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Biological models

Y Krylova, V Polyakova, I Kvetnoy, I Kogan, L Dzhemlikhanova, D Niauri, A Gzgzyan, E Ailamazyan
: Abstracts Background: Implantation failure of in vitro fertilization (IVF) cycles is recognized as one of key problems in contemporary reproductive medicine. Implantation itself is a multifactorial process and one can hardly expect to find a single criterion for the endometrium receptivity. Endometrium biopsy still remains the most applicable technique to diagnose abnormalities causing decrease or complete loss of endometrial receptivity. MATERIALS AND METHODS: We have studied 95 endometrial biopsy samples from 45 patient with I/II stage endometriosis and 40 controls from October 2014 to December 2015...
October 2016: Gynecological Endocrinology
Justin A Lemkul, Alexander D MacKerell
Mg2+ ions are important in biological systems, particularly in stabilizing compact RNA folds. Mg2+ is strongly polarizing, and representing its interactions in heterogeneous environments is a challenge for empirical force field development. To date, the most commonly used force fields in molecular dynamics simulations utilize a pairwise-additive approximation for electrostatic interactions, which cannot account for the significant polarization response in systems containing Mg2+. In the present work, we refine the interactions of Mg2+ with water, Cl- ions, and nucleic acid moieties using a polarizable force field based on the classical Drude oscillator model...
October 19, 2016: Journal of Physical Chemistry. B
Martina F Callaghan, Siawoosh Mohammadi, Nikolaus Weiskopf
Quantitative MRI (qMRI) provides standardized measures of specific physical parameters that are sensitive to the underlying tissue microstructure and are a first step towards achieving maps of biologically relevant metrics through in vivo histology using MRI. Recently proposed models have described the interdependence of qMRI parameters. Combining such models with the concept of image synthesis points towards a novel approach to synthetic qMRI, in which maps of fundamentally different physical properties are constructed through the use of biophysical models...
October 18, 2016: NMR in Biomedicine
Jeganathan Manivannan, Manjunath Prashanth, Venkatesan Saravana Kumar, Manickaraj Shairam, Jayachandran Subburaj
Since there is no precise therapy for treating vascular calcification by directly targeting the vascular wall, we aim to unveil novel drug targets through mining the molecular effect of a high phosphate environment on vascular cells through computational methods. Here, we hypothesize that manipulation of the vascular pathogenic network by small molecule therapeutics predicted from prior knowledge might offer great promise. With this, we intend to understand the publicly available transcriptomic data of vascular smooth muscle cells and endothelial cells exposed to the high phosphate induced vascular calcification milieu and to re-examine the above published experiments for reasons different from those examined in the previous studies through multilevel systems biological understanding...
October 18, 2016: Molecular BioSystems
Yum Eryanti, Adel Zamri, Neni Frimayanti, Unang Supratman, Tati Herlina
The dataset of curcumin derivatives consists of 45 compounds (Table 1) with their anti cancer biological activity (IC50) against P388 cell line. 45 curcumin derivatives were used in the model development where 30 of these compounds were in the training set and the remaining 15 compounds were in the test set. The development of the QSAR model involved the use of the multiple linear regression analysis (MLRA) method. Based on the method, r(2) value, r(2)(CV) value of 0.81, 0.67 were obtained. The QSAR model was also employed to predict the biological activity of compounds in the test set...
December 2016: Data in Brief
Su Jin Kang, Ji Yeon Seo, Kye Man Cho, Chang Kwon Lee, Jeong Hwan Kim, Jong-Sang Kim
A new type of doenjang was manufactured by mixing soaked soybean, koji (Rhizopus oryzae), cheonggukjang (Bacillus amyloliquefaciens MJ1-4 and B. amyloliquefaciens EMD17), and Pichia farinosa SY80 as a yeast, salt, and water, followed by fermentation with koji that was made by fermenting whole wheat with R. oryzae. The mixed culture doenjang was designed to have a more palatable flavor and stronger biological activities than the conventional product. The extract of mixed culture doenjang showed higher antioxidant activity than the commercial doenjang as evaluated by the ferric reducing antioxidant power assay although it was not significantly different from the commercial product in 2,2-diphenyl-1-picrylhydrazyl and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) radical scavenging activities...
September 2016: Preventive Nutrition and Food Science
Alexey L Chernobrovkin, Roman A Zubarev
While the focus of attempts to classify cell death programs has finally shifted in 2010s from microscopy-based morphological characteristics to biochemical assays, more recent discoveries have put the underlying assumptions of many such assays under severe stress, mostly because of the limited specificity of the assays. On the other hand, proteomics can quantitatively measure the abundances of thousands of proteins in a single experiment. Thus proteomics could develop a modern alternative to both semiquantitative morphology assessment as well as single-molecule biochemical assays...
2016: Cell Death Discovery
Eduard Poltavskiy, J David Spence, Jeehyoung Kim, Heejung Bang
In the modern era, with high-throughput technology and large data size, associational studies are actively being generated. Some have statistical and clinical validity and utility, or at least have biologically plausible relationships, while others may not. Recently, the potential effect of birth month on lifetime disease risks has been studied in a phenome-wide model. We evaluated the associations between birth month and 5 cardiovascular disease-related outcomes in an independent registry of 8,346 patients from Ontario, Canada in 1977-2014...
2016: Online Journal of Public Health Informatics
Michael Popovich, Brandy Altstadter, Lara Hargraves Popovich, B S Biology
The Health Information Technology for Economic and Clinical Health (HITECH) Act encourages health information exchange between clinical care and public health through Meaningful Use measures. Meaningful Use specifically identifies objectives to support a number of public health programs including immunizations, cancer registries, syndromic surveillance, and disease case reports. The objective is to improve public and population health. Stage 2 of Meaningful Use focused on compliance to sending of information to public health...
2016: Online Journal of Public Health Informatics
Matthew L Paff, Scott L Nuismer, Andrew D Ellington, Ian J Molineux, Ryan H May, James J Bull
BACKGROUND: We propose, model, and implement a novel system of population-level intervention against a virus. One context is a treatment against a chronic infection such as HIV. The underlying principle is a form of virus 'wars' in which a benign, transmissible agent is engineered to protect against infection by and spread of a lethal virus. In our specific case, the protective agent consists of two entities, a benign virus and a gene therapy vector mobilized by the benign virus. RESULTS: Numerical analysis of a mathematical model identified parameter ranges in which adequate, population-wide protection is achieved...
2016: Journal of Biological Engineering
Liu Chunbao, Li Li, Lei Yulong, Liu Changsuo, Zhang Yubo
Fish-like, dolphin-like, and bionic nonsmooth surfaces were employed in a hydraulic torque converter to achieve drag reduction and performance improvement, which were aimed at reducing profile loss, impacting loss and friction loss, respectively. YJSW335, a twin turbine torque converter, was bionically designed delicately. The biological characteristics consisted of fish-like blades in all four wheels, dolphin-like structure in the first turbine and the stator, and nonsmooth surfaces in the pump. The prediction performance of bionic YJSW335, obtained by computational fluid dynamics simulation, was improved compared with that of the original model, and then it could be proved that drag reduction had been achieved...
2016: Applied Bionics and Biomechanics
Athanassios D Velentzas, Panagiotis D Velentzas, Niki E Sagioglou, Eumorphia G Konstantakou, Athanasios K Anagnostopoulos, Maria M Tsioka, Vassiliki E Mpakou, Zoe Kollia, Christos Consoulas, Lukas H Margaritis, Issidora S Papassideri, George Th Tsangaris, Evangelia Sarantopoulou, Alkiviadis-Constantinos Cefalas, Dimitrios J Stravopodis
Drosophila chorion represents a model biological system for the in vivo study of gene activity, epithelial development, extracellular-matrix assembly and morphogenetic-patterning control. It is produced during the late stages of oogenesis by epithelial follicle cells and develops into a highly organized multi-layered structure that exhibits regional specialization and radial complexity. Among the six major proteins involved in chorion's formation, the s36 and s38 ones are synthesized first and regulated in a cell type-specific and developmental stage-dependent manner...
October 18, 2016: Scientific Reports
Qing Zhang, Qing Zhang, Yanxing Guan, Shaozheng Liu, Qingjie Chen, Xiangmin Li
BACKGROUND This study was specifically designed to develop a new 99mTc compound with 3-amino-4-[2-(2-methyl-5-nitro-1H-imidazol)-ethylamino]-4-oxo-butyrate (5-ntm-asp) and to verify whether this compound is feasible to be a radiopharmaceutical for hypoxic tumors. MATERIAL AND METHODS Metronidazole derivative 5-ntm-asp was synthesized and then radio-labeled by Na [99mTcO4], forming 99mTc-5-ntm-asp. Another two complexes of 99mTc-2- and 99mTc-5-nitroimidazole-iminodiacetic acid (99mTc-2-ntm-IDA and 99mTc-5-ntm-IDA) were also synthesized based on previous studies...
October 18, 2016: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Gavin D Merrifield, James Mullin, Lindsay Gallagher, Carl Tucker, Maurits A Jansen, Martin Denvir, William M Holmes
Increasing scientific interest in the zebrafish as a model organism across a range of biomedical and biological research areas raises the need for the development of in vivo imaging tools appropriate to this subject. Development of the embryonic and early stage forms of the subject can currently be assessed using optical based techniques due to the transparent nature of the species at these early stages. However this is not an option during the juvenile and adult stages when the subjects become opaque. Magnetic Resonance Imaging (MRI) techniques would allow for the longitudinal and non-invasive assessment of development and health in these later life stages...
October 14, 2016: Magnetic Resonance Imaging
Mamatha Bhat, Peter Ghali, Benoît Dupont, Roy Hilzenrat, Mahmood Tazari, André Roy, Prosanto Chaudhury, Fernando Alvarez, Michel Carrier, Marc Bilodeau
BACKGROUND & AIMS: Patients listed with exception points for Hepatocellular carcinoma (HCC) have been more likely to be transplanted than those listed for chronic liver failure (LF) based on the Model for End-Stage Liver Disease (MELD) score. The aim of this study was to determine outcomes in the 5-year experience of a scoring system designed to reflect heterogeneity of tumor load of patients listed for HCC. METHODS: A novel MELD exception point system based on size and number of HCC was implemented in July 2009...
October 14, 2016: Journal of Hepatology
Antoine Wystrach, Konstantinos Lagogiannis, Barbara Webb
Taxis behaviour in Drosophila larva is thought to consist of distinct control mechanisms triggering specific actions. Here we support a simpler hypothesis: that taxis results from direct sensory modulation of continuous lateral oscillations of the anterior body, sparing the need for 'action selection'. Our analysis of larvae motion reveals a rhythmic, continuous lateral oscillation of the anterior body, encompassing all head-sweeps, small or large, without breaking the oscillatory rhythm. Further, we show that an agent-model that embeds this hypothesis reproduces a surprising number of taxis signatures observed in larvae...
October 18, 2016: ELife
Zheng Liu, Cristina Gutierrez-Vargas, Jia Wei, Robert A Grassucci, Noel Espina, Susan Madison-Antenucci, Liang Tong, Joachim Frank
With the advance of new instruments and algorithms, and the accumulation of experience over decades, single-particle cryo-EM has become a pivotal part of structural biology. Recently, we determined the structure of a eukaryotic ribosome at 2.5 Å for the large subunit. The ribosome was derived from Trypanosoma cruzi, the protozoan pathogen of Chagas disease. The high-resolution density map allowed us to discern a large number of unprecedented details including rRNA modifications, water molecules, and ions such as Mg(2+) and Zn(2+) ...
October 17, 2016: Protein Science: a Publication of the Protein Society
Pedro David Carvalho, Cátia Duarte, Elsa Vieira-Sousa, Luís Cunha-Miranda, Pedro Avila-Ribeiro, Helena Santos, Miguel Bernardes, Maria José Santos, Marcos Cerqueira, Margarida Mateus, Patrícia Nero, Ana Águeda, José António Pereira da Silva, Pedro Machado
Psoriatic arthritis (PsA) is a chronic inflammatory rheumatic disease with a broad clinical spectrum. PsA can affect the axial skeleton, peripheral joints, entheses, synovial sheaths of tendons, skin, nails and extra-articular organs. Tumour necrosis factor alpha blockers (TNF blockers) were a breakthrough development in the treatment of PsA. Identifying predictors of response to biological therapies in patients with PsA is of utmost importance, especially in view of the costs and potential side effects of these agents...
August 17, 2016: Acta Reumatológica Portuguesa
Yang Liu, Xia Peng, Xiaocong Guan, Dong Lu, Yong Xi, Shiyu Jin, Hui Chen, Limin Zeng, Jing Ai, Meiyu Geng, Youhong Hu
FGF receptors (FGFRs) are tyrosine kinases that are overexpressed in diverse tumors by genetic alterations such as gene amplifications, somatic mutations and translocations. Owing to this characteristic, FGFRs are attractive targets for cancer treatment. It has been demonstrated that most multi-targeted, ATP competitive tyrosine kinase inhibitors are active against FGFRs as well as other kinases. The design of new and more selective inhibitors of FGFRs, which might be reduced off-target and side effects, is a difficult yet significant challenge...
October 4, 2016: European Journal of Medicinal Chemistry
Alessio Soggiu, Cristian Piras, Viviana Greco, Paola Devoto, Andrea Urbani, Luigino Calzetta, Marco Bortolato, Paola Roncada
The enzyme 5α-reductase (5αR) catalyzes the conversion of progesterone and testosterone into neuroactive steroids implicated in a wide array of behavioral functions. The prototypical 5αR inhibitor, finasteride (FIN), is clinically approved for the treatment of androgenic alopecia and benign prostatic hyperplasia. Recent evidence has shown that FIN, albeit generally well tolerated, can induce untoward psychological effects in a subset of patients; furthermore, this drug may have therapeutic efficacy for a number of different neuropsychiatric conditions, ranging from Tourette syndrome to schizophrenia...
October 6, 2016: Psychoneuroendocrinology
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