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https://www.readbyqxmd.com/read/28095781/link-prediction-in-drug-target-interactions-network-using-similarity-indices
#1
Yiding Lu, Yufan Guo, Anna Korhonen
BACKGROUND: In silico drug-target interaction (DTI) prediction plays an integral role in drug repositioning: the discovery of new uses for existing drugs. One popular method of drug repositioning is network-based DTI prediction, which uses complex network theory to predict DTIs from a drug-target network. Currently, most network-based DTI prediction is based on machine learning - methods such as Restricted Boltzmann Machines (RBM) or Support Vector Machines (SVM). These methods require additional information about the characteristics of drugs, targets and DTIs, such as chemical structure, genome sequence, binding types, causes of interactions, etc...
January 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28088632/nanosized-complexation-assemblies-housed-inside-reverse-micelles-churn-out-monocytic-delivery-cores-for-bendamustine-hydrochloride
#2
Yuvraj Singh, Anumandla Chandrashekhar, Jaya Gopal Meher, K K Durga Rao Viswanadham, Vivek K Pawar, Kavit Raval, Komal Sharma, Pankaj K Singh, Animesh Kumar, Manish K Chourasia
OBJECTIVE: We explore a plausible method of targeting bendamustine hydrochloride (BM) to circulatory monocytes by exploiting their intrinsic endocytic/phagocytic capability. METHODS: We do so by complexation of sodium alginate and chitosan inside dioctyl sulfo succinate sodium (AOT) reverse micelles to form bendamustine hydrochloride loaded nanoparticles (CANPs). Dynamic light scattering, electrophoretic mobility and UV spectroscopy were used to detail intra-micellar complexation dynamics and to prove that drug was co-captured during interaction of carbohydrate polymers...
January 11, 2017: European Journal of Pharmaceutics and Biopharmaceutics
https://www.readbyqxmd.com/read/28074015/electron-absorbed-fractions-in-an-image-based-microscopic-skeletal-dosimetry-model-of-chinese-adult-male
#3
Shenshen Gao, Li Ren, Rui Qiu, Zhen Wu, Chunyan Li, Junli Li
Based on the Chinese reference adult male voxel model, a set of microscopic skeletal models of Chinese adult male is constructed through the processes of computed tomography (CT) imaging, bone coring, micro-CT imaging, image segmentation, merging into macroscopic bone model and implementation in Geant4. At the step of image segmentation, a new bone endosteum (BE) segmentation method is realized by sampling. The set of model contains 32 spongiosa samples with voxel size of 19 μm cubes. The microscopic spongiosa bone data for Chinese adult male are provided...
January 10, 2017: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/28053904/comparative-study-on-the-osseointegration-of-implants-in-dog-mandibles-according-to-the-implant-surface-treatment
#4
Wook-Jae Yoon, Su-Gwan Kim, Ji-Su Oh, Jae-Seek You, Kyung-In Jeong, Sung-Chul Lim, Mi-Ae Jeong
OBJECTIVES: This study compared the impact of implant surface treatment on the stability and osseointegration of implants in dog mandibles. MATERIALS AND METHODS: Six adult dogs received a total of 48 implants that were prepared using four different surface treatments; resorbable blast media (RBM), hydroxyapatite (HA), hydrothermal-treated HA, and sand blasting and acid etching (SLA). Implants were installed, and dogs were separated into 2- and 4-week groups. Implant stability was evaluated via Periotest M, Osstell Mentor, and removal torque analyzers...
December 2016: Journal of the Korean Association of Oral and Maxillofacial Surgeons
https://www.readbyqxmd.com/read/28052885/a-micronutrient-fortified-young-child-formula-improves-the-iron-and-vitamin-d-status-of-healthy-young-european-children-a-randomized-double-blind-controlled-trial
#5
Marjolijn D Akkermans, Simone Rbm Eussen, Judith M van der Horst-Graat, Ruurd M van Elburg, Johannes B van Goudoever, Frank Brus
BACKGROUND: Iron deficiency (ID) and vitamin D deficiency (VDD) are common among young European children because of low dietary intakes and low compliance to vitamin D supplementation policies. Milk is a common drink for young European children. Studies evaluating the effect of milk fortification on iron and vitamin D status in these children are scarce. OBJECTIVE: We aimed to investigate the effect of a micronutrient-fortified young-child formula (YCF) on the iron and vitamin D status of young European children...
January 4, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/27992656/meta-regression-of-a-dose-response-relationship-of-methotrexate-in-mono-and-combination-therapy-in-dmard-naive-early-rheumatoid-arthritis-patients
#6
S A Bergstra, C F Allaart, T Stijnen, Rbm Landewé
OBJECTIVE: To investigate a possible short term dose-response relationship of initial treatment with methotrexate in monotherapy and combination therapy in recent onset rheumatoid arthritis (RA) patients. METHODS: A systematic literature search was performed on trials and cohorts including early, Disease Modifying Antirheumatic Drugs (DMARD) naive RA patients, treated with methotrexate, with data on clinical results within 6 months from treatment start. Cohen's effect sizes were calculated for the HAQ, ESR/CRP and/or DAS/DAS28 in 4 treatment groups: methotrexate monotherapy, or methotrexate in combination with synthetic (cs)DMARDs, biologic (b)DMARDs or glucocorticoids...
December 19, 2016: Arthritis Care & Research
https://www.readbyqxmd.com/read/27983605/effect-of-the-crac-peptide-vlnyyvw-on-mptp-opening-in-rat-brain-and-liver-mitochondria
#7
Tamara Azarashvili, Olga Krestinina, Yulia Baburina, Irina Odinokova, Vladimir Akatov, Igor Beletsky, John Lemasters, Vassilios Papadopoulos
The translocator protein (TSPO; 18 kDa) is a high-affinity cholesterol-binding protein located in the outer membrane of mitochondria. A domain in the C-terminus of TSPO was characterized as the cholesterol recognition/interaction amino acid consensus (CRAC). The ability of the CRAC domain to bind to cholesterol led us to hypothesize that this peptide may participate in the regulation of mitochondrial membrane permeability. Herein, we report the effect of the synthetic CRAC peptide, VLNYYVW, on mitochondrial permeability transition pore (mPTP) opening...
December 13, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27960519/confined-acoustic-phonons-in-colloidal-nanorod-heterostructures-investigated-by-nonresonant-raman-spectroscopy-and-finite-elements-simulations
#8
Mario Miscuglio, Miao-Ling Lin, Francesco Di Stasio, Ping-Heng Tan, Roman Krahne
Lattice vibrational modes in cadmium chalcogenide nanocrystals (NCs) have a strong impact on the carrier dynamics of excitons in such confined systems and on the optical properties of these nanomaterials. A prominent material for light emitting applications are CdSe/CdS core-shell dot-in-rods. Here we present a detailed investigation of the acoustic phonon modes in such dot-in-rods by nonresonant Raman spectroscopy with laser excitation energy lower than their bandgap. With high signal-to-noise ratio in the frequency range from 5-50 cm(-1), we reveal distinct Raman bands that can be related to confined extensional and radial-breathing modes (RBM)...
December 14, 2016: Nano Letters
https://www.readbyqxmd.com/read/27941224/selective-coherent-phonon-mode-generation-in-single-wall-carbon-nanotubes
#9
Ahmad R T Nugraha, Eddwi H Hasdeo, Riichiro Saito
The pulse-train technique within ultrafast pump-probe spectroscopy is theoretically investigated to excite a specific coherent phonon mode while suppressing the other phonon modes generated in single-wall carbon nanotubes (SWNTs). In particular, we focus on the selectivity of the radial breathing mode (RBM) and the G-band for a given SWNT. We find that if the repetition period of the pulse train matches with the integer multiple of the RBM phonon period, the RBM amplitude can be maintained while the amplitudes of the other modes are suppressed...
February 8, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/27896213/bone-cutting-capacity-and-osseointegration-of-surface-treated-orthodontic-mini-implants
#10
Ho-Young Kim, Sang-Cheol Kim
OBJECTIVE: The objective of the study was to evaluate the practicality and the validity of different surface treatments of self-drilling orthodontic mini-implants (OMIs) by comparing bone cutting capacity and osseointegration. METHODS: Self-drilling OMIs were surface-treated in three ways: Acid etched (Etched), resorbable blasting media (RBM), partially resorbabla balsting media (Hybrid). We compared the bone cutting capacity by measuring insertion depths into artificial bone (polyurethane foam)...
November 2016: Korean Journal of Orthodontics
https://www.readbyqxmd.com/read/27871994/root-bark-of-morus-alba-ameliorates-the-depressive-like-behaviors-in-diabetic-rats
#11
Mei Ye, Yuting Ke, Bingyang Liu, Yanyan Yuan, Fuyan Wang, Shizhong Bu, Yisheng Zhang
Diabetes-induced depression is one of the severe chronic complications of diabetes mellitus. Up to now, there are only a few effective medicines to prevent or manage the co-morbidity of diabetes and depression. The present study was to investigate the effect of root bark of Morus alba (RBM) on depressive-like behaviors in the diabetic rats established by a high fat diet and a low dose of streptozotocin. Depressive-like behaviors were measured by the open field test, locomotor activity test and forced swimming test...
January 10, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/27858555/the-occurrence-of-progressive-bone-loss-around-the-anodized-surface-implants-and-rbm-implants-a-retrospective-cohort-study
#12
Hee-Chang Kim, Shin-Young Park, Min-Su Han, Yong-Moo Lee, Young Ku, In-Chul Rhyu, Yang-Jo Seol
BACKGROUND: This study was performed to evaluate the occurrence of progressive bone loss around implants with different implant surfaces. METHODS: We retrospectively examined 2,517 implants in 903 patients, including 1,147 anodized-surface implants in 454 patients and 1,370 resorbable blasting media (RBM)-surface implants in 449 patients, which were placed from January 2006 to December 2010. Through regular check-up radiographs and records, the presence of progressive bone loss up to more than 50% of the fixture length was investigated...
November 18, 2016: Journal of Periodontology
https://www.readbyqxmd.com/read/27842489/a-novel-phase-variant-of-the-cholera-pathogen-shows-stress-adaptive-cryptic-transcriptomic-signatures
#13
Bliss Lambert, Maheshi Dassanayake, Dong-Ha Oh, Shana B Garrett, Sang-Yeol Lee, Gregg S Pettis
BACKGROUND: In a process known as phase variation, the marine bacterium and cholera pathogen Vibrio cholerae alternately expresses smooth or rugose colonial phenotypes, the latter being associated with advanced biofilm architecture and greater resistance to ecological stress. To define phase variation at the transcriptomic level in pandemic V. cholerae O1 El Tor strain N16961, we compared the RNA-seq-derived transcriptomes among the smooth parent N16961, its rugose derivative (N16961R) and a smooth form obtained directly from the rugose at high frequencies consistent with phase variation (N16961SD)...
November 14, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27815431/leukaemia-mortality-and-low-dose-ionising-radiation-in-the-wismut-uranium-miner-cohort-1946-2013
#14
Michaela Kreuzer, Christina Sobotzki, Nora Fenske, James W Marsh, Maria Schnelzer
OBJECTIVES: To examine the risk of death from leukaemia in relation to occupational chronic low-level external and internal radiation exposure in a cohort of 58 972 former German uranium miners with mortality follow-up from 1946 to 2013. METHODS: The red bone marrow (RBM) dose from low-linear energy transfer (LET) (mainly external γ-radiation) and high-LET (mainly radon gas) radiation was estimated based on a job-exposure matrix and biokinetic/dosimetric models...
November 4, 2016: Occupational and Environmental Medicine
https://www.readbyqxmd.com/read/27814835/what-makes-rbm-online-special-the-chief-editor-s-point-of-view
#15
EDITORIAL
Bart C J M Fauser
No abstract text is available yet for this article.
November 2016: Reproductive Biomedicine Online
https://www.readbyqxmd.com/read/27807906/activin-a-and-follistatin-in-patients-with-asthma-does-severity-make-the-difference
#16
Anastasia Papaporfyriou, Petros Bakakos, Konstantinos Kostikas, Georgios Papatheodorou, Georgios Hillas, Rodoula Trigidou, Patroklos Katafigiotis, Nikolaos G Koulouris, Spyros A Papiris, Stelios Loukides
BACKGROUND AND OBJECTIVE: Activin A is a pleiotropic cytokine holding a fundamental role in inflammation and tissue remodelling. Follistatin can modulate the bioactivity of activin. We aimed to measure activin A and follistatin in sputum supernatants and bronchoalveolar lavage (BAL) of asthmatic patients and to determine the possible associations with severity as well as with inflammatory and remodelling indices. METHODS: A total of 58 asthmatic patients (33 with severe refractory asthma (SRA)) and 10 healthy controls underwent sputum induction for % cells, activin A, follistatin, eosinophilic cationic protein (ECP), transforming growth factor beta 1 (TGF-β1), IL-13 and IL-8 measurements...
November 2, 2016: Respirology: Official Journal of the Asian Pacific Society of Respirology
https://www.readbyqxmd.com/read/27796954/using-3d-culture-of-primary-mammary-epithelial-cells-to-define-molecular-entities-required-for-acinus-formation-analyzing-map-kinase-phosphatases
#17
Malgorzata Gajewska, Sara McNally
Three-dimensional (3D) cell cultures on reconstituted basement membrane (rBM) enable the study of complex interactions between extracellular matrix (ECM) components and epithelial cells, which are crucial for the establishment of cell polarity and functional development of epithelia. 3D cultures of mammary epithelial cells (MECs) on Matrigel (a laminin-rich ECM derived from the Engelbreth-Holm-Swarm (EHS) murine tumor) promote interactions of MECs with the matrix via integrins, leading to formation of spherical monolayers of polarized cells surrounding a hollow lumen (acini)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27795425/recombinant-receptor-binding-domains-of-multiple-middle-east-respiratory-syndrome-coronaviruses-mers-covs-induce-cross-neutralizing-antibodies-against-divergent-human-and-camel-mers-covs-and-antibody-escape-mutants
#18
Wanbo Tai, Yufei Wang, Craig A Fett, Guangyu Zhao, Fang Li, Stanley Perlman, Shibo Jiang, Yusen Zhou, Lanying Du
: Middle East respiratory syndrome coronavirus (MERS-CoV) binds to cellular receptor dipeptidyl peptidase 4 (DPP4) via the spike (S) protein receptor-binding domain (RBD). The RBD contains critical neutralizing epitopes and serves as an important vaccine target. Since RBD mutations occur in different MERS-CoV isolates and antibody escape mutants, cross-neutralization of divergent MERS-CoV strains by RBD-induced antibodies remains unknown. Here, we constructed four recombinant RBD (rRBD) proteins with single or multiple mutations detected in representative human MERS-CoV strains from the 2012, 2013, 2014, and 2015 outbreaks, respectively, and one rRBD protein with multiple changes derived from camel MERS-CoV strains...
January 1, 2017: Journal of Virology
https://www.readbyqxmd.com/read/27778399/effect-of-substituents-and-initial-degree-of-functionalization-of-alkylated-single-walled-carbon-nanotubes-on-their-thermal-stability-and-photoluminescence-properties
#19
Yutaka Maeda, Yuya Takehana, Jing-Shuang Dang, Mitsuaki Suzuki, Michio Yamada, Shigeru Nagase
Alkylated single-walled carbon nanotubes (SWNTs) have been thermally treated to determine the influence of substituents and the degree of functionalization on their thermal stability and photoluminescence (PL) properties. Alkylated SWNTs were prepared by treating SWNTs with sodium naphthalenide and alkyl bromide. The defunctionalization of the alkylated SWNTs was monitored by absorption and Raman spectra. Selective recovery of the characteristic absorption and radial breathing mode peaks was observed during the thermal treatment, which indicates that the thermal stability of the alkylated SWNTs decreases with increases in SWNT diameter and degree of functionalization...
October 24, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27711454/calculation-of-raman-parameters-of-real-size-zigzag-n-0-single-walled-carbon-nanotubes-using-finite-size-models
#20
Teobald Kupka, Michal Stachów, Leszek Stobiński, Jakub Kaminský
Structural and selected Raman features of pristine single-walled carbon nanotubes (SWCTNs) with diameters from 0.4 to 1.2 nm and total lengths up to 2.15 nm were studied using the density functional theory (DFT) at the UB3LYP/6-31G* level. Models of different lengths (1, 4, 6 and 10 adjacent bamboo-units) of zigzag (n, 0) SWCNTs, for n ranging from 5 to 15, were studied. Highly systematic changes of individual CC bond lengths and angles along the nanotube axis were observed and described for the longest models...
September 14, 2016: Physical Chemistry Chemical Physics: PCCP
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