gebhart/patrepeval huggingface dataset:
Message and time efficient multi-broadcast schemes (2013)

We consider message and time efficient broadcasting and multi-broadcasting in wireless ad-hoc networks, where a subset of nodes, each with a unique rumor, wish to broadcast their rumors to all destinations while minimizing the total number of transmissions and total time until all rumors arrive to their destination. Under centralized settings, we introduce a novel approximation algorithm that provides almost optimal results with respect to the number of transmissions and total time, separately. Later on, we show how to efficiently implement this algorithm under distributed settings, where the nodes have only local information about their surroundings. In addition, we show multiple approximation techniques based on the network collision detection capabilities and explain how to calibrate the algorithms' parameters to produce optimal results for time and messages.
Digoxin-Quinidine Interaction (1979)

Several recent reports have shown that plasma concentrations of digoxin increase when quinidine is administered along with digoxin; the present study was designed to explore the pharmacokinetics of this digoxin-quinidine interaction in six subjects. The elimination half-life of digoxin, although variable, did not change appreciably (42 vs. 44 hours) when quinidine was administered. Other pharmacokinetic values were substantially reduced in the presence of quinidine: total body clearance (from 3.08 to 1.96 ml per minute per kilogram), renal clearance (from 1.64 to 1.09 ml per minute per kilogram) and volume of distribution (from 10.87 to 7.35 liters per kilogram). The results may be explained by the displacement of digoxin from binding sites in tissue by quinidine, causing a rise in the plasma concentration of digoxin. The reduction in renal clearance of digoxin may result also from inhibition of renal secretion of digoxin by quinidine.
Optimized assay for thymidine kinase and its application to the detection of antibodies against herpes simplex virus type 1- and 2-induced thymidine kinase (1980)

An optimized assay for herpes simplex virus type 1- and 2-induced deoxythymidine kinase (dTk) is described which used [125I]iododeoxyuridine (IUdr) as a substrate. Values for Km and Vsat were determined for both viral and cellular dTK, using either deoxythymidine or IUdR as a substrate. A comparison between the two substrates revealed that higher reaction velocities and lower Km values were obtained with IUdR. A standard assay was designed which uses 10(-7) M IUdR as a substrate. This assay can detect herpes simplex-induced dTK from as few as two infected cells and is several orders of magnitude more sensitive than conventional dTK assays which use 10(-5) M dT as a substrate. An easily detectable blocking activity, which was shown to be mainly confined to the immunoglobulin G antibody class, was found in most human sera which were positive for complement-fixing antibody against herpes simplex virus.
Cationic emulsifiers in cosmetics (1966)

Surface active chemicals are conveniently classified as anionic, nonionic, cationic or ampholytic depending upon their ionization properties in solution. Molecules, of surface active chemicals which ionize, are anionic or cationic according to which ion contains the hydrophobic grouping. Compounds uch as soaps, alkyl sulphonates, alkyl aryl sulphonates, salts of sulphated alcohols, etc. are anionic as the negative ion contains the hydrophobic, long chain grouping, e.g. (CH a. (CH•)•6 COO)Iqa + sodium soap of fatty acid (CH a. (CH2)•.• OSOa)Na+ sodium cetyl sulphate When the ion containing the hydrophobic, long chain group, is positive the compounds are cationic, e.g.
A Proposal To Reclassify Nocardia pinensis Blackall et al. as Skermania piniformis gen. nov., comb. nov. (1997)

The type strain of Nocardia pinensis was the subject of chemotaxonomic and 16S ribosomal DNA sequencing studies. The resultant nucleotide sequence was aligned with the sequences of representatives of the genera Corynebacterium, Dietzia, Gordona, Mycobacterium, Nocardia, Rhodococcus, and Tsukamurella, and phylogenetic trees were generated by using the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, and neighbor-joining methods. It was evident from the phylogenetic analyses that N. pinensis represents a distinct phyletic line that is most closely associated with the Gordona clade. This genealogical evidence, together with chemotaxonomic and phenotypic data derived from this and previous studies, indicates that N. pinensis merits generic status within the family Nocardiaceae. Therefore, we propose that N. pinensis Blackall et al. 1989 be reclassified as Skermania piniformis gen. nov., comb. nov. The type strain of Skermania piniformis cleaved an array of conjugated substrates based on the fluorophores 7-amino-4-methylcoumarin and 4-methylumbelliferone.
Design and fpga implementation of an embedded real-time biologically plausible spiking neural network processor (2005)

The implementation of a large scale, leaky-integrate-and-fire neural network processor using the Xilinx Virtex-II family of field programmable gate array (FPGA) is presented. The processor has been designed to model biologically plausible networks of spiking neurons in real-time to assist with the control of a mobile robot. The real-time constraint has led to a re-evaluation of some of the established architectural and algorithmic features of previous spiking neural network based hardware. The design was coded and simulated using Handel-C hardware description language (HDL) and the DK3 design suite from Celoxica. The processor has been physically implemented and tested on a RC200 development board, also from Celoxica.
Interleukin-4 protects double-negative and CD4 single-positive thymocytes from dexamethasone-induced apoptosis (1993)

Glucocorticoid hormones (GCH) and anti-CD3 monoclonal antibodies (MoAbs) induce in mouse thymocytes and T-cell tumor lines an active process of cell death called apoptosis. Interleukins (IL), including IL-1 and IL-2, have been reported to inhibit such apoptosis. In this study we show that IL-4 also reduced the DNA fragmentation characteristic of dexamethasone (DEX)-induced apoptosis in thymocytes. This effect, studied in both time-course and dose-response experiments, was also detected at low IL-4 concentrations (1 U/mL) and against high DEX levels (10(-7) mol/L). The effect of IL-4 was blocked by an anti-IL-4 but not by an anti-IL-1 alpha MoAb, and was thus both specific and direct. Phenotypic analysis showed that IL-4 protects predominantly CD4-CD8- and CD4+CD8- cells. Our findings suggest that intrathymic T-cell development may be influenced by IL-4.
Monoclonal anti-histone autoantibodies derived from murine models of lupus. (1984)

We characterized three monoclonal antibodies with histone reactivity which were derived from spleen cells obtained from unmanipulated NZB/NZW or MRL/1 mice. By using an enzyme-linked immunosorbent assay, we noted that all three antibodies reacted with chromatin histones as well as with total histones extracted from chromatin. None of the antibodies appeared to require DNA as part of the antigen. One antibody (BWH-1) recognized a determinant present in the nucleosome core H2A-H2B complex but showed little reactivity with any of the individual histones (H1, H2A, H2B, H3, or H4). In contrast, the other two monoclonal antibodies each recognized multiple individual histones in a unique pattern. Antibody MH-1 reacted with H2A, H2B, and H3; antibody MH-2 reacted with H2A, H3, and H4. MH-1 demonstrated cross-reactivity with poly-1-lysine but not poly-1-arginine or protamine sulfate; the opposite pattern of cross-reactivity was observed with MH-2. The antigenic determinants recognized by MH-2 were all trypsin-sensitive, suggesting that these determinants were present on the N-terminal regions of the respective individual histones. These studies revealed markedly different specificities of anti-histone monoclonal antibodies derived from murine models of systemic lupus erythematosus. These and other similarly derived antibodies may provide interesting tools to understand the specificity and biologic importance of anti-histone autoantibodies in different diseases.
Original Article: Enhanced expression of cytokines may play a fundamental role in the mechanisms of immunologically mediated recurrent spontaneous abortion (1997)

In view of the proven findings that cytokines do have detrimental effects on implantation, trophoblast proliferation, embryo development and fetal survival, our results suggest a potential mechanism of immunologic recurrent abortion which involves the secretion of IL-1 beta, TNF alpha, IFN gamma and other cytokines by activated endometrial lymphocytes and macrophages in response to either trophoblast or sperm antigens and these cytokines could partially defuse or penetrate into the systemic circulation.
A Model of the Intracellular Response of an Olfactory Neuron in Caenorhabditis elegans to Odor Stimulation (2012)

We developed a mathematical model of a hypothetical neuronal signal transduction pathway to better understand olfactory perception in Caenorhabditis elegans. This worm has only three pairs of olfactory receptor neurons. Intracellular Ca(2+) decreases in one pair of olfactory neurons in C. elegans, the AWC neurons, following application of an attractive odor and there is a transient increase in intracellular Ca(2+) following removal of odor. The magnitude of this increase is positively correlated with the duration of odor stimulation. Additionally, this Ca(2+) transient is induced by a cGMP second messenger system. We identified likely candidates for the signal transduction molecules functioning in this system based on available gene expression and physiological data from AWCs. Our model incorporated a G-protein-coupled odor receptor, a G-protein, a guanylate cyclase as the G-protein effector, and a single phosphodiesterase. Additionally, a cyclic-nucleotide-gated ion channel and a voltage-gated ion channel that mediated calcium influx were incorporated into the model. We posited that, upon odor stimulation, guanylate cyclase was suppressed by the G-protein and that, upon cessation of the stimulus, the G-protein-induced suppression ceased and cGMP synthesis was restored. A key element of our model was a Ca(2+)-dependent negative feedback loop that ensured that the calcium increases were transient. Two guanylate cyclase-activating proteins acted on the effector guanylate cyclase to negatively regulate cGMP signaling and the resulting calcium influx. Our model was able to closely replicate in silico three important features of the calcium dynamics of AWCs. Specifically, in our simulations, [Ca(2+)] increased rapidly and reached its peak within 10 s after the odor stimulus was removed, peak [Ca(2+)] increased with longer odor exposure, and [Ca(2+)] decreased during a second stimulus that closely followed an initial stimulus. However, application of random background signal ('noise') showed that certain components of the pathway were particularly sensitive to this noise.
Improving effective bandwidth through compiler enhancement of global and dynamic cache reuse (2000)

While CPU speed has been improved by a factor of 6400 over the past twenty years, memory bandwidth has increased by a factor of only 139 during the same period. Consequently, on modern machines the limited data supply simply cannot keep a CPU busy, and applications often utilize only a few percent of peak CPU performance. The hardware solution, which provides layers of high-bandwidth data cache, is not effective for large and complex applications primarily for two reasons: far-separated data reuse and large-stride data access. The first repeats unnecessary transfer and the second communicates useless data. Both waste memory bandwidth.\nThis dissertation pursues a software remedy. It investigates the potential for compiler optimizations to alter program behavior and reduce its memory bandwidth consumption. To this end, this research has studied a two-step transformation strategy: first fuse computations on the same data and then group data used by the same computation. Existing techniques such as loop blocking can be viewed as an application of this strategy within a single loop nest. In order to carry out this strategy to its full extent, this research has developed a set of compiler transformations that perform computation fusion and data grouping over the whole program and during the entire execution. The major new techniques and their unique contributions are: Maximal loop fusion : an algorithm that achieves maximal fusion among all program statements and bounded reuse distance within a fused loop. Inter-array data regrouping : the first to selectively group global data structures and to do so with guaranteed profitability and compile-time optimality. Locality grouping and dynamic packing: the first set of compiler-inserted and compiler-optimized computation and data transformations at run time.\nThese optimizations have been implemented in a research compiler and evaluated on real-world applications on SGI Origin2000. The result shows that, on average, the new strategy eliminates 41% of memory loads in regular applications and 63% in irregular and dynamic programs. As a result, the overall execution time is shortened by 12% to 77%.\nIn addition to compiler optimizations, this research has developed a performance model and designed a performance tool. The former allows precise measurement of the memory bandwidth bottleneck; the latter enables effective user tuning and accurate performance prediction for large applications: neither goal was achieved before this thesis.
Automatic Age Detection Using Text Readability Features. (2015)

In this paper, we present the results of automatic age detection based on very short texts as about 100 words per author. Instead of widely used n-grams, only text readability features are used in current study. Training datasets presented two age groups children and teens up to age 16 and adults 20 years and older. Logistic Regression, Support Vector Machines, C4.5, k-Nearest Neighbor, Naive Bayes, and Adaboost algorithms were used to build models. All together ten different models were evaluated and compared. Model generated by Support Vector Machine with Adaboost yield to f-score 0.94, Logistic regression to 0.93. A prototype age detection application was built using the best model.
Direct polarization switching in semiconductor lasers (1984)

Direct polarization switching controlled by the level of the injection current is achieved in InGaAsP lasers operating near the polarization transition temperature. The laser output can be switched from a pure TM00 mode at low injection currents to a TE00 mode at high currents with high extinction ratios and nanosecond response time. Conditions for polarization switching in InGaAsP and AlGaAs lasers at room temperature are also discussed.
An EWOD Droplet Microfluidic Chip with Integrated Local Temperature Control for Multiplex Proteomics (2009)

We present a microfluidic chip for multiplex thermal processing of discrete micro- and nano-liter sample droplets driven by electrowetting-on-dielectric (EWOD). The system features local temperature control integrated on chip in addition to the basic fluidic functionalities previously reported for EWOD devices [1]. Multifunctioning indium-tin-oxide (ITO) electrodes serve as optically transparent resistive heaters, temperature sensors, and EWOD actuation pads. With a 1 μL sample, heaters reach programmed set points in a few seconds and stabilize to ±1 °C. We demonstrate automated on-chip proteomics sample processing and direct characterization by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The results, showing increased insulin disulfide reduction efficiency with heater temperatures from 22 to 130 °C, highlight the efficacy of the chip.
The Antiallodynic Effects of Intrathecal Cholinesterase Inhibitors in a Rat Model of Neuropathic Pain  (1999)

These experiments suggest that intrathecal edrophonium or neostigmine produces an antagonism on touch-evoked allodynia at the spinal level in a rat model of neuropathic pain and that the antiallodynic action of cholinesterase inhibitors is probably mediated by a spinal muscarinic system, especially at the M1 receptor subtype.
<i>Bacillus subtilis</i> antibiotics: structures, syntheses and specific functions (2005)

The endospore-forming rhizobacterium Bacillus subtilis- the model system for Gram-positive organisms, is able to produce more than two dozen antibiotics with an amazing variety of structures. The produced anti-microbial active compounds include predominantly peptides that are either ribosomally synthesized and post-translationally modified (lantibiotics and lantibiotic-like peptides) or non-ribosomally generated, as well as a couple of non-peptidic compounds such as polyketides, an aminosugar, and a phospholipid. Here I summarize the structures of all known B. subtilis antibiotics, their biochemistry and genetic analysis of their biosyntheses. An updated summary of well-studied antibiotic regulation pathways is given. Furthermore, current findings are resumed that show roles for distinct B. subtilis antibiotics beyond the "pure" anti-microbial action: Non-ribosomally produced lipopeptides are involved in biofilm and swarming development, lantibiotics function as pheromones in quorum-sensing, and a "killing factor" effectuates programmed cell death in sister cells. A discussion of how these antibiotics may contribute to the survival of B. subtilis in its natural environment is given.
Towards Intraoperative Quantification of Atrial Fibrosis Using Light-Scattering Spectroscopy and Convolutional Neural Networks (2021)

Light-scattering spectroscopy (LSS) is an established optical approach for characterization of biological tissues. Here, we investigated the capabilities of LSS and convolutional neural networks (CNNs) to quantitatively characterize the composition and arrangement of cardiac tissues. We assembled tissue constructs from fixed myocardium and the aortic wall with a thickness similar to that of the atrial free wall. The aortic sections represented fibrotic tissue. Depth, volume fraction, and arrangement of these fibrotic insets were varied. We gathered spectra with wavelengths from 500-1100 nm from the constructs at multiple locations relative to a light source. We used single and combinations of two spectra for training of CNNs. With independently measured spectra, we assessed the accuracy of the CNNs for the classification of tissue constructs from single spectra and combined spectra. Combined spectra, including the spectra from fibers distal from the illumination fiber, typically yielded the highest accuracy. The maximal classification accuracy of the depth detection, volume fraction, and permutated arrangements was (mean ± standard deviation (stddev)) 88.97 ± 2.49%, 76.33 ± 1.51%, and 84.25 ± 1.88%, respectively. Our studies demonstrate the reliability of quantitative characterization of tissue composition and arrangements using a combination of LSS and CNNs. The potential clinical applications of the developed approach include intraoperative quantification and mapping of atrial fibrosis, as well as the assessment of ablation lesions.
A Numerical Classification Method for Partitioning of a Large Multidimensional Mixed Data Set (1979)

Sometimes the problem of data classification arises without any knowledge of the underlying classes. Furthermore, not enough sample data from the classes may be available to develop reliable parametric estimates and, hence, data classification rules. However, when the size of the mixed data to be classified is large, computer aided techniques for displaying data with histograms and frequency tables can be exploited to compensate partially for the lack of class knowledge and sample data. Based on this concept, a numerical classification procedure is developed and is described in this paper. The classification rule is completely data directed and utilizes the data marginal distributions in a sequential manner. The technique was employed for partitioning certain remotely sensed multispectral scanner data for a number of sites in the U.S. and was found to be fairly competitive when compared to some commonly used parametric approaches utilizing training sample data.
Cerivastatin triggers tumor-specific apoptosis with higher efficacy than lovastatin (2001)

The statin family of drugs inhibits 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase, the rate-limiting enzyme of the mevalonate pathway, and is used clinically as a safe and effective approach in the control of hypercholesterolemia. We have shown previously (Dimitroulakos, J., Nohynek, D., Backway, K. L., Hedley, D. W., Yeger, H., Freedman, M. H., Minden, M D., and Penn, L. Z. Increased sensitivity of acute myelogenous leukemias to lovastatin-induced apoptosis: a potential therapeutic approach. Blood, 93: 1308-1318, 1999) that lovastatin, a prototypic member of the statin family, can induce apoptosis of human acute myeloid leukemia (AML) cells in a sensitive and specific manner. In the present study, we evaluated the relative potency and mechanism of action of the newer synthetic statins, fluvastatin, atorvastatin, and cerivastatin, to trigger tumor-specific apoptosis. Cerivastatin is at least 10 times more potent than the other statins at inducing apoptosis in AML cell lines. Cerivastatin-induced apoptosis is reversible with the addition of the immediate product of the HMG-CoA reductase reaction, mevalonate, or with a distal product of the pathway, geranylgeranyl pyrophosphate. This suggests protein geranylgeranylation is an essential downstream component of the mevalonate pathway for cerivastatin similar to lovastatin-induced apoptosis. The enhanced potency of cerivastatin expands the number of AML patient samples as well as the types of malignancies, which respond to statin-induced apoptosis with acute sensitivity. Cells derived from acute lymphocytic leukemia are only weakly sensitive to lovastatin cytotoxicity but show robust response to cerivastatin. Importantly, cerivastatin is not cytotoxic to nontransformed human bone marrow progenitors. These results strongly support the further testing of cerivastatin as a novel anticancer therapeutic alone and in combination with other agents in vivo.
Light shift compensation in a Rb gas cell frequency standard with two-laser-pumping (2002)

One of the most important physical processes that occurs in Rb frequency standards is the light shift, which depends strongly on the intensity and the optical frequency detuning of the pumping light. This paper presents a method to compensate the light shift by means of two-laser-pumping. The two-laser-pumping schemes will also improve the signal-to-noise ratio since almost all atoms can be pumped to the desired state.