gebhart/patrepeval huggingface dataset:
New Phototriggers 9:  <i>p</i>-Hydroxyphenacyl as a C-Terminal Photoremovable Protecting Group for Oligopeptides (2000)

In our search for a more versatile protecting group that would exhibit fast release rates for peptides, we have designed and developed the p-hydroxyphenacyl (pHP) group as a new photoremovable protecting group. We report the application of this protecting group for the dipeptide Ala-Ala (1) and for the nonapeptide bradykinin (2), two representative peptides that demonstrate C-terminus “caging” and photorelease. The synthesis of these p-hydroxyphenacyl esters was accomplished in good yields by DBU-catalyzed displacement of bromide from p-hydroxyphenacyl bromide. As in the case of caged γ-amino acids 11 (pHP glu) and 12 (pHP GABA) and caged nucleotide 17 (pHP ATP) reported earlier,1,2 irradiations of the p-hydroxyphenacyl esters of 1 and 2 actuate the release of the peptides with rate constants that are consistently greater than 108 s-1 and appearance efficiencies (Φapp) that range from 0.1 to 0.3. Release of the substrate is accompanied by a deep-seated rearrangement of the protecting group into the near-UV silent p-hydroxyphenylacetic acid (6). Quenching studies of pHP Ala-Ala (7) with either sodium 2-naphthalenesulfonate or potassium sorbate gave good Stern−Volmer kinetics yielding a rate constant for release of 1.82 × 108 s-1. Quenching of the phosphorescence emission from pHP Ala-Ala (7, ET = 70.1 kcal/mol) and pHP GABA (12, ET = 68.9 kcal/mol) were also observed. The biological efficacy of bradykinin released from pHP bradykinin (9) was examined on single rat sensory neurons grown in tissue culture. A single 337 nm flash (<1 ns) released sufficient bradykinin from the p-hydroxyphenacyl protected nonapeptide to activate cell-surface bradykinin receptors as indicated by a rapid increase in the intracellular calcium concentration. A selective antagonist of type 2 bradykinin receptors blocked the biological response. From these results, it is apparent that flash photolysis of p-hydroxyphenacyl protected peptides provides a powerful tool for the rapid and localized activation of biological receptors.
A knowledge system for automatic finite element mesh generation: AMEKS (1988)

An Automated MEshing Knowledge System that automatically generates quadrilateral finite element meshes is discussed in this paper.
Surface plasmonic enhanced polarimetric longwave infrared photodetection with band pass spectral filtering (2012)

In this paper, we report a surface plasmonic enhanced polarimetric longwave infrared (LWIR) photodetector. Polarization-selective detection of LWIR incidence with different polarizations is achieved at different plasmonic resonant modes. Band-pass spectral filtering is also provided at the plasmonic resonant modes by the plasmonic enhancement. The extinction ratio (ER) of the polarimetric detection and its limiting factor is discussed.
Cooperative Neural Network Background Model for Multi-Modal Video Surveillance (2011)

This paper proposed a new cooperative background model for multi-modal video surveillance based on probability neural network (PNN). Firstly, probability of being foreground was estimated in visible and infrared channel, and post processed separately. Then, every pixel was classified into foreground, background, and change pixels by fusing this information, and foreground pixels were segmented into motion regions. Thirdly, adaptive learning rate was computed for every frame and every pixel based on frame motion difference and pixel classification result, and background model for every channel was updated. Experimental results on well-known benchmark image sequences show that the proposed algorithm can detect motion region more precisely.
Collaborative multimedia systems: synthesis of media objects (1998)

When a group {/1,..., l/sub n/} of individuals wishes to collaboratively construct a complex multimedia document, the first requirement is that they be able to manipulate media-objects created by one another. For instance, if individual L/sub j/ wishes to access some media objects present at participant l/sub k/'s site, he must be able to: 1) retrieve this object from across the network, 2) ensure that the object is in a form that is compatible with the viewing/editing resources he has available at his node, and 3) ensure that the object has the desired quality (such as image size and resolution). Furthermore, he must be able to achieve these goals at the lowest possible cost. In this paper, we develop a theory of media objects, and present optimal algorithms for collaborative object sharing/synthesis of the sort envisaged above. We then extend the algorithms to incorporate quality constraints (such as image size) as well as distribution across multiple nodes. The theoretical model is validated by an experimental implementation that supports the theoretical results.
Characterization of the Region Involved in CD3 Pairwise Interactions within the T Cell Receptor Complex (1998)

Assembly of the six-chain T cell antigen receptor-CD3 complex takes place by pairwise interactions. Thus, CD3-epsilon interacts with either CD3-gamma or CD3-delta, and these dimers then associate with the TCR heterodimer (alpha.beta or gamma.delta) and the CD3-zeta homodimer to constitute a full complex. We have now mapped the site in CD3-epsilon responsible for the interaction with CD3-gamma and CD3-delta by analysis of a series of deletional mutants encompassing the most conserved regions. We found that the highly conserved juxtamembrane domain is mainly responsible for the interaction. Thus, deletion of this 16-amino acid extracellular sequence resulted in the inhibition of up to 95% of the CD3-epsilon/gamma interaction. A highly conserved sequence is also present in both CD3-gamma and CD3-delta, suggesting that the domain in these two chains may reciprocally be involved in the interaction with CD3-epsilon. Indeed, an immobilized synthetic peptide corresponding to the CD3-gamma sequence specifically associated to a bacterially expressed CD3-epsilon protein, suggesting the 16-amino acid domain is sufficient to promote CD3-epsilon/CD3-gamma assembly. The conservation of the motif in the CD3 chains suggest that, in addition to CD3-epsilon/CD3-gamma and CD3-epsilon/CD3-delta interactions, it may also mediate homotypic interactions. Indeed, it is shown that it mediates the formation of disulfide-linked homodimers and that the formation of homo- and heterodimers are mutually excluded. Finally, this domain contains a Cys-X-X-Cys sequence that resembles that of p56(lck), which is responsible for the interaction with the cytoplasmic tails of CD4 and CD8. Since the replacement of the two cysteines (Cys97 and Cys100) in CD3-epsilon by alanines strongly inhibited pair formation, the existence of a Cys-X-X-Cys motif involved in protein-protein interactions is suggested.
Immunopathogenesis of IBD: Batf as a Key Driver of Disease Activity (2016)

Targeting Batf in IBD emerges as an attractive therapeutic approach disabling colitogenic T cell activities while sparing off-target effects in the intestinal epithelial cell compartment.
Electrical effects in bone (1988)

This paper presents a review of the work carried out on the electromechanical properties of bone over the past three decades. Research in this field has established the piezoelectric nature of bone and identified collagen as the generating source in dry bone. Some of the characteristics of the strain generated potential (SGP) signal from dry and hydrated bone were found to be unaccountable in terms of a classical piezoelectric theory. Modifications of the theory were suggested and in the case of fully hydrated bone, a new mechanism (streaming potential) has emerged. The paper also reports on recent developments in the field and presents results from microstructural (osteonic) studies and from fluid-filled bone. The review indicates the need for actual in vivo work because most of the reported data were obtained, in the last decade, from in vitro work and were considered valid in vivo. Modelling of the mechanism which produces the SGP has been considered to explain the characteristics of these potentials. A representative model recently developed by the present authors and co-workers is reported. This model relates the generated potential to reorientation of spontaneous dipoles and differentiates between the generated and recorded signal, thus identifying effects from the measuring circuitry. The clinical aspects of electricity of bone in assisting fracture healing and the different techniques employed are mentioned briefly. Emphasis on new techniques of piezoelectric implants and their future development is also reported.
Primary tumors of the lung other than lung cancer (1993)

Neoplasms of the lung other than lung cancer are rare and have varying biologic behavior. Diffuse malignant mesothelioma remains a difficult clinical problem, with efforts directed at combined modality therapy. A nude mouse xenograft model may hold promise in the identification of active chemotherapy agents. Continuing evidence suggests that typical and atypical pulmonary carcinoids represent a spectrum of neuroendocrine disease, with small cell lung cancer representing the most virulent subtype. Therapy for advanced invasive thymoma includes neoadjuvant chemotherapy, surgery, and postoperative radiation. Nonseminomatous germ cell neoplasms of the mediastinum respond much less favorably to cisplatin-based chemotherapy than do similar tumors arising elsewhere, and new advances in treatment are needed. Rare mesenchymal tumors usually respond favorably to surgical excision.
On the Effects of Economic Integration on Greenfield Investments and Cross-border Mergers and Acquisitions Location Pattern (2005)

This paper investigates the linkages between economic integration and horizontal Foreign Direct Investment (FDI) location. In a three-country partial equilibrium model with differentiated Cournot and Bertrand competition, we incorporate the two main FDI modes: Greenfield Investment (G.I.) and crossborder Merger and Acquisition (M&A). We also allow regionally-based firms to invest outside the regional area. Economic integration characterized by internal and external transaction costs may affect entry modes (G.I. vs. M&A) and its location (intra -extra regional flows). Our findings suggest the existence of complex linkages between economic integration and FDI location pattern depending simultaneously on set-up fixed costs, the competitive mode of market interaction and the product differentiation. However, the role of cross-border M&A as well as the importance of FDI outflows from the regional area is highlighted.
Rapid location of mount points (1989)

Abstract ‘Mount points’ allow more storage to be grafted into tree‐structured hierarchical file systems. Administrative tasks use their locations, which are tabulated in a file. In our System V Unix environment, this file was occasionally removed. Getmnt was written to recover the information. Getmnt has had three significant versions. The original version ( getmnt1 ) was a highly optimized naive tree traversal. Getmnt3 improved the real time performance by a mean factor of 7 by pruning unnecessary branches from the traversal. Getmnt3 doubled getmnt2's speed, with a change from depth‐first to breadth‐first search. On our development system, getmnt1 required 647.6 s to run, whereas getmnt3 required 42.53 s.
Efficient real-time modelling of substrate coupling in large mixed-signal Spice designs, using analogue HDL (1998)

In large mixed-signal circuits, digitally-injected substrate noise has recently been recognised as a key problem for circuit designers. However, no published procedure exists which allows circuit designers to efficiently model the substrate noise and coupling to the analogue circuitry in large mixed-signal Spice designs. Such a methodology is presented and is extended to employ novel analogue HDL (hardware description language) models, providing real-time capability. The efficiency and practicality of the proposed methodology are demonstrated in two example circuits.
Intermodulation Distortion Analysis of MESFET Amplifiers Using the Volterra Series Representation (1980)

Third-order intermodulation distortion generated in a MESFET amplifer is analyzed by means of the Volterra series representation. A transistor model is used which enables direct analytical determination of the nonlinear elements from small-signal measurements. The four nonlinearities considered are the gate capacitance, transconductance, drain feedback capacitance, and output conductance. Volterra transfer functions are derived for a simplified model and closed-form expressions for the third-order intermodulation ratio and intercept point are determined. The equations show the dependence of distortion on frequency, terminating impedances, and transistor parameters. Principal sources of distortion are identified and the influence of device parameters and network terminations is investigated. Experimental verification on specific MESFET amplifiers, with 2-mu m and 1-mu m gate devices, comparing predicted and measured intermodulation products for various load conditions is presented.
Study of the presalt dolomite reservoir prediction in the East Margin of Pre-Caspian Basin (2012)

Thick salt domes developed in the east margin of the Pre-Caspian basin during Permian, leading to seismic events distortion in presalt layers. The main oil-bearing beds are the fracture-pore type of Carboniferous dolomite with strong heterogeneity, which also caused difficulties in presalt carbonate reservoir prediction. To solve these problems, a set of carbonate reservoir seismic prediction methods were presented in thick salt domes areas. Reverse-time migration imaging was used to eliminate interference caused by thick salt domes and to enhance the presalt seismic quality; the cavernous dolomite areas were predicted qualitatively; forward modeling was applied to analyze the seismic response pattern; non-leaner neural network method based on seismic multi-attribute was employed to carry out three-parameter inversion and quantitatively predict dolomite reservoirs. The actual application shows the methods produce a good prediction for dolomite reservoirs in the east margin of the Pre-Caspian basin.
Marketing Applications of Social Tagging Networks (2012)

This dissertation focuses on marketing applications of social tagging networks. Social tagging is a new way to share and categorize content, allowing users to express their perceptions and feelings with respect to concepts such as brands and firms with their own keywords, “tags.” The associative information in social tagging networks provides marketers with a rich source of information reflecting consumers’ mental representations of a brand/firm/product. The first essay presents a methodology to create “social tag maps,” brand associative networks derived from social tags. The proposed approach reflects a significant improvement towards understanding brand associations compared to conventional techniques (e.g., brand concept maps and recent text mining techniques), and helps marketers to track real-time updates in a brand’s associative network and dynamically visualize the relative competitive position of their brand. The second essay investigates how information contained in social tags acts as proxy measures of brand assets that track and predict the financial valuation of firms using the data collected from a social bookmarking website, del.icio.us, for 61 firms across 16 industries. The results suggest that brand asset metrics based on social tags explain stock return. Specifically, an increase in social attention and connectedness to competitors is shown to be positively related to stock return for less prominent brands, while for prominent brands associative uniqueness and evaluation valence is found to be more significantly related to stock return. The findings suggest to marketing practitioners a new way to proactively improve brand assets for impacting a firm’s financial performance. The third essay investigates whether the position of products on social tagging networks can predict sales dynamics. We find that (1) books in long tail can increase sales by being strongly linked to well-known keywords with high degree centrality and (2) top sellers can be better sellers by creating dense content clusters rather than connecting them to well-known keywords with high degree centrality. Our findings suggest that marketing managers better understand a user community’s perception of products and potentially influence product sales by taking into account the positioning of their products within social tagging networks.
Evidence of Remediation-Induced Alteration of Subsurface Poly- and Perfluoroalkyl Substance Distribution at a Former Firefighter Training Area (2014)

Poly- and perfluoroalkyl substances (PFASs) are a class of fluorinated chemicals that are utilized in firefighting and have been reported in groundwater and soil at several firefighter training areas. In this study, soil and groundwater samples were collected from across a former firefighter training area to examine the extent to which remedial activities have altered the composition and spatial distribution of PFASs in the subsurface. Log Koc values for perfluoroalkyl acids (PFAAs), estimated from analysis of paired samples of groundwater and aquifer solids, indicated that solid/water partitioning was not entirely consistent with predictions based on laboratory studies. Differential PFAA transport was not strongly evident in the subsurface, likely due to remediation-induced conditions. When compared to the surface soil spatial distributions, the relative concentrations of perfluorooctanesulfonate (PFOS) and PFAA precursors in groundwater strongly suggest that remedial activities altered the subsurface PFAS distribution, presumably through significant pumping of groundwater and transformation of precursors to PFAAs. Additional evidence for transformation of PFAA precursors during remediation included elevated ratios of perfluorohexanesulfonate (PFHxS) to PFOS in groundwater near oxygen sparging wells.
Sustained Reductions in Invasive Pneumococcal Disease in the Era of Conjugate Vaccine (2009)

Dramatic reductions in IPD after PCV7 introduction in the United States remain evident 7 years later. IPD rates caused by serotype 19A and other non-PCV7 types have increased but remain low relative to decreases in PCV7-type IPD.
Tunable Er <sup>3+</sup> -doped fibre ring laser usingfibre gratingincorporated by optical circulator or fibre coupler (1995)

Efficient narrow linewidth Er3+-doped fibre ring lasers using a single fibre Bragg grating incorporated by a fibre optical circulator or a fibre coupler are investigated. Tunability of the fibre lasers is obtained by compressing the fibre grating in a specially designed unit. Tunabilities of 18 and 12 nm are achieved for fibre ring lasers with an optical circulator and fibre coupler, respectively.
Code density optimization for embedded DSP processors using data compression techniques (2002)

We address the problem of code size minimization in VLSI systems with embedded DSP processors. Reducing code size reduces the production cost of embedded systems. We use data compression methods to develop code size minimization strategies. We present a framework for code size minimization where the compressed data consists of a dictionary and a skeleton. The dictionary can be computed using popular text compression algorithms. We describe two methods to execute the compressed code that have varying performance characteristics and varying degrees of freedom in compressing the code. Experimental results obtained with a TMS320C25 code generator are presented.
Conserved residues in the <i>Plasmodium vivax</i> Duffy-binding protein ligand domain are critical for erythrocyte receptor recognition (2004)

Malaria merozoite invasion of human erythrocytes depends on recognition of specific erythrocyte surface receptors by parasite ligands. Plasmodium vivax merozoite invasion is totally dependent on the recognition of the Duffy blood group antigen by the parasite ligand Duffy-binding protein (DBP). Receptor recognition by P. vivax relies on a cysteine-rich domain, the DBL domain or region II, at the N terminus of the extracellular portion of DBP. The minimal region of the DBP implicated for receptor recognition lies between cysteines 4 and 8 of the DBL domain, which is a region that also has the highest rate of allelic polymorphisms among parasite isolates. We previously found that allelic polymorphisms in this region altered the P. vivax DBL domain antigenic character, which contrasts with changes in receptor specificity attributed to polymorphisms in some homologous ligands of Plasmodium falciparum. To further investigate the relative importance of conserved and polymorphic residues within this DBL central region, we identified residues critical for receptor recognition by site-directed mutagenesis. Seventy-seven surface-predicted residues of the Sal-1 DBL domain were substituted with alanine and assayed for erythrocyte binding activity by expression of the mutant proteins on the surface of transiently transfected COS cells. The functional effect of alanine substitution varied from nil to complete loss of DBL erythrocyte-binding activity. Mutations that caused loss of ligand function mostly occurred in discontinuous clusters of conserved residues, whereas nearly all mutations in polymorphic residues did not affect erythrocyte binding. These data delineate DBL domain residues essential for receptor recognition.
International Randomized Clinical Trial, Stroke Inpatient Rehabilitation With Reinforcement of Walking Speed (SIRROWS), Improves Outcomes (2010)

Background. Feedback about performance may optimize motor relearning after stroke. Objectives . Develop an international collaboration to rapidly test the potential efficacy of daily verbal feedback about walking speed during inpatient rehabilitation after stroke, using a protocol that requires no research funds. Methods . This phase 2, single-blinded, multicenter trial randomized inpatients to either feedback about self-selected fast walking speed (daily reinforcement of speed, DRS) immediately after a single, daily 10-m walk or to no reinforcement of speed (NRS) after the walk, performed within the context of routine physical therapy. The primary outcome was velocity for a 15.2-m (50-foot) timed walk at discharge. Secondary outcomes were walking distance in 3 minutes, length of stay (LOS), and level of independence (Functional Ambulation Classification, FAC). Results. Within 18 months, 179 participants were randomized. The groups were balanced for age, gender, time from onset of stroke to entry, initial velocity, and level of walking-related disability. The walking speed at discharge for DRS (0.91 m/s) was greater ( P = .01) than that for NRS (0.72 m/s). No difference was found for LOS. LOS for both DRS and NRS was significantly shorter, however, for those who had mean walking speeds >0.4 m/s at entry. The DRS group did not have a higher proportion of FAC independent walkers ( P = .1) and did not walk longer distances ( P = .09). Conclusions. An Internet-based collaboration of 18 centers found that feedback about performance once a day produced gains in walking speed large enough to permit unlimited, slow community ambulation at discharge from inpatient rehabilitation.