gebhart/patrepeval huggingface dataset:
Construction of a Multifunctional Enzyme Complex via the Strain-Promoted Azide–Alkyne Cycloaddition (2013)

Inspired by the multienzyme complexes occurring in nature, enzymes have been brought together in vitro as well. We report a co-localization strategy milder than nonspecific cross-linking, and free of any scaffold and affinity tags. Using non-natural amino acid incorporation, two heterobifunctional linkers, and the strain-promoted azide-alkyne cycloaddition as conjugation reaction, three metabolic enzymes are linked together in a controlled manner. Conjugate formation was demonstrated by size-exclusion chromatography and gel electrophoresis. The multienzyme complexes were further characterized by native mass spectrometry. It was shown that the complexes catalyzed the three-step biosynthesis of piceid in vitro with comparable kinetic behavior to the uncoupled enzymes. The approach is envisioned to have high potential for various biotechnological applications, in which multiple biocatalysts collaborate at low concentrations, in which diffusion may be limited and/or side-reactions are prone to occur.
Acellular<i>Bordetella pertussis</i>vaccine enhances mucosal interleukin-10 production, induces apoptosis of activated Th1 cells and attenuates colitis in Gαi2-deficient mice (2005)

Mice deficient for the inhibitory G protein subunit alpha2 (Galphai2(-/-)) spontaneously develop a progressive inflammatory bowel disease resembling ulcerative colitis, and have a T helper 1 (Th1)-dominated immune response prior to onset of colitis, which is further augmented after the onset of disease. The present study was performed to investigate whether the Galphai2(-/-) mice were able to down-regulate the Th1-dominated inflammatory mucosal immune response and/or induce an anti-inflammatory Th2/T regulatory response and thereby diminish the severity of colitis following treatment with acellular Bordetella pertussis vaccine. The acellular vaccine against B. pertussis, the causative agent of whooping cough, has been demonstrated to induce a Th2-mediated response in both man and mice. We therefore treated Galphai2(-/-) mice intraperitoneally with a three-component acellular B. pertussis vaccine. The treated Galphai2(-/-) mice showed significantly increased interleukin (IL)-10 production in intestinal tissue, associated with significantly reduced colitis and decreased mortality, compared to untreated Galphai2(-/-) mice. The attenuation of colitis in Galphai2(-/-) mice was due, at least partly, to the B. pertussis surface antigen filamentous haemagglutinin (FHA), which almost completely inhibited proliferation of CD4(+) T cells and stimulated apoptosis of activated CD4(+) T helper 1 cells. In conclusion, the three-component acellular B. pertussis vaccine containing filamentous haemagglutinin increases the production of IL-10 in the intestinal mucosa, induces apoptosis of activated Th1 cells and attenuates colitis in Galphai2(-/-) mice.
Serum‐Free Media (2005)

The disadvantages of serum are described, including variability, shelf life, availability, effect on down-stream processing, and potential for contamination. The development of selective media and the control of proliferation and differentiation are cites as further advantages, while the cost, availability, and multiplicity of media required, are cited among disadvantages. The components that replace serum, including adhesion factors, growth factors, hormones and nutrients, are described, with an extensive table listing growth factors and their actions. Advice is given on selecting a serum-free medium and serum substitutes, and how to adapt an existing cell line to serum-free conditions. The chapter concludes with development and preparation of serum-free media and a brief introduction to protein-free media.
Changeable production systems in the machinery and equipment industry — Success factors: It-integration and real-time capable production planning and control (2011)

The German machinery and equipment industry is set in a dynamic market with challenging requirements. Short delivery times and high delivery reliability are key factors for purchase decisions. Therefore it is crucial for succeeding in the market to meet these requirements with efficient business processes and high developed skills for a quick reaction on changes (ability to coordinate). For this reason the research project “WInD” — Changeable production systems through integrated IT-structures and real-time capable production planning and control in the conceptual framework “research for the production of tomorrow” aims to improve the ability of coordination in production networks in the machinery and equipment industry through the integration of the internal and external information flow between companies as well as realizing a real-time capable production planning and control method.
Notice of Retraction: A 210 GHz Fully-Integrated OOK Transceiver for Short-Range Wireless Chip-to-Chip Communication in 40 nm CMOS Technology (2015)

Retracted.
<title>Lapse observation algorithm for lung cancer detection using 3D thoracic helical CT images</title> (1998)

In this paper, we present a lapse observation algorithm for lung cancer detection using 3D thoracic helical CT images. Purpose of this study is to detect the interval change that exist between time different images of same patient. We employed two methods to detect the interval change. The first method is 3D local template matching method. We tried to detect the movement of blood vessel and other organs by this method. The second method is subtraction method. We tried to detect the new shadow by this method. The subtraction technique is the common method which detects the interval change. If the two images are produced in an identical manner, the subtraction image derived from a pair of thin slice CT with time difference having an uniform zero pixel value except for regions with interval changes. However, the same 3D thoracic images are not obtained. Therefore, we study the method to correct the location between 3D thoracic images with time difference.
Quantitative determination of urea concentrations in cell culture medium (2009)

Urea is the major nitrogenous end product of protein metabolism in mammals. Here, we describe a quantitative, sensitive method for urea determination using a modified Jung reagent. This assay is specific for urea and is unaffected by ammonia, a common interferent in tissue and cell cultures. We demonstrate that this convenient colorimetric microplate-based, room temperature assay can be applied to determine urea synthesis in cell culture.
Real-Time Measurement of Small-Crack Opening Behavior Using an Interferometric Strain/Displacement Gage (1992)

A procedure for real-time measurement of the opening displacement of small fatigue cracks is reviewed. The method employs a computerized, laser-based, interferometric strain/displacement gage (ISDG) to monitor the relative displacement between two tiny indentations placed across small surface cracks. Complete load versus crack opening displacement curves are obtained for surface cracks of length ranging from 50 μm to several millimetres. The method is applicable to naturally or artificially initiated cracks in smooth or notched specimens. The load-displacement measurements provide a detailed record of crack closure behavior, and estimates of crack size are obtained from measurements of elastic compliance. The resolution of the opening displacement measurements is on the order of 5 nm. Computerization of the system allows measurements to be obtained in real time, facilitating feedback control of testing. Four versions of the ISDG that are used in different laboratories are described. The instrument's characteristics are presented along with some practical considerations associated with its use. Examples from studies of a number of materials are included to demonstrate applications of the ISDG to the measurement of closure, crack shape, and to automation of small-crack testing.
Reshaping cache misses to improve row-buffer locality in multicore systems (2013)

Optimizing cache locality has always been important since the emergence of caches, and numerous cache locality optimization schemes have been published in compiler literature. However, in modern architectures, cache locality is not the only factor that determines memory system performance. Many emerging multicores employ banked memory systems and each bank is attached a row-buffer that holds the most-recently accessed memory row (page). A last-level cache miss that also misses in the row-buffer can experience much higher latency than a cache miss that hits in the row-buffer. Consequently, optimizing for row-buffer locality can be as important as optimizing for cache locality. Targeting emerging multicores and multithreaded applications, this paper presents a compiler-directed row-buffer locality optimization strategy. This strategy modifies the memory layout of data to increase the number of row-buffer hits without increasing the number of misses in the on-chip cache hierarchy. We implemented our proposed optimization strategy in an open-source compiler and tested its effectiveness in improving the row-buffer performance using a set of multithreaded applications. Our results indicate that the proposed approach improves the average data access latency by about 29%, and this translates, on average, to about 15% improvement in execution time.
Towards a Theory of Insider Threat Assessment (2005)

Insider attacks are a well-known problem acknowledged as a threat as early as 1980s. The threat is attributed to legitimate users who abuse their privileges, and given their familiarity and proximity to the computational environment, can easily cause significant damage or losses. Due to the lack of tools and techniques, security analysts do not correctly perceive the threat, and hence consider the attacks as unpreventable. In this paper, we present a theory of insider threat assessment. First, we describe a modeling methodology which captures several aspects of insider threat, and subsequently, show threat assessment methodologies to reveal possible attack strategies of an insider.
Material classification based on multi-band polarimetric images fusion (2006)

Polarization imparted by surface reflections contains unique and discriminatory signatures which may augment spectral target-detection techniques. With the development of multi-band polarization imaging technology, it is becoming more and more important on how to integrate polarimetric, spatial and spectral information to improve target discrimination. In this study, investigations were performed on combining multi-band polarimetric images through false color mapping and wavelet integrated image fusion method. The objective of this effort was to extend the investigation of the use of polarized light to target detection and material classification. As there is great variation in polarization in and between each of the bandpasses, and this variation is comparable to the magnitude of the variation intensity. At the same time, the contrast in polarization is greater than for intensity, and that polarization contrast increases as intensity contrast decreases. It is also pointed out that chromaticity can be used to make targets stand out more clearly against background, and material can be divided into conductor and nonconductor through polarization information. So, through false color mapping, the difference part of polarimetric information between each of the bandpasses and common part of polarimetric information in each of the bandpasses are combined, in the resulting image the conductor and nonconductor are assigned different color. Then panchromatic polarimetric images are fused with resulting image through wavelet decomposition, the final fused image have more detail information and more easy identification. This study demonstrated, using digital image data collected by imaging spectropolarimeter, multi-band imaging polarimetry is likely to provide an advantage in target detection and material classification.
SVM for learning with label proportions (2013)

We study the problem of learning with la-bel proportions in which the training data is provided in groups and only the propor-tion of each class in each group is known. We propose a new method called proportion-SVM, or ∝SVM, which explicitly models the latent unknown instance labels together with the known group label proportions in a large-margin framework. Unlike the existing works, our approach avoids making restric-tive assumptions about the data. The ∝SVM model leads to a non-convex integer program-ming problem. In order to solve it efficiently, we propose two algorithms: one based on simple alternating optimization and the other based on a convex relaxation. Extensive ex-periments on standard datasets show that ∝SVM outperforms the state-of-the-art, es-pecially for larger group sizes. 1.
Microsoft COCO: Common Objects in Context (2014)

RU-AI dataset is constructed based on three large publicly available datasets: Flickr8K, COCO, and Places205, by adding their corresponding machine-generated pairs.
Deep Reinforcement Learning Attention Selection for Person Re-Identification (2017)

Existing person re-identification (re-id) methods assume the provision of accurately cropped person bounding boxes with minimum background noise, mostly by manually cropping. This is significantly breached in practice when person bounding boxes must be detected automatically given a very large number of images and/or videos processed. Compared to carefully cropped manually, auto-detected bounding boxes are far less accurate with random amount of background clutter which can degrade notably person re-id matching accuracy. In this work, we develop a joint learning deep model that optimises person re-id attention selection within any auto-detected person bounding boxes by reinforcement learning of background clutter minimisation subject to re-id label pairwise constraints. Specifically, we formulate a novel unified re-id architecture called Identity DiscriminativE Attention reinforcement Learning (IDEAL) to accurately select re-id attention in auto-detected bounding boxes for optimising re-id performance. Our model can improve re-id accuracy comparable to that from exhaustive human manual cropping of bounding boxes with additional advantages from identity discriminative attention selection that specially benefits re-id tasks beyond human knowledge. Extensive comparative evaluations demonstrate the re-id advantages of the proposed IDEAL model over a wide range of state-of-the-art re-id methods on two auto-detected re-id benchmarks CUHK03 and Market-1501.
Design for Cascade of Crossflow Direct Contact Membrane Distillation (2007)

The use of crossflow direct contact membrane distillation (XF-DCMD) modules allows lower velocities and volumetric flows on the brine side while still maintaining good heat-transfer coefficients. The key to using these modules in energy-efficient processes requires that the heat be recovered from the hot distillate exit stream with close temperatures of approach. This is best accomplished in a cascade of crossflow modules arranged in a manner approaching the behavior of countercurrent DCMD modules. A short-cut design method is presented to determine the number of such identical modules needed to extract maximum heat recovery between an inlet and exit brine temperature. This method is dependent on two observations: (1) existence of a unique relationship between brine temperature drop across a stage (ΔTstage) and the temperature of closest approach between brine and distillate streams at the top of the stage (ΔTend), which defines an operating line; (2) ΔTend remains relatively constant from stage to stage. As in other thermal processes, there is a tradeoff between energy efficiency and area (here, membrane area). The optimum will be a function of the relative costs of energy and membrane area. For brine entrance and exit temperatures of 95 °C and 32−38 °C, respectively, and a specific stage area of 2.9 m2/(mt/h), the optimum number of stages moves from six to two as the price of energy decreases from $4 US/mt steam equivalent to $0.73 US/mt steam equivalent.
Selenium Assimilation and Nutrient Element Uptake in White Clover and Tall Fescue under the Influence of Sulphate Concentration and Selenium Tolerance of the Plants (1992)

Tall fescue (Festuca arundinacea Schreb.) and white clover (Trifolium repens L.) were examined for Se assimilation and nutrient element uptake. Substantial Se tolerance difference was found between the two species. An inverse relationship between Se accumulation and Se tolerance suggests an exclusion mechanism that restricts Se uptake by the plant with greater Se tolerance. A positive relationship between the increase of protein Se concentration and growth inhibition in the plants suggests that assimilation of Se into proteins is responsible for the Se toxic effect and this study indicates that the antagonistic effect of sulphate is responsible for reducing Se toxicity at the protein level. No evidence that a Se exclusion mechanism which excludes Se from incorporating into protein, such as that found in Astragalus species, plays any major role of Se tolerance in these two species. Under Se treatment, plant tissue Ca concentration was increased, but P concentration was decreased. A higher Fe concentration was found in white clover which increased with increasing tissue Se concentration. Copper, Mn, and Zn concentrations only increased in the white clover under conditions of severe growth inhibition.
Neural Aspects of Inhibition Following Emotional Primes in Depressed Adolescents (2015)

Adults diagnosed with major depressive disorder (MDD) have been found to be characterized by selective attention to negative material and by impairments in their ability to disengage from, or inhibit the processing of, negative stimuli. Altered functioning in the frontal executive control network has been posited to underlie these deficits in cognitive functioning. We know little, however, about the neural underpinnings of inhibitory difficulties in depressed adolescents. We used functional magnetic resonance imaging in 18 adolescents diagnosed with MDD and 15 age- and gender-matched healthy controls (CTLs) while they performed a modified affective Go/No-Go task that was designed to measure inhibitory control in the presence of an emotional distractor. Participants were presented with either a happy or a sad face, followed by a go or a no-go target to which they either made or inhibited a motor response. A group (MDD, CTL) by valence (happy, sad) by condition (go, no-go) analysis of variance indicated that MDD adolescents showed attenuated BOLD response in the right dorsolateral prefrontal cortex (DLPFC) and in the occipital cortex bilaterally, to no-go targets that followed a sad, but not a happy, face. Adolescents diagnosed with MDD showed anomalous recruitment of prefrontal control regions during inhibition trials, suggesting depression-associated disruption in neural underpinnings of the inhibition of emotional distractors. Given that the DLPFC is associated with the maintenance of goal-relevant information, it is likely that sad faces differentially capture attention in adolescents with MDD and interfere with task demands requiring inhibition.
Mixtures of palm kernel oil with cocoa butter and milk fat in compound coatings (1997)

Abstract Thermal behavior of binary mixtures of palm kernel oil (PKO), cocoa butter (CB), and anhydrous milk fat was used to study mixed‐lipid crystallization. This study was related to the physical properties of compound coatings made with these fats. Phase behavior was studied by evaluating changes in melting behavior with composition and time, by creating isosolid diagrams, and by monitoring polymorphic behavior. For binary mixtures, multiple melting peaks and eutectic formation were observed for 30–50% addition levels of CB to PKO, but not for addition of milk fat to PKO. For compound coatings and binary mixtures, made with the same fat composition, hardness of compound coatings increased as solid fat content (SFC) at 25°C of binary mixtures increased. Also, as SFC at 25°C of the binary mixtures increased, induction time for bloom formation and time to fully bloom for compound coatings decreased. Observation of eutectic behavior for binary mixtures indicated softness in a compound coating with the same fat composition, but the converse was not necessarily true.
Junction barrier Schottky rectifier with an improved P-well region (2012)

A junction barrier Schottky (JBS) rectifier with an improved P-well on 4H—SiC is proposed to improve the VF—IR trade-off and the breakdown voltage. The reverse current density of the proposed JBS rectifier at 300 K and 800 V is about 3.3×10−8 times that of the common JBS rectifier at no expense of the forward voltage drop. This is because the depletion layer thickness in the P-well region at the same reverse voltage is larger than in the P+ grid, resulting in a lower spreading current and tunneling current. As a result, the breakdown voltage of the proposed JBS rectifier is over 1.6 kV, that is about 0.8 times more than that of the common JBS rectifier due to the uniform electric field. Although the series resistance of the proposed JBS rectifier is a little larger than that of the common JBS rectifier, the figure of merit (FOM) of the proposed JBS rectifier is about 2.9 times that of the common JBS rectifier. Based on simulating the values of susceptibility of the two JBS rectifiers to electrostatic discharge (ESD) in the human body model (HBM) circuits, the failure energy of the proposed JBS rectifier increases 17% compared with that of the common JBS rectifier.
Crystal Structure of the N-terminal Domain of the Group B Streptococcus Alpha C Protein (2005)

Group B Streptococcus (GBS) is the leading cause of bacterial pneumonia, sepsis, and meningitis among neonates and an important cause of morbidity among pregnant women and immunocompromised adults. Invasive diseases due to GBS are attributed to the ability of the pathogen to translocate across human epithelial surfaces. The alpha C protein (ACP) has been identified as an invasin that plays a role in internalization and translocation of GBS across epithelial cells. The soluble N-terminal domain of ACP (NtACP) blocks the internalization of GBS. We determined the 1.86-A resolution crystal structure of NtACP comprising residues Ser(52) through Leu(225) of the full-length ACP. NtACP has two domains, an N-terminal beta-sandwich and a C-terminal three-helix bundle. Structural and topological alignments reveal that the beta-sandwich shares structural elements with the type III fibronectin fold (FnIII), but includes structural elaborations that make it unique. We have identified a potential integrin-binding motif consisting of Lys-Thr-Asp(146), Arg(110), and Asp(118). A similar arrangement of charged residues has been described in other invasins. ACP shows a heparin binding activity that requires NtACP. We propose a possible heparin-binding site, including one surface of the three-helix bundle, and nearby portions of the sandwich and repeat domains. We have validated this prediction using assays of the heparin binding and cell-adhesion properties of engineered fragments of ACP. This is the first crystal structure of a member of the highly conserved Gram-positive surface alpha-like protein family, and it will enable the internalization mechanism of GBS to be dissected at the atomic level.
OFA Short Course Preview (2005)

Murine typhus should be considered in the differential diagnosis of aseptic meningitis and meningoencephalitis. Early diagnosis and treatment can prevent death and long-term morbidity.