gebhart/patrepeval huggingface dataset:
Identification of a New Epitope in uPAR as a Target for the Cancer Therapeutic Monoclonal Antibody ATN-658, a Structural Homolog of the uPAR Binding Integrin CD11b (αM) (2014)

The urokinase plasminogen activator receptor (uPAR) plays a role in tumor progression and has been proposed as a target for the treatment of cancer. We recently described the development of a novel humanized monoclonal antibody that targets uPAR and has anti-tumor activity in multiple xenograft animal tumor models. This antibody, ATN-658, does not inhibit ligand binding (i.e. uPA and vitronectin) to uPAR and its mechanism of action remains unclear. As a first step in understanding the anti-tumor activity of ATN-658, we set out to identify the epitope on uPAR to which ATN-658 binds. Guided by comparisons between primate and human uPAR, epitope mapping studies were performed using several orthogonal techniques. Systematic site directed and alanine scanning mutagenesis identified the region of aa 268-275 of uPAR as the epitope for ATN-658. No known function has previously been attributed to this epitope Structural insights into epitope recognition were obtained from structural studies of the Fab fragment of ATN-658 bound to uPAR. The structure shows that the ATN-658 binds to the DIII domain of uPAR, close to the C-terminus of the receptor, corroborating the epitope mapping results. Intriguingly, when bound to uPAR, the complementarity determining region (CDR) regions of ATN-658 closely mimic the binding regions of the integrin CD11b (αM), a previously identified uPAR ligand thought to be involved in leukocyte rolling, migration and complement fixation with no known role in tumor progression of solid tumors. These studies reveal a new functional epitope on uPAR involved in tumor progression and demonstrate a previously unrecognized strategy for the therapeutic targeting of uPAR.
P‐58: Resolution Evaluation of MPC Displays (2011)

Abstract In this paper, we evaluate the resolution characteristics of multi‐primary color (MPC) display systems. We have previously shown that the four primary color (4PC) displays increase effective resolution in the luminance domain to twice that of conventional RGB‐based displays with 4PC‐specialized sub‐pixel rendering we proposed. We improve this rendering method to allow apply five or more primary color systems and compare several rendering methods using the resolution characteristics of each display obtained by computational simulation.
Efficient Processing of Skyline Queries Using MapReduce (2017)

The skyline operator has attracted considerable attention recently due to its broad applications. However, computing a skyline is challenging today since we have to deal with big data. For data-intensive applications, the MapReduce framework has been widely used recently. In this paper, we propose the efficient parallel algorithm SKY-MR <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> for processing skyline queries using MapReduce. We first build a quadtree-based histogram for space partitioning by deciding whether to split each leaf node judiciously based on the benefit of splitting in terms of the estimated execution time. In addition, we apply the dominance power filtering method to effectively prune non-skyline points in advance. We next partition data based on the regions divided by the quadtree and compute candidate skyline points for each partition using MapReduce. Finally, we check whether each skyline candidate point is actually a skyline point in every partition using MapReduce. We also develop the workload balancing methods to make the estimated execution times of all available machines to be similar. We did experiments to compare SKY-MR <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> with the state-of-the-art algorithms using MapReduce and confirmed the effectiveness as well as the scalability of SKY-MR <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> .
Two-dimensional spectral shearing interferometry (2DSI) for ultrashort pulse characterization (2006)

We present a new pulse characterization method based on two-dimensional spectral shearing interferometry with zero delay. It features simple calibration, greatly relaxed spectrometer resolution, and is well suited for few-cycle laser pulses.
Novel Therapies in the Treatment of Multiple Myeloma (2009)

Multiple myeloma (MM) is a clonal B-cell malignancy characterized by aberrant expansion of plasma cells within bone marrow and extramedullary sites. In 2009, 20,580 new cases of MM and 10,580 deaths from the disease occurred in the United States. Treatment traditionally consists of systemic chemotherapy, with adjunctive use of radiation or surgery in selected cases associated with extramedullary disease. The therapeutic landscape in MM has changed markedly in the past decade with the introduction of the novel immunomodulatory agents thalidomide and lenalidomide, and the first-in-class proteasome inhibitor bortezomib. Although MM remains an incurable malignancy, new approaches to therapy incorporating these agents have produced significantly higher response rates and improved intervals of both progression-free and overall survival in the context of randomized, controlled trials. In aggregate, the use of novel therapies in MM has been associated with substantial improvements in patient outcome.
Spectral contrast optical coherence tomography angiography (Conference Presentation) (2019)

A new method is presented, called Spectral Contrast Optical Coherence Tomography, which utilizes the visible spectrum of blood instead of doppler or speckle contrast to locate blood vessels. This is seen as a significant improvement for OCT angiography, since sample motion no longer affects vessel contrast, repetitive scanning is not required, and non-flowing blood can be imaged. A visible Optical Coherence Tomography system from 500-700 nm was used and the differential spectral intensity of two short time Fourier Transform Kaiser sampling windows centered at 557 nm and 620 nm provided contrast revealing blood vessel location. This approach allows for single-scan endogenous contrast angiography all the way down to the capillary level. We demonstrate the method by imaging the vasculature of human oral mucosa and the lymphatics and vasculature of freshly sacrificed mouse tissue.
Blind Deblurring and Denoising of Images Corrupted by Unidirectional Object Motion Blur and Sensor Noise (2016)

Low light photography suffers from blur and noise. In this paper, we propose a novel method to recover a dense estimate of spatially varying blur kernel as well as a denoised and deblurred image from a single noisy and object motion blurred image. A proposed method takes the advantage of the sparse representation of double discrete wavelet transform-a generative model of image blur that simplifies the wavelet analysis of a blurred image-and the Bayesian perspective of modeling the prior distribution of the latent sharp wavelet coefficient and the likelihood function that makes the noise handling explicit. We demonstrate the effectiveness of the proposed method on moderate noise and severely blurred images using simulated and real camera data.
Truncated Nucleosides as A<sub>3</sub> Adenosine Receptor Ligands: Combined 2-Arylethynyl and Bicyclohexane Substitutions (2012)

C2-Arylethynyladenosine-5'-N-methyluronamides containing a bicyclo[3.1.0]hexane ((N)-methanocarba) ring are selective A(3) adenosine receptor (AR) agonists. Similar 4'-truncated C2-arylethynyl-(N)-methanocarba nucleosides containing alkyl or alkylaryl groups at the N(6) position were low-efficacy agonists or antagonists of the human A(3)AR with high selectivity. Higher hA(3)AR affinity was associated with N(6)-methyl and ethyl (K(i) 3-6 nM), than with N(6)-arylalkyl groups. However, combined C2-phenylethynyl and N(6)-2-phenylethyl substitutions in selective antagonist 15 provided a K(i) of 20 nM. Differences between 4'-truncated and nontruncated analogues of extended C2-p-biphenylethynyl substitution suggested a ligand reorientation in AR binding, dominated by bulky N(6) groups in analogues lacking a stabilizing 5'-uronamide moiety. Thus, 4'-truncation of C2-arylethynyl-(N)-methanocarba adenosine derivatives is compatible with general preservation of A(3)AR selectivity, especially with small N(6) groups, but reduced efficacy in A(3)AR-induced inhibition of adenylate cyclase.
Model-based delay-distortion optimization for video streaming using packet interleaving (2003)

Bursty channel losses have been shown generally to produce larger total mean-square error distortion in streaming video than an equivalent number of isolated losses. The paper proposes a simple packet interleaving scheme to combat the effect of bursty losses by dispersing them. The optimal interleaver for minimizing the expected total distortion of the decoded video, subject to a delay constraint, is determined using a model that accurately predicts the expected distortion for different packet loss patterns. Compared to other forms of error-resilience, packet interleaving has the advantages of (1) simplicity and (2) not requiring any extra bitrate. For a simple burst loss channel, where each loss event has 100 ms duration, packet interleaving can provide between 0.24 dB and 0.87 dB gain over conventional non-interleaved streaming, at the expense of a delay increase of 400 ms.
Analysis of Monoclonal Antibody Sequence and Post-translational Modifications by Time-controlled Proteolysis and Tandem Mass Spectrometry (2015)

Methodology for sequence analysis of ∼150 kDa monoclonal antibodies (mAb), including location of post-translational modifications and disulfide bonds, is described. Limited digestion of fully denatured (reduced and alkylated) antibody was accomplished in seconds by flowing a sample in 8murea at a controlled flow rate through a micro column reactor containing immobilized aspergillopepsin I. The resulting product mixture containing 3-9 kDa peptides was then fractionated by capillary column liquid chromatography and analyzed on-line by both electron-transfer dissociation and collisionally activated dissociation mass spectrometry (MS). This approach enabled identification of peptides that cover the complete sequence of a murine mAb. With customized tandem MS and ProSightPC Biomarker search, we verified 95% amino acid residues of this mAb and identified numerous post-translational modifications (oxidized methionine, pyroglutamylation, deamidation of Asn, and several forms ofN-linked glycosylation). For disulfide bond location, native mAb is subjected to the same procedure but with longer digestion times controlled by sample flow rate through the micro column reactor. Release of disulfide containing peptides from accessible regions of the folded antibody occurs with short digestion times. Release of those in the interior of the molecule requires longer digestion times. The identity of two peptides connected by a disulfide bond is determined using a combination of electron-transfer dissociation and ion-ion proton transfer chemistry to read the two N-terminal and two C-terminal sequences of the connected peptides.
Experimental characterization of a biomimetic differential microphone diaphragm. (2008)

The identification of mechanical properties for a microphone diaphragm based on the coupled ears of the fly Ormia ochracea and fabricated out of polycrystalline silicon is described. An acoustic test setup using a laser vibrometer has been developed that facilitates the characterization of the diaphragm on a bare die level. A major problem with using a laser vibrometer for acoustic measurement of microstructures is the close working distance between the sensor head and test device, resulting in measurements corrupted by reflections. Time select windowing procedures are often used to obtain anechoic response estimates from measurements taken in reverberant environments, but are not effective for characterization at lower frequencies or testing of lightly damped structures where the time window length needs to be more than the reverberation time. It is shown that the reflections from the measured response of the biologically inspired diaphragm can be reduced through comparison methods for the calibration of the sound field using a closely placed probe microphone and a commercially available pressure differential microphone. Equivalent mechanical parameters for the diaphragm are estimated with a least squares identification procedure. Characterization results for a diaphragm with two different back volume configurations are compared. [Work supported by NIH.]
An investigation of the potential of rapid prototyping technology for image‐guided surgery (2006)

Image-guided surgery can be broken down into two broad categories: frame-based guidance and frameless guidance. In order to reduce both the invasive nature of stereotactic guidance and the cost in equipment and time, we have developed a new guidance technique based on rapid prototyping (RP) technology. This new system first builds a computer model of the patient anatomy and then fabricates a physical reference frame that provides a precise and unique fit to the patient anatomy. This frame incorporates a means of guiding the surgeon along a preplanned surgical trajectory. This process involves (1) obtaining a high-resolution CT or MR scan, (2) building a computer model of the region of interest, (3) developing a surgical plan and physical guide, (4) designing a frame with a unique fit to the patient's anatomy with a physical linkage to the surgical guide, and (5) fabricating the frame using an RP unit. Software was developed to support these processes. To test the accuracy of this process, we first scanned and reproduced a plastic phantom fabricated to validate the system's ability to build an accurate virtual model. A target on the phantom was then identified, a surgical approach planned, a surgical guide designed, and the accuracy and precision of guiding a probe to that target were determined. Steps 1 through 5 were also evaluated using a head phantom. The results show that the RP technology can replicate an object from CT scans with submillimeter resolution. The fabricated reference frames, when positioned on the surface of the phantom and used to guide a surgical probe, can position the probe tip with an accuracy of 1.7 mm at the probe tip. These results demonstrate that the RP technology can be used for the fabrication of customized positioning frames for use in image-guided surgery.
Enhanced generation of entangled‐photon pairs from a cavity system (2006)

Abstract We have theoretically studied efficiency of entangled‐photon generation from a quantum well embedded in a microcavity, and have found considerable enhancement of the efficiency. We have determined an optimal condition for achieving the strong enhancement, which is qualitatively understood from a characteristic feature of the cavity QED. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Recent Trends in Leather Making: Processes, Problems, and Pathways (2004)

Leather processing has emerged as an important economic activity in several developing countries. Awareness of environmental problems has increased considerably and during recent years protecting environment has become a global issue. Currently the leather processing industry is going through a phase change due to global environmental regulations. The article summarizes the current leather processing methods with their rationale and environmental problems. It has been revealed that pretanning and tanning processes contribute 80–90% of the total pollution load (BOD, COD, TS, TDS, Cr, S2−, sludge, etc.). Further, toxic gases like ammonia and hydrogen sulfide are also emitted. Volatile organic compounds, heavy metals, and carcinogenic arylamines from posttanning and finishing operations are also creating severe concern. Apart from this, a great deal of solid wastes like lime sludge from tannery and chrome sludge from effluent treatment plants are being generated. Advanced processing techniques as well as effluent treatment strategies for combating environmental and human health risks are reviewed in detail. The leather processing industry in various countries, however, is facing a serious challenge from the public and government. This is in spite of the implementation of several advanced processing techniques and treatment systems. Hence, there is a need to revamp leather processing methods anew for the sustainability of leather industry. Some of the novel concepts in leather processing are briefly mentioned and discussed.
UQJG (2021)

An SQL assertion is a declarative statement about data that must always be satisfied in any database state. Assertions were introduced in the SQL92 standard but no commercial DBMS has implemented them so far. Some approaches have been proposed to incrementally determine whether a transaction violates an SQL assertion, but they assume that transactions are applied in isolation, hence not considering the problem of concurrent transaction executions that collaborate to violate an assertion. This is the main stopper for its commercial implementation. To handle this problem, we have developed a technique for efficiently serializing concurrent transactions that might interact to violate an SQL assertion.
Plastic optical fibre with improved transmittance (1979)

A low-loss plastic optical fibre has been manufactured employing polystyrene as core material. The minimum transmission loss was 140 dB/km at 670 nm, and intrinsic material loss of polystyrene was estimated to be 105 dB/km.
Lunar Brightness Temperature Model Based on the Microwave Radiometer Data of Chang’e-2 (2017)

The brightness temperature (TB) data of the Moon acquired by the microwave radiometer (MRM) on-board the Chinese Chang'e-2 (CE-2) lunar probe are valuable and comprehensive data, which can be helpful in studying the physical properties of the lunar regolith, such as thickness, physical temperature, and dielectric constant. To construct the accurate and high-resolution lunar TB model with the TB data obtained by the MRM on-board CE-2, 2401 tracks of the original TB data are quantized by using the hour angle processing, and the hierarchical MK splines function (HMKSF) method is presented, which uses a hierarchy of coarse-to-fine control lattices to generate a sequence of TB model functions. The TB model constructor is the sum of the TB model functions derived at each level of the hierarchy. In addition, the lunar TB models with a resolution of 0.5°×0.5° in all four frequency channels are constructed for both the daytime and the nighttime. The obtained models show rich information, e.g., the global distribution of TB over the lunar surface, the effect of frequency on the TB model.
Molecular cloning and functional expression of the human sodium channel β<sub>1B</sub> subunit, a novel splicing variant of the β<sub>1</sub> subunit (2003)

The voltage gated sodium channel comprises a pore-forming alpha subunit and regulatory beta subunits. We report here the identification and characterization of a novel splicing variant of the human beta1 subunit, termed beta1B. The 807 bp open reading frame of the human beta1Beta subunit encodes a 268 residue protein with a calculated molecular mass of 30.4 kDa. The novel human beta1B subunit shares an identical N-terminal half (residues 1-149) with the human beta1 subunit, but contains a novel C-terminal half (residues 150-268) of less than 17% sequence identity with the human beta1 subunit. The C-terminal region of the human beta1B is also significantly different from that of the rat beta1A subunit, sharing less than 33% sequence identity. Tissue distribution studies reveal that the human beta1Beta subunit is expressed predominantly in human brain, spinal cord, dorsal root ganglion and skeletal muscle. Functional studies in oocytes demonstrate that the human beta1B subunit increases the ionic current when coexpressed with the tetrodotoxin sensitive channel, NaV1.2, without significantly changing voltage dependent kinetics and steady-state properties, thus distinguishing it from the human beta1 and rat beta1A subunits.
Transplantation of Human Embryonic Stem Cell-Derived Oligodendrocyte Progenitors into Rat Spinal Cord Injuries Does not Cause Harm (2006)

Demyelination contributes to loss of function following spinal cord injury. We have shown previously that transplantation of human embryonic stem cell-derived oligodendrocyte progenitors into adult rat 200 kD contusive spinal cord injury sites enhances remyelination and promotes recovery of motor function. Previous studies using oligodendrocyte lineage cells have noted a correlation between the presence of demyelinating pathology and the survival and migration rate of the transplanted cells. The present study compared the survival and migration of human embryonic stem cell-derived oligodendrocyte progenitors injected 7 days after a 200 or 50 kD contusive spinal cord injury, as well as the locomotor outcome of transplantation. Our findings indicate that a 200 kD spinal cord injury induces extensive demyelination, whereas a 50 kD spinal cord injury induces no detectable demyelination. Cells transplanted into the 200 kD injury group survived, migrated, and resulted in robust remyelination, replicating our previous studies. In contrast, cells transplanted into the 50 kD injury group survived, exhibited limited migration, and failed to induce remyelination as demyelination in this injury group was absent. Animals that received a 50 kD injury displayed only a transient decline in locomotor function as a result of the injury. Importantly, human embryonic stem cell-derived oligodendrocyte progenitor transplants into the 50 kD injury group did not cause a further decline in locomotion. Our studies highlight the importance of a demyelinating pathology as a prerequisite for the function of transplanted myelinogenic cells. In addition, our results indicate that transplantation of human embryonic stem cell-derived oligodendrocyte progenitor cells into the injured spinal cord is not associated with a decline in locomotor function.
High-power all-fiber passively Q-switched laser using a doped fiber as a saturable absorber: numerical simulations (2011)

We report a design for a power-scalable all-fiber passively Q-switched laser that uses a large mode area Yb-doped fiber as a gain medium adiabatically tapered to an unpumped single-mode Yb-doped fiber, which serves as a saturable absorber. Through the use of a comprehensive numerical simulator, we demonstrate a passively Q-switched 1030 nm pulsed laser with 14 ns pulse duration and 0.5 mJ pulse energy operating at 200 kHz repetition rate. The proposed configuration has a potential for orders of magnitude of improvement in both the pulse energies and durations compared to the previously reported result. The key mechanism for this improvement relates to the ratio of the core areas between the pumped inverted large mode area gain fiber and the unpumped doped single-mode fiber.
Adaptive, efficient, parallel execution of parallel programs (2014)

Future multicore processors will be heterogeneous, be increasingly less reliable, and operate in dynamically changing operating conditions. Such environments will result in a constantly varying pool of hardware resources which can greatly complicate the task of efficiently exposing a program's parallelism onto these resources. Coupled with this uncertainty is the diverse set of efficiency metrics that users may desire. This paper proposes Varuna, a system that dynamically, continuously, rapidly and transparently adapts a program's parallelism to best match the instantaneous capabilities of the hardware resources while satisfying different efficiency metrics. Varuna is applicable to both multithreaded and task-based programs and can be seamlessly inserted between the program and the operating system without needing to change the source code of either.