gebhart/patrepeval huggingface dataset:
Tuning non-linear adaptive compensators in non-ideal noise environment (1998)

Adaptive compensation has been popular in a variety of biomedical signal processing applications. One of the major limitations of this method is the requirement for a primary signal + noise channel and a secondary noise channel, with the noises in the two channels being strongly correlated. In the majority of real-life biomedical applications this requirement can rarely be fulfilled since the secondary channel inevitably contains certain representation of the signal from the primary channel thus jeopardizing the adaptive compensation process. In the present work we describe a method for tuning an adaptive compensator containing a non-linear real-time multiplier in the reference channel in such non-ideal noise environment. The method is based on iterative adjustments of an exponential non-linear function which modifies in real-time the signal-to-noise balance in the reference channel in favor of the noise, preserving the correlation of the latter with the noise in the primary (signal + noise) channel but diminishing the signal content in the reference channel. Sets of model signals and noises are used to illustrate this methodology with a particular emphasis on biomedical signal applications. A quantitative description of the iterative tuning procedure is provided and the capabilities and limitations of this novel method for adaptive compensation are outlined.
Laboratory phlebotomy. College of American Pathologists Q-Probe study of patient satisfaction and complications in 23,783 patients. (1991)

Outpatients from 630 institutions participated in a phlebotomy module of Q-Probes, a quality assurance program of the College of American Pathologists, Northfield, Ill. This module assessed patient outcome measurements of complications, discomfort, and satisfaction with the phlebotomy procedure. Of the 29,700 ostensibly healthy individuals registered, 80.1% returned postcards containing measurements and assessments they made about the procedure and information recorded by the phlebotomist. The median time required for phlebotomy was 6 minutes, with 25% of patients requiring less than 5 minutes and 10% more than 21 minutes for completion of the procedure. The average number of phlebotomy attempts per patient was 1.03, with 95 patients (0.4%) experiencing three to 11 attempts. Ecchymoses occurred in 4048 (16.6%) attempts, with the median size of ecchymosis being 15.1 mm. On the average, an outstanding employee was identified by patients 46.6% of the time. The discomfort caused by the needle puncture was more than expected by 35.3% of patients. Although 98.6% of the patients were satisfied, 336 patients were dissatisfied with the procedure. We conclude that the technical skills of phlebotomists and patient satisfaction with phlebotomy are outstanding, but that patient discomfort from the procedure needs to be minimized.
HW2VEC: A Graph Learning Tool for Automating Hardware Security (2021)

The time-to-market pressure and continuous growing complexity of hardware designs have promoted the globalization of the Integrated Circuit (IC) supply chain. However, such globalization also poses various security threats in each phase of the IC supply chain. Although the advancements of Machine Learning (ML) have pushed the frontier of hardware security, most conventional ML-based methods can only achieve the desired performance by manually finding a robust feature representation for circuits that are non-Euclidean data. As a result, modeling these circuits using graph learning to improve design flows has attracted research attention in the Electronic Design Automation (EDA) field. However, due to the lack of supporting tools, only a few existing works apply graph learning to resolve hardware security issues. To attract more attention, we propose HW2VEC, an open-source graph learning tool that lowers the threshold for newcomers to research hardware security applications with graphs. HW2VEC provides an automated pipeline for extracting a graph representation from a hardware design in various abstraction levels (register transfer level or gate-level netlist). Besides, HW2VEC users can automatically transform the non-Euclidean hardware designs into Euclidean graph embeddings for solving their problems. In this paper, we demonstrate that HW2VEC can achieve state-of-the-art performance on two hardware security-related tasks: Hardware Trojan Detection and Intellectual Property Piracy Detection. We provide the time profiling results for the graph extraction and the learning pipelines in HW2VEC.
CCL2 Accelerates Microglia-Mediated Aβ Oligomer Formation and Progression of Neurocognitive Dysfunction (2009)

We posit that CCL2 facilitates Abeta oligomer formation in microglia and propose that such events accelerate memory dysfunction by affecting Abeta seeding in the brain.
Maintenance versus Induction Therapy Choice on Outcomes after Autologous Transplantation for Multiple Myeloma (2016)

Bortezomib (V), lenalidomide (R), cyclophosphamide (C), and dexamethasone (D) are components of the most commonly used modern doublet (RD, VD) or triplet (VRD, CVD) initial induction regimens before autologous hematopoietic cell transplantation (AHCT) for multiple myeloma (MM) in the United States. In this study we evaluated 693 patients receiving "upfront" AHCT after initial induction therapy with modern doublet or triplet regimens using data reported to the Center for International Blood and Marrow Transplant Research from 2008 to 2013. Analysis was limited to those receiving a single AHCT after 1 line of induction therapy within 12 months from treatment initiation for MM. In multivariate analysis, progression-free survival (PFS) and overall survival were similar irrespective of induction regimen. However, high-risk cytogenetics and nonreceipt of post-transplant maintenance/consolidation therapy were associated with higher risk of relapse. Patients receiving post-transplant therapy had significantly improved 3-year PFS versus no post-transplant therapy (55% versus 39%, P = .0001). This benefit was most evident in patients not achieving at least a complete response post-AHCT (P = .005). In patients receiving upfront AHCT, the choice of induction regimen (doublet or triplet therapies) appears to be of lower impact than use of post-transplant therapy.
Flagellin A Gene Restriction Fragment Length Polymorphism Patterns of Campylobacter spp. Isolates from Broiler Production Sources (1997)

The purpose of this study was to determine the potential reservoirs for Campylobacter spp. that provide the initial sources involved with broiler chicken colonization during poultry production. We characterized the flagellin A gene (flaA) of the organism by restriction fragment length polymorphism (RFLP) for 59 isolates of the bacterium provided during an epidemiological study. Isolates were obtained from three broiler production houses existing at separate locations. They were cultured and isolated from other (nonbroiler) domestic farm animals, wild birds, rodents, feed, farmers' boots, chicken feathers, and chicken intestinal materials. Eight distinctive flaA types were found in two of the houses. In one house, at least five flaA types (4, 6, 8, 15, and 21) were characterized from the poultry production environment, with three types isolated and identified from the chicken intestinal tract. flaA type 15 was found in flies, on boots, and in chicken intestinal samples. In another house, a distinctive diversity of flaA types existed (4, 7, 43, and 53). At least three flaA types found in samples from chicken intestinal tracts were also found in warm-blooded animals outside of the poultry house (domesticated animals, wild birds, and vermin).
Universal vaccination of H5N1 hemagglutinin (2013)

T nature of influenza virus to randomly mutate and evolve into new types with diverse antigenic determinants is an important challenge in the control of influenza infection. Particularly, variations within the amino acid sequences of major neutralizing epitopes of influenza virus hemagglutinin (HA) hindered the development of universal vaccines against H5N1 lineages. Based on distribution analyses of the identified major neutralizing epitopes of hemagglutinin, we selected three vaccine strains that cover the entire variants in the neutralizing epitopes among the H5N1 lineages. HA proteins of selected vaccine strains were expressed on the baculovirus surface (BacHA), and the preclinical efficacy of the vaccine formulations was evaluated in a mouse model. The combination of three selected vaccine strains could effectively neutralize viruses from clades 1, 2.1, 2.2, 4, 7, and 8 of influenza H5N1 viruses. In contrast, a vaccine formulation containing only adjuvanted monovalent BacHA (mono-BacHA) or a single strain of inactivated whole viral vaccine was able to neutralize only clade 1 (homologous), clade 2.1, and clade 8.0 viruses. Also, the trivalent BacHA vaccine was able to protect 100% of the mice against challenge with three different clades (clade 1.0, clade 2.1, and clade 7.0) of H5N1 strains compared to mono-BacHA or inactivated whole viral vaccine. The present findings provide a rationale for the development of a universal vaccine against H5N1 lineages. Furthermore, baculoviruses displaying HA will serve as an ideal choice for a vaccine in prepandemic or pandemic situations and expedite vaccine technology without the requirement of high-level-biocontainment facilities or tedious protein purification processes. Fang He et al., J Clin Cell Immunol 2013, 4:5 http://dx.doi.org/10.4172/2155-9899.S1.014
Zotarolimus, a Novel Sirolimus Analogue With Potent Anti-proliferative Activity on Coronary Smooth Muscle Cells and Reduced Potential for Systemic Immunosuppression (2007)

Sirolimus (rapamycin) is an immunosuppressant used in preventing allograft rejection and in drug-eluting stents to prevent restenosis after angioplasty. Zotarolimus, an analogue of sirolimus, was designed to have a shorter in vivo half-life. Zotarolimus was found to be mechanistically similar to sirolimus in having high-affinity binding to the immunophilin FKBP12 and comparable potency for inhibiting in vitro proliferation of both human and rat T cells. Rat pharmacokinetic studies with intravenous dosing demonstrated terminal elimination half-lives of 9.4 hours and 14.0 hours for zotarolimus and sirolimus, respectively. Given orally, T1/2 values were 7.9 hours and 33.4 hours, respectively. Consistent with its shorter duration, zotarolimus showed a corresponding and statistically significant 4-fold reduction in potency for systemic immunosuppression in 3 rat disease models. Pharmacokinetic studies in cynomolgus monkey underpredicted the half-life difference between zotarolimus and sirolimus apparent from recent clinical data. In vitro inhibition of human coronary artery smooth muscle cell proliferation by zotarolimus was comparable to sirolimus. Drug-eluting stents for local delivery of zotarolimus to the vessel wall of coronary arteries are in clinical development. The pharmacological profile of zotarolimus suggests it may be advantageous for preventing restenosis with a reduced potential for causing systemic immunosuppression or other side effects.
Coverage and Energy Analysis of Mobile Sensor Nodes in Obstructed Noisy Indoor Environment: A Voronoi Approach (2020)

The rapid deployment of wireless sensor network (WSN) poses the challenge of finding optimal locations for the network nodes, especially so in (i) unknown and (ii) obstacle-rich environments. This paper addresses this challenge with BISON (Bio-Inspired Self-Organizing Network), a variant of the Voronoi algorithm. In line with the scenario challenges, BISON nodes are restricted to (i) locally sensed as well as (ii) noisy information on the basis of which they move, avoid obstacles and connect with neighboring nodes. Performance is measured as (i) the percentage of area covered, (ii) the total distance traveled by the nodes, (iii) the cumulative energy consumption and (iv) the uniformity of nodes distribution. Obstacle constellations and noise levels are studied systematically and a collision-free recovery strategy for failing nodes is proposed. Results obtained from extensive simulations show the algorithm outperforming previously reported approaches in both, convergence speed, as well as deployment cost.
Collision avoidance norms in trajectory planning (2011)

This paper studies norms that quantify safety of robotic vehicle trajectories. The main motivation behind this work is to automate the process of selecting safe motions in complex state spaces such as ones arising from environments cluttered with obstacles or when trajectories lie close to the permitted boundary of configuration space. An autonomous vehicle can plan obstacle-free trajectories in a known environment but the inherent uncertainty in sensing and motion could render these trajectories unsafe during execution. Therefore, in the presence of uncertainty it is crucial to predict in real-time the safety of planned trajectories through appropriate metrics or norms. There are a number of standard methods to weigh risks associated with vehicle behavior, for instance, based on the minimum distance to the closest obstacles, or on the average distance to obstacles along the trajectory. In this paper we study generalization of such norms based on the theory of Sobolev spaces. In particular, H <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</sup> Sobolev norms applied to the distance-to-obstacle function along a trajectory are based not only on its spatial properties but also on its time variation or frequency components. We show that this extra information renders an H <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> norm more effective for quantifying risk compared to the standard L <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</sup> norms. This is demonstrated for an analytical example as well as for a semi-realistic helicopter flying through an obstacle terrain.
High‐performance water purification and desalination by solar‐driven interfacial evaporation and photocatalytic VOC decomposition enabled by hierarchical TiO 2 ‐CuO nanoarchitecture (2021)

Solar-driven interfacial evaporation for clean water generation has drawn significant attention as a promising and environmentally friendly avenue to tackle the global issue of water scarcity. The collected condensate can be free from most pollutants and impurities of diverse undrinkable water sources, such as heavy metals, organic dyes, minerals, and salts. However, when water is contaminated by volatile organic compounds (VOCs), this approach is ineffective because VOCs also evaporate and even can be enriched in the condensate. Here, we demonstrate TiO2-loaded CuO nanowire-covered Cu foam (TiO2-CuO-Cufoam) for efficient solar-driven interfacial evaporation and synchronous removal of VOCs via photocatalytic degradation. The TiO2-CuO-Cufoam nanoarchitecture possesses high solar absorption, quasi-one-dimensional water pathway, super-hydrophilicity for ultrafast water transport, long-term stability, and potential for cost-effective and scalable production for both VOC removal and desalination, meeting World Health Organization potable water standards. Our TiO2-CuO-Cufoam evaporator simultaneously demonstrates high solar evaporation efficiency of 86.6% and efficiency of 80.0% for the removal of VOCs under one sun (i.e., 1 kW m−2). This result may open new opportunities for energy-efficient, clean water generation from real-world water sources using solar energy. Novelty Statement TiO2-loaded CuO nanowire-covered Cu foam (TiO2-CuO-Cufoam) was obtained through the facile and green synthesis process. The TiO2-CuO-Cufoam nanoarchitecture possesses high solar absorption due to surface nanostructuring, quasi-one-dimensional water pathway for localized thermal management, super-hydrophilicity for ultrafast water transport, TiO2-CuO heterojunction for enhanced photodegradation of VOCs without consumption of chemical reagents, long-term stability, and potential for cost-effective and scalable production. The nanoarchitecture is employed for clean water generation from real-world water sources.
Fine Resolution Position Estimation Using Kalman Filtering (2019)

This paper is focused on using an inertial measurement unit (IMU) processed with the Kalman filter to provide fine resolution position estimates. The method is designed to provide position estimates between global positioning system (GPS) position updates. The goal is to have the GPS provide position data on a course scale while the IMU data is used to estimate the position on a finer scale. By integrating both the GPS and IMU, a more precise position estimate on a fine scale can be achieved that cannot be accomplished using the sensors independently.
Learning the min-max gait comfort region when wearing shoes (2020)

Shoe-embedded sensors are a recent, common and convenient choice for devices intended for locomotion-related applications. They are advantageous, compared to other wearable devices, since they allow performing gait assessment in real-world environments, recognizing the user walking pattern in real-time and directly on the feet level. However, shoe with embedded sensors, while providing affore-mentioned advantages, must in no way disturb the walk. In this paper, we present a simple, reliable and cheap method to check whether, and in which manner, the shoe affects the gait. The ultimate goal of the developed methodology is to provide a way to assess the performance of an innovative sole adaptable to changes in the external environment and in the dynamic state of the user. The proposed method is based on using a 2D camera to monitor three geometrical angles (knee, ankle, shoe) which reflect, in a simple but exhaustive manner, the lower limb behavior during the gait cycle. The ability of the shoe not to affect the normal gait is tested by comparison between the three angles trends of a person wearing the shoe and the person's min-max gait comfort regions, with respect to the three angles. Min-max comfort regions are learned through real experiments on different subjects and shoes.
Solution structure of the fifth repeat of factor H: a second example of the complement control protein module (1992)

Modules which share the same consensus sequence are assumed to have common structural features, at the secondary and tertiary level. In order to test the extent of such similarities, it is necessary to examine the structures of several examples from each module family. Recently, the first three-dimensional structure of a complement control protein (CCP) module (the 16th repeat of human factor H, H16) was determined using a combination of two-dimensional NMR and simulated annealing [Norman, D.G., Barlow, P.N., Baron, M., Day, A.J., Sim, R.B., & Campbell, I.D. (1991) J. Mol. Biol. 219, 717-725]. Using the same techniques, the three-dimensional structure of a second CCP module (the 5th repeat of human factor H, H5) has now been determined. The primary sequence of H5 contains 17 residues which are identical and in equivalent position to those in H16. Thirteen of these 17 are part of the consensus sequence. The similarities between the secondary structure of H5 and that of H16 are extensive. This implies that the consensus sequence dictates a particular secondary structure. The tertiary structure of H5, a compact hydrophobic core wrapped in beta-strand and sheet, bears much overall resemblance to that of H16. However, there is a deletion in the first strand of H5, and an insertion in a loop, resulting in slightly shorter overall length. This is associated with a rearrangement of residues within the hydrophobic core. The side chain of the highly conserved Tyr29, which occupies a central position within the core of H16, lies on the periphery of the core of H5.
Overexpression of Bacillus thuringiensis HknA, a histidine protein kinase homology, bypasses early Spo mutations that result in CryIIIA overproduction (1994)

The Bacillus thuringiensis CryIIIA insecticidal crystal protein (ICP) is a vegetatively expressed protein that is toxic to coleopteran insect larvae. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the asporogenous B. thuringiensis subsp. morrisoni strain EG1351, which harbors the native cryIIIA-encoding 88-MDa plasmid, showed a 2.5-fold overproduction of the CryIIIA protein compared with that of an isogenic wild-type strain. Further studies showed that neither CryIIIA protein synthesis nor CryIIIA protein processing was affected in strain EG1351 during vegetative growth. In an attempt to characterize the EG1351 mutation by complementation of function, the hknA gene was identified and cloned from a B. thuringiensis cosmid library. Primer extension analysis of hknA mRNA in wild-type B. thuringiensis demonstrated that the hknA gene is transcribed during vegetative growth from a sigma A-like promoter. Multiple copies of either the hknA gene or the Bacillus subtilis kinA (spoIIJ) gene were shown to bypass the sporulation defect in strain EG1351 as well as a spo0F mutation in B. thuringiensis EG1634. Additional studies showed that the hknA gene was not defective in strain EG1351. The results of this study suggest that hknA encodes a novel histidine protein kinase involved in B. thuringiensis sporulation. We also propose that the CryIIIA-overproducing phenotype of strain EG1351 is most likely due to a defect in the phosphorylation of Spo0A and confirm that CryIIIA production is not dependent on sporulation.
Short-Stability Study of Rifaximin-Based Samples (2020)

It is worth considering the development of these products, since the design process of formulation and pharmaceutical technology is financially more attractive than the development of new drugs that require high levels of investment in research and development, innovation of public policies, and regulatory actions.
Synthesis and Small-Angle X-ray Scattering Investigations of Ureido-Pyrimidone Hydrogen Bonding Star and Linear Poly(ethylene-co-propylene)s (2006)

Copolymers of poly(ethylene) and poly(propylene) having ureido-pyrimidone (UPy) hydrogen bonding moieties were synthesized and their bulk morphological behavior characterized. Anionic polymerization techniques allowed the synthesis of copolymers having well-defined linear, telechelic, and star architectures in which the UPy functional groups were located at the ends of the polymer chains. Small-angle x-ray scattering was used to characterize the bulk morphologies of these materials, which were found to be microphase separated, with the hydrogen bonding UPy moieties segregating from the copolymer bulk. The characteristic length scale observed varied substantially, depending on the molecular architecture, and is most likely correlated with the separation between microphase separated UPy-rich domains.
Optical biopsy of in vivo tissue using optical coherence tomography (1996)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1997.