keyword
MENU ▼
Read by QxMD icon Read
search

Structure prediction

keyword
https://www.readbyqxmd.com/read/29169108/identification-of-mutagenic-transformation-products-generated-during-oxidation-of-3-methyl-4-nitrophenol-solutions-by-orbitrap-tandem-mass-spectrometry-and-quantitative-structure-activity-relationship-analyses
#1
Taku Matsushita, Shiho Honda, Taisuke Kuriyama, Yuki Fujita, Takashi Kondo, Yoshihiko Matsui, Nobutaka Shirasaki, Hirokazu Takanashi, Takashi Kameya
We used Ames assays to investigate the effects of ozonation (designated O3), ozonation followed by chlorination (O3/Cl), an advanced oxidation process (AOP, UV/H2O2), and AOP followed by chlorination (AOP/Cl) on the mutagenicity of solutions of 3-methyl-4-nitrophenol (3M4NP), a major environmental degradation product of the organophosphorus insecticide fenitrothion. Whereas O3 did not induce mutagenicity, O3/Cl, AOP, and AOP/Cl converted 3M4NP into mutagenic transformation products (TPs). Using liquid chromatography-mass spectrometry, we detected a total of 138 peaks in the solutions subjected to O3/Cl, AOP, and AOP/Cl...
November 14, 2017: Water Research
https://www.readbyqxmd.com/read/29169074/flow-stagnation-volume-and-abdominal-aortic-aneurysm-growth-insights-from-patient-specific-computational-flow-dynamics-of-lagrangian-coherent-structures
#2
Florian Joly, Gilles Soulez, Damien Garcia, Simon Lessard, Claude Kauffmann
Abdominal aortic aneurysms (AAA) are localized, commonly-occurring dilations of the aorta. When equilibrium between blood pressure (loading) and wall mechanical resistance is lost, rupture ensues, and patient death follows, if not treated immediately. Experimental and numerical analyses of flow patterns in arteries show direct correlations between wall shear stress and wall mechano-adaptation with the development of zones prone to thrombus formation. For further insights into AAA flow topology/growth interaction, a workout of patient-specific computational flow dynamics (CFD) is proposed to compute finite-time Lyapunov exponents and extract Lagrangian-coherent structures (LCS)...
November 6, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29169034/greater-cortical-thickness-within-the-limbic-visceromotor-network-predicts-higher-levels-of-trait-emotional-awareness
#3
Ryan Smith, Sahil Bajaj, Natalie S Dailey, Anna Alkozei, Courtney Smith, Anna Sanova, Richard D Lane, William D S Killgore
Previous studies of trait emotional awareness (EA) have not yet examined whether differences in cortical structure might account for differences in EA. Based on previous research on the relationship between EA and both emotion conceptualization and visceromotor control processes, we tested two hypotheses in a sample of 26 healthy participants: that higher EA would be predicted by greater cortical thickness within (1) regions of the default mode network (DMN; linked with conceptualization processes), and/or (2) regions of the limbic network (linked with affect generation and visceromotor control processes)...
November 20, 2017: Consciousness and Cognition
https://www.readbyqxmd.com/read/29168914/shortfall-of-b3lyp-in-reproducing-nmr-jch-couplings-in-some-isomeric-epoxy-structures-with-strong-stereoelectronic-effects-a-benchmark-study-of-dft-functionals
#4
Ryszard B Nazarski, Jasper Adamson, Jüri Jarvet, Tõnis Pehk Pehk, Riina Aav
Unprecedented scattered plots of calculated vs. measured 2,3JCHs in six densely oxygen-functionalized epoxides were found with some B3LYP protocols, an effect attributed to stereoelectronic effects in play. Hence, 27 other exchange-correlation density functionals (xc DFs) were benchmarked in this work. Very good results were achieved with mPW1PW91 and PBE0 used in conjunction with the pcJ-1 basis set (BS) of moderate size. A statistical analysis of 53 relationships between the predicted and observed 2,3JCH sets is presented...
November 23, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/29168743/synthesis-and-anticandidal-activity-evaluation-of-new-benzimidazole-thiazole-derivatives
#5
Zafer Asım Kaplancıklı, Serkan Levent, Derya Osmaniye, Begüm Nurpelin Sağlık, Ulviye Acar Çevik, Betül Kaya Çavuşoğlu, Yusuf Özkay, Sinem Ilgın
Azole-based antifungal agents constitute one of the important classes of antifungal drugs. Hence, in the present work, 12 new benzimidazole-thiazole derivatives 3a-3l were synthesized to evaluate their anticandidal activity against C.albicans, C.glabrata, C.krusei, and C.parapsilopsis. The structures of the newly synthesized compounds 3a-3l were confirmed by IR, ¹H-NMR, (13)C-NMR, and ESI-MS spectroscopic methods. ADME parameters of synthesized compounds 3a-3l were predicted by an in-slico study and it was determined that all synthesized compounds may have a good pharmacokinetic profile...
November 23, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29168281/a-review-of-urban-impacts-on-avian-life-history-evolution-does-city-living-lead-to-slower-pace-of-life
#6
REVIEW
Tuul Sepp, Kevin J McGraw, Ants Kaasik, Mathieu Giraudeau
The concept of a pace-of-life syndrome describes inter- and intraspecific variation in several life-history traits along a slow-to-fast pace-of-life continuum, with long lifespans, low reproductive and metabolic rates, and elevated somatic defences at the slow end of the continuum and the opposite traits at the fast end. Pace-of-life can vary in relation to local environmental conditions (e.g. latitude, altitude), and here we propose that this variation may also occur along an anthropogenically modified environmental gradient...
November 23, 2017: Global Change Biology
https://www.readbyqxmd.com/read/29168072/estimates-for-the-acoustical-stimulation-and-heating-of-multiphase-biotissue
#7
T I Zohdi, R Krone
Low-intensity, unfocused, ultrasound-induced diathermy can produce undesired temperature increases at the interface of adjacent tissues within the body; particularly, at the interface of soft tissue and bone. This study provides a computational framework for predicting an upper bound on the temperature profile within a multiphase system composed of gel pad (water), tissue and bone from an input of acoustic energy, at frequencies and power levels consistent with applications of therapeutic hyperthermia. The model consists of solving a (one-dimensional) spatially discretized bioheat transfer equation via finite-difference method and updating the solution in time with a forward-Euler scheme...
November 22, 2017: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/29168071/influence-of-functionally-graded-pores-on-bone-ingrowth-in-cementless-hip-prosthesis-a-finite-element-study-using-mechano-regulatory-algorithm
#8
Faris Tarlochan, Hassan Mehboob, Ali Mehboob, Seung-Hwan Chang
Cementless hip prostheses with porous outer coating are commonly used to repair the proximally damaged femurs. It has been demonstrated that stability of prosthesis is also highly dependent on the bone ingrowth into the porous texture. Bone ingrowth is influenced by the mechanical environment produced in the callus. In this study, bone ingrowth into the porous structure was predicted by using a mechano-regulatory model. Homogenously distributed pores (200 and 800 [Formula: see text]m in diameter) and functionally graded pores along the length of the prosthesis were introduced as a porous coating...
November 22, 2017: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/29167982/successional-changes-in-trophic-interactions-support-a-mechanistic-model-of-post-fire-population-dynamics
#9
Annabel L Smith
Models based on functional traits have limited power in predicting how animal populations respond to disturbance because they do not capture the range of demographic and biological factors that drive population dynamics, including variation in trophic interactions. I tested the hypothesis that successional changes in vegetation structure, which affected invertebrate abundance, would influence growth rates and body condition in the early-successional, insectivorous gecko Nephrurus stellatus. I captured geckos at 17 woodland sites spanning a succession gradient from 2 to 48 years post-fire...
November 22, 2017: Oecologia
https://www.readbyqxmd.com/read/29167930/planarian-cholinesterase-molecular-and-functional-characterization-of-an-evolutionarily-ancient-enzyme-to-study-organophosphorus-pesticide-toxicity
#10
Danielle Hagstrom, Siqi Zhang, Alicia Ho, Eileen S Tsai, Zoran Radić, Aryo Jahromi, Kelson J Kaj, Yingtian He, Palmer Taylor, Eva-Maria S Collins
The asexual freshwater planarian Dugesia japonica has emerged as a medium-throughput alternative animal model for neurotoxicology. We have previously shown that D. japonica are sensitive to organophosphorus pesticides (OPs) and characterized the in vitro inhibition profile of planarian cholinesterase (DjChE) activity using irreversible and reversible inhibitors. We found that DjChE has intermediate features of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). Here, we identify two candidate genes (Djche1 and Djche2) responsible for DjChE activity...
November 22, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/29167570/different-protein-protein-interface-patterns-predicted-by-different-machine-learning-methods
#11
Wei Wang, Yongxiao Yang, Jianxin Yin, Xinqi Gong
Different types of protein-protein interactions make different protein-protein interface patterns. Different machine learning methods are suitable to deal with different types of data. Then, is it the same situation that different interface patterns are preferred for prediction by different machine learning methods? Here, four different machine learning methods were employed to predict protein-protein interface residue pairs on different interface patterns. The performances of the methods for different types of proteins are different, which suggest that different machine learning methods tend to predict different protein-protein interface patterns...
November 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29167557/factors-affecting-gebv-accuracy-with-single-step-bayesian-models
#12
Lei Zhou, Raphael Mrode, Shengli Zhang, Qin Zhang, Bugao Li, Jian-Feng Liu
A single-step approach to obtain genomic prediction was first proposed in 2009. Many studies have investigated the components of GEBV accuracy in genomic selection. However, it is still unclear how the population structure and the relationships between training and validation populations influence GEBV accuracy in terms of single-step analysis. Here, we explored the components of GEBV accuracy in single-step Bayesian analysis with a simulation study. Three scenarios with various numbers of QTL (5, 50, and 500) were simulated...
November 23, 2017: Heredity
https://www.readbyqxmd.com/read/29167364/fear-of-predation-shapes-social-network-structure-and-the-acquisition-of-foraging-information-in-guppy-shoals
#13
Matthew J Hasenjager, Lee A Dugatkin
Spatio-temporal variation in predation risk is predicted to select for plastic anti-predator responses, which may in turn impact the fine-scale social structure of prey groups and processes mediated by that structure. To test these predictions, we manipulated the ambient predation risk experienced by Trinidadian guppy (Poecilia reticulata) groups before quantifying their social networks and recording individual latencies to approach and solve a novel foraging task. High-risk conditions drove the formation of social networks that were more strongly assorted by body size than those exposed to low ambient risk and promoted longer durations of contact between preferred partners...
November 29, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29167180/asymmetry-of-inverted-topology-repeats-in-the-ae1-anion-exchanger-suggests-an-elevator-like-mechanism
#14
Emel Ficici, José D Faraldo-Gómez, Michael L Jennings, Lucy R Forrest
The membrane transporter anion exchanger 1 (AE1), or band 3, is a key component in the processes of carbon-dioxide transport in the blood and urinary acidification in the renal collecting duct. In both erythrocytes and the basolateral membrane of the collecting-duct α-intercalated cells, the role of AE1 is to catalyze a one-for-one exchange of chloride for bicarbonate. After decades of biochemical and functional studies, the structure of the transmembrane region of AE1, which catalyzes the anion-exchange reaction, has finally been determined...
November 22, 2017: Journal of General Physiology
https://www.readbyqxmd.com/read/29167151/substituted-cysteine-accessibility-and-cross-linking-identify-an-exofacial-cleft-in-the-7-th-and-8-th-helices-of-the-proton-coupled-folate-transporter-slc46a1
#15
Srinivas Aluri, Rongbao Zhao, Andras Fiser, I David Goldman
The proton-coupled folate transporter (PCFT-SLC46A1) is required for folate transport across the apical membrane of the small intestine and across the choroid plexus. This study focuses on the structure/function of the 7(th) transmembrane domain (TMD), and its relationship to the 8th TMD as assessed by the substituted cysteine accessibility method (SCAM) and dicysteine cross-linking. Nine exofacial residues (I278C; H281C-L288C) of 23 residues in the 7(th) TMD were accessible to 2-((Biotinoyl)amino)ethyl methanethiosulfonate (MTSEA-biotin)...
November 22, 2017: American Journal of Physiology. Cell Physiology
https://www.readbyqxmd.com/read/29167050/insecure-attachment-style-and-cumulative-traumatic-life-events-in-patients-with-somatoform-pain-disorder-a-cross-sectional-study
#16
Yeliz Nacak, Eva Morawa, Daniela Tuffner, Yesim Erim
OBJECTIVE: Current models assume somatoform pain disorder (SPD) to be the result of a complex interaction between bio- and psychosocial factors, but the etiology is still not well understood. This study aimed to investigate the distribution of attachment style and the frequency of traumatic life events, especially childhood adversities, in patients with SPD compared to healthy controls. METHODS: We compared 65 patients with SPD (confirmed by Structured Clinical Interview, SCID-I) to 65 age- and gender-matched healthy controls...
December 2017: Journal of Psychosomatic Research
https://www.readbyqxmd.com/read/29166618/ipsc-based-compound-screening-and-in%C3%A2-vitro-trials-identify-a-synergistic-anti-amyloid-%C3%AE-combination-for-alzheimer-s-disease
#17
Takayuki Kondo, Keiko Imamura, Misato Funayama, Kayoko Tsukita, Michiyo Miyake, Akira Ohta, Knut Woltjen, Masato Nakagawa, Takashi Asada, Tetsuaki Arai, Shinobu Kawakatsu, Yuishin Izumi, Ryuji Kaji, Nobuhisa Iwata, Haruhisa Inoue
In the process of drug development, in vitro studies do not always adequately predict human-specific drug responsiveness in clinical trials. Here, we applied the advantage of human iPSC-derived neurons, which offer human-specific drug responsiveness, to screen and evaluate therapeutic candidates for Alzheimer's disease (AD). Using AD patient neurons with nearly 100% purity from iPSCs, we established a robust and reproducible assay for amyloid β peptide (Aβ), a pathogenic molecule in AD, and screened a pharmaceutical compound library...
November 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/29166323/strength-affect-regulation-and-subcortical-morphology-in-military-pilots
#18
David Cárdenas, Iker Madinabeitia, Jesús Vera, José Cesar Perales, Amador García-Ramos, Enrique Ortega, Elvira Catena-Verdejo, Andrés Catena
INTRODUCTION: Previous studies have shown links of body composition and fitness measures with brain structure, as well as with different aspects of emotional adjustment and well-being. However, the possible role of trait emotion-regulation success in the relationship between fitness/body composition and emotion-related subcortical structures have never been directly addressed METHODS: 23 elite helicopter pilots were assessed in fat mass percentage, an endurance test to volitional exhaustion, bench-press power output, and negative urgency (trait affect regulation failure)...
November 20, 2017: Medicine and Science in Sports and Exercise
https://www.readbyqxmd.com/read/29166097/volatility-of-the-catalytic-hydrogenation-products-of-1-4-bis-phenylethynyl-benzene
#19
Hom N Sharma, Elizabeth A Sangalang, Cheng K Saw, Gareth A Cairns, William McLean, Robert S Maxwell, Long N Dinh
Measurements of equilibrium vapor pressures by effusion thermogravimetry and melting points by differential scanning calorimetry reveal that the melting temperature and equilibrium vapor pressures of 1,4-bis(phenylethynyl)benzene (DEB) do not vary monotonically with the hydrogenation extent. Contrary to intuition which suggests increasing volatility with hydrogenation, results indicate decreasing volatility for the first two hydrogenation steps before a non-monotonic upward trend, in which trans-isomers are less volatile...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166078/perspective-theory-and-simulation-of-hybrid-halide-perovskites
#20
Lucy D Whalley, Jarvist M Frost, Young-Kwang Jung, Aron Walsh
Organic-inorganic halide perovskites present a number of challenges for first-principles atomistic materials modeling. Such "plastic crystals" feature dynamic processes across multiple length and time scales. These include the following: (i) transport of slow ions and fast electrons; (ii) highly anharmonic lattice dynamics with short phonon lifetimes; (iii) local symmetry breaking of the average crystallographic space group; (iv) strong relativistic (spin-orbit coupling) effects on the electronic band structure; and (v) thermodynamic metastability and rapid chemical breakdown...
June 14, 2017: Journal of Chemical Physics
keyword
keyword
59621
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"