gebhart/patrepeval huggingface dataset:
The surface of β‐sheet proteins contains amphiphilic regions which may provide clues about protein folding (1996)

A major bottleneck in the field of biochemistry is our limited understanding of the processes by which a protein folds into its native conformation. Much of the work on this issue has focused on the conserved core of the folded protein. However, one might imagine that a ubiquitous motif for unaided folding or for the recognition of chaperones may involve regions on the surface of the native structure. We explore this possibility by an analysis of the spatial distribution of regions with amphiphilic alpha-helical potential on the surface of beta-sheet proteins. All proteins, including beta-sheet proteins, contain regions with amphiphilic alpha-helical potential. That is, any alpha-helix formed by that region would be amphiphilic, having both hydrophobic and hydrophilic surfaces. In the three-dimensional structure of all beta-sheet proteins analyzed, we have found a distinct pattern in the spatial distribution of sequences with amphiphilic alpha-helical potential. The amphiphilic regions occur in ring shaped clusters approximately 20 to 30 A in diameter on the surface of the protein. In addition, these regions have a strong preference for positively charged amino acids and a lower preference for residues not favorable to alpha-helix formation. Although the purpose of these amphiphilic regions which are not associated with naturally occurring alpha-helix is unknown, they may play a critical role in highly conserved processes such as protein folding.
Reply: “The Physiatry Workforce in 2019 and Beyond Part 2: Modeling Results” (2021)

Bryan, Katherine M. MS; Jumreornvong, Oranicha BA; Katz, Nicole B. BS; Sarno, Danielle L. MD; Ulep, Robin D. MD; Verduzco-Gutierrez, Monica MDAuthor Information
The flux-reversal machine: a new brushless doubly-salient permanent-magnet machine (1997)

A new brushless doubly-salient permanent-magnet machine called the flux-reversal machine is described. Design, analysis, construction, and experimental results for a prototype machine built as a single-phase, high-speed generator are presented. Qualitative comparisons are made with the other types of brushless machines in its class, using the flux-MMF diagram technique. An elementary CAD program developed for designing flux-reversal machines and the associated drive electronics is also described.
Function merging by sequence alignment (2019)

Resource-constrained devices for embedded systems are becoming increasingly important. In such systems, memory is highly restrictive, making code size in most cases even more important than performance. Compared to more traditional platforms, memory is a larger part of the cost and code occupies much of it. Despite that, compilers make little effort to reduce code size. One key technique attempts to merge the bodies of similar functions. However, production compilers only apply this optimization to identical functions, while research compilers improve on that by merging the few functions with identical control-flow graphs and signatures. Overall, existing solutions are insufficient and we end up having to either increase cost by adding more memory or remove functionality from programs. We introduce a novel technique that can merge arbitrary functions through sequence alignment, a bioinformatics algorithm for identifying regions of similarity between sequences. We combine this technique with an intelligent exploration mechanism to direct the search towards the most promising function pairs. Our approach is more than 2.4x better than the state-of-the-art, reducing code size by up to 25%, with an overall average of 6%, while introducing an average compilation-time overhead of only 15%. When aided by profiling information, this optimization can be deployed without any significant impact on the performance of the generated code.
Object Handling by Coordinated Multiple Mobile Manipulators Without Force/Torque Sensors (2008)

The coordinated control algorithm for multiple mobile manipulators without force/torque sensors handling a single object in coordination controls individual mobile manipulators as if the grasping point has impedance dynamics by using the real manipulator’s dynamics. Mobile manipulators handle the object in coordination using the leader-follower control algorithm we propose, based on impedance dynamics. After discussing the effect of parameter error and how to reduce it, we confirm the proposed control algorithm’s feasibility in experiments using two mobile manipulators.
Euclidean Distances in Quantized Spaces with Pre-stored Components for MIMO Detection (2007)

This paper proposes a technique to reduce the complexity involved in the maximum likelihood detection of multiple input multiple output (MIMO) spatial multiplexing systems. Both the received lattice and the components of the received signal are quantized, corresponding to a mapping into a multidimensional space divided into hypercubes. In the new space the maximum likelihood detection criterion can be applied making use of a small look-up table storing all the exact possible distance components in each dimension of the quantized space. The number of pre-stored elements can be as small as the number of quantization levels per dimension. This procedure eliminates the multiplications involved in the calculation of the squared Euclidean distances. The impact of the quantization error is assessed by means of simulations over fast flat fading channels. Near optimum performance is achieved with only 5 bits representing each dimension of the received signal.
The coccidioidal complement fixation and immunodiffusion-complement fixation antigen is a chitinase (1992)

Culture filtrates and autolysates of Coccidioides immitis have provided suitable crude antigens for the serodiagnosis and prognosis of coccidioidomycosis. One of these, a heat-labile antigen which participates in the immunodiffusion reaction corresponding to the complement fixation reaction (IDCF), has been characterized as a 110-kDa native protein that, when subjected to reducing conditions and heat, yields a 48-kDa component. The present report provides serologic and biochemical evidence that this antigen is a chitinase. This chitinase, isolated from 48-h culture filtrate of the spherule-endospore-phase C. immitis by affinity adsorption to chitin, formed a line of identity with the IDCF reference antigen and participated in the complement fixation reaction with human serum. It lost its enzymatic as well as antigenic activity when heated, but when not heated it retained its enzymatic activity even when precipitated with coccidiodal antibody present in human serum. This chitinase represents a significant serodiagnostic substance and may be important in the morphogenesis of C. immitis.
Hashing with Mutual Information (2019)

Binary vector embeddings enable fast nearest neighbor retrieval in large databases of high-dimensional objects, and play an important role in many practical applications, such as image and video retrieval. We study the problem of learning binary vector embeddings under a supervised setting, also known as hashing. We propose a novel supervised hashing method based on optimizing an information-theoretic quantity, mutual information. We show that optimizing mutual information can reduce ambiguity in the induced neighborhood structure in the learned Hamming space, which is essential in obtaining high retrieval performance. To this end, we optimize mutual information in deep neural networks with minibatch stochastic gradient descent, with a formulation that maximally and efficiently utilizes available supervision. Experiments on four image retrieval benchmarks, including ImageNet, confirm the effectiveness of our method in learning high-quality binary embeddings for nearest neighbor retrieval.
Determining the degree of crosslinking of ethylene vinyl acetate photovoltaic module encapsulants—A comparative study (2013)

A total of 16 analytical methods, spanning from classical solvent extraction over different thermo-analytic and mechanical approaches to acoustic and optical spectroscopy, have been evaluated as to their ability to determine the crosslinking state of ethylene vinyl acetate (EVA), the prevailing encapsulant for photovoltaics applications. The key objective of this work was to create a systematic and comprehensive comparison, using a unified set of traceable test samples covering the full range of realistically occurring degrees of EVA crosslinking. A majority number of these tested methods proved fundamentally suitable for detecting changes in the polymer properties during crosslinking based on the effect e.g. its mechanical properties or its crystallinity. Interestingly, when investigated in detail, most of the methods showed mutually different dependencies on the lamination time, indicating a complex range of effects of the chemical crosslinking on the properties and behaviour of the material. Furthermore, Raman spectroscopy could be identified as a potential new method for measuring the degree of crosslinking in-line in the PV module manufacturing process, thus providing an interesting approach for improving process control in PV module processing.
Spatially Resolved Electronic Structures of Atomically Precise Armchair Graphene Nanoribbons (2012)

Graphene has attracted much interest in both academia and industry. The challenge of making it semiconducting is crucial for applications in electronic devices. A promising approach is to reduce its physical size down to the nanometer scale. Here, we present the surface-assisted bottom-up fabrication of atomically precise armchair graphene nanoribbons (AGNRs) with predefined widths, namely 7-, 14- and 21-AGNRs, on Ag(111) as well as their spatially resolved width-dependent electronic structures. STM/STS measurements reveal their associated electron scattering patterns and the energy gaps over 1 eV. The mechanism to form such AGNRs is addressed based on the observed intermediate products. Our results provide new insights into the local properties of AGNRs, and have implications for the understanding of their electrical properties and potential applications.
On the Application of Situational Language Teaching Method to Mongolian English Majors (2017)

The traditional English teaching method has gradually been replaced by new teaching methods in English class. Situational Language Teaching Method is a way to activate the teaching of language knowledge through the design of authentic and concrete situation. A survey is carried out in Inner Mongolia University for Nationalites. It investigates the practical application of Situational Language Teaching Method among Mongolian English majors in this university. Through the analysis of the questionnaire results, the paper reveals the obstacles existing in the application of the method, namely: passive participation due to improper text parsing; weakening role of teachers; and ineffective transfer among language, image and meaning. At the same time, it puts forward appropriate strategies to solve the problems during the application of SLT to Mongolian English majors.
A Reproducible Model of Middle Cerebral Artery Occlusion in Mice: Hemodynamic, Biochemical, and Magnetic Resonance Imaging (1998)

A reproducible model of thread occlusion of the middle cerebral artery (MCA) was established in C57 Black/6J mice by matching the diameter of the thread to the weight of the animals. For this purpose, threads of different diameter (80 to 260 microns) were inserted into the MCA of animals of different weights (18 to 33 g), and the success of vascular occlusion was evaluated by imaging the ischemic territory on serial brain sections with carbon black. Successful occlusion of the MCA resulted in a linear relationship between body weight and thread diameter (r = 0.46, P < 0.01), allowing precise selection of the appropriate thread size. Laser-Doppler measurements of CBF, neurological scoring, and 2,3,5-triphenyltetrazolium chloride staining confirmed that matching of animal weight and suture diameter produced consistent cerebral infarction. Three hours after MCA occlusion, imaging of ATP, tissue pH, and cerebral protein synthesis allowed differentiation between the central infarct core, in which ATP was depleted, and a peripheral penumbra with reduced protein synthesis and tissue acidosis but preserved ATP content. Perfusion deficits and ischemic tissue alterations could also be detected by perfusion- and diffusion-weighted magnetic resonance imaging, demonstrating the feasibility of dynamic evaluations of infarct evolution. The use of multiparametric imaging techniques in this improved MCA occlusion model opens the way for advanced pathophysiological studies of stroke in gene-manipulated animals.
Commentary on “A roadmap for the prevention of dementia II. Leon Thal Symposium 2008.” The Multidomain Alzheimer Preventive Trial (MAPT): A new approach to the prevention of Alzheimer's disease (2009)

The MAPT Study is the first preventive trial involving multidomain interventions. Final results should be available in 2013.
Development and Application of a Flexible and Efficient Environment for Aerodynamic Shape Optimisation (2006)

Within the next few years numerical shape optimisation based on high fidelity methods is likely to play a strategic role in future aircraft design. In this context, suitable tools have to be developed for solving aerodynamic shape optimisation problems. Based on the unstructured RANS solver TAU, the major key components recently developed, e.g. the free form deformation or the adjoint approach, are described in detail and applied for optimising the DLR-F6 wing-body aircraft configuration. The flexibility and efficiency of the meshing procedure, the optimisation strategy, tha adjoint approach and the parametrisation have been assessed.
Effects of amino acid infusions on cell metabolism in hemodialyzed patients with uremia. (1983)

Eighteen uremic patients received i.v. infusions of a mixture of amino acids three times per week for 3 months in an effort to improve cellular amino acid imbalance and related cell bioactivities. They were a subset of 42 uremic patients stabilized by maintenance hemodialysis and were characterized by reduced cellular levels of threonine, isoleucine, methionine, and ornithine, with increased levels of aspartate, glycine, arginine, tyrosine, and phenylalanine. Protein synthesis (3H-leucine incorporation), energy level [energy charge = (ATP + 1/2 ADP)-(ATP + ADP + AMP)], and activity of the rate-limiting glycolytic enzyme pyruvate kinase were reduced in these patients compared with 32 control normal subjects. The circulating leukocyte (88 +/- 5% granulocytes) was used as a cell model. Previously, multiple regression best-subset analysis showed that a combination of the cell levels of aspartate, valine, isoleucine, ornithine, lysine, and tryptophan could "explain" 40% of the variance in protein synthesis in these patients. Similarly, a combination of the levels of aspartate, glutamic acid, glycine, ornithine, and arginine were "predictive" of the level of energy charge. We hypothesized that protein synthesis and energy level would be improved if the amino acid infusions normalized the intracellular levels of those amino acids that were predictive of the bioactivities. After 3 months of amino acid infusions, levels of the predictive intracellular amino acids were not improved, but deviated further from baseline values. Failure to detect significant improvement in the cell bioactivities is attributed to inability to correct the imbalance in the intracellular amino acid pool.
Physico-Chemical Properties and Sensory Characteristics of Dehydrated Guava Concentrate: Effect of Drying Method and Maltodextrin Concentration (2011)

Dehydration of guava juice into powdered particles gives a considerable reduction in volume and is an effective method of prolonging the shelf life. Therefore, a research study was conducted to determine the effect of different drying methods and the addition of drying aids on the physico-chemical proper-ties and sensory characteristics of dehydrated guava concentrate. Instant guava-drink-powder samples were obtained by dehydrating the concentrated guava juice using freeze drying, spray drying and tunnel drying techniques. Guava juice at 10.5°Brix was used to prepare the fruit powders. A significant reduction (p<0.05) in titratable acidity of 0.22% as citric acid and an increase in pH of 0.44 after drying of guava juice indicated that some acids were lost during the drying process. The oxidative loss of ascorbic acid was considerably lower in freeze drying (18.8%) compared to tunnel drying (32.2%). Spray dried powders were obtained from the guava juice with different maltodextrin concentrations as drying aids. When 30% maltodextrin was added to guava juice, the solubility of powder was 95% whereas, adding 60% maltodextrin decreased the solubility to 86%. The chromametric parameters L* (lightness), a* (redness) and b* (yellowness) were found to be significantly (p<0.05) affected by drying methods. Twenty trained sensory panellists ranked the juice prepared from the freeze dried powder as the highest and there were no significant differences (p>0.05) between the juice prepared from spray drying of guava juice upto 50% added maltodextrin. The freeze dried product had superior nutritional and sensory qualities, however spray dried product was stable and more economical to produce free-flowing guava powder with good stability. Key words: Freeze drying; guava-drink-powder; maltodextrin; spray drying DOI: http://dx.doi.org/10.4038/tare.v13i2.3138 Tropical Agricultural Research and Extension 13(2) 2010 pp.48-54
Generation of Flavor Compounds by the Reaction of 2-Deoxyglucose with Selected Amino Acids (1997)

The volatile compounds generated by the reaction of 2-deoxyglucose with glutamine, glutamic acid, asparagine, and aspartic acid were studied. The nitrogen-containing compounds identified included pyrazines, pyridines, and pyrroles. Non-nitrogen-containing volatiles included aldehydes, ketones, cyclic compounds, furans, and aromatic compounds. As in the case with glucose, higher pHs were favorable to the formation of pyrazines in the reaction systems containing 2-deoxyglucose. Asparagine, glutamine, and asparatic acid produced similar amounts of pyrazines at pH 8.0. In general, lower pHs favor the generation of non-nitrogen-containing compounds. The reaction of 2-deoxyglucose with the selected amino acids produced only about 1% of the amount of pyrazines generated in the systems containing glucose under the same reaction conditions. The results indicated that the 2-hydroxy group on the glucose molecule is essential for the effective generation of flavor compounds. Keywords: 2-Deoxyglucose; flavor compounds; Maillard reaction; pyrazines
Use of feedforward in idle speed control for a direct injection spark ignition engine during lean burn (2002)

The use of reference feedforward control is investigated in the idle speed problem for a direct-injection spark-ignition engine during lean burn. This additional control signal is added to improve the speed and air-fuel ratio transient responses due to large load torque disturbances. A baseline control design is given, and a feedforward algorithm is presented and added to the baseline controller. The design is illustrated through simulations of step responses due to disturbances in load torque. With feedforward in the air control loop, the maximum engine speed droop is decreased more than 20%, while also improving the setpoint control of air-fuel ratio.
Growth conditions for wurtzite zinc oxide films in aqueous solutions (2002)

A pH above 9.0 was essential for the formation of wurtzite zinc oxide (ZnO) in aqueous solution systems. The addition of complexing agents to decrease the deposition rate was required for the direct growth of ZnO on the surface of substrates through heterogeneous nucleation. The nucleation of the crystals was promoted by undercoats derived from zinc acetate. Wurtzite ZnO films consisting of hexagonal columns with diameters of 20–100 nm were successfully prepared on various substrates under suitable conditions.
Analysis of Decision Boundaries Generated by Constructive Neural Network Learning Algorithms (1995)

Constructive learning algorithms offer an approach to incremental construction of near-minimal artificial neural networks for pattern classification. Examples of such algorithms include Tower, Pyramid, Upstart, and Tiling algorithms which construct multilayer networks of threshold logic units (or, multi-layer perceptrons). These algorithms differ in terms of the topology of the networks that they construct which in turn biases the search for a decision boundary that correctly classifies the training set. This paper presents an analysis of such algorithms from a geometrical perspective. This analysis helps in a better characterization of the search bias employed by the different algorithms in relation to the geometrical distribution of examples in the training set. Simple experiments with non linearly separable training sets support the results of mathematical analysis of such algorithms. This suggests the possibility of designing more efficient constructive algorithms that dynamically choose among different biases to build near-minimal networks for pattern classification.
Solubility Studies of Oleanolic Acid and Betulinic Acid in Aqueous Solutions and Plant Extracts of <i>Viscum album</i> L. (2007)

Mistletoe (Viscum album L.) contains the triterpene acids oleanolic acid (OA) and betulinic acid (BA), which were found to have anti-tumour properties. In this study, the solubilities of OA and BA were studied in water (up to 0.02 microg/mL in each case) and in alkaline solutions of 10 mM trisodium phosphate (pH 11.5; OA: 77.2 microg/mL; BA: 40.1 microg/mL). Furthermore, triterpene acids were quantified in aqueous mistletoe extracts (pH 7.3; drug to extract ratio 1:25). OA (1.1 microg/mL) and BA (0.9 microg/mL) were extracted with a yield of less than 5%. Preparing plant extracts with basic pH values resulted in a triterpene acid content of 9.3 microg/mL OA and 5.2 microg/mL BA (pH 12.1), reaching neither the solubility limits nor a complete extraction of the plant material. The triterpene acid content of neutral plant extracts above the solubility limit could be due to interactions with biocolloids. Interaction studies were performed by gel permeation chromatography. Different mechanisms of the dissolution at pH 7.3 and pH 10.2 are discussed.