gebhart/patrepeval huggingface dataset:
Exploration of geosmin synthase from Streptomyces peucetius ATCC 27952 by deletion of doxorubicin biosynthetic gene cluster (2009)

Thorough investigation of Streptomyces peucetius ATCC 27952 genome revealed a sesquiterpene synthase, named spterp13, which encodes a putative protein of 732 amino acids with significant similarity to S. avermitilis MA-4680 (SAV2163, GeoA) and S. coelicolor A3(2) (SCO6073). The proteins encoded by SAV2163 and SCO6073 produce geosmin in the respective strains. However, the spterp13 gene seemed to be silent in S. peucetius. Deletion of the doxorubicin gene cluster from S. peucetius resulted in increased cell growth rate along with detectable production of geosmin. When we over expressed the spterp13 gene in S. peucetius DM07 under the control of an ermE* promoter, 2.4 +/- 0.4-fold enhanced production of geosmin was observed.
Common bean breeding to improve red grain lines (2011)

The purpose of this study was to evaluate the performance potential of red bean lines, derived from populations of the first cycle of recurrent selection in the common bean breeding program of the Federal University of Viçosa, Minas Gerais. In the F3:5, F3:6 and F3:7 generations, 243 families from 18 segregating populations were evaluated. These families were conducted by the bulk-within-families method and from the best, 154 lines were obtained and evaluated in the dry season of 2006 (F7: 9) and of 2007 (F7: 10), Coimbra - MG. The estimates of genetic and phenotypic parameters revealed variability among families. The method bulk within F3-derived families proved useful for bean breeding. The most promising lines that may be included in future tests of value for cultivation and use (VCU), and will possibly be recommended for planting in the state of Minas Gerais, were derived from the populations Vermelhinho/AN9022180//Vermelhinho/Vermelho2157, Vermelhinho//Vermelhinho/ IAPAR81,Vermelhinho/LR720982// Vermelhinho/AB136 and Vermelhinho/AB136//Vermelhinho/ Vermelho2157.
Tracking Surface Glycans on Live Cancer Cells with Single‐Molecule Sensitivity (2014)

Using a combination of metabolically labeled glycans, a bioorthogonal copper(I)-catalyzed azide-alkyne cycloaddition, and the controlled bleaching of fluorescent probes conjugated to azide- or alkyne-tagged glycans, a sufficiently low spatial density of dye-labeled glycans was achieved, enabling dynamic single-molecule tracking and super-resolution imaging of N-linked sialic acids and O-linked N-acetyl galactosamine (GalNAc) on the membrane of live cells. Analysis of the trajectories of these dye-labeled glycans in mammary cancer cells revealed constrained diffusion of both N- and O-linked glycans, which was interpreted as reflecting the mobility of the glycan rather than to be caused by transient immobilization owing to spatial inhomogeneities on the plasma membrane. Stochastic optical reconstruction microscopy (STORM) imaging revealed the structure of dynamic membrane nanotubes.
A Direct-Current-Comparator Ratio Bridge for Four-Terminal Resistance Measurements (1966)

A ratio bridge has been built which compares four-terminal resistances by measuring the current ratio corresponding to voltage drop equality. A current ratio, corresponding to turns ratio, is automatically maintained by a self-balancing direct current comparator and is adjustable in part-per-million steps. The two current sources are isolated so that, at balance, there is no current in the potential circuit. The bridge can be direct reading in either resistance or conductance ratio. The bridge makes use of the ability of a self-balancing direct current comparator to measure and compare accurately the ratio of two isolated direct currents. A detailed description of the bridge is presented with an analysis of its accuracy limitations. In its optimum operating range accuracies of better than one part per million can be achieved. The bridge is particularly suited to the scaling of resistance standards from one hundred ohms to a fraction of a milliohm. It can be used at any ratio up to one thousand to one. It permits the calibration of low value shunts at full operating current with an accuracy limited only by their noise level and stability.
Universal real-time navigational assistance (URNA) (2007)

We describe a complete hardware/software system, dubbed Universal Real-Time Navigational Assistance (URNA), which enables communication of relevant location-aware information to a blind person carrying a Bluetooth-enabled cell phone. Although URNA can be used for a number of different applications (e.g., an information kiosk at a shopping mall or public transit information at a bus stop), we concentrate on the challenging case of an urban intersection. Information provided to the user as he or she approaches the intersection includes a description of the intersection topology and real-time notification of the state of the traffic lights. The main FPGA-based control board (NavCon) interfaces with a traffic controller and with the Bluetooth modules, which are each mounted atop the intersection's pedestrian heads (pedheads) - the lights signaling a pedestrian when to "WALK" or "DON'T WALK". The cell phone software (PedNav), written in Java 2 Micro Edition (J2ME), uses Text-To-Speech (TTS) for presenting the information transmitted by NavCon to the blind user.
Organic Compounds FT-IR Spectroscopy (2012)

General spectral range of electromagnetic radiation with a wavelength greater than 750 nm (i.e. with the number of wavelength below 13000 cm-1) bears the name of the domain infrared (IR). In this field samples absorb electromagnetic radiation due to transitions of vibration of the structure of molecules, molecular transitions in vibrations crystalline network (if the sample is in the solid state of aggregation) or due to transitions of molecular rotation. Subdomain of spectral wavelengths between 2500 50000 nm (respectively the wave numbers 4000 to 200 cm-1) bears the name of the middle infrared domain.
Non-majority magnetic logic gates: a review of experiments and future prospects for ‘shape-based’ logic (2011)

We discuss the experimental demonstration of non-majority, two-input, nanomagnet logic (NML) AND and OR gates. While gate designs still can incorporate the symmetric, rounded-rectangle magnets used in the three-input majority gate experiments by Imre (2006 Science 311 205-8), our new designs also leverage magnets with an edge that has a well-defined 'slant'. In rectangular and ellipsoid nanomagnets, the easy axis of the device coincides with its longer edge. For a magnet with a slanted edge, the easy and hard axes are 'tilted', and magnetic fields applied along the (geometrical) hard axis alone can set the easy axis magnetization state. This switching phenomenon can be employed to realize NML Boolean logic gates with both reduced footprints and critical path delays. Experimental demonstrations of two-input AND and OR gates are supported by corresponding micromagnetic simulations with temperature effects associated with a 300 K environment. Simulations suggest that the time evolution of experimentally demonstrated structures is correct, and that designs can also tolerate clock field misalignment. Additionally, simulations suggest that a slanted-edge 'compute magnet' can (i) be driven by two anti-ferromagnetically ordered lines of NML devices (for input) and (ii) drive an anti-ferromagnetically ordered line (for output). Both are essential if slanted-edge devices are to be used in NML circuits. We conclude with a discussion of extensibility and scaling prospects for shape-based computation with nanomagnets.
Nicotine‐induced Protection Against Glutamate Cytotoxicity (1996)

Cortical neurodegeneration in Alzheimer's disease (AD) is suggested to be attributable not only to beta-protein but also to glutamate. Although degeneration of cholinergic projection to the cerebral cortex is recognized to be one of the most prominent pathological changes in AD, there is only limited information concerning the cholinergic interaction with the cortical neurodegeneration. This study was performed to examine the protective effect of nicotine against glutamate-induced cytotoxicity using rat cultured cortical neurons. The cell viability was significantly reduced when cultures were briefly exposed to glutamate or N-methyl-D-aspartate (NMDA). The simultaneous addition of nicotine did not reduce glutamate cytotoxicity. In contrast, the simultaneous application of NMDA receptor antagonists such as MK-801 reduced glutamate cytotoxicity. Incubating the cultures with nicotine (10 microM) for 0.5-24 h prior to glutamate exposure reduced its cytotoxicity. Neuroprotection by nicotine was dependent on both the concentration and incubation period. In contrast to nicotine, muscarine (10 microM) weakly potentiated glutamate cytotoxicity. The neuroprotective effect of nicotine against glutamate cytotoxicity was antagonized by hexamethonium but not by artopine. Nicotine prevented NMDA cytotoxicity but did not affect cytotoxicity induced by either kainate or alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA). Cell viability was significantly reduced by a brief exposure of cultures to ionomycin, a calcium ionophore. Ionomycin-induced cytotoxicity was abolished by removing Ca2+ from incubating medium. S-nitrosocysteine (SNOC), which spontaneously releases nitric oxide (NO), also induced delayed cell death. Nicotine prevented ionomycin-induced cytotoxicity without affecting SNOC-induced cytotoxicity. These results suggest that nicotinic cholinergic receptor stimulation induces neuroprotection against glutamate cytotoxicity by its inhibitory action on NO-formation. Therefore, we propose that acetylcholine, acting through nicotinic cholinergic receptors, can function as a putative neuroprotective factor against neurodegeneration caused by the excessive release of glutamate and/or NMDA receptor activation.
Effects of 5‐[S‐(2,4‐dinitrophenyl)‐thio]‐2′‐deoxyuridine analog incorporation on the structure and stability of DNA hybrids: implications for the design of nucleic acid probes (1999)

Labeled nucleic acid probes are used as diagnostic tools by detecting changes in gene expression upon hybridization to target RNAs or DNAs that are related to specific disease genes. 5-[S-(2,4-Dinitrophenyl)-thio]-2′-deoxyuridine analog represents an excellent nucleic acid label, containing the DNP group which functions both as a probe and as a precursor for the introduction of a variety of fluorescent groups. This study describes thermal denaturation hybridization experiments with oligonucleotides containing the 5-[S-(2,4-dinitrophenyl)-thio]-2′-deoxyuridine analog. Using molecular modeling techniques, the effects of this analog on the hybrid structure and stability were examined, including (i) analog conformation, (ii) hydrogen bonding, (iii) stacking interactions and (iv) hybrid helical geometry. This analog does not prohibitively affect the hybrid thermal stability and incorporation of the analog does not compromise the structural integrity of the double helix. In particular, the sequence-dependence of the analog effects and the dependence on the modification site relative to the end(s) of the helix were investigated. Findings described here should provide guidelines in the rational design of nucleic acid probes. Copyright © 1999 John Wiley & Sons, Ltd.
Modeling of pseudoacoustic P-waves in orthorhombic media with a low-rank approximation (2013)

ABSTRACT Wavefield extrapolation in pseudoacoustic orthorhombic anisotropic media suffers from wave-mode coupling and stability limitations in the parameter range. We use the dispersion relation for scalar wave propagation in pseudoacoustic orthorhombic media to model acoustic wavefields. The wavenumber-domain application of the Laplacian operator allows us to propagate the P-waves exclusively, without imposing any conditions on the parameter range of stability. It also allows us to avoid dispersion artifacts commonly associated with evaluating the Laplacian operator in space domain using practical finite-difference stencils. To handle the corresponding space-wavenumber mixed-domain operator, we apply the low-rank approximation approach. Considering the number of parameters necessary to describe orthorhombic anisotropy, the low-rank approach yields space-wavenumber decomposition of the extrapolator operator that is dependent on space location regardless of the parameters, a feature necessary for orthorhombic anisotropy. Numerical experiments that the proposed wavefield extrapolator is accurate and practically free of dispersion. Furthermore, there is no coupling of qSv and qP waves because we use the analytical dispersion solution corresponding to the P-wave.
An architecture for real-time multimedia communication systems (1990)

A multimedia communication system includes both the communication protocols used to transport the real-time data and the distributed computing system (DCS) within which any applications using the protocols must execute. The architecture presented attempts to integrate these communications protocols with the DCS in a smooth fashion in order to ease the writing of multimedia applications. Two issues are identified as being essential to the success of this integration: the synchronization of related real-time data streams, and the management of heterogeneous multimedia hardware. The synchronization problem is tackled by defining explicit synchronization properties at the presentation level and by providing control and synchronization operations within the DCS which operate in terms of these properties. The heterogeneity problems are addressed by separating the data transport semantics (protocols themselves) from the control semantics (protocol interfaces).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
MPINet: Metabolite Pathway Identification via Coupling of Global Metabolite Network Structure and Metabolomic Profile (2014)

High-throughput metabolomics technology, such as gas chromatography mass spectrometry, allows the analysis of hundreds of metabolites. Understanding that these metabolites dominate the study condition from biological pathway perspective is still a significant challenge. Pathway identification is an invaluable aid to address this issue and, thus, is urgently needed. In this study, we developed a network-based metabolite pathway identification method, MPINet, which considers the global importance of metabolites and the unique character of metabolomic profile. Through integrating the global metabolite functional network structure and the character of metabolomic profile, MPINet provides a more accurate metabolomic pathway analysis. This integrative strategy simultaneously captures the global nonequivalence of metabolites in a pathway and the bias from metabolomic experimental technology. We then applied MPINet to four different types of metabolite datasets. In the analysis of metastatic prostate cancer dataset, we demonstrated the effectiveness of MPINet. With the analysis of the two type 2 diabetes datasets, we show that MPINet has the potentiality for identifying novel pathways related with disease and is reliable for analyzing metabolomic data. Finally, we extensively applied MPINet to identify drug sensitivity related pathways. These results suggest MPINet's effectiveness and reliability for analyzing metabolomic data across multiple different application fields.
Dynamic trace-based analysis of vectorization potential of applications (2012)

Recent hardware trends with GPUs and the increasing vector lengths of SSE-like ISA extensions for multicore CPUs imply that effective exploitation of SIMD parallelism is critical for achieving high performance on emerging and future architectures. A vast majority of existing applications were developed without any attention by their developers towards effective vectorizability of the codes. While developers of production compilers such as GNU gcc, Intel icc, PGI pgcc, and IBM xlc have invested considerable effort and made significant advances in enhancing automatic vectorization capabilities, these compilers still cannot effectively vectorize many existing scientific and engineering codes. It is therefore of considerable interest to analyze existing applications to assess the inherent latent potential for SIMD parallelism, exploitable through further compiler advances and/or via manual code changes.
Immunocompetence in lung cancer.Relationship to extent of tumor burden and histologic type (1989)

In vitro assays of immunocompetence were done in 60 patients with differing extents of tumor load and various histologic types of lung cancer and were compared to values obtained for 60 normal controls. Profound alterations in monoclonal antibody-defined T-lymphocytes and circulating B-cells were seen. All patients showed impaired blastogenic response to the mitogens used with the exception of a normal response to pokeweed mitogen (PWM) in patients with localized disease. Increase levels of serum IgG were seen in patients with localized disease whereas high levels of IgA was seen in patients with more advanced disease. Distant metastases were associated with low IgM levels. All patients studied regardless of stage and histologic type had elevated levels of circulating immunocomplexes. These findings indicate gross immunologic abnormalities in these patients.
Opportunities and challenges for location aware computing in the construction industry (2005)

This paper describes the opportunities for location aware computing to enhance information capture and use within the construction industry. The construction industry is characterized as being slow to take up innovative mobile ICT, despite the highly mobile workforce who must collaborate with a range of on and off-site personnel, and make use of large volumes of information. Based on fieldwork and workshop activities within COMIT (a large-scale mobile IT project within the construction industry), the information used within two key business processes - health and safety audits, and site design problem resolution - is outlined, and the opportunities for support by location aware computing discussed. Some potential challenges are also identified, as is the need to understand how to provide real value (as opposed to just information) to the end user.
Preparative electrochromatography of proteins in various types of porous media (2000)

The performance of commercial and enzymatically modified size-exclusion (SE) gels in electrochromatography was compared for preparative protein separations. Dextran and agarose-based SE gels were subjected to enzymatic digestion under mild conditions. This treatment partially hydrolyzed the gel matrix modifying its pore size distribution. Enzymatic treatment of agarose-based SE gels was found to increase the resolution of the separation. Successful separation of preparative amounts of the A and B forms of beta-lactoglobulin (difference in electrophoretic mobility of 8.5%) was achieved with a high degree of purity using agarose-based SE gels. The four major whey proteins, beta-lactoglobulin, alpha-lactalbumin, BSA and immunoglobulins, were purified from an acid whey preparation. The degree of retention of a protein in electrochromatography followed their free-solution electrophoretic mobility (mu) when the protein was able to enter the gel pores and the ratio of diffusion/mu when the protein was excluded.
Organic Electronics: Facile Photo‐Crosslinking of Azide‐Containing Hole‐Transporting Polymers for Highly Efficient, Solution‐Processed, Multilayer Organic Light Emitting Devices (Adv. Funct. Mater. 48/2014) (2014)

B. Ma, B. J. Kim, and co-workers report a novel platform of photo-crosslinkable azide (N3) functional hole conducting polymers (X-PTPA) for use in highly efficient, solution-processed, multi-layer OLEDs. On page 7588 the X-PTPA with 5 mol% of N3 group can be crosslinked via mild UV irradiation at short exposure time. A twofold enhancement of device performance is achieved with X-PTPA layer over the control device without X-PTPA.
Monoclonal antibody profiling of cell surface proteins associated with the viral biofilms on HTLV-1 transformed cells (2015)

Human T lymphotropic virus 1 (HTLV-1) is a pathogenic retrovirus that spreads predominantly via cell-to-cell contact. Two models of cell-to-cell virus transmission are proposed: virological synapse (VS) and viral biofilms (VB). Both infectious structures can be involved in transmission and synergistically enhance HTLV-1 spread between cells. Although transmission of virus via VB has been reported, the molecular composition of VB remains poorly understood. In this study we generated new anti-VB monoclonal antibodies (MAbs) and screenedthem along with a panel of anti-human cluster of differentiation (CD) MAbs to select antigens associated with VB. Among four MAbs generated against VB, two MAbs were identified as anti-CD25 (IL-2RA). We found that antigens CD4, CD150, CD25, CD70, and CD80 were enriched in VB. We also determined that expression of viral protein Tax, a central molecule in HTLV-1 transmission, upregulates intercellular adhesion molecule 1 (ICAM-1), CD95, CD25, CD70, and CD80. Whether these antigens are essential for VB formation and HTLV-1 infection remains unknown and will be determined in further experiments.
The Vote Tallying Chip: A Custom Integrated Circuit. (1984)

A custom integrated circuit with applications to computer vision has been designed and fabricated. It is the first generation of a series of circuits that can act as specialized hardware for finding maxima in a distribution that is constructed by vote tallying. Many applications in artificial intelligence use peaks of histograms or areas of high density in distribution as the basis for decisions. This series of designs is meant to operate in those domains where histograms are constructed by tallying samples. The current design simply constructs the histogram given a stream of samples. An extension of content addressable memory is used to tally the samples. The design has been made fast by extensive use of pipelining. Keywords include: VLSI, Hough Transform, Cluster Analysis, Histogram, Artificial Intelligence, Computer Vision, and Systollic Array.
Tactical Shipping and Scheduling at Polaroid with Dual Lead-Times (2002)

which we developed a supply chain model to provide decision support for planning production and transportation. Production occurs in Asia to serve world-wide demand. Production planners must determine both the production quantities as well as whether to ship by sea or by air. We develop a model to optimize a static version of this problem and then show how to use this static model in a dynamic setting. We test the model with data from Polaroid and show its effectiveness. Index Terms—dual replenishment modes, inventory and transportation planning, supply chain application, supply chain modeling I.
Support for comprehensive reuse (1991)

Reuse of products, processes and other knowledge will be the key to enable the software industry to achieve the dramatic improvement in productivity and quality required to satisfy anticipated growing demands. Although experience shows that certain kinds of reuse can be successful, general success has been elusive. A software life-cycle technology that allows comprehensive reuse of all kinds of software-related experience could provide the means of achieving the desired order-of-magnitude improvements. In this paper, we introduce a comprehensive framework of models, model-based characterisation schemes, and support mechanisms for better understanding, evaluating, planning and supporting all aspects of reuse.