Mathematical Model and Simulation of a Pneumatic Apparatus for In-Drilling Alignment of an Inertial Navigation Unit during Horizontal Well Drilling

Conventional methods in horizontal drilling processes incorporate magnetic surveying techniques for determining the position and orientation of the bottom-hole assembly (BHA). Such means result in an increased weight of the drilling assembly, higher cost due to the use of non-magnetic collars necessary for the shielding of the magnetometers, and significant errors in the position of the drilling bit. A fiber-optic gyroscope (FOG) based inertial navigation system (INS) has been proposed as an alternative to magnetometer -based downhole surveying. The utilizing of a tactical-grade FOG based surveying system in the harsh downhole environment has been shown to be theoretically feasible, yielding a significant BHA position error reduction (less than 100m over a 2-h experiment). To limit the growing errors of the INS, an in-drilling alignment (IDA) method for the INS has been proposed. This article aims at describing a simple, pneumatics-based design of the IDA apparatus and its implementation downhole. A mathematical model of the setup is developed and tested with Bloodshed Dev-C++. The simulations demonstrate a simple, low cost and feasible IDA apparatus.

Operational Methods in the Environment of a Computer Algebra System

This article presents the principal results of the doctoral thesis “Direct Operational Methods in the Environment of a Computer Algebra System” by Margarita Spiridonova (Institute of mathematics and Informatics, BAS), successfully defended before the Specialised Academic Council for Informatics and Mathematical Modelling on 23 March, 2009.

Transitive state alignment for the quantum jensen-shannon kernel

Kernel methods provide a convenient way to apply a wide range of learning techniques to complex and structured data by shifting the representational problem from one of finding an embedding of the data to that of defining a positive semidefinite kernel. One problem with the most widely used kernels is that they neglect the locational information within the structures, resulting in less discrimination. Correspondence-based kernels, on the other hand, are in general more discriminating, at the cost of sacrificing positive-definiteness due to their inability to guarantee transitivity of the correspondences between multiple graphs. In this paper we generalize a recent structural kernel based on the Jensen-Shannon divergence between quantum walks over the structures by introducing a novel alignment step which rather than permuting the nodes of the structures, aligns the quantum states of their walks. This results in a novel kernel that maintains localization within the structures, but still guarantees positive definiteness. Experimental evaluation validates the effectiveness of the kernel for several structural classification tasks. © 2014 Springer-Verlag Berlin Heidelberg.

Smoke rings:towards a comprehensive tobacco free policy for the Olympic Games

Background The tobacco industry has long sought affiliation with major sporting events, including the Olympic Games, for marketing, advertising and promotion purposes. Since 1988, each Olympic Games has adopted a tobacco-free policy. Limited study of the effectiveness of the smoke-free policy has been undertaken to date, with none examining the tobacco industry's involvement with the Olympics or use of the Olympic brand. Methods and Findings A comparison of the contents of Olympic tobacco-free policies from 1988 to 2014 was carried out by searching the websites of the IOC and host NOCs. The specific tobacco control measures adopted for each Games were compiled and compared with measures recommended by the WHO Tobacco Free Sports Initiative and Article 13 of the Framework Convention on Tobacco Control (FCTC). This was supported by semi-structured interviews of key informants involved with the adoption of tobacco-free policies for selected games. To understand the industry's interests in the Olympics, the Legacy Tobacco Documents Library (http://legacy.library.ucsf.edu) was systematically searched between June 2013 and August 2014. Company websites, secondary sources and media reports were also searched to triangulate the above data sources. This paper finds that, while most direct associations between tobacco and the Olympics have been prohibited since 1988, a variety of indirect associations undermine the Olympic tobacco-free policy. This is due to variation in the scope of tobacco-free policies, limited jurisdiction and continued efforts by the industry to be associated with Olympic ideals. Conclusions The paper concludes that, compatible with the IOC's commitment to promoting healthy lifestyles, a comprehensive tobacco-free policy with standardized and binding measures should be adopted by the International Olympic Committee and all national Olympic committees.

Serum-free process development:improving the yield and consistency of human mesenchymal stromal cell production

Background aims: The cost-effective production of human mesenchymal stromal cells (hMSCs) for off-the-shelf and patient specific therapies will require an increasing focus on improving product yield and driving manufacturing consistency. Methods: Bone marrow-derived hMSCs (BM-hMSCs) from two donors were expanded for 36 days in monolayer with medium supplemented with either fetal bovine serum (FBS) or PRIME-XV serum-free medium (SFM). Cells were assessed throughout culture for proliferation, mean cell diameter, colony-forming potential, osteogenic potential, gene expression and metabolites. Results: Expansion of BM-hMSCs in PRIME-XV SFM resulted in a significantly higher growth rate (P < 0.001) and increased consistency between donors compared with FBS-based culture. FBS-based culture showed an inter-batch production range of 0.9 and 5 days per dose compared with 0.5 and 0.6 days in SFM for each BM-hMSC donor line. The consistency between donors was also improved by the use of PRIME-XV SFM, with a production range of 0.9 days compared with 19.4 days in FBS-based culture. Mean cell diameter has also been demonstrated as a process metric for BM-hMSC growth rate and senescence through a correlation (R² = 0.8705) across all conditions. PRIME-XV SFM has also shown increased consistency in BM-hMSC characteristics such as per cell metabolite utilization, in vitro colony-forming potential and osteogenic potential despite the higher number of population doublings. Conclusions: We have increased the yield and consistency of BM-hMSC expansion between donors, demonstrating a level of control over the product, which has the potential to increase the cost-effectiveness and reduce the risk in these manufacturing processes.

Targeted mass spectrometry methods for detecting oxidative post-translational modifications

Oxidative post-translational modifications (oxPTMs) can alter the function of proteins, and are important in the redox regulation of cell behaviour. The most informative technique to detect and locate oxPTMs within proteins is mass spectrometry (MS). However, proteomic MS data are usually searched against theoretical databases using statistical search engines, and the occurrence of unspecified or multiple modifications, or other unexpected features, can lead to failure to detect the modifications and erroneous identifications of oxPTMs. We have developed a new approach for mining data from accurate mass instruments that allows multiple modifications to be examined. Accurate mass extracted ion chromatograms (XIC) for specific reporter ions from peptides containing oxPTMs were generated from standard LC-MSMS data acquired on a rapid-scanning high-resolution mass spectrometer (ABSciex 5600 Triple TOF). The method was tested using proteins from human plasma or isolated LDL. A variety of modifications including chlorotyrosine, nitrotyrosine, kynurenine, oxidation of lysine, and oxidized phospholipid adducts were detected. For example, the use of a reporter ion at 184.074 Da/e, corresponding to phosphocholine, was used to identify for the first time intact oxidized phosphatidylcholine adducts on LDL. In all cases the modifications were confirmed by manual sequencing. ApoB-100 containing oxidized lipid adducts was detected even in healthy human samples, as well as LDL from patients with chronic kidney disease. The accurate mass XIC method gave a lower false positive rate than normal database searching using statistical search engines, and identified more oxidatively modified peptides. A major advantage was that additional modifications could be searched after data collection, and multiple modifications on a single peptide identified. The oxPTMs present on albumin and ApoB-100 have potential as indicators of oxidative damage in ageing or inflammatory diseases.

Free radical reaction products and antioxidant capacity in beating heart coronary artery surgery compared to conventional bypass

Oxygen-derived free radicals are important agents of tissue injury during ischemia and reperfusion. The aim of this study was to investigate changes in protein and lipid oxidation and antioxidant status in beating heart coronary artery surgery and conventional bypass and to compare oxidative stress parameters between the two bypass methods. Serum lipid hydroperoxide, nitric oxide, protein carbonyl, nitrotyrosine, vitamin E, and β-carotene levels and total antioxidant capacity were measured in blood of 30 patients undergoing beating heart coronary artery surgery (OPCAB, off-pump coronary artery bypass grafting) and 12 patients undergoing conventional bypass (CABG, on-pump coronary artery bypass grafting). In the OPCAB group, nitric oxide and nitrotyrosine levels decreased after reperfusion. Similarly, β-carotene level and total antioxidant capacity also decreased after anesthesia and reperfusion. In the CABG group, nitric oxide and nitrotyrosine levels decreased after ischemia and reperfusion. However, protein carbonyl levels elevated after ischemia and reperfusion. Vitamin E, β-carotene, and total antioxidant capacity decreased after ischemia and reperfusion. Significantly decreased nitration and impaired antioxidant status were seen after reperfusion in both groups. Moreover, elevated protein carbonyls were found in the CABG group. The off-pump procedure is associated with lower degree of oxidative stress than on-pump coronary surgery. © 2011 Pleiades Publishing, Ltd.

Detergent-free membrane protein purification

Membrane proteins are localised within a lipid bilayer; in order to purify them for functional and structural studies the first step must involve solubilising or extracting the protein from these lipids. To date this has been achieved using detergents which disrupt the bilayer and bind to the protein in the transmembrane region. However finding conditions for optimal extraction, without destabilising protein structure is time consuming and expensive. Here we present a recently-developed method using a styrene maleic acid (SMA) co-polymer instead of detergents. The SMA co-polymer extracts membrane proteins in a small disc of lipid bilayer which can be used for affinity chromatography purification, thus enabling the purification of membrane proteins while maintaining their native lipid bilayer environment.

A földrajzi távolság, a kulturális hasonlóság és a szabadkereskedelem hatása a borkereskedelemre = Effects on the global wine trade of geographical distance, cultural and linguistic similarity, and free trade

A globalizálódó világgazdaságban a vezető bortermelő országok egyre jelentősebb borkereskedelmet bonyolítanak le egymás között. Míg Európában a fogyasztók egyre kevesebb bort vásárolnak, addig Amerikában és Ázsiában a bor iránti kereslet folyamatosan bővül: a borkereskedelem földrajzi átrendeződése zajlik. A kulturális hasonlóság és a földrajzi távolság kereskedelemre gyakorolt hatását gyakran a kereskedelemelméletek gravitációs modelljével elemzik. E tanulmány azt vizsgálja, hogy a fő borexportáló országok közötti földrajzi távolság, kulturális hasonlóság és szabadkereskedelem milyen hatással van a nemzetközi borkereskedelemre, annak költségeire. A regressziós becslés eredményei alátámasztják, hogy a borkereskedelem költségei alacsonyabbak, ha a kereskedelmi partnerek kulturálisan hasonlók, földrajzilag közel helyezkednek el egymáshoz, vagy van tengeri kikötőjük, tagjai a WTO-nak, illetve ha kötöttek egymással regionális kereskedelmi megállapodást. Ezenkívül megállapítható, hogy az angolszász, a latin-amerikai és az európai kulturális klaszterek elsősorban egymással kereskednek. A kutatás számos kulturális változó alkalmazásával és több ökonometriai modell, illetve becslési eljárás nagymintás tesztelésével gazdagítja a szakirodalmat. ____ In a globalizing world, major wine-producing countries export considerable quantities to the global wine market and turn over a notable trade, but in what happens European wine regions differ markedly from the New World. Here major wine producers suffered a remarkable fall in domestic wine consumption in recent decades, while New World wine producers increased their production potential and generated new foreign demand. The changes have been joined by geographical relocation of wine consumption and exports. The gravity equation can be derived from demand-side or supply-side theory-consistent estimation methods that suggest relationships between the size of the economies, geographical distances, cultural similarities, and size of their trade. The paper analyses the effects of cultural and geographical proximity, free trade, and linguistic similarity on bilateral trade in the main wine-producing countries, using a cross-section gravity model for 2012. The results suggest that larger countries export more wine, while transport costs rise in line with geographical distance and are higher for landlocked trading partners. Wine export costs are lower if trading partners are culturally similar, share a dominant religion, or are both WTO members with regional trade agreements. Anglo-Saxon, Germanic, Latin American and Latin European countries mainly trade wines within their groups. The paper looks to extend the number of trading partners, investigate the effect of language clusters, and confirm that the results are robust by different econometric methodologies.

Relative basicities of free base porphyrins; understanding the role of macrocyclic distortion

Porphyrins have been the center of numerous investigations in different areas of chemistry, geochemistry, and the life sciences. In nature the conformation of the porphyrin macrocycle varies, depending on the function of its apoenzyme. It is believed that the conformation of the porphyrin ring is necessary for the enzyme to achieve its function and modify its reactivity. It is important to understand how the conformation of the porphyrin ring will influence its properties. ^ In synthetic porphyrins particular conformations and ring deformations can be achieved by peripheral substitution, metallation, core substitution, and core protonation among other alterations of the macrocycle. The macrocyclic distortions will affect the ring current, the ability of pyrroles to intramolecularly hydrogen bond and the relative basicity of each of the porphyrins. To understand these effects different theoretical models are used. The ground state structure of each of 19 free base porphyrins is determined using molecular mechanics (MM+) and semiempirical methods (PM3). The energetics of deformation of the macrocyclic core is calculated by carrying out single point energy calculations for the conformation achieved by each synthetic compound. Enthalpies of solution and enthalpies of protonation of 10 porphyrins with varying degrees of macrocyclic deformation and varying electron withdrawing groups in the periphery are determined using solution calorimetry. Using Hess's Law, the relative basicity of each of the different free base porphyrins is calculated. NMR results are described, including the determination of free energies of activation of ring tautomerization and hydrogen bonding for several compounds. It was found that in the absence of electronic effects, the greater macrocyclic deformation, the greater the basicity of the porphyrins. This basicity is attenuated by the presence of electron withdrawing groups and ability to of the macrocycle to intramolecularly hydrogen bond. ^

Factors affecting the alignment of *grades and reading scores for third-grade students on the Florida Comprehensive Assessment Test

The purpose of this study was to aid in understanding the relationship between current Reading report card grading practices and standards-based state standardized testing results in Reading and factors associated with the alignment of this relationship. Report card and Florida Comprehensive Assessment Test (FLAT) data for 2004 were collected for 1064 third grade students in nine schools of one feeder pattern in Florida's Miami-Dade County Public Schools. A Third Grade Teacher Questionnaire was administered to 48 Reading teachers. The questionnaire contained items relating to teachers' education, teaching experience, grading practices, and beliefs about the FCAT, instructional Reading activities, methods, and materials. ^ Findings of this study support a strong relationship between report card grades and FCAT Reading achievement levels. However, individual school correlational analysis showed significant differences among schools' alignment measures. Higher teacher alignment between grades and FCAT levels was associated with teachers spending more time on individualized methods of Reading instruction and to teachers feeling there was not enough time to teach and help individual students. Lower teacher alignment of grades and achievement levels was associated with teachers taking homework into account in the final Reading grade. Teacher alignment of grades and achievement levels was not associated with teacher beliefs concerning the FCAT, instructional activities in Reading and Language Arts, the Reading program used, the model of delivery of the Reading program, instruction or type of instructional planning done by the teachers. ^ This study highlights the need for further investigations related to determining additional teacher factors that may affect the alignment relationship between report card grades and standards-based state standardized testing results. ^

Relative basicities of free base porphyrins : understanding the role of macrocyclic distortion

Porphyrins have been the center of numerous investigations in different areas of chemistry, geochemistry, and the life sciences. In nature the conformation of the porphyrin macrocycle varies, depending on the function of its apoenzyme. It is believed that the conformation of the porphyrin ring is necessary for the enzyme to achieve its function and modify its reactivity. It is important to understand how the conformation of the porphyrin ring will influence its properties. In synthetic porphyrins particular conformations and ring deformations can be achieved by peripheral substitution, metallation, core substitution, and core protonation among other alterations of the macrocycle. The macrocyclic distortions will affect the ring current, the ability of pyrroles to intramolecularly hydrogen bond and the relative basicity of each of the porphyrins. To understand these effects different theoretical models are used. The ground state structure of each of 19 free base porphyrins is determined using molecular mechanics (MM+) and semiempirical methods (PM3). The energetics of deformation of the macrocyclic core is calculated by carrying out single point energy calculations for the conformation achieved by each synthetic compound. Enthalpies of solution and enthalpies of protonation of 10 porphyrins with varying degrees of macrocyclic deformation and varying electron withdrawing groups in the periphery are determined using solution calorimetry. Using Hess's Law, the relative basicity of each of the different free base porphyrins is calculated. NMR results are described, including the determination of free energies of activation of ring tautomerization and hydrogen bonding for several compounds. It was found that in the absence of electronic effects, the greater macrocyclic deformation, the greater the basicity of the porphyrins. This basicity is attenuated by the presence of electron withdrawing groups and ability to of the macrocycle to intramolecularly hydrogen bond.

On Provable Algorithms for Determination of Continuous Protein Interdomain Motions from Residual Dipolar Couplings

Dynamics of biomolecules over various spatial and time scales are essential for biological functions such as molecular recognition, catalysis and signaling. However, reconstruction of biomolecular dynamics from experimental observables requires the determination of a conformational probability distribution. Unfortunately, these distributions cannot be fully constrained by the limited information from experiments, making the problem an ill-posed one in the terminology of Hadamard. The ill-posed nature of the problem comes from the fact that it has no unique solution. Multiple or even an infinite number of solutions may exist. To avoid the ill-posed nature, the problem needs to be regularized by making assumptions, which inevitably introduce biases into the result.

Here, I present two continuous probability density function approaches to solve an important inverse problem called the RDC trigonometric moment problem. By focusing on interdomain orientations we reduced the problem to determination of a distribution on the 3D rotational space from residual dipolar couplings (RDCs). We derived an analytical equation that relates alignment tensors of adjacent domains, which serves as the foundation of the two methods. In the first approach, the ill-posed nature of the problem was avoided by introducing a continuous distribution model, which enjoys a smoothness assumption. To find the optimal solution for the distribution, we also designed an efficient branch-and-bound algorithm that exploits the mathematical structure of the analytical solutions. The algorithm is guaranteed to find the distribution that best satisfies the analytical relationship. We observed good performance of the method when tested under various levels of experimental noise and when applied to two protein systems. The second approach avoids the use of any model by employing maximum entropy principles. This 'model-free' approach delivers the least biased result which presents our state of knowledge. In this approach, the solution is an exponential function of Lagrange multipliers. To determine the multipliers, a convex objective function is constructed. Consequently, the maximum entropy solution can be found easily by gradient descent methods. Both algorithms can be applied to biomolecular RDC data in general, including data from RNA and DNA molecules.

High-speed label-free functional photoacoustic microscopy of mouse brain in action.

We present fast functional photoacoustic microscopy (PAM) for three-dimensional high-resolution, high-speed imaging of the mouse brain, complementary to other imaging modalities. We implemented a single-wavelength pulse-width-based method with a one-dimensional imaging rate of 100 kHz to image blood oxygenation with capillary-level resolution. We applied PAM to image the vascular morphology, blood oxygenation, blood flow and oxygen metabolism in both resting and stimulated states in the mouse brain.