gebhart/patrepeval huggingface dataset:
Oncogenic AKAP9-BRAF fusion is a novel mechanism of MAPK pathway activation in thyroid cancer (2005)

Genes crucial for cancer development can be mutated via various mechanisms, which may reflect the nature of the mutagen. In thyroid papillary carcinomas, mutations of genes coding for effectors along the MAPK pathway are central for transformation. BRAF point mutation is most common in sporadic tumors. By contrast, radiation-induced tumors are associated with paracentric inversions activating the receptor tyrosine kinases RET and NTRK1. We report here a rearrangement of BRAF via paracentric inversion of chromosome 7q resulting in an in-frame fusion between exons 1–8 of the AKAP9 gene and exons 9–18 of BRAF. The fusion protein contains the protein kinase domain and lacks the autoinhibitory N-terminal portion of BRAF. It has elevated kinase activity and transforms NIH3T3 cells, which provides evidence, for the first time to our knowledge, of in vivo activation of an intracellular effector along the MAPK pathway by recombination. The AKAP9-BRAF fusion was preferentially found in radiation-induced papillary carcinomas developing after a short latency, whereas BRAF point mutations were absent in this group. These data indicate that in thyroid cancer, radiation activates components of the MAPK pathway primarily through chromosomal paracentric inversions, whereas in sporadic forms of the disease, effectors along the same pathway are activated predominantly by point mutations.
Experimental observation on the random dopant fluctuation of small scale trigate CMOS devices (2012)

The random dopant fluctuation is one of the most important issues for sub-50nm CMOS technologies in terms of the device architecture and manufacturing. This paper will demonstrate the methodology to understand the dopant fluctuation via a purely experimental approach. It will be demonstrated in advanced bulk-trigate devices. The discrete dopant distribution along the channel direction can be determined. Boron clustering effect in nMOSFETs can be reasonably explained which results in a larger Vth variation, in comparison to that of pMOSFETs. Moreover, experiments have been extended to the advanced bulk-trigate CMOS devices. The sidewall roughness effect in trigate has also been studied. This approach provides a direct-observation of the random dopant fluctuation (RDF) and is useful for the gate oxide quality monitoring of future generation trigate devices.
Modeling and Optimization of Desalting Process in Oil Industry (2009)

Throughout a very long piping network crude oil in Saudi Arabia is sent to Gas Oil Separation&#13;\nPlant called GOSP. The main objectives of the GOSP are:&#13;\n- Separation of the associated gas through pressure drop in two series stages one to 120&#13;\npsig and the other to 50 psig.&#13;\n- Separation of water by gravity separators called High Pressure Production Trap (HPPT),&#13;\nDehydrator, Desalter and Water Oil Separator (WOSEP).&#13;\n- Reducing salt concentration to less than 10 PTB utilizing wash water and demulsifier.&#13;\nDuring the desalting process, the challenge is to overcome the existence of an emulsion layer at&#13;\nthe interface between oil and water. In petroleum industry normally emulsions encountered are&#13;\nsome kind of water droplets dispersed in a continuous phase of oil. In crude oil emulsions,&#13;\nemulsifying agents are present at the oil-water interface, hindering this coalescence process.&#13;\nSuch agents include scale and clay particles, added chemicals or indigenous crude oil&#13;\ncomponents like asphaltenes, resins, waxes and naphthenic acids.&#13;\nMany techniques made available to gas oil separation plant operators to minimize the effect of&#13;\ntight emulsions. These techniques include injection of demulsifier, increasing oil temperature,&#13;\ngravity separation in large vessels with high retention time as well as electrostatic voltage. From&#13;\nexperience and studies these variables have been already optimized to a good extent; however,&#13;\nfrom the believe that knowledge never stop, this study is conducted targeting enhancing the&#13;\ndemulsifier control and optimizing the wash water rate.&#13;\nThe objective of this study is to design an Artificial Neural Network (ANN) trained on data set&#13;\nto cover wide operating range of all parameters effecting demulsifier dosage. This network will&#13;\nbe used to work as a control black box inside the controller in which all effecting parameters are&#13;\ninputs and the demulsifier dosage is the controller output. Testing this control scheme showed an&#13;\neffective reduction in demulsifier consumption rate compared to the existing linear method.&#13;\nResults also, showed that the existing control strategy is highly conservative to prevent the salt&#13;\nfrom exceeding the limit. The generated function from the ANN was used also to optimize the&#13;\namount of fresh water added to wash the salty crude oil. Finally, another ANN was developed to&#13;\ngenerate an online estimate of the salt content in the produced oil.
Preparation and Characterisation of New Titanium Based Alloys for Orthopaedic and Dental Applications (2006)

Various types of titanium alloys with high strength and low elastic modulus and, at the same time, vanadium and aluminium free have been developed as surgical biomaterials in recent years. Moreover, porous metals are promising hard tissue implants in orthopaedic and dentistry, where they mimic the porous structure and the low elastic modulus of natural bone. In the present study, new biocompatible Ti-based alloy foams with approximate relative densities of 0.4, in which Sn and Nb were added as alloying metals, were synthesised through powder metallurgy method. The new alloys were prepared by mechanical alloying and subsequently sintered at high temperature using a vacuum furnace. The characteristics and the processability of the ball milled powders and the new porous titanium-based alloys were characterised by X-ray diffraction, optical microscopy and scanning electron microscopy .The mechanical properties of the new titanium alloys were examined by Vickers microhardness measurements and compression testing.
A Systematic Laboratory Approach to Low-Cost, High-Performance Chemical Flooding (2009)

Summary We present a systematic study of laboratory tests of alternative chemical formulations for a chemical flood design and application. Aqueous and microemulsion phase behavior tests have previously been shown to be a rapid, inexpensive, and highly effective means to select the best chemicals and minimize the need for relatively expensive coreflood tests. Microemulsion phase behavior testing was therefore conducted using various combinations of surfactants, cosolvents, and alkalis with a particular crude oil and in reservoir conditions of interest. Branched alcohol propoxy sulfates and internal olefin sulfonates showed high performance in these tests, even when mixed with both conventional and novel alkali agents. Systematic screening methods helped tailor and fine tune chemical mixtures to perform well under the given design constraints. The best chemical formulations were validated in coreflood experiments, and compared in terms of both oil recovery and surfactant retention in cores. Each of the four best formulations tested in corefloods gave nearly 100% oil recovery and very low surfactant adsorption. The two formulations with conventional and novel alkali agents gave almost zero surfactant retention. In standard practice, soft water must be used with alkali, but we show how alkali-surfactant-polymer (ASP) flooding can be used in this case even with very hard saline brine.
Cryptosporidiosis in Neonatal Calves Food animal practice (2010)

Cryptosporidiosis in calves is an ongoing problem, primarily because of the high prevalence and high morbidity associated with the infection. This article summarizes current knowledge of the host/parasite interactions associated with cryptosporidiosis. The infection process in intestinal mucosa, the pathophysiology of the disease process, and the immune responses initiated in the calf to control the infection are discussed. Methods for diagnosing C. parvum infection, treatments that have been tried, and management controls are also examined.
Comparative Research on Basic Composition and Processing Properties of Inulin and Inulin Granules (2013)

In order to investigate the feasibility of alternative of Inulin and Inulin Granules in processing applied, the influence of the processing properties of inulin and Inulin Granules has carried on the comparative analysis in experiment .The results show that, in gel application of raw material, the gel formed at the concentration of 40%, and took 6 hours for gelation. All of Inulin Granules and inulin in gel processing properties differences were not significant, can replace each other. Applications in raw Water Holding Capability, which can replace each other in a certain extent; The pervious to light transmittance, freeze-thaw stability and acid stability was no significant difference; The viscosity of both all can reach more than 140 MPa·S, conform to the viscosity of colloid product specifications.
Diagnostic Accuracy of The 13C-Urea Breath Test for Childhood Helicobacter Pylori Infection: A Multicenter Japanese Study (2002)

The 13C-UBT with a cutoff value of 3.5 per thousand is an accurate diagnostic method for active H. pylori infection. The test with the NDIRS method is inexpensive and might be widely applied in clinical practice.
The application of CaSO4:Dy (TLD‐900) to diagnostic x‐ray exposures (1983)

The properties of a new commercial thermoluminescent dosimeter, CaSO4:Dy without a LiF binder (TLD-900) was studied for low-exposure measurements in diagnostic radiology. The former TLD-900 had a LiF binder (herein referred to as "TLD-900/LiF"). The principle features of this dosimeter are its high sensitivity to low-energy radiation and its relatively low fading which permits measurements down to less than 2.6 X 10(-8) C kg (0.1 mR) with an accuracy better than 20%. The characteristics, annealing procedures, light sensitivity, energy response, reproducibility, and fading, of TLD-900 are discussed and compared with TLD-900/LiF. When the precautions presented in this paper are used, the dosimeters can be used for the measurement of x-ray exposures.
Gas turbine ceramic-coated-vane concept with convection-cooled porous metal core (1981)

Analysis and flow experiments on a ceramic-coated-porous-metal vane concept indicated the feasibility, from a heat transfer standpoint, of operating in a high-temperature (1644 K; 2500 deg F) gas turbine cascade facility. The heat transfer and pressure drop calculations provided a basis for selecting the ceramic layer thickness (to 2.03 mm; 0.08 in.), which was found to be the dominant factor in the overall heat transfer coefficient. Also an approximate analysis of the heat transfer in the vane trailing edge revealed that with trailing-edge ejection the ceramic thickness could be reduced to 0.254 mm (0.01 in.) in this portion of the vane. (Author)
Structure and expression profile of the cinnamyl alcohol dehydrogenase gene and its association with lignification in the sorghum (Sorghum bicolor (L.) Moench) bmr-6 mutant (2010)

Lignin, one of the major components of plant cell walls, has negative impacts on forage digestibility and bioethanol production through fermentation. Understanding the regulatory mechanism of lignin biosynthesis is essential to developing plants with altered lignin contents. The sorghum (Sorghum bicolor [L.] Moench) brown-midrib-6 mutant (bmr-6) has reduced levels of several key enzymes in the lignin biosynthesis pathway. Among the genes encoding these enzymes, the gene for cinnamyl alcohol dehydrogenase (CAD; EC 1.1.1.195) contains a nonsense mutation (responsible for bmr-6) that results in reduced CAD gene transcript levels. We found that the CAD coding region was 4225 bp and consisted of four exons separated by three introns. Bioinformatic analysis of the 5′-flanking region identified several putative binding sites for transcription factors. Moreover, a cross-species comparison of CAD genomic DNA sequences revealed evolutionary and structural variation among plant taxa. The expression level of the CAD gene was much lower in bmr-6 than in normal isoline (N-6) in root, stem, leaf, and midrib. Expression levels of other lignin biosynthesis genes were comparable in bmr-6 and N-6. These results suggest that the depression of CAD enzymatic activity in bmr-6 could affect enzymatic activity and post-translational regulation of other enzymes related to lignin biosynthesis.
Lesions of the amygdala central nucleus interfere with blockade of satiation for peanut oil by Na-2-mercaptoacetate (2000)

Previous research suggests that the amygdala central nucleus (CN) is an important neuroanatomical substrate for energy balance, and the detection of lipoprivic state signals in particular. We recently demonstrated that rats with selective lesions of the CN did not show enhanced conditioned responding toward oil-predicting stimuli after administration of the lipoprivic agent, Na-2-mercaptoacetate (MA; Benoit, Morell, & Davidson, 1999). In the present experiment, rats with lesions of the CN were trained in such a way that a stimulus predicted the delivery of either sucrose pellets or peanut oil under food deprivation. They were then given access to the foods under food satiation after an injection of either saline or MA. Finally, rats received a behavioral test for learned satiation responses to the stimulus (i.e., reduced responding) in the absence of food or MA. Results showed that MA blocked acquisition of satiation responses in rats trained with peanut oil, but not sucrose. Rats with lesions of the CN, however, acquired satiation responses equally, regardless of macronutrient or treatment. These data extend previous findings suggesting that the CN is a critical brain structure for rats’ ability to detect lipoprivation and introduce an additional behavioral paradigm for the study of macronutrient selection.
UAV Elasticity Formation Extension Consensus Control based on Joint Errors (2018)

To solve the problem of the lack communication for UAV (unmanned aerial vehicle) formation control, this paper proposed a control method for formation based on the joint errors. This method is essentially an extension of the consensus control theory. Based on the position of the UAV, an elastic look-ahead point is set. By using the position and velocity errors of each UAV, a linear state equation with the joint errors is established. The error feedbacks between other UAV s in the formation are introduced and an elasticity extension consensus controller is designed. The classic consistency controller is a special case for the extended consensus control in the case of some errors unknown. The stability of the system is verified by the Hurwitz stability analysis method. The conclusion is shown that if the system is stable, not only should there be a directed spanning tree, its elastic distance should also be a positive real number. The simulations show that when the nodes lose some communications, with the extensional controller the system can not only maintain a stable formation, but also the elasticity formation can adapt to the speed change of the leader.
Microbial cleavage of various organophosphorus insecticides (1979)

Bacteria able to utilize Aspon, Azodrin, Dasanit, diazinon, malathion, Orthene, parathion, Trithion, dimethoate, Dylox, methyl parathion, and Vapona as sole phosphorus sources were isolated from soil and sewage. Individual isolates used from 3 to 10 of these insecticides as sole phosphorus sources. The extent of growth of two Pseudomonas strains in media containing diazinon and malathion was in the range expected from the amount of insecticide supplied, and their proliferation resulted in disappearance of the chemical. Resting cells of the pseudomonads derived from cultures grown on diazinon or malathion but not orthophosphate caused extensive destruction of these two organophosphates in the presence or absence of chloramphenicol. Extracts of the two bacteria derived from organophosphate-grown cultures catalyzed the disappearance of Aspon, Azodrin, Dasanit, diazinon, malathion, Orthene, parathion, and Trithion but not dimethoate, Dylox, methyl parathion, and Vapona. Results from gas chromatographic analysis suggested that the extracts formed dimethyl phosphate from azodrin, dimethyl phosphorodithioate from malathion, diethyl phosphorodithioate from Trithion, and diethyl phosphorothioate from Dasanit, diazinon, and parathion. Dimethyl phosphate, dimethyl phosphorothioate , dimethyl phosphorodithioate, diethyl phosphate, and diethyl phosphorothioate were not used by the pseudomonads as sole phosphorus sources.
Antibody CDR loops as ensembles in solution vs. canonical clusters from X-ray structures (2020)

In the past decade, the relevance of antibodies as therapeutics has increased substantially. Therefore, structural and functional characterization, in particular of the complementarity-determining regions (CDRs), is crucial to the design and engineering of antibodies with unique binding properties. Various studies have focused on classifying the CDR loops into a small set of main-chain conformations to facilitate antibody design by assuming that certain sequences can only adopt a limited number of conformations. Here, we present a kinetic classification of CDR loop structures as ensembles in solution. Using molecular dynamics simulations in combination with strong experimental structural information, we observe conformational transitions between canonical clusters and additional dominant solution structures in the micro-to-millisecond timescale for all CDR loops, independent of length and sequence composition. Besides identifying all relevant conformations in solution, our results revealed that various canonical cluster medians actually belong to the same kinetic minimum. Additionally, we reconstruct the kinetics and probabilities of the conformational transitions between canonical clusters, and thereby extend the model of static canonical structures to reveal a dynamic conformational ensemble in solution as a new paradigm in the field of antibody structure design.<b>Abbreviations:</b> CDR: Complementary-determining region; Fv: Antibody variable fragment; PCCA: Perron cluster analysis; tICA: Time-lagged independent component analysis; V<sub>H</sub>: Heavy chain variable region; V<sub>L</sub>: Light chain variable region.
Response of two strains of large white male turkeys to amino acid levels when diets are changed at three- or four-week intervals (1997)

A study was conducted to evaluate the amino acid recommendations of the NRC (1994) when diets were changed at 3- or 4-wk intervals. Diets formulated to provide from 90 to 115% of recommended amino acid levels were fed to Nicholas (NIC) and British United Turkey (BUT) Large White males from day-old to 24 wk of age; samples of turkeys were processed at 18 and 24 wk. Results indicated that the amino acid levels suggested by NRC are adequate to support maximum body weight gain, feed conversion, and dressing percentage of Large White males grown to 18 or 24 wk when fed on 4-wk intervals. An approximately 5% higher level of amino acids was required to maximize breast yield. When feeds were changed at 3-wk intervals, higher levels of amino acids were required to maximize performance; however, there did not seem to be any difference in the response of the two strains of turkeys to different levels of amino acids in this study.
The Emergence of Market Economies in Eastern Europe (1992)

Contributors Preface 1. Introduction: The Journey to a Market Economy: Christopher Clague Part I: The Problem of the Transition 2. The Next Decade in Central and Eastern Europe: Lawrence Summers 3. Evolution in Economics and in the Economic Reform of the Centrally Planned Economies: Peter Murrell 4. The Hidden Path to a Successful Economy: Mancur Olson 5. Organizations as Property: Economic Analysis of Property Law Applied to Privatization: Robert Cooter 6. The Transition to a Market Economy: Alan Walters Part II: Macroeconomic Policy and Financial Discipline 7. Taxation, Money, and Credit in a Liberalizing Socialist Economy: Robert McKinnon 8. Stabilization and Liberalization Policies for Economics in Transition: Latin American Lessons for Eastern Europe: Sebastian Edwards 9. The Design of Financial Systems for the Newly Emerging Democracies of Eastern Europe: Joseph E. Stiglitz Part III: Government Policy Toward the Private Sector: Antitrust Policy and the Safety Net 10. Anti-Monopoly Policies and Institutions: Robert Willig 11. The Safety Net During Transformation: Hungary: David Newbery 12. Institutions for the New Private Sector: Anne Krueger Part IV: The Privatization Process 13. Privatization in East European Transformation: Stanley Fischer 14. The Political Economy of Transition in Eastern Europe: Packaging Enterprises for Privatization: Gordon Rausser and Leo Simon 15. Privatization in East-Central Europe: Avoiding Major Mistakes: Jan Winiecki 16. The Political Economy of Privatization: Poland, Hungary, and Czechoslovakia: Scott Thomas 17. Strategies for the Transition: Arnold Harberger 18. Institutions and the Transition to a Market Economy: Andras Nagy Part V: Conclusions 19. Lessons for Emerging Market Economies in Eastern Europe: Gordon Rausser References.