gebhart/patrepeval huggingface dataset:
Active Site Protection of Proteolytic Enzymes by Poly(ethylene glycol) Surface Modification (1993)

A method to prevent the loss of enzymatic activity of proteolytic enzymes toward high molecular weight substrates that occurs upon derivatiza tion with monomethoxypoly(ethylene glycol) (mPEG) is described. It is based on the heterogenous phase enzyme modification after the enzyme is bound to an active site inhibitor immobilized on an insoluble resin. This procedure pro tects the active site and the surrounding area from mPEG linkage. Trypsin modified by mPEG in a heterogeneous phase, using benzamidine bound to Sepharose maintained a high degree of its ability to hydrolize large molecular weight substrates, such as bovine serum albumin or casein, compared to the mPEG derivatives obtained without any protection or with free benzamidine in solution.
Anisotropic Magnetism in Field-Structured Composites (1999)

Magnetic field-structured-composites (FSCs) are made by structuring magnetic particle suspensions in uniaxial or biaxial (e.g. rotating) magnetic fields, while polymerizing the suspending resin. A uniaxial field produces chain-like particle structures, and a biaxial field produces sheet-like particle structures. In either case, these anisotropic structures affect the measured magnetic hysteresis loops, with the magnetic remanence and susceptibility increased significantly along the axis of the structuring field, and decreased slightly orthogonal to the structuring field, relative to the unstructured particle composite. The coercivity is essentially unaffected by structuring. We present data for FSCs of magnetically soft particles, and demonstrate that the altered magnetism can be accounted for by considering the large local fields that occur in FSCs. FSCS of magnetically hard particles show unexpectedly large anisotropies in the remanence, and this is due to the local field effects in combination with the large crystalline anisotropy of this material.
A device to assess the severity of peripheral edema (2007)

Peripheral edema causes swelling in extremities that often indicates the presence of a serious medical condition. Currently, clinicians visually observe fluctuations in edema symptoms to assess edema severity. The subjective nature of these assessments hinders clinicians from accurately communicating a patient's condition to other medical professionals and leads to inconsistencies in medical treatment. To eliminate subjectivity in edema measurement, we developed a handheld device that uses a manually depressed probe to objectively measure the depth of pitting from edema and the force required to depress the tissue, which correlate directly to edema severity. Clinicians can collect these values from the device over time to monitor a patient's progress and improve the accuracy of medical diagnosis.
Enzymes for the Homeland Defense: Optimizing Phosphotriesterase for the Hydrolysis of Organophosphate Nerve Agents (2012)

Phosphotriesterase (PTE) from soil bacteria is known for its ability to catalyze the detoxification of organophosphate pesticides and chemical warfare agents. Most of the organophosphate chemical warfare agents are a mixture of two stereoisomers at the phosphorus center, and the S(P)-enantiomers are significantly more toxic than the R(P)-enantiomers. In previous investigations, PTE variants were created through the manipulation of the substrate binding pockets and these mutants were shown to have greater catalytic activities for the detoxification of the more toxic S(P)-enantiomers of nerve agent analogues for GB, GD, GF, VX, and VR than the less toxic R(P)-enantiomers. In this investigation, alternate strategies were employed to discover additional PTE variants with significant improvements in catalytic activities relative to that of the wild-type enzyme. Screening and selection techniques were utilized to isolate PTE variants from randomized libraries and site specific modifications. The catalytic activities of these newly identified PTE variants toward the S(P)-enantiomers of chromophoric analogues of GB, GD, GF, VX, and VR have been improved up to 15000-fold relative to that of the wild-type enzyme. The X-ray crystal structures of the best PTE variants were determined. Characterization of these mutants with the authentic G-type nerve agents has confirmed the expected improvements in catalytic activity against the most toxic enantiomers of GB, GD, and GF. The values of k(cat)/K(m) for the H257Y/L303T (YT) mutant for the hydrolysis of GB, GD, and GF were determined to be 2 × 10(6), 5 × 10(5), and 8 × 10(5) M(-1) s(-1), respectively. The YT mutant is the most proficient enzyme reported thus far for the detoxification of G-type nerve agents. These results support a combinatorial strategy of rational design and directed evolution as a powerful tool for the discovery of more efficient enzymes for the detoxification of organophosphate nerve agents.
1.55-&#x03BC;m polarization-insensitive quantum dot semiconductor optical amplifier (2008)

A 1.55-mum polarization-insensitive quantum dot semiconductor optical amplifier was realized for the first time by applying columnar dots surrounded by tensile-strained side-barriers. The polarization dependent gain was only 0.4 dB at 1.55 mum.
Tree array quantum cascade laser (2009)

A monolithic coupling scheme for mid-infrared quantum cascade laser arrays is investigated with respect to brightness enhancement. The tree-shaped resonator enables parallel coupling of six laser elements into a single element by means of several Y-junctions. Phase-locking is observed on the basis of far field analysis, and leads to in-phase emission on both sides of the device. The experimental results match calculated far field profiles and demonstrate a high level of modal control when driven far above threshold. Whereas optical power measurements confirm negligible coupling losses, the slope efficiency is below the theoretically expected value, which is attributed to modal competition. Additional evaluation of near fields and spectral characteristics provides background on the modal dynamics of the sophisticated cavity and reveals limitations to coherent beam combining. The findings pave the way to improved coupling efficiency and brightness scaling of a single facet emitting compact quantum cascade laser array.
Dynamic variations in optical properties of graphene oxide in response to gas exposure as determined from thin-film interference (2018)

An approach is presented for measuring the dynamic variations in refractive index (RI) of Graphene Oxide (GO) based optical gas‐sensors [1‐ 3] upon their exposure to gases, using thin‐film interference method [4]. The approach is simple yet effective, and also is physically integratable into the sensing system, a required attribute for being able to measure the dynamically changing RI in response to the ongoing interactions with the analyte. The details can be found in our journal paper [5].
Synthesis and Biological Activity of 3,4‐Dihydroquinazolines for Selective T‐Type Ca<sup>2+</sup> Channel Blockers. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
WE‐G‐211‐05: Advances in X‐Ray Luminescence Computed Tomography: Towards In‐Vivo Imaging of Radioluminescent Nanophosphors (2011)

Purpose: Radioluminescent nanophosphors (RLNPs) show great promise for imaging biological processes in vivo, at the molecular level, and for enhancing the delivery of cytotoxic therapy within the target volume of a radiation treatment. As progress is made towards these goals, there is a need for an imaging modality that can quantitatively measure the distribution of RLNPs in vivo, with high sensitivity and spatial resolution. X‐ray luminescence computed tomography (XLCT) is best placed to meet all these requirements. In this scheme, collimated beams of X‐ray radiation selectively excite RLNPs, producing optical light within a narrowly‐defined volume. Optical measurements of the photons diffusing out of the subject can be interpreted as projective measurements and reconstructed into tomographic images. Methods: As a proof of concept, we built a prototype XLCT system and acquired projective data for near‐IR‐emitting RLNPs embedded in various phantoms. A novel reconstruction scheme that includes a model of light propagation in biological tissue was developed and evaluated on XLCT scans with sparse angular sampling. Results: Imaging in an optically‐diffusive medium shows that imaging performance is not affected by optical scatter; furthermore, the linear response of the reconstructed images suggests that XLCT is capable of quantitative imaging. Reconstruction that combines models of light and X‐ray propagation in tissue was found more accurate for sparsely‐sampled datasets. Conclusion: Based on phantom experiments, we found XLCT to be a feasible approach for imaging RLNPs tomographically. As we advance towards our goal of imaging RLNPs in live animals, we are designing and building a new imaging set‐up with improved X‐ray collimation and light collection efficiency.
Distributed optimization in multi-agent robotics for industry 4.0 warehouses (2018)

Robotic automation is being increasingly proselytized in the industrial and manufacturing sectors to increase production efficiency. Typically, complex industrial tasks cannot be satisfied by individual robots, rather coordination and information sharing is required. Centralized robotic control and coordination is ill-advised in such settings, due to high failure probabilities, inefficient overheads and lack of scalability. In this paper, we model the interactions among robotic units using intelligent agent based interactions. The autonomous behavior of these agents requires task/resource allocation to be performed via distributed algorithms. We use the motivating example of warehouse inventory automation to optimally allocate and distribute delivery tasks among multiple robotic agents. The optimization is decomposed using primal and dual decomposition techniques to operate in minimal latency, minimal battery usage or maximal utilization scenarios. These techniques may be applied to multiple deployments involving coordination and task allocation between autonomous agents.
A great depth class V flextensional transducer design (1993)

Flextensional transducers consist of a piezoelectric or magnetostrictive driver and a mechanical shell. The shell, excited on its first bending mode, amplifies the acoustic radiation. In a first part, the coupling between the driver and the shell is analyzed. The relative resonance frequency of each element determines the resonance frequency of the transducer and its radiated acoustic power. Furthermore, in most cases, operating depth is a significant limitation in the design of this kind of source—classical flextensional transducers on the work market are typically depth limited at about 200 or 300 m. To avoid the effects of the hydrostatic pressure, mechanical filters have been developed. The aim of these devices is to make the driver and the shell independent under static conditions. An equivalent scheme model is used to understand and to design this filtering element. Theoretical results are presented and a great depth class V flextensional transducer has been developed using this original technology. Its acoustic and static behaviors have been optimized with an axisymmetric B.E.M./F.E.M. numerical code. Finally, theoretical results are discussed in comparison with experimental ones obtained with the CERDSM facilities in Castillon Lake. Finally acoustic performances of this low-frequency, high power, and great depth transducer are shown. [Work supported by DRET.]
Spur-reduction techniques for PLLs using sub-sampling phase detection (2010)

In PLL designs, a wide loop bandwidth is often desired as it offers fast settling time, reduces on-chip loop filter area and sensitivity of the VCO to pulling. The reference spur is a major issue when the bandwidth is increased, because ripples on the VCO control line undergo less filtering by the loop filter. This paper proposes design techniques based on sub-sampling phase detection to reduce the reference spur of a 2.2GHz PLL to −80dBc at a high loop-bandwidth-to-reference-frequency ratio (f <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">BW</inf> /f <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ref</inf> ) of 1/20.
<i>Arabidopsis</i> ecotypes and mutants that are recalcitrant to <i>Agrobacterium</i> root transformation are susceptible to germ‐line transformation (2000)

Germ-line transformation (vacuum infiltration) is frequently used to transform Arabidopsis thaliana using Agrobacterium tumefaciens. We have recently identified several Arabidopsis ecotypes and T-DNA-tagged mutants that are recalcitrant to Agrobacterium-mediated transformation of cut root segments. Some of these ecotypes and mutants are deficient in their ability to bind bacteria. Some are deficient in T-DNA integration. We report here that using a germ-line transformation protocol we transformed these ecotypes and mutants, including attachment- and integration-defective Arabidopsis plants, with a frequency similar to that of highly susceptible wild-type plants. However, we could not transform otherwise highly susceptible Arabidopsis plants by germ-line or root transformation using several vir and attachment-deficient Agrobacterium mutants. These results indicate that certain plant factors important for transformation may exist in germ-line tissue but may be lacking in some somatic cells.
Design and development of proton exchange membrane fuel cell using open pore cellular foam as flow plate material (2014)

Our results confirmed the correlation among rCBV measurements, VEGF expression, and histopathologic grade in nonenhancing gliomas. PWI may add useful data to the preoperative assessment of nonenhancing gliomas. Its contribution in predicting tumor behavior and patient prognosis remains to be determined.
Stabilization of the photoluminescence from porous silicon: The competition between photoluminescence and dissolution (1997)

Two experiments are reported which demonstrate the means to stabilize the photoluminescence from an electrochemically etched (100) Si surface (porous silicon). The strong stabilizing influence of small quantities of water on a nonaqueous [2 mol/ℓ HF in methylcyanide (MeCN)] etching process and the stabilizing effect of hydrochloric acid on a porous silicon surface photoluminescing in solution are described. Mechanisms consistent with these observations are considered as they are commensurate with a silicon oxyhydride emitting species.
Abstract 3982: Cancer genome sequencing analysis, storage, discovery and delivery (2012)

Abstract Genome instability and structural rearrangement is a distinctive hallmark of the cancer genome. With next-gen sequencing technologies, our ability to measure structural rearrangements that occur throughout tumorigenesis and progression has improved significantly, while creating an urgent need for rearrangement discovery, analysis, and visualization methods to aid in our understanding of these events. We have developed a sequencing analysis pipeline that streamlines the discovery of an individual tumor's mutations, small indels, copy number alterations, allele-specific amplifications and deletions, and genomic rearrangements. Rearrangements are refined to base-pair precision using unmapped, putative split reads found in the vicinity of the breakpoint. Results are presented in an interactive, web-based genome browser that provides analysis and visualization of both high-level, processed results as well as the raw data from which they were derived. From the web-based interface, results from multiple samples can be aggregated into user-defined sample cohorts to help identify features that are shared among a significant number of the samples. Using this sequencing analysis pipeline, we discovered high-confident, small- and large-scale somatic events in 17 whole genome glioblastoma multiforme (GBM) tumor samples from The Cancer Genome Atlas (TCGA) project, using their matched normal sequences to filter out germline variants. Among many interesting structural aberrations identified in these samples, we find four samples exhibiting EGFR amplifications and the presence of the EGFRvIII mutant, characterized by the in-frame deletion of exons 2-7 to produce a constitutively active form of the receptor. Comparing the read support of the EGFRvIII-associated breakpoints to the number of normally-mapped reads in the neighborhood suggest that, in all cases, the EGFRvIII mutant emerges after the amplification of wild-type EGFR, existing as a small fraction of total number of EGFR copies. In other samples, evidence of high copy number amplicons containing both MDM2 and EGFR are discovered at detectable levels in the blood sequencing data, raising the possibility that patient-specific PCR-based assays could be developed to quantitate the presence of somatic rearrangements as a proxy to monitor the progression of brain tumors. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3982. doi:1538-7445.AM2012-3982
A conditional enhancement-layer quantizer for the scalable MPEG advanced Audio Coder (2002)

We propose an efficient enhancement-layer quantizer which considerably improves the bit rate scalability of the multi-layer Advanced Audio Coder (AAC). The scheme exploits the statistical dependence of the enhancement-layer signal on the base-layer quantization parameters. It fundamentally extends the prior work on compander domain scalability, which was shown to be asymptotically optimal for entropy coded uniform scalar quantizer, to systems with non-uniform base-layer quantization. We show that an enhancement-layer quantization which is conditional on the base-layer information can be efficiently implemented within the AAC framework to achieve major performance gains. Moreover, in the important case that the source is well modeled as Laplacian, we show that the optimal conditional quantizer is implementable by only two distinct switchable quantizers depending on whether or not the base-layer quantizer employed the “zero dead-zone.” Hence, major savings in bit rate are recouped at virtually no additional computational cost. For example, the proposed four layer scalable coder consisting of 16kbps layers achieves performance close to a 60kbps non-scalable coder on the standard test database of 44.1kHz audio.
Liquid-like Solids Support Cells in 3D (2016)

The demands of tissue engineering have driven a tremendous amount of research effort in 3D tissue culture technology and, more recently, in 3D printing. The need to use 3D tissue culture techniques more broadly in all of cell biology is well-recognized, but the transition to 3D has been impeded by the convenience, effectiveness, and ubiquity of 2D culture materials, assays, and protocols, as well as the lack of 3D counterparts of these tools. Interestingly, progress and discoveries in 3D bioprinting research may provide the technical support needed to grow the practice of 3D culture. Here we investigate an integrated approach for 3D printing multicellular structures while using the same platform for 3D cell culture, experimentation, and assay development. We employ a liquid-like solid (LLS) material made from packed granular-scale microgels, which locally and temporarily fluidizes under the focused application of stress and spontaneously solidifies after the applied stress is removed. These rheological properties enable 3D printing of multicellular structures as well as the growth and expansion of cellular structures or dispersed cells. The transport properties of LLS allow molecular diffusion for the delivery of nutrients or small molecules for fluorescence-based assays. Here, we measure viability of 11 different cell types in the LLS medium, we 3D print numerous structures using several of these cell types, and we explore the transport properties in molecular time-release assays.
Flow‐lysometry for cytoplasmic analysis of single cells in large populations (2013)

Presented is a single‐cell analyser to measure cytoplasmic components in large cell populations. This technology, flow‐lysometry, uses a flow‐cell that performs three functions (cell detection, cell lysis and component sensing) in a continuous microfluidic channel. This flow‐cell can be coupled and synchronised with classical flowcytometry, thus offering high‐throughput measurements of various cytoplasmic compounds in combination with cell‐surface markers. The measurement of cytoplasmic markers in the cytosol of red blood cells was shown to verify population analysis of individual cells in mixed‐cell populations. This work presents an approach to characterise complex cell populations to extend measurements in cell biology.
Dopants effect on the band structure of PbTe thermoelectric material (2012)

PbTe is a promising thermoelectric material and its dimensionless figure of merit, zT, can be enhanced by optimizing the band structure near the Fermi level via chemical doping. This letter describes the dopants effect on bandgap, Eg, and effective mass, m*, for disordered La- and I-doping, based on theoretical calculations. Eg increases with increasing La and decreases with increasing I concentration. While m* increases upon La-doping, I-doping does not change m* noticeably. The calculated results are qualitatively consistent with the experimental results and explain the higher zT, up to 1.4 at 800 K, observed in I-doping PbTe compared to La-doping.
Compartment-Selective Sensitivity of Cardiovascular Morphogenesis to Combinations of Retinoic Acid Receptor Gene Mutations (1997)

Several aspects of normal cardiovascular development require signaling by the vitamin A metabolite retinoic acid. We have previously established germ-line mutations in mice in the genes that encode the RAR alpha 1, RAR beta, and RXR alpha retinoic acid receptors as a means of studying the function of these receptors in vivo. Although mutation of RXR alpha results in fetal ventricular defects, the RAR alpha 1 and RAR beta mutations are apparently nonphenotypic in the heart and elsewhere. In this study, we have established and analyzed combinations of these receptor gene mutations. Malformations of the ventricular chamber (chamber hypoplasia and muscular ventricular septal defects), conotruncus (double-outlet right ventricle, transposition, and membranous ventricular septal defects), aortic sac (persistent truncus arteriosus and aorticopulmonary window), and aortic arch-derived arteries were recovered in various combinations of the RAR alpha 1, RAR beta, and RXR alpha gene mutations. Depending on the combination of receptor mutations, selective defects were obtained in specific cardiovascular compartments, suggestive of differential expression or function of each receptor within domains of the developing heart.