Prioritizing Chemicals for Risk Assessment Using Chemoinformatics: Examples from the IARC Monographs on Pesticides.

Environ Health Perspect. 2016 May 10;

Authors: Guha N, Guyton KZ, Loomis D, Barupal DK

Abstract
BACKGROUND: Identifying cancer hazards is the first step towards cancer prevention. The IARC Monographs Programme, which has evaluated nearly 1000 agents for carcinogenic potential since 1971, typically selects agents for hazard identification on the basis of public nominations, expert advice, published data on carcinogenicity, and public health importance.
OBJECTIVES: Here we present a novel and complementary strategy for identifying agents for hazard evaluation using chemoinformatics, database integration and automated text mining.
DISCUSSION: To inform selection among a broad range of pesticides nominated for evaluation, we identified and screened nearly 6000 relevant chemical structures, thereafter systematically compiled information on 980 pesticides, creating chemical similarity network maps that allowed cluster visualization by chemical similarity, pesticide class, and publicly available information concerning cancer epidemiology, cancer bioassays, and carcinogenic mechanisms. For the IARC Monograph meetings that took place in March and June 2015, this approach supported high priority evaluation of glyphosate, malathion, parathion, tetrachlorvinphos, diazinon, DDT, lindane, and 2,4-D.
CONCLUSIONS: This systematic approach, accounting for chemical similarity and overlaying multiple data sources, can be used by risk assessors as well as researchers to systematize, inform and increase efficiency in selecting and prioritizing agents for hazard identification, risk assessment, regulation or further investigation. This approach could be extended to an array of outcomes and agents, including occupational carcinogens, drugs, and foods.

PMID: 27164621 [PubMed - as supplied by publisher]

Convex biclustering.

Biometrics. 2016 May 10;

Authors: Chi EC, Allen GI, Baraniuk RG

Abstract
In the biclustering problem, we seek to simultaneously group observations and features. While biclustering has applications in a wide array of domains, ranging from text mining to collaborative filtering, the problem of identifying structure in high-dimensional genomic data motivates this work. In this context, biclustering enables us to identify subsets of genes that are co-expressed only within a subset of experimental conditions. We present a convex formulation of the biclustering problem that possesses a unique global minimizer and an iterative algorithm, COBRA, that is guaranteed to identify it. Our approach generates an entire solution path of possible biclusters as a single tuning parameter is varied. We also show how to reduce the problem of selecting this tuning parameter to solving a trivial modification of the convex biclustering problem. The key contributions of our work are its simplicity, interpretability, and algorithmic guarantees-features that arguably are lacking in the current alternative algorithms. We demonstrate the advantages of our approach, which includes stably and reproducibly identifying biclusterings, on simulated and real microarray data.

PMID: 27163413 [PubMed - as supplied by publisher]

BioCreative V CDR task corpus: a resource for chemical disease relation extraction.

Database (Oxford). 2016;2016

Authors: Li J, Sun Y, Johnson RJ, Sciaky D, Wei CH, Leaman R, Davis AP, Mattingly CJ, Wiegers TC, Lu Z

Abstract
Community-run, formal evaluations and manually annotated text corpora are critically important for advancing biomedical text-mining research. Recently in BioCreative V, a new challenge was organized for the tasks of disease named entity recognition (DNER) and chemical-induced disease (CID) relation extraction. Given the nature of both tasks, a test collection is required to contain both disease/chemical annotations and relation annotations in the same set of articles. Despite previous efforts in biomedical corpus construction, none was found to be sufficient for the task. Thus, we developed our own corpus called BC5CDR during the challenge by inviting a team of Medical Subject Headings (MeSH) indexers for disease/chemical entity annotation and Comparative Toxicogenomics Database (CTD) curators for CID relation annotation. To ensure high annotation quality and productivity, detailed annotation guidelines and automatic annotation tools were provided. The resulting BC5CDR corpus consists of 1500 PubMed articles with 4409 annotated chemicals, 5818 diseases and 3116 chemical-disease interactions. Each entity annotation includes both the mention text spans and normalized concept identifiers, using MeSH as the controlled vocabulary. To ensure accuracy, the entities were first captured independently by two annotators followed by a consensus annotation: The average inter-annotator agreement (IAA) scores were 87.49% and 96.05% for the disease and chemicals, respectively, in the test set according to the Jaccard similarity coefficient. Our corpus was successfully used for the BioCreative V challenge tasks and should serve as a valuable resource for the text-mining research community.Database URL: http://www.biocreative.org/tasks/biocreative-v/track-3-cdr/.

PMID: 27161011 [PubMed - in process]

Clinical Management of Head and Neck Cancer Cases: Role of Pharmacogenetics of CYP2 and GSTs.

Oncol Res Treat. 2016;39(4):221-6

Authors: Ruwali M, Dhawan A, Pant MC, Rahman Q, Khurana SM, Parmar D

Abstract
Head and neck squamous cell carcinoma (HNSCC) describes a wide range of malignant tumors which originate in the upper aerodigestive tract and have a multifactorial origin involving both genetic and lifestyle risk factors. The clinical management of head and neck cancer involves surgery, radiotherapy, and chemotherapy. With the advances in treatment strategies for HNSCC, newer targeted therapies are adding to the progress already achieved in the multimodality management of patients although the problems of differences in drug response and adverse drug reactions are still grave concerns. Cancer pharmacogenomics has fast emerged as a new and promising field for the early identification of genetic markers that can predict drug response or toxicity. This could greatly help in identifying genetic markers useful for the selection of optimal drugs, dose, and treatment duration on an individual basis resulting in improved drug efficacy and decreased toxicity. This review focuses on the various treatment modalities available for the clinical management of HNSCC followed by a description of the contribution of genetic variations to chemotherapeutic toxicity and response. Furthermore, studies addressing the association of genetic variants of drug-metabolizing enzymes with treatment response in head and neck cancer are also discussed.

PMID: 27160276 [PubMed - in process]

Recent advances in large-scale protein interactome mapping.

F1000Res. 2016;5

Authors: Mehta V, Trinkle-Mulcahy L

Abstract
Protein-protein interactions (PPIs) underlie most, if not all, cellular functions. The comprehensive mapping of these complex networks of stable and transient associations thus remains a key goal, both for systems biology-based initiatives (where it can be combined with other 'omics' data to gain a better understanding of functional pathways and networks) and for focused biological studies. Despite the significant challenges of such an undertaking, major strides have been made over the past few years. They include improvements in the computation prediction of PPIs and the literature curation of low-throughput studies of specific protein complexes, but also an increase in the deposition of high-quality data from non-biased high-throughput experimental PPI mapping strategies into publicly available databases.

PMID: 27158474 [PubMed]

Dental and dentofacial problems in a female child with Toriello-Carey -syndrome: changes in 3 years.

Spec Care Dentist. 2016 May 9;

Authors: Tirali RE, İlhan B, Şar Ç, Çehreli SB

Abstract
Toriello-Carey syndrome is a rare disease whose clinical manifestations are midline facial defects, laryngeal and pharyngeal hypoplasia, cardiac defect, and corpus callosum hypoplasia. Literature states that clinical manifestations are more evident in males. This is the second report in the literature which describes the dental and dentofacial -features in an 8-year-old female patient with Toriello-Carey syndrome.

PMID: 27159668 [PubMed - as supplied by publisher]

Paraneoplastic stiff person syndrome: Inpatient rehabilitation outcomes of a rare disease from two cancer rehabilitation programmes.

J Rehabil Med. 2016 May 3;

Authors: Robinson Smith S, Fu JB

Abstract
Paraneoplastic stiff person syndrome is a rare, but debilitating, manifestation of cancer, characterized by painful extremities, truncal and facial spasms. The resultant functional impairment may necessitate comprehensive rehabilitation and symptom management. This case series describes the acute inpatient rehabilitation courses of 2 patients at different tertiary care referral cancer rehabilitation programmes, including work-up and diagnosis, medical management of symptoms, and functional outcomes. Both patients had a reduction in symptom burden and an improvement in motor function as a result of multidisciplinary acute inpatient rehabilitation.

PMID: 27157044 [PubMed - as supplied by publisher]

Chronic recurrent multifocal osteomyelitis: a rare skeletal disorder.

BMJ Case Rep. 2015;2015

Authors: Aygun D, Barut K, Camcioglu Y, Kasapcopur O

Abstract
Chronic recurrent multifocal osteomyelitis (CRMO) is a rare non-infectious inflammatory bone disease of unknown aetiology. CRMO mainly affects the metaphyses of long bones and spine in children and young adolescents. It presents with recurrent episodes of bone pain and fever, resembling bacterial osteomyelitis, but cultures of lesions are sterile and it is unresponsive to antibiotic therapy. We report a case of a 3-year-old boy diagnosed with CRMO, who was initially treated for bacterial osteomyelitis, and received prolonged antibiotic therapy for chronic pain, and swelling of mandible and ulna. CRMO should be kept in mind in the differential diagnosis of chronic bone pain and osteomyelitis unresponsive to antibiotic treatment.

PMID: 26307646 [PubMed - indexed for MEDLINE]

Report on the EUROMAC McArdle Exercise Testing Workshop, Madrid, Spain, 11-12 July 2014.

Neuromuscul Disord. 2015 Sep;25(9):739-45

Authors: Quinlivan R, Lucia A, Scalco RS, Santalla A, Pattni J, Godfrey R, Marti R, Workshop Participants

PMID: 26159598 [PubMed - indexed for MEDLINE]

Breast: Sezary Syndrome: A Unique Presentation.

Breast J. 2015 Jul-Aug;21(4):423-7

Authors: Bedayat A, Mirzabeigi M, Yu H, Hultman R, MacMaster S

Abstract
Sezary syndrome is a subtype of cutaneous T cell lymphoma which usually presents as generalized skin disease with erytheroderma. Distal organ involvement is rare and is usually a late finding in the course of the disease. Breast involvement is extremely rare. Herein, we present a case report of a patient whose initial presentation involved an intramammary lymph node prior to the onset of more characteristic skin disease. Sezary syndrome was confirmed by cythopathologic findings.

PMID: 25939954 [PubMed - indexed for MEDLINE]

Activation of sirtuin 1 as therapy for the peroxisomal disease adrenoleukodystrophy.

Cell Death Differ. 2015 Nov;22(11):1742-53

Authors: Morató L, Ruiz M, Boada J, Calingasan NY, Galino J, Guilera C, Jové M, Naudí A, Ferrer I, Pamplona R, Serrano M, Portero-Otín M, Beal MF, Fourcade S, Pujol A

Abstract
Oxidative stress and mitochondrial failure are prominent factors in the axonal degeneration process. In this study, we demonstrate that sirtuin 1 (SIRT1), a key regulator of the mitochondrial function, is impaired in the axonopathy and peroxisomal disease X-linked adrenoleukodystrophy (X-ALD). We have restored SIRT1 activity using a dual strategy of resveratrol treatment or by the moderate transgenic overexpression of SIRT1 in a X-ALD mouse model. Both strategies normalized redox homeostasis, mitochondrial respiration, bioenergetic failure, axonal degeneration and associated locomotor disabilities in the X-ALD mice. These results indicate that the reactivation of SIRT1 may be a valuable strategy to treat X-ALD and other axonopathies in which the control of redox and energetic homeostasis is impaired.

PMID: 25822341 [PubMed - indexed for MEDLINE]

Use of Pharmacogenomics and Biomarkers in the Development of New Drugs for Alzheimer Disease in Japan.

Clin Ther. 2015 Aug;37(8):1627-31

Authors: Otsubo Y

Abstract
PURPOSE: Pharmacogenomics (PGx) and biomarkers have been utilized for improving the benefit/risk ratios of drugs and the efficiency of drug development. In the development of drugs for Alzheimer disease (AD), a number of clinical trials have failed to demonstrate clinical efficacy. To overcome this circumstance, the importance of using PGx/biomarkers for enhancing recruitment into clinical trials and for evaluating the efficacy of treatments has been increasingly recognized. In this article, the current status and examples of the use of PGx/biomarkers in Japan for drug development are explained.
METHODS: Guidelines, notifications, and administrative notices related to PGx/biomarkers were downloaded from the Web sites of the Pharmaceuticals and Medical Devices Agency (PMDA), the US Food and Drug Administration, and the European Medicines Agency. Data from clinical studies of AD drugs were obtained from the review reports of the PMDA. To analyze the current status of the use of PGx/biomarkers in Japan, "Issues to Consider in the Clinical Evaluation and Development of Drugs for Alzheimer's Disease (Interim Summary)" was also downloaded from PMDA Web site.
FINDINGS: There are 2 major measures of utilizing PGx/biomarkers for drug development: (1) biomarker qualification and (2) companion diagnostics. Recently, the PMDA issued a number of guidelines and notifications for their practical use. Although examples of qualified PGx/biomarkers and approved companion diagnostics are limited at present, it is expected that the use of PGx/biomarkers for the development of drugs against AD would increase.
IMPLICATIONS: For promoting the use of PGx/biomarkers in the development of drugs against AD, PGx/biomarkers should be qualified as early as possible. To that end, accumulating data on PGx/biomarkers from nonclinical or clinical trials and the concurrent development of reliable diagnostics in the early stage of the development process are indispensable. It is important to strengthen collaboration among the academia, industries, and regulatory agencies, followed by the establishment of an effective guideline in the area of AD.

PMID: 25963998 [PubMed - indexed for MEDLINE]

The Contribution of Transcriptomics to Biomarker Development in Systemic Vasculitis and SLE.

Curr Pharm Des. 2015;21(17):2225-35

Authors: Flint SM, McKinney EF, Lyons PA, Smith KG

Abstract
A small but increasing number of gene expression based biomarkers are becoming available for routine clinical use, principally in oncology and transplantation. These underscore the potential of gene expression arrays and RNA sequencing for biomarker development, but this potential has not yet been fully realized and most candidates do not progress beyond the initial report. The first part of this review examines the process of gene expression- based biomarker development, highlighting how systematic biases and confounding can significantly skew study outcomes. Adequate validation in an independent cohort remains the single best means of protecting against these concerns. The second part considers gene-expression based biomarkers in Systemic Lupus Erythematosus (SLE) and systemic vasculitis. The type 1 interferon inducible gene signature remains by far the most studied in autoimmune rheumatic disease. While initially presented as an objective, blood-based biomarker of active SLE, subsequent research has shown that it is not specific to SLE and that its association with disease activity is considerably more nuanced than first thought. Nonetheless, it is currently under evaluation in ongoing trials of anti-interferon therapy. Other candidate markers of note include a prognostic CD8+ T-cell gene signature validated in SLE and ANCA-associated vasculitis, and a disease activity biomarker for SLE derived from modules of tightly correlated genes.

PMID: 25771200 [PubMed - indexed for MEDLINE]

Providing family-centred care for rare diseases in maternity services: Parent satisfaction and preferences when dysmelia is identified.

Women Birth. 2016 May 4;

Authors: Johnson J, Adams-Spink G, Arndt T, Wijeratne D, Heyhoe J, Taylor P

Abstract
PROBLEM AND BACKGROUND: Dysmelia is usually detected prenatally or postnatally in maternity services. The provision of family-centred care for parents at the time of initial diagnosis is crucial to facilitate decision making, access to appropriate services, and the provision of parental care-giving, but no research has investigated parent experiences or preferences in this population.
AIMS: The current research aimed to address this by investigating satisfaction with service, occurrence of signposting and preferences in this group.
METHODS: Two online surveys were conducted. In the first survey (n=417), parents reported whether they were offered signposting information and their level of satisfaction with the service they received when initially diagnosed. In the second survey (n=130), a subgroup of participants who completed the first survey reported their preferences for signposting and health service access after diagnosis.
FINDINGS: On average, participants were less than satisfied with the service they received and only 27% were offered signposting information. Satisfaction was higher amongst parents who had been offered signposting information. 91% of parents said they would have wanted signposting information and 67% would have wanted access to a support group.
CONCLUSIONS: There is a need to improve the family-centeredness of care when dysmelia is identified. Offering signposting information to relevant third-sector organisations may increase parent satisfaction and address parent preferences. These findings could have implications for parents of children with other rare diseases identified in maternity services.

PMID: 27156021 [PubMed - as supplied by publisher]

[Pulmonary MALT lymphoma and paraneoplastic syndromes].

Rev Mal Respir. 2016 May 4;

Authors: Monge E, Coolen-Allou N, Mascarel P, Gazaille V

Abstract
INTRODUCTION: Primary pulmonary lymphoma is a rare disease; diagnosis is often delayed because of atypical clinical presentation and slow progression.
OBSERVATION: A 42-year-old woman consulted because of haemoptysis. Chest CT-scan showed multiple nodular calcified masses. A lung biopsy led to the diagnosis of pulmonary amyloidosis with pulmonary MALT lymphoma (mucosa-associated lymphoid tissue). The patient developed two paraneoplastic syndromes: a hypertrophic osteoarthropathy and mucinosis.
CONCLUSION: Multiple nodular amyloidosis can be a mode of presentation for pulmonary lymphoma. Paraneoplastic syndromes must be systematically considered and can help in early diagnosis of the disease and its relapse.

PMID: 27155897 [PubMed - as supplied by publisher]

Putting the Genome in Context: Gene-Environment Interactions in Type 2 Diabetes.

Curr Diab Rep. 2016 Jul;16(7):57

Authors: Franks PW, Paré G

Abstract
The genome is often the conduit through which environmental exposures convey their effects on health and disease. Whilst not all diseases act by directly perturbing the genome, the phenotypic responses are often genetically determined. Hence, whilst diseases are often defined has having differing degrees of genetic determination, genetic and environmental factors are, with few exceptions, inseparable features of most diseases, not least type 2 diabetes. It follows that to optimize diabetes, prevention and treatment will require that the etiological roles of genetic and environmental risk factors be jointly considered. As we discuss here, studies focused on quantifying gene-environment and gene-treatment interactions are gathering momentum and may eventually yield data that helps guide health-related choices and medical interventions for type 2 diabetes and other complex diseases.

PMID: 27155607 [PubMed - as supplied by publisher]

Polypharmacology in Drug Development: A Minireview of Current Technologies.

ChemMedChem. 2016 May 6;

Authors: Tan Z, Chaudhai R, Zhang S

Abstract
Polypharmacology, the process in which a single drug is able to bind to multiple targets specifically and simultaneously, is an emerging paradigm in drug development. The potency of a given drug can be increased through the engagement of multiple targets involved in a certain disease. Polypharmacology may also help identify novel applications of existing drugs through drug repositioning. However, many problems and challenges remain in this field. Rather than covering all aspects of polypharmacology, this Minireview is focused primarily on recently reported techniques, from bioinformatics technologies to cheminformatics approaches as well as text-mining-based methods, all of which have made significant contributions to the research of polypharmacology.

PMID: 27154144 [PubMed - as supplied by publisher]

Spinal cord ependymoma: a review of the literature and case series of ten patients.

J Neurooncol. 2016 May 6;

Authors: Celano E, Salehani A, Malcolm JG, Reinertsen E, Hadjipanayis CG

Abstract
Spinal cord ependymoma (SCE) is a rare tumor that is most commonly low-grade. Complete surgical resection has been established as first-line treatment and can be curative. However, SCEs tend to recur when complete tumor resection is not possible. Evidence supporting the use of adjuvant radiation and chemotherapy is not definitive. We review the most recent literature on SCE covering a comprehensive range of topics spanning the biology, presentation, clinical management, and outcomes. In addition, we present a case series of ten SCE patients with the goal of contributing to existing knowledge of this rare disease.

PMID: 27154165 [PubMed - as supplied by publisher]

Integrating pharmacogenomics into clinical practice: promise vs reality.

Am J Med. 2016 May 4;

Authors: St Sauver JL, Bielinski SJ, Olson JE, Bell EJ, Mc Gree ME, Jacobson DJ, McCormick JB, Caraballo PJ, Takahashi PY, Roger VL, Rohrer Vitek CR

Abstract
BACKGROUND: Limited information is available regarding primary care clinicians' response to pharmacogenomic Clinical Decision Support (PGx-CDS) alerts integrated in the electronic health record.
METHODS: In February 2015, 159 clinicians in the Mayo Clinic primary care practice were sent e-mail surveys to understand their perspectives on the implementation and use of pharmacogenomic testing in their clinical practice. Surveys assessed how the clinicians felt about pharmacogenomics and whether they thought electronic PGx-CDS alerts were useful. Information was abstracted on the number of CDS alerts the clinicians received between October, 2013 and the date their survey was returned. CDS alerts were grouped into two categories: alert recommended caution using the prescription or the alert recommended an alternate prescription. Finally, data were abstracted regarding whether the clinician changed their prescription in response to the alert recommendation.
RESULTS: The survey response rate was 57% (n=90). Overall, 52% of the clinicians did not expect to use or did not know whether they would use pharmacogenomic information in their future prescribing practices. Additionally, 53% of the clinicians felt that the alerts were confusing, irritating, frustrating, or that it was difficult to find additional information. Finally, only 30% of the clinicians that received a CDS alert changed their prescription to an alternative medication.
CONCLUSIONS: Our results suggest a lack of clinician comfort with integration of pharmacogenomic data into primary care. Further efforts to refine PGx-CDS alerts to make them as useful and user-friendly as possible are needed to improve clinician satisfaction with these new tools.

PMID: 27155109 [PubMed - as supplied by publisher]

Personalized asthma therapy in blacks-the role of genetic ancestry.

J Allergy Clin Immunol. 2016 May;137(5):1370-1372

Authors: Dunn RM, Wechsler ME

PMID: 27155033 [PubMed - as supplied by publisher]