gebhart/patrepeval huggingface dataset:
Phage-directed synthesis of copper sulfide: structural and optical characterization (2013)

The growth of crystalline copper sulfide using a viral template was investigated using sequential incubation in CuCl2 and Na2S precursors. Non-specific electrostatic attraction between a genetically-modified M13 bacteriophage and copper cations in the CuCl2 precursor caused phage agglomeration and bundle formation. Following the addition of Na2S, polydisperse nanocrystals 2-7 nm in size were found along the length of the viral scaffold. The structure of the copper sulfide material was identified as cubic anti-fluorite type Cu1.8S, space group Fm3[overline]m. Strong interband absorption was observed within the ultraviolet to visible range with an onset near 800 nm. Furthermore, free carrier absorption, associated with the localized surface plasmon resonance of the copper sulfide nanocrystals, was seen in the near infrared with absorbance maxima at 1060 nm and 3000 nm, respectively.
Shorter failure analysis using a new application of IDDQ for defect localization in ICs (1998)

Recent progress with I<SUB>DDQ</SUB> testing has demonstrated the ability to identify a majority of defects in logic ICs. I<SUB>DDQ</SUB> testing has also been integrated in fault simulators embedded with automatic test pattern generation algorithms to further extend defect coverage. However, this progress has not eliminated the complex task of defect localization on the silicon level of ICs. Duration and accuracy of localization have a direct impact on the cost of failure analysis. Faster, better localization means shorter failure analysis and turn around time which in turn impacts the yield and reliability of IC production lines. To respond to this challenge, a new application of I<SUB>DDQ</SUB> tests has been developed to accelerate the localization task and to directly impact IC production yields and reliability. In this paper, we will present a novel voltage contrast method for high speed defect localization. Using the same test pattern as that used to identify a faulty circuit, the equipotential line of the failure can be located using only a failed circuit. Comparing the equipotential line with the fault simulator output, the site of the simulated defect corresponding to the physical failure can be extracted, and local deprocessing with a FIB can be used on the failed circuit to physically reveal the defect with an improved turn around time.
Maximum A-Posteriori Estimation in Linear Models With a Gaussian Model Matrix (2007)

We consider the Bayesian inference of a random Gaussian vector in a linear model with a Gaussian model matrix. We derive the maximum a-posteriori (MAP) estimator for this model and show that it can be found using a simple line search over a unimodal function that can be efficiently evaluated. Next, we discuss the application of this estimator in the context of near-optimal detection of near-Gaussian-digitally modulated signals and demonstrate through simulations that the MAP estimator outperforms the standard linear MMSE estimator in terms of mean square error (MSE) and bit error rate (BER).
Application of a birdcage coil at 3 tesla to imaging of the human knee using MRI (1999)

A transceive RF birdcage coil designed for very high field with a novel matching scheme was implemented with the specific geometry chosen for the human knee. This coil design incorporates a hinge for greater patient accessibility. Volunteer human subjects were studied using spin-echo and 3D gradient echo sequences for image acquisition. The higher signal-to-noise and improved tissue contrast obtained from this high-field system, coupled with the optimized coil design, improves visualization of the structural detail in articular cartilage, which is not seen well at conventional field strengths. This has important clinical implications, as newer medical and surgical treatments become available for the treatment of early cartilage degeneration. Magn Reson Med 42:215-221, 1999.
Opportunistic medium access for wireless networking adapted to decentralized CSI (2006)

Relative to a centralized operation, opportunistic medium access capitalizing on decentralized multiuser diversity in a channel-aware homogeneous slotted Aloha system with analog-amplitude channels has been shown to incur only partial loss in throughput due to contention. In this context, we provide sufficient conditions for stability as well as upper bounds on average queue sizes, and address three equally important questions. The first one is whether there exist decentralized scheduling algorithms for homogeneous users with higher throughputs than available ones. We prove that binary scheduling maximizes the sum-throughput. The second issue pertains to heterogeneous systems where users may have different channel statistics. Here we establish that binary scheduling not only maximizes the sum of the logs of the average throughputs, but also asymptotically guarantees fairness among users. The last issue we address is extending the results to finite state Markov chain (FSMC) channels. We provide a convex formulation of the corresponding throughput optimization problem, and derive a simple binary-like access strategy
Ultrafast-UV laser integrating cavity device for inactivation of SARS-CoV-2 and other viruses (2022)

Ultraviolet (UV) irradiation-based methods used for viral inactivation have provided an important avenue targeting severe acute respiratory-syndrome coronavirus-2 (SARS-CoV-2) virus. A major problem with state-of-the-art UV inactivation technology is that it is based on UV lamps, which have limited efficiency, require high power, large doses, and long irradiation times. These drawbacks limit the use of UV lamps in air filtering systems and other applications. To address these limitations, herein we report on the fabrication of a device comprising a pulsed nanosecond 266 nm UV laser coupled to an integrating cavity (LIC) composed of a UV reflective material, polytetrafluoroethylene. Previous UV lamp inactivation cavities were based on polished walls with specular reflections, but the diffuse reflective UV ICs were not thoroughly explored for virus inactivation. Our results show that LIC device can inactivate several respiratory viruses including SARS-CoV-2, at ~ 1 ms effective irradiation time, with > 2 orders of magnitude higher efficiency compared to UV lamps. The demonstrated 3 orders of magnitude cavity enhancement relative to direct exposure is crucial for the development of efficient real-time UV air and water purification systems. To the best of our knowledge this is the first demonstration of LIC application for broad viral inactivation with high efficiency.
Emergence of influenza A viruses (2001)

Pandemic influenza in humans is a zoonotic disease caused by the transfer of influenza A viruses or virus gene segments from animal reservoirs. Influenza A viruses have been isolated from avian and mammalian hosts, although the primary reservoirs are the aquatic bird populations of the world. In the aquatic birds, influenza is asymptomatic, and the viruses are in evolutionary stasis. The aquatic bird viruses do not replicate well in humans, and these viruses need to reassort or adapt in an intermediate host before they emerge in human populations. Pigs can serve as a host for avian and human viruses and are logical candidates for the role of intermediate host. The transmission of avian H5N1 and H9N2 viruses directly to humans during the late 1990s showed that land-based poultry also can serve between aquatic birds and humans as intermediate hosts of influenza viruses. That these transmission events took place in Hong Kong and China adds further support to the hypothesis that Asia is an epicentre for influenza and stresses the importance of surveillance of pigs and live-bird markets in this area.
Cardiac output monitoring by long time interval analysis of a radial arterial blood pressure waveform with correction for arterial compliance changes using pulse transit time (2011)

We previously developed a technique for estimating relative cardiac output (CO) change by long time interval analysis of a radial arterial blood pressure waveform. This technique analyzes the slow, beat-to-beat changes in the waveform to circumvent the confounding wave reflections but assumes constant arterial compliance (AC). Here, we sought to correct the CO estimates of the technique for potential AC changes using pulse transit time--a conveniently measured index of AC. For proof-of-concept, we compared the original and corrected techniques using invasive swine hemodynamic data. The corrected technique reduced the overall calibrated CO estimation error by 18% relative to the original technique.
Performance of networks using wavelength converters based on four-wave mixing in semiconductor optical amplifiers (1999)

In this paper, we examine the blocking performance of networks in which connections may be blocked due to either insufficient capacity or due to limitations in the transmission network. We use analytical expressions and network simulations to examine blocking in networks in which the quality of the received signal may be so poor that the connection is effectively blocked. In particular, we apply our analysis to networks which use wavelength converters based on four-wave mixing (FWM) in semiconductor optical amplifiers. We show that the performance improvements obtained using these wavelength converters can be significant, but this depends on whether the network uses fixed-frequency or tunable transmitters and receivers.
Hot-Carrier Relaxation in CdSe/CdS Core/Shell Nanoplatelets (2019)

We present time-resolved photoluminescence (PL) spectroscopy of a series of colloidal CdSe/CdS core/shell nanoplatelets with different core and shell thicknesses. Exciton numbers are determined from the integrated PL intensities, and carrier temperatures are determined from the high-energy exponential tail of the PL spectra. For times between 10 and 1000 ps, the measured carrier relaxation dynamics are well described by a simple model of Auger reheating: biexcitonic Auger recombination continually increases the average energy of the carriers (while decreasing their number), and this reheating sets a bottleneck to cooling through electron–phonon coupling. For times between 1 and 10 ps, the relaxation dynamics are consistent with electron–phonon coupling, where the bottleneck is now the decay of the longitudinal optical phonon population. Comparison of relaxation dynamics to recombination dynamics reveals changes in the carrier–phonon coupling for shell thicknesses greater than 4 monolayers.
Machine learning surrogate models for prediction of point defect vibrational entropy (2020)

The temperature variation of the defect densities in a crystal depends on vibrational entropy. This contribution to the system thermodynamics remains computationally challenging as it requires a diagonalization of the system's Hessian which scales as $O({N}^{3})$ for a crystal made of $N$ atoms. Here, to circumvent such a heavy computational task and make it feasible even for systems containing millions of atoms, the harmonic vibrational entropy of point defects is estimated directly from the relaxed atomic positions through a linear-in-descriptor machine learning approach of order $O(N)$. With a size-independent descriptor dimension and fixed model parameters, an excellent predictive power is demonstrated on a wide range of defect configurations, supercell sizes, and external deformations well outside the training database. In particular, formation entropies in a range of $250{k}_{B}$ are predicted with less than $1.6{k}_{B}$ error from a training database whose formation entropies span only $25{k}_{B}$ (training error less than $1.0{k}_{B}$). This exceptional transferability is found to hold even when the training is limited to a low-energy superbasin in the phase space while the tests are performed for a different liquid-like superbasin at higher energies.
Use of Porous Tantalum Metaphyseal Cones for Severe Tibial Bone Loss During Revision Total Knee Replacement (2008)

At the time of short-term follow-up, the porous tantalum metaphyseal tibial cones effectively provided structural support for the tibial implants in this series. The potential for long-term biologic fixation may provide durability for these tibial reconstructions. Long-term follow-up and comparison with alternative reconstructive techniques will be required to evaluate the true effectiveness of this treatment approach.
Computers in the Professional Practice of Design (1994)

&lt;p&gt;While CADD technology is becoming commonplace in most design firms today, the wherewithal to take full advantage of computer technology generally as a business tool is often missing. This book will give the reader that “holistic''information on how to integrate the CADD function with other common applications--from word processing of construction documents to creating project budget spreadsheets to project management to database management. The book will touch on examples of commonly used software packages and hardware platforms, but will otherwise treat those subjects generically. &lt;/p&gt;
Levonadifloxacin, a Novel Benzoquinolizine Fluoroquinolone, Modulates Lipopolysaccharide-Induced Inflammatory Responses in Human Whole-Blood Assay and Murine Acute Lung Injury Model (2020)

Fluoroquinolones are reported to possess immunomodulatory activity; hence, a novel benzoquinolizine fluoroquinolone, levonadifloxacin, was evaluated in lipopolysaccharide-stimulated human whole-blood (HWB) and mouse acute lung injury (ALI) models. Levonadifloxacin significantly mitigated the inflammatory responses in an HWB assay through inhibition of proinflammatory cytokines and in the ALI model by lowering lung total white blood cell count, myeloperoxidase, and cytokine levels. The immunomodulatory effect of levonadifloxacin, along with promising antibacterial activity, is expected to provide clinical benefits in the treatment of infections.
1X deep-UV lithography with chemical amplification for 1-micron DRAM production (1990)

This paper describes methods used and results obtained in the production of 1-megabit (Mb) DRAM chips, using a chemically amplified tertiary-butoxy carhonyl hydroxystyrene (t-BOC) resist and 1X lithography. 'Flie internally developed resist provided high sensitivity and contrast, for I rn resolution on a Perkin Elmer Micralign model 500 (PE 500) in the deep UV. Characterization, and modification of the PE 500 were required for this first application in the deep UV. The manufacturing process had photo limited yield in excess of 95% with throughput of 100 wafers per hour.
Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations (2007)

Escape from T cell-mediated immune responses affects the ongoing evolution of rapidly evolving viruses such as HIV. By applying statistical approaches that account for phylogenetic relationships among viral sequences, we show that viral lineage effects rather than immune escape often explain apparent human leukocyte antigen (HLA)-mediated immune-escape mutations defined by older analysis methods. Phylogenetically informed methods identified immune-susceptible locations with greatly improved accuracy, and the associations we identified with these methods were experimentally validated. This approach has practical implications for understanding the impact of host immunity on pathogen evolution and for defining relevant variants for inclusion in vaccine antigens.
Asymmetric distribution of type IV pili triggered by directional light in unicellular cyanobacteria (2017)

The type IV pili (T4P) system is a supermolecular machine observed in prokaryotes. Cells repeat the cycle of T4P extension, surface attachment, and retraction to drive twitching motility. Although the properties of T4P as a motor have been scrutinized with biophysics techniques, the mechanism of regulation remains unclear. Here we provided the framework of the T4P dynamics at the single-cell level in <i>Synechocystis</i> sp. PCC6803, which can recognize light direction. We demonstrated that the dynamics was detected by fluorescent beads under an optical microscope and controlled by blue light that induces negative phototaxis; extension and retraction of T4P was activated at the forward side of lateral illumination to move away from the light source. Additionally, we directly visualized each pilus by fluorescent labeling, allowing us to quantify their asymmetric distribution. Finally, quantitative analyses of cell tracking indicated that T4P was generated uniformly within 0.2 min after blue-light exposure, and within the next 1 min the activation became asymmetric along the light axis to achieve directional cell motility; this process was mediated by the photo-sensing protein, PixD. This sequential process provides clues toward a general regulation mechanism of T4P system, which might be essentially common between archaella and other secretion apparatuses.
Characterization of Enkephalin Release from Rat Striatum (1981)

Using antisera specific for methionine- and leucine-enkephalin, we studied the characteristics of the release of these peptides from rat striatal slices. Only 2-3% of the total tissue stores of enkephalin could be released by potassium-depolarization; similar percentages were released from globus pallidus, thalamus, and nucleus accumbens. Enkephalin release from hippocampus could not be detected. The striatal release of both enkephalins was affected similarly by changes in potassium and calcium levels in the superfusion medium. Lithium has no effect on either basal or potassium-stimulated release; tyr-arg did not affect basal release of either peptide. Striatal enkephalin levels were stable during the short-term incubation periods used in these experiments.
Material Optimisation for Optical Data Storage (2005)

High throughput synthesis and screening methodologies of optical data storage materials have allowed an in depth study of more than 4000 compositions. We report on the optical and electrical compositional dependence of these materials.
Polysialyltransferase: A New Target in Metastatic Cancer (2012)

Polysialic acid (polySia) is a carbohydrate polymer critical for neuronal cell migration and axon pathfinding in embryonic development. Besides brain regions requiring persistent neuronal plasticity, polySia is essentially absent from the adult body. However, polySia is aberrantly re-expressed on many tumours, where it decorates the surface of NCAM (neuronal cell adhesion molecule) and modulates cell adhesion, migration and invasion. PolySia-NCAM expression is strongly associated with poor clinical prognosis and correlates with aggressive and invasive disease in many cancers, including lung cancer, neuroblastoma and gliomas. The synthesis of polySia is mediated by two polysialyltransferases (polySTs), ST8SiaIV (PST) and particularly ST8SiaII (STX) in cancer cells. The demonstration that polyST knock-down negates events associated with tumour cell dissemination indicates that PST and STX are validated targets. Selective inhibition of polySTs therefore presents a therapeutic opportunity to inhibit tumour invasion and metastasis.
ATP Modulates Subunit-Subunit Interactions in an ATP-binding Cassette Transporter (MalFGK2) Determined by Site-directed Chemical Cross-linking (2000)

The binding protein-dependent maltose transport system of enterobacteria (MalFGK(2)), a member of the ATP-binding cassette (ABC) transporter superfamily, is composed of two integral membrane proteins, MalF and MalG, and of two copies of an ATPase subunit, MalK, which hydrolyze ATP, thus energizing the translocation process. In addition, an extracellular (periplasmic) substrate-binding protein (MalE) is required for activity. Ligand translocation and ATP hydrolysis are dependent on a signaling mechanism originating from the binding protein and traveling through MalF/MalG. Thus, subunit-subunit interactions in the complex are crucial to the transport process but the chemical nature of residues involved is poorly understood. We have investigated the proximity of residues in a conserved sequence ("EAA" loop) of MalF and MalG to residues in a helical segment of the MalK subunits by means of site-directed chemical cross-linking. To this end, single cysteine residues were introduced into each subunit at several positions and the respective malF and malG alleles were individually co-expressed with each of the malK alleles. Membrane vesicles were prepared from those double mutants that contained a functional transporter in vivo and treated with Cu(1,10-phenanthroline)(2)SO(4) or bifunctional cross-linkers. The results suggest that residues Ala-85, Lys-106, Val-114, and Val-117 in the helical segment of MalK, to different extents, participate in constitution of asymmetric interaction sites with the EAA loops of MalF and MalG. Furthermore, both MalK monomers in the complex are in close contact to each other through Ala-85 and Lys-106. These interactions are strongly modulated by MgATP, indicating a structural rearrangement of the subunits during the transport cycle. These data are discussed with respect to current transport models.
Director Structures of Cholesteric Diffraction Gratings (2001)

Abstract We study director structures of electrically-controlled cholesteric diffraction gratings (CDG's). The cholesteric liquid crystal (LC) is confined between two transparent non-patterned electrodes with either planar or homeotropic anchoring. In cells with planar alignment, the applied electric field causes reorientation of the initial (zero field) planar state and creates one-dimensionally modulated structures in the plane of the cell. The modulations occur via two distinct scenarios: (I) nucleation and expansion of ‘stripes’ and (II) undulation of quasinematic layers in the plane normal to the cell's plates. In the cells with homeotropic surface alignment, modulated structures exist without applied voltage. Magnetic field is used to provide uniform orientation of these structures. Confocal microscope studies and computer simulations are carried out to reveal the fine structure of the CDG's.
Performance analysis of a QAM adaptive receiver for 1.6 Mbps digital subscriber line transmission (2003)

The asymmetric digital subscriber line service attempts to provide 1.6 Mb/s data transmission over a single twisted-pair copper loop for distances up to 18000 ft. The authors investigate the various system components necessary to realize such a system on a single integrated circuit. They discuss the modulation format, adaptive equalization and its convergence, and system sensitivity to sampling phase error. A comparison of conventional quadrature amplitude modulation (QAM) and pulse amplitude modulation (PAM) schemes is presented. It is concluded that a QAM-based system can meet the system objectives. The use of fractionally spaced equalization and error prediction as means of improving SNR and reducing the hardware complexity is investigated for such a system. It is shown that with 6 T/2-spaced feedforward equalizer taps, eight decision-feedback equalizer taps, and two error predictor taps, the proposed digital QAM system can achieve performance close to that of an ideal infinite-length equalizer.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>