gebhart/patrepeval huggingface dataset:
Quantitative Cell-based Protein Degradation Assays to Identify and Classify Drugs That Target the Ubiquitin-Proteasome System (2011)

We have generated a set of dual-reporter human cell lines and devised a chase protocol to quantify proteasomal degradation of a ubiquitin fusion degradation (UFD) substrate, a ubiquitin ligase CRL2(VHL) substrate, and a ubiquitin-independent substrate. Well characterized inhibitors that target different aspects of the ubiquitin-proteasome system can be distinguished by their distinctive patterns of substrate stabilization, enabling assignment of test compounds as inhibitors of the proteasome, ubiquitin chain formation or perception, CRL activity, or the UFD-p97 pathway. We confirmed that degradation of the UFD but not the CRL2(VHL) or ubiquitin-independent substrates depends on p97 activity. We optimized our suite of assays to establish conditions suitable for high-throughput screening and then validated their performance by screening against 160 cell-permeable protein kinase inhibitors. This screen identified Syk inhibitor III as an irreversible p97/vasolin containing protein inhibitor (IC(50) = 1.7 μM) that acts through Cys-522 within the D2 ATPase domain. Our work establishes a high-throughput screening-compatible pipeline for identification and classification of small molecules, cDNAs, or siRNAs that target components of the ubiquitin-proteasome system.
Capitalize on dimensionality increasing techniques for improving face recognition grand challenge performance (2006)

This paper presents a novel pattern recognition framework by capitalizing on dimensionality increasing techniques. In particular, the framework integrates Gabor image representation, a novel multiclass Kernel Fisher Analysis (KFA) method, and fractional power polynomial models for improving pattern recognition performance. Gabor image representation, which increases dimensionality by incorporating Gabor filters with different scales and orientations, is characterized by spatial frequency, spatial locality, and orientational selectivity for coping with image variabilities such as illumination variations. The KFA method first performs nonlinear mapping from the input space to a high-dimensional feature space, and then implements the multiclass Fisher discriminant analysis in the feature space. The significance of the nonlinear mapping is that it increases the discriminating power of the KFA method, which is linear in the feature space but nonlinear in the input space. The novelty of the KFA method comes from the fact that 1) it extends the two-class kernel Fisher methods by addressing multiclass pattern classification problems and 2) it improves upon the traditional Generalized Discriminant Analysis (GDA) method by deriving a unique solution (compared to the GDA solution, which is not unique). The fractional power polynomial models further improve performance of the proposed pattern recognition framework. Experiments on face recognition using both the FERET database and the FRGC (Face Recognition Grand Challenge) databases show the feasibility of the proposed framework. In particular, experimental results using the FERET database show that the KFA method performs better than the GDA method and the fractional power polynomial models help both the KFA method and the GDA method improve their face recognition performance. Experimental results using the FRGC databases show that the proposed pattern recognition framework improves face recognition performance upon the BEE baseline algorithm and the LDA-based baseline algorithm by large margins.
A Study of High Frequency Voltage Effects in Medium Voltage Cable Terminations (2008)

High-power voltage sourced converters(VSC’s) are becoming increasingly prevalent in modern transmission systems. These systems primarily use switching schemes generating kHz range harmonics, which may be magnified by one or more system resonances. Despite the high frequency harmonics, VSC systems widely use insulated equipment designed for operation at power frequencies; this includes critical substation components such as medium voltage polymeric cables and terminations. The stress grading systems of non-geometric (compact) cable terminations are susceptible to insulation degradation and eventual flashover failure, under high frequency harmonic stresses. As such, the present work studies high frequency voltage effects in cross-linked polyethylene cable terminations, and their relationship to stress grading (SG) design and material properties. Finite element modeling (FEM) has been used to analyze electric field and resistive heating in termination designs, in response to parametric variations in SG material properties. Experimental studies investigate thermal behaviour in a variety of commercial termination designs, using a high voltage, high frequency test setup developed to replicate conditions of high frequency harmonic resonance in a VSC system. \n \nThe study results show that high frequency voltage application increases the electric field, resistive heating, and surface temperature rise, in non-geometric (compact) termination designs using field-dependant stress grading materials. Geometric (stress cone) designs are insensitive to high frequency harmonics; however, they have disadvantages compared to compact designs, making them a less practical long-term solution for high frequency applications. Among non-geometric designs, the field-dependent electrical conductivity σ (E), the permittivity ε, and the temperature dependencies of σ (E) and ε strongly influence the termination electrical and thermal behaviour under high frequency stress. Since thermal hotspots in cable termination SG areas may lead to material degradation and eventual failure, recommendations are made for an optimal non-geometric stress grading design, for terminations operating in environments where high frequency harmonics may be present.
Corporate branding versus product branding in emerging markets (2006)

Purpose To build a conceptual framework for the development of branding strategy from the pint of view of a Western firm entering a market in a developing economy. Design/methodology/approach An extensive literature review brings together two research streams, market entry and branding strategy, with particular reference to corporate branding versus product branding. Findings The choice of branding strategy is determined in the conditions under study by five antecedent factors and three moderating variables, which are expressed as a visual model and eight propositions. Practical implications In a rapidly developing world, this framework and the literature review from which it is derived offer applicable marketing intelligence to planners of branding strategies for international markets. The eight propositions suggest fruitful directions for further academic research. Originality/value Draws together two streams within the marketing literature in an original way, and offers a framework for the conceptualisation of an important element of marketing strategy in challenging market conditions.
Thermodynamic Properties of Pd‐X‐Alloys, with X = Gd, Y, Ce (1983)

Abstract Electromotive force measurements on cells with a CaF 2 solid electrolyte were used to determine the activities of Gd, Y, and Ce in Pd‐rich alloys between 700°C and 800°C. The thermodynamic properties of these alloys are characterized by extreme negative deviations from ideal mixing behavior, up to −400 kJ/mol for the partial molar excess Gibbs energy of Ce and up to −320 kJ/mol for Gd and Y. The high thermodynamic stability of these alloys is attributed to a transfer of valence electrons to the electron gas of the alloy. At infinite dilution the resulting bonding contribution to the partial excess free energy is determined by the difference of the Fermi levels of the components and the valency of the solute. Including the size difference of the components as an additional effect, the mixing behavior of the alloys can be well described. – Within the homogeneity ranges of the intermetallic phases Pd 3 Y and Pd 3 Gd the activities of the unnoble components increase by more than ten orders or magnitude.
A Vortex Whistle (1954)

Simple whistles have been constructed that produce sound by the escape of a vortex from the open end of a tube. The whistle operates equally well on either air or water. When the frequency that is produced by the passage of either air or water is plotted against the volume rate of fluid flow, it is found that the frequency depends almost linearly on the rate of flow and that the number of cycles produced by the flow of a unit volume of air is nearly the same as that produced by the flow of a unit volume of water. Measurements have been made relating the frequency of the sound produced to different pressures of air applied to the whistle.
The algofunctional indices for hip and knee osteoarthritis. (1997)

The severity or algofunctional indices for hip and knee osteoarthritis (OA) have been used in Europe for about 10 years. They were validated, then published between 1982 and 1987. They are useful mainly as outcome measures in OA trials, and also for appraising the severity of patient function: a score above 11-12 points after appropriate treatment indicates surgery. Most patients recruited in OA trials have a score of 9-11 (SD 2.3 to 3.8), decreasing about 30 to 40% with the active drug. The effect size reaches 1.3 to 1.8. The indices have 2 advantages: they are structured separately for hip and for knee OA and the same instrument serves as a measure of severity (disability scale) and as an outcome measurement tool in trials.
European Citizenship: The IGC and Beyond (1997)

This paper examines two aspects of the 'citizenship dimension' of the IGC agenda, in the light of a broader argument about the role of citizenship of the Union in feeding the construction and development of a 'European polity'. It is argued that citizenship was always likely to become a salient issue of debate in the 1990s EU, but that the concept which exists so far in Treaty form is extremely weak in nature. Against this background, the paper develops the arguments in favour of amendments to the EU Treaties to incorporate a 'non-discrimination' clause and enhanced individual access to EU institutional documents, concluding that such changes represent a fundamental aspect of polity-formation within the EU, so far as concerns the vital role of citizens.
Effect of Delayed Peripheral Nerve Repair on Nerve Regeneration, Schwann Cell Function and Target Muscle Recovery (2013)

Despite advances in surgical techniques for peripheral nerve repair, functional restitution remains incomplete. The timing of surgery is one factor influencing the extent of recovery but it is not yet clearly defined how long a delay may be tolerated before repair becomes futile. In this study, rats underwent sciatic nerve transection before immediate (0) or 1, 3, or 6 months delayed repair with a nerve graft. Regeneration of spinal motoneurons, 13 weeks after nerve repair, was assessed using retrograde labeling. Nerve tissue was also collected from the proximal and distal stumps and from the nerve graft, together with the medial gastrocnemius (MG) muscles. A dramatic decline in the number of regenerating motoneurons and myelinated axons in the distal nerve stump was observed in the 3- and 6-months delayed groups. After 3 months delay, the axonal number in the proximal stump increased 2-3 folds, accompanied by a smaller axonal area. RT-PCR of distal nerve segments revealed a decline in Schwann cells (SC) markers, most notably in the 3 and 6 month delayed repair samples. There was also a progressive increase in fibrosis and proteoglycan scar markers in the distal nerve with increased delayed repair time. The yield of SC isolated from the distal nerve segments progressively fell with increased delay in repair time but cultured SC from all groups proliferated at similar rates. MG muscle at 3- and 6-months delay repair showed a significant decline in weight (61% and 27% compared with contra-lateral side). Muscle fiber atrophy and changes to neuromuscular junctions were observed with increased delayed repair time suggestive of progressively impaired reinnervation. This study demonstrates that one of the main limiting factors for nerve regeneration after delayed repair is the distal stump. The critical time point after which the outcome of regeneration becomes too poor appears to be 3-months.
The rural-urban fringe problem: Farm, suburban, and city interests have interdependence in decisions on expenditure of public money for public services (1959)

California Agriculture - All Issues
B cell depletion with ublituximab reshapes the T cell profile in multiple sclerosis patients (2019)

Multiple sclerosis (MS) is a demyelinating disease of the central nervous system, thought to be mediated by myelin-specific CD4+ T cells. However, B cell depletion has proven to be an effective therapy for MS, but the mechanism is not well understood. This study was designed to determine how B cell depletion changes lymphocyte profiles. During a phase IIa clinical trial with ublituximab, a novel CD20 antibody, blood was collected from 48 MS patients at 11 time points over 24 weeks and the lymphocyte profiles were analyzed by flow cytometry. The percentage of naïve CD4+ and CD8+ T cells increased, while the percentage of both effector and central memory T cells declined. CD4+ Th1 effector cells decreased, while there was a significant increase in CD4+ regulatory T cells. The depletion of B cells had a favorable shift in the lymphocyte landscape, reducing the number of naïve T cells becoming activated and transitioning to memory T cells. The ratio of Th1 cells to CD4+ regulatory T cells declined, suggesting that immune regulation was being restored. These data suggest that loss of B cells as antigen presenting cells is a major mechanism of action for the beneficial effects of CD20 antibody therapy in MS.
Differences in the chemical and catalytic characteristics of two crystallographically ‘identical’ enzyme catalytic sites. Characterization of actinidin and papain by a combination of pH-dependent substrate catalysis kinetics and reactivity probe studies targeted on the catalytic-site thiol group and its immediate microenvironment (1987)

The characteristics of actinidin (EC 3.4.22.14) and papain (EC 3.4.22.2), two cysteine proteinases whose catalytic-site regions appear to superimpose to a degree that approaches atomic co-ordinate accuracy of both crystal structures, were evaluated by determining (a) the pH-dependence in acid media of the acylation process of the catalytic act (k+2/Ks) using N alpha-benzoyl-L-arginine p-nitroanilide (L-Bz-Arg-Nan) as substrate and (b) the sensitivity of the reactivity of the catalytic-site thiol group and its pH-dependence to structural change in small, thiol-specific, two-protonic-state reactivity probes (2,2'-dipyridyl disulphide and methyl 2-pyridyl disulphide) where enzyme-probe contacts should be restricted to areas close to the catalytic site. Distortion of the catalytic sites of the two enzymes at pH less than 4 was evaluated over time-scales appropriate for both stopped-flow reactivity probe kinetics (less than or equal to 1-2 s) and steady-state substrate catalysis kinetics (3-5 min) by using the 2,2'-dipyridyl disulphide monocation as a titrant for non-distorted catalytic sites. This permitted a lower pH limit to be defined for valid kinetic analysis of both types. The behaviour of the enzymes at pH less than 4 requires a kinetic model in which the apparently biomolecular reaction of enzyme with probe reagent is separated from the process leading to loss of conformational integrity by a potentially reversible step. The acylation of actinidin with L-Bz-Arg-Nan in acidic media occurs in two protonic states, one produced by raising the pH across pKa less than 4 which probably characterizes the formation of -S-/-ImH+ ion pair (pKa approx. 3) and the other, of higher reactivity, produced by raising the pH across pKa 5.5, which may characterize rearrangement of catalytic-site geometry. The pH-dependence of the acylation of papain by L-Bz-Arg-Nan is quite different and is not influenced by protonic dissociation with pKa values in the range 5-6. The earlier conclusion that the acylation of papain depends on two protonic dissociations each with pKa approx. 4 was confirmed. This argument is now more firmly based because titration with 2,2'-dipyridyl disulphide permits the loss of conformational integrity to be taken into account in the analysis of the kinetic data at very low pH. Methyl 2-pyridyl disulphide was synthesized by reaction of pyridine-2-thione with methyl methanethiolsulphonate and its pKa at I = 0.1 was determined by spectral analysis at 307 nm to be 2.8.(ABSTRACT TRUNCATED AT 400 WORDS)
Computational Studies of Protein Folding (1996)

This review describes computational approaches to the determination of protein structure from sequence. The emphasis is on reduced protein models that are sufficiently accurate to represent protein structure at low resolution, yet are computationally efficient enough to allow the extensive search of phase space required to locate the global minimum from an unfolded state. A discussion of both potential functions and algorithmic simulation strategies for such models are presented, along with a number of specific models that have been developed and successfully applied to proteins as large as myoglobin. The results indicate that significant progress is being made in understanding the requirements for computational prediction of protein structure.
Nanosphere lithography for optical fiber tip nanoprobes (2016)

This paper reports a simple and economical method for the fabrication of nanopatterned optical fiber nanotips. The proposed patterning approach relies on the use of the nanosphere lithography of the optical fiber end facet. Polystyrene (PS) nanospheres are initially self-assembled in a hexagonal array on the surface of water. The created pattern is then transferred onto an optical fiber tip (OFT). The PS monolayer colloidal crystal on the OFT is the basic building block that is used to obtain different periodic structures by applying further treatment to the fiber, such as metal coating, nanosphere size reduction and sphere removal. Ordered dielectric and metallo-dielectric sphere arrays, metallic nanoisland arrays and hole-patterned metallic films with feature sizes down to the submicron scale are achievable using this approach. Furthermore, the sizes and shapes of these periodic structures can be tailored by altering the fabrication conditions. The results indicate that the proposed self-assembly approach is a valuable route for the development of highly repeatable metallo-dielectric periodic patterns on OFTs with a high degree of order and low fabrication cost. The method can be easily extended to simultaneously produce multiple fibers, opening a new route to the development of fiber-optic nanoprobes. Finally, we demonstrate the effective application of the patterned OFTs as surface-enhanced Raman spectroscopy nanoprobes.
Thermodynamics of the carbon dioxide system in the oceans (1995)

In the next ten years, a number of studies on the carbonate system are planned as part of the JGOFS/WOCE programs. The carbon dioxide system will be studied by measuring at least two of the controlling parameters; pH, total alkalinity (TA), total inorganic CO2 (TCO2), and the fugacity of CO2 (fCO2). The other parameters can be calculated using thermodynamic relations. In the present paper the thermodynamic equations necessary to characterize the CO2 system in the oceans as a function of salinity and temperature are given. This includes equations for the dissociation of carbonic acid, boric acid, phosphoric acid, silicic acid, water, hydrogen sulfide, and ammonia in seawater as a function of temperature (0 to 45°C) and salinity (0 to 45). The equations are of the form ln Ki = A + BT + C ln T, where A, B, and C are functions of salinity. Equations are also given for calculating the effect of temperature and salinity on the fugacity and pH of seawater using the carbonic acid constants of Roy et al. (1993a).
Automated capillary electrochromatography: reliability and reproducibility studies (1996)

The routine application of capillary electrochromatography (CEC) is demonstrated by incorporating 75 μm I.D. capillaries packed with 3 μm octadecylsilica (ODS) particles into a commercial CZE instrument. A mixture of several neutral compounds is separated into its components with an average efficiency up to 181 000 plates/m in less than 8 min. Hundreds of consecutive runs are performed over a period of weeks from which it is concluded that the reproducibility of the capacity factors is better than 2% and that CEC separations can be achieved in a reliable and routine manner.
Parameters affecting hybridization of nucleic acids blotted onto nylon or nitrocellulose membranes. (1990)

Nine different nylon and nitrocellulose membranes were compared utilizing four different methods of attaching the nucleic acid target. Nylon membranes repeatedly demonstrated increased sensitivity as compared to nitrocellulose membranes. Sensitivity could also be enhanced by mildly denaturing the target prior to attachment onto the membrane. This was achieved by either UV cross-linking or baking.
Terrain Roughness Measurement from Elevation Maps (1990)

The Autonomous Planetary Rover Project at Carnegie Mellon University is investigating the use of geometric information obtained from terrain elevation maps for mobile robot planning and control. We review how surface geometry has been characterized by surface roughness parameters, and why several of these parameters must be combined to form a vector roughness measurement. Next we propose a technique to localize and extract the intrinsic roughness from terrain elevation maps, and show how this can be used to characterize terrain.
Latest advances in high voltage, drift free, 4H-SiC PiN diodes (2004)

The 4H-SiC PiN diode is an attractive choice as a high power rectifier. 4H-SiC material technology has advanced to allow the realization of high power PiN diodes. In order to fabricate PiN diodes, nitrogen doped epilayers were grown on conducting 4HN SiC substrates. Stacking fault affect the device performance. Blocking capability, forward and reverse characteristics are explained. Long term forward voltage stability measurements were made on these devices by applying a constant forward current density.