gebhart/patrepeval huggingface dataset:
<i>Chlamydia</i>Vaccine: Progress and Challenges (2014)

The accumulated body of evidence has provided important guiding principles for Chlamydia vaccine development. They are: (i) whole-organism vaccine preparations may be efficacious, as animal studies and the trachoma trials have suggested; (ii) a multisub-unit component vaccine should likely include combinations of serovar/biovar-specific protective antigens; and (iii) the prevention of pathological sequelae and the reduction of the incidence of infection should be the driving forces in vaccine development. Live chlamydial infections induce the best protective immunity in both humans and mice when compared to immunization with either dead organisms or component antigens. In a gel electrophoresis and immunoblotting approach, chlamydial antigens derived from purified organisms or Chlamydia-infected cells are subjected to two-dimensional gel electrophoresis (2D-GE) and then probed with sera from Chlamydia-seropositive humans. Chlamydial proteins are labeled during growth with radioactive amino acids, and individual antigens from lysed chlamydial organisms or Chlamydia-infected cells that are recognized by patient sera are first immunoprecipitated and then resolved using 2D-GE. A genome expression library screen for immunogenicity followed by DNA immunization has been used to identify four housekeeping genes that induced robust protective immunity against Chlamydia abortus lung infection in mice. Collectively, contemporary technologies have enabled considerable progress in Chlamydia vaccine development in the recent past, but several issues remain to be addressed before advancing the identified antigens into human clinical trials.
HA22 (R490A) is a recombinant immunotoxin with increased anti-tumor activity and therapeutic index (2004)

Proc Amer Assoc Cancer Res, Volume 45, 2004

622 

RFB4 (dsFv)-PE38 (BL22) is a recombinant immunotoxin containing an anti-CD22 variable domain (Fv) fused to a 38-kDa form of Pseudomonas exotoxin A (PE). BL22 has been evaluated in a Phase I clinical trial at the National Cancer Institute in patients with hematological malignancies. BL22 is able to induce a high complete remission rate in patients with purine analogue-resistant HCL. This finding establishes the concept that immunotoxins can produce clinical benefit to patients with advanced malignancies. Our laboratory recently made a mutant immunotoxin, HA22, with improved affinity and cytotoxic activity using a combination of phage display and hot spot mutagenesis techniques. HA22 is derived from BL22 and has three mutations in the heavy chain CDR3 that result in its increased activity. Previous studies using native PE showed that destruction of a protease sensitive site in domain 3 by deleting arginine 490 increased the half-life of PE in the circulation of mice. Several factors are thought to control the lifetime of proteins in the circulation and inactivation or degradation of proteins by proteolysis could be one of them. We have now extended these studies to immunotoxins. For this purpose we have chosen HA22 and made a new mutant in which arginine 490 is changed to alanine. We chose to mutate R490 to A rather than delete it to diminish possible changes in protein structure. We found that HA22 (R490A) is ∼2-fold more active than HA22 on several CD22-positive cell lines. Surprisingly, the plasma half-life of HA22 (490A) was not increased. It was 18.8 min compared to a half -life of 21.9 min for HA22. When injected into mice HA22 and HA22 (R490A) had very similar toxicities with an LD50 of about 1.3 mg/kg for each. However, HA22 (R490A) had a more potent anti-tumor activity than HA22 against CA46 tumors in mice reflecting its increased cytotoxic activity in cell culture. These studies show that protein engineering can be used to increase the efficacy of recombinant immunotoxins. Furthermore because HA22 (490A) has increased anti-tumor activity and not increased animal toxicity, immunotoxins with this mutation are better candidates for clinical development.
Targeting Recruitment of Disruptor of Telomeric Silencing 1-like (DOT1L) (2013)

The MLL fusion proteins, AF9 and ENL, activate target genes in part via recruitment of the histone methyltransferase DOT1L (disruptor of telomeric silencing 1-like). Here we report biochemical, biophysical, and functional characterization of the interaction between DOT1L and MLL fusion proteins, AF9/ENL. The AF9/ENL-binding site in human DOT1L was mapped, and the interaction site was identified to a 10-amino acid region (DOT1L865-874). This region is highly conserved in DOT1L from a variety of species. Alanine scanning mutagenesis analysis shows that four conserved hydrophobic residues from the identified binding motif are essential for the interactions with AF9/ENL. Binding studies demonstrate that the entire intact C-terminal domain of AF9/ENL is required for optimal interaction with DOT1L. Functional studies show that the mapped AF9/ENL interacting site is essential for immortalization by MLL-AF9, indicating that DOT1L interaction with MLL-AF9 and its recruitment are required for transformation by MLL-AF9. These results strongly suggest that disruption of interaction between DOT1L and AF9/ENL is a promising therapeutic strategy with potentially fewer adverse effects than enzymatic inhibition of DOT1L for MLL fusion protein-associated leukemia.
Study of a new route by which to make fully cured thermoplastic elastomers with plastics and ultrafine powdered rubber (2003)

Abstract A series of fully cured thermoplastic elastomers (TPEs) have been developed by mixing plastics and fully cured, ultra‐fine powdered rubbers (UFPRs). The fully cured UFPRs were prepared by the irradiation of rubber latexes and drying of the irradiated rubber latexes. The average particle size of the UFPRs ranged from 50 to 500nm. The influences of the dose rate, absorbed dose and content of cross‐linking agent on the cross‐linking of rubber latexes were studied. It was found that a new type of TPEs with excellent properties can be easily made by blending UFPRs with plastics.
Study on volume production of uniform wafer-level micro glass cavities by a chemical foaming process (CFP) (2013)

In this paper, an improved chemical foaming process (CFP) for wafer-level glass cavities will be demonstrated for volume production in a clean room. First of all, suitable foaming agents transferring techniques are investigated to avoid powder pollution to the chips in a clean room. In addition, the precise controlling of the sizes of the glass cavities is studied theoretically and experimentally. The shapes, morphology and sizes of the glass cavities formed by the improved CFP are characterized by AFM and digital 3D microscopy. A theoretical model for precisely predicting the final shapes and sizes are established. Moreover, glass cavities with uniform structures and precisely controlled sizes at a 4-inch wafer are prepared successfully. The improved CFP will provide a novel volume-production technique for micro-machining of glass, which has many applications in MEMS and MOEMS.
Preliminary field results of an ultra-wideband (10-620 MHz) stepped-frequency ground penetrating radar (2002)

The authors present the results from preliminary field trials using a newly developed ultra-wideband, stepped-frequency ground penetrating radar system. This system has been developed to improve the maximum penetration depth capability in ground penetrating radar (GPR) applications without degradation of resolving power. To achieve this, they have based their system on the stepped-frequency radar technique operating across the 10-620 MHz frequency band. The stepped-frequency technique offers substantial benefits over existing time-domain (impulse) GPR systems. The main advantage of the technique is that it is relatively easy with current technologies to efficiently sample ultra-wideband signals with low speed analog-to-digital converters. Also, due to transmission of long duration waveforms, a high average transmitted power is much easier to obtain than for short-pulse and impulse waveforms. The stepped-frequency technique offers other potential advantages for GPR such as a variable dwell time on each frequency, and more flexibility in signal processing such as the ability to correct for system errors. Their system can operate over multi-octave bands within the 10-620 MHz frequency range. The radar has the capability to employ a short range gate (/spl sim/10 ns duration) at each frequency step which can suppress unwanted strong signals (e.g. direct wave between antennas) relative to weak reflections from deep targets. Field trials of the radar have demonstrated the effectiveness of gating and of the system as a whole.
Superposition of Broadcast and Unicast in Wireless Cellular Systems (2008)

Practical application of superposition coding in multiplexing broadcast and unicast for OFDM-based mobile cellular systems is discussed. Superposition coding, whose gain is increased as the superposed signals have larger difference in signal-to interference-plus-noise ratio, is well matched for unicast and broadcast in a single-frequency network configuration. Combined with interference cancellation technique, broadcast signals from multiple base stations can be cancelled in a single step, minimizing the interference from broadcast to unicast. Issues related with scheduling and strategy for time, frequency and power resource sharing between broadcast and unicast are discussed. The application of superposed broadcast and unicast is then extended to MIMO systems. Simulation results in a practical mobile cellular environment are also provided, showing significant throughput gain of superposed broadcast and unicast.
A Marine Natural Product Inhibitor of Kinesin Motors (1998)

Members of the kinesin superfamily of motor proteins are essential for mitotic and meiotic spindle organization, chromosome segregation, organelle and vesicle transport, and many other processes that require microtubule-based transport. A compound, adociasulfate-2, was isolated from a marine sponge, Haliclona (also known as Adocia) species, that inhibited kinesin activity by targeting its motor domain and mimicking the activity of the microtubule. Thus, the kinesin-microtubule interaction site could be a useful target for small molecule modulators, and adociasulfate-2 should serve as an archetype for specific inhibitors of kinesin functions.
Effective collection metasearch in a hierarchical environment (2002)

We compare standard global IR searching with user-centric localized techniques to address the database selection problem. We conduct a series of experiments to compare the retrieval effectiveness of three separate search modes applied to a hierarchically structured data environment of textual database representations. The data environment is represented as a tree-like directory containing over 15,000 unique databases and over 100,000 total leaf nodes. Our search modes consist of varying degrees of browse and search, from a global search at the root node to a refined search at a sub-node using dynamically-calculated inverse document frequencies (idfs) to score candidate databases for probable relevance. Our findings indicate that a browse and search approach that relies upon localized searching from sub-nodes is capable of producing the most effective results.
Rational Design of In Situ Monolithic Imprinted Polymer Membranes for the Potentiometric Sensing of Diethyl Chlorophosphate – a Chemical Warfare Agent Simulant (2009)

Abstract Molecularly imprinted polymer membrane was prepared by semicovalent imprinting strategy wherein i) the template diethyl chlorophosphate (DCP), (a simulant of organophosphorous nerve agents), is covalently linked to the reactive functional monomer vinyl aniline (VA) during imprinting step followed by noncovalent rebinding and ii) in situ polymerization via single pot synthesis in presence of additional functional monomer, 2‐hydroxyethyl methacrylate (HEMA) and crosslinking monomer, ethylene glycol dimethacrylate (EGDMA) after addition of 2‐nitrophenyl octyl ether (NPOE) and 2,2′‐azobisisobutyronitrile (AIBN) as plasticizer and initiator respectively. The resulting membrane is integrated with a potentiometric transducer while designing a DCP sensor. The fabricated sensor responds over a wider concentration range of 10 −6 –10 −2 M with a lower detection limit of 10 −6 M (0.17 ppm). In addition, in situ monolithic membrane based sensor was designed by adopting noncovalent imprinting strategy also. A detailed comparison is made between semicovalent and noncovalent in situ membrane based sensors on the prime sensor performance criteria such as sensitivity, selectivity, working range, response time, reusability and reversibility. Again, the relative merits and demerits of semicovalent vis‐à‐vis noncovalent strategy based in situ monolithic membrane sensors were also highlighted. The probable molecular recognition mechanism is also discussed.
Visually estimating workpiece pose in a robot hand using the feature points method (1978)

An automatic method of visually estimating the pose of a workpiece in a robot hand has been developed. This method is not subject to the constraint that the workpiece have one of a finite number of states in the robot hand. Workpiece pose is estimated using the three dimensional locations of workpiece feature points. Workpiece features can be located in space by image feature tracking during a known arm motion and by using trigonometric relations. The correspondence to features on a model of the workpiece can be established by using transformations which verify interfeature distances and angles. The ability to estimate workpiece pose is necessary to enable robots to accomplish many industrial tasks.
Three‐dimensional pixel configurations for optical outcoupling of OLED displays—optical simulation (2019)

Abstract Because of considerations on image quality and fabrication/integration compatibility, current active‐matrix OLED displays (AMOLEDs) hardly adopt any effective light outcoupling techniques/structures, and it remains an unsolved critical technical issue. Recently, through optical simulation, we proposed a three‐dimensional (3D) pixel configuration as a potential and promising way to boost light outcoupling of OLED display pixels. By extending the bottom reflective electrode to bank slope of the pixel definition layer (PDL) and selectively filling the bank opening (concave area) with high‐index filler to form the optically reflective concave structure, it is possible to give several‐fold light extraction enhancement. In this paper, we further extend the simulation work by evaluating effects of more realistic graded bank slopes vs straight bank slope, less challenging nonpatterned (blanket) high‐index filler vs patterned filler, and real OLED layer stacks and properties. The optical simulation clearly reveals that light extraction enhancement can be mostly kept with more realistic graded bank profiles and even less ideal (but also less challenging) nonpatterned filler can provide substantial extraction enhancement. The graded bank structure also provides beneficial effects on viewing characteristics.
Adaptive Multi-Resolution Myocardial Motion Analysis of B-Mode Echocardiography Images using Combined Local/Global Optical Flow (2008)

Since myocardial motion is directly related to cardiac vascular supply, it can be helpful in diagnosing the heart abnormalities. The most comprehensive and available imaging study of the cardiac function is echocardiography and therefore it is important to make the echocardiography motion more quantitative. To overcome the sensitivity to shear, rotation and wide range of motion, we propose an adaptive hybrid method based on combined local global (CLG) optical flow in combination with adaptive multi-resolution spatiotemporal spline moments. In adaptive multi-resolution strategy the coarse moments are applied on the coarse moving regions and the fine moments are applied on the fine moving areas. The fine and coarse moving regions are obtained using motion segmentation. The evaluation was performed on simulated, synthetic, real data. The proposed method achieved rotational error of 2.8 degrees per frame and amplitude error of 2.2 percent per frame. These results demonstrate a better performance with respect to other B-Mode echocardiography motion estimation techniques such as Lucas-Kanade, Horn-Shunck and spatiotemporal affine technique.
Structured Variational Distributions in VIBES (2003)

Variational methods are becoming increasingly popular for the approximate solution of complex probabilistic models in machine learning, computer vision, information retrieval and many other fields. Unfortunately, for every new application it is necessary first to derive the specific forms of the variational update equations for the particular probabilistic model being used, and then to implement these equations in applicationspecific software. Each of these steps is both time consuming and error prone. We have therefore recently developed a general purpose inference engine called VIBES [1] (‘Variational Inference for Bayesian Networks’) which allows a wide variety of probabilistic models to be implemented and solved variationally without recourse to coding. New models are specified as a directed acyclic graph using an interface analogous to a drawing package, and VIBES then automatically generates and solves the variational equations. The original version of VIBES assumed a fully factorized variational posterior distribution. In this paper we present an extension of VIBES in which the variational posterior distribution corresponds to a sub-graph of the full probabilistic model. Such structured distributions can produce much closer approximations to the true posterior distribution. We illustrate this approach using an example based on Bayesian hidden Markov models. 1
Join algorithms on GPUs: A revisit after seven years (2015)

Implementing database operations on parallel platforms has gain a lot of momentum in the past decade. A number of studies have shown the potential of using GPUs to speed up database operations. In this paper, we present empirical evaluations of a state-of-the-art work published in SIGMOD'08 on GPU-based join processing. In particular, this work presents four major join algorithms and a number of join-related primitives on GPUs. Since 2008, the compute capabilities of GPUs have increased following a pace faster than that of the multi-core CPUs. We run a comprehensive set of experiments to study how join operations can benefit from such rapid expansion of GPU capabilities. Our experiments on today's mainstream GPU and CPU hardware show that the GPU join program achieves up to 20X speedup in end-to-end running time over a highly-optimized CPU version. This is significantly better than the 7X performance gap reported in the original paper. We also present improved GPU programs that take advantage of new GPU hardware/software features such as read-only data cache, large L2 cache, and shuffle instructions. By applying such optimizations, extra performance improvement of 30-52% is observed in various components of the GPU program. Finally, we evaluate the same program from a few other perspectives including energy efficiency, floatingpoint performance, and program development considerations to further reveal the advantages and limitations of using GPUs for database operations. In summary, we find that today's GPUs are significantly faster in floating point operations, can process more on-board data, and achieve higher energy efficiency than modern CPUs.
A male genital tract‐specific carbohydrate epitope on human CD52: Implications for immunocontraception (2002)

The identification of unique sperm surface epitopes that are not expressed or exposed in the female reproductive tract is a key element in the development of antibody-based contraceptives. Western blotting and immunohistochemistry were performed to define the tissue distribution of the S19 epitope, which has been proposed as a target for immunocontraception. S19 is an IgG1 murine monoclonal antibody (mAb) directed to an N-linked carbohydrate epitope on a 15-25 kDa glycoprotein, sperm agglutination antigen-1 (SAGA-1), containing a peptide core identical to that of the lymphocytic surface protein CD52. In this study, the S19 epitope was shown to be absent from human lymphocytes, demonstrating a distinction between this epitope and the CAMPATH epitope that is recognized by an antibody against the terminal tripeptide and GPI-anchor of CD52. Further tissue specificity analysis identified the S19 epitope in the epithelium of the human epididymis and vas deferens, as well as on both epididymal and ejaculated spermatozoa. In contrast, the S19 epitope was absent in the five human female reproductive tract and 18 other somatic tissues tested. These results support the use of the S19 epitope as a contraceptive immunogen and the suitability of the S19 mAb as an intravaginal contraceptive. To test the agglutinating activity of the S19 mAb in a formulation designed for vaginal use, S19 mAb were bound to the surface of Novasomes, a multilamellar liposome delivery vehicle. S19-Novasome formulations agglutinated human spermatozoa and were as effective as unbound S19 mAb, demonstrating the feasibility of spermistatic contraceptives targeted to the male reproductive tract specific carbohydrate epitope.
OFDM for next generation optical communication systems (2008)

A number of different forms of Orthogonal Frequency Division Multiplexing (OFDM) have recently been developed for application in a range of optical systems. In this presentation the key differences between these are explained. Analytical techniques developed for conventional optical modulation formats cannot always be applied successfully to optical OFDM. For example, in calculating the effect of nonlinearities in OFDM, the overall shrinkage or rotation of the constellation may be a significant effect. Depending on the properties of phase noise, the distortion caused may be easily corrected in the digital section of the OFDM receiver.
Optimal successive group decoder for the slow-fading multiple access channel (2006)

We consider a slow-fading narrowband multiple access channel (MAC) in which multiple users, each equipped with multiple transmit antennas, communicate to a receiver equipped with multiple receive antennas. The users are unaware of the channel state information (CSI) whereas the receiver knows it perfectly and employs the successive group decoder (SGD). We obtain achievable outage probabilities for the case where an outage must be declared simultaneously for all users (common outage) as well as the case where outages can be declared individually for each user (individual outage). We then derive the optimum successive group decoder (OSGD) which simultaneously minimizes the common outage probability and the individual outage probability of each user, over all successive group decoders of permissible decoding complexity. For each channel realization, the OSGD is also shown to maximize the minimum of the per-user error exponents of all users not in outage. An adaptive SGD is derived which retains the outage optimality of the OSGD but also minimizes the expected decoding complexity. Asymptotically tight affine approximations are then obtained for the weighted sum common and individual outage capacities and the symmetric outage capacities. Simulation results with practical LDPC outer codes show that the OSGD results in greatly improved performance at low decoding complexities.
Notch Signaling in Leukemia (2007)

Recent discoveries indicate that gain-of-function mutations in the Notch1 receptor are very common in human T cell acute lymphoblastic leukemia/lymphoma. This review discusses what these mutations have taught us about normal and pathophysiologic Notch1 signaling, and how these insights may lead to new targeted therapies for patients with this aggressive form of cancer.