gebhart/patrepeval huggingface dataset:
Mapping the Ig superantigen-binding site of HIV-1 gp120 (1995)

The envelope glycoprotein, gp120, of HIV-1 has recently been identified as a member of the new family of Ig superantigens (Ig-SAg). This classification is based on the selective binding of gp120 to an unusually high proportion of endogenous, nonimmune Ig, and the selective activation of nonimmune B cells by gp120 in vitro. Many, if not all of the nonimmune Ig that bind to gp120 are members of the VH3 Ig gene family. The aim of this study was to determine the epitope on gp120 that was responsible for its Ig-SAg binding activity. To do this, we utilized a panel of 30 peptides derived from gp160 in a competition-binding assay. For five Igs that were tested, as well as for polyclonal serum IgM, two overlapping peptides (each 20 amino acids in length) were identified that were potent inhibitors of gp120 binding. Similarly, the 10 amino acid overlap region of these two peptides had inhibitory activity. Thus, this decamer sequence represented the optimal Ig-SAg epitope or mimotope. The amino acid residue at position 1 of the decamer, and to a lesser extent at position 10, was critical for peptide binding. In addition to this decamer peptide, other peptides that shared modest sequence homology were also selectively inhibitory for specific Ig samples. These findings provide the first definition of an Ig-SAg ligand at the peptide level and will facilitate further structural and biologic characterization of this new class of pathogenic Ags.
Limitations to the Power Output and Efficiency of Mid-Infrared Quantum Cascade Lasers Imposed by Transport (2010)

We use a density-matrix framework to evaluate the wallplug efficiency of mid-infrared quantum cascade lasers. We assess the limitations to maximum current and internal efficiency, imposed by injection coupling and current leakage, respectively.
Treatment of AL Amyloidosis with 4′-Iodo-4′-Deoxydoxorubicin: An Update (1999)

To the Editor:

Amyloidosis formed by monoclonal immunoglobulin light chain (AL) is a rapidly progressive disease in most patients, causing organ failure and death within 1 to 3 years of diagnosis.[1][1] [2][2] The logical therapeutic target in this type of amyloidosis is the elimination of the
Microwave plasma-assisted premixed flame combustion (2006)

A compact microwave plasma/combustion torch has been operated at atmospheric pressure in both plasma-only and plasma-assisted premixed combustion modes. The torch burns CH4∕O2 mixtures with plasma enhancement that modifies combustion, flame structure, flame size, and flame power density. The microwave energy also extends the fuel-lean burn limits.
Ultrafast Beam Switching Using Coupled VCSELs (2001)

The ability to steer or switch propagation direction of a laser beam in a controllable way is very important for many applications, and especially for optical interconnect networks. Beam scanning and steering in edge emitting lasers have been realized using thermal control [1] and spatial phase controlling technique [2]. For optical interconnect application, all the well-known advantageous attributes of VCSELs make them especially appealing elements for such networks. For this reason, routers integrated together with VCSELs that can be controlled electronically are especially important to reduce the overall volume of interconnect network. By creating a phase shift in part of a VCSEL, it was demonstrated [3] that up to 2GHz beam switching can be achieved with maximum swing angle of about 3 degree.
O(log n) dynamic router-tables for prefixes and ranges (2004)

Two versions of the Internet (IP) router-table problem are considered. In the first, the router table consists of n pairs of tuples of the form (p, a), where p is an address prefix and a is the next-hop information. In this version of the router-table problem, we are to perform the following operations: insert a new tuple, delete an existing tuple, and find the tuple with longest matching-prefix for a given destination address. We show that each of these three operations may be performed in O(log n) time in the worst case using a priority-search tree. In the second version of the router-table problem considered by us, each tuple in the table has the form (r, a), where r is a range of destination addresses matched by the tuple. The set of tuples in the table is conflict-free. For this version of the router-table problem, we develop a data structure that employs priority-search trees as well as red-black trees. This data structure permits us to perform each of the operations insert, delete, and find the tuple with most-specific matching-range for a given destination address in O(log n) time each in the worst case. The insert and delete operations preserve the conflict-free property of the set of tuples. Experimental results are also presented.
Direct growth of single-crystalline III–V semiconductors on amorphous substrates (2016)

The III-V compound semiconductors exhibit superb electronic and optoelectronic properties. Traditionally, closely lattice-matched epitaxial substrates have been required for the growth of high-quality single-crystal III-V thin films and patterned microstructures. To remove this materials constraint, here we introduce a growth mode that enables direct writing of single-crystalline III-V's on amorphous substrates, thus further expanding their utility for various applications. The process utilizes templated liquid-phase crystal growth that results in user-tunable, patterned micro and nanostructures of single-crystalline III-V's of up to tens of micrometres in lateral dimensions. InP is chosen as a model material system owing to its technological importance. The patterned InP single crystals are configured as high-performance transistors and photodetectors directly on amorphous SiO2 growth substrates, with performance matching state-of-the-art epitaxially grown devices. The work presents an important advance towards universal integration of III-V's on application-specific substrates by direct growth.
An Opto-Electro-Mechanical Phase Shifter (2015)

We demonstrate an opto-electro-mechanical phase shifter. A suspended microbridge is electrostatically actuated to strongly-interact with a weakly-confined waveguide mode. The resulting effective index tuning substantially exceeds that achievable with thermo-optic and electro-optic approaches.
Line network network (LNN): an alternative in-fixture calibration procedure (1997)

An alternative method for a network analyzer calibration is evaluated. This line network network (LNN) method avoids de-embedding of the device under test (DUT) and it allows the characterization of an unknown two-port inserted between an arbitrary number of cascaded unknown two-ports. An unknown obstacle must be moved on a transmission line into three positions. The LNN calibration technique delivers the electrical wavelength or the relative dielectric constant of the transmission line and the scattering parameters of the obstacle. Since the connectors do not have to be exchanged, nonreproducibilities of the connectors are only a minor problem. Additionally, a double-calibration technique is presented. The double-calibration technique is used to employ the LNN method on both sides of the two-port DUT in order to perform an error-corrected measurement. Experimental results compare the LNN method with the tru-reflect-line (TRL) method particularly for an in-fixture calibration.
Automated analysis of cervix images to grade the severity of cancer (2011)

This paper discusses a method to objectively analyze the severity of cancer in images obtained from cervix. We propose a novel method to identify the transformation zone in post Lugol's iodine images and acetic acid images that are obtained from the cervix to grade the severity of cancer. We segment the Lugol's iodine image to identify the abnormal tissues and map them to acetic acid images to accurately identify the abnormal tissues in post acetic acid images as well. This information is further used to obtain an opacity difference score that could be used for grading the cancer.
Biologically Active <sup>11</sup>C-Labeled Amides Using Palladium-Mediated Reactions with Aryl Halides and [<sup>11</sup>C]Carbon Monoxide (1999)

Using [11C]carbon monoxide in palladium-mediated synthesis, six amides were labeled with 11C. Phenyl and benzyl halides with halides as additional substituents were carbonylated and reacted with primary and secondary amines. Four of the selected amides were receptor ligands, one was a precursor to a receptor ligand, and one was a model compound. The 11C-labeled amides were obtained with good to almost quantitative radiochemical yields with specific activities up to 1000 GBq/μmol. The radiochemical purity of the final products exceeded 98%. In one case, the corresponding 13C-substituted compound was produced to verify the position of the label. In a typical experiment starting with 5.0 GBq of [11C]carbon monoxide, 2.2 GBq of LC-purified N-(2-aminoethyl)-4-chloro[carbonyl-11C]benzamide was obtained within 15 min from the start of the carbonylation reaction (74% decay-corrected radiochemical yield). The presented approach gives significant new possibilities for 11C-labeling and is seen to be valuable also for synthesis of 13C- and 14C-substituted compounds.
Dynamic Physical Constraints: Emulating Hard Surfaces with High Realism (2012)

In this paper, we present a novel haptic technique for emulating hard surfaces with high realism; such a technique has significant potential utility in certain orthopedic surgery applications such as joint replacement surgery where the goal is to prevent incursions beyond a virtual surface during bone cutting operations. The Dynamic Physical Constraint (DPC) concept uses a unidirectional physical constraint that is actively positioned to limit movement between two manipulator links; the concept is applicable to providing virtual constraints in both 2D and 3D workspaces. Simulation results demonstrate the potential feasibility of the concept, and a prototype device was built for testing. The DPC device provides a convincing sensation of a real, hard virtual surface which can be smoothly tracked when the end effector is in contact with the surface. Incursion across the surface with the prototype was well submillimetric and within the accuracy constraints required for joint replacement applications.
Fracture characterization at multiple scales using borehole images, sonic logs, and walkaround vertical seismic profile (2009)

We present a quantitative forward-modeling methodology to link and interpret several measurements relevant to mechanical properties of fractures such as borehole images, sonic anisotropy logs, and borehole seismic anisotropy. The analysis is applied to a case study from a north African tight gas field using data from a vertical well. Two studies are conducted independently using the same geological fracture data to model fracture-induced anisotropy. In the first study, we use the orientation of the natural and drilling-induced fractures interpreted on the image log to model the azimuthal fracture-induced anisotropy at the sonic scale. The mechanical effects of natural and drilling-induced fractures are treated using different compliance parameters for each fracture type. We show that modeled sonic fast shear azimuths could be biased by the presence of noncompliant fractures in each fracture type, and we propose an empirical selection criterion to reject noncompliant fractures prior to compliance estimation. Then, we estimate the fracture compliances and confirm that natural open fractures have larger compliances than drilling-induced fractures. In the second study, we apply interpreted borehole images toward modeling of the azimuthal vertical seismic profile (VSP) attributes as a function of source azimuthal position. Natural fractures inside a window of height, h, and located at depth, d, are included, and several volume sizes and positions (i.e., h and d) are considered. We find a good agreement between modeled and observed transverse-over-radial displacement trends using natural fractures within windows located at the depth of the VSP receiver, and having window heights on the order of one to two VSP shear wavelengths.
Downhole vertical seismic profile survey reveals structure near borehole (1982)

A vertical seismic profile (VSP) survey can be useful for obtaining subsurface structural information in the immediate vicinity of the borehole. Such information has much higher vertical and horizontal resolution than that of conventional surface seismic data. Ray-tracing techniques allow the interpreter to compare synthetic VSP data from a structural model with the actual VSP field data. Additionally, the vertical seismic profile common-depth-point (VSPCDP) stack procedure effectively determines what the model should be by transforming VSP data into a high-resolution miniseismic section in the vicinity of the boreholes.
Immunization with a Combination of Integral Chlamydial Antigens and a Defined Secreted Protein Induces Robust Immunity against Genital Chlamydial Challenge (2010)

We have previously demonstrated the efficacy of recombinant chlamydial protease-like activity factor (rCPAF; a secreted chlamydial protein) in inducing antigen-specific CD4+ T cell/gamma interferon (IFN-gamma)-mediated but not antibody-mediated chlamydial clearance and reduction of upper genital tract (UGT) pathological sequelae. Since chlamydial integral antigens may induce neutralizing antibody protection, we further evaluated induction of protective immunity using a combination of rCPAF and UV-inactivated chlamydial elementary bodies (UV-EB) against vaginal chlamydial challenge in comparison to immunization with the individual components or live EB. The rCPAF-UV-EB immunization induced a significantly enhanced anti-UV-EB cellular and antibody response and a reduced anti-CPAF cellular and antibody response, compared to immunization with the respective individual components. Moreover, vaccination with UV-EB and rCPAF-UV-EB induced serum antibodies that neutralized chlamydial infectivity. The rCPAF-UV-EB immunization resulted in a significant reduction of vaginal chlamydial shedding and induced earlier bacterial clearance than vaccination of mice with the individual components. Importantly, the UGT sequelae were significantly reduced in mice immunized with rCPAF or rCPAF-UV-EB, but not in those immunized with UV-EB alone, and approached the levels of protection induced by live EB. These results collectively suggest that a combination of neutralizing antibodies induced by integral chlamydial antigens and cell-mediated responses induced by secreted proteins such as CPAF induces optimal protective immunity against genital chlamydial infections.
Endogenous fluorescence lifetime of viable cells by flow cytometry (2008)

Autofluorescence emission is commonly measured in flow cytometry and is used as a negative control in protocols that explore binding of exogenous fluorophores to cell receptors or other targets of interest. The presence of intrinsic fluorophores however may burden complex cytometry applications. For example it may be difficult to resolve fluorescence signals from multi-intensity and multi-color measurements when the de-convolved fluorescence in question falls close to the autofluorescence background. One possible solution to intensity and spectral overlap problems in flow cytometry is to acquire fluorescence decay kinetic measurements. To this end we focus on advancing time-dependent flow cytometry and conduct measurements of endogenous fluorescence lifetime. Instrument developments to a phase-sensitive flow cytometry (PSFC) system were coupled with lifetime measurements of intrinsic fluorophores from viable cell samples. The average lifetime of >300,000 individual rat fibroblast cells was measured at discrete wavelengths ranging from 457- to 785-nm using a 10-MHz intensity-modulated excitation beam. AC amplitude, DC, and phase-shift were resolved and the average lifetime from excitable endogenous species was measured. The lifetime results ranged from 1- to 6-ns over the broad spectral range. Cataloging lifetime values prefaces the use of phase-sensitive techniques in more complex systems and provides a priori measurements necessary for PSFC filtering known lifetime signals from Raman, or other emission and scattering events.
Cloning and Expression of a Novel K+ Channel Regulatory Protein, KChAP (1998)

Voltage-gated K+ (Kv) channels are important in the physiology of both excitable and nonexcitable cells. The diversity in Kv currents is reflected in multiple Kv channel genes whose products may assemble as multisubunit heteromeric complexes. Given the fundamental importance and diversity of Kv channels, surprisingly little is known regarding the cellular mechanisms regulating their synthesis, assembly, and metabolism. To begin to dissect these processes, we have used the yeast two-hybrid system to identify cytoplasmic regulatory molecules that interact with Kv channel proteins. Here we report the cloning of a novel gene encoding a Kv channel binding protein (KChAP, for K+ channel-associated protein), which modulates the expression of Kv2 channels in heterologous expression system assays. KChAP interacts with the N termini of Kvalpha2 subunits, as well as the N termini of Kvalpha1 and the C termini of Kvbeta subunits. Kv2.1 and KChAP were coimmunoprecipitated from in vitro translation reactions supporting a direct interaction between the two proteins. The amplitudes of Kv2. 1 and Kv2.2 currents are enhanced dramatically in Xenopus oocytes coexpressing KChAP, but channel kinetics and gating are unaffected. Although KChAP binds to Kv1.5, it has no effect on Kv1.5 currents. We suggest that KChAP may act as a novel type of chaperone protein to facilitate the cell surface expression of Kv2 channels.
A high data transfer rate frequency shift keying demodulator chip for the wireless biomedical implants (2003)

This paper describes a high-rate frequency shift keying (FSK) data transfer protocol and demodulator circuit for wireless operated biomedical implants in need of data transfer rates above 1 Mbit/sec. The demodulator circuit receives the serial data bit stream from an FSK carrier signal in the 2/spl sim/20 MHz range, which is used to power the implant through inductive coupling. The circuitry has been designed and fabricated in the University of Michigan's single metal, dual-poly 3 /spl mu/m CMOS process and has been tested fully functional.
A new absorption heat pump (1998)

A new absorption heat pump is being developed that uses a new organometallic liquid absorbent and hydrogen or nitrogen gas as a refrigerant. The organometallic liquid is environmentally clean, has {approximately}1.3 wt.% hydrogen uptake capacity, and has {Delta}H/c{sub p} {approximately} 10--15 times higher than that of ammonia/water, so more compact, higher power density heat pumps are possible. The compressor-driven and heat-driven heat pumps are described and analyzed. The analysis indicates that high efficiencies are possible.
Full‐waveform based microseismic event detection and signal enhancement: An application of the subspace approach (2014)

ABSTRACT Microseismic monitoring has proven invaluable for optimizing hydraulic fracturing stimulations and monitoring reservoir changes. The signal to noise ratio of the recorded microseismic data varies enormously from one dataset to another, and it can often be very low, especially for surface monitoring scenarios. Moreover, the data are often contaminated by correlated noises such as borehole waves in the downhole monitoring case. These issues pose a significant challenge for microseismic event detection. In addition, for downhole monitoring, the location of microseismic events relies on the accurate polarization analysis of the often weak P‐wave to determine the event azimuth. Therefore, enhancing the microseismic signal, especially the low signal to noise ratio P‐wave data, has become an important task. In this study, a statistical approach based on the binary hypothesis test is developed to detect the weak events embedded in high noise. The method constructs a vector space, known as the signal subspace, from previously detected events to represent similar, yet significantly variable microseismic signals from specific source regions. Empirical procedures are presented for building the signal subspace from clusters of events. The distribution of the detection statistics is analysed to determine the parameters of the subspace detector including the signal subspace dimension and detection threshold. The effect of correlated noise is corrected in the statistical analysis. The subspace design and detection approach is illustrated on a dual‐array hydrofracture monitoring dataset. The comparison between the subspace approach, array correlation method, and array short‐time average/long‐time average detector is performed on the data from the far monitoring well. It is shown that, at the same expected false alarm rate, the subspace detector gives fewer false alarms than the array short‐time average/long‐time average detector and more event detections than the array correlation detector. The additionally detected events from the subspace detector are further validated using the data from the nearby monitoring well. The comparison demonstrates the potential benefit of using the subspace approach to improve the microseismic viewing distance. Following event detection, a novel method based on subspace projection is proposed to enhance weak microseismic signals. Examples on field data are presented, indicating the effectiveness of this subspace‐projection‐based signal enhancement procedure.
Simulator to evaluate tsunami warning performance for coastal HF radars (2016)

The four-decade old prediction that coastal HF radars intended for current mapping could detect and warn of tsunamis via their orbital velocities has been confirmed by dozens of offline observations over the past four years. A detection method for SeaSonde systems (of which 600 now operate worldwide) has shown how the unique (but often weak) tsunami signal can be pulled out of background currents and noise by a “q-factor” pattern recognition algorithm. As with any event detector, one must trade off probability of detection with false alarm rate. We developed and describe here a simulator, that allows one to optimize tsunami performance based on local bathymetry and background conditions. Running on real-time systems in the field, it correlates false-alarm and detection probabilities with the background, injecting a simulated model-derived tsunami signal into noise and echo normally used for current mapping. This allows optimizing algorithm performance and detection thresholds masked by background. Minimal tsunami-intensity is predictable at a given site. Filters that correlate alert spikes with other information (e.g., seismic events) further reduce false alarms, so that robust warnings are passed along to our TWCs (tsunami warning centers). Our company has begun an official partnership with NOAA's NWS and NOS to evolve this capability into TWC operations.
Heterologous Expression, Purification, and Characterization of a Highly Active Xylose Reductase from <i>Neurospora crassa</i> (2005)

A xylose reductase (XR) gene was identified from the Neurospora crassa whole-genome sequence, expressed heterologously in Escherichia coli, and purified as a His6-tagged fusion in high yield. This enzyme is one of the most active XRs thus far characterized and may be used for the in vitro production of xylitol.
Cross-Linked Polybenzimidazole Membranes for Fuel Cells (2007)

Polybenzimidazole membranes have been covalently cross-linked after casting. The membranes exhibit much-improved chemical stability and mechanical strength. This allows the membrane to be doped at higher acid levels and therefore possess higher proton conductivity and potentially increased durability in fuel cells.