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https://www.readbyqxmd.com/read/27934891/structure-determination-of-molecules-in-an-alignment-laser-field-by-femtosecond-photoelectron-diffraction-using-an-x-ray-free-electron-laser
#1
Shinichirou Minemoto, Takahiro Teramoto, Hiroshi Akagi, Takashi Fujikawa, Takuya Majima, Kyo Nakajima, Kaori Niki, Shigeki Owada, Hirofumi Sakai, Tadashi Togashi, Kensuke Tono, Shota Tsuru, Ken Wada, Makina Yabashi, Shintaro Yoshida, Akira Yagishita
We have successfully determined the internuclear distance of I2 molecules in an alignment laser field by applying our molecular structure determination methodology to an I 2p X-ray photoelectron diffraction profile observed with femtosecond X-ray free electron laser pulses. Using this methodology, we have found that the internuclear distance of the sample I2 molecules in an alignment Nd:YAG laser field of 6 × 10(11) W/cm(2) is elongated by from 0.18 to 0.30 Å "in average" relatively to the equilibrium internuclear distance of 2...
December 9, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27934019/experimental-and-computational-analysis-of-protein-stabilization-by-gly-to-d-ala-substitution-a-convolution-of-native-state-and-unfolded-state-effects
#2
Junjie Zou, Benben Song, Carlos Simmerling, Daniel Raleigh
The rational and predictable enhancement of protein stability is an important goal in protein design. Most efforts target the folded state, however stability is the free energy difference between the folded and unfolded states thus both are suitable targets. Strategies directed at the unfolded state usually seek to decrease chain entropy by introducing cross-links or by replacing glycines. Cross-linking has led to mixed results. Replacement of glycine with an l-amino acid, while reducing the entropy of the unfolded state, can introduce unfavorable steric interactions in the folded state, since glycine is often found in conformations that require a positive φ angle such as helical C-capping motifs or type I' and II″ β-turns...
December 7, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27925317/toward-arbitrary-direction-energy-harvesting-through-flexible-piezoelectric-nanogenerators-using-perovskite-pbtio3-nanotube-arrays
#3
Young Bum Lee, Jin Kyu Han, Suttinart Noothongkaew, Seong Ku Kim, Wooseok Song, Sung Myung, Sun Sook Lee, Jongsun Lim, Sang Don Bu, Ki-Seok An
New fiber-type piezoelectric nanogenerator devices consisting of radially aligned perovskite PbTiO3 nanotubes are designed for energy harvesting from arbitrary mechanical motion. The free-standing fiber-type nanogenerators generate constant amount of electric power by bending or wind motion regardless of direction, thus, extending the possibility of their practical applications.
December 7, 2016: Advanced Materials
https://www.readbyqxmd.com/read/27924268/effects-of-the-difference-in-similarity-measures-on-the-comparison-of-ligand-binding-pockets-using-a-reduced-vector-representation-of-pockets
#4
Tsukasa Nakamura, Kentaro Tomii
Comprehensive analysis and comparison of protein ligand-binding pockets are important to predict the ligands which bind to parts of putative ligand binding pockets. Because of the recent increase of protein structure information, such analysis demands a fast and efficient method for comparing ligand binding pockets. Previously we proposed a fast alignment-free method based on a simple representation of a ligand binding pocket with one 11-dimensional vector, which is suitable for such analysis. Based on that method, we conducted this study to expand and revise similarity measures of binding pockets and to investigate the effects of those modifications with two datasets for improving the ability to detect similar binding pockets...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27921162/multicentre-randomized-trial-of-the-ajust%C3%A2-single-incision-sling-compared-to-the-align%C3%A2-transobturator-tape-sling
#5
Jordi Sabadell, Marta Palau-Gené, Eva Huguet, Anabel Montero-Armengol, Sabina Salicrú, Jose L Poza
INTRODUCTION AND HYPOTHESIS: Tension-free suburethral tapes have become the first-line surgical treatment for female stress urinary incontinence. Single-incision midurethral slings (SIMS) were introduced with the aim of offering similar efficacy with reduced morbidity, particularly postoperative pain. The objective of this study was to compare the effectiveness and complications of the Ajust™ SIMS and the Align™ transobturator tape sling. METHODS: We performed a randomized controlled trial with a noninferiority design...
December 5, 2016: International Urogynecology Journal
https://www.readbyqxmd.com/read/27918587/an-alignment-free-algorithm-in-comparing-the-similarity-of-protein-sequences-based-on-pseudo-markov-transition-probabilities-among-amino-acids
#6
Yushuang Li, Tian Song, Jiasheng Yang, Yi Zhang, Jialiang Yang
In this paper, we have proposed a novel alignment-free method for comparing the similarity of protein sequences. We first encode a protein sequence into a 440 dimensional feature vector consisting of a 400 dimensional Pseudo-Markov transition probability vector among the 20 amino acids, a 20 dimensional content ratio vector, and a 20 dimensional position ratio vector of the amino acids in the sequence. By evaluating the Euclidean distances among the representing vectors, we compare the similarity of protein sequences...
2016: PloS One
https://www.readbyqxmd.com/read/27916118/an-in%C3%A2-vitro-approach-for-lipolysis-measurement-using-high-resolution-mass-spectrometry-and-partial-least-squares-based-analysis
#7
Wen-Qi Chang, Jian-Liang Zhou, Yi Li, Zi-Qi Shi, Li Wang, Jie Yang, Ping Li, Li-Fang Liu, Gui-Zhong Xin
The elevation of free fatty acids (FFAs) has been regarded as a universal metabolic signature of excessive adipocyte lipolysis. Nowadays, in vitro lipolysis assay is generally essential for drug screening prior to the animal study. Here, we present a novel in vitro approach for lipolysis measurement combining UHPLC-Orbitrap and partial least squares (PLS) based analysis. Firstly, the calibration matrix was constructed by serial proportions of mixed samples (blended with control and model samples). Then, lipidome profiling was performed by UHPLC-Orbitrap, and 403 variables were extracted and aligned as dataset...
January 15, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/27911524/nanobubble-fragmentation-and-bubble-free-channel-shear-localization-in-helium-irradiated-submicron-sized-copper
#8
Ming-Shuai Ding, Lin Tian, Wei-Zhong Han, Ju Li, Evan Ma, Zhi-Wei Shan
Helium bubbles are one of the typical radiation microstructures in metals and alloys, significantly influencing their deformation behavior. However, the dynamic evolution of helium bubbles under straining is less explored so far. Here, by using in situ micromechanical testing inside a transmission electron microscope, we discover that the helium bubble not only can coalesce with adjacent bubbles, but also can split into several nanoscale bubbles under tension. Alignment of the splittings along a slip line can create a bubble-free channel, which appears softer, promotes shear localization, and accelerates the failure in the shearing-off mode...
November 18, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27910561/orientation-free-and-differentially-pumped-addition-of-a-low-flux-reactive-gas-beam-to-a-surface-analysis-system
#9
Colin Harthcock, Abdolreza Jahanbekam, Jeremy R Eskelsen, David Y Lee
We describe an example of a piecewise gas chamber that can be customized to incorporate a low flux of gas-phase radicals with an existing surface analysis chamber for in situ and stepwise gas-surface interaction experiments without any constraint in orientation. The piecewise nature of this gas chamber provides complete angular freedom and easy alignment and does not require any modification of the existing surface analysis chamber. In addition, the entire gas-surface system is readily differentially pumped with the surface chamber kept under ultra-high-vacuum during the gas-surface measurements...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27909073/accuracy-of-outpatient-service-data-for-activity-based-funding-in-new-south-wales-australia
#10
Esther N Munyisia, David Reid, Ping Yu
BACKGROUND: Despite increasing research on activity-based funding (ABF), there is no empirical evidence on the accuracy of outpatient service data for payment. OBJECTIVE: This study aimed to identify data entry errors affecting ABF in two drug and alcohol outpatient clinic services in Australia. METHODS: An audit was carried out on healthcare workers' (doctors, nurses, psychologists, social workers, counsellors, and aboriginal health education officers) data entry errors in an outpatient electronic documentation system...
December 1, 2016: HIM Journal
https://www.readbyqxmd.com/read/27900266/ankle-arthrodesis-a-systematic-approach-and-review-of-the-literature
#11
REVIEW
Youichi Yasui, Charles P Hannon, Dexter Seow, John G Kennedy
Ankle arthrodesis is a common treatment used for patients with end-stage ankle arthritis (ESAA). The surgical goal of ankle arthrodesis is to obtain bony union between the tibia and talus with adequate alignment [slight valgus (0°-5°)], neutral dorsiflexion, and slight external rotation positions) in order to provide a pain-free plantigrade foot for weightbearing activities. There are many variations in operative technique including deferring approaches (open or arthroscopic) and differing fixation methods (internal or external fixation)...
November 18, 2016: World Journal of Orthopedics
https://www.readbyqxmd.com/read/27899557/alignment-free-d_2-oligonucleotide-frequency-dissimilarity-measure-improves-prediction-of-hosts-from-metagenomically-derived-viral-sequences
#12
Nathan A Ahlgren, Jie Ren, Yang Young Lu, Jed A Fuhrman, Fengzhu Sun
Viruses and their host genomes often share similar oligonucleotide frequency (ONF) patterns, which can be used to predict the host of a given virus by finding the host with the greatest ONF similarity. We comprehensively compared 11 ONF metrics using several k-mer lengths for predicting host taxonomy from among ∼32 000 prokaryotic genomes for 1427 virus isolate genomes whose true hosts are known. The background-subtracting measure [Formula: see text] at k = 6 gave the highest host prediction accuracy (33%, genus level) with reasonable computational times...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899282/bindprofx-assessing-mutation-induced-binding-affinity-change-by-protein-interface-profiles-with-pseudo-counts
#13
Peng Xiong, Chengxin Zhang, Wei Zheng, Yang Zhang
Understanding how gene-level mutations affect the binding affinity of protein-protein interactions is a key issue of protein engineering. Due to the complexity of the problem, using physical force field to predict the mutation-induced binding free-energy change remains challenging. In this work, we present a renewed approach to calculate the impact of gene mutations on the binding affinity through the structure-based profiling of protein-protein interfaces, where the binding free-energy change (ΔΔG) is counted as the logarithm of relative probability of mutant amino acids over wild-type ones in the interface alignment matrix; three pseudo counts are introduced to alleviate the limit of the current interface library...
November 26, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27898695/dcite-measuring-necessary-cladistic-information-can-help-you-reduce-polytomy-artefacts-in-trees
#14
Michael J Wise
Biologists regularly create phylogenetic trees to better understand the evolutionary origins of their species of interest, and often use genomes as their data source. However, as more and more incomplete genomes are published, in many cases it may not be possible to compute genome-based phylogenetic trees due to large gaps in the assembled sequences. In addition, comparison of complete genomes may not even be desirable due to the presence of horizontally acquired and homologous genes. A decision must therefore be made about which gene, or gene combinations, should be used to compute a tree...
2016: PloS One
https://www.readbyqxmd.com/read/27896447/novel-extended-sequons-of-human-n-glycosylation-sites-improve-the-precision-of-qualitative-predictions-an-alignment-free-study-of-pattern-recognition-using-protdcal-protein-features
#15
Yasser B Ruiz-Blanco, Yovani Marrero-Ponce, Enrique García-Hernández, James Green
N-Glycosylation is a common post-translational modification that plays an important role in the proper folding and function of many proteins. This modification is largely dependent on the presence of a sequence motif called a "sequon" defined as Asn-Xxx-Ser/Thr. However, evidence has shown that the presence of such a "sequon" is insufficient to determine the occurrence of N-glycosylation with high precision. This study aims to elucidate patterns that can more accurately predict N-glycosylation sites in human proteins...
November 28, 2016: Amino Acids
https://www.readbyqxmd.com/read/27894944/surface-projected-flair-supr-flair-analysis-a-novel-tool-for-advanced-imaging-of-epilepsy
#16
Francesco Cardinale, Stefano Francione, Luciana Gennari, Alberto Citterio, Maurizio Sberna, Laura Tassi, Roberto Mai, Ivana Sartori, Lino Nobili, Massimo Cossu, Laura Castana, Giorgio Lo Russo, Nadia Colombo
OBJECTIVE: The objective of this pilot retrospective study is to describe the SUrface-PRojected FLuid-Attenuation-Inversion-Recovery (SUPR-FLAIR) analysis, a novel method mainly aimed at revealing cortical areas with subtle signal hyper-intensity. METHODS: Images from 101 healthy controls and ten patients suffering from drug-resistant partial epilepsy were retrospectively post-processed. Brain surface was reconstructed from a 3D T1-weighted fast field echo (3D T1W-FFE) MRI scan...
November 25, 2016: World Neurosurgery
https://www.readbyqxmd.com/read/27893177/efficient-charge-transfer-and-fine-tuned-energy-level-alignment-in-a-thf-processed-fullerene-free-organic-solar-cell-with-11-3-efficiency
#17
Zhong Zheng, Omar M Awartani, Bhoj Gautam, Delong Liu, Yunpeng Qin, Wanning Li, Alexander Bataller, Kenan Gundogdu, Harald Ade, Jianhui Hou
Fullerene-free organic solar cells show over 11% power conversion efficiency, processed by low toxic solvents. The applied donor and acceptor in the bulk heterojunction exhibit almost the same highest occupied molecular orbital level, yet exhibit very efficient charge creation.
November 28, 2016: Advanced Materials
https://www.readbyqxmd.com/read/27893003/navigation-guidance-during-free-flap-mandibular-reconstruction-a-cadaveric-trial
#18
R Alex Harbison, Xiao-Feng Shan, Zachary Douglas, Scott Bevans, Yangming Li, Kris S Moe, Neal Futran, Jeffrey J Houlton
Importance: Segmental mandibulectomy for tumors that distort the buccal surface of the mandible present a reconstructive challenge. Objective: To determine whether mandible alignment after navigation-guided mandible reconstruction is better than alignment after non-template-assisted freehand reconstruction and as good as template-assisted reconstruction in a cadaveric trial. Design, Setting, and Participants: A cadaveric trial using 10 specimens was conducted at a tertiary academic center...
November 17, 2016: JAMA Otolaryngology—Head & Neck Surgery
https://www.readbyqxmd.com/read/27891298/pt-decorated-g-c3n4-tio2-nanotube-arrays-with-enhanced-visible-light-photocatalytic-activity-for-h2-evolution
#19
Zhi-Da Gao, Yong-Fang Qu, Xuemei Zhou, Lei Wang, Yan-Yan Song, Patrik Schmuki
Aligned TiO2 nanotube layers (TiNTs) grown by self-organizing anodization of a Ti-substrate in a fluoride-based electrolyte were decorated with graphitic-phase C3N4 (g-C3N4) via a facile chemical vapor deposition approach. In comparison with classical TiO2 nanotubes (anatase), the g-C3N4/TiNTs show an onset of the photocurrent at 2.4 eV (vs. 3.2 eV for anatase) with a considerably high photocurrent magnitude in the visible range. After further decoration with Pt nanoparticles, we obtained a visible-light responsive platform that showed, compared with g-C3N4-free TiNTs, a strong enhancement for photoelectrochemical and bias-free H2 evolution (15...
June 2016: ChemistryOpen
https://www.readbyqxmd.com/read/27885474/comparison-of-mri-defined-back-muscles-volume-between-patients-with-ankylosing-spondylitis-and-control-patients-with-chronic-back-pain-age-and-spinopelvic-alignment-matched-study
#20
Doo Hee Bok, Jihye Kim, Tae-Hwan Kim
PURPOSE: To compare MRI-defined back muscle volume between AS patients and age, and spinopelvic alignment matched control patients with chronic back pain. METHODS: 51 male patients with AS were enrolled. Age and spinopelvic alignment matched controls (male) were found among non-AS patients with chronic back pain. After matching procedure, fully matched controls were found in 31 of 51 AS patients (60.8%), who represent AS patients without deformity. However, matched controls were not found in 20 of 51 AS patients (39...
November 24, 2016: European Spine Journal
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