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In silico

Juri A Steiner, Patrik Christen, Remo Affentranger, Stephen J Ferguson, G Harry van Lenthe
Insufficient primary stability of screws in bone leads to screw loosening and failure. Unlike conventional continuum finite-element models, micro-CT based finite-element analysis (micro-FE) is capable of capturing the patient-specific bone micro-architecture, providing accurate estimates of bone stiffness. However, such in silico models for screws in bone highly overestimate the apparent stiffness. We hypothesized that a more accurate prediction of primary implant stability of screws in bone is possible by considering insertion-related bone damage...
February 27, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
Ana B Arroyo, Salam Salloum-Asfar, Carlos Pérez-Sánchez, Raúl Teruel-Montoya, Silvia Navarro, Nuria García-Barberá, Ginés Luengo-Gil, Vanessa Roldán, John-Bjarne Hansen, Chary López-Pedrera, Vicente Vicente, Rocío González-Conejero, Constantino Martínez
The increased risk of cardiovascular events in older men is multifactorial, but the significant reduction of testosterone levels has been involved. As this hormone regulates the expression of TFPI by unknown mechanisms, we aimed to evaluate the role of miRNAs in the regulation of TFPIα expression under normal conditions and in response to androgens. In silico studies allowed the selection of 4 miRNAs as potential TFPIα regulators. Only miR-27a/b-3p significantly reduced TFPIα expression in two endothelial cell lines...
February 27, 2017: Scientific Reports
Suheda Erener, Ashish Marwaha, Rusung Tan, Constadina Panagiotopoulos, Timothy J Kieffer
Type 1 diabetes (T1D) is an autoimmune disease that is clinically silent until the majority of β cells are destroyed. There is an unmet need for reliable and cost-effective biomarkers to predict and diagnose diabetes at an early stage. A number of stable microRNAs (miRNAs) have been reported in serum and plasma and are now being investigated as biomarkers of different diseases. We measured the levels of 745 miRNAs in sera of children with recent-onset T1D and age-matched controls using locked nucleic acid-enhanced (LNA-enhanced) quantitative PCR profiling...
February 23, 2017: JCI Insight
Stine Harder, Rasmus R Paulsen, Martin Larsen, Søren Laugesen, Michael Mihocic, Piotr Majdak
Individual head-related transfer functions (HRTFs) are essential in applications like fitting hearing-assistive devices (HADs) for providing accurate sound localization performance. Individual HRTFs are usually obtained through intricate acoustic measurements. This paper investigates the use of a three-dimensional (3D) head model for acquisition of individual HRTFs. Two aspects were investigated; whether a 3D-printed model can replace measurements on a human listener and whether numerical simulations can replace acoustic measurements...
June 2016: Computer Aided Design
Sebastián Cerminati, Florencia Eberhardt, Claudia E Elena, Salvador Peirú, María E Castelli, Hugo G Menzella
Enzymatic degumming using phospholipase C (PLC) enzymes may be used in environmentally friendly processes with improved oil recovery yields. In this work, phosphatidylinositol-specific phospholipase C (PIPLC) candidates obtained from an in silico analysis were evaluated for oil degumming. A PIPLC from Lysinibacillus sphaericus was shown to efficiently remove phosphatidylinositol from crude oil, and when combined with a second phosphatidylcholine and phosphatidylethanolamine-specific phospholipase C, the three major phospholipids were completely hydrolyzed, providing an extra yield of oil greater than 2...
February 25, 2017: Applied Microbiology and Biotechnology
Karin Weisser, Sabine Stübler, Walter Matheis, Wilhelm Huisinga
As a potentially toxic agent on nervous system and bone, the safety of aluminium exposure from adjuvants in vaccines and subcutaneous immune therapy (SCIT) products has to be continuously re-evaluated, especially regarding concomitant administrations. For this purpose, knowledge on absorption and disposition of aluminium in plasma and tissues is essential. Pharmacokinetic data after vaccination in humans, however, are not available, and for methodological and ethical reasons difficult to obtain. To overcome these limitations, we discuss the possibility of an in vitro-in silico approach combining a toxicokinetic model for aluminium disposition with biorelevant kinetic absorption parameters from adjuvants...
February 22, 2017: Regulatory Toxicology and Pharmacology: RTP
Brian D Clarke, Kenneth A McColl, Alister C Ward, Timothy J Doran
Viral haemorrhagic septicaemia virus (VHSV) represents an important disease of finfish. To explore the potential of shRNAs to combat this disease nucleotide sequences of either the VHSV glycoprotein (G) or polymerase (L) gene were targeted. To test their function, shRNAs were expressed in zebrafish epithelial ZF-4 cells utilizing the zebrafish U6-2 promoter. Five of the six shRNA molecules successfully reduced VHSV replication by between 2 and 4 logs in titre relative to an irrelevant control shRNA at all MOIs and also reduced viral CPE at the highest MOI...
February 22, 2017: Antiviral Research
Hongru Feng, Yuan Lin, Yuzhen Sun, Huiming Cao, Jianjie Fu, Ke Gao, Aiqian Zhang
Short chain perfluorinated sulfonic acids (PFSAs) that were introduced as alternatives for perfluorooctane sulfonic acid (PFOS) have been widely produced and used. However, few studies have investigated the environmental process of short chain PFSAs, and the related adsorption mechanisms still need to be uncovered. The water-oxide interface is one of the major environmental interfaces that plays an important role in affecting the adsorption behaviour and transport potential of the environmental pollutant. In this study, we performed molecular dynamics simulations and quantum chemistry calculations to investigate the adsorption mechanisms of five PFSAs and their adsorption on hydrated hematite surface as well...
February 14, 2017: Water Research
Bin Zhang, Ning Wang, Cunlong Zhang, Chunmei Gao, Wei Zhang, Kang Chen, Weibin Wu, Yuzong Chen, Chunyan Tan, Feng Liu, Yuyang Jiang
Sorafenib was the only small-molecule drug approved by FDA for treatment of the advanced hepatocellular carcinoma (HCC). Recent study indicated that YM155 was a promising agent for HCC cells with high survivin expression, however, the antitumor activity needs to be further improved. Based on molecular docking and rational design method, a series of multi-substituted benzyl acridone derivatives were designed and synthesized. MTT assay indicated that some of the synthesized compounds displayed better antiproliferative activity against HepG2 cells than YM155...
February 17, 2017: European Journal of Medicinal Chemistry
Mikhail Krasavin, Mikhail Korsakov, Zhanna Zvonaryova, Evgenii Semyonychev, Tiziano Tuccinardi, Stanislav Kalinin, Muhammet Tanç, Claudiu T Supuran
Three distinct series of isoxazole-based primary mono- and bis-sulfonamides have been synthesized via direct sulfochlorination, each of them delivering nanomolar inhibitors of human carbonic anhydrase. Certain pronounced SAR trends have been established and rationalized by in silico docking. These findings expand the structure-activity knowledge base for heterocycle-containing sulfonamide carbonic anhydrase inhibitors and further validate the power of direct electrophilic sulfochlorination as a means of introducing the pharmacophoric primary sulfonamide group into structurally diverse aromatic precursors...
February 13, 2017: Bioorganic & Medicinal Chemistry
Muhammad Ilyas, Ali Khaqan, Jamshed Iqbal, Raja Ali Riaz
Continuous adjustment of Propofol in manual delivery of anesthesia for conducting a surgical procedure overburdens the workload of an anesthetist who is working in a multi-tasking scenario. Going beyond manual administration and Target Controlled Infusion, closed-loop control of Propofol infusion has the potential to offer several benefits in terms of handling perturbations and reducing the effect of inter-patient variability. This paper proposes a closed-loop automated drug administration approach to control Depth Of Hypnosis in anesthesia...
March 2017: Brazilian Journal of Anesthesiology
Xiaobing Chen, Bojian Xie, Liang Cao, Feng Zhu, Beibei Chen, Huifang Lv, Xingxing Fan, Lili Han, Liangyu Bie, Xinguang Cao, Xiaokun Shen, Feilin Cao
The Regorafenib is a broad-spectrum kinase inhibitor that has been approved to treat colorectal cancer (CRC). However, evidences have shown that the agent is also implicated in drug interaction with microRNA-21 (miR-21), an oncogenic miRNA which plays a key role in resisting programmed cell death in CRC cells. Here, we supposed that, instead of kinase inhibition, Regorafenib can directly bind to and then stabilize miR-21 pre-element, thus preventing RNase Dicer-meditated cleavage of the pre-element to mature miR-21...
February 10, 2017: Journal of Molecular Graphics & Modelling
Andrea Guala, Carlo Camporeale, Luca Ridolfi, Luca Mesin
Everyday clinical cardiovascular evaluation is still largely based on brachial systolic and diastolic pressures. However, several clinical studies have demonstrated the higher diagnostic capacities of the aortic pressure, as well as the need to assess the aortic mechanical properties (e.g., by measuring the aortic pulse wave velocity). In order to fill this gap, we propose to exploit a set of easy-to-obtain physical characteristics to estimate the aortic pressure and pulse wave velocity. To this aim, a large population of virtual subjects is created by a validated mathematical model of the cardiovascular system...
February 21, 2017: Medical Engineering & Physics
Rahul Suryawanshi, Sushama Jadhav, Nandini Makwana, Dipen Desai, Devidas Chaturbhuj, Archana Sonawani, Susan Idicula-Thomas, Vanangamudi Murugesan, Seturam B Katti, Srikanth Tripathy, Ramesh Paranjape, Smita Kulkarni
Rapid emergence of drug resistance is crucial in management of HIV infection limiting implementation of efficacious drugs in the ART regimen. Designing new molecules against HIV drug resistant strains is utmost essential. Based on the anti-HIV-1 activity, we selected four 4-thiazolidinone derivatives (S009-1908, S009-1909, S009-1911, S009-1912) and studied their interaction with reverse transcriptase (RT) from a panel of 10 clinical isolates (8 nevirapine resistant and two susceptible) using in silico methods, and inhibition pattern using in vitro cell based assays...
February 15, 2017: Bioorganic Chemistry
Fatma Bastaki, Madiha Mohamed, Pratibha Nair, Fatima Saif, Ethar M Mustafa, Sami Bizzari, Mahmoud T Al-Ali, Abdul Rezzak Hamzeh
BACKGROUND: Clinical and molecular heterogeneity is a prominent characteristic of congenital ichthyoses, with the involvement of numerous causative loci. Mutations in these loci feature in autosomal recessive congenital ichthyoses (ARCIs) quite variably, with certain genes/mutations being more frequently uncovered in particular populations. METHODS: In this study, we used whole exome sequencing as well as direct Sanger sequencing to uncover four novel mutations in ARCI-related genes, which were found in families from the United Arab Emirates...
February 24, 2017: International Journal of Dermatology
Sandeep Kumar Panda, Rajani Kanta Mahapatra
With the enormous genetic plasticity of malaria parasite, the challenges of developing a potential malaria vaccine candidate with highest efficacy still remain. This study has incorporated a bioinformatics-based screening approach to explore potential vaccine candidates in Plasmodium falciparum proteome. A systematic strategy was defined to screen proteins from the Malaria Parasite Metabolic Pathways (MPMP) database, on the basis of surface exposure, non-homology with host proteome, orthology with related Plasmodium species, and MHC class I and II binding promiscuity...
February 24, 2017: Parasitology Research
Chiara Pagliarani, Marco Vitali, Manuela Ferrero, Nicola Vitulo, Marco Incarbone, Claudio Lovisolo, Giorgio Valle, Andrea Schubert
Grapevine (Vitis vinifera L.) is routinely grafted and rootstocks inducing drought tolerance represent a source for adapting vineyards to climate change in temperate areas. Our goal was to investigate drought stress effects on miRNA abundance in a drought-resistant grapevine rootstock, M4 (Vitis vinifera X Vitis berlandieri), compared with a commercial cultivar, Cabernet Sauvignon (CS), by using their auto- and reciprocal grafts. RNA extracted from roots and leaves of droughted and irrigated plants of different graft combinations was used to prepare cDNA libraries for small RNA sequencing, and to analyse miRNAs by Real Time PCR (RT-qPCR)...
February 24, 2017: Plant Physiology
Z Pourhashem, M Mehrpouya, N Yardehnavi, A Eslamparast, F Kazemi-Lomedasht
HER3 is an important therapeutic target in cancer treatments. HER3 Nanobodies (Nbs) are a novel class of antibodies with several competitive advantages over conventional antibodies. A peptidomimetic derived from these Nbs can be considered to be a small peptide mimicking some of the molecular recognition interactions of a natural peptide or protein in a three-dimensional (3D) space, with a receptor that has improved properties. In this study, we introduce a new approach to design a peptidomimetic derived from HER3 Nb through an in silico analysis...
February 10, 2017: Computational Biology and Chemistry
Mohtashim Lohani, Anupam Dhasmana, Shafiul Haque, Mohd Wahid, Arshad Jawed, Sajad A Dar, Raju K Mandal, Mohammed Y Areeshi, Saif Khan
Clostridium difficile is an enteric pathogen that causes approximately 20% to 30% of antibiotic-associated diarrhea. In recent years, there has been a substantial rise in the rate of C. difficile infections as well as the emergence of virulent and antibiotic resistant C. difficile strains. So, there is an urgent need for the identification of therapeutic potential targets and development of new drugs for the treatment and prevention of C. difficile infections. In the current study, we used a hybrid approach by combining sequence similarity-based approach and protein-protein interaction network topology-based approach to identify and characterize the potential drug targets of C...
February 21, 2017: Journal of Microbiological Methods
Hong Wang, Hewei Zheng, Chenguang Wang, Xiaoyan Lu, Xueying Zhao, Xia Li
LncRNAs fulfill a wide range of regulatory functions at almost every process of gene expression. While derived from secondary structural features, lncRNAs may function as landing pads for transcription factors (TFs). In this paper, we detected the global structural landscape of 20,338 lncRNAs by utilizing a thermodynamic model, and identified the lncRNA and TF interactions. The accessibility analysis of full sequences as well as potential TF-binding fragments shows a large percentage of structural flanking sequence around the TF binding sites...
February 21, 2017: Biochemical and Biophysical Research Communications
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