gebhart/patrepeval huggingface dataset:
Development and validation of an electronic phenotyping algorithm for chronic kidney disease. (2014)

Twenty-six million Americans are estimated to have chronic kidney disease (CKD) with increased risk for cardiovascular disease and end stage renal disease. CKD is frequently undiagnosed and patients are unaware, hampering intervention. A tool for accurate and timely identification of CKD from electronic medical records (EMR) could improve healthcare quality and identify patients for research. As members of eMERGE (electronic medical records and genomics) Network, we developed an automated phenotyping algorithm that can be deployed to identify rapidly diabetic and/or hypertensive CKD cases and controls in health systems with EMRs It uses diagnostic codes, laboratory results, medication and blood pressure records, and textual information culled from notes. Validation statistics demonstrated positive predictive values of 96% and negative predictive values of 93.3. Similar results were obtained on implementation by two independent eMERGE member institutions. The algorithm dramatically outperformed identification by ICD-9-CM codes with 63% positive and 54% negative predictive values, respectively.
Propelling SAT and SAT-based BMC using careset (2010)

We introduce the notion of careset, a subset of variables in a Boolean formula that must be assigned in any satisfying assignment. We propose a restricted branching technique in a CDCL solver (i.e., DPLL-based SAT solver with clause learning) such that every decision path is prefixed with decisions on such a careset. Although finding a non-trivial careset may not be tractable in general, we demonstrate that for a SAT-based bounded model checking (BMC) application we can derive it automatically from the sequential behaviors of programs. Our proposed branching technique significantly reduces the search effort of a CDCL solver, and leads to a performance improvement of 1--2 orders of magnitude over well-known heuristics, and over top-ranked solvers of SAT2009 competition, that do not exploit system-level information. We also discuss the proof complexity of such a restricted CDCL solver.
A stirrer for magnetohydrodynamically controlled minute fluidic networks (2002)

Magnetohydrodynamics may potentially provide a convenient means for controlling fluid flow and stirring fluids in minute fluidic networks. The branches of such fluidic networks consist of conduits with rectangular cross sections. Each conduit has two individually controlled electrodes positioned along opposing walls and additional disk-shaped electrodes deposited in the conduit’s interior away from its sidewalls. The network is positioned in a uniform magnetic field. When one applies a potential difference between a disk-shaped electrode and two wall electrodes acting in tandem, circulatory motion is induced in the conduit. When the potential difference alternates periodically across two or more such configurations, complicated (chaotic) motions evolve. As the period of alternation increases, so does the complexity of the flow. We derive a two-dimensional, time-independent expression for the magnetohydrodynamic creeping flow around a centrally positioned disk-shaped electrode in the limit of zero radius. With the aid of this expression, the trajectories of passive tracers are computed as functions of the alternations protocol and the electrodes’ locations. The theoretical results are qualitatively compared with flow visualization experiments.
Taming hardware event samples for FDO compilation (2010)

Feedback-directed optimization (FDO) is effective in improving application runtime performance, but has not been widely adopted due to the tedious dual-compilation model, the difficulties in generating representative training data sets, and the high runtime overhead of profile collection. The use of hardware-event sampling to generate estimated edge profiles overcomes these drawbacks. Yet, hardware event samples are typically not precise at the instruction or basic-block granularity. These inaccuracies lead to missed performance when compared to instrumentation-based [email protected] In this paper, we use multiple hardware event profiles and supervised learning techniques to generate heuristics for improved precision of basic-block-level sample profiles, and to further improve the smoothing algorithms used to construct edge profiles. We demonstrate that sampling-based FDO can achieve an average of 78% of the performance gains obtained using instrumentation-based exact edge profiles for SPEC2000 benchmarks, matching or beating instrumentation-based FDO in many cases. The overhead of collection is only 0.74% on average, while compiler based instrumentation incurs 6.8%-53.5% overhead (and 10x overhead on an industrial web search application), and dynamic instrumentation incurs 28.6%-1639.2% overhead.
2.9 A 2GHz 244fs-resolution 1.2ps-Peak-INL edge-interpolator-based digital-to-time converter in 28nm CMOS (2016)

Digital-to-time converters (DTC) generate a clock with a time delay (or phase shift) based on a digital input code. They can be used in clock-and-data-recovery (CDR) circuits [1,2], in the feedback or reference path of a phase-locked loop (PLL) [3,4] or as direct phase modulators in outphasing transmitters (OT) [5]. While DTCs in PLLs often operate close to the reference oscillator frequency, CDR and OT DTCs are required to operate at frequencies in the GHz range. DTCs are often built using a multistage segmented architecture, employing separate coarse and fine delay tuning.
Regulation of Cancer Aggressive Features in Melanoma Cells by MicroRNAs (2011)

MicroRNAs (miRNAs) are small non-coding RNAs with regulatory roles, which are involved in a broad spectrum of physiological and pathological processes, including cancer. A common strategy for identification of miRNAs involved in cell transformation is to compare malignant cells to normal cells. Here we focus on identification of miRNAs that regulate the aggressive phenotype of melanoma cells. To avoid differences due to genetic background, a comparative high-throughput miRNA profiling was performed on two isogenic human melanoma cell lines that display major differences in their net proliferation, invasion and tube formation activities. This screening revealed two major cohorts of differentially expressed miRNAs. We speculated that miRNAs up-regulated in the more-aggressive cell line contribute oncogenic features, while the down-regulated miRNAs are tumor suppressive. This assumption was further tested experimentally on five candidate tumor suppressive miRNAs (miR-31, -34a, -184, -185 and -204) and on one candidate oncogenic miRNA (miR-17-5p), all of which have never been reported before in cutaneous melanoma. Remarkably, all candidate Suppressive-miRNAs inhibited net proliferation, invasion or tube formation, while miR-17-5p enhanced cell proliferation. miR-34a and miR-185 were further shown to inhibit the growth of melanoma xenografts when implanted in SCID-NOD mice. Finally, all six candidate miRNAs were detected in 15 different metastatic melanoma specimens, attesting for the physiological relevance of our findings. Collectively, these findings may prove instrumental for understanding mechanisms of disease and for development of novel therapeutic and staging technologies for melanoma.
Mobile location management in ATM networks (1997)

This paper presents two mobile location management algorithms for ATM (asynchronous transfer mode) networks based on the PNNI (private network-to-network interface) standard. The first solution is called the mobile PNNI scheme because it builds on the PNNI routing protocol. It uses limited-scope (characterized by a parameter S) reachability updates, forwarding pointers, and a route optimization procedure. The second solution is called the LR (location registers) scheme because it introduces location registers (such as the cellular home and visitor location registers) into the PNNI standards-based hierarchical networks. This scheme uses a hierarchical arrangement of location registers with the hierarchy limited to a certain level S. Analytical models are set up to compare the average move, search, and total costs per move of these two schemes for different values of the CMR (call-to-mobility ratio), and to provide guidelines for selecting parameters of the algorithms. Results show that at low CMRs (CMR<0.025), the LR scheme performs better than the mobile PNNI scheme. We also observe that the two schemes show a contrasting behavior in terms of the value to be used for the parameter S to achieve the least average total cost. At low CMRs, the parameter S should be high for the mobile PNNI scheme, but low for the LR scheme, and vice versa for high CMRs.
Homogeneous-homeotropic fluorescent liquid crystal cells (1981)

Theoretical and experimental contrast ratios are compared for homogeneous-to-homeotropic liquid-crystal cells containing fluorescent dye molecules activated by ultraviolet light. Two-color fluorescent displays are described in which one active fluor dissolved in the liquid crystal is used as a UV shutter to switch a passive fluor external to the cell. Contrast ratios of about 8 have been achieved simultaneously for both colors, if two polarizers are used and about 7, if only one polarizer is employed.
<title>UV-shifted durable silver coating for astronomical mirrors</title> (2000)

Silver has the highest reflectance of all of the materials, but it tarnishes in the presence of sulfides, chlorides, and oxides in the atmosphere. Also, the silver reflectance is very low at wavelengths below 400 nm making aluminum more desirable mirror coating for the UV region. We have found a way to prevent silver tarnishing by sandwiching the silver layer between two thin layers of NiCrN<SUB>x</SUB>, and to extend the metal's high reflectance down to 200 nm by depositing the (thin) Ag layer on top of Al. Thus, the uv is transmitted through the thin Ag layer below 400 nm wavelength, and is reflected from the Al layer underneath. This UV-shifted durable coating provides a valuable alternative to the aluminum coating for telescope mirror coatings where high throughput and durability are important considerations. The throughput for a telescope with, say, six reflections from silver coatings is (0.97)<SUP>6</SUP> equals 83% compared to (0.92)<SUP>6</SUP> equals 60% for aluminum coatings, or 28% less. The use of silver coatings allows more photons to be collected by primary mirror. Aluminum also has a reflectance dip at 850 nm caused by inter-band transitions which is eliminated by placing the thin Ag layer on top. This paper describes a non-tarnishing silver coating having high reflectance down into the UV region. The average specular reflectance is 70% - 97% in the near-UV, 95% - 99% in the visible region, and >= 99% in the infrared region covering the total wavelength range 200 nm to 10,000 nm.
Bi-criteria studies of mesh network restoration path-length versus capacity tradeoffs (2002)

Mesh-restorable networks are of interest as an alternative to rings for DWDM-based optical networks. We study the capacity design of mesh networks using a bi-criteria formulation to explore the optimal trade-off between restoration capacity and restoration path lengths.
Promotion of Flowering by Apple Latent Spherical Virus Vector and Virus Elimination at High Temperature Allow Accelerated Breeding of Apple and Pear (2016)

Plant viral vectors are superior tools for genetic manipulation, allowing rapid induction or suppression of expression of a target gene in plants. This is a particularly effective technology for use in breeding fruit trees, which are difficult to manipulate using recombinant DNA technologies. We reported previously that if apple seed embryos (cotyledons) are infected with an Apple latent spherical virus (ALSV) vector (ALSV-AtFT/MdTFL1) concurrently expressing the Arabidopsis thaliana florigen (AtFT) gene and suppressing the expression of the apple MdTFL1-1 gene, the period prior to initial flowering (generally lasts 5-12 years) will be reduced to about 2 months. In this study, we examined whether or not ALSV vector technology can be used to promote flowering in pear, which undergoes a very long juvenile period (germination to flowering) similar to that of apple. The MdTFL1 sequence in ALSV-AtFT/MdTFL1 was replaced with a portion of the pear PcTFL1-1 gene. The resulting virus (ALSV-AtFT/PcTFL1) and ALSV-AtFT/MdTFL1 were used individually for inoculation to pear cotyledons immediately after germination in two inoculation groups. Those inoculated with ALSV-AtFT/MdTFL1 and ALSV-AtFT/PcTFL1 then initiated flower bud formation starting one to 3 months after inoculation, and subsequently exhibited continuous flowering and fruition by pollination. Conversely, Japanese pear exhibited extremely low systemic infection rates when inoculated with ALSV-AtFT/MdTFL1, and failed to exhibit any induction of flowering. We also developed a simple method for eliminating ALSV vectors from infected plants. An evaluation of the method for eliminating the ALSV vectors from infected apple and pear seedlings revealed that a 4-week high-temperature (37°C) incubation of ALSV-infected apples and pears disabled the movement of ALSV to new growing tissues. This demonstrates that only high-temperature treatment can easily eliminate ALSV from infected fruit trees. A method combining the promotion of flowering in apple and pear by ALSV vector with an ALSV elimination technique is expected to see future application as a new plant breeding technique that can significantly shorten the breeding periods of apple and pear.
Crystal structure of a thermostable type B DNA polymerase from <i>Thermococcus gorgonarius</i> (1999)

Most known archaeal DNA polymerases belong to the type B family, which also includes the DNA replication polymerases of eukaryotes, but maintain high fidelity at extreme conditions. We describe here the 2.5 A resolution crystal structure of a DNA polymerase from the Archaea Thermococcus gorgonarius and identify structural features of the fold and the active site that are likely responsible for its thermostable function. Comparison with the mesophilic B type DNA polymerase gp43 of the bacteriophage RB69 highlights thermophilic adaptations, which include the presence of two disulfide bonds and an enhanced electrostatic complementarity at the DNA-protein interface. In contrast to gp43, several loops in the exonuclease and thumb domains are more closely packed; this apparently blocks primer binding to the exonuclease active site. A physiological role of this "closed" conformation is unknown but may represent a polymerase mode, in contrast to an editing mode with an open exonuclease site. This archaeal B DNA polymerase structure provides a starting point for structure-based design of polymerases or ligands with applications in biotechnology and the development of antiviral or anticancer agents.
Liquid-Tunable Frequency Selective Surfaces (2010)

In this letter, a new technique for designing tunable frequency selective surfaces (FSSs) with the second-order band-pass response is presented and experimentally verified. The technique is applied to an FSS utilizing nonresonant, subwavelength, constituting unit cells. Frequency tuning is achieved by adjusting the location of a liquid metal slug within capillary tubes embedded between the FSS's metallic layers. A wideband flexible frequency tuning covering nearly the entire X band is tested in a waveguide environment and excellent agreement between the measured and simulated results is demonstrated.
Deriving document structure from prosodic cues (2001)

This study presents an approach for prosody-driven segmentation of speech data. The model is based solely on F contours and RMS envelopes. Phoneme or word information from a speech recognizer is unneccesary. Using data from German broadcast news, we show how this prosodic information can be exploited to retrieve structural information of the spoken text. The suitability of the CART-like algorithm for utterance boundary prediction has been evaluated on 7 five-minutes-news-reports, using 28 reports as training material for the classification tree. Sentence boundaries were predicted with a precision of 93%, at a recall of 88%.
Design of aberrationless aspheric unstable resonators (1992)

We present a method for designing aspheric mirrors for unstable-resonator lasers to yield an arbitrary laser mode inside the resonator. Both analytical and numerical examples are given of aberration-compensated resonators, including solid resonators whose modes, on refraction through the output coupler, have identically zero spherical aberration.
Empirical Analysis of Hardware-Assisted GPU Virtualization (2019)

The increasing use of Graphics Processing Unit (GPUs) for accelerating compute intensive tasks and graphics-related computations has led to their inclusion in High Performance Clusters and Cloud setups. Several cloud vendors provide virtual machine instances with GPU capabilities. With the advent of virtualization aware GPU hardware (NVIDIA vGPUs), allocating and sharing physical GPU among virtual machines has become easier and cost-efficient. The sharing mechanism and extent of sharing are determined by the vGPU scheduling algorithm and a configurable vGPU profile. As part of this work, we present a thorough empirical study of the hardware-assisted virtualized GPU setups. In particular, we quantify the virtualization overheads, study the interference effects of concurrently executing homogeneous and heterogeneous workloads, and impact of vGPU scheduling algorithms. We also demonstrate that the best vGPU configuration parameters are sensitive to the mix of workload characteristics that share the GPU. Our study also compares the performance of vGPU based virtualization with PCI passthrough based direct GPU assignment to virtual machines. Based on our evaluation using heterogeneous workloads setups and varying vGPU configurations, we observe that the virtualization overheads are up to 7% (in terms of reduced memory availability) and up to 20% increase in execution times. Further, we demonstrate using our setups, that co-placing of heterogeneous workloads can improve the efficiency of GPU multiplexing and decrease execution times to as low as 20% as compared to homogeneous workload placements.
Network Loss Inference Using Unicast End-to-End Measurement (2000)

The fundamental objective of this work is to determine the extent to which unicast, end-to-end network measurement is capable of determining internal network losses. The major contributions of this paper are two-fold: we formulate a measurement procedure for network loss inference based on end-to-end packet pair measurements, and we develop a statistical modeling and computation framework for inferring internal network loss characteristics. Simulation experiments demonstrate the potential of our new framework. 1.
New Synthetic Surfactants – Basic Science (2005)

The hydrophobic surfactant proteins, SP-B and SP-C, promote adsorption of surface-active lipids to the air-liquid interface of the alveoli and are essential for alveolar stability and gas exchange. Synthetic surfactant preparations must contain at least one of these hydrophobic proteins, or analogs thereof, to have optimal effects when administered into the airways of patients with lung diseases. However, development of clinically active artificial surfactants has turned out to be more complicated than initially anticipated since the native hydrophobic proteins are structurally complex or unstable in pure form. The proteins have been replaced by different analogs which have the right conformation without forming oligomers. Increased understanding of the surfactant proteins will hopefully lead to development of effective synthetic surfactants which can be produced in large quantities for treatment of a wide range of respiratory disorders. Furthermore, the lipid composition seems to be important, as well as a high lipid concentration in the suspension. For successful treatment of many respiratory diseases, it is also desirable that the synthetic surfactant resists inactivation by plasma components leaking into the alveoli.
ATRP with Alkyl Pseudohalides Acting as Initiators and Chain Transfer Agents: When ATRP and RAFT Polymerization Become One (2012)

Abstract All controlled radical polymerization (CRP) procedures rely on a dynamic and rapid equilibrium between dormant and active species. This equilibrium can be established through different mechanisms and all the resulting CRP processes have their own advantages and limitations. Therefore, it becomes interesting to investigate the possibility of combining CRP techniques to eliminate specific drawbacks of each individual procedure. Atom transfer radical polymerization (ATRP) with alkyl pseudohalides acting as initiators and chain transfer agents was developed for that purpose. The process relies on a dual mechanism involving both activationdeactivation and reversible additionfragmentation chain transfer (RAFT). This peculiar characteristic of ATRP with alkyl pseudohalides acting as chain transfer agents made it possible to overcome some of the limitations typically associated with conventional ATRP and RAFT polymerization as well as to prepare new responsive materials.
Comparison of three inverse Fourier transform techniques to determine the second-order optical nonlinearity profile of thin films (2004)

We compare the predictions of three inverse Fourier transform (IFT) Maker fringe techniques that we have developed over the last 2 years to measure uniquely and accurately the second-order nonlinearity spatial profile of thin films. These techniques involve clamping two wafers with unknown nonlinearity profiles together to form a sandwich structure and measuring its Maker fringe (MF) spectrum. As a result of interference between the two nonlinear films, these spectra contain information on both the magnitude and phase of the FT of the two unknown profiles. These FT magnitude and phase can be processed numerically and the full FT is inverted to recover the profiles. In the first method the samples are different, in the second one they are identical, and in the third technique one of the two wafers has a known profile. The latter methods are advantageous because they require a single MF measurement, and consequently, their algorithms are simpler, and data processing is much faster. We present experimental evidence using thermally poled silica samples showing that when all three techniques are applied to the same sample, they yield very similar profiles, which gives credence to all three techniques.
Impulse Line Blocking Diagnosis of Digital differential pressure transmitter (2006)

Differential pressure transmitter with an orifice has achieved great field performance and success in flow measurement as a reliable field flow meter. However, blockage in impulse line attached to transmitter is sometime caused by precipitating or solidifying liquids. The pressure signals have random fluctuation signals due to a turbulent flow in a pipeline, and in case of impulse line blockage, the fluctuation signals vary from that of normal conditions. Mean square of differential pressure fluctuation has formerly been used to evaluate the blocking state. However, mean square of differential pressure fluctuation is strongly affected by flow rate. Then we have developed a new diagnostic technique, in which a specific parameter F called 'blockage factor' indicates the extent of each impulse line blockage. Dp transmitter EJX series is able to measure not only the differential pressure but also the static pressure at high and low pressure sides of orifice by means of silicon resonant pressure sensor. EJX makes it possible to calculate statistical variables F by using three pressure signals. We confirmed that blockage can be detected by using statistical variables F. Thus, impulse line blocking diagnosis of digital differential pressure transmitter contributes to predicting blockage in impulse line and saving maintenance cost