Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Mutations in RNA Polymerase Beta Subunit Gene Encoding Resistance to Rifampin in Mycobacterium tuberculosis by DNA Microarray

Abstract Rapid and efficient diagnosis is essential in the management of drug‐resistant tuberculosis. A DNA microarray technique based on differential hybridization method was described in the present study for detecting mutations in the RNA polymerase beta subunit (rpoB) gene of Mycobacterium tuberculosis (M. tuberculosis) cultures and in clinical specimens. The mutations in rpoB confer resistance to rifampin, an important first‐line antituberculosis drug. The differential hybridization approach was mainly based on the effect of a single base mismatch on the melting temperature of the hybridized DNA; therefore, any point mutation of rpoB gene resulting in the rifampin resistance can be detected efficiently. The development of the DNA microarray involves the design of dozens of oligonucleotide probes for identifying rifampin‐resistant and ‐sensitive strains. The method comprises isolating genomic DNA from the samples containing M. tuberculosis cells, amplifying rpoB gene coding sequence to produce fluorescently labelled product, and hybridization with the oligonucleotide arrays. The results demonstrated the capability of DNA microarray to provide important clinically relevant information about the rpoB gene of mycobacterial organisms. The DNA microarray offers a reliable diagnostic test for rapidly detecting multidrug resistance caused by gene mutations of mycobacteria.
On the Fluctuations that Order and Frustrate Liquid Water

At ambient conditions, water sits close to phase coexistence with its crystal. More so than in many other materials, this fact is manifested in the fluctuations that maintain a large degree of local order in the liquid. These fluctuations and how they result in long-ranged order, or its absence, are emergent features of many interacting molecules. Their study therefore requires using the tools of statistical mechanics for their their systematic understanding. In this dissertation we develop such an understanding. In particular, we focus on collective behavior that emerges in liquid and solid water. At room temperatures, the thermophysical properties of water are quantified and rationalized with simple molecular models. A key feature of these models is the correct characterization of the competition between entropic forces of packing and the energetic preference for tetrahedral order. At cold temperatures, the properties of ice surfaces are studied with statistical field theory. The theory we develop for the long wavelength features of ice interfaces allows us to explain the existence of a premelting layer on the surface of ice and the stability of ice in confinement. In between these extremes, the dynamics of supercooled water are considered. A detailed theory for the early stages of coarsening is developed and used to explain the peculiar observation of a transient second liquid state of water. When coarsening dynamics are arrested, the result is the formation of a glassy states of water. We show that out-of-equilibrium the phase diagram for supercooled water exhibits a rich amount of structure, including a triple point between two glass phases of water and the liquid. At the end, we explore possible technological implications for the interplay between ordering and frustration in studies of water at metal interfaces.
International Journal of Food Engineering Dynamic Viscoelastic Properties of Rice Kernels Studied by Dynamic Mechanical Analyzer

Dynamic viscoelastic properties of brown rice kernels were investigated using a dynamic mechanical analyzer (DMA). In order to meet the sample requirements for the DMA and prevent moisture loss of rice kernels during the DMA measurements, necessary precautions were taken. To prevent moisture loss of rice kernels during the DMA measurements at temperatures ranging from room temperature to 120 degrees centigrade, rice kernels were wrapped with a thin layer of sealing film. Then the wrapped rice kernels were additionally covered with an aluminum foil. Two ends of the wrapped brown rice kernels were cut with a razor blade; subsequently both ends of the cut rice kernels were filed using fine sandpaper to produce near cylindrical rice kernels with parallel ends. The storage modulus of the rice kernels decreased with increasing temperature and moisture content. The loss modulus and the tan delta (loss factor) of the rice kernels as a function of temperature showed clear peaks, which are associated with the glass transition of rice kernels. Two rice varieties had been investigated, and the results showed that the dynamic viscoelastic properties of these rice samples were not significantly different. The glass transition temperatures for the long-grain rice kernels with the moisture contents of 17.4, 13.8, and 10.9 wt. % were determined as 45, 58, and 66 degrees centigrade, respectively.
Transport and fate of veterinary sulfonamide antibiotics in soil

······························································································ i ZUSAMMENFASSUNG ················································································ iv ACKKNOWLEDGEMENTS ··········································································· viii TABLE OF CONTENTS ················································································· x LIST OF TABLES ······················································································· xiii LIST OF FIGURES ······················································································ xiv LIST OF ABBREVIATIONS ··········································································· xvi LIST OF SYMBOLS ···················································································· xvii 1. General introduction ··················································································· 1 1.1. Occurrence and origin of veterinary antibiotics in environment ························· 1 1.2. Significance of veterinary sulfonamide antibiotics for environmental and ecotoxicological issues ········································································ 2 1.3. Property of target sulfonamide antibiotics ·················································· 5 1.4. Overview of this thesis ········································································· 7 1.4. 1 Study area ·················································································· 7 1.4. 2 Objectives and hypotheses ······························································· 8 1.4. 3 Methods and results ······································································· 12 1.4. 3.1 Effect of soil structure and pH on transport of sulfonamide antibiotics ····· 12 1.4. 3.2 Transport of sulfonamide antibiotics in crop fields during monsoon season 16 1.4. 3.3 Sulfadimethoxine transport in soil columns in relation to sorbable and nonsorbable tracers ··········································································· 20 1.5. List of manuscripts and specification of individual contributions ······················· 23 1.6. References ······················································································· 25 2. Effect of soil structure and pH on transport of sulfonamide antibiotics ························ 33 2.
Spectroscopy with Laser-cooled Francium and Progress on Atomic Parity Non-conservation

Title of dissertation: SPECTROSCOPY WITH LASER-COOLED FRANCIUM AND PROGRESS ON ATOMIC PARITY NON-CONSERVATION Jiehang Zhang, Doctor of Philosophy, 2015 Dissertation directed by: Professor Luis A. Orozco Joint Quantum Institute, University of Maryland Department of Physics and National Institute of Standards and Technology Francium, the heaviest alkali, possesses a unique combination of structural simplicity and great sensitivity to effects such as atomic parity non-conservation (APNC). We report in this thesis our progress towards measuring weak-interaction physics in a low energy system: the francium atom. We have built a new generation of high-efficiency laser cooling and trapping facility at TRIUMF national laboratory in Canada. We constructed a precision science chamber and demonstrate francium atom transfer into the precision trap, where the electromagnetic field environments can be exquisitely controlled such that weak-interaction studies via optical and microwave excitations can take place. We perform laser spectroscopy measurements of the hyperfine structure and isotope shifts in a chain of francium isotopes near the neutron closed shell (N = 126), including both ground and isomeric nuclear states. These measurements provide a basis for benchmarking state of the art atomic theory, as well as future nuclear structure calculations in Fr, necessary for interpreting the weak-interaction studies. These developments lay important foundations for precision parity non-conservation measurements with francium.
Microfabricated rubidium dielectric barrier discharge light sources for portable atomic clocks

Keywords: atomic clocks ; rubidium ; dielectric barrier discharge ; microfabrication ; anodic bonding ; rf plasma ; solder sealing ; double-resonance These Ecole polytechnique federale de Lausanne EPFL, n° 5702 (2013)Programme doctoral Microsystemes et MicroelectroniqueFaculte des sciences et techniques de l'ingenieurInstitut de microtechniqueLaboratoire des microsystemes pour les technologies spatialesJury: P.-A. Farine (president), D. Briand, G. Mileti, A. Weis Public defense: 2013-4-12 Reference doi:10.5075/epfl-thesis-5702Print copy in library catalog Record created on 2013-03-27, modified on 2017-05-10
One-dimensional graphene nanoribbons hybridized with carbon nanotubes as cathode and anode interfacial layers for high performance solar cells

Solution processible graphene oxide nanoribbons (GONRs) with a continuous one-dimensional length and the remaining carbon nanotubes (CNTs) have been synthesized from the partial unzipping of multiwalled carbon nanotubes (MWCNTs). Such low-cost GONRs hybridized with CNTs (GONR/CNTs) show solution processibility as well as a tunable work function and multifunctional interfacial modification in polymer solar cells (PSCs) due to well-defined nanoribbons containing CNTs with a continuous one-dimensional length that promote charge transport, different from the GONRs unzipped from single-walled carbon nanotubes that tend to form a large amount of graphene oxide pieces. Incorporation of the GONR/CNTs into solution processed PSCs as an electron transporting layer (ETL) and hole transporting layer (HTL) simultaneously delivers a high device performance with long-term stability. The results demonstrate that multifunctional GONR/CNTs unzipped from MWCNTs would be promising interfacial materials for solution processed high performance PSCs.
Single-particle motion and heat transfer in fluidized beds

Fluidized beds are particularly favored as chemical reactors because of their ability to exchange heat through immersed heat-exchange surfaces. However, little is known about how the heat-exchange process works on a single-particle level. The most commonly applied theory of fluidized bed heat exchange is that developed by Mickley and Fairbanks in the 1950s—the so-called packet model. The work described in this article is an attempt to understand the process of heat transfer by solids convection, using positron emission particle tracking to follow the trajectory of a single tracer particle in the bed. In particular, the residence time of particles in the vicinity of the surface is determined here for the first time. Using these data, the observed heat-transfer variations are interpreted mechanistically. © 2006 American Institute of Chemical Engineers AIChE J, 2006
Crystal structure, magnetic susceptibility and electrical conductivity of EuAuGe: a new ordered version of the CeCu2-type structure

The ternary germanide EuAuGe has been prepared from the elemental components in a tantalum tube at 1070 K. It was investigated by X-ray diffraction on both powder and single crystals. The crystal structure was determined from four-circle diffractometer data: Imm2, a= 460.1(1) pm, b= 737.1(1) pm, c= 788.1(2) pm, V= 0.2673(2) nm3, Z= 4, R= 0.0288 for 1069 F2 values and 22 variables. EuAuGe crystallizes in a new ternary ordered version of the CeCu2 type. Its structure is compared with the related TiNiSi-type. Susceptibility measurements show Curie-Weiss behaviour above 40 K with µexp= 7.4(1)µB, indicating Eu2+. EuAuGe orders ferromagnetically at Tc= 34(1) K. Electrical conductivity measurements are compatible with metallic behaviour.
An ab Initio and Classical Molecular Dynamics Investigation of the Structural and Vibrational Properties of Talc and Pyrophyllite

The structural and vibrational properties of two uncharged 2:1 phyllosilicates, talc and pyrophyllite, are investigated via ab initio and classical molecular dynamics simulations. The quantum mechanical simulations are based on plane−wave pseudopotential density functional theory (DFT), which is shown to be sufficiently accurate in predicting the clay mineral structural and vibrational properties. The classical molecular dynamics (MD) simulations, using the CLAYFF force field, faithfully reproduce the crystal structures with relatively simple analytical functions that include primarily nonbonded interactions. The adsorption properties in these clay minerals are strongly dependent upon the disposition of the hydroxyl group in the octahedral sheet. With the assistance of molecular simulation, the relationship between the hydroxyl group vibrational modes and the molecular-scale structure is explored. The talc hydroxyl groups are oriented perpendicular to the ab plane, while the presence of the dioctahedral v.
Coexistence of competing consumers on a single resource in a hybrid model

The question of whether and how two competing consumers can coexist on a single limiting resource has a long tradition in ecological theory. We build on a recent seasonal (hybrid) model for one consumer and one resource, and we extend it by introducing a second consumer. Consumers reproduce only once per year, the resource reproduces throughout the"summer" season. When we use linear consumer reproduction between years, we find explicit expressions for the trivial and semi-trivial equilibria, and we prove that there is no positive equilibrium generically. When we use non-linear consumer reproduction, we determine conditions for which both semi-trivial equilibria are unstable. We prove that a unique positive equilibrium exists in this case, and we find an explicit analytical expression for it. By linear analysis and numerical simulation, we find bifurcations from the stable equilibrium to population cycles that may appear through period-doubling or Hopf bifurcations. We interpret our results in terms of climate change that changes the length of the"summer" season.
Evaluation of an induction‐assisted friction stir welding technique for super duplex stainless steels

The microstructure changes and the mechanical properties of a friction stir welded (FSW) super duplex stainless steel (GX2CrNiMoN26‐7‐4) were analyzed. A PCBN tool was used to weld 5‐mm‐thick plates at a constant rotational speed of 300 rpm, at 100 and 200 mm/min, under two different conditions: conventional FSW and Induction‐Assisted FSW (IA‐FSW). Preheating technique allows welding with a reduction in forge forces close to 31% at the same welding speed, or doubling speed (200 mm/min) at the same axial force, obtaining sound welds. No sigma phase was detected in the welds, and the clear grain size reduction led to an increase in mean hardness value and the tensile strength of the stir zone. Ferrite percentage was found to be between 50 and 70% through the welds. Copyright © 2014 John Wiley & Sons, Ltd.
An Investigation of the Relationship Between Structural Disruption and Functional Connectivity in Multiple Sclerosis and its Effect on Cognition

Although previous research has established a link between structural damage and functional reorganization in Multiple Sclerosis, it remains unclear what mediates this link and how it affects people with MS. Using neuroimaging techniques such as MRI and fMRI, it is possible to examine several resting state functional networks to determine whether certain networks of brain activity differ in how they functionally change in response to structural damage brought about by MS. Using a general linear model, we were able to show that there exists a significant relationship between structural and functional connectivity among nine resting state networks. This relationship was strongest among more abstract higher order networks such as the default mode network or the executive control network. Changes in functional connectivity may also help explain the concept of cognitive reserve in MS, where some people show less cognitive dysfunction despite a similar amount of white and grey matter atrophy. We again used a general linear model to measure the interaction between structural and functional connectivity as it pertains to cognitive processing speed, and found that preservation of functional connectivity helps moderate cognitive reserve in people with MS.
M ar 2 01 4 Toward transferable interatomic van der Waals potentials : The role of multipole electrostatics and many-body dispersion without electrons

We estimate polarizabilities of atoms in molecules without electron density, using a Voronoi partitioning approach instead. The resulting atomic dispersion coefficients are calculated, as well as many-body dispersion effects on intermolecular potential energies. We also estimate contributions from multipole electrostatics and compare them to dispersion. We assess the performance of the resulting intermolecular potential from dispersion and electrostatics for more than 1,300 neutral and charged, small organic molecular dimers. Applications to water clusters, the benzene crystal, the anti-cancer drug ellipticine—intercalated between two Watson-Crick DNA base pairs, as well as six macro-molecular host-guest complexes highlight the potential of this method and help to identify points of future improvement. Overall, the method achieves an accuracy well within sophisticated empirical force fields, such as OPLS and Amber FF03, while exhibiting a simple parametrization protocol without the need for experimental input.
Catalyst Deactivation Simulation Through Carbon Deposition in Carbon Dioxide Reforming over Ni/CaO-Al2O3 Catalyst

Major problem in CO2 reforming of methane (CORM) process is coke formation which is a carbonaceous residue that can physically cover active sites of a catalyst surface and leads to catalyst deactivation. A key to develop a more coke-resistant catalyst lies in a better understanding of the methane reforming mechanism at a molecular level. Therefore, this paper is aimed to simulate a micro-kinetic approach in order to calculate coking rate in CORM reaction. Rates of encapsulating and filamentous carbon formation are also included. The simulation results show that the studied catalyst has a high activity, and the rate of carbon formation is relatively low. This micro-kinetic modeling approach can be used as a tool to better understand the catalyst deactivation phenomena in reaction via carbon deposition. Copyright © 2011 BCREC UNDIP. All rights reserved. ( Received: 10th May 2011; Revised: 16th August 2011; Accepted: 27th August 2011 ) [ How to Cite : I. Istadi, D.D. Anggoro, N.A. S. Amin, and D.H. W. Ling. (2011). Catalyst Deactivation Simulation Through Carbon Deposition in Carbon Dioxide Reforming over Ni/CaO-Al2O3 Catalyst. Bulletin of Chemical Reaction Engineering & Catalysis , 6 (2): 129-136. doi:10.9767/bcrec.6. 2.1213. 129-136 ] [How to Link / DOI: http://dx.doi. org/10.9767/bcrec.6. 2.1213. 129-136 || or local: http://ejournal.undip. ac.id/index.php/bcrec/article/view/1213 ] | View in |
Water Deficit Effect on Ratio of Seed to Berry Fresh Weight and Berry Weight Uniformity in Winegrape cv. Merlot

The objective of this research was to investigate the effect of vine water deficit on berry tissue components and berry weight uniformity at maturity. Field-grown grapevines cv. Merlot (Vitis vinifera L.) were differentially irrigated over six consecutive years to maintain a high or low level of vine water stress from fruit set until harvest and clusters were sampled at maturity in the third and fifth year. Detached berries were individually weighed to assess weight uniformity within each irrigation regime and to obtain a sample of similar weight berries from each level of irrigation. Vine water deficit was associated with up to a 27% increase in the proportion of seed to total berry fresh weight regardless of berry size. Berry weight within each irrigation regime was distributed normally and water deficit did not affect berry weight uniformity at maturity. Results have implications for winemaking because a greater ratio of seed to total berry fresh weight alters the proportion of seed-derived relative to skin-derived compounds present during fermentation.
Determination of AlAs mole fraction in AlxGa1−xAs using Raman spectroscopy and x‐ray diffraction

High resolution x‐ray diffraction (HRXRD) is used to accurately determine the AlAs mole fraction in AlxGa1−xAs samples over the complete alloy range. The AlAs mole fraction error in the HRXRD measurement is estimated to be less than 0.0035. A small bowing in the variation of the alloy lattice constant with changing AlAs mole fraction is observed. The HRXRD characterized samples are used in Raman spectroscopy to calibrate the variation in the longitudinal optical (LO) GaAs and AlAs modes with varying alloy composition. Empirical expressions for the variation in the LO modes are found, with mole fraction errors of less than 0.03. Raman spectroscopy is a relatively simple nondestructive measurement and the expressions developed here allow for the fast determination of AlAs mole fraction in AlxGa1−xAs samples. The Raman data is compared to a theoretical dependence for a two phonon mode alloy crystal with excellent results.