gebhart/patrepeval huggingface dataset:
A novel thermostable polymerase for RNA and DNA loop-mediated isothermal amplification (LAMP) (2014)

Meeting the goal of providing point of care (POC) tests for molecular detection of pathogens in low resource settings places stringent demands on all aspects of the technology. OmniAmp DNA polymerase (Pol) is a thermostable viral enzyme that enables true POC use in clinics or in field by overcoming important barriers to isothermal amplification. In this paper, we describe the multiple advantages of OmniAmp Pol as an isothermal amplification enzyme and provide examples of its use in loop-mediated isothermal amplification (LAMP) for pathogen detection. The inherent reverse transcriptase activity of OmniAmp Pol allows single enzyme detection of RNA targets in RT-LAMP. Common methods of nucleic acid amplification are highly susceptible to sample contaminants, necessitating elaborate nucleic acid purification protocols that are incompatible with POC or field use. OmniAmp Pol was found to be less inhibited by whole blood components typical in certain crude sample preparations . Moreover, the thermostability of the enzyme compared to alternative DNA polymerases (Bst) and reverse transcriptases allows pretreatment of complete reaction mixes immediately prior to amplification, which facilitates amplification of highly structured genome regions. Compared to Bst, OmniAmp Pol has a faster time to result, particularly with more dilute templates. Molecular diagnostics in field settings can be challenging due to the lack of refrigeration. The stability of OmniAmp Pol is compatible with a dry format that enables long term storage at ambient temperatures. A final requirement for field operability is compatibility with either commonly available instruments or, in other cases, a simple, inexpensive, portable detection mode requiring minimal training or power. Detection of amplification products is shown using lateral flow strips and analysis on a real-time PCR instrument. Results of this study show that OmniAmp Pol is ideally suited for low resource molecular detection of pathogens.
Knowledge-based navigation of complex information spaces (1996)

While the explosion of on-line information has brought new opportunities for finding and using electronic data, it has also brought to the forefront the problem of isolating useful information and making sense of large multi-dimension information spaces. We have built several developed an approach to building data &quot;tour guides,&quot; called FindMe systems. These programs know enough about an information space to be able to help a user navigate through it. The user not only comes away with items of useful information but also insights into the structure of the information space itself. In these systems, we have combined ideas of instance-based browsing, structuring retrieval around the critiquing of previously-retrieved examples, and retrieval strategies, knowledge-based heuristics for finding relevant information. We illustrate these techniques with several examples, concentrating especially on the RentMe system, a FindMe system for helping users find suitable rental apartments in the Chica...
HORNET-A packet-switched WDM network: optical packet transmission and recovery (1999)

The hybrid optoelectronic ring network (HORNET) is a novel packet-switched wavelength-division-multiplexed metropolitan area network (MAN). HORNET uses a combination of optical and electronic packet-switching and an optical carrier sense multiple access with collision avoidance (CSMA/CA) media access scheme to efficiently provide large bandwidth to many users. The HORNET optical packets consist of 2.5-Gb/s payload data, an embedded 2.5-GHz clock tone, and a subcarrier-multiplexed (SCM) header for CSMA/CA. We are constructing an experimental testbed to demonstrate the ability of HORNET nodes to transmit and receive packets, to recover the destination node address carried by the SCM header, and to perform fast clock and data recovery with minimal overhead within the HORNET packet receiver.
A new approach in the development of no-flow underfill materials for both eutectic and lead-free solders with high melting temperature (2002)

No-flow underfill technology has been drawing attention due to its potential advantages over conventional underfill technology and several no-flow underfill materials have been developed and reported. However, most of these materials are unsuitable for lead-free solder applications that usually have higher melting temperatures than eutectic solder. Due to increasing environmental concerns, demand for friendly lead-free solders has increased. This paper demonstrates the study of two new formulas of no-flow underfill developed for lead-free solders with melting point around 220/spl deg/C. These novel formulas use a liquid curing catalyst to provide ease in preparation of the no-flow underfill materials and more choice in combining fluxing agents. In this study, the curing kinetics, glass transition temperature (T/sub g/), thermal expansion coefficient (TCE), storage modulus (E') and loss modulus (E") of these materials were studied with differential scanning calorimetry (DSC), thermo-mechanical analysis (TMA), and dynamic-mechanical analysis (DMA). The pot-life in terms of viscosity of these materials was characterized with a stress rheometer. The adhesive strength of the material on the surface of silicon chip was studied with a die-shear instrument. The materials curing kinetics were studied with DSC. The materials compatibility to the solder penetration and wetting on copper clad during solder reflow was investigated with both eutectic and no-lead solders on copper laminated FR-4 organic boards and heated in a reflow oven.
Nonisocyanate polyurethanes for adhesives and coatings (2002)

Polyurethane adhesives and coatings are widely used in Microelectronics and Photonics. The novel matrix of advanced nonisocyanate polyurethane (NIPU) coatings and adhesives are formed from two oligomers, one of them contains terminated cyclocarbonate groups (CC-oligomer), second terminated primary amines groups. As a result of forming an intramolecular bond and blockage of carbonyl oxygen it is considerably lowers the susceptibility of the whole urethane group to hydrolysis. We have elaborated a few technologies for the synthesis of CC-oligomers with different structures that give us possibility for preparing coatings from high elastic to very hard. By the data of IR-spectroscopy investigation the process of curing different CC-oligomers and primary amine oligomers was studied and give us all the needed information for many coating compositions' preparing according a lot of requests for a wide spectrum of industrial, decorative and another types of coatings. The chemical resistance and permeability of hybrid nonisocyanate polyurethane (HNIPU) coatings is 1.5-2.5 times better in comparison with conventional polyurethane coatings of the similar structure without the intermolecular hydrogen bond. Corrosive passive adhesives were prepared by a new method of their synthesis the method of multiplication. In the report will present the data of their testing by ASTM, DIN and BS. At the end of 2001 the industrial production of different nonisocyanate polyurethane systems for coating, adhesives and sealant will be established in the USA.
Novel, Highly Potent Adenosine Deaminase Inhibitors Containing the Pyrazolo[3,4-<i>d</i>]pyrimidine Ring System. Synthesis, Structure−Activity Relationships, and Molecular Modeling Studies (2005)

This study reports the synthesis of a number of 1- and 2-alkyl derivatives of the 4-aminopyrazolo[3,4-d]pyrimidine (APP) nucleus and their evaluation as inhibitors of ADA from bovine spleen. The 2-substituted aminopyrazolopyrimidines proved to be potent inhibitors, most of them exhibiting K(i) values in the nanomolar/subnanomolar range. In this series the inhibitory activity is enhanced with the increase in length of the alkyl chain, reaching a maximum with the n-decyl substituent. Insertion of a 2'-hydroxy group in the n-decyl chain gave 3k, whose (R)-isomer displayed the highest inhibitory potency of the series (K(i) 0.053 nM), showing an activity 2 orders of magnitude higher than that of (+)-EHNA (K(i) 1.14 nM), which was taken as the reference standard. Docking simulations of aminopyrazolopyrimidines into the ADA binding site were also performed, to rationalize the structure-activity relationships of this class of inhibitors.
Rapid Synthesis of New DNMT Inhibitors Derivatives of Procainamide (2011)

DNA methyltransferases (DNMTs) are responsible for DNA methylation, an epigenetic modification involved in gene regulation. Families of conjugates of procainamide, an inhibitor of DNMT1, were conceived and produced by rapid synthetic pathways. Six compounds resulted in potent inhibitors of the murine catalytic Dnmt3A/3L complex and of human DNMT1, at least 50 times greater than that of the parent compounds. The inhibitors showed selectivity for C5 DNA methyltransferases. The cytotoxicity of the inhibitors was validated on two tumour cell lines (DU145 and HCT116) and correlated with the DNMT inhibitory potency. The inhibition potency of procainamide conjugated to phthalimide through alkyl linkers depended on the length of the linker; the dodecane linker was the best.
Coupled surface-subsurface flow hydrodynamic model for surface irrigation (2013)

<abstract> <bold>Abstract.</bold> The coupled surface-subsurface flow model for surface irrigation can effectively simulate the non-linear interaction processes of surface-subsurface flow as well as the soil moisture redistribution processes. In this study, a new coupled surface-subsurface flow hydrodynamic model is constructed based on the governing equations of a 1D complete hydrodynamic model, which is solved using the hybrid numerical method, and a 1D subsurface flow model, which is solved using a proposed finite-volume method with fourth-order accuracy. The surface water depth obtained from the continuous equation of the complete hydrodynamic model for surface irrigation is set as the upper boundary condition, and the infiltration water depth value is calculated using the subsurface flow model. Subsequently, the modified new surface water depth is obtained and is still set as the upper boundary condition for the subsurface flow model, the next new surface water depth can then be obtained. In this iteration process, the convergence of surface and infiltration water depth is reached. The converged surface water depth is then fed back to the momentum conservation equation of the complete hydrodynamic model for surface irrigation to maintain the momentum conservation. Then, the coupled surface-subsurface flow can be simulated and the coupling process ia labeled hybrid coupling method. The validation results showed that the proposed coupled model has better simulation accuracy and stability than that of two existed internal iterative coupled models. Moreover, the computational efficiency of the proposed coupled model is 0.7 times higher than those of the other two coupled models.
Simple forms for equations of rays in gradient-index lenses (1990)

The calculation of the shape of an optical ray in a gradient-index lens is often greatly simplified by the use of formalism in which the equation governing the ray assumes the form of Newton’s law of motion. A new justification of this method is presented, and the method is applied to a gradient-index lens with cylindrical symmetry.
High efficiency electron spin polarization analyzer based on exchange scattering at Fe∕W(001) (2008)

We report on a compact electron spin analyzer based on exchange scattering from a magnetic surface. The heart of the detector is an Fe(001) thin film grown on W(001) with chemisorbed oxygen in the p(1 x 1) structure. The device is mounted at the exit of an energy dispersive analyzer and works at a scattering energy of about 13.5 eV. Its figure of merit is 2 x 10(-3), combined with an excellent stability of more than 2 weeks in UHV.
Compiler-directed data prefetching in multiprocessors with memory hierarchies (2014)

Memory hierarchies are used by multiprocessor systems to reduce large memory access times. It is necessary to automatically manage such a hierarchy, to obtain effective memory utilization. In this paper, we discuss the various issues involved in obtaining an optimal memory management strategy for a memory hierarchy. We present an algorithm for finding the earliest point in a program that a block of data can be prefetched. This determination is based on the control and data dependencies in the program. Such a method is an integral part of more general memory management algorithms. We demonstrate our method's potential by using static analysis to estimate the performance improvement afforded by our prefetching strategy and to analyze the reference patterns in a set of Fortran benchmarks. We also study the effectiveness of prefetching in a realistic shared-memory system using an RTL-level simulator and real codes. This differs from previous studies by considering prefetching benefits in the presence of network contention.
Pneumatic low-coherence interferometry otoscope to quantify tympanic membrane mobility and middle ear pressure (2018)

Pneumatic otoscopy to assess the mobility of the tympanic membrane (TM) is a highly recommended diagnostic method of otitis media (OM), a widespread middle ear infection characterized by the fluid accumulation in the middle ear. Nonetheless, limited depth perception and subjective interpretation of small TM displacements have challenged the appropriate and efficient examination of TM dynamics experienced during OM. In this paper, a pneumatic otoscope integrated with low coherence interferometry (LCI) was adapted with a controlled pressure-generating system to record the pneumatic response of the TM and to estimate middle ear pressure (MEP). Forty-two ears diagnosed as normal (n = 25), with OM (n = 10), or associated with an upper respiratory infection (URI) (n = 7) were imaged with a pneumatic LCI otoscope with an axial, transverse, and temporal resolution of 6 µm, 20 µm, and 1 msec, respectively. The TM displacement under pneumatic pressure transients (a duration of 0.5 sec with an intensity of ± 150 daPa) was measured to compute two metrics (compliance and amplitude ratio). These metrics were correlated with peak acoustic admittance and MEP from tympanometry and statistically compared via Welch's <i>t-</i>test. As a result, the compliance represents pneumatic TM mobility, and the amplitude ratio estimates MEP. The presence of a middle ear effusion (MEE) significantly decreased compliance (p<0.001). The amplitude ratio of the OM group was statistically less than that of the normal group (p<0.01), indicating positive MEP. Unlike tympanometry, pneumatic LCI otoscopy quantifies TM mobility as well as MEP regardless of MEE presence. With combined benefits of pneumatic otoscopy and tympanometry, pneumatic LCI otoscopy may provide new quantitative metrics for understanding TM dynamics and diagnosing OM.
COIL technology development at Boeing (2002)

The historical COIL contributions at the McDonnell Douglas Research Laboratory, the Rocketdyne Division of Rockwell International and Boeing's Laser and Electro-Optic Systems organization are briefly described. The latter organization now contains the capabilities of the two heritage organizations. Boeing's new high pressure sealed COIL is also described.
Neurosecretory-like material in 3rd- and 4th-stage<i>Dirofilaria immitis</i>larvae (Nematoda: Filarioidea) (1989)

Phase-interference microscopic examination of the infective, post-infective 3rd-stage and 4th-stage larvae of Dirofilaria immitis has identified a single cell body in each of the paired lateral amphidial nerves which undergoes characteristic morphological change during the development from 3rd- to 4th-stage larvae. Acetaldehyde-fuchsin staining of worm sections revealed fuchsinophilic material in the precise location of the amphidial nerve-cell bodies observed by phase-interference microscopy. This material was found in 70% of infective larvae recovered from mosquitoes and in 100% of larvae recovered from micropore chambers 24 h after implantation into BALB/C mice. In pre-moult larvae recovered at 42 h (Experiment 1) and at 48 h (Experiment 2) fuchsinophilic material was demonstrable, but no staining was observed in those larvae in which separation of the 3rd- and 4th-stage cuticles had occurred. No such material was observed in 4th-stage larvae recovered from chambers after 74 h, and in these larvae the amphidial nerve-cell bodies were not discernible. These cytological observations are consistent with a cycle of elaboration and release of neurosecretion associated with moulting in D. immitis.
APPLICATION OF MODIFIED ATMOSPHERE PACKAGING AND HUMIDITY CONTROL TO EXTEND THE STORAGE LIFE OF GRAPE VARIETIES GROWN IN EASTERN UNITED STATES - A COMPARATIVE STUDY (1990)

In 1987, 1988, and 1989, the behavior of four different table grape varieties including Alden, Concord, Himrod, and Vanessa were studied during storage at 0°C. The first objective of our study was to determine the behavior of table grapes in modified atmosphere packages in terms of general acceptance. After three years of experimenting with these three films we were able to obtain a modified atmosphere of about 3% O 2 and 10-15% CO 2 at 0°C using a 3 mil thickness LDPE. Our second objective was to use moisture absorbents as a means of reducing the relative humidity inside the void volume of a package by the inclusion of different desiccants in the package to establish a desirable relative humidity. Examining different storage characteristics, our data showed that `Himrod', `Vanessa', and `Concord' grape clusters stored in the presence of KNO 3 and KCl had better quality compared to grape clusters stored in the presence of other sorption compounds or controls with no sorbants.
Opportunistic traffic scheduling in cellular data networks (2012)

Cellular data networks are experiencing a serious capacity crunch in the face of exponential increase in mobile data traffic volume. New traffic management techniques are needed to improve network and user perceived performance. In this work, we consider the existence of a higher-layer, agent-based scheduling system that could potentially delay scheduling of low priority flows at peak loads. The priorities are assumed to be user or application tagged, either automatically or manually. The general goal is to potentially move the low priority flows in time and space opportunistically to reduce the overall resource needs. We develop and evaluate two scheduling schemes - one based on a straightforward greedy method that requires real-time load monitoring and the other based on model-based estimation of traffic loads and subscriber mobility based on historical data. Simulation results using a large-scale cellular network trace data collected inside a nationwide network show the potential of these approaches in reducing base station resource requirements. This indirectly demonstrates that if providers can incentivize subscribers to tag certain flows as low priority, they can potentially accommodate a significant number of additional subscribers in the same network without expending any additional resource.
Multilevel dynamic bandwidth allocation using buffer observation for cousin-fair access systems (2011)

This paper proposes two techniques for reducing the buffer size and computational complexity of an aggregation layer-2 switch (L2SW) in access systems by using buffer observation and multilevel dynamic bandwidth allocation (DBA). The conventional architecture for providing cousin fairness, which realizes fairness among multiple passive optical network (PON) branches, needs a huge buffer in an L2SW that depends on the number of optical network units (ONUs). Our proposal reduces the required buffer size for an L2SW that depends on the number of optical subscriber units (OSUs), which is much smaller than the number of ONUs. The proposed techniques reduce by more than two thirds the amount of unfairly distributed bandwidth caused by the lack of cousin fairness. A simulation result obtained with our proposed approach shows improved cousin fairness among multiple PON branches with a smaller buffer.
Interleukin 10 (IL-10), not IL-4 or interferon-gamma production, correlates with progression of joint destruction in rheumatoid arthritis. (2001)

Both interleukin 4 (IL-4) and IL-10, separately and in combination, and under in vitro and in vivo conditions in animals, have been reported to inhibit characteristics of rheumatoid arthritis (RA) and experimentally induced arthritis. We investigated if IL-10 and IL-4 production, as well as interferon-gamma (IFN-gamma) production, opposing IL-4, were related to RA disease variables. A method was chosen to exclude the influence of age and disease duration.We selected RA patients with mild and severe disease. Inclusion criteria were erythrocyte sedimentation rate (ESR) < or = 28 mm/h and > or = 50, C-reactive protein (CRP) < or = 20 and > or = 30, Thompson joint score < or = 60 and > or = 100 and radiographic joint damage score, Sharp score < or = 30 and > or = 40. Age and disease duration were restricted: 30 to 70 years and 5 to 15 years, respectively. Peripheral blood mononuclear cells were isolated and the ex vivo 48 h production of T cell IL-10, IL-4, and IFN-gamma (after CD3-CD28 stimulation) was assessed and was correlated to clinical variables.Only IL-10 production differed significantly between the 2 groups of RA patients, being highest in the "mild" group. Taking all patients together, a strong negative correlation was found between IL-10 production and radiographic joint damage (r = -0.53, p < 0.001) as well as progression of joint damage (r = -0.56, p < 0.0001). Similar negative correlations, although less powerful, were found between IL-10 production and ESR, CRP, and Thompson joint score. No correlation was found for IFN-gamma, IL-4, or the ratio of the 2 with disease activity variables or joint damage.The findings suggest that the high IL-10 production found in patients with RA may be protective, especially against progression of joint destruction in RA.
Morphus: Supporting Online Reconfigurations in Sharded NoSQL Systems (2015)

While sharded NoSQL stores offer high availability, reconfiguration operations present a major pain point in deployments today. For instance, in order to change a configuration setting such as the shard (or primary) key of a database table, the prevalent solutions entail shutting down the database, exporting and re-importing the table, and restarting the database. This goes against the NoSQL philosophy of high availability of data. Our system, called Morph us, provides support towards reconfigurations for NoSQL stores in an online manner. Morphus allows read and write operations to continue concurrently with the data transfer among servers. Morphus works for NoSQL stores that feature master-slave replication, range partitioning, and flexible data placement. This paper presents: i) a systems architecture for online reconfigurations, incorporated into Mongo DB, and ii) optimal algorithms for online reconfigurations. Our evaluation using realistic workloads shows that Morphus completes reconfiguration efficiently, offers high availability, and incurs low overhead for reads and writes.