gebhart/patrepeval huggingface dataset:
The <i>Francisella</i> Pathogenicity Island (2007)

The Francisella pathogenicity island (FPI) is a cluster of 16-19 genes, which is found duplicated in most of the Francisella genomes that have been sequenced. Although 16 FPI genes are highly conserved there are 2-3 putative genes that are absent or interrupted by stop codons in some strains. Francisella strains with experimentally induced mutations in FPI genes are highly attenuated in virulence and show defects in intramacrophage growth. There is experimental evidence indicating that the regulation of most FPI genes is affected by the presence of the virulence regulator MglA and by the concentration of iron in the growth medium. Although studies of mRNA expression show that essentially all FPI genes are transcribed, only a handful of FPI-encoded proteins have been detected by biochemical methods. The cumulative biochemical and genetic data to date have not yet been able to ascribe a biochemical function to any of the FPI-encoded proteins. However, bioinformatics analysis suggests that some of the FPI-encoded proteins are part of a type VI secretion system.
A semi-naïve Bayesian method incorporating clustering with pair-wise constraints for auto image annotation (2004)

We propose a novel approach for auto image annotation. In our approach, we first perform the segmentation of images into regions, followed by clustering of regions, before learning the relationship between concepts and region clusters using the set of training images with pre-assigned concepts. The main focus of this paper is two-fold. First, in the learning stage, we perform clustering of regions into region clusters by incorporating pair-wise constraints which are derived by considering the language model underlying the annotations assigned to training images. Second, in the annotation stage, we employ a semi-naïve Bayes model to compute the posterior probability of concepts given the region clusters. Experiment results show that our proposed system utilizing these two strategies outperforms the state-of-the-art techniques in annotating large image collection.
Paging scheme for high-speed portable Internet (HPi) system (2006)

In order to overcome the drawbacks and combine the advantages of both 3G packet-switched mobile communication systems and WLAN, high-speed portable Internet (HPi) system based on 2.3 GHz bandwidth and IEEE 802.16e has been developed in Korea. In this paper, we propose a new paging scheme helping provide various packet data services including Internet services regardless of location for HPi. High-speed portable Internet (HPi) system defines idle mode for conserving power and operational resources. So we need to propose a paging mechanism for idle
Condensed tannins in horse bean seeds: Chemical structure and apparent effects on poultry (1977)

Abstract The seed‐coats of numerous varieties of horse beans contain condensed tannins of the proanthocyanidin type. These polymers consist of molecules of flavan‐3‐ols (catechin, gallocatechin) and flavan‐3,4‐diols (leucocyanidin, leucodelphinidin). Condensed tannins of horse bean seeds appear to depress the growth of muscovy ducklings, to cause a reduction in the weight of eggs produced by laying hens and to decrease the digestibility of nitrogen compounds in growing chicks.
Discriminative training of language models for speech recognition (2002)

In this paper we describe how discriminative training can be applied to language models for speech recognition. Language models are important to guide the speech recognition search, particularly in compensating for mistakes in acoustic decoding. A frequently used measure of the quality of language models is the perplexity; however, what is more important for accurate decoding is not necessarily having the maximum likelihood hypothesis, but rather the best separation of the correct string from the competing, acoustically confusible hypotheses. Discriminative training can help to improve language models for the purpose of speech recognition by improving the separation of the correct hypothesis from the competing hypotheses. We describe the algorithm and demonstrate modest improvements in word and sentence error rates on the DARPA Communicator task without any increase in language model complexity.
Regulator of G Protein Signaling 6 (RGS6) Induces Apoptosis via a Mitochondrial-dependent Pathway Not Involving Its GTPase-activating Protein Activity (2010)

Regulator of G protein signaling 6 (RGS6) is a member of a family of proteins called RGS proteins, which function as GTPase-activating proteins (GAPs) for Gα subunits. Given the role of RGS6 as a G protein GAP, the link between G protein activation and cancer, and a reduction of cancer risk in humans expressing a RGS6 SNP leading to its increased translation, we hypothesized that RGS6 might function to inhibit growth of cancer cells. Here, we show a marked down-regulation of RGS6 in human mammary ductal epithelial cells that correlates with the progression of their transformation. RGS6 exhibited impressive antiproliferative actions in breast cancer cells, including inhibition of cell growth and colony formation and induction of cell cycle arrest and apoptosis by mechanisms independent of p53. RGS6 activated the intrinsic pathway of apoptosis involving regulation of Bax/Bcl-2, mitochondrial outer membrane permeabilization (MOMP), cytochrome c release, activation of caspases-3 and -9, and poly(ADP-ribose) polymerase cleavage. RGS6 promoted loss of mitochondrial membrane potential (ΔΨ(m)) and increases in reactive oxygen species (ROS). RGS6-induced caspase activation and loss of ΔΨ(m) was mediated by ROS, suggesting an amplification loop in which ROS provided a feed forward signal to induce MOMP, caspase activation, and cell death. Loss of RGS6 in mouse embryonic fibroblasts dramatically impaired doxorubicin-induced growth suppression and apoptosis. Surprisingly, RGS6-induced apoptosis in both breast cancer cells and mouse embryonic fibroblasts does not require its GAP activity toward G proteins. This work demonstrates a novel signaling action of RGS6 in cell death pathways and identifies it as a possible therapeutic target for treatment of breast cancer.
MIOpen: An Open Source Library For Deep Learning Primitives (2020)

Deep Learning has established itself to be a common occurrence in the business lexicon. The unprecedented success of deep learning in recent years can be attributed to: an abundance of data, availability of gargantuan compute capabilities offered by GPUs, and adoption of open-source philosophy by the researchers and industry. Deep neural networks can be decomposed into a series of different operators. MIOpen, AMD's open-source deep learning primitives library for GPUs, provides highly optimized implementations of such operators, shielding researchers from internal implementation details and hence, accelerating the time to discovery. This paper introduces MIOpen and provides details about the internal workings of the library and supported features. MIOpen innovates on several fronts, such as implementing fusion to optimize for memory bandwidth and GPU launch overheads, providing an auto-tuning infrastructure to overcome the large design space of problem configurations, and implementing different algorithms to optimize convolutions for different filter and input sizes. MIOpen is one of the first libraries to publicly support the bfloat16 data-type for convolutions, allowing efficient training at lower precision without the loss of accuracy.
Device-parameter estimation with on-chip variation sensors considering random variability (2011)

Device-parameter monitoring sensors inside a chip are gaining its importance as the post-fabrication tuning is becoming of a practical use. In estimation of variational parameters using on-chip sensors, it is often assumed that the outputs of variation sensors are not affected by random variations. However, random variations can deteriorate the accuracy of the estimation result. In this paper, we propose a device-parameter estimation method with on-chip variation sensors explicitly considering random variability. The proposed method derives the global variation parameters and the standard deviation of the random variability using the maximum likelihood estimation. We experimentally verified that the proposed method can accurately estimate variations, whereas the estimation result deteriorates when neglecting random variations. We also demonstrate an application result of the proposed method to test chips fabricated in a 65-nm process technology.
Micromotor fabrication (1992)

Micromotor fabrication and related issues are discussed. The micromotors under study are of the variable-capacitance side-drive type with salient-pole and wobble (harmonic) designs. Polysilicon surface micromachining forms the basis of the micromotor fabrication process. In this process, LPCVD heavily phosphorus-doped polysilicon is used for the structural parts, LPCVD silicon nitride is used for electrical isolation, and CVD low-temperature oxide is used to as the sacrificial material. The fabrication process affects the performance characteristics of the micromotor through the reproduction accuracy of the design geometry and through the modification of the characteristics of contacting surfaces. Pattern definition and delineation are among the most critical steps of the micromotor fabrication process because of the increasing surface topography during fabrication and the large film thicknesses utilized. The release and testing process can affect the frictional characteristics of the micromotor significantly, determining success or failure of operation by dielectric excitation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
GPU implementation of volume reconstruction and object detection in Digital Holographic Microscopy (2010)

Using Digital Holographic Microscopy (DHM) we can gather information from a whole volume and thus we can avoid the small depth of field constraint of the conventional microscopes. This way a volume inspection system can be constructed, which is capable to find, segment, collect, and later classify those objects that flow through an inspection chamber. Digital hologram reconstruction and processing, however, require considerable computational resources. We are developing volume reconstruction and object detection algorithms that can speed up considerably by parallel hardware implementation. Therefore, we put these tasks into operation on a GPU. As data transfer of the reconstructed planes would slow down the algorithm, all the reconstruction, object detection processes are to be completed on the parallel hardware, while fine tuning of object reconstruction and classification will be done on a CPU later. The actual speed up of the GPU implemented algorithm comparing to its conventional CPU realization depends on the applied hardware devices. So far we reached a 10 times acceleration value.
<scp>d</scp>‐glufosinate as a male sterility agent for hybrid seed production (2010)

A chemical male sterility system based on anther-localized conversion of the inactive D-enantiomer of the herbicide, glufosinate (2-amino-4-(methylphosphinyl)-butanoate) to the phytotoxic L is described. Highly pure D-glufosinate was isolated in >98% enantiomeric excess from the racemate via fermentation with a strain of Escherichia coli expressing the PAT (L-glufosinate N-acetyl transferase) gene and purification of the unreacted D-enantiomer from the broth by ion exchange. A modified (F58K, M213S) form of the D-amino acid oxidase (DAAO) (EC 1.4.3.3) from Rhodosporidium toruloides was designed, tested in vitro and found to efficiently oxidize D-glufosinate to its 2-oxo derivative [2-oxo-4-(methylphosphinyl)-butanoic acid]. Tobacco (Nicotiana tabacum) plants were transformed to express this modified oxidase under control of the TAP1 tapetum-specific promoter. A number of the resultant transgenic lines exhibited complete male sterility that persisted for two or more weeks immediately following foliar treatment with 75 or 200 g/ha of D-glufosinate without exhibiting obvious phytotoxic symptoms or any measurable decline in female fertility. Similarly, plants containing the same construct and, additionally, a PAT gene expressed from a plastocyanin promoter exhibited significantly reduced male fertility and no reduction in female fertility following foliar application of racemic glufosinate. Thus, foliar application of d-glufosinate either purified or as the commercial herbicide, combined with anther expression of a modified DAAO promises to provide a cost-effective conditional chemical male sterility system with the characteristics necessary for practical F₁ hybrid seed production.
Photo-induced force for spectroscopic imaging at the nanoscale (2016)

Photo-induced force microscopy (PiFM) is a new scan probe method that enables imaging with spectroscopic contrast at the nanoscale. The operating principle of PiFM is based on the coupling between a sharp atomic tip and a polarizable object, as mediated by the electromagnetic field in the vicinity of the tip-sample junction. In this contribution, we develop a description of the photo-induced force in the limit where the tip and object can be approximated as dipoles. This description provides an insightful picture of the forces at play in the tip-sample junction in terms of the gradient and scattering forces. We consider various approximations that are relevant to experimental conditions. The theoretical approach described here successfully explains the previous spectroscopic PiFM measurements in the visible and in the near-IR range, and the anticipated spectral information that can be retrieved under mid infrared illumination.
Thickness dependence of structural and piezoelectric properties of epitaxial Pb(Zr0.52Ti0.48)O3 films on Si and SrTiO3 substrates (2006)

We report the structural and longitudinal piezoelectric responses (d33) of epitaxial Pb(Zr0.52Ti0.48)O3 (PZT) films on (001) SrTiO3 and Si substrates in the thickness range of 40nm–4μm. With increasing film thickness the tetragonality of PZT was reduced. The increase in d33 value with increasing film thicknesses was attributed to the reduction of substrate constraints and softening of PZT due to reduced tetragonality. The d33 values of PZT films on Si substrates (∼330pm∕V) are higher than those on SrTiO3 substrates (∼200pm∕V). The epitaxial PZT films on silicon will lead to the fabrication of high performance piezoelectric microelectromechanical devices.
Cascaded Multilevel Inverter Employing Three-Phase Transformers and Single DC Input (2009)

This paper proposes an isolated cascaded multilevel inverter employing low-frequency three-phase transformers and a single DC input power source. The proposed circuit configuration can reduce a number of transformers compared with traditional three-phase multilevel inverters using single-phase transformers. It controls switching phase angles to obtain an optimal switching pattern identified with the fundamental frequency of the output voltage. Owing to this control strategy, harmonic components of the output voltage and switching losses can be diminished considerably. To verify the performance of the proposed approach, we implemented computer-aided simulations and experiments using a prototype.
Description of Experimental Television Transmitting Apparatus (1933)

A description is given of an experimental television transmitter. This equipment was installed in the Empire State Building and was used in making practical tests on an experimental television system. The installation included facilities for radiating sound and picture signals from studio and from motion picture film. The general considerations underlying the design and performance of television terminal and transmitting apparatus for this experimental system are reviewed.
Fast self-organization by the probing algorithm (1989)

A new computational algorithm, the probing algorithm, is introduced for the subproblem of finding the best matching unit in Kohonen's self-organization procedure (Self-Organization and Associative Memory, Springer-Verlag, 1988). It is compared to exhaustive search and to four other algorithms and shown to be roughly six to 10 times faster for the case of high-dimensional vectors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
PHYSIOLOGICAL AND PHARMACOLOGICAL REGULATION OF HUMAN SALIVARY ELECTROLYTE CONCENTRATIONS; WITH A DISCUSSION OF ELECTROLYTE CONCENTRATIONS OF SOME OTHER EXOCRINE SECRETIONS 1 (1955)

The electrolyte content of paraffin-stimulated, whole, mixed saliva obtained from patients with congestive heart failure is characterized by lower sodium, lower chloride, and higher potassium concentrations than saliva of normal subjects (1). Since these data suggested possible increased adrenal cortical activity in patients with heart failure, desoxycorticosterone acetate (DCA) was administered to nineteen normal subjects. It also seemed of interest to study additional pharmacological and physiological mechanisms that may play a role in the regulation of salivary electrolyte concentrations. Thus, the aims of this communication are to present: 1) Data on normal salivary concentrations of sodium, chloride, and potassium; 2) data relating to physiological mechanisms regulating the concentrations of salivary electrolytes; and 3) the effects on salivary elec- trolytes of three pharmacologic agents: desoxycorticosterone acetate (DCA), pilocarpine, and Mercuhydrin@. METHODS Approximately 30 ml. of saliva were collected in the morning from fasting subjects who chewed paraffin for 15 to 20 minutes following a preliminary mouth wash with water. Where indicated, normal subjects chewed paraffin for two consecutive ten-minute periods. Whole, mixed saliva was analyzed. Sodium and potassium concentrations were measured with an internal standard Perkin 52A flame photometer; chloride concentrations,
Changes in Conformation and Subunit Assembly of Cod Myosin at Low and High pH and after Subsequent Refolding (2003)

Conformational and structural changes of cod myosin at pH 2.5 and 11 and after subsequent pH readjustment to pH 7.5 were studied. Results suggest that on acid unfolding, the myosin rod may fully dissociate due to electrostatic repulsion within the coiled coil, while it does not dissociate at alkaline pH. Both pHs led to significant conformational changes in the globular head fraction of the myosin heavy chains, suggesting that it takes on a molten globular configuration. A large part of the myosin light chains are lost on both pH treatments. On pH readjustment to neutrality, the heavy chains take on a structural form similar to the native state with the coiled-coil rod reassociating from acid pH while leaving the globular head less packed, more hydrophobic and structurally less stable. The irreversible change brought about in the globular head region leads to the failure of light chains to reassemble onto it, a drastic loss in ATPase activity, and more exposure of reactive thiol groups. The acid and alkali processes therefore lead to substantial changes in the globular part of the myosin molecule and perhaps more importantly to different molecular changes in myosin, depending on which pH treatment is employed.
Comparison of Quantitative Coronary Angiography, Intravascular Ultrasound, and Coronary Pressure Measurement to Assess Optimum Stent Deployment (1999)

In this study, using a coil stent, both IVUS and coronary pressure measurement were of similar value with respect to the assessment of optimum stent deployment. Therefore, coronary pressure measurement can be used as a cheap and rapid alternative to IVUS for that purpose.
Discovery and development of antipicornaviral agents. (1993)

The rhinovirus and enterovirus members of the picornavirus family are responsible for the majority of the mild upper respiratory infections most often referred to as the common cold as well as more serious illnesses including myocarditis. Much progress has been made in the identification and development of antiviral agents which specifically target the capsid of the picornaviruses. Preclinical and clinical efficacy data will be discussed on the WIN series of antiviral agents which were the result of a conventional drug discovery approach. The design of new agents is being assisted by the availability of atomic resolution data on the interaction of this class of antiviral agents with the viral capsid.
Query Performance Tuning in Supply Chain Analytics (2011)

Data explosion with knowledge shortage is becoming increasingly prominent. By utilizing business intelligence technology, supply chain analytics turns data into business insights and optimizes supply chain management decisions. Firstly, this paper describes the levels of Business Intelligence analytics, and formulates the architecture of supply chain analytics topics, then explains the analytics details of each topic. Furthermore, as OLAP is the most important decision support analysis tools of which query performance directly impacts the quality of analytics system end user experience, this paper proposes a variety of tuning technologies to accelerate query performance, including optimizing design of dimension, table aggregations, partitions, column store and tuning server resources technologies etc. A use scenario shows performance can be dramatically improved by dropping the processing time from previous 6-8 seconds to less than 0.1 seconds when aggregating 20+ million business transaction records.
Effect of Vitamins A and E on Nitric Oxide Production by Blood Mononuclear Leukocytes from Neonatal Calves Fed Milk Replacer (1998)

This study evaluated the effects of dietary vitamin A and E on the in vitro capacity of blood mononuclear leukocytes from calves to produce nitric oxide. Calves fed milk replacer received 100 IU/d of vitamin E as RRR-alpha-tocopherol or RRR-alpha-tocopheryl acetate and 0, 1700, 34,000, or 68,000 IU of vitamin A as retinyl acetate. Leukocytes from calves produced greater amounts of nitric oxide relative to leukocytes from adult cattle. The greater production of nitric oxide by calf leukocytes may be typical of the immature neonatal immune system. Nitric oxide production by calves fed RRR-alpha-tocopherol and either 1700 or 34,000 IU of vitamin A was less than that of calves in other groups and was more typical of production by leukocytes from cows. Our data suggest that optimal amounts of dietary vitamins A and E prompt the maturation of this response toward one that is more typical of adult cattle. Leukocytes from 1-wk-old calves produced less nitric oxide and were less responsive to stimuli than were leukocytes from older calves, a possible consequence of suppressive factors that were present in the ingested colostrum or in the circulation at birth.