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https://www.readbyqxmd.com/read/29297376/investigations-on-factors-influencing-hpo-based-semantic-similarity-calculation
#1
Jiajie Peng, Qianqian Li, Xuequn Shang
BACKGROUND: Although disease diagnosis has greatly benefited from next generation sequencing technologies, it is still difficult to make the right diagnosis purely based on sequencing technologies for many diseases with complex phenotypes and high genetic heterogeneity. Recently, calculating Human Phenotype Ontology (HPO)-based phenotype semantic similarity has contributed a lot for completing disease diagnosis. However, factors which affect the accuracy of HPO-based semantic similarity have not been evaluated systematically...
September 20, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29262338/homeostatic-control-of-hpo-mst-kinase-activity-through-autophosphorylation-dependent-recruitment-of-the-stripak-pp2a-phosphatase-complex
#2
Yonggang Zheng, Bo Liu, Li Wang, Huiyan Lei, Katiuska Daniela Pulgar Prieto, Duojia Pan
The Hippo pathway controls organ size and tissue homeostasis through a kinase cascade leading from the Ste20-like kinase Hpo (MST1/2 in mammals) to the transcriptional coactivator Yki (YAP/TAZ in mammals). Whereas previous studies have uncovered positive and negative regulators of Hpo/MST, how they are integrated to maintain signaling homeostasis remains poorly understood. Here, we identify a self-restricting mechanism whereby autophosphorylation of an unstructured linker in Hpo/MST creates docking sites for the STRIPAK PP2A phosphatase complex to inactivate Hpo/MST...
December 19, 2017: Cell Reports
https://www.readbyqxmd.com/read/29250549/identifying-human-phenotype-terms-by-combining-machine-learning-and-validation-rules
#3
Manuel Lobo, Andre Lamurias, Francisco M Couto
Named-Entity Recognition is commonly used to identify biological entities such as proteins, genes, and chemical compounds found in scientific articles. The Human Phenotype Ontology (HPO) is an ontology that provides a standardized vocabulary for phenotypic abnormalities found in human diseases. This article presents the Identifying Human Phenotypes (IHP) system, tuned to recognize HPO entities in unstructured text. IHP uses Stanford CoreNLP for text processing and applies Conditional Random Fields trained with a rich feature set, which includes linguistic, orthographic, morphologic, lexical, and context features created for the machine learning-based classifier...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29241324/repeatedly-heated-palm-kernel-oil-induces-hyperlipidemia-atherogenic-indices-and-hepatorenal-toxicity-in-rats-beneficial-role-of-virgin-coconut-oil-supplementation
#4
Ademola C Famurewa, Onyebuchi E Nwankwo, Abiola M Folawiyo, Emeka C Igwe, Michael A Epete, Odomero G Ufebe
BACKGROUND: The literature reports that the health benefits of vegetable oil can be deteriorated by repeated heating, which leads to lipid oxidation and the formation of free radicals. Virgin coconut oil (VCO) is emerging as a functional food oil and its health benefits are attributed to its potent polyphenolic compounds. We investigated the beneficial effect of VCO supplementation on lipid profile, liver and kidney markers in rats fed repeatedly heated palm kernel oil (HPO). METHODS: Rats were divided into four groups (n = 5)...
October 2017: Acta Scientiarum Polonorum. Technologia Alimentaria
https://www.readbyqxmd.com/read/29231729/simulation-of-calcium-phosphate-species-in-aqueous-solution-force-field-derivation
#5
Raffaella Demichelis, Natalya A Garcia, Paolo Raiteri, Riccardo Innocenti Malini, Colin L Freeman, John H Harding, Julian D Gale
A new force field has been derived for the aqueous calcium phosphate system that aims to reproduce the key thermodynamic properties of the system, including free energies of hydration of the ions and the solubility of the solid mineral phases. Interactions of three phosphate anions (PO 3-, HPO 2- and H PO -) with water were calibrated through comparison with the results 4424 obtained from ab initio molecular dynamics using both GGA and hybrid density functional theory with dispersion corrections. In the solid state, the force field has been evaluated by benchmarking against experiment and other existing models and is shown to reproduce the structural and mechanical properties well, despite the primary focus being on thermodynamics...
December 12, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29213997/cloning-optimization-of-induction-conditions-and-purification-of-mycobacterium-tuberculosis-rv1733c-protein-expressed-in-escherichia-coli
#6
Mitra Ashayeri-Panah, Fereshteh Eftekhar, Bahram Kazemi, Joan Joseph
Background and Objectives: Rv1733c is a latency antigen from Mycobacterium tuberculosis, a probable integral-membrane protein with promiscuous T-cell and B-cell epitopes, making it a potential vaccine candidate against tuberculosis. This study aimed to clone and optimize the expression of recombinant Rv1733c in Escherichia coli for purification. Materials and Methods: Chemically synthesized rv1733c coding sequence was cloned in pET-23a(+) followed by transforming E...
April 2017: Iranian Journal of Microbiology
https://www.readbyqxmd.com/read/29207981/an-ontology-aware-integration-of-clinical-models-terminologies-and-guidelines-an-exploratory-study-of-the-scale-for-the-assessment-and-rating-of-ataxia-sara
#7
Haitham Maarouf, María Taboada, Hadriana Rodriguez, Manuel Arias, Ángel Sesar, María Jesús Sobrido
BACKGROUND: Electronic rating scales represent an important resource for standardized data collection. However, the ability to exploit reasoning on rating scale data is still limited. The objective of this work is to facilitate the integration of the semantics required to automatically interpret collections of standardized clinical data. We developed an electronic prototype for the Scale of the Assessment and Rating of Ataxia (SARA), broadly used in neurology. In order to address the modeling challenges of the SARA, we propose to combine the best performances from OpenEHR clinical archetypes, guidelines and ontologies...
December 6, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/29193559/evaluation-of-exome-filtering-techniques-for-the-analysis-of-clinically-relevant-genes
#8
Kristin D Kernohan, Taila Hartley, Najmeh Alirezaie, Care Rare Canada Consortium, Peter N Robinson, David A Dyment, Kym M Boycott
A significant challenge facing clinical translation of exome sequencing is meaningful and efficient variant interpretation. Each exome contains ∼500 rare coding variants; laboratories must systematically and efficiently identify which variant(s) contribute to the patient's phenotype. In silico filtering is an approach that reduces analysis time while decreasing the chances of incidental findings. We retrospectively assessed 55 solved exomes using available datasets as in silico filters: Online Mendelian Inheritance in Man (OMIM), Orphanet, Human Phenotype Ontology (HPO), andRadboudumc University Medical Center curated panels...
November 30, 2017: Human Mutation
https://www.readbyqxmd.com/read/29162690/multiple-pathways-in-pressure-induced-phase-transition-of-coesite
#9
Wei Liu, Xuebang Wu, Yunfeng Liang, Changsong Liu, Caetano R Miranda, Sandro Scandolo
High-pressure single-crystal X-ray diffraction method with precise control of hydrostatic conditions, typically with helium or neon as the pressure-transmitting medium, has significantly changed our view on what happens with low-density silica phases under pressure. Coesite is a prototype material for pressure-induced amorphization. However, it was found to transform into a high-pressure octahedral (HPO) phase, or coesite-II and coesite-III. Given that the pressure is believed to be hydrostatic in two recent experiments, the different transformation pathways are striking...
November 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29125115/roles-of-hypothalamic-pituitary-adrenal-axis-and-hypothalamus-pituitary-ovary-axis-in-the-abnormal-endocrine-functions-in-patients-with-polycystic-ovary-syndrome
#10
Fan Wang, Zheng-Hong Zhang, Kai-Zhuan Xiao, Zheng-Chao Wang
Polycystic ovary syndrome(PCOS) is a common reproductive endocrine disease in women of childbearing age. While it can be affected by a variety of factors,its pathophysiology remains unclear. Its clinical features mainly include anovulation,hyperandrogenism,and hyperinsulinemia,which are closely related with abnormal neuroendocrine system. Hypothalamic-pituitary-gonadal axis(HPG) plays a crucial regulatory role in various life activities in mammals. In particular,hypothalamic-pituitary-adrenal(HPA) axis and hypothalamus-pituitary-ovary(HPO) axis can be abnormal in PCOS patients...
October 30, 2017: Zhongguo Yi Xue Ke Xue Yuan Xue Bao. Acta Academiae Medicinae Sinicae
https://www.readbyqxmd.com/read/29077208/clinical-efficacy-of-a-next-generation-sequencing-gene-panel-for-primary-immunodeficiency-diagnostics
#11
W Rae, D Ward, C Mattocks, R J Pengelly, E Eren, S V Patel, S N Faust, D Hunt, A P Williams
Primary immunodeficiencies (PIDs) are rare monogenic inborn errors of immunity that result in impairment of functions of the human immune system. PIDs have a broad phenotype with increased morbidity and mortality and treatment choices are often complex. With increased accessibility of next-generation sequencing the rate of discovery of genetic causes for PID has increased exponentially. Identification of an underlying monogenic diagnosis provides important clinical benefits for patients with the potential to alter treatments, facilitate genetic counselling, and pre-implantation diagnostics...
October 27, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29071997/-effect-of-electroacupuncture-on-hypothalamus-pituitary-ovary-hpo-axis-in-rats-with-peri-menopausal-depression
#12
Xi-Rong Jiang, Lu Ren, Chun-Ri Li
OBJECTIVE: To observe the effect of electroacupuncture (EA) on the hormones derived from the hypothalamus-pituitary-ovary (HPO) axis, so as to explore the neuroendocrine mechanism induced by EA on rats with perimenopausal depression disorder. METHODS: Sixty female sprague-dawley rats were randomly divided into blank control group, model group, sham-operation (sham) group, clomipramine group, and electroacupuncture (EA) group, with 12 rats in each group. Perimenopausal depression model was established by bilateral ovariectomy combined with chronic unpredictable stimulation...
February 25, 2017: Zhen Ci Yan Jiu, Acupuncture Research
https://www.readbyqxmd.com/read/29063556/knowledge-representation-and-management-it-s-time-to-integrate
#13
F Dhombres, J Charlet
Objectives: To select, present, and summarize the best papers published in 2016 in the field of Knowledge Representation and Management (KRM). Methods: A comprehensive and standardized review of the medical informatics literature was performed based on a PubMed query. Results: Among the 1,421 retrieved papers, the review process resulted in the selection of four best papers focused on the integration of heterogeneous data via the development and the alignment of terminological resources. In the first article, the authors provide a curated and standardized version of the publicly available US FDA Adverse Event Reporting System...
August 2017: Yearbook of Medical Informatics
https://www.readbyqxmd.com/read/29031632/separate-transcriptionally-regulated-pathways-specify-distinct-classes-of-sister-dendrites-in-a-nociceptive-neuron
#14
Barbara M J O'Brien, Sierra D Palumbos, Michaela Novakovic, Xueying Shang, Lakshmi Sundararajan, David M Miller
The dendritic processes of nociceptive neurons transduce external signals into neurochemical cues that alert the organism to potentially damaging stimuli. The receptive field for each sensory neuron is defined by its dendritic arbor, but the mechanisms that shape dendritic architecture are incompletely understood. Using the model nociceptor, the PVD neuron in C. elegans, we determined that two types of PVD lateral branches project along the dorsal/ventral axis to generate the PVD dendritic arbor: (1) Pioneer dendrites that adhere to the epidermis, and (2) Commissural dendrites that fasciculate with circumferential motor neuron processes...
October 13, 2017: Developmental Biology
https://www.readbyqxmd.com/read/29025394/prediction-of-human-phenotype-ontology-terms-by-means-of-hierarchical-ensemble-methods
#15
Marco Notaro, Max Schubach, Peter N Robinson, Giorgio Valentini
BACKGROUND: The prediction of human gene-abnormal phenotype associations is a fundamental step toward the discovery of novel genes associated with human disorders, especially when no genes are known to be associated with a specific disease. In this context the Human Phenotype Ontology (HPO) provides a standard categorization of the abnormalities associated with human diseases. While the problem of the prediction of gene-disease associations has been widely investigated, the related problem of gene-phenotypic feature (i...
October 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29017443/a-new-synonym-substitution-method-to-enrich-the-human-phenotype-ontology
#16
Maria Taboada, Hadriana Rodriguez, Ranga C Gudivada, Diego Martinez
BACKGROUND: Named entity recognition is critical for biomedical text mining, where it is not unusual to find entities labeled by a wide range of different terms. Nowadays, ontologies are one of the crucial enabling technologies in bioinformatics, providing resources for improved natural language processing tasks. However, biomedical ontology-based named entity recognition continues to be a major research problem. RESULTS: This paper presents an automated synonym-substitution method to enrich the Human Phenotype Ontology (HPO) with new synonyms...
October 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28993190/secretome-from-hypoxia-conditioned-adipose-derived-mesenchymal-stem-cells-promotes-the-healing-of-gastric-mucosal-injury-in-a-rodent-model
#17
Xianfeng Xia, Philip Wai Yan Chiu, Ping Kuen Lam, Wai Ching Chin, Enders Kwok Wai Ng, James Yun Wong Lau
Studies have indicated that the definitive engraftment and transdifferentiation potential of stem cells do not seem crucial for its property of tissue repair. Our previous study showed that transplantation of adipose-derived mesenchymal stem cells (ADMSCs) enhanced the healing of sutured gastric perforation. This study aimed to investigate the paracrine role of ADMSCs in the experimental gastric mucosal injury. Normoxia-conditioned medium (Nor CM) and hypoxia (HPO) CM were obtained after culturing ADMSCs in 20% O2 and 5% O2 for 48h...
October 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28991988/citrate-addition-increased-phosphorus-bioavailability-and-enhanced-gasoline-bioremediation
#18
Tingting Chen, Courtney Philips, Jordan Hamilton, Blaine Chartbrand, Jay Grosskleg, Kris Bradshaw, Trevor Carlson, Karen Timlick, Derek Peak, Steven D Siciliano
Phosphorus (P) bioavailability often limits gasoline biodegradation in calcareous cold-region soils. One possible method to increase P bioavailability in such soils is the addition of citrate. Citrate addition at the field scale may increase hydrocarbon degradation by: (i) enhancing inorganic and organic P dissolution and desorption, (ii) increasing hydrocarbon bioavailability, and/or (iii) stimulating microbial activity. Alternatively, citrate addition may inhibit activity due to competitive effects on carbon metabolism...
September 2017: Journal of Environmental Quality
https://www.readbyqxmd.com/read/28946786/preaxial-polydactyly-of-the-foot
#19
Elise B Burger, Martijn Baas, Steven E R Hovius, A Jeannette M Hoogeboom, Christianne A van Nieuwenhoven
Background and purpose - Preaxial polydactyly of the foot is a rare malformation and clinicians are often unfamiliar with the associated malformations and syndromes. In order to give guidelines for diagnostics and referral to a clinical geneticist, we provide an overview of the presentation using a literature review and our own patient population. Patients and methods - The literature review was based on the Human Phenotype Ontology (HPO) project. From the HPO dataset, all phenotypes describing preaxial polydactyly were obtained and related diseases were identified and selected...
September 26, 2017: Acta Orthopaedica
https://www.readbyqxmd.com/read/28937253/sirt1-mediates-improvement-in-cognitive-defects-induced-by-focal-cerebral-ischemia-following-hyperbaric-oxygen-preconditioning-in-rats
#20
P Ding, D Ren, S He, M He, G Zhang, Y Chen, H Sang, Z Peng, W Yan
Hyperbaric oxygen preconditioning (HBO-PC) has been proposed as a safe and practical approach for neuroprotection in ischemic stroke. However, it is not known whether HPO-PC can improve cognitive deficits induced by cerebral ischemia, and the mechanistic basis for any beneficial effects remains unclear. We addressed this in the present study using rats subjected to middle cerebral artery occlusion (MCAO) as an ischemic stroke model following HBO-PC. Cognitive function and expression of phosphorylated neurofilament heavy polypeptide (pNF-H) and doublecortin (DCX) in the hippocampus were evaluated 14 days after reperfusion and after short interfering RNA-mediated knockdown of sirtuin1 (Sirt1)...
September 22, 2017: Physiological Research
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