, confirmed the complete healing of the patient. BTX-A has been shown to be effective in the treatment of painful localized contractures even in the absence of neurological lesions. Therefore, BTX-A could be a feasible option to treat painful localized contractures that do not respond to standard treatments. Further investigations are suggested to better identify appropriate dosages and the best inoculation schedule.

Comparison among Different Types, Dosages and Duration of Interferon Therapy in Chronic Hepatitis C

In an attempt to determine the best therapeutic protocol for the treatment of chronic hepatitis C with interferon (IFN), we reported our experience comparing the efficacy of IFN at the usual dose and duration, i.e. 3 million units (MU) three times weekly for 6 months, with the immediate and long-term effects of different types, dosages and duration of IFN therapy. 300 patients with chronic hepatitis C were randomly assigned to five groups of 60 subjects each and treated as follows: group A - recombinant IFN alpha (rIFNalpha) 3MU three times weekly for 6 months; group B - rIFNalpha 6MU three times weekly for 6 months; group C - rIFNalpha 3MU 3 times weekly for 12 months; group D - lymphoblastoid IFN (L-IFN) 6MU three times weekly for 6 months; group E - L-IFN 3MU three times weekly for 12 months. The diagnosis of hepatitis was based on clinical, serological and histological data in all patients. A 'biochemical response' was defined as the normalisation of alanine aminotransferase (ALT) values, and a 'complete response' as the normalisation of ALT with disappearance of serum hepatitis C virus (HCV)-RNA. A 'sustained response' was defined as the persistence of ALT normalisation and undetectable viraemia 2 years after the end of treatment. The five groups were homogeneous. The incidence of dropouts was 8%, and IFN treatment was interrupted for adverse effects in 11% of the patients. In group A, 55% of the patients showed a 'biochemical response' and 31% of the subjects demonstrated a 'complete response'. In group B, a 'biochemical response' was observed in 61% and a 'complete response' in 36% of the cases. In group C, 77% of the subjects showed a 'biochemical response', with a 'complete response' seen in 40%. In group D, we observed a 'biochemical response' in 55% of the patients and a 'complete response' in 33%. In group E, 79% of the subjects had a 'biochemical response', and a 'complete response' was seen in 38%. At the end of the treatment-free follow-up the percentage of patients with a sustained response was 24% in group A, 28% in group B, 35% in group C, 27% in group D and 33% in group E. Therefore, a longer period of IFN treatment seems to provide higher percentages of sustained response than the usual 6-month duration, independently of the type of IFN. Moreover, the patients treated with a higher dosage (6MU 3 times weekly) for 6 months showed a slightly better sustained response rate compared with the usual dose. In conclusion, even if the differences among the response rates in the five groups were not statistically significant, we recommend a 12-month regimen, possibly using higher dosages at least in the first 4 to 6 months of treatment.

Pulmonary hypertension in primary Sjögren’s syndrome: report of a case and review of the literature

A 61-year-old female with a history of vaginal dryness, Raynaud's phenomenon, xerostomia and xerophthalmia presented with exertional dyspnoea and weakness. Laboratory and instrumental examinations enabled us to make the diagnosis of primary Sjögren's syndrome, while cardiologic and imaging investigations evidenced isolated pulmonary hypertension and ruled out pulmonary fibrosis. Oral anticoagulant and furosemide therapy induced a partial improvement of exertional dyspnoea and weakness.

Encephalopathy associated with Hashimoto's thyroiditis: an additional case

A 35-year-old female with a history of Hashimoto's thyroiditis (HT) presented with episodic dysphasia and a burst of axial jerks with abdominal muscle contraction and asymmetric blepharospasm as manifestations of encephalopathy associated with HT. Brain magnetic resonance imaging (MRI) showed scattered supratentorial white matter hyperintense T2 foci. Brain single photon emission computerized tomography (SPECT) demonstrated a cortical hypoperfusion in the upper frontal and parietal areas. Corticosteroid therapy induced a rapid improvement of the clinical picture.

Long-term maintenance treatment in ulcerative colitis: a 10-year follow-up

BACKGROUND

With the extensive use of mesalamine, the natural history of ulcerative colitis is probably changed.

AIM

To evaluate the relapse rate and the duration of remission in patients with ulcerative colitis on maintenance treatment with mesalamine.

PATIENTS AND METHODS

Enrolled in the study were 95 patients divided into 4 groups according to macroscopic location of the disease and treated with the same therapy starting from the date of enrolment. Patients in all 4 groups were followed-up until relapse occurred. The disease activity was evaluated by the Clinical Activity Index and Endoscopic Index. Patients suitable for recruitment showed a Clinical Activity Index and Endoscopic Index lower than 6 and 4, respectively. The patients with ulcerative pancolitis or left-sided colitis were treated with 1.6 g/day while the cases with proctosigmoiditis or proctitis were treated with 5-acetylsalicylic acid enemas 4 g/day Each patient was evaluated with clinical and endoscopic assessment at a 6-month interval. Relapse was defined as an increase in Clinical Activity Index and Endoscopic Index, of more than 6 and 4, respectively.

RESULTS

Five patients dropped-out. All enrolled patients showed a clinical and/or endoscopic relapse within 10 years, the majority 2 or 3 years after diagnosis: pancolitis and left-sided colitis within 2-3 years and patients with distal colitis within 9-10 years.

CONCLUSIONS

A relapse was observed in most cases within 3 years, and in all recruited patients within a space of ten years. The extent of the disease in the colon is an important prognostic factor, as patients with distal colitis showed a lesser tendency to relapse.

Suicidal poisoning with barium chloride

A 49-year-old male pharmacist suffering from depression phoned the emergency services telling of how he had ingested barium chloride. He was found semicomatose in bed and resuscitation attempts were to no avail and he died at the scene. A white plastic container labelled "Barium chloride... Poison", and a book with a writing on a blank page... "give sulphate... SO(4)" were found. At autopsy, 1l of whitish-yellow fluid was found in the stomach. Autopsy barium levels were: blood 9.9mg/l; bile 8.8mg/l; urine 6.3mg/l; gastric 10.0g/l. Cause of death was given as cardiorespiratory arrest due to barium chloride poisoning. The issue of barium toxicity in a variety of itatrogenic and non itatrogenic situation is discussed together with the two only other cases of suicidal barium ingestion, and the feasibility of early intervention at the scene by an emergency team.

Crohn disease of the small bowel: spiral CT evaluation after oral hyperhydration with isotonic solution

PURPOSE

Our aim was to evaluate the accuracy of spiral CT study of small-bowel Crohn disease with use of oral hyperhydration with isoosmotic solution.

METHOD

We prospectively analyzed 33 consecutive patients and 10 control subjects with spiral CT after oral administration of 2,000 ml of polyethylene glycol electrolyte-balanced solution. The CT diagnoses were compared with the results of conventional radiologic oral barium examination (33 cases), ileum colonoscopy (8 cases), and surgery (4 cases).

RESULTS

The final diagnoses were Crohn disease (14 cases), no small-bowel disease (16 cases), cancer of ileocecal valve (1 case), carcinosis of mesenteric root (1 case), and intestinal lymphangiectasia (1 case). In the control group, no abnormalities of the small bowel were found. The sensitivity of spiral CT was 85.7%, specificity 100%, positive predictive value 100%, negative predictive value 90%, and diagnostic accuracy 93.9%.

CONCLUSION

Our method allowed adequate distension of the small bowel for spiral CT studies, thus resulting in a safe and effective alternative to small-bowel spiral CT enema, which can be used in patients that refuse the nasojejunal balloon catheter.

High-dose interferon plus ribavirin in chronic hepatitis C not responding to recombinant alpha-interferon

BACKGROUND

Recently, the combination treatment of recombinant alpha-interferon plus ribavirin has been proposed for chronic hepatitis C patients unresponsive to previous therapy with recombinant alpha-interferon alone.

AIM

To determine the effectiveness of the combination therapy for the re-treatment of chronic hepatitis C patients unresponsive to previous interferon therapy. Immediate and long-term follow-up data are reported.

PATIENTS AND METHODS

A series of 100 patients with chronic hepatitis C not responding to recombinant alpha-interferon 3 MU tiw, were randomly assigned to two groups of 50 patients each: Group A, treated with recombinant alpha-interferon therapy for an additional six months but at a double dosage (6 MU tiw) in association with ribavirin. Group B, same treatment as group A but without ribavirin. All patients responsive to therapy were then followed-up for at least 12 months. At the end of the treatment and at the end of the follow-up period, we distinguished between complete responses (return to normal of alanine aminotransferase with undetectable serum HCV-RNA] and biochemical responses (return to normal of alanine aminotransferase still with detectable viraemia).

RESULTS

Side-effects were observed only in patients treated with recombinant alpha-interferon plus ribavirin: 12% discontinued the therapy due to haemolytic anaemia. In group A, the percentages of end-of-treatment complete response, end-of-treatment biochemical response, sustained complete response, and sustained biochemical response, were 38%, 20%, 8%, and 14%, respectively, whilst in group B, these percentages were 12%, 16%, 6%, and 16%, respectively.

CONCLUSION

The results indicate that in patients with chronic hepatitis C unresponsive to previous recombinant alpha-interferon therapy, re-treatment with higher recombinant alpha-interferon doses, either alone or in combination with ribavirin, lead to mild long-term benefit. However, the satisfactory end of treatment complete response in group A suggests that a significant percentage of patients are sensitive to the combination therapy; and that a more aggressive therapeutic protocol in this selected subset of patients could result in a larger number of long-lasting responses leading, in turn, to a more favourable cost-effect ratio.

Does the initial location of Crohn's disease have an influence on the time-to-relapse in patients under maintenance treatment with oral mesalamine?

The aim of this study was to determine the possible influence of the initial location of Crohn's disease (CD) on the time-to-relapse in patients with quiescent CD treated only with oral mesalamine (5-ASA). We divided 74 consecutive patients in clinical remission into three groups according to the initial location of CD. Group A consisted of 30 cases with an ileal location; group B, 18 with ileocolonic location; and group C, 26 with a colonic location. The patients entered the study if they were in clinical and endoscopic remission for at least 3 months. Relapse was defined by CD Activity Index > or = 150, CD Endoscopic Index of Severity > or =4, and by an abnormal increase of C-reactive protein, white blood cell count, and erythrocyte sedimentation rate; moreover, if it was confirmed by x-ray and/or endoscopy. Time-to-relapse was defined as the interval between the date of enrollment and the date of relapse. The patients with an ileal location showed a relapse within 5 years, with a time-to-relapse of 1 year in 26% of cases, 2 years in 85%, 3 years in 92%, and 4 years in 96%. The patients with ileocolonic location showed a relapse within 4 years, with time-to-relapse of 1 year in 39% of cases, 2 years in 89%, and 3 years in 94%. The cases with a colonic location showed a relapse within 6 years, with time-to-relapse of 1 year in 33% of cases, 2 years in 71%, 3 years in 79%, and 4 years in 87%. Surgical treatment was necessary in 37% of the cases with an ileal location, in 44% with ileocolonic location, and 17% with a colonic location. In conclusion, even if our data lack a statistical significance, we have found that the initial anatomic involvement is not a valid parameter to predict the relapse risk in a homogeneous group under continuous treatment with oral 5-ASA, although ileocolonic location seems to have a more aggressive course.

Interferon plus ribavirin in chronic hepatitis C non-responders to recombinant alpha-interferon

The aim of this study was to evaluate the most appropriate therapeutic protocol for patients with chronic hepatitis C not responding to a previous course of recombinant interferon alpha-2b (rIFN). Sixty patients were randomly assigned to two groups of 30 subjects each: group A was treated with double dose of the same type of rIFN (6 MU t.i.w.) plus ribavirin for 6 months; group B was treated with the same rIFN dose and duration as group A, but without ribavirin. An end of treatment complete response (ETCR) was defined as alanine transaminase (ALT) normalization with undetectable serum HCV-RNA at the end of the treatment, while an end of treatment biochemical response (ETBR) as ALT normalization with still detectable viraemia. The two groups were homogeneous. The patients with ETCR or ETBR were than followed-up for at least 1 year. A sustained biochemical response (SBR) was defined as the persistence of normal ALT with still detectable viraemia after a 12-month follow-up, and a sustained complete response (SCR) as the persistence of normal ALT with undetectable viraemia. Side-effects were only observed in patients treated with rIFN plus ribavirin: four cases (13%) discontinued the therapy owing to haemolytic anaemia. Combination therapy induced an ETCR in 11 patients (37%) and an ETBR in six (20%), while a SCR was observed in two subjects (7%) and a SBR in four (13%). The use of a double dose of rIFN alone obtained an ETCR in four cases (13%) and an ETBR in five (17%), with a SCR in two (7%) and a SBR in three (10%). Hence, both combination therapy and single treatment with higher rIFN doses were unable to show statistically significant long-term benefits in patients with chronic hepatitis C resistant to a previous course of rIFN treatment.

Clinical efficacy and tolerability of a steady dosage schedule of local nasal immunotherapy. Results of preseasonal treatment in grass pollen rhinitis

BACKGROUND

Local nasal immunotherapy (LNIT) is an effective and safe alternative to conventional subcutaneous immunotherapy. A specific nasal provocation test (SNPT) could be used to indicate the optimal subclinical dose to carry out LNIT.

OBJECTIVE

We hypothesize that LNIT could be carried out with only one predefined dose for all patients, so we have evaluated the efficacy and the tolerability of LNIT administered at steady dosages in patients with seasonal allergic rhinitis.

METHODS

Twenty grass pollen-sensitized patients suffering from seasonal allergic rhinitis were studied in a randomized, double-blind, placebo-controlled trial. The treatment was carried out according to a schedule based on the administration of a steady subclinical dosage of the allergenic extract, selected on the basis of the sensitivity threshold of the SNPT. The patients were divided into two groups of 10 people each, which were treated either with grass pollen extract in a hydroglyceric solution or with placebo.

RESULTS

During the peak pollen period, with regard to the placebo (P) group, in the grass treated (GT) group a significant decrease of both nasal symptoms (P = .021) and consumption of antihistamines (P = 0.047) was found. Furthermore, only in the GT group was the provocative dose assessed by the SNPT significantly lower (P = .049) at the end of the treatment. In this group of patients an inverse correlation between such provocative dose and the nasal symptom score reported during the peak pollen period was also evidenced (r = 0.708; P = .038). Adverse reactions to LNIT were mild, rare, and did not interfere with the completion of the therapeutic schedule.

CONCLUSIONS

Our study indicates that LNIT, when administered at steady dosages, may be proposed as a treatment for grass pollen seasonal allergic rhinitis as it appears to be effective and well tolerated.

Colonic disease in cirrhotic patients with portal hypertension: an endoscopic and clinical evaluation

Fifty cirrhotic patients with portal hypertension but without colonic or systemic disease underwent lower gastrointestinal endoscopy in order to investigate the effects, if any, of portal hypertension on the colon. Fifty patients without liver or systemic disease, examined by colonoscopy because of irritable bowel syndrome in the same period served as controls. Rectosigmoid varices were observed in 34% of the cirrhotic patients and 2% of the controls. Hemorrhoids were observed in 70% of the cirrhotic patients and 48% of the controls. Multiple vascular-appearing lesions were found in 16% of the cirrhotic patients and 6% of the controls. Nonspecific inflammatory changes were noted in 10% of the cirrhotic patients and 4% of the controls. Simultaneous presence, in the same patient, of rectosigmoid varices, hemorrhoids, multiple vascular-appearing lesions, and nonspecific inflammatory changes, was observed in only five (10%) of the cirrhotic patients. We found polyps in 12% of the cirrhotic patients and 14% of the controls, and a malignant tumor in 4% of the cirrhotic patients. The patients with normal colonoscopic findings were 8% of the cirrhotic patients and 36% of the controls. All patients and controls were followed up for 1 year; there was no gastrointestinal hemorrhage among controls, whereas 34% of the cirrhotic patients had an upper gastrointestinal hemorrhage (88% from esophageal varices, 12% from the stomach) and 4% had a lower gastrointestinal hemorrhage (one from rectosigmoid varices and one from nonspecific inflammatory lesions). Colonic lesions were significantly more frequent in the cirrhotic patients (92%) than in the control group (64%); however, such lesions did not seem specific to the disease and were not statistically correlated with the degree of esophageal varices by Child's grading, the etiology of cirrhosis, or the bleeding risk from the lower gastrointestinal tract.

On the employment of lambda carrageenan in a matrix system. III. Optimization of a lambda carrageenan-HPMC hydrophilic matrix

The lambda carrageenan/HPMC ratio in matrix tablets has been optimized in order to obtain pH-independent release profiles of chlorpheniramine maleate, a freely soluble drug. Release profiles in acidic (pH1.2) and neutral (pH 6.8) media were fitted according to the Weibull and the power law models. Model independent parameters(t50% and the percentage of drug released after 2 h) were also calculated. The Weibull parameters were found suitable to describe the dependence of the release profiles on matrix composition. Preparation and testing of the optimized formulation showed linear and pH-independent release profiles lasting about 24 h, in good accordance with the values predicted by the optimization procedure.

Evaluation of clinical patterns in ulcerative colitis: a long-term follow-up

The aim of this prospective research was to compare, in a seven-year follow-up, the clinical outcome of ulcerative pancolitis with that of non-progressive ulcerative colitis. The activity of the disease was evaluated by a Clinical Activity Index and an Endoscopic Index. Of 112 cases of ulcerative colitis observed, 95 showed no change in extent and were studied as examples of non-progressive UC, and in this group the extension of the disease was: pancolitis in 19%, left-sided colitis in 39%, proctosigmoiditis in 17% and proctitis in 25%. A colectomy had to be performed in 5%. None of the enrolled cases developed a cancer during the follow-up. The patients with ulcerative pancolitis or left-sided colitis were treated with 5-ASA 1.6 g/day in a delayed-release formulation, while the cases with proctosigmoiditis or proctitis were treated with 5-ASA enemas 4 g/day. The cases with more than one relapse/year were 39%. The proportion of patients with only one relapse/year was 53%. The patients with steady remission for all the seven years of the trial were only 8%, but with a statistically significant difference between the groups with initial diagnosis of proctosigmoiditis or proctitis and the group with initial diagnosis of pancolitis or left-sided colitis (12% versus 5%). Among the cases with continuous remission, 37% showed colonic alterations, with an endoscopic score higher than 4 but a clinical score less than 6. Side-effects were observed in 6% patients but without treatment withdrawal. Non-progressive ulcerative colitis throughout the colon has a relatively good prognosis which seems to be independent of the location of the disease, even if we have found a statistically significant higher percentage of cases with steady remission among the patients with more distal disease.

[Cervical pain and proprioceptive sensitivity]

With the intent of estimating the proprioceptive sensitivity of the cervical rachis, the Authors subjected 17 healthy volunteers and 20 patients suffering from various cervical disorders to a clinical head positioning test, which was previously experimented upon by several french Authors was modified under certain aspects by our equipe. The test, consists in flexion and extension of the head after maximal rotations to the left and right, then repositioning the head at the starting point "0" which corresponds to the crossing point of two orthogonal axis of a target. The positions are marked on the target by a laser beam situated on the helmet worn by the subject undergoing testing. The results obtained corresponding to the errors committed regarding point "0", permit us to confirm the reliability of the test and significant definitions between the control group and the patients suffering from cervical disorders.

Dissolution enhancement of an insoluble drug by physical mixture with a superdisintegrant: optimization with a simplex lattice design

The aim of the present work was to optimize a tablet formulation containing a physical mixture of a practically insoluble drug (prednisone) with a superdisintegrant (croscarmellose sodium) and two filler-binders characterized by differing water solubility (dicalcium phosphate dihydrate and anhydrous beta-lactose). Crushing strength, disintegration, and dissolution were measured for 10 formulations distributed over a factor space according to a simplex lattice design for a special cubic model. Multiple linear regression analysis was used to assess the best fit for each variable. The model predicted that increasing the amount of disintegrant to a critical amount (50%) would result in reduced disintegration time for dicalcium phosphate/beta-lactose ratios > 0.3, no changes in disintegration time for ratios < 0.3, and for all ratios an improvement in dissolution at 10 min. Crushing strength values of dicalcium phosphate increased with increasing disintegration concentration but not for beta-lactose tablets. The physical mixture of a practically insoluble drug with a superdisintegrant was confirmed as a valid approach to the improvement of dissolution, even in presence of other components. The solubility of the filler-binders influenced the minimum amount of disintegrant needed; when a soluble diluent was used, the amount of disintegrant required was reduced.