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https://www.readbyqxmd.com/read/28821842/direct-learning-hidden-excited-state-interaction-patterns-from-ab-initio-dynamics-and-its-implication-as-alternative-molecular-mechanism-models
#1
Fang Liu, Likai Du, Dongju Zhang, Jun Gao
The excited states of polyatomic systems are rather complex, and often exhibit meta-stable dynamical behaviors. Static analysis of reaction pathway often fails to sufficiently characterize excited state motions due to their highly non-equilibrium nature. Here, we proposed a time series guided clustering algorithm to generate most relevant meta-stable patterns directly from ab initio dynamic trajectories. Based on the knowledge of these meta-stable patterns, we suggested an interpolation scheme with only a concrete and finite set of known patterns to accurately predict the ground and excited state properties of the entire dynamics trajectories, namely, the prediction with ensemble models (PEM)...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821738/directly-monitor-protein-rearrangement-on-a-nanosecond-to-millisecond-time-scale
#2
Eric H-L Chen, Tony T-Y Lu, Jack C-C Hsu, Yufeng Jane Tseng, T-S Lim, Rita P-Y Chen
In order to directly observe the refolding kinetics from a partially misfolded state to a native state in the bottom of the protein-folding funnel, we used a "caging" strategy to trap the β-sheet structure of ubiquitin in a misfolded conformation. We used molecular dynamics simulation to generate the cage-induced, misfolded structure and compared the structure of the misfolded ubiquitin with native ubiquitin. Using laser flash irradiation, the cage can be cleaved from the misfolded structure within one nanosecond, and we monitored the refolding kinetics of ubiquitin from this misfolded state to the native state by photoacoustic calorimetry and photothermal beam deflection techniques on nanosecond to millisecond timescales...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28820586/dissociation-chemistry-of-3-oxetanone-in-the-gas-phase
#3
Sumitra Godara, Pooja Verma, Manikandan Paranjothy
3-Oxetanone is a strained cyclic molecule which plays an important role in synthetic chemistry. A few studies exist in the literature about the equilibrium properties of this molecule and the dissociation patterns of substituted 3-oxetanones. For the unsubstituted 3-oxetanone, formation of ketene (CH2CO) and formaldehyde (HCHO) was considered to be the major dissociation pathway. In a recent work, pyrolysis products of 3-oxetanone molecule in the gas phase were investigated by Fourier transform infrared spectroscopy and photoionization mass spectrometry...
August 18, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28820492/variation-in-the-ovine-kap6-3-gene-krtap6-3-is-associated-with-variation-in-mean-fibre-diameter-associated-wool-traits
#4
Shaobin Li, Huitong Zhou, Hua Gong, Fangfang Zhao, Jiqing Wang, Yuzhu Luo, Jon G H Hickford
Polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) analysis was used to investigate variation in the ovine KAP6-3 gene (KRTAP6-3) in 383 Merino × Southdown-cross lambs from four sire-lines, and to determine whether this variation affects wool traits. Five PCR-SSCP banding patterns, representing five different nucleotide sequences, were detected, including four previously identified (named A, B, C, and F) variants and one newly identified (named G) variant. A new non-synonymous single nucleotide polymorphism (SNP) and a 45-bp deletion were detected in variant G...
August 18, 2017: Genes
https://www.readbyqxmd.com/read/28820347/association-between-eye-diagnosis-and-positive-syphilis-test-results-in-a-large-urban-sexually-transmitted-infection-primary-care-clinic-population
#5
Ann-Marie Lobo, Yan Gao, Laura Rusie, Magda Houlberg, Supriya D Mehta
In 2015, the Centers for Disease Control and Prevention (CDC) and the American Academy of Ophthalmology (AAO) released clinical advisories on rising cases of ocular syphilis. We examined the association between eye disease and syphilis infection among primary care and sexually transmitted infection (STI) clinic patients attending an urban lesbian, gay, bisexual, transgender (LGBT) health center. We conducted a retrospective medical record review of all patients who underwent syphilis testing at Howard Brown Health between 1 January 2010 and 31 December 2015...
January 1, 2017: International Journal of STD & AIDS
https://www.readbyqxmd.com/read/28820124/bacillus-wudalianchiensis-sp-nov-isolated-from-grass-soils-of-the-wudalianchi-scenic-area
#6
Bo Liu, Guo-Hong Liu, Cetin Sengonca, Peter Schumann, Jie-Ping Wang, Yu-Jing Zhu, Hai-Feng Zhang
A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium, designated FJAT-27215T, was isolated from grass soil collected from Wudalianchi in the Heilongjiang Province of China. Growth was observed at 10-60 °C (optimum 30 °C), in 0 and 3.0 % NaCl (optimum 0 %) and at pH 5.0-10.0 (optimum 7.0), respectively. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the isoprenoid quinone was MK7. The main fatty acids were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, and iso-C16 : 0...
August 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28820123/laceyella-thermophila-sp-nov-a-thermophilic-bacterium-isolated-from-a-hot-spring
#7
Hong Ming, Wei-Li Ji, Shuai Li, Zhuo-Li Zhao, Ling-Yu Zhang, Xiao-Lin Meng, En-Min Zhou, Guo-Xing Nie, Wen-Jun Li
A novel themophilic bacterium, designated YIM 79486T, was isolated from a sediment sample collected from Jinze hot spring in Tengchong county, Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequence analysis revealed that strain YIM 79486T should be assigned to the genus Laceyella and formed a monophyletic clade with the type strain Laceyella putida KCTC 3666T (98.7 % similarity). Strain YIM 79486T formed white aerial mycelium and brown substrate mycelium. Abundant endospores were produced on short sporophores...
August 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28820105/roseomonas-hibiscisoli-sp-nov-isolated-from-the-rhizosphere-of-mugunghwa-hibiscus-syriacus
#8
Zheng-Fei Yan, Pei Lin, Chang-Tian Li, MooChang Kook, Qi-Jun Wang, Tae-Hoo Yi
A Gram-stain-negative, aerobic, non-motile and coccoid to short-rod-shaped bacterial strain (THG-N2.22T) was isolated from the rhizosphere of Mugunghwa (Hibiscus syriacus). Growth occurred at 20-40 °C (optimum 28 °C), at pH 5-9 (optimum 7) and with 0-4 % (w/v) NaCl (optimum 1 %). Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-N2.22T were identified as Roseomonas rhizosphaerae YW11T (98.5 % similarity), Roseomonas rubra S5T (98.5 %), Roseomonas cervicalis ATCC 49957T (98...
August 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28820097/emticicia-soli-sp-nov-a-novel-member-of-the-family-flexibacteraceae-isolated-from-tetrabromobisphenol-a-contaminated-soil
#9
Qing Chen, Xiao-Xia Zang, Xing Hang, Hong-Mei Wang, Wei-Bin Jia, Shun-Peng Li, Jian-Dong Jiang, Kai Chen
Bacterial strain ZZ-4T, a Gram-stain-negative, aerobic, non-spore-forming, non-motile, non-flagellated, rod-shaped bacterium, was isolated from tetrabromobisphenol A-contaminated soil in PR China. The taxonomic position of this strain was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ZZ-4T was a member of the genus Emticicia and showed the highest sequence similarity to Emticicia fontis IMCC1731T (98.0 %) and Emticicia ginsengisoli Gsoil 085T (97...
August 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28820092/rhizobium-wenxiniae-sp-nov-an-endophytic-bacterium-isolated-from-maize-root
#10
Jun-Lian Gao, Pengbo Sun, Xu-Ming Wang, Fan-Yang Lv, Xiao-Jie Mao, Jian-Guang Sun
A novel Gram-stain-negative, aerobic, rod-shaped strain designated 166T was isolated from surface-sterilized root tissue of maize planted in the Fangshan District of Beijing, PR China. The 16S rRNA gene sequence analysis indicated that strain 166T belongs to the genus Rhizobium and is closely related to Rhizobium cellulosilyticum ALA10B2T and Rhizobium yantingense H66T with sequence similarities of 98.8 and 98.3 %, respectively. According to atpD and recA sequence analysis, the highest sequence similarity between strain 166T and R...
August 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28820088/bacillus-praedii-sp-nov-isolated-from-purplish-paddy-soil
#11
Bo Liu, Guo-Hong Liu, Cetin Sengonca, Peter Schumann, Jie-Ping Wang, Yu-Jing Zhu, Qin-Ying Liu, Ming-Kuang Wang
A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium, designated strain FJAT-25547T, was isolated from the purplish paddy soil collected from Linshan Township, Yanting Prefecture of Sichuan Province in PR China (31° 16' N 105° 27' E). Growth was achieved aerobically at temperatures between 15 and 40 °C (optimum 30 °C), with between 0 and 10.0 % NaCl (w/v) (optimum 4 %) and in the range of pH 5.0-12.0 (optimum pH 9.0). The cell-wall peptidoglycan contained meso-diaminopimelic acid, and the main isoprenoid quinone was MK-7...
August 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28819652/quantitative-first-principles-calculations-of-valence-and-core-excitation-spectra-of-solid-c60
#12
F Fossard, G Hug, K Gilmore, J J Kas, J J Rehr, F D Vila, E L Shirley
We present calculated valence and C 1s near-edge excitation spectra of solid C60 and experimental results measured with high-resolution electron energy-loss spectroscopy. The near-edge calculations are carried out using three different methods: solution of the Bethe-Salpeter equation (BSE) as implemented in the OCEAN suite (Obtaining Core Excitations with ab initio methods and the NIST BSE solver), the excited-electron core-hole approach (XCH), and the constrained-occupancy method using the Stockholm-Berlin core-excitation code, StoBe...
March 2017: Physical Review. B
https://www.readbyqxmd.com/read/28819297/energy-free-machine-learning-force-field-for-aluminum
#13
Ivan Kruglov, Oleg Sergeev, Alexey Yanilkin, Artem R Oganov
We used the machine learning technique of Li et al. (PRL 114, 2015) for molecular dynamics simulations. Atomic configurations were described by feature matrix based on internal vectors, and linear regression was used as a learning technique. We implemented this approach in the LAMMPS code. The method was applied to crystalline and liquid aluminum and uranium at different temperatures and densities, and showed the highest accuracy among different published potentials. Phonon density of states, entropy and melting temperature of aluminum were calculated using this machine learning potential...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818987/response-assessment-of-68-ga-dota-e-c-rgdfk-2-pet-ct-for-lung-adenocarcinoma-patients-treated-with-nintedanib-plus-docetaxel
#14
Oscar Arrieta, Francisco O Garcia-Perez, David Michel-Tello, Laura-Alejandra Ramirez-Tirado, Quetzali Pitalua-Cortes, Graciela Cruz-Rico, Eleazar-Omar Macedo-Perez, Andres F Cardona, Jaime de la Garza-Salazar
Nintedanib is an oral angiokinase inhibitor used as a second-line treatment for non-small-cell lung cancer (NSCLC). New radiotracers, such as (68)Ga-DOTA-E-[c(RGDfK)]2, that target αvβ3 integrin might impact the clinical practice as a non-invasive method for assessing angiogenesis inhibitors. Methods: From July 2014 through October 2015, 38 patients received second-line nintedanib plus docetaxel. All the patients underwent PET/CT with (68)Ga-DOTA-E-[c(RGDfK)]2 radiotracer and blood-sample tests to quantify angiogenesis factors (FGF, VEGF and PDGF-AB) prior to and after completing 2 therapy cycles...
August 17, 2017: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
https://www.readbyqxmd.com/read/28818563/-lower-lymphocyte-response-in-severe-cases-of-acute-bronchiolitis-due-to-respiratory-syncytial-virus
#15
José Miguel Ramos-Fernández, David Moreno-Pérez, Cristina Antúnez-Fernández, Guillermo Milano-Manso, Ana María Cordón-Martínez, Antonio Urda-Cardona
INTRODUCTION: Acute bronchiolitis (AB) of the infant has a serious outcome in 6-16% of the hospital admitted cases. Its pathogenesis and evolution is related to the response of the T lymphocytes. The objective of the present study is to determine if the lower systemic lymphocytic response is related to a worse outcome of AB in hospitalised infants. PATIENTS AND METHOD: Retrospective observational-analytical study of cases-controls nested in a cohort of patients admitted due to RSV-AB between the period from October 2010 to March 2015...
August 14, 2017: Anales de Pediatría: Publicación Oficial de la Asociación Española de Pediatría (A.E.P.)
https://www.readbyqxmd.com/read/28817949/linear-trend-in-single-case-visual-and-quantitative-analyses
#16
Rumen Manolov
The frequently used visual analysis of single-case data focuses on data aspects such as level, trend, variability, overlap, immediacy of effect, and consistency of data patterns; most of these aspects are also commonly quantified besides inspecting them visually. The present text focuses on trend, because even linear trend can be operatively defined in several different ways, while there are also different approaches for controlling for baseline trend. We recommend using a quantitative criterion for choosing a trend line fitting technique and comparing baseline and intervention slopes, instead of detrending...
August 1, 2017: Behavior Modification
https://www.readbyqxmd.com/read/28817869/re-impact-of-combination-therapy-5-alpha-reductase-inhibitors-5-ari-plus-alpha-blockers-ab-on-erectile-dysfunction-and-decrease-of-libido-in-patients-with-luts-bph-a-systematic-review-with-meta-analysis
#17
https://www.readbyqxmd.com/read/28817775/departure-from-a-spherically-symmetric-ground-state-in-a-system-with-a-half-filled-shell-the-case-example-of-berkelium-iv-iodate
#18
Mark A Silver, Samantha K Cary, Alejandro J Garza, Ryan E Baumbach, Alexandra A Arico, Gregory A Galmin, Kuan-Wen Chen, Jason A Johnson, Jamie C Wang, Ronald J Clark, Alexander Chemey, Teresa M Eaton, Matthew L Marsh, Kevin Seidler, Shane S Galley, Lambertus van de Burgt, Ashley L Gray, David E Hobart, Kenneth Hanson, Shelley M van Cleve, Frédéric Gendron, Jochen Autschbach, Gustavo E Scuseria, Laurent Maron, Manfred Speldrich, Paul Kögerler, Cristian Celis-Barros, Dayán Paéz-Hernandéz, Ramiro Arratia-Perez, Michael Ruf, Thomas E Albrecht-Schmitt
The reaction of 249Bk(OH)4 with iodate under hydrothermal conditions results in the formation of Bk(IO3)3 as the major product with trace amounts of Bk(IO3)4 also crystallizing from the reaction mixture. The structure of Bk(IO3)3 consists of nine-coordinate BkIII cations that are bridged by iodate anions to yield layers that are isomorphous with those found for AmIII, CfIII, and with lanthanides that possess similar ionic radii. Bk(IO3)4 was expected to adopt the same structure as M(IO3)4 (M = Ce, Np, Pu), but instead parallels the structural chemistry of the smaller ZrIV cation...
August 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28817773/surface-reaction-barriometry-methane-dissociation-on-flat-and-stepped-transition-metal-surfaces
#19
Davide Migliorini, Helen Jane Chadwick, Francesco Nattino, Ana Gutiérrez-Gonzáles, Eric Dombrowski, Eric A High, Han Guo, Arthur L Utz, Bret Earl Jackson, Rainer D Beck, Geert-Jan Kroes
Accurately simulating heterogeneously catalyzed reactions requires reliable barriers for molecules reacting at defects on metal surfaces, such as steps. However, first principles methods capable of computing these barriers to chemical accuracy have yet to be demonstrated. We show that state-resolved molecular beam experiments combined with ab initio molecular dynamics using specific reaction parameter density functional theory (SRP-DFT) can determine the molecule-metal surface interaction with the required reliability...
August 17, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28817382/quantum-mechanical-force-fields-for-condensed-phase-molecular-simulations
#20
Timothy J Giese, Darrin M York
Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application...
August 17, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
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