gebhart/patrepeval huggingface dataset:
Characterization of uptake and hydrolysis of fluorescein diacetate and carboxyfluorescein diacetate by intracellular esterases in Saccharomyces cerevisiae, which result in accumulation of fluorescent product (1995)

Flow cytometry is a rapid and sensitive method which may be used for the detection of microorganisms in foods and drinks. A key requirement for this method is a sufficient fluorescence staining of the target cells. The mechanism of staining of the yeast Saccharomyces cerevisiae by fluorescein diacetate (FDA) and 5- (and 6-)carboxyfluorescein diacetate (cFDA) was studied in detail. The uptake rate of the prefluorochromes increased in direct proportion to the concentration and was not saturable, which suggests that transport occurs via a passive diffusion process. The permeability coefficient for cFDA was 1.3 x 10(-8) m s-1. Once inside the cell, the esters were hydrolyzed by intracellular esterases and their fluorescent products accumulated. FDA hydrolysis (at 40 degrees C) in cell extracts could be described by first-order reaction kinetics, and a rate constant (K) of 0.33 s-1 was calculated. Hydrolysis of cFDA (at 40 degrees C) in cell extracts was described by Michaelis-Menten kinetics with an apparent Vmax and Km of 12.3 nmol.min-1.mg of protein-1 and 0.29 mM, respectively. Accumulation of fluorescein was most likely limited by the esterase activity, since transport of FDA was faster than the hydrolysis rate. In contrast, accumulation of carboxyfluorescein was limited by the much slower transport of cFDA through the cell envelope. A simple mathematical model was developed to describe the fluorescence staining. The implications for optimal staining of yeast cells with FDA and cFDA are discussed.
On the information rate of speech communication (2017)

The key to the success of speech-based technology is an understanding of human speech communication. While significant advances have been made, a unified theory of speech communication that is both comprehensive and quantitative is yet to emerge. In this paper we approach speech communication from an information theoretical perspective. Without relying on prior knowledge of speech production, language, or auditory processing, we develop a new methodology for measuring the information rate of speech. Instead we rely on having recordings of multiple talkers saying the same utterance. In general, our results are consistent with a linguistic understanding of speech communication.
Algebraic multigrid (AMG). An introduction with applications (2022)

Since the early nineties, there has been a strongly increasing demand for more efficient methods to solve large sparse and unstructured linear systems of equations. For practically relevant problem sizes, classical one-level methods had already reached their limits and new hierarchical algorithms had to be developed in order to allow an efficient solution of even larger problems. The purpose of this paper is to give an elementary introduction to the first hierarchical and purely matrix-based approach, algebraic multigrid (AMG). The main idea behind AMG is to extend the classical ideas of geometric multigrid (smoothing and coarse-grid correction) to certain classes of algebraic systems of equations. Besides its robustness and efficiency, the main practical advantage of AMG is that it can directly be applied, for instance, to solve various types of elliptic partial differential equations discretized on unstructured meshes, both in 2D and 3D. Since AMG does not make use of any geometric information, it is a \\plug-in" solver which can even be applied to problems without any geometric background, provided that the underlying matrix satisfies certain properties. Although the development of AMG goes back to the early eighties, it still provides one of the most efficient algebraic methods to solve corresponding problems. Compared to the original approach, however, several modifications and extensions have been introduced. In addition to the theoretical basics of AMG, we present a concrete algorithm in some detail and demonstrate its robustness and efficiency by means of a variety of typical applications.
First Judicial District of Pennsylvania (2003)

My sincere appreciation is extended to everyone who contributed to this National Center for State Courts, Court Executive Development Program, Phase III, project: Providing Electronic Access to Justice in the First Judicial District of Pennsylvania, Philadelphia Court of Common Pleas, Trial Division – Civil. A very special thanks is extended to the following individuals for providing their unwavering support and invaluable contributions to this research project, for without which this would not have been possible:
Membrane technology applications in the food industry: Present and future (1990)

This presentation provides an overview of present, near-term, and potential applications of membrane technology in the food industry. This presentation is based on a comprehensive survey of membrane applications and research in the food industry prepared by EG G Idaho, Inc. for the US Department of Energy, Office of Industrial Programs. 2 refs., 3 tabs.
Thermal cycling-hyperthermia in combination with polyphenols, epigallocatechin gallate and chlorogenic acid, exerts synergistic anticancer effect against human pancreatic cancer PANC-1 cells (2019)

Hyperthermia (HT) has shown feasibility and potency as an anticancer therapy. Administration of HT in the chemotherapy has previously enhanced the cytotoxicity of drugs against pancreatic cancer. However, the drugs used when conducting these studies are substantially conventional chemotherapeutic agents that may cause unwanted side effects. Additionally, the thermal dosage in the treatment of cancer cells could also probably harm the healthy cells. The purpose of this work was to investigate the potential of the two natural polyphenolic compounds, epigallocatechin gallate (EGCG) and chlorogenic acid (CGA), as heat synergizers in the thermal treatment of the PANC-1 cells. Furthermore, we have introduced a unique strategy entitled the thermal cycling-hyperthermia (TC-HT) that is capable of providing a maximum synergy and minimal side effect with the anticancer compounds. Our results demonstrate that the combination of the TC-HT and the CGA or EGCG markedly exerts the anticancer effect against the PANC-1 cells, while none of the single treatment induced such changes. The synergistic activity was attributed to the cell cycle arrest at the G2/M phase and the induction of the ROS-dependent mitochondria-mediated apoptosis. These findings not only represent the first in vitro thermal synergistic study of natural compounds in the treatment of pancreatic cancer, but also highlight the potential of the TC-HT as an alternative strategy in thermal treatment.
Clocked-sense-amplifier-based smart-pixel optical receivers (1996)

We introduce the concept of synchronous smart-pixel optical receivers, and present the first use of a clocked-sense amplifier as a smart-pixel optical receiver. Such a receiver uses the controlled application of positive feedback to obtain low-power compact digital amplification. We describe the design and simulation of two types of optical receivers based on a clamped bit-line sense amplifier (CBLSA), and a conventional sense amplifier (CSA). Both of these circuits have been realized in 0.8 micron-linewidth foundry CMOS with hybrid-bonded GaAs-AlGaAs MQW detectors and modulators attached to the circuit. Operation in excess of 750 Mb/s is demonstrated, within a layout area of 44 μm×22 μm, with a bias-dependent estimated power dissipation of 1 to 2 mW. Operation with one or two input beams is possible, with approximate minimum detected photocurrent levels at 320 Mb/s of 8 μA (/spl sim/100 fJ) for single-beam operation and 2.5 μA/beam (/spl sim/30 fJ/beam) for two-beam operation, all in the CBLSA-based circuit.
Staphylococcal plasmids that replicate and express erythromycin resistance in both Streptococcus pneumoniae and Escherichia coli. (1982)

Plasmid pSA5700 from Staphylococcus aureus coding for erythromycin (EmR) and chloramphenicol (CmR) resistance was transformed into Streptococcus pneumoniae. High-copy-number and EmR constitutive mutants of this plasmid were isolated. Transformation frequencies in S. pneumoniae as high as 70% were obtained with a constitutive plasmid as donor DNA, into a recipient cell containing a resident, inducible, high-copy-number plasmid. With the aid of these high frequencies, the site of constitutive mutations could be mapped via a simple marker rescue technique that uses purified restriction endonuclease-generated fragments. One of the EmR constitutive mutants, pFB9, a plasmid originating from a Gram-positive host, was shown to replicate and express EmR and CmR in a Gram-negative organism, Escherichia coli. Four derivatives of pFB9 containing large (0.6-0.9 megadalton) insertion sequences that arose spontaneously in E. coli demonstrated unusual transforming activity, as well as enhanced EmR, in E. coli. The inserted elements mapped to the region in front of the EmR gene. Three of these inserted elements had the size and restriction patterns of insertion sequence IS1, IS2, and IS5. Plasmid pFB9 and derivatives are useful for isolation of new insertion sequences and for comparison of gene expression and illegitimate recombination between Gram-positive and Gram-negative species.
Effects of <i>Yucca shidigera</i> Extract on Growth, Nitrogen Retention, Ammonia Excretion, and Toxicity in Channel Catfish <i>Ictalurus punctatus</i> and Hybrid Tilapia <i>Oreochromis mossambicus × O. niloticus</i> (2003)

Abstract Nitrogenous waste control in aquaculture systems is necessary to maintain healthy animals and to meet effluent standards. Decreased ammonia production has been attained in traditional livestock production systems by adding extracts of Yucca shidigera to the feed or storage lagoon system. An extract of Yucca shidigera was fed to post yolk‐sac and juvenile channel catfish Ictalurus punctatus and hybrid tilapia Oreochrornis mossambicus × O. niloticus to determine the effects on growth, nitrogen retention, ammonia excretion, and toxicity. Post yolk‐sac channel catfish fry fed the 1.0‐g yucca extract/kg as an agar coating were the only group of experimental organisms that had significantly greater weight gains compared to the control and 0.5‐g yucca extract/kg diet groups after 12 wk. Significantly lower fecal nitrogen concentrations were obtained from catfish fed diets containing yucca extract compared to the control groups, although no differences between fecal nitrogen concentrations for catfish fed diets with either 0.5‐g or 1.0‐g yucca extract/kg diet occurred. Ammonia excretion rates were significantly lower for catfish fed diets containing yucca extract compared to the control group. Accordingly, fish fed diets containing the yucca extract had significantly greater whole‐body protein composition, while lipid levels were significantly lower. No significant differences in proximate composition occurred for fish fed any of the diets containing yucca extract, though growth rates were significantly higher than the controls. This study demonstrated that a yucca extract can be used in the diet of channel catfish, and increased growth and decreased ammonia concentrations can be obtained in rearing systems.
Expression and Function of Tec, Itk, and Btk in Lymphocytes: Evidence for a Unique Role for Tec (2004)

The Tec protein tyrosine kinase is the founding member of a family that includes Btk, Itk, Bmx, and Txk. Btk is essential for B-cell receptor signaling, because mutations in Btk are responsible for X-linked agammaglobulinemia (XLA) in humans and X-linked immunodeficiency (xid) in mice, whereas Itk is involved in T-cell receptor signaling. Tec is expressed in both T and B cells, but its role in antigen receptor signaling is not clear. In this study, we show that Tec protein is expressed at substantially lower levels in primary T and B cells relative to Itk and Btk, respectively. However, Tec is up-regulated upon T-cell activation and in Th1 and Th2 cells. In functional experiments that mimic Tec up-regulation, we find that Tec overexpression in lymphocyte cell lines is sufficient to induce phospholipase Cgamma (PLC-gamma) phosphorylation and NFAT (nuclear factor of activated T cells) activation. In contrast, overexpression of Btk, Itk, or Bmx does not induce NFAT activation. Tec-induced NFAT activation requires PLC-gamma, but not the adapters LAT, SLP-76, and BLNK, which are required for Btk and Itk to couple to PLC-gamma. Finally, we show that the unique effector function for Tec correlates with a unique subcellular localization. We hypothesize that Tec functions in activated and effector T lymphocytes to induce the expression of genes regulated by NFAT transcription factors.
Simulation of yield/cost learning curves with Y4 (1997)

This paper describes a prototype of a discrete event simulator-Y4 (yield forecaster)-capable of simulating defect related yield loss and manufacturing cost as a function of time, for a multiproduct IC manufacturing line. The methodology of estimating yield and cost is based on mimicking the operation and characteristics of a manufacturing line in the time domain. The paper presents a set of models that take into account the effect of particles introduced during wafer processing as well as changes in their densities due to process improvements. These models also illustrate a possible way of accounting for the primary attributes of fabrication, product, and failure analysis which affect yield learning. A spectrum of results are presented for a manufacturing scenario to demonstrate the usefulness of the simulator in formulating IC manufacturing strategies.
Explaining Disparities between Actual and Hypothetical Stated Values: Further Investigation Using Meta-Analysis (2004)

Spurred by the need to account for non-market values in various policy applications, a lively and extended debate has surrounded the presence and magnitude of hypothetical bias in stated value studies (e.g., applications of the survey-based contingent valuation method). Using the rapidly accumulating set of comparison studies, List and Gallet (2001) conducted an initial meta-analysis of the experimental protocol that may be influencing the disparity between real and hypothetical values in stated value studies. We expand the original meta-analysis by using a significantly larger (29%) data set, including variables to account for referendum formats, certainty corrections, and cheap talk scripts.
Computer-Assisted Design of Image Classification Algorithms: Dynamic and Static Fitness evaluations in a Scaffolded Genetic Programming Environment (1996)

This paper discusses several issues in applying genetic programming to image classification problems in geoscience and remote sensing. In particular, this paper examines the role in using dynamic and static fitness evaluation functions. This paper also examines a few of the aspects in human-computer interactions that facilitate computer-assisted learning and problem solving (i.e., scaffolding) for our system. We describe a possible means for visualizing and summarizing a solution space without having to resort to an exhaustive search of individuals.
Cathodic Protection of Concrete Bridge Members Containing Mild Reinforcing Steel (1990)

Impressed current cathodic protection has been successfully used for over a decade to effectively mitigate corrosion of reinforcing steel in chloride-contaminated concrete structures. The problems associated with the corrosion of reinforcing steel in concrete and the validity of cathodic protection are discussed. A comprehensive review of the several types of cathodic protection systems and their component parts which have been used in the last 14 years to minimize salt-induced deterioration of reinforced concrete structures is presented.
Genealogy of mammalian cysteine proteinase inhibitors (1985)

A model for the evolution of mammalian cysteine proteinase inhibitors has been constructed on the basis of sequence homology. This model suggests that the diversity of cysteine proteinase inhibitors has evolved from two ancestral units forming the building blocks of stefin and cystatin. Gene triplication of the archetypal inhibitor generated the kininogen heavy chain which contains three cystatin-like copies. Hence, the superfamily of mammalian cysteine proteinase inhibitors is constituted by at least three distinct families, with stefin, cystatin and kininogen as their prototypes.
A Planning and Optimization Framework for Hybrid Ultra-Dense Network Topologies (2018)

The deployment of small cells has been a critical upgrade in fourth-generation mobile networks as they provide macrocell traffic offloading gains, improved spectrum reuse and reduce coverage holes. The need for small cells will be even more critical in fifth-generation networks due to the introduction of higher spectrum bands, which necessitate denser network deployments to support larger traffic volumes per unit area. A network densification scenario envisioned for evolved fourth and fifth generation networks is the deployment of ultra-dense networks with small cell site densities exceeding 90 sites/km <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> (or inter-site distances of less than 112 m). The careful planning and optimization of ultra-dense networks topologies have been known to significantly improve the achievable performance compared to completely random (unplanned) ultra-dense network deployments by various third-party stakeholders (e.g. homeowners). However, these well-planned and optimized ultra-dense network deployments are difficult to realize in practice due to various constraints, such as limited or no access to preferred optimum small cell site locations in a given service area. The hybrid ultra-dense network topologies provide an interesting trade-off, whereby, an ultra-dense network may constitute a combination of operator optimized small cell deployments that are complemented by random small cell deployments by third-parties. In this study, an ultra-dense network multiobjective optimization framework and post-deployment power optimization approach are developed for realization and performance comparison of random, optimized and hybrid ultra-dense network topologies in a realistic urban case study area. The results of the case study demonstrate how simple transmit power optimization enable hybrid ultra-dense network topologies to achieve performance almost comparable to optimized topologies whilst also providing the convenience benefits of random small cell deployments.
Monoamine Transporters: From Genes to Behavior (2003)

Modulation of fast neurotransmission by monoamines is critically involved in numerous physiological functions and pathological conditions. Plasma membrane monoamine transporters provide one of the most efficient mechanisms controlling functional extracellular monoamine concentrations. These transporters for dopamine (DAT), serotonin (SERT), and norepinephrine (NET), which are expressed selectively on the corresponding neurons, are established targets of many psychostimulants, antidepressants, and neurotoxins. Recently, genetic animal models with targeted disruption of these transporters have become available. These mice have provided opportunities to investigate the functional importance of transporters in homeostatic control of monoaminergic transmission and to evaluate, in an in vivo model system, their roles in physiology and pathology. The use of these mice as test subjects has been helpful in resolving several important issues on specificity and mechanisms of action of certain pharmacological agents. In the present review, we summarize recent advances in understanding the physiology and pharmacology of monoamine transporters gained in mice with targeted genetic deletion of DAT, SERT, and NET.
Biaxial Strain Effects on Cells from the Inner and Outer Regions of the Meniscus (2006)

During knee joint loading, the fibrocartilaginous menisci experience significant spatial variations in mechanical stimuli. Meniscus cells also exhibit significant variations in biosynthesis and gene expression depending on their location within the tissue. These metabolic patterns are consistent with a more chondrocytic phenotype for cells located within the avascular inner two-thirds compared with a more fibroblastic phenotype for cells within the vascularized outer periphery. The spatial distribution of cell biosynthesis and gene expression patterns within the meniscus suggest that cells may exhibit intrinsically different responses to mechanical stimuli. The objective of our study was to test for intrinsic differences in the responsiveness of these meniscus cell populations to an equivalent mechanical stimulus. Cellular biosynthesis and gene expression for extracellular matrix proteins in isolated inner and outer meniscus cells in monolayer were quantified following cyclic biaxial stretch. The results demonstrate that inner and outer meniscus cells exhibit significant differences in matrix biosynthesis and gene expression regardless of stretching condition. Both inner and outer meniscus cells responded to stretch with increased nitric oxide production and total protein synthesis. The results suggest that inner and outer meniscus cells may respond similarly to biaxial stretch in vitro with measures of biosynthesis and gene expression.
A Naphthalimide-Based Glyoxal Hydrazone for Selective Fluorescence Turn-On Sensing of Cys and Hcy (2012)

A fluorescent turn-on probe for Cys/Hcy based on inhibiting the C═N isomerization quenching process by an intramolecular hydrogen bond was reported. The probe exhibited higher selectivity toward Cys/Hcy over other amino acids as well as thiol-containing compounds.
Spatial-Temporal Transformer for Dynamic Scene Graph Generation (2021)

Dynamic scene graph generation aims at generating a scene graph of the given video. Compared to the task of scene graph generation from images, it is more challenging because of the dynamic relationships between objects and the temporal dependencies between frames allowing for a richer semantic interpretation. In this paper, we propose Spatial-temporal Transformer (STTran), a neural network that consists of two core modules: (1) a spatial encoder that takes an input frame to extract spatial context and reason about the visual relationships within a frame, and (2) a temporal decoder which takes the output of the spatial encoder as input in order to capture the temporal dependencies between frames and infer the dynamic relationships. Furthermore, STTran is flexible to take varying lengths of videos as input without clipping, which is especially important for long videos. Our method is validated on the benchmark dataset Action Genome (AG). The experimental results demonstrate the superior performance of our method in terms of dynamic scene graphs. Moreover, a set of ablative studies is conducted and the effect of each proposed module is justified. Code available at: https://github.com/yrcong/STTran.
Crossing the Line: Crowd Counting by Integer Programming with Local Features (2013)

We propose an integer programming method for estimating the instantaneous count of pedestrians crossing a line of interest in a video sequence. Through a line sampling process, the video is first converted into a temporal slice image. Next, the number of people is estimated in a set of overlapping sliding windows on the temporal slice image, using a regression function that maps from local features to a count. Given that count in a sliding window is the sum of the instantaneous counts in the corresponding time interval, an integer programming method is proposed to recover the number of pedestrians crossing the line of interest in each frame. Integrating over a specific time interval yields the cumulative count of pedestrian crossing the line. Compared with current methods for line counting, our proposed approach achieves state-of-the-art performance on several challenging crowd video datasets.