gebhart/patrepeval huggingface dataset:
Leveraging a high resolution microfluidic assay reveals insights into pathogenic fungal spore germination (2016)

Germination of spores into actively growing cells is a process essential for survival and pathogenesis of many microbes. Molecular mechanisms governing germination, however, are poorly understood in part because few tools exist for evaluating and interrogating the process. Here, we introduce an assay that leverages developments in microfluidic technology and image processing to quantitatively measure germination with unprecedented resolution, assessing both individual cells and the population as a whole. Using spores from Cryptococcus neoformans, a leading cause of fatal fungal disease in humans, we developed a platform to evaluate spores as they undergo morphological changes during differentiation into vegetatively growing yeast. The assay uses pipet-accessible microdevices that can be arrayed for efficient testing of diverse microenvironmental variables, including temperature and nutrients. We discovered that temperature influences germination rate, a carbon source alone is sufficient to induce germination, and the addition of a nitrogen source sustains it. Using this information, we optimized the assay for use with fungal growth inhibitors to pinpoint stages of germination inhibition. Unexpectedly, the clinical antifungal drugs amphotericin B and fluconazole did not significantly alter the process or timing of the transition from spore to yeast, indicating that vegetative growth and germination are distinct processes in C. neoformans. Finally, we used the high temporal resolution of the assay to determine the precise defect in a slow-germination mutant. Combining advances in microfluidics with a robust fungal molecular genetic system allowed us to identify and alter key temporal, morphological, and molecular events that occur during fungal germination.
Activation Functions: Comparison of trends in Practice and Research for Deep Learning (2018)

Deep neural networks have been successfully used in diverse emerging domains to solve real world complex problems with may more deep learning(DL) architectures, being developed to date. To achieve these state-of-the-art performances, the DL architectures use activation functions (AFs), to perform diverse computations between the hidden layers and the output layers of any given DL architecture. This paper presents a survey on the existing AFs used in deep learning applications and highlights the recent trends in the use of the activation functions for deep learning applications. The novelty of this paper is that it compiles majority of the AFs used in DL and outlines the current trends in the applications and usage of these functions in practical deep learning deployments against the state-of-the-art research results. This compilation will aid in making effective decisions in the choice of the most suitable and appropriate activation function for any given application, ready for deployment. This paper is timely because most research papers on AF highlights similar works and results while this paper will be the first, to compile the trends in AF applications in practice against the research results from literature, found in deep learning research to date.
The Effect of pH on the Adsorption and Transport of Phosphonate Scale Inhibitor Through Porous Media (1993)

Abstract This paper presents results and analysis for several cycles of low concentration phosphonate (DETPMP) inhibitor floods in highly reproducible sandpacks. The central objective of this work is to present a detailed study of the effects of solution pH on the adsorption behaviour of phosphonate inhibitor. Displacements at constant near neutral and low pH conditions and in pH gradients have been carried out The latter type of flood is analysed in terms of coupled adsorption where the adsorption isotherm is a function of both inhibitor concentration and [H+] (or pH). The main finding is that phosphonate inhibitor adsorption level is higher at lower pH values. Non-equilibrium adsorption is also evident in the low pH floods. The floods are simulated and analysed using a non-equilibrium, coupled adsorption numerical model which reproduced most of the main features observed in the experiments. The modelling also leads to some novel interpretations of the experimental results which are then tested by further experiments. In order to put this study in a practical context, some further sensitivities, to calcium ion concentartion and pH on high concentration phosphonate adsorption, are also presented in this work. Again, it is shown that the pH and [Ca++] effects exert a coupled influence on phosphonate adsorption.
Two-Step Dynamic Encoding for Linear Decompressors (2014)

In this paper, a new linear decompress or is presented. A specific two-step encoding is incorporated in the implication process to exploit the degree of freedom during ATPG. The proposed decompress or achieves on average 247X test application time reduction for 10 industrial cores. A comparison with multiple seeds per pattern shows that the proposed decompress or achieves higher test application time reduction with fewer test patterns for 7 out of 10 industrial cores.
Designing a distributed queue (2002)

A common paradigm for distributed computing is the producer-consumer model. One set of processes produce objects (data, resources, or tasks) that are consumed by another set of processes. We present a simple algorithm for implementing a distributed queue. This algorithm has several parameters that need to be tuned, such as the number of probes to find an object, the amount of buffering, and the connectivity between the producers and the consumers. We provide an analytical model that predicts performance and based on the analytical model we provide recommendations for setting the parameters. Our analytical model is validated by a comparison to simulation results.
Visualization Support for Interactive Query Refinement (2005)

It has been well documented that Web searchers have difficulties crafting queries to fulfill their information needs. In this work, we use a concept knowledge base generated from the ACM computing classification system to generate a query space that represents the query terms in relation to the concepts they describe and the other terms that are related to these concepts. A visual representation of this query space allows the user to interpret the relationships between their query terms and the query space. Interactive query refinement within this visual representation takes advantage of the user's visual information processing abilities, and allows the user to choose terms that accurately represent their information need. A preview of the search results from Google provides the user with an indication of the current state of their query refinement process. This work allows the user to take an active role in the information retrieval process, supporting the fundamental shift from information retrieval systems to information retrieval support systems.
Investigations into Possible Alternative Decontamination Methods for <i>Salmonella enteritidis</i> on the Surface of Table Eggs (2003)

Investigations into various alternative techniques for decontamination of the surfaces of artificially contaminated shell eggs were carried out. Ionized air, exposure to ozone in a dry atmosphere and use of a commercial herbal antibacterial product were not effective. Application of ozone in a humid environment was only partially effective but a commercial ionized water anolyte was highly effective in eliminating Salmonella from egg surfaces.
Release of atherosclerotic debris after transluminal angioplasty. (1982)

To determine if there is release of endothelial cells or plaque contents after percutaneous transluminal angioplasty, effluent from atherosclerotic segments of the aorta and iliac arteries of rabbits were collected before and after angioplasty. No endothelial cells or cholesterol plates were identified in the preangioplasty effluents. Only a few single endothelial cells and cholesterol crystals were found in effluents after angioplasty. We conclude that embolization of endothelial fragments and cholesterol plates occurs during angioplasty, but only to a minor degree, and is probably not clinically important.
VALINE-RESISTANCE, A POTENTIAL MARKER IN PLANT CELL GENETICS. I. DISTINCTION BETWEEN TWO TYPES OF VALINE-RESISTANT TOBACCO MUTANTS ISOLATED FROM PROTOPLAST-DERIVED CELLS (1985)

In previous experiments, seven lines of valine-resistant plants were regenerated from protoplast-derived haploid tobacco mesophyll cells which had been UV mutagenized and submitted to selection by toxic concentrations of valine. In this study we described the transmission of valine-resistance to progeny and a preliminary phenotypical and biochemical characterization of the resistant plants.-Two types were thus distinguished among the seven mutant lines. Valine-resistance of the mutants of the first type (three lines) was transmitted as a single Mendelian dominant character (Vr1), whereas valine-resistance of the second type (four lines) was transmitted as a digenic recessive character (vr2 and vr3). Allelism tests revealed that the four recessive mutant lines yielded resistant progeny when intercrossed and, therefore, bear recessive mutant alleles at the same two unlinked loci.-When cultured at a density of 100 cell/ml, protoplast-derived cells of mutants of the first type had a low level of resistance to valine, whereas protoplast-derived cells of mutants of the second type displayed a high level of resistance to valine and to other amino acids.-According to the results of (14)C-labelled amino acid uptake experiments, the amino acid resistance of mutants of the second type, but not valine-resistance of the first type, could be accounted for by reduced uptake of several amino acids. Possible uses of valine-resistance as a marker in plant cell genetics are discussed.
Effect of catabolic plasmids on physiological parameters and efficiency of oil destruction by Pseudomonas bacteria (2007)

The ability of microbial degraders of polycyclic aromatic hydrocarbons to grow at 24°C in liquid mineral medium supplemented with oil as the sole source of carbon and energy was studied. Growth characteristics (CFU) and the level of oil destruction by plasmid-bearing and plasmid-free strains were determined after seven days of cultivation. The presence of catabolic plasmids in the degrader strains, including rhizosphere pseudomonads, was shown to increase cell growth and enhance the level of oil degradation. Strain Pseudomonas chlororaphis BS1391 bearing plasmid pBS216 was found to be the most effective oil degrader.
Selective growth of human mast cells induced by Steel factor, IL-6, and prostaglandin E2 from cord blood mononuclear cells (1996)

To establish the method for generating a large number of mature human mast cells, we cultured cord blood mononuclear cells (CBMC) in several conditions in the presence of Steel factor (SF). Among several cytokines tested, IL-6 enhanced SF-dependent mast cell growth from purified CD34+ cells for more than 8 wk in culture. When CBMC were cultured instead of CD34+ cells, IL-6 enhanced the mast cell development in the presence but not in the absence of PGE2. PGE2 enhanced the SF- and IL-6-dependent development of mast cells from CBMC probably by blocking granulocyte-macrophage CSF (GM-CSF) secretion from accessory cells, because 1) PGE2, or anti-GM-CSF enhanced the mast cell development induced by SF and IL-6 from CBMC, but not from CD34+ cells; 2) GM-CSF inhibited the enhancing effect of IL-6 on the mast cell development from CD34+ cells; and 3) PGE2 inhibited GM-CSF secretion from CBMC. The mast cells cultured in the presence of SF, IL-6, and PGE2 for >10 wk were 99% pure, and seemed to be functionally mature, because 1) they contained 5.62 micrograms of histamine and 3.46 micrograms of tryptase per 10(6) cells; and 2) when sensitized with human IgE and then challenged with anti-human IgE, the cells released a variety of mediators such as histamine, and an increase in intracellular Ca2+ was found in advance of the activation of membrane movement by using a confocal laser-scanning microscope. Electron-microscopic analysis revealed that some of the cultured mast cells are morphologically mature since they filled with scroll granules and contained crystal granules.
Efficacy and safety of a quick drying rubbing type povidone-iodine alcoholic disinfectant solution. (1993)

The efficacy and safety of a quick drying rubbing type disinfectant (HAD Hand Wash) composed of a povidone-iodine (PVP-I) and ethanol were evaluated in the disinfection of transient skin flora on fingers of 30 medical staff of our department. Three millilitres of HAD solution was rubbed onto the hands for three minutes several times a day over a four week period. Bacteriological effects were evaluated twice, on the first day and after four weeks, by the palm stamp method. The rate of colonies sterilized (bacterial reduction rate) after the use of HAD Hand Wash was 86.9 +/- 21.2% (mean +/- SD) on the first measurement, and 91.5% +/- 12.8% at four weeks. Staphylococcus epidermidis was isolated most frequently and this was eradicated in 83.3% of subjects, the bacterial reduction rate 99.7%. Staphylococcus aureus was originally isolated in 14 subjects and was eradicated in 13; the bacterial colony reduction rate was 99.9% showing high antiseptic efficacy. Although the bacterial reduction rate for Bacillus sp. was a rather low, 75.8-100%, this result was not considered problematic from the clinical standpoint. There were no side effects like chapping in spite of an average 104 applications of HAD Hand Wash during the 4-week test period. From these results, HAD Hand Wash was considered highly effective and safe.
Prevention of Fatty Liver and Maintenance of Systemic Valine Depletion Using a Newly Developed Dual Infusion System (1995)

Administration of low concentrations of valine via the portal vein simultaneous with central venous administration of valine-depleted TPN solution may prevent fatty liver.
Syntheses of Benzoquinolizine Derivatives. II (1959)

In order to obtain amebacidal agent, 2-dimethylaminoethyl-3-methyl-9, 10-dimethoxy-1, 2, 3, 4, 6, 7-hexahydro-11bH-benzo [a] quinolizine (IX) was prepared. Dieckmann con-densation of ethyl N-(3, 4-dimethoxyphenethyl)-N-(ethoxycarbonylpropyl) malonamate (I) afforded a β-ketoester (II), soluble in dilute sodium hydroxide solution and giving positive reaction to ferric chloride. Ketonic decomposition of (II) with 10% acetic acid followed by dehydrative condensation with ethyl cyanoacetate, and subsequent esterification, decarboxylation, and reduction afforded the carboxylic acid (VI). Cyclization and reduction of (VI) gave the quinolizine ester which was further derived to the amine (IX). The condensate (Xa) obtained from 3, 4-dimethoxyphenethylamine, 1, 1, 2-ethanetricarboxylic acid, and formaldehyde underwent automatic decarboxylation to form an aminodicarboxylic acid (XIa). Its esterification and condensation with ethoxycarbonylacetyl chloride gave the amide (XII) which was derived to the ketoester (XIV) as above, converted to the thioketal, and desulfurized and reduced to the homo acid (XVI). The use of 1, 1, 3-propanetricarboxylic acid gave an aminotricarboxylic acid (Xb) which was boiled with 60% acetic acid to effect decarboxylation and cyclization to form the lactam (XVIII) and its Arndt reaction gave the homo acid amide (XX). The compounds (XVI) and (XX) are intermediate for the preparation of the objective amine (A).
Block and Stream Ciphers and the Creatures in Between (2007)

In this paper we define a notion of leak extraction from a block cipher. We demonstrate this new concept on an example of AES. A result is LEX: a simple AES-based stream cipher which is at least 2.5 times faster than AES both in software and in hardware.
Pt-Based ORR Catalyst on Carbon-Supported Amorphous Niobium Oxide Support (2013)

This work uses a carbon-supported amorphous conductive metal oxide as Pt-based catalyst support for ORR in PEMFC. Amorphous conductive metal oxides have neither grain boundaries, nor the long-range atomic order to be easily transformed into insulating crystalline structure, i.e. amorphous niobium oxides are resistant to oxygen incorporation, thus preserving the structural stability and electric conductivity.
Discovery of 4‐Benzylamino‐Substituted α‐Carbolines as a Novel Class of Receptor Tyrosine Kinase Inhibitors (2010)

Within the last decade, interest in the development of new anticancer drugs increased mainly from emerging resistance against established drugs, which were found to be limited by the multidrug resistance (MDR) phenomenon. Several anticancer targets have been investigated for the development of structurally new drugs which were thought to be unaffected by the MDR phenomenon. Receptor tyrosine kinases (RTKs) make up one interesting group of anticancer targets. The overexpression and mutation of RTKs lead to an ongoing stimulus of cell growth and cancer progression. Early approaches to selective inhibition of single RTKs were generally disappointing in clinical studies, due in part to occurring resistance. Therefore, a new strategy involves the identification of multi-kinase inhibitors to slow the development of potential resistance. Moreover, the expected side effects of the first nonselective inhibitors were less dramatic than had been expected. We have discovered novel 4-benzylamino-α-carbolines as a new class of RTK inhibitors. Docking studies suggest a binding mode to the addressed target structures of the epidermal growth factor receptor (EGFR) and to the vascular endothelial growth factor receptor 2 (VEGFR2). Selectivity profiling against a panel of kinases and antiproliferative studies have highlighted one inhibitor, active in the nanomolar range, as a highly interesting candidate for further clinical studies.
Transport critical current densities of partially aligned bulk samples of YBa2Cu3O7−<i>x</i> superconductors (1990)

Temperature and magnetic field dependence of critical current densities (Jc) of partially oriented bulk YBa2Cu3O7−x samples are presented. A series of partially oriented samples has been fabricated by repeating the steps of the solid-state reaction method. X ray and Raman studies detect the orientation of the grains on the surface and in the bulk of the samples. Jc increases with the degree of alignment of the microcrystals, up to a factor of three. The effect of partial bulk-preferred orientation on the critical current anisotropy is also studied.
Fourier Transform Infrared Spectroscopic Study of the Role of Tartaric Acid in Glass-ionomer Dental Cements (1988)

(+)-Tartaric acid is incorporated into glass-ionomer dental cements to control the setting characteristics. FTIR has been used to examine the cements as they set, and has confirmed previous results that (+)-tartaric acid reacts more readily with the glass than does poly(acrylic acid), thereby delaying the setting of the cement. Subsequently, ions released by the glass become available for reaction with the polyacid, and gelation occurs. (+)-Tartaric acid not only reacts rapidly to yield calcium tartrate, but also enhances the rate at which aluminum polyacrylate is formed within the cement. Mesotartaric acid, by contrast, while rapidly forming calcium tartrate, does not enhance the rate of aluminum polyacrylate formation. As a result, this latter isomer merely suppresses the setting process; unlike (+)-tartaric acid, it does not also sharpen the set.
Cold load pickup issues (2009)

The goal of this paper is provide an understanding of the cold load pickup phenomenon and the options available with modern protective relays so improvements in the protection of distribution circuits can be achieved.
Additive Manufacturing of Batteries (2019)

Abstract Additive manufacturing, i.e., 3D printing, is being increasingly utilized to fabricate a variety of complex‐shaped electronics and energy devices (e.g., batteries, supercapacitors, and solar cells) due to its excellent process flexibility, good geometry controllability, as well as cost and material waste reduction. In this review, the recent advances in 3D printing of emerging batteries are emphasized and discussed. The recent progress in fabricating 3D‐printed batteries through the major 3D‐printing methods, including lithography‐based 3D printing, template‐assisted electrodeposition‐based 3D printing, inkjet printing, direct ink writing, fused deposition modeling, and aerosol jet printing, are first summarized. Then, the significant achievements made in the development and printing of battery electrodes and electrolytes are highlighted. Finally, major challenges are discussed and potential research frontiers in developing 3D‐printed batteries are proposed. It is expected that with the continuous development of printing techniques and materials, 3D‐printed batteries with long‐term durability, favorable safety as well as high energy and power density will eventually be widely used in many fields.
Theory of Probability, A Critical Introductory Treatment. (1975)

Part 7 A preliminary survey: heads and tails - preliminary considerations heads and tails - the random process laws of large numbers the central limit theorem. Part 8 Random processes with independent increments: the case of asymptotic normality the Wiener-Levy process behaviour and asymptotic behaviour ruin problems ballot problems. Part 9 An introduction to other types of stochastic process: Markov processes stationary processes. Part 10 Problems in higher dimensions: second-order characteristics and the normal distribution the discrete case the continuous case the case of spherical symmetry. Part 11 Inductive reasoning, statistical inference: the basic formulation and preliminary clarifications the case of independence and the case of dependence exchangeability. Part 12 Mathematical statistics: the scope and limits of the treatment the likelihood principle and sufficient statistics a Bayesian approach to estimation and hypothesis testing the connections with decision theory.
Cytomegalovirus InducesInterferon-Stimulated Gene Expression and Is Attenuated by Interferon in the DevelopingBrain (2006)

Cytomegalovirus (CMV) is considered the most common infectious agent causing permanent neurological dysfunction in the developing brain. We have previously shown that CMV infects developing brain cells more easily than it infects mature brain cells and that this preference is independent of the host B- and T-cell responses. In the present study, we examined the innate antiviral defenses against mouse (m) and human (h) CMVs in developing and mature brain and brain cells. mCMV infection induced interferon (IFN)-stimulated gene expression by 10- to 100-fold in both glia- and neuron-enriched cultures. Treatment of primary brain cultures with IFN-alpha, -beta, and -gamma or a synthetic RNA, poly(I:C), reduced the number of mCMV-infected cells, both in older cells and in fresh cultures from embryonic mouse brains. When a viral dose that killed almost all unprotected cells was used, IFN-protected cells had a natural appearance, and when they were tested with whole-cell patch clamp recording, they appeared physiologically normal with typical resting membrane potentials and action potentials. mCMV infection increased expression of representative IFN-stimulated genes (IFIT3, OAS, LMP2, TGTP, and USP18) in both neonatal and adult brains to similarly large degrees. The robust upregulation of gene expression in the neonatal brain was associated with a much higher degree of viral replication at this stage of development. In contrast to the case for downstream gene induction, CMV upregulated IFN-alpha/beta expression to a greater degree in the adult brain than in the neonatal brain. Similar to the case with cultured brain cells, IFN treatment of the developing brain in vivo depressed mCMV replication. In parallel work with cultured primary human brain cells, IFN and poly(I:C) treatment reduced hCMV infection and prevented virus-mediated cell death. These results suggest that coupling IFN administration with current treatments may reduce CMV infections in the developing brain.