gebhart/patrepeval huggingface dataset:
Improved specificity and sensitivity when using pronase-digested lymphocytes to perform flow-cytometric crossmatch prior to renal transplantation (2002)

Abstract Several laboratories have resorted to flow-cytometric crossmatch (FCXM) in an effort to prevent hyperacute and accelerated renal allograft rejections. The currently employed FCXM has problems with both false-positive and -negative reactions, largely as a result of irrelevant IgG binding to Fc IgG receptors. In 1980, we circumvented this problem by digesting Fc IgG receptors with pronase, and demonstrated that, with immunofluorescnce microscopy (IF), detection of IgG anti-HLA antibodies was highly sensitive and specific. In 1995, we introduced the pronase technique to FCXM and showed that this enzyme did not decrease HLA expression. We present herein a prospective study at our institution to determine whether FCXM using pronase-digested (PD) lymphocytes is as sensitive and more specific than FCXM with undigested (UD) lymphocytes when compared with the highly sensitive and specific IF assay. In analyzing the 186 donor-specific prerenal-transplant crossmatches, we found that PD FCXM was as sensitive and specific as IF and was able to detect weak IgG anti-HLA antibodies that bound to B cells. Fourteen of these patients would have been denied transplants if one were to have relied on UD FCXM. The data clearly indicate that PD FCXM can reliably be used to detect weak IgG anti-HLA antibodies before renal transplantation.
Fundamental examination of hybrid‐type double three‐phase stepping motor (2007)

Abstract Resolution of the hybrid‐type stepping motor can be improved either by increasing the number of rotor teeth or by increasing the number of phases. But the number of rotor teeth can be increased only to a certain degree limited by obvious constraints of mechanical machining, while an increase in the number of rotor teeth causes the deterioration of high‐speed characteristics. On the other hand, an increase of the number of phases leads to higher production costs due to a greater complexity of the drive circuit. Copyright © 2004 Wiley Periodicals, Inc. In this paper, we examine a double three‐phase stepping motor having two sets of three‐phase stator windings as a means of improving the resolution of HB‐type stepping motors. The step angle of the proposed motor is half that of the three‐phase stepping motor with the same number of rotor teeth. The proposed double three‐phase motor is implemented in two types of the magnetic path configuration (multiphase magnetic path type and uniphase magnetic path type). Methods of selection of the number of rotor teeth and the stator pole pitch for the double three‐phase stepping motor of both types of the magnetic path are discussed, and characteristics of the motors having the multiphase magnetic path are compared with those of motors with the uniphase magnetic path. © 2007 Wiley Periodicals, Inc. Electr Eng Jpn, 159(2): 72– 79, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/eej.20442
Flask for the Drying of Biological Material (2004)

Recent advances in the stabilization of eukaryotic cells during desiccation provide possibilities for present and future pharmaceutical and biomedical applications. Such applications require strict adherence to sterility. Devices for the sterile processing of biological samples during drying and rehydration are lacking, however. An ideal device suitable for these procedures, especially for use in freeze-drying, would maintain sterility, allow sterile temperature sampling during the drying procedure, allow for microscopic analysis in the dry and rehydrated state, and allow for subsequent use in cell and tissue culture following rehydration. Furthermore, since the initial hydration of samples from the vapor phase (pre-hydration) is often useful to preserve sample integrity prior to complete rehydration, the device must prevent contamination during this process. We have developed a device suitable for these tasks. The Biomaterial Desiccation, Rehydration, and Imaging Flask (BioDRI™ Flask) fulfills all of the above mentioned requirements. It maintains sterility during drying, pre-hydration, and rehydration. It further enables adequate, sterile temperature sampling and microscopy. The design proves to be multi-functional, and allows for adequate drying by multiple methods, including freeze-drying, air-drying, and vacuum-drying—all of which are useful in the desiccation of biological samples. We believe that the BioDRI Flask will provide many applications in the field of biostabilization by drying.
Structure-Based Enhancement of Boronic Acid-Based Inhibitors of AmpC β-Lactamase (1998)

The expression of beta-lactamases is the most common form of bacterial resistance to beta-lactam antibiotics. To combat these enzymes, agents that inhibit (e.g. clavulanic acid) or evade (e.g. aztreonam) beta-lactamases have been developed. Both the beta-lactamase inhibitors and the beta-lactamase-resistant antibiotics are themselves beta-lactams, and bacteria have responded to these compounds by expressing variant enzymes resistant to inhibition (e.g. IRT-3) or that inactivate the beta-lactamase-resistant antibiotic (e.g. TEM-10). Moreover, these compounds have increased the frequency of bacteria with intrinsically resistant beta-lactamases (e.g. AmpC). In an effort to identify non-beta-lactam-based beta-lactamase inhibitors, we used the crystallographic structure of the m-aminophenylboronic acid-Escherichia coli AmpC beta-lactamase complex to suggest modifications that might enhance the affinity of boronic acid-based inhibitors for class C beta-lactamases. Several types of compounds were modeled into the AmpC binding site, and a total of 37 boronic acids were ultimately tested for beta-lactamase inhibition. The most potent of these compounds, benzo[b]thiophene-2-boronic acid (36), has an affinity for E. coli AmpC of 27 nM. The wide range of functionality represented by these compounds allows for the steric and chemical "mapping" of the AmpC active site in the region of the catalytic Ser64 residue, which may be useful in subsequent inhibitor discovery efforts. Also, the new boronic acid-based inhibitors were found to potentiate the activity of beta-lactam antibiotics, such as amoxicillin and ceftazidime, against bacteria expressing class C beta-lactamases. This suggests that boronic acid-based compounds may serve as leads for the development of therapeutic agents for the treatment of beta-lactam-resistant infections.
Assay Systems for the Growth Hormone-Binding Protein (1994)

The first method used for detection of growth hormone-binding protein (GHBP) in biological fluids was based on the incubation of the sample with radiolabeled GH followed by separation of bound and free GH by gel exclusion chromatography. Recently, other methods have been developed which are faster and easier to use. These methods include variants of the original binding/column assay (e.g., separation of bound and free GH is obtained by immunoprecipitation, charcoal adsorption, ion exchange chromatography, or HPLC), and a ligand-mediated immunofunctional assay (LIFA), in which a monoclonal antibody is used to capture the GHBP on a microtiter plate; all binding sites are saturated with GH and an anti-GH antibody is used to detect the amount of GH (endogenous and exogenous) bound to the GHBP. To permit comparison of results obtained by different methods we have cross-validated the LIFA with two different binding assays: (i) the original long column assay (column assay), and (ii) an assay based on immunoprecipitation (RIPA) of the GH/GHBP complex with an anti-GHBP antibody.
A class of micromachined gyroscopes with increased parametric space (2003)

This paper reports a design concept for MEMS gyroscopes based on increasing the degrees-of-freedom of the oscillatory system by the use of two independently oscillating interconnected proof masses. The 4-DOF dynamical system eliminates the necessity for mode-matching due to its wide operation frequency range, and reduces the damping sensitivity problem by operating away from resonance. Thus, inherent disturbance rejection is achieved, providing reduced sensitivity to structural and thermal parameter fluctuations. The basic operational principles of the design concept were experimentally demonstrated, including the wide operation frequency band, and dynamic amplification providing high oscillation amplitudes without resonance.
Remote sensing and precision nematicide applications for Rotylenchulus reniformis management in cotton (2004)

Summary Site-specific management of cotton pests is practised in Mississippi using remote sensing to direct spatially variable pesticide applications. Remotely sensed imagery is correlated with crop growth parameters using Normalised Difference Vegetation Index (NDVI) values to create prescription maps for bi-modal or multi-modal distributions. This technology is being examined using the spatial distribution of the reniform nematode (Rotylenchu-lus reniformis). Reflectance properties exhibited by R. reniformis-infected cotton plants are being acquired with hyperspectral spectroradiometers using both airborne and ground platforms. Specific reflectance data are used to develop self-organised maps (SOM). SOM are used to determine relationships between cotton plant stress and nematode population numbers. A Matlab based hyperspectral toolkit (MHTK) operating with SOM analysis is used to identify the specific spectral bands associated with R. reniformis. This will be instrumental in providing nematode numbers for use in generating nematode contour maps for global positioning system (GPS) directed variable rate technology (VRT) nematicide applications. Hyperspectral data may provide useful remote-sensing tools reducing the time consuming and costly grid sampling process required in precision nematicide applications.
First-in-human, Randomized, Double-blind Clinical Trial of Differentially Adjuvanted PAMVAC, A Vaccine Candidate to Prevent Pregnancy-associated Malaria (2019)

EudraCT 2015-001827-21; ClinicalTrials.gov NCT02647489.
Multi-institutional evaluation of deep brain stimulation targeting using probabilistic connectivity-based thalamic segmentation (2011)

This report identifies and provides preliminary external validation of a novel means of targeting a patient-specific therapeutic thalamic target for the treatment of tremor based on individualized analysis of thalamic connectivity patterns. This novel thalamic targeting approach is based on identifying the thalamic region with the highest probability of connectivity with premotor and supplementary motor cortices. This approach may prove to be advantageous over traditional preoperative methods of indirect targeting, providing patient-specific targets that could improve the precision, efficacy, and efficiency of deep brain stimulation surgery. Prospective evaluation and development of methodologies to make these analyses more widely available to neurosurgeons are likely warranted.
Superconducting Nanowire Single-Photon Detectors (2011)

Superconducting nanowire single-photon detectors show exceptional performance for quantum information processing, but several developments promise further progress, including new signal-amplification methods and efficient devices in the mid-infrared.
Advanced Motion-Constrained AV1 Encoder for 8K 360 VR Tiled Streaming (2019)

This paper presents the advanced motion-constrained AV1 encoder for a 360 8K VR streaming application. Currently, 360 8K VR streaming faces problems in limited network bandwidth, limited server-side computing power that makes difficult to serve ultra-high resolution videos to a large number of clients, and limiting power of a consumer electronic device to decode the stream. We propose a motion-constrained AV1 encoder that can solve these problems. The proposed method is composed of three different restrictions: motion vector search range, AV1 encoding options, and constrained loop filters in the boundary region of tiles. The experimental results show the average BDBR overhead of the proposed method with various tiles is 10.00% with saving 17.30% encoding time compared to the existing AV1 encoder. Also, the proposed AV1 encoder improves the BDBR by an average of 12.50% compared to a motion-constrained HEVC encoder.
Natural Language Interfaces with Fine-Grained User Interaction (2018)

The rapidly increasing ubiquity of computing puts a great demand on next-generation human-machine interfaces. Natural language interfaces, exemplified by virtual assistants like Apple Siri and Microsoft Cortana, are widely believed to be a promising direction. However, current natural language interfaces provide users with little help in case of incorrect interpretation of user commands. We hypothesize that the support of fine-grained user interaction can greatly improve the usability of natural language interfaces. In the specific setting of natural language interface to web APIs, we conduct a systematic study to verify our hypothesis. To facilitate this study, we propose a novel modular sequence-to-sequence model to create interactive natural language interfaces. By decomposing the complex prediction process of a typical sequence-to-sequence model into small, highly-specialized prediction units called modules, it becomes straightforward to explain the model prediction to the user, and solicit user feedback to correct possible prediction errors at a fine-grained level. We test our hypothesis by comparing an interactive natural language interface with its non-interactive version through both simulation and human subject experiments with real-world APIs. We show that with the interactive natural language interface, users can achieve a higher success rate and a lower task completion time, which lead to greatly improved user satisfaction.
Imidazo[1,2-a]quinoxalines Derivatives Grafted with Amino Acids: Synthesis and Evaluation on A375 Melanoma Cells (2018)

Imiqualines (imidazoquinoxaline derivatives) are anticancer compounds with high cytotoxic activities on melanoma cell lines. The first generation of imiqualines, with two lead compounds (EAPB0203 and EAPB0503), shows remarkable in vitro (IC<sub>50</sub> = 1 570 nM and IC<sub>50</sub> = 200 nM, respectively, on the A375 melanoma cell line) and in vivo activity on melanoma xenografts. The second generation derivatives, EAPB02302 and EAPB02303, are more active, with IC<sub>50</sub> = 60 nM and IC<sub>50</sub> = 10 nM, respectively, on A375 melanoma cell line. The aim of this study was to optimize the bioavailability of imiqualine derivatives, without losing their intrinsic activity. For that, we achieved chemical modulation on the second generation of imiqualines by conjugating amino acids on position 4. A new series of twenty-five compounds was efficiently synthesized by using microwave assistance and tested for its activity on the A375 cell line. In the new series, compounds <b>11a</b>, <b>9d</b> and <b>11b</b> show cytotoxic activities less than second generation compounds, but similar to that of the first generation ones (IC<sub>50</sub> = 403 nM, IC<sub>50</sub> = 128 nM and IC<sub>50</sub> = 584 nM, respectively). The presence of an amino acid leads to significant enhancement of the water solubility for improved drugability.
Puncturing for finite length low-density parity-check codes (2004)

In this paper we study and propose an algorithm to puncture finite length low density parity check (LDPC) codes (Ha, J, et al., 2002). The introduced puncturing criterion results in good performance (for 1024 and 4096 bits) when compared with both random puncturing and dedicated LDPC codes, i.e. unpunctured codes designed for a given rate. The comparison also shows that the proposed punctured LDPC codes have better block-error rates than the dedicated codes because of longer effective block lengths of the high-rate puncturing. Although we apply the idea for regular LDPC codes, we can easily modify the idea for irregular LDPC codes.
Pellicle for F 2 laser lithography (2000)

The two possible 157nm-pellicle membrane materials are discussed. Currently polymers have considerable absorption at 157nm. The F<SUB>2</SUB> laser durability evaluation was carried out for the polymer with the least absorption. The polymer membrane suffered severe damage after short irradiation. What is the most important for the polymer membrane is to reduce the absorption at 157nm in order to increase the transmission and to improve the durability. Modified fused silica is the material for mask substrate for F<SUB>2</SUB> laser lithography. This fused silica shows good laser durability, but stringent tolerances are required when the fused silica plate is applied for pellicle membrane. Thickness uniformity and bending of plate are discussed.
A novel catalyst-free synthesis of vertically aligned silicon nanowire–carbon nanotube heterojunction arrays for high performance electron field emitters (2011)

A novel, catalyst-free strategy for the direct synthesis of vertically aligned silicon nanowire-carbon nanotube (SiNW-CNT) heterojunction arrays is presented. Such a heterojunction with the junction area in the nanoscale displays enhanced field emission characteristics at low turn-on field, with a nearly three times increase in the field enhancement factor.
Birefringence correction for single-mode fiber couplers (1983)

Stabilized single-mode fiber couplers will find increasing application in interferometric sensors and in data bus distribution systems. These couplers have been fabricated by a variety of methods, ineluding etching and subsequent encapsulation,1 polishing,2 and fusion.3 Although little data have been published, it has become evident that these types of coupler typically do not preserve optical polarization through the coupler. Instead linearly polarized inputs are often transformed to highly elliptical states upon exiting the coupler. Since these couplers are often used in series and the coupling fraction typically varies with the Input polarization state, these effects lead to reduced sensitivity and polarization noise In Interferometers and to nonoptimum coupling fractions in fiber data buses.
<title>Multichannel detection for correlated non-Gaussian random processes based on innovations</title> (1993)

This paper addresses the problem of multichannel signal detection in additive correlated non- Gaussian noise using the innovations approach. While this problem has been addressed extensively for the case of additive Gaussian noise, the corresponding problem for the non- Gaussian case has received limited attention. This is due to the fact that there is no unique specification for the joint probability density function (PDF) of N correlated non-Gaussian random variables. We overcome this problem by using the theory of spherically invariant random processes (SIRP) and derive the innovations based detectors. It is found that the optimal estimators for obtaining the innovations processes are linear and that the resulting detector is canonical for the class of PDFs arising from SIRPs.
SiC Microsensor with Piezoresistive Diamond Sensing Elements (1992)

Advanced microfabrication processes have been developed for novel high temperature pressure sensors utilizing diamond and SiC materials. Such sensors represent a new generation of high temperature piezoresistive sensors. The accomplishments of Phase I include the following: (a) Growth of polycrystalline diamond on Beta-SiC substrates. (b) The first isolated p-type diamond resistive elements grown on intrinsic diamond. (c) Establishment of microfabrication processes for sensor manufacture. (d) Demonstration of a large piezoresistive effect in poly-diamond. (e) Demonstration of a new field- assisted-bonding process which allows dielectrically isolated SiC elements to be formed.
A Stereoselective Synthesis of 4′‐ <i>α</i> ‐Fluoro‐methyl Carbocyclic Nucleoside Analogs (2023)

Abstract The 4′ position modifications in carbocyclic nucleosides have not been investigated much as potential antiviral agents. Due to the higher ring strain and torsion of the cyclopentyl carbocyclic ring, it is not easy to carry out the modification at the 4′ position. Therefore, there is a need for a procedure that may tackle the synthesis of 4′ position substituted carbocyclic pentyl ring. In this communication, a stereoselective synthesis of 4′‐ α ‐fluoro‐methyl carbocyclic nucleosides has been reported. A stereoselective synthesis of the 4‐ α ‐fluoro‐methyl carbocyclic sugar moiety ( 16 ) was carried out via carbocyclic ketone 1 . The oxidation of the 5‐methyl hydroxy of 9 followed by the aldol condensation gave a diol 11 , which via selective protection followed by selective fluorination, yielded a MOM‐protected 4‐ α ‐fluoro‐methyl carbocyclic ring ( 16 ). Compound 16 served as a key intermediate for the synthesis of purines ( 21 & 24 ) and pyrimidine ( 28 & 31 ) nucleosides. The described synthesis may be utilized to construct the various 4′ position modified carbocyclic nucleos(t)ides for an elaborated structure‐activity relationship (SAR) as an antiviral and anticancer agent.
The structural basis for the anti-inflammatory activity of sialylated antibodies (THER5P.822) (2014)

Abstract Antibodies (Ab) mediate pro-inflammatory effector functions through the engagement of Fc receptors (FcγRs) expressed on leukocytes. A complex, N-linked glycan attached to the Fc domain of IgG regulates the interaction to FcγRs by maintaining the Fc in a biologically active conformation. However, attaching sialic acid sugar residues to this Fc-associated glycan reduces affinity for FcγRs and confers binding to an alternate class of receptors, the C-type lectins (DC-SIGN). This switch in receptor specificity coincides with a switch in effector function in vivo as sialylated IgG (sFc) suppresses inflammation in mouse models of autoimmunity. The structural mechanism that regulates the sialic acid-dependent change in Ab effector function remains poorly understood. Biophysical analysis reveals that sialylation destabilizes the Fc fragment by increasing the hydrophobic surface area exposed to solvent. Upon solving a crystal structure of sFc, we observe that this loss of stability correlates with inter-domain flexibility such that the sFc in the crystal is found in both “open” and “closed” states. Mutagenic analysis of sFc further identifies key contact sites between the Fc-glycan and the Fc-backbone necessary to induce this conformational change and attain anti-inflammatory activity in vivo. These studies demonstrate that the conformational diversity of the Fc fragment serves as a general strategy to shift receptor specificity in order to effect different immunological outcomes.
Shape-based Matching of ECG Recordings (2007)

An electrocardiogram (ECG) is an important and commonly used diagnostic aid in cardiovascular disease diagnosis. Physicians routinely perform diagnosis by a simple visual examination of ECG waveform shapes. In this paper, we address the problem of shape-based retrieval of ECG recordings, both digital and scanned from paper, to infer similarity in diagnosed diseases. Specifically, we use the knowledge of ECG recording structure to segment and extract curves representing various recording channels from ECG images. We then present a method of capturing the perceptual shape similarity of ECG waveforms by combining shape matching with dynamic time warping. The shape similarity of each recording channel is combined to develop an overall shape similarity measure between ECG recordings. Results are presented that demonstrate the method on shape-based matching of various cardiovascular diseases.