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https://www.readbyqxmd.com/read/28092632/the-tilt-dependent-potential-of-mean-force-of-a-pair-of-dna-oligomers-from-all-atom-molecular-dynamics-simulations
#1
Ruggero Cortini, Xiaolin Cheng, Jeremy C Smith
Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups...
January 16, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28092439/molecular-details-of-the-ph-domain-of-acap1-bar-ph-protein-binding-to-pip-containing-membrane
#2
Chun Chan, Lanyuan Lu, Fei Sun, Jun Fan
ACAP1 proteins were previously reported to specifically bind PIP2-containing cell membranes and form well-structured protein lattices in order to conduct membrane tubulation. We carried out molecular dynamics simulations to characterize orientation of the PH domains with respect to the BAR domains inside the protein dimer. Followed by molecular dynamics simulations, we present a comprehensive orientation analysis of PH domain under different states including unbound and bound with lipids. We have examined two binding pockets on the PH domain and present PMF profiles of the two pockets to account for their preference to PIP2 lipids...
January 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28088626/characterization-and-source-apportionment-of-pm2-5-based-on-error-estimation-from-epa-pmf-5-0-model-at-a-medium-city-in-china
#3
Baoshuang Liu, Jianhui Wu, Jiaying Zhang, Lu Wang, Jiamei Yang, Danni Liang, Qili Dai, Xiaohui Bi, Yinchang Feng, Yufen Zhang, Qinxun Zhang
Heze city, a medium-size city in Shandong province, Eastern China. Ambient PM2.5 samples were collected in urban area of Heze from August 2015 to April 2016, and chemical species and sources of PM2.5 were investigated in this paper. The results indicated that the average concentration of PM2.5 was 100.9 μg/m(3) during the sampling period, and the water-soluble ions, carbonaceous species included elemental carbon (EC) and organic carbon (OC), as well as elements contributed 32.7-51.7%, 16.3% and 12.5%, respectively, to PM2...
January 12, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28074258/the-treatment-options-for-posterior-malleolar-fractures-in-tibial-spiral-fractures
#4
Jialiang Guo, Lei Liu, Zongyou Yang, Zhiyong Hou, Wei Chen, Yingze Zhang
PURPOSE: The posterior malleolar fracture (PMF) in tibial spiral fractures are a common type of complication that occurs in tibial fractures. However, the indication of fixation for posterior fractures is still under debate and varies between different surgeons'. It is not unusual to find the smaller PMF (<25%), which could be treated conservatively within guidelines, treated with internal fixation in clinic. The aim of this study is to evaluate the clinical outcomes of tibial spiral fractures with PMF and provide proper guidance for the treatment of this special fracture...
January 10, 2017: International Orthopaedics
https://www.readbyqxmd.com/read/28073798/effectiveness-of-a-lumbopelvic-monitor-and-feedback-device-to-change-postural-behaviour-a-protocol-for-the-elf-cluster-randomised-controlled-trial
#5
Daniel Cury Ribeiro, Stephan Milosavljevic, J Haxby Abbott
INTRODUCTION: Low back pain (LBP) is the most common, costly and disabling musculoskeletal disorder worldwide, and is prevalent in healthcare workers. Posture is a modifiable risk factor for LBP shown to reduce the prevalence of LBP. Our feasibility research suggests that postural feedback might help healthcare workers avoid hazardous postures. The Effectiveness of Lumbopelvic Feedback (ELF) trial will investigate the extent to which postural monitor and feedback (PMF) can reduce exposure to hazardous posture associated with LBP...
January 10, 2017: BMJ Open
https://www.readbyqxmd.com/read/28068569/quantification-of-ph-dependent-speciation-of-organic-compounds-with-spectroscopy-and-chemometrics
#6
Thomas Ritschel, Kai Uwe Totsche
Fluorescence and UV/Vis spectra of aqueous solutions with numerous organic compounds are a superposition of single spectra of the chemical species present. Thus, an isolation of individual spectra with chemometrics is required for their quantification. We investigated UV/Vis spectra and fluorescence excitation-emission matrices of vanillic acid, salicylic acid, phenoxyacetic acid and phthalic acid with positive matrix factorization (PMF) and non-negativity constrained parallel factor analysis (PARAFAC) in combination with the law of mass action...
December 30, 2016: Chemosphere
https://www.readbyqxmd.com/read/28051297/source-apportionment-of-atmospheric-polychlorinated-biphenyls-in-new-jersey-1997-2011
#7
Pornsawai Praipipat, Qing Yu Meng, Robert J Miskewitz, Lisa A Rodenburg
Concentrations of polychlorinated biphenyls (PCBs) in the Delaware River currently exceed the Water Quality Criteria of 16 pg/L for the sum of PCBs due in part to atmospheric deposition. The purpose of this work was to use a source apportionment tool called Positive Matrix Factorization (PMF) to identify the sources of PCBs to the atmosphere in this area and determine whether their concentrations are declining over time. The data set was compiled by the Delaware Atmospheric Deposition Network (DADN) from samples taken in Camden, NJ from 1999 to 2011 and New Brunswick, NJ from 1997 to 2011...
January 4, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28050371/haemostatic-profile-in-patients-of-myeloproliferative-neoplasms-a-tertiary-care-centre-experience
#8
Yatendra Parashar, Rashmi Kushwaha, Ashutosh Kumar, Kamal Agarwal, U S Singh, Mili Jain, S P Verma, A K Tripathi
INTRODUCTION: Patients of MPN commonly present with abnormalities in laboratory coagulation tests that are consistent with hypercoagulable state. Some individuals with MPN exhibit a pattern of exclusive bleeding or thrombotic events; many others have both bleeding and thrombosis during the course of the disease. AIM: This study was undertaken to assess the haemostatic defects and platelet functions in patients of MPN. MATERIALS AND METHODS: One year prospective study was conducted at a tertiary care centre in North India in Department of Pathology in collaboration with Department of Clinical Haematology...
November 2016: Journal of Clinical and Diagnostic Research: JCDR
https://www.readbyqxmd.com/read/28043820/kinase-signaling-and-targeted-therapy-for-primary-myelofibrosis
#9
REVIEW
Qiong Yang, John D Crispino, Qiang Jeremy Wen
The myeloproliferative neoplasms (MPNs) are somatic mutation-driven hematological malignancies characterized by bone marrow fibrosis and the accumulation of atypical megakaryocytes with reduced polyploidization in the primary myelofibrosis (PMF) subtype of the MPNs. Increasing evidence points to a dominant role of abnormal megakaryocytes (MK) in disease initiation and progression. Here we review the literature related to kinase signaling pathways relevant to megakaryocyte differentiation and proliferation, including Aurora A kinase, RhoA/ROCK and JAK/STAT, as well as the activities of their targeted inhibitors in models of the disease...
December 30, 2016: Experimental Hematology
https://www.readbyqxmd.com/read/28043705/characteristics-of-pahs-in-street-dust-of-beijing-and-the-annual-wash-off-load-using-an-improved-load-calculation-method
#10
Yingxia Li, Ningning Song, Yang Yu, Zhifeng Yang, Zhenyao Shen
A significant amount of polycyclic aromatic hydrocarbons (PAHs) adsorbed in street dust ends up in runoff. Accordingly, evaluating the content, possible wash-off load and constituent risks associated with street dust is critical for urban runoff usage. Based on the PAH concentrations examined in this study, different risk assessment methods were applied and the differences among results were analyzed. An improved PAH wash-off calculation method was established and the annual PAH wash-off load was obtained. In addition, emission sources were diagnosed based on isomer ratios and PMF methods...
December 30, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/28035152/pulsed-magnetic-field-improves-seed-quality-of-aged-green-pea-seeds-by-homeostasis-of-free-radical-content
#11
Jyotsna Bhardwaj, Anjali Anand, V K Pandita, Shantha Nagarajan
To elucidate the mechanism responsible for magnetic field induced seed invigoration in aged seeds an experiment was conducted on six year old garden pea seeds stored under controlled (20 °C and 40% RH) condition. Aged seeds were magnetoprimed by exposing to pulsed magnetic field (PMF) of 100 mT for 1 h in three pulsed modes. The 6 min on and off PMF showed significant improvement in germination (7.6%) and vigor (84.8%) over aged seeds. Superoxide and hydrogen peroxide production increased in germinating primed seeds by 27 and 52%, respectively, over aged seeds...
November 2016: Journal of Food Science and Technology
https://www.readbyqxmd.com/read/28033555/unbinding-pathway-energy-of-glyphosate-from-the-epsps-enzyme-binding-site-characterized-by-steered-molecular-dynamics-and-potential-of-mean-force
#12
Moacir F Ferreira, Eduardo F Franca, Fábio L Leite
The quantification of herbicides in the environment, like glyphosate, is extremely important to prevent contamination. Nanobiosensors stands out in the quantization process, because of the high selectivity, sensitivity and short response time of the method. In order to emulate the detection of glyphosate using a specific nanobiossensor through an Atomic Force Microscope (AFM), this work carried out Steered Molecular Dynamics simulations (SMD) in which the herbicide was unbinded from the active site of the enzyme 5- enolpyruvylshikimate 3 phosphate synthase (EPSPS) along three different directions...
November 21, 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28031530/a-novel-assay-to-detect-calreticulin-mutations-in-myeloproliferative-neoplasms
#13
Valentina Rosso, Jessica Petiti, Enrico Bracco, Roberto Pedrola, Francesca Carnuccio, Elisabetta Signorino, Sonia Carturan, Chiara Calabrese, Giada Bot-Sartor, Michela Ronconi, Anna Serra, Giuseppe Saglio, Francesco Frassoni, Daniela Cilloni
The myeloproliferative neoplasms are chronic myeloid cancers divided in Philadelphia positive (Ph+), chronic myeloid leukemia, or negative: polycythemia vera (PV) essential thrombocythemia (ET), and primary myelofibrosis (PMF). Most Ph negative cases have an activating JAK2 or MPL mutation. Recently, somatic mutations in the calreticulin gene (CALR) were detected in 56-88% of JAK2/MPL-negative patients affected by ET or PMF. The most frequent mutations in CARL gene are type-1 and 2. Currently, CALR mutations are evaluated by sanger sequencing...
December 23, 2016: Oncotarget
https://www.readbyqxmd.com/read/28028559/real-world-epidemiology-of-myeloproliferative-neoplasms-a-population-based-study-in-korea-2004-2013
#14
Ja Min Byun, Young Jin Kim, Taemi Youk, John Jeongseok Yang, Jongha Yoo, Tae Sung Park
Myeloproliferative neoplasms (MPNs), with an expected increment in number, impose substantial economic and social burdens. To this end, we conducted a nationwide population-based descriptive epidemiology study. We also investigated medical cost associated with MPNs. Prevalence was the highest for essential thrombocythemia (ET) (range 4.1-9.0 per 100,000), followed by polycythemia vera (PV) (range 2.8-5.4 per 100,000) and primary myelofibrosis (PMF) (range 0.5-0.9 per 100,000). ET incurred the highest cumulative total cost at US$35 million and the most frequent hospital visits, while PMF incurred the highest average cost per person at US$5000...
December 27, 2016: Annals of Hematology
https://www.readbyqxmd.com/read/28028029/genetic-basis-and-molecular-pathophysiology-of-classical-myeloproliferative-neoplasms
#15
William Vainchenker, Robert Kralovics
The genetic landscape of classical myeloproliferative neoplasm (MPN) is in large part elucidated. The MPN restricted driver mutations including those in JAK2, calreticulin (CALR) and MPL abnormally activate the cytokine receptor/JAK2 pathway and their downstream effectors, more particularly the STATs. The most frequent mutation, JAK2V617F, activates the three main myeloid cytokine receptors (EPOR, G-CSFR and MPL) whereas CALR or MPL mutants are restricted to MPL activation. This explains why JAK2V617F is associated with polycythemia vera (PV), essential thrombocythemia (ET) and primary myelofibrosis (PMF) whereas CALR and MPL mutants are found in ET and PMF...
December 27, 2016: Blood
https://www.readbyqxmd.com/read/28027559/the-contribution-of-hereditary-thrombophilia-to-increasing-the-frequency-of-thrombosis-in-patients-with-ph-negative-myeloproliferative-neoplasms-including-the-victims-from-the-chornobyl-accident
#16
O Y Mishcheniuk, V M Shkarupa, O M Kostukevich, L V Neumerzhitcka, S M Kravchenko, S V Klymenko
OBJECTIVE: The definition of a contribution of the carriage of the G1691A allele of thecoagulation factor V gene and the G20210A allele of the coagulation factor II gene in the development of thrombosis in Ph negative myeloprolifer ative neoplasms (MPN) patients, who were irradiated in the dose range 0,001 0,99 Gy and who were not. MATERIALS AND METHODS: The clinical and molecular genetic characteristics of patients with radiation associated and spontaneous polycythemia vera (PV), essential trombotsytemiya (ET) and primary myelofibrosis (PMF) were ana lyzed...
December 2016: Problemy Radiat︠s︡iĭnoï Medyt︠s︡yny Ta Radiobiolohiï
https://www.readbyqxmd.com/read/28025866/proliferative-characteristics-of-philadelphia-negative-myeloproliferative-neoplasms-clinical-implications
#17
D Šefer, S Bižić-Radulović, N Kraguljac-Kurtović, A Bogdanović, V Čokić, P Miljić, B Beleslin-Čokić, V Knežević, O Mitrović-Ajtić, D Leković, M Gotić
INTRODUCTION: Philadelphia-negative myeloproliferative neoplasms (Ph(-) MPN) are characterized by overproduction of one or more blood cell lines. METHODS: We studied the proliferative characteristics of 91 patients with de novo Ph(-) MPN. Colony-forming cells (CFC) and endogenous colonies (EC), from bone marrow (BM) and/or peripheral blood (PB), were analyzed by colony assay based on methylcellulose. The level of circulating CD34(+) cells was determined by flow cytometry...
December 26, 2016: International Journal of Laboratory Hematology
https://www.readbyqxmd.com/read/28024121/sodium-binding-sites-and-permeation-mechanism-in-the-nachbac-channel-a-molecular-dynamics-study
#18
Carlo Guardiani, P Mark Rodger, Igor A Khovanov
NaChBac was the first discovered sodium voltage dependent channel, yet computational studies are still limited due to the lack of a crystal structure. In this work a pore-only construct built using the NavMs template was investigated using unbiased Molecular Dynamics and Metadynamics. The Potential of Mean Force (PMF) from the unbiased run features four minima, three of which correspond to sites IN, CEN and HFS discovered in NavAb. During the run the Selectivity Filter (SF) is spontaneously occupied by two ions and frequent access of a third one is often observed...
December 26, 2016: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28013504/macromolecule-biosynthesis-assay-and-fluorescence-spectroscopy-methods-to-explore-antimicrobial-peptide-mode-s-of-action
#19
Bimal Jana, Kristin Renee Baker, Luca Guardabassi
Antimicrobial peptides (AMPs) are viable alternatives to the currently available antimicrobials, and numerous studies have investigated their possible use as therapeutic agents for specific clinical applications. AMPs are a diverse class of antimicrobials that often act upon the bacterial cell membrane but may exhibit additional modes of action. Identification of the multiple modes of action requires a comprehensive study at subinhibitory concentrations and careful data analysis since additional modes of action can be eclipsed by AMP action on the cell membrane...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28013356/diuretic-effect-of-extracts-fractions-and-two-compounds-2%C3%AE-3%C3%AE-19%C3%AE-trihydroxy-urs-12-en-28-oic-acid-and-5-hydroxy-3-6-7-8-4-pentamethoxyflavone-from-rubus-rosaefolius-sm-rosaceae-leaves-in-rats
#20
Priscila de Souza, Thaise Boeing, Lincon Bordignon Somensi, Camile Cecconi Cechinel-Zanchett, Jairo Kenupp Bastos, Marcel Petreanu, Rivaldo Niero, Valdir Cechinel-Filho, Luisa Mota da Silva, Sérgio Faloni de Andrade
Although diuretics have been widely used to treat hypertension along with others cardiovascular and renal disorders, no scientific data have been recorded to support the diuretic properties of Rubus rosaefolius Sm. (Rosaceae), a plant popularly used in Brazil to treat hypertension. Male Wistar rats were orally treated with: vehicle; hydrochlorothiazide; aqueous (AERR) and methanolic (MERR) extracts; dichloromethane (DCM), hexane (HEX) and ethyl acetate (EA) fractions; and the isolated compounds 2α,3β,19α-trihydroxy-urs-12-en-28-oic acid (TUA) and 5-hydroxy-3,6,7,8,4'-pentamethoxyflavone (PMF)...
December 24, 2016: Naunyn-Schmiedeberg's Archives of Pharmacology
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