gebhart/patrepeval huggingface dataset:
Two Approaches to Enhance the Processivity and Salt Tolerance of Staphylococcus aureus DNA Polymerase (2019)

In this article, two engineering-strategies were carried out to enhance the processivity of the DNA polymerase used in recombinase polymerase amplification (RPA). We demonstrate that covalent linkage of a non-specific, double-stranded DNA binding protein, Sso7d, to the large fragment of Staphylococcus aureus Pol I (Sau) caused a moderate enhancement of processivity and a significant improvement in the salt tolerance of Sau. Meanwhile, we provide evidence suggesting that insertion of the thioredoxin-binding domain from bacteriophage T7 DNA polymerase into the analogous position of the large fragment of Sau dramatically enhanced the processivity and mildly increased the salt tolerance of Sau when a host DNA binding protein, thioredoxin, was annexed. Both of these two strategies did not improve the amplifying performance of Sau in RPA, indicating that optimum processivity is crucial for amplifying efficiency.
Tissue reactions to bacteria-challenged implantable leads with enhanced infection resistance (1998)

Tissue reactions to implantable pacemaker leads were investigated in an early infection model in rabbits. Both standard leads and surface-modified leads were used. The surface modification technique was applied to achieve controlled release of the antibiotic gentamicin. The insulating polyurethane tubing material of the leads was provided with an acrylic acid/acrylamide copolymer surface graft and then loaded with gentamicin. Implantation periods varied from day 4, to week 3 1/2, to week 10. We investigated tissue reactions in the absence of an infectious challenge and also the efficacy of surface-modified leads in preventing infection after challenge with Staphylococcus aureus was evaluated. It was demonstrated that the applied surface modification did not induce adverse effects although during early postimplantation an increase in infiltration of granulocytes and macrophages and wound fluid and fibrin deposition were observed. After bacterial challenge, standard leads were heavily infected at each explantation period, denoted by abscesses, cellular debris, and bacterial colonies. In contrast, little or no infection was observed, either macroscopically or by bacterial cultures, with the surface-modified leads. Microscopy showed little evidence of the bacterial challenge, and that primarily at day 4. It was concluded that the applied surface modification demonstrated enhanced infection resistance and thus represents a sound approach to the battle against infectious complications with biomaterials.
Dual-fiber point diffraction interferometer to measure the wavefront aberration of an imaging system (2020)

A dual-fiber point diffraction interferometer is built to measure the wavefront aberration of an imaging system with high precision. The optical intensity of the test light and reference light are controlled independently, so that high interference contrast can be obtained. The interferometer has several advantages: high precision, a flexible structure, and a quasi-common optical path. System errors of the interferometer that influence the measurement accuracy are considered and calibrated. In the experiments, a projection lens with numerical aperture of 0.3 is measured. The measured wavefront error is 1.5 nm rms, and the measurement repeatability is 35 pm rms.
Composite silicide gate electrodes&#8212;Interconnections for VLSI device technologies (1980)

A potentially severe limit on density, performance, and wirability of polysilicon-gate technologies for VLSI applications, is the high resistivity of polycrystalline silicon. Composite structures of highly conductive molybdenum or tungsten disilicide on top of polysilicon (polycide) are shown to be a viable alternative gate electrode and interconnect level. Sheet resistance values of 1-3 Ω/□ for an integrated structure are easily attainable. IGFET devices fabricated to channel lengths of ≥ 1.4 µm show the polycide devices to be indistinguishable from normal polysilicon gate devices.
Very concurrent mark-&-sweep garbage collection without fine-grain synchronization (1998)

We describe a new incremental algorithm for the concurrent reclamation of a program's allocated, yet unreachable, data. Our algorithm is a variant of mark-&-sweep collection that---unlike prior designs---runs mutator, marker, and sweeper threads concurrently without explicit fine-grain synchronization on shared-memory multiprocessors. A global, but infrequent, synchronization coordinates the per-object coloring marks used by the three threads; fine-grain synchronization is achieved without locking via the basic memory consistency guarantees commonly provided by multiprocessor hardware. We have implemented two versions of this algorithm (called VCGC): in the Inferno operating system and in the SML/NJ ML compiler. Measurements, compared to a sequential generational collector, indicate that VCGC can substantially reduce worst-case pause latencies as well as reduce overall memory usage. We remark that the degrees of freedom on the rates of marking and sweeping enable exploration of a range of resource tradeoffs, but makes "optimal" tuning for even a small set of applications difficult.
Interleukin-2 induced immune effects in human immunodeficiency virus-infected patients receiving intermittent interleukin-2 immunotherapy (2001)

To characterize the immunological effects of intermittent IL-2 therapy, which leads to selective increases in CD4+ T lymphocytes in HIV-infected patients, 11 patients underwent extensive immunological evaluation. While IL-2 induced changes in both CD4+ and CD8+ cell number acutely, only CD4+ cells showed sustained increases following discontinuation of IL-2. Transient increases in expression of the activation markers CD38 and HLA-DR were seen on both CD4+ and CD8+ cells, but CD25 (a chain of the IL-2 receptor) increased exclusively on CD4+ cells. This increase in CD25 expression was sustained for months following discontinuation of IL-2, and was seen in naive as well as memory cells. IL-2 induced cell proliferation, but tachyphylaxis to these proliferative effects developed after 1 week despite continued IL-2 administration. It thus appears that sustained CD25 expression selectively on CD4+ cells is a critical component of the immunological response to IL-2, and that intermittent administration of IL-2 is necessary to overcome the tachyphylaxis to IL-2-induced proliferation.
Gas generators produce hydrogen-rich fuel (1975)

Resulting fuel, which is produced from gasoline and water, can be burned by gasoline engines with significantly reduced pollution and improved fuel economy.
Accelerating Relational Databases by Leveraging Remote Memory and RDMA (2016)

Memory is a crucial resource in relational databases (RDBMSs). When there is insufficient memory, RDBMSs are forced to use slower media such as SSDs or HDDs, which can significantly degrade workload performance. Cloud database services are deployed in data centers where network adapters supporting remote direct memory access (RDMA) at low latency and high bandwidth are becoming prevalent. We study the novel problem of how a Symmetric Multi-Processing (SMP) RDBMS, whose memory demands exceed locally-available memory, can leverage available remote memory in the cluster accessed via RDMA to improve query performance. We expose available memory on remote servers using a lightweight file API that allows an SMP RDBMS to leverage the benefits of remote memory with modest changes. We identify and implement several novel scenarios to demonstrate these benefits, and address design challenges that are crucial for efficient implementation. We implemented the scenarios in Microsoft SQL Server engine and present the first end-to-end study to demonstrate benefits of remote memory for a variety of micro-benchmarks and industry-standard benchmarks. Compared to using disks when memory is insufficient, we improve the throughput and latency of queries with short reads and writes by 3X to 10X, while improving the latency of multiple TPC-H and TPC-DS queries by 2X to 100X.
Microbial de-mannosylation and mannosylation of teicoplanin derivatives. (1991)

The single components of the teicoplanin complex, glycopeptide antibiotics active against Gram-positive bacteria, can be converted in the corresponding de-mannosyl derivatives by cultures of Nocardia orientalis NRRL 2450 or Streptomyces candidus NRRL 3218. Conversely, teicoplanin aglycone and other teicoplanin de-mannosyl derivatives can be converted in the corresponding teicoplanin mannosyl derivatives by cultures of Actinoplanes teichomyceticus ATCC 31121. The biological transformation yields are approximately 40% for de-mannosylation and 90% for mannosylation. The processes allow for the preparation of gram quantities of the de-mannosyl derivatives of teicoplanin and of teicoplanin mannosyl derivatives. De-mannosyl teicoplanin and teicoplanin mannosyl-pseudoaglycone were not amenable to preparation by either acidic or basic chemical hydrolysis.
Silicon-based nanowires from silicon wafers catalyzed by cobalt nanoparticles in a hydrogen environment (2005)

We present here the synthesis of silicon-based nanowires directly from silicon wafers at high temperatures and in the presence of cobalt nanoparticles and hydrogen gas. All three ingredients were critical to the growth of Si-based nanowires, which were between 5-60 nm in diameter and microm-mm long. Both heavily coiled and straight Si-based nanowires were made. Experimental evidence suggested that the sources of silicon for the nanowires growth were in the gas phase.
The Value of Rate Regularity and Multiplicity Measures to Detect Ventricular Tachycardia in the Presence of Atrial Fibrillation or Flutter (1994)

The predominant cause of inappropriate therapy by implantable antitachycardia devices with pacing and nonpacing cardioverter defibrillators, is mistaking a fast ventricular response during atrial fibrillation or flutter with true ventricular tachycardia (VT). The distinction between these arrhythmias is an important consideration in addressing the problem of reducing false-positives in detection mechanisms for implantable devices. Dual chamber analysis that examines atrial and ventricular event ratios has been proposed as a solution to this problem, but would still fail in distinguishing paroxysmal VT requiring treatment from a fast but otherwise benign ventricular response during atrial fibrillation or flutter. In this study, two methods for discriminating these tachyarrhythmias were evaluated. Method 1 examined ventricular rate and rate regularity as a method for VT detection. Method 2 combined rate and regularity as well as an additional multiplicity criterion for recognition of atrial flutter with a fast ventricular response. In 20 patients, Method 1 had 100% sensitivity of VT detection and 80% specificity for detection of atrial fibrillation or flutter. Method 2 had 90% sensitivity and 90% specificity. These results suggest that use of these algorithms in future implantable devices would result in a decrease in false-positive device therapies.
Micro-UV detector (2004)

A lightweight, tactical biological agent detection network offers the potential for a detect-to-warn capability against biological aerosol attacks. Ideally, this capability can be achieved by deploying the sensors upwind from the protected assets. The further the distance upwind, the greater the warning time. The technological challenge to this concept is the biological detection technology. Here, cost, size and power are major factors in selecting acceptable technologies. This is in part due to the increased field densities needed to cover the upwind area and the fact that the sensors, when deployed forward, must operate autonomously for long periods of time with little or no long-term logistical support. The Defense Advanced Research Project Agency’s (DARPA) Solid-state Ultraviolet Optical Source (SUVOS) program offers an enabling technology to achieving a detector compatible with this mission. As an optical source, these devices emit excitation wavelengths known to be useful in the detection of biological aerosols. The wavelength band is absorbed by the biological aerosol and results in visible fluorescence. Detection of a biological aerosol is based on the observed intensity of this fluorescence signal compared to a background reference. Historically this has been accomplished with emission sources that are outside the boundaries for low cost, low power sensors. The SUVOS technology, on the other hand, provides the same basic wavelengths needed for the detection process in a small, low power package. ECBC has initiated an effort to develop a network array based on micro UV detectors that utilize the SUVOS technology. This paper presents an overview of the micro UV detector and some of the findings to date. This includes the overall design philosophy, fluid flow calculations to maximize presentation of aerosol particles to the sources, and the fluorescence measurements.
Prefix coding of hierarchical categories for publish-subscribe in mobile wireless environments (2015)

This paper proposes an algorithm called MACH for coding a hierarchical category structure to enable prefix matching between a publication and a subscription. Compared to fixed-length coding, the MACH algorithm generates shorter code lengths without losing the efficiency of matching. In addition, the MACH algorithm automatically identifies the bits that are not necessary for prefix matching. These bits are saved to allow growth of categories. The bit saving is prioritized according to a configurable criterion. Experiments with real world data and synthetic data are conducted to evaluate the benefit of the proposed algorithm.
A Machine Learning Solution for Operational Remote Sensing of Active Wildfires (2020)

Quantitative wildfire behavior data is invaluable for model development and real-time situational awareness during a fire emergency. However, there exists at present no scalable solution to acquire consistent information about active forest fires that is both spatially and temporally explicit. Spaceborne sensors must meet exigent tradeoffs between spatial and temporal resolution, and there is no single platform that allows detailed measurement of fire behaviour from space. To overcome this limitation, we developed a machine learning solution designed to leverage the complementary features of various remote sensing platforms. Our system relies on a machine learning algorithm to statistically downscale Geostationary (GEO) satellite imagery and continuously monitor active fire location with the spatial resolution typical of Low Earth Orbit (LEO) sensors. In order to achieve this, the model trains on LEO imagery, land use information, vegetation properties, and terrain data. This paper describes the system architecture and demonstrates its performance in two case studies. Results presented here prove the viability of the proposed strategy and encourage further development.
A novel redundancy technique for mobile networks (2002)

In a mobile network, the information transmission is done in a relatively noise and burst-error prone shared medium. The two methods commonly used to recover the transmission errors are automatic retransmission request (ARQ) and forward error correction (FEC). The ARQ is issued when errors exceed beyond those that can be corrected by FEC. ARQ implies re-transmission, which wastes a considerable amount of bandwidth and battery energy and creates an undesirable long delay, and can't be tolerated for certain services. We describe a spatial redundancy scheme in a mobile cellular network which is shown to greatly decrease the handoff call termination probability, the forced new call blocking probability and the ARQ probability. The basic idea is to add minimal number of redundant stations (Standby Stations: SS) at strategic locations in the cellular network topology. One of the potential location is the corner where the three adjacent three cells meet. Each SS could be "listening" and quietly monitoring activities on adjacent cells. These strategic locations could also be based on ground and signal profiles, so that fading signals could be easily restored by the SS.
Meningococcal Vaccines (2004)

Monovalent serogroup C conjugate vaccines have been successful in reducing the burden of serogroup C meningococcal disease among infants, older children, and adults in the United Kingdom and Canada. Tetravalent serogroup A/C/W/Y conjugate vaccines are in late stage development. The use of serogroup B capsular polysaccharide as the basis for a vaccine for prevention of serogroup B meningococcal disease has proved problematic. The recent sequencing of the serogroup B genome led to the identification of additional, genome-derived, neisserial antigens, through a process called "reverse vaccinology."
Numerical stability analysis of floating-point computations using software model checking (2010)

Software model checking has recently been successful in discovering bugs in production software. Most tools have targeted heap related programming mistakes and control-heavy programs. However, real-time and embedded controllers implemented in software are susceptible to computational numeric instabilities. We target verification of numerical programs that use floating-point types, to detect loss of numerical precision incurred in such programs. Techniques based on abstract interpretation have been used in the past for such analysis. We use bounded model checking (BMC) based on Satisfiability Modulo Theory (SMT) solvers, which work on a mixed integer-real model that we generate for programs with floating points. We have implemented these techniques in our software verification platform. We report experimental results on benchmark examples to study the effectiveness of model checking on such problems, and the effect of various model simplifications on the performance of model checking.
Droplet displacements and oscillations induced by ultrasonic surface acoustic waves: A quantitative study (2010)

We present an experimental study of a droplet interacting with an ultrasonic surface acoustic wave. Depending on the amplitude of the wave, the drop can either experience an internal flow with its contact line pinned, or (at higher amplitude) move along the direction of the wave also with internal flow. Both situations come with oscillations of the drop free surface. The physical origins of the internal mixing flow as well as the drop displacement and surface waves are still not well understood. In order to give insights of the underlying physics involved in these phenomena, we carried out an experimental and numerical study. The results suggest that the surface deformation of the drop can be related to a combination between acoustic streaming effect and radiation pressure inside the drop.
NMR Signal Amplification by Reversible Exchange of Sulfur‐Heterocyclic Compounds Found In Petroleum (2016)

NMR hyperpolarization via Signal Amplification by Reversible Exchange (SABRE) was employed to investigate the feasibility of enhancing the NMR detection sensitivity of sulfur-heterocycles (specifically 2-methylthiophene and dibenzothiophenes), a family of compounds typically found in petroleum and refined petroleum products. SABRE hyperpolarization of sulfur-heterocycles (conducted in seconds) offers potential advantages of providing structural information about sulfur-containing contaminants in petroleum, thereby informing petroleum purification and refining to minimize sulfur content in refined products such as gasoline. Moreover, NMR spectroscopy sensitivity gains endowed by hyperpolarization potentially allows for performing structural assays using inexpensive, low-magnetic-field (<i>ca</i>. 1 T) high-resolution NMR spectrometers ideally suited for industrial applications in the field.
Efficient Approach to Scheduling of Transient Processes for Time-Constrained Single-Arm Cluster Tools With Parallel Chambers (2018)

In wafer manufacturing, extensive research on the operations of cluster tools under the steady state has been reported. However, with the shrinking down of wafer lot size, such tools are frequently required to switch from handling one lot of wafers to another, resulting in more transient processes, including start-up and close-down ones. Also, wafer residency time constraint is critical for many wafer fabrication processes. To cope with the transient scheduling problem of time-constrained single-arm cluster tools with parallel chambers, based on a generalized backward strategy, this paper first builds timed Petri net models for these two transient processes. Then, two linear programs are derived for the first time to search a feasible schedule with a minimal makespan. Two industrial examples are given to demonstrate the effectiveness of the obtained results at last.
Multi-Parameter Aerosol Scattering Sensor (2011)

This work relates to the development of sensors that measure specific aerosol properties. These properties are in the form of integrated moment distributions, i.e., total surface area, total mass, etc., or mathematical combinations of these moment distributions. Specifically, the innovation involves two fundamental features: a computational tool to design and optimize such sensors and the embodiment of these sensors in actual practice. The measurement of aerosol properties is a problem of general interest. Applications include, but are not limited to, environmental monitoring, assessment of human respiratory health, fire detection, emission characterization and control, and pollutant monitoring. The objectives for sensor development include increased accuracy and/or dynamic range, the inclusion in a single sensor of the ability to measure multiple aerosol properties, and developing an overall physical package that is rugged, compact, and low in power consumption, so as to enable deployment in harsh or confined field applications, and as distributed sensor networks. Existing instruments for this purpose include scattering photometers, direct-reading mass instruments, Beta absorption devices, differential mobility analyzers, and gravitational samplers. The family of sensors reported here is predicated on the interaction of light and matter; specifically, the scattering of light from distributions of aerosol particles. The particular arrangement of the sensor, e.g. the wavelength(s) of incident radiation, the number and location of optical detectors, etc., can be derived so as to optimize the sensor response to aerosol properties of practical interest. A key feature of the design is the potential embodiment as an extremely compact, integrated microsensor package. This is of fundamental importance, as it enables numerous previously inaccessible applications. The embodiment of these sensors is inherently low maintenance and high reliability by design. The novel and unique features include the underlying computational underpinning that allows the optimization for specific applications, and the physical embodiment that affords the construction of a compact, durable, and reliable integrated package. The advantage appears in the form of increased accuracy relative to existing instruments, and the applications enabled by the physical attributes of the resulting configuration
Active Tera Hertz (THz) spoof surface plasmon polariton (SSPP) switch comprising the perfect conductor meta-material (2009)

The feasibility of realizing an active Tera Hertz (THz) switch by utilizing artificially corrugated perfect conductor meta-materials is reported in this paper by demonstrating that the strongly localized THz spoof surface plasmon polariton (SSPP) modes can be easily controlled by changing the refractive index of dielectrics inside a longitudinal metallic structure with a periodic array of grooves. Specifically, the paper shows that incorporation of electro-optical (EO) material such as a nematic liquid crystal (N-LC) into the plasmonic gap leads to a highly compact and efficient THz switch that is activated by a low voltage control-signal.