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Structure prediction

Matthew J Mason, Hannah L Cornwall, Ewan St J Smith
Although increasingly popular as a laboratory species, very little is known about the peripheral auditory system of the naked mole-rat, Heterocephalus glaber. In this study, middle and inner ears of naked mole-rats of a range of ages were examined using micro-computed tomography and dissection. The ears of five other bathyergid species (Bathyergus suillus, Cryptomys hottentotus, Fukomys micklemi, Georychus capensis and Heliophobius argenteocinereus) were examined for comparative purposes. The middle ears of bathyergids show features commonly found in other members of the Ctenohystrica rodent clade, including a fused malleus and incus, a synovial stapedio-vestibular articulation and the loss of the stapedius muscle...
2016: PloS One
Duyu Chen, Wen Yih Aw, Danelle Devenport, Salvatore Torquato
In proliferating epithelia of mammalian skin, cells of irregular polygon-like shapes pack into complex, nearly flat two-dimensional structures that are pliable to deformations. In this work, we employ various sensitive correlation functions to quantitatively characterize structural features of evolving packings of epithelial cells across length scales in mouse skin. We find that the pair statistics in direct space (correlation function) and Fourier space (structure factor) of the cell centroids in the early stages of embryonic development show structural directional dependence (statistical anisotropy), which is a reflection of the fact that cells are stretched, which promotes uniaxial growth along the epithelial plane...
December 6, 2016: Biophysical Journal
Christina Grønberg, Oleg Sitsel, Erik Lindahl, Pontus Gourdon, Magnus Andersson
Cu(+)-specific P-type ATPase membrane protein transporters regulate cellular copper levels. The lack of crystal structures in Cu(+)-binding states has limited our understanding of how ion entry and binding are achieved. Here, we characterize the molecular basis of Cu(+) entry using molecular-dynamics simulations, structural modeling, and in vitro and in vivo functional assays. Protein structural rearrangements resulting in the exposure of positive charges to bulk solvent rather than to lipid phosphates indicate a direct molecular role of the putative docking platform in Cu(+) delivery...
December 6, 2016: Biophysical Journal
Emad Mohamed Elgendy, Yasuha Arai, Norihito Kawashita, Tomo Daidoji, Tatsuya Takagi, Madiha Salah Ibrahim, Takaaki Nakaya, Yohei Watanabe
Highly pathogenic avian influenza virus H5N1 infects a wide range of host species, with a few cases of sporadic pigeon infections reported in the Middle East and Asia. However, the role of pigeons in the ecology and evolution of H5N1 viruses remains unclear. We previously reported two H5N1 virus strains, isolated from naturally infected pigeons in Egypt, that have several unique mutations in their viral polymerase genes. Here, we investigated the effect of these mutations on H5N1 polymerase activity and viral growth and identified three mutations that affected viral polymerase activity...
December 7, 2016: Journal of General Virology
Hanno Schmiedt, Per Jensen, Stephan Schlemmer
The concept of molecular structure is traditionally considered to be virtually fundamental. However, it breaks down in extremely flexible molecules, whose dynamics are governed by large-amplitude motions. For the dynamics of molecules with free internal rotations, we therefore propose a five-dimensional rigid rotor model, with states characterized by two generalized angular momentum quantum numbers and a rotational constant B. The quantum numbers characterize a 5D angular-momentum vector, super-j, which describes collective rotations that involve both the internal and the overall rotation...
November 25, 2016: Physical Review Letters
A V Poshakinskiy, A N Poddubny, A Fainstein
We demonstrate that the parity-time symmetry for sound is realized in laser-pumped multiple-quantum-well structures. Breaking of the parity-time symmetry for the phonons with wave vectors corresponding to the Bragg condition makes the structure a highly selective acoustic wave amplifier. Single-mode distributed feedback phonon lasing is predicted for structures with realistic parameters.
November 25, 2016: Physical Review Letters
Wenliang Zhang, J T Park, Xingye Lu, Yuan Wei, Xiaoyan Ma, Lijie Hao, Pengcheng Dai, Zi Yang Meng, Yi-Feng Yang, Huiqian Luo, Shiliang Li
The origin of nematic order remains one of the major debates in iron-based superconductors. In theories based on spin nematicity, one major prediction is that the spin-spin correlation length at (0,π) should decrease with decreasing temperature below the structural transition temperature T_{s}. Here, we report inelastic neutron scattering studies on the low-energy spin fluctuations in BaFe_{1.935}Ni_{0.065}As_{2} under uniaxial pressure. Both intensity and spin-spin correlation start to show anisotropic behavior at high temperature, while the reduction of the spin-spin correlation length at (0,π) happens just below T_{s}, suggesting the strong effect of nematic order on low-energy spin fluctuations...
November 25, 2016: Physical Review Letters
Isabel Reinecke, Marcus-Hillert Schultze-Mosgau, Rüdiger Nave, Heinz Schmitz, Bart A Ploeger
Pharmacokinetics (PK) of anastrozole (ATZ) and levonorgestrel (LNG) released from an intravaginal ring (IVR) intended to treat endometriosis symptoms were characterized, and the exposure-response relationship focusing on the development of large ovarian follicle-like structures was investigated by modeling and simulation to support dose selection for further studies. A population PK analysis and simulations were performed for ATZ and LNG based on clinical phase 1 study data from 66 healthy women. A PK/PD model was developed to predict the probability of a maximum follicle size ≥30 mm and the potential contribution of ATZ beside the known LNG effects...
December 7, 2016: Journal of Clinical Pharmacology
Leonardo Correa, Bruno Borguesan, Camilo Farfan, Mario Inostroza-Ponta, Marcio Dorn
Memetic Algorithms are population-based metaheuristics intrinsically concerned with exploiting all available knowledge about the problem under study. The incorporation of problem domain knowledge is not an optional mechanism, but a fundamental feature of the Memetic Algorithms. In this paper, we present a Memetic Algorithm to tackle the three-dimensional protein structure prediction problem. The method uses a structured population and incorporates a Simulated Annealing algorithm as a local search strategy, as well as ad-hoc crossover and mutation operators to deal with the problem...
December 2, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Jeremy Brown, Conor O'Brien, Sarah Leung, Kristoffel Dumon, David Lee, Katherine Kuchenbecker
OBJECTIVE: Most trainees begin learning robotic minimally invasive surgery by performing inanimate practice tasks with clinical robots such as the Intuitive Surgical da Vinci. Expert surgeons are commonly asked to evaluate these performances using standardized five-point rating scales, but doing such ratings is time consuming, tedious, and somewhat subjective. This article presents an automatic skill evaluation system that analyzes only the contact force with the task materials, the broad-bandwidth accelerations of the robotic instruments and camera, and the task completion time...
December 2, 2016: IEEE Transactions on Bio-medical Engineering
Chengwu Yang, Xiaojuan Yu, Stefan Heißler, Alexei Nefedov, Sara Colussi, Jordi Llorca, Alessandro Trovarelli, Yuemin Wang, Christof Wöll
The surface atomic arrangement of metal oxides determines their physical and chemical properties, and the ability to control and optimize structural parameters is of crucial importance for many applications, in particular in heterogeneous catalysis and photocatalysis. Whereas the structures of macroscopic single crystals can be determined with established methods, for nanoparticles (NPs), this is a challenging task. Herein, we describe the use of CO as a probe molecule to determine the structure of the surfaces exposed by rod-shaped ceria NPs...
December 7, 2016: Angewandte Chemie
Enoch Teye-Kwadjo, Ashraf Kagee, Hermann Swart
BACKGROUND: Growing cross-sectional research shows that the theory of planned behaviour (TPB) is robust in predicting intentions to use condoms and condom use behaviour. Yet, little is known about the TPB's utility in explaining intentions to use condoms and condom use behaviour over time. METHODS: This study used a longitudinal design and latent variable structural equation modelling to test the longitudinal relationships postulated by the TPB. School-going youths in Ghana provided data on attitudes, subjective norms, perceived control, intentions, and behaviour regarding condom use at three time points, spaced approximately three months apart...
December 7, 2016: Applied Psychology. Health and Well-being
Cedric Tan Kai Wei, Philippa Doyle, Emma Bagshaw, David S Richardson, Stuart Wigby, Tommaso Pizzari
In structured populations, competition for reproductive opportunities should be relaxed among related males. The few tests of this prediction often neglect the fact that sexual selection acts through multiple mechanisms, both before and after mating. We performed experiments to study the role of within-group male relatedness across pre- and postcopulatory mechanisms of sexual selection in social groups of red junglefowl, Gallus gallus, in which two related males and one unrelated male competed over females unrelated to all the males...
December 7, 2016: Evolution; International Journal of Organic Evolution
Alexandra C H Nowakowski, Katelyn Y Graves
We assess how well differences in ethnoracial background may predict timing of menopause among females in the USA and whether or not inflammatory biomarker levels appear to mediate these overall associations. We use data from the National Social Life, Health, and Aging Project (NSHAP) to model apparent net effects from race on menopausal onset, as well as possible mediating influences from the inflammatory biomarker C-reactive protein (CRP). Using continuous time event history analysis, we assess and frame overall relationships between race and menopausal age...
December 6, 2016: Journal of Racial and Ethnic Health Disparities
María José Soler, Carmen Dasí, Juan Carlos Ruiz, Teresa Cervera
This study presents a normative database of Spanish restricted length word stems that provides useful information for the selection of stimuli in memory experiments with Word Stem Completion (WSC) tasks. The database includes indices relative to stems (total baseline completion, priming baseline completion, priming, number of completions, ratio between given and deleted letters, and syllabic structure), and indices relative to characteristics of the words used to obtain the stems (frequency, familiarity, number of meanings, length, number of syllables, arousal, and valence)...
December 6, 2016: Behavior Research Methods
Baptiste Schindler, Gina Renois-Predelus, Nassiba Bagdadi, Sihem Melizi, Loïc Barnes, Stéphane Chambert, Abdul-Rahman Allouche, Isabelle Compagnon
We report an original MS-based hyphenated method for the elucidation of the epimerization in GAG fragments. It consists of measuring simultaneously the MS/MS spectrum and the gas phase IR spectrum to gain direct structural information. This is possible using a customized MS instrument, modified to allow injection of a tunable IR laser inside of the instrument for in situ spectroscopy of trapped ions. The proof of principle of this approach is performed in the case of a hyaluronic acid tetrasaccharide standard...
December 7, 2016: Glycoconjugate Journal
José Carlos Ferrão, Mónica Duarte Oliveira, Filipe Janela, Henrique M G Martins
BACKGROUND: EHR systems have high potential to improve healthcare delivery and management. Although structured EHR data generates information in machine-readable formats, their use for decision support still poses technical challenges for researchers due to the need to preprocess and convert data into a matrix format. During our research, we observed that clinical informatics literature does not provide guidance for researchers on how to build this matrix while avoiding potential pitfalls...
December 7, 2016: Applied Clinical Informatics
Qiaoqiao Teng, Han Vinh Huynh
The properties and reactivities of transition metal complexes are rooted in the stereoelectronic properties of their ligands. While the bulk of a ligand can be easily evaluated and compared by the drawing of its Lewis structure, prediction on the electronic contributions is often less straightforward. Thus, several electronic parameters have been developed for the experimental evaluation of ligands throughout the years. This article accounts for the most recent one developed by the Huynh group, which employs (13)C NMR spectroscopy to determine ligand donor strengths using N-heterocyclic carbene complexes...
December 7, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Masaaki Kotera, Susumu Goto
Metabolic pathway reconstruction presents a challenge for understanding metabolic pathways in organisms of interest. Different strategies, i.e., reference-based vs. de novo, must be used for pathway reconstruction depending on the availability of well-characterized enzymatic reactions. If at least one enzyme is already known to catalyze a reaction, its amino acid sequence can be used as a reference for identifying homologous enzymes in the genome of an organism of interest. Where there is no known enzyme able to catalyze a corresponding reaction, however, the reaction and the corresponding enzyme must be predicted de novo from chemical transformations of the putative substrate-product pair...
2016: Biophysics and Physicobiology
Takako Sakano, Md Iqbal Mahamood, Takefumi Yamashita, Hideaki Fujitani
The accurate prediction of a ligand-protein complex structure is important for computer-assisted drug development. Although many docking methods have been developed over the last three decades, the success of binding structure prediction remains greatly limited. The purpose of this study was to demonstrate the usefulness of molecular dynamics (MD) simulation in assessing a docking pose predicted using a docking program. If the predicted pose is not unstable in an aqueous environment, MD simulation equilibrates the system and removes the ligand from the predicted position...
2016: Biophysics and Physicobiology
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