gebhart/patrepeval huggingface dataset:
Induction of Strong Protection by Vaccination with Partially Attenuated Serotype 1 Marek's Disease Viruses (2002)

Studies were conducted to better understand the relationship among Marcek's disease (MD) vaccine strains between induction of protective immunity and the degree of attenuation (or virulence). To obtain viruses at different stages of attenuation, very virulent plus MD strains 584A and 648A and selected clones of these strains were serially passaged in chicken and duck cells. These viruses were considered fully attenuated after passage for 70-100 times in chicken embryo cell cultures until they no longer induced gross lesions in susceptible, maternal antibody-negative (ab-) chickens. Lower passages of the same strains were considered partially attenuated, provided their virulence was less than that of the parent strain. Four of five partially attenuated preparations derived from MD virus strains 584A and 648A or the previously attenuated Md11 strain induced 28%-62% higher levels of protection in maternal antibody-positive (ab+) chickens against virulent MD challenge than the fully attenuated counterpart viruses. The partially attenuated 584A/d2/3 strain replicated in chickens but was totally nonprotective. Data from two subsequent trials in ab+ chickens confirmed that protection induced by the partly attenuated (passage 80) preparations was 79% and 118% higher, respectively, than that induced by the fully attenuated (passage 100) preparations of strain 648A. However, in one trial with ab- chickens, no difference in protection between partially and fully attenuated virus was observed. Strong protection (up to 85%) against highly virulent challenge also was provided by preparations of 648A at passages 40-60, which were moderately oncogenic when used alone. Partially attenuated strains tended to replicate to higher titers in both ab+ and ab- chickens compared with fully attenuated vaccines. Also, ab+ and ab- chickens vaccinated with partially attenuated strains developed three- to nine fold more extensive microscopic lesions in peripheral nerves at 14 and 22 days after virulent challenge than chickens vaccinated with fully attenuated strains. When measured in ab+ chickens, loss of lesion induction by 648A was achieved 30 passages earlier (at passage 70) than when measured in ab- chickens. Thus, maternal antibodies appeared to abrogate the pathogenicity of some partially attenuated strains. These studies establish for MD the principle that at least some partially attenuated MD viruses may replicate better and induce stronger immunity against virulent challenge than fully attenuated preparations of the same strain, at least when tested in ab+ chickens. Moreover, depending on passage level, partially attenuated vaccine strains may be relatively innocuous for ab+ chickens, causing few or no lesions.
Chitin utilization by marine bacteria. A physiological function for bacterial adhesion to immobilized carbohydrates. (1991)

Chitin turnover is essential for recycling carbon and nitrogen in marine ecosystems. A key step in this process is the adhesion of marine bacteria to chitin-containing particulates. Vibrio species were therefore surveyed for their ability to bind to immobilized carbohydrates, and one, Vibrio furnissii, adhered to glycosides of three sugars, N-acetylglucosamine (the preferred ligand), D-mannose, and D-glucose. A single Ca(2+)-requiring lectin is responsible for binding to the three sugars. Cells adhering to the chitin analogue divided at the same rate as cells in liquid culture. The first progeny of adherent cells continued to bind to the beads, but the population gradually shifted to a large fraction of free swimming cells, a process that may be necessary for colonization. Metabolic energy is required for cell adhesion to the glycosides, and transient (or no) adhesion occurred in incomplete growth media. The results were explained by studying met and pro mutants. Both the initiation and maintenance of lectin-mediated adhesion requires continuous protein synthesis; expression of lectin activity is a major priority of these cells and functions under conditions adequate for minimal protein synthesis, but insufficient to support cell growth. The adhesion/deadhesion apparatus is apparently used to continuously monitor the nutrient status of the environment, i.e. as a nutrient sensorium. In incomplete medium, cells deadhere, presumably to migrate to a more favorable environment.
Delegation Assistance (2009)

Today's IT systems typically comprise a fine-grained access control mechanism based on complex policies. The strict enforcement of these policies, at runtime, always contains the risk of hindering people in their regular work. An efficient support for assisted delegation can help in resolving the conflict between too tight access control and the required flexibility as well as support the resolution of conflicts. Here, assisted delegation means that, additional to denying the access, a user is informed about a list of users that could either grant him access to the requested resource or which could execute this task in behalf of the user. In this paper, we present an approach for determining a set of users which are able to resolve an access control conflict. This set is based on various information sources and are ordered with respect to different distance functions. We show that one distance function can be used to serve different types of contextual input, e.g., role hierarchies, geospatial information as well as shared business object structure data or social network graphs.
Boosting the energy efficiency and power performance of neutral aqueous organic redox flow batteries (2017)

A neutral aqueous organic redox flow battery demonstrated an unprecedented 79% energy efficiency at 60 mA cm<sup>−2</sup> and 122.7 mW cm<sup>−2</sup> power density.
Biopsy-guided learning with deep convolutional neural networks for Prostate Cancer detection on multiparametric MRI (2017)

Prostate Cancer (PCa) is highly prevalent and is the second most common cause of cancer-related deaths in men. Multiparametric MRI (mpMRI) is robust in detecting PCa. We developed a weakly supervised computer-aided detection (CAD) system that uses biopsy points to learn to identify PCa on mpMRI. Our CAD system, which is based on a deep convolutional neural network architecture, yielded an area under the curve (AUC) of 0.903±0.009 on a receiver operation characteristic (ROC) curve computed on 10 different models in a 10 fold cross-validation. 9 of the 10 ROCs were statistically significantly different from a competing support vector machine based CAD, which yielded a 0.86 AUC when tested on the same dataset (α = 0.05). Furthermore, our CAD system proved to be more robust in detecting high-grade transition zone lesions.
QMOS digital logic circuit design (2000)

This paper presents results of work to explore the feasibility of using resonant tunnelling diodes (RTDs) and conventional MOSFETs for the development of digital logic circuits. Based on the use of RTDs and MOSFETs, two different logic design styles—fixed pull-down and fixed pull-up—are proposed and evaluated. Fixed pull-up gates perform better than their CMOS counterparts with similar device sizes. Since the proposed fixed pull-down style avoids the use of series MOSFETs, for large fan-in gates it yields significantly better performance than the corresponding CMOS gates.
Plasmalemmal Vesicle Associated Protein (PLVAP) as a therapeutic target for treatment of hepatocellular carcinoma (2014)

The results of this study suggest that anti-PLVAP Fab-TF may be used to treat HCC cases for which transcatheter arterial chemoembolization (TACE) is currently used and potentially avoid the drawback of high viscosity of chemoembolic emulsion for TACE to improve therapeutic outcome. Anti-PLVAP Fab-TF may become a viable therapeutic agent in patients with advanced disease and compromised liver function.
Validation of a new algorithm for the BPM-100 electronic oscillometric office blood pressure monitor (2001)

This study illustrates a new method for developing and testing a change in an algorithm for an oscillometric BP monitor utilizing collected and stored electronic data and demonstrates that the new algorithm meets the AAMI standard and BHS protocol.
Lifelong update of semantic maps in dynamic environments (2020)

A robot understands its world through the raw information it senses from its surroundings. This raw information is not suitable as a shared representation between the robot and its user. A semantic map, containing high-level information that both the robot and user understand, is better suited to be a shared representation. We use the semantic map as the user-facing interface on our fleet of floor-cleaning robots. Jitter in the robot's sensed raw map, dynamic objects in the environment, and exploration of new space by the robot are common challenges for robots. Solving these challenges effectively in the context of semantic maps is key to enabling semantic maps for lifelong mapping. First, as a robot senses new changes and alters its raw map in successive runs, the semantics must be updated appropriately. We update the map using a spatial transfer of semantics. Second, it is important to keep semantics and their relative constraints consistent even in the presence of dynamic objects. Inconsistencies are automatically determined and resolved through the introduction of a map layer of meta-semantics. Finally, a discovery phase allows the semantic map to be updated with new semantics whenever the robot uncovers new information. Deployed commercially on thousands of floor-cleaning robots in real homes, our user-facing semantic maps provide a intuitive user experience through a lifelong mapping robot.
Performance estimation of diagnostic tests for cervical precancer based on fluorescence spectroscopy: effects of tissue type, sample size, population, and signal-to-noise ratio (1999)

Fluorescence spectroscopy may provide a cost-effective tool to improve precancer detection. We describe a method to estimate the diagnostic performance of classifiers based on optical spectra, and to explore the sensitivity of these estimations to factors affecting spectrometer cost. Fluorescence spectra were obtained at three excitation wavelengths in 92 patients with an abnormal Papanicolaou smear and 51 patients with no history of an abnormal smear. Bayesian classification rules were developed and evaluated at multiple misclassification costs. We explored the sensitivity of classifier performance to variations in tissue type, sample size, tested population, signal to noise ratio (SNR), and number of excitation and emission wavelengths. Sensitivity and specificity could be evaluated within +/- 7%. Minimal decrease in diagnostic performance is observed as SNR is reduced to 15, the number of excitation-emission wavelength combinations is reduced to 15 or the number of excitation wavelengths is reduced to one. Diagnostic performance is compromised when ultraviolet excitation is not included. Significant spectrometer cost reduction is possible without compromising diagnostic ability. Decision-analytic methods can be used to rate designs based on incremental cost-effectiveness.
Literature review and fundamental approaches for vehicle and tire state estimation (2018)

Most modern day automotive chassis control systems employ a feedback control structure. Therefore, real-time estimates of the vehicle dynamic states and tire-road contact parameters are invaluable for enhancing the performance of vehicle control systems, such as anti-lock brake system (ABS) and electronic stability program (ESP). Today's production vehicles are equipped with onboard sensors (e.g. a 3-axis accelerometer, 3-axis gyroscope, steering wheel angle sensor, and wheel speed sensors), which when used in conjunction with certain model-based or kinematics-based observers can be used to identify relevant tire and vehicle states for optimal control of comfort, stability and handling. Vehicle state estimation is becoming ever more relevant with the increased sophistication of chassis control systems. This paper presents a comprehensive overview of the state-of-the-art in the field of vehicle and tire state estimation. It is expected to serve as a resource for researchers interested in developing vehicle state estimation algorithms for usage in advanced vehicle control and safety systems.
An Acousto-Optic Processor For Inspecting Cigarette Labels (1990)

An acousto-optic correlator is considered to verify that the correct text is present on a product and that the text is not skewed or blurred or mispositioned beyond allowed tolerances. For the case study considered, 20 possible labels exist and the presence of the correct one is to be verified. We need not determine which wrong label is present, although this is possible with modifications. We address the resolution and quantization requirements and the capacity of the system. Initial simulation results and real-time laboratory test results are provided. A space and frequency-multiplexed acousto-optic processor is used and described.
Phosphorylation of the Herpes Simplex Virus Tegument Protein VP22 Has No Effect on Incorporation of VP22 into the Virus but Is Involved in Optimal Expression and Virion Packaging of ICP0 (2005)

Herpes simplex virus VP22 is a major tegument protein of unknown function. Very recently, we reported that the predominant effect of deleting the VP22 gene was on the expression, localization, and virion incorporation of ICP0. In addition, the Delta22 virus replicated poorly in epithelial MDBK cells. We have also previously shown that VP22 interacts with the tegument protein VP16 and the cellular microtubule network. While the majority of VP22 in infected cells is highly phosphorylated, the nonphosphorylated form of VP22 is the predominant species in the virion, suggesting a differential requirement for phosphorylation through virus replication. Hence, to study the significance of VP22 phosphorylation, we have now constructed two recombinant viruses expressing green fluorescent protein-VP22 (G22) in which the previously identified serine phosphorylation sites have been mutated either to alanine to abolish the phosphorylation status of VP22 (G22P-) or to glutamic acid to mimic permanent phosphorylation (G22P+). Localization studies indicated that the G22P- protein associated tightly with microtubules in some infected cells, suggesting that VP22 phosphorylation may control its interaction with the microtubule network. By contrast, VP22 phosphorylation had no effect on its ability to interact with VP16 and, importantly, had no effect on the relative packaging of VP22. Intriguingly, virion packaging of ICP0 was reduced in the G22P+ virus while ICP0 expression was reduced in the G22P- virus, suggesting that these two ICP0 defects, previously observed in the Delta22 virus, were attributable to different forms of VP22. Furthermore, the Delta22 virus replication defect in MDBK cells correlated with the expression of constitutively charged VP22 in the G22P+ virus. Taken together, these results suggest an important role for VP22 phosphorylation in its relationship with ICP0.
On optimal decision thresholds for soft-decision error correction decoding in fiberoptic communication systems (2004)

We propose a practical way for selecting multiple decision thresholds maximizing mutual information. We show that when soft-decision error correction performance approaches Shannon limit, optimal thresholds converge to the ones maximizing mutual information.
Characterizing adaptive video streaming control systems (2015)

Adaptive video streaming systems aim at providing the best user experience given the user device and the network available bandwidth. To the purpose, a controller selecting the video bitrate from a discrete set ℒ has to be designed. The control goal is to maximize the video bitrate while avoiding playback interruptions and minimizing video bitrate switches. In the literature two different approaches, which we name rate-based actuation and level-based actuation, have been explored. The first one adapts both the received rate and the video bitrate, whereas the second acts only on the video bitrate. In this paper we advocate the adoption of level-based actuation controllers and we propose a hybrid dynamical system that models the essential features of such a class of controllers. With this model we are able to derive the minimum obtainable video bitrate switching frequency which can be considered as a benchmark for any level-based actuation controller. Finally, we show how to design the video level set ℒ to obtain a performance trade-off between switching frequency and storage cost requirements at the servers. The theoretical results are validated through numerical simulation and experimental evaluation.
A Semianalytical Model for Production Simulation From Nonplanar Hydraulic-Fracture Geometry in Tight Oil Reservoirs (2015)

Summary Two key technologies such as horizontal drilling and hydraulic fracturing have led to the economic production of unconventional resources such as shale gas and tight oil. In reality, a nonplanar hydraulic-fracture geometry with varying fracture width and fracture permeability is created during the hydraulic-fracturing process. However, it is challenging to simulate well performance from the nonplanar fracture geometry. For the sake of simplicity, the nonplanar fracture geometry is often represented by ideal planar fracture geometry with constant fracture width, which one can easily handle analytically, semianalytically, and numerically. However, such ideal fracture geometry is inadequate to capture the physics of the transient flow behavior of the nonplanar fracture geometry. Although significant efforts were made in recent years to numerically model well performance from the complex fracture geometry, these approaches are still challenging to model the nonplanar fracture geometry with varying width because of a large considerable fracture-gridding issues and an expensive computation cost. In addition, the effect of nonplanar fracture geometry on well productivity and transient flow behavior was not reported in the literature. Hence, a model to handle the nonplanar fracture geometry by considering varying fracture width and fracture permeability is still lacking in the petroleum industry. Zhou et al. (2014) proposed a semianalytical model to handle the complex fracture geometry with constant fracture width. However, the semianalytical model did not consider the effects of stress-dependent fracture conductivity and the nonplanar fracture geometry as well as planar fracture geometry with varying fracture width along the fracture. In this work, we extended the semianalytical model to simulate production from the nonplanar fracture geometry as well as planar fracture geometry with varying width. In addition, the effect of stress-dependent fracture conductivity was implemented in the model. We verified the semianalytical model against a numerical reservoir simulator for single planar fracture with constant width. We performed two case studies. The first case contains a comparison of two planar fractures, one with constant fracture width and another with varying fracture width. In the second study, we compared two fractures with different fracture geometries such as planar fracture geometry and nonplanar fracture geometry, which were generated from the fracture-propagation model. In addition, transient flow regimes were investigated on the basis of a log-log graph of the dimensionless pressure drop and pressure-drop derivative vs. the dimensionless time. This work can provide critical insights into understanding the well performance from tight oil reservoirs with the nonplanar hydraulic-fracture geometry.
An enzyme regulating triacylglycerol composition is encoded by the <i>ROD1</i> gene of <i>Arabidopsis</i> (2009)

The polyunsaturated fatty acids (PUFAs) linoleic acid (18:2) and alpha-linolenic acid (18:3) in triacylglycerols (TAG) are major factors affecting the quality of plant oils for human health, as well as for biofuels and other renewable applications. These PUFAs are essential fatty acids for animals and plants, but also are the source of unhealthy trans fats during the processing of many foodstuffs. PUFAs 18:2 and 18:3 are synthesized in developing seeds by the desaturation of oleic acid (18:1) esterified on the membrane lipid phosphatidylcholine (PC) on the endoplasmic reticulum. The reactions and fluxes involved in this metabolism are incompletely understood, however. Here we show that a previously unrecognized enzyme, phosphatidylcholine:diacylglycerol cholinephosphotransferase (PDCT), encoded by the Arabidopsis ROD1 gene, is a major reaction for the transfer of 18:1 into PC for desaturation and also for the reverse transfer of 18:2 and 18:3 into the TAG synthesis pathway. The PDCT enzyme catalyzes transfer of the phosphocholine headgroup from PC to diacylglycerol, and mutation of rod1 reduces 18:2 and 18:3 accumulation in seed TAG by 40%. Our discovery of PDCT is important for understanding glycerolipid metabolism in plants and other organisms, and provides tools to modify the fatty acid compositions of plant oils for improved nutrition, biofuel, and other purposes.
5α-reductase from radical prostatectomy tissue and utilization of testosterone and androstenedione to produce DHT: A dual isotope method and preliminary results. (2015)

58 Background: Previous work has shown that 5α-reductase prefers androstenedione (AD) in favor of testosterone (T) for dihydrotestosterone (DHT) synthesis in castration-resistant prostate cancer. Yet, 5α-reductase substrate preference in the setting of localized prostate tissue has yet to be fully elucidated. We propose a novel ex-vivo method for tracking steroid handling by the prostate and report our preliminary findings. Methods: Prostate tissue from the peripheral and transitional zones of patients who underwent radical prostatectomy (RP) for localized prostate cancer were incubated in media, along with ( 3 H)-labeled AD and ( 14 C)-labeled T. Media was collected after 7, 24 and 48 hours of incubation, treated with glucuronidase and high performance liquid chromatography (HPLC) was used to identify steroids tagged with either 3 H or 14 C. Results: In total, 11 patients were consented for tissue procurement at the time of RP. Qualitatively, both AD and T are utilized by the prostate to produce DHT. Over time, concentrations of tritiated AD decreased, while concentrations of tritiated T, 5α-androstanedione and DHT rose. Similarly, concentrations of 14 C-T decreased over a 48-hour period, while AD, 5α-androstanedione and DHT increased. Conclusions: We describe a dual isotope method for characterizing androgen handling by prostate tissue from patients with localized prostate cancer, using 2-channel radiolabel detection. Preliminary results show that both AD and T can be utilized by localized prostate cancer tissue. Future work will focus on determining if different phenotypes of androgen handling exist among various patient genotypes and cancer risk groups.