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Filiz Karakas, Ipek Imamoglu, Kadir Gedik
Receptor models were typically used in air pollution studies and few publications are available for Positive Matrix Factorization (PMF) that consider the details of parameters and procedures in evaluating the trace organic pollutants in sediments. In this study, environmental fate and source composition of Lake Eymir sediments contaminated by polychlorinated biphenyls (PCBs) were explored by applying two PMF models, Paatero's PMF2 and United States Environmental Protection Agency's (US EPA) EPA-PMF3. PMF2 and EPA-PMF3 rely on different algorithms; Paatero's algorithm and multilinear engine algorithm, respectively...
October 12, 2016: Environmental Pollution
Jiangbo Lu, Yu Li, Hongsheng Yang, Dongbo Min, Weiyong Eng, Minh Do
Though many tasks in computer vision can be formulated elegantly as pixel-labeling problems, a typical challenge discouraging such a discrete formulation is often due to computational efficiency. Recent studies on fast cost volume filtering based on efficient edge-aware filters provide a fast alternative to solve discrete labeling problems, with the complexity independent of the support window size. However, these methods still have to step through the entire cost volume exhaustively, which makes the solution speed scale linearly with the label space size...
October 11, 2016: IEEE Transactions on Pattern Analysis and Machine Intelligence
Daniel Xia, Robert P Hasserjian
Polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF) are myeloproliferative neoplasms characterized by recurrent somatic mutations in JAK2, CALR, and MPL. This short review addresses 1) the spectrum of mutations seen in PV, ET, and PMF, 2) the emerging genotype-phenotype correlations, 3) the current role of molecular testing in disease classification and management, and 4) several important considerations for selecting an appropriate molecular test. In our view, sequential testing algorithms and simultaneous assessment of multiple mutations by next-generation sequencing are both valid approaches to testing...
October 11, 2016: American Journal of Hematology
Jaiprakash, Amrita Singhai, Gazala Habib, Ramya Sunder Raman, Tarun Gupta
Fine aerosol fraction (particulate matter with aerodynamic diameter <= 1.0 μm (PM)1.0) over the Indian Institute of Technology Delhi campus was monitored day and night (10 h each) at 30 m height from November 2009 to March 2010. The samples were analyzed for 5 ions (NH4(+), NO3(-), SO4(2-), F(-), and Cl(-)) and 12 trace elements (Na, K, Mg, Ca, Pb, Zn, Fe, Mn, Cu, Cd, Cr, and Ni). Importantly, secondary aerosol (sulfate and nitrate) formation was observed during dense foggy events, supporting the fog-smog-fog cycle...
October 10, 2016: Environmental Science and Pollution Research International
Katsuto Takenaka
Myeloproliferative neoplasms (MPNs) are chronic hematopoietic stem cell disorders, including polycythemia vera, essential thrombocytosis, and primary myelofibrosis. The JAK2V617F mutation was identified in 2005, followed by the discovery of the JAK2 exon12, MPNW515 mutation, and CALR mutation. About 90% of patients with BCR/ABL negative MPNs have been shown to have one of these driver mutations. In addition, mutations in epigenetic regulators and RNA splicing genes were found to co-exist with driver mutations and to play critical roles in the disease progression of MPNs...
2016: [Rinshō Ketsueki] the Japanese Journal of Clinical Hematology
Geun-Hye Yu, Seungshik Park, Kwon-Ho Lee
In this study, 24 h size-segregated particulate matter (PM) samples were collected between September 2012 and August 2013 at an urban site in Korea to investigate seasonal mass size distributions of PM and its water-soluble components as well as to infer the possible sources of size-resolved water-soluble organic carbon (WSOC) using a positive matrix factorization (PMF) model. The potential source contribution function (PSCF) was also computed to identify the possible source regions of size-resolved WSOC. The seasonal average contribution of water-soluble organic matter to PM1...
October 12, 2016: Environmental Science. Processes & Impacts
Debabrata Pramanik, Prabal K Maiti
Various unique physical, chemical, mechanical and electronic properties of carbon nanotubes (CNTs) make them very useful materials for diverse potential application in many fields. Experimentally synthesized CNTs are generally found in bundle geometry with a mixture of different chiralities and present a unique challenge to separate them. In this paper we have proposed the PAMAM dendrimer to be an ideal candidate for this separation. To estimate the efficiency of the dendrimer for the dispersion of CNTs from the bundle geometry, we have calculated potential of mean forces (PMF)...
September 26, 2016: Soft Matter
Bharath Kumar, Abhishek Chakraborty, S N Tripathi, Deepika Bhattu
Non-refractory submicron (NR-PM1) aerosols were measured during the late winter period (February-March) via an Aerodyne High Resolution Time of Flight Aerosols Mass Spectrometer (HR-ToF-AMS) along with Black Carbon (BC) and trace gasses in an industrial city, Kanpur, situated in the Gangetic Plain (GP) of India. The composition of NR-PM1 aerosols was dominated by organics (54%), followed by inorganics (36%), and BC (10%). Source apportionment via Positive Matrix Factorization (PMF) of AMS measured organic aerosols (OAs) revealed 6 factors...
October 12, 2016: Environmental Science. Processes & Impacts
Nupur Bansal, Zheng Zheng, David S Cerutti, Kenneth M Merz
We review our performance in the SAMPL5 challenge for predicting host-guest binding affinities using the movable type (MT) method. The challenge included three hosts, acyclic Cucurbit[2]uril and two octa-acids with and without methylation at the entrance to their binding cavities. Each host was associated with 6-10 guest molecules. The MT method extrapolates local energy landscapes around particular molecular states and estimates the free energy by Monte Carlo integration over these landscapes. Two blind submissions pairing MT with variants of the KECSA potential function yielded mean unsigned errors of 1...
October 3, 2016: Journal of Computer-aided Molecular Design
Limin Hu, Xuefa Shi, Shuqing Qiao, Tian Lin, Yuanyuan Li, Yazhi Bai, Bin Wu, Shengfa Liu, Narumol Kornkanitnan, Somkiat Khokiattiwong
Surface sediments obtained from a matrix of 92 sample sites in the Gulf of Thailand (GOT) were analyzed for a comprehensive study of the distribution, sources, and mass inventory of polycyclic aromatic hydrocarbons (PAHs) to assess their input pathways and impacts of the regional land-based energy structure on the deposition of PAHs on the adjacent continental margins. The concentration of 16 PAHs in the GOT ranged from 2.6 to 78.1ng/g (dry weight), and the mean concentration was 19.4±15.1ng/g. The spatial distribution pattern of 16 PAH was generally consistent with that of sediment grain size, suggesting the influence of regional hydrodynamic conditions...
September 30, 2016: Science of the Total Environment
Geoffry A Davis, Atsuko Kanazawa, Mark Aurel Schöttler, Kaori Kohzuma, John E Froehlich, A William Rutherford, Mio Satoh-Cruz, Deepika Minhas, Stefanie Tietz, Amit Dhingra, David M Kramer
The thylakoid proton motive force (pmf) generated during photosynthesis is the essential driving force for ATP production; it is also a central regulator of light capture and electron transfer. We investigated the effects of elevated pmf on photosynthesis in a library of Arabidopsis thaliana mutants with altered rates of thylakoid lumen proton efflux, leading to a range of steady-state pmf extents. We observed the expected pmf-dependent alterations in photosynthetic regulation, but also strong effects on the rate of photosystem II (PSII) photodamage...
October 4, 2016: ELife
Nariyoshi Matsumoto, Sayaka Mori, Hiroo Hasegawa, Daisuke Sasaki, Hayato Mori, Kazuto Tsuruda, Daisuke Imanishi, Yoshitaka Imaizumi, Tomoko Hata, Norihito Kaku, Kousuke Kosai, Naoki Uno, Yasushi Miyazaki, Katsunori Yanagihara
INTRODUCTION: Recently, novel calreticulin (CALR) mutations were discovered in Janus kinase 2 (JAK2) non-mutated myelofibrosis (PMF) and essential thrombocythemia (ET) cases, with a frequency of 60-80%. We examined clinical correlations and CALR mutation frequency in our myeloproliferative neoplasms (MPN) cases, and introduce an effective test method for use in clinical practice. METHODS: We examined 177 samples previously investigated for the JAK2 mutation for differential diagnosis of MPN...
November 1, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
Juli-Anne Gardner, Jason D Peterson, Scott A Turner, Barbara L Soares, Courtney R Lancor, Luciana L Dos Santos, Prabhjot Kaur, Deborah L Ornstein, Gregory J Tsongalis, Francine B de Abreu
OBJECTIVES: To describe three methods used to screen for frameshift mutations in exon 9 of the CALR gene. METHODS: Genomic DNA from 47 patients was extracted from peripheral blood and bone marrow using the EZ1 DNA Blood Kit (Qiagen, Valencia, CA) and quantified by the Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen, San Diego, CA). After clinical history, cytogenetics, and molecular tests, patients were diagnosed with either clonal or nonclonal hematologic diseases...
October 2016: American Journal of Clinical Pathology
D P Fields, G S Mitchell
Spinal metabotropic serotonin receptors encode transient experiences into long-lasting changes in motor behavior (i.e. motor plasticity). While interactions between serotonin receptor subtypes are known to regulate plasticity, the significance of molecular divergence in downstream G protein coupled receptor signaling is not well understood. Here we tested the hypothesis that distinct cAMP dependent signaling pathways differentially regulate serotonin-induced phrenic motor facilitation (pMF); a well-studied model of spinal motor plasticity...
September 20, 2016: Neuropharmacology
Yong Hyun Kim, Hong Kwon, Jeongjun Kim, Kwang Yong Song
High-sensitivity distributed measurement of hydrostatic pressure is experimentally demonstrated by optical time-domain analysis of Brillouin dynamic grating (BDG) in polarization maintaining fibers (PMF's). The spectral shift of the BDG in four different types of PMF's are investigated under hydrostatic pressure variation from 14.5 psi (1 bar) to 884.7 psi (61 bar) with less than 2 m spatial resolution. The pressure sensitivity of BDG frequency is measured to be ‒1.69, + 0.65, + 0.78, and + 0.85 MHz/psi for a PM photonic crystal fiber (PM-PCF), two Bow-tie fibers, and a PANDA fiber, respectively, which is about 65 to 169 times larger than that of Brillouin frequency-based pressure sensing...
September 19, 2016: Optics Express
Hummad Habib Qazi, Abu Bakar Mohammad, Harith Ahmad, Mohd Zamani Zulkifli
A D-shaped polarization-maintaining fiber (PMF) as fiber optic sensor for the simultaneous monitoring of strain and the surrounding temperature is presented. A mechanical end and edge polishing system with aluminum oxide polishing film is utilized to perform sequential polishing on one side (lengthwise) of the PMF in order to fabricate a D-shaped cross-section. Experimental results show that the proposed sensor has high sensitivity of 46 pm/µε and 130 pm/°C for strain and temperature, respectively, which is significantly higher than other recently reported work (mainly from 2013) related to fiber optic sensors...
2016: Sensors
F Xing, Y N Lin, Q Sun, L Qin, Y J Jia, D L Zhang, K Ru
Objective: To characterize the molecular profile in patients with Ph negative myeloproliferative neoplasms (MPN) by exploring 49 gene mutations. Methods: Targeted gene sequencing were performed to analyze 49 MPN-associated genes in 51 patients with Ph negative MPN, of which CARL (exon 9), NPM1 (exon 12) and CEBPA (TAD, BZIP domains) were investigated by using Sanger sequencing simultaneously, while FLT3-ITD was assessed by PCR method. Results: Mutations were detected in 73.5% (36/49) of genes, and the mutational rates of JAK2-V617F, CALR (exon 9) and MPL were 60...
September 8, 2016: Zhonghua Bing Li Xue za Zhi Chinese Journal of Pathology
Lasun T Ogundele, Oyediran K Owoade, Felix S Olise, Philip K Hopke
To identify the potential sources responsible for the particulate matter emission from secondary iron and steel smelting factory environment, PM2.5 and PM2.5-10 particles were collected using the low-volume air samplers twice a week for a year. The samples were analyzed for the elemental and black carbon content using x-ray fluorescence spectrometer and optical transmissometer, respectively. The average mass concentrations were 216.26, 151.68, and 138. 62 μg/m(3) for PM2.5 and 331.36, 190.01, and 184.60 μg/m(3) for PM2...
October 2016: Environmental Monitoring and Assessment
Vitalij Novickij, Audrius Grainys, Eglė Lastauskienė, Rūta Kananavičiūtė, Dovilė Pamedytytė, Lilija Kalėdienė, Jurij Novickij, Damijan Miklavčič
Electroporation is a phenomenon occurring due to exposure of cells to Pulsed Electric Fields (PEF) which leads to increase of membrane permeability. Electroporation is used in medicine, biotechnology, and food processing. Recently, as an alternative to electroporation by PEF, Pulsed ElectroMagnetic Fields (PEMF) application causing similar biological effects was suggested. Since induced electric field in PEMF however is 2-3 magnitudes lower than in PEF electroporation, the membrane permeabilization mechanism remains hypothetical...
2016: Scientific Reports
Venkat Reddy Pannala, Amadou K S Camara, Ranjan K Dash
Cytochrome c oxidase (CcO) catalyzes the exothermic reduction of O2 to H2O by utilizing electrons from cytochrome c, and hence plays a crucial role in ATP production. Although details on the enzyme structure and redox centers involved in O2 reduction have been known, there still remains a considerable ambiguity on its mechanism of action, e.g. the number of sequential electrons donated to O2 in each catalytic step, the sites of protonation and proton pumping, and nitric oxide (NO) inhibition mechanism. In this work, we developed a thermodynamically-constrained mechanistic mathematical model for the catalytic action of CcO based on available kinetic data...
September 15, 2016: Journal of Applied Physiology
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