gebhart/patrepeval huggingface dataset:
Regulation of Glutamine and Glutamate Metabolism by GlnR and GlnA in Streptococcus pneumoniae (2006)

Several genes involved in nitrogen metabolism are known to contribute to the virulence of pathogenic bacteria. Here, we studied the function of the nitrogen regulatory protein GlnR in the Gram-positive human pathogen Streptococcus pneumoniae. We demonstrate that GlnR mediates transcriptional repression of genes involved in glutamine synthesis and uptake (glnA and glnPQ), glutamate synthesis (gdhA), and the gene encoding the pentose phosphate pathway enzyme Zwf, which forms an operon with glnPQ. Moreover, the expression of gdhA is also repressed by the pleiotropic regulator CodY. The GlnR-dependent regulation occurs through a conserved operator sequence and is responsive to the concentration of glutamate, glutamine, and ammonium in the growth medium. By means of in vitro binding studies and transcriptional analyses, we show that the regulatory function of GlnR is dependent on GlnA. Mutants of glnA and glnP displayed significantly reduced adhesion to Detroit 562 human pharyngeal epithelial cells, suggesting a role for these genes in the colonization of the host by S. pneumoniae. Thus, our results provide a thorough insight into the regulation of glutamine and glutamate metabolism of S. pneumoniae mediated by both GlnR and GlnA.
Dzelarhons: Myths of the Northwest Coast. Anne Cameron. (1988)

and self-willed; most admirable perhaps, Heloise, who is given
Embedding expert knowledge and hypothetical data bases into a data base system (1980)

This paper is concerned with adding knowledge to a data base management system and suggests two appropriate mechanisms, namely hypothetical data bases (HDB's) and experts. Herein we indicate the need for HDB's and define the extensions that are needed to a data base system to support HDB's.In addition, we suggest that the notion of "experts" is an appropriate way to add semantic knowledge to a data base system. Unlike most other proposals which extend an underlying data model to capture more meaning, our proposal does not require extensions to the schema. Moreover, the DBMS does not even have to know how an expert functions. In this paper we define an expert and indicate how it would be added to one existing data base system.
Super-resolution from a low- and partial high-resolution image pair (2014)

The classical super-resolution (SR) setting starts with a set of low-resolution (LR) images related by subpixel shifts and tries to reconstruct a single high-resolution (HR) image. In some cases, partial observations about the HR image are also available. Trying to complete the missing HR data without any reference to LR ones is an inpainting (or completion) problem. In this paper, we consider the problem of recovering a single HR image from a pair consisting of a complete LR and incomplete HR image pair. This setting arises in particular when one wants to fuse image data captured at two different resolutions. We propose an efficient algorithm that allows to take advantage of both image data by first learning nonlocal interactions from an interpolated version of the LR image using patches. Those interactions are then used by a convex energy function whose minimization yields a super-resolved complete image.
A semantic modeling approach for video retrieval by content (2003)

A knowledge-based approach to model and retrieve video data by content is developed. Selected objects of interest in a video sequence are described and stored in a database. This database forms the object layer. On top of this layer we define the schema layer used to capture the structured abstractions of the objects stored in the object layer. We propose two abstract languages on the basis of description logics: one for describing the contents of these layers, and the other more expressive, for making queries. The query language provides possibilities for navigation of the schema through forward and backward traversal of links, sub-setting of attributes, and constraints on links.
What Reassorts When Reovirus Genome Segments Reassort? (1995)

The members of several families of RNA-containing viruses possess segmented genomes that consist of from 2 to 12 genome segments. These viruses have the problem of assembling their genome segments into sets that contain one of each, a process that is usually referred to as assortment. Viruses appear to solve this problem in two ways, exemplified by influenza virus, on the one hand, and by reovirus, on the other. Influenza virus possesses eight species of negative stranded genome segments, each tightly associated with the nucleocapsid protein NP(1).
Increasing Hospitalization and Death Possibly Due to<i>Clostridium difficile</i>Diarrheal Disease (1998)

This study calculated yearly estimated national hospital discharge (1985 to 1994) and age-adjusted death rates (1980 to 1992) due to bacterial, viral, protozoal, and ill-defined enteric pathogens. Infant and young child hospitalization (but not death) rates in each category increased more than 50% during 1990 to 1994. Age-adjusted death and hospitalization rates due to enteric bacterial infections and hospitalizations due to enteric viral infections have increased since 1988. The increases in hospitalization and death rates from enteric bacterial infections were due to a more than eightfold increase in rates for specified enteric bacterial infections that were uncoded during this period (ICD9 00849). To identify bacterial agents responsible for most of these infections, hospital discharges and outpatient claims (coded with more detail after 1992) were examined for New Mexico's Lovelace Health Systems for 1993 to 1996. Of diseases due to uncoded enteric pathogens, 73% were due to Clostridium difficile infection. Also, 88% of Washington State death certificates (1985 to 1996) coded to unspecified enteric pathogen infections (ICD0084) listed C. difficile infection.
High performance packaging system for superconducting electronics (1999)

We demonstrate a packaging system/test probe suitable for testing complex, large scale superconducting integrated circuits with thousands of Josephson junctions. The cryopackage is designed to work with a 1 cm superconducting die, with liquid He immersion cooling using a standard storage dewar. The package has 80 high-speed input-output lines (DC to 20 GHz) which connect the chip to room temperature electronics. The tip of the cryopackage, containing the chip, is shielded from the ambient magnetic field with two mumetal cylinders and contains a built-in coil, which provides in-situ degaussing of the inner shield. To clear flux trapped in the chip being tested, the probe contains a novel gas manifold and a system of heaters. During the defluxing operation, a heater evaporates liquid helium inside the chip enclosure, the expanding vapor purging the liquid from the sample cell and warming the chip above its transition temperature. Once the chip is defluxed, the liquid helium is allowed back into the cell, at a rate slow enough to avoid trapping flux in the chip while it is cooled. The process can be automated and does not require any movement of the probe once inserted in the dewar.
A survey of prophet inequalities in optimal stopping theory (1992)

This paper surveys the origin and development of what has come to be known as prophet inequalities in optimal stopping theory. Included is a review of all published work to date on these problems, in­ cl uding extensions and variations, descriptions and examples of the main proof techniques, and a list of a number of basic open problems.
An experimental technique and a model for studying the operation of harmonic side-drive micrometers (1993)

The operation of harmonic side-drive micrometers is studied through gear ratio measurements and modeling of the micrometer dynamics. A simple experiment in which the wobble micromotor gear ratio is measured as a function of excitation voltage and pattern is used to characterize micromotor operation. This experiment in conjunction with the micromotor dynamic model presented can be used to study friction at the micromotor bearing and bushing contacts by fitting the model to the experiment. The model accounts for sliding and rolling of the rotor on the bearing, and sliding of the rotor on the bushing. The model can be used in conjunction with the experiment to estimate the bearing coefficient of friction and the bushing friction force. For micromotor operation in nitrogen gas, a polysilicon on polysilicon coefficient of friction of 0.36-0.4 is estimated. The bushing frictional force is found to consist of a constant term and a term that depends on the square of the excitation voltage.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Bisphenol A in combination with insulin can accelerate the conversion of 3T3-L1 fibroblasts to adipocytes (2002)

The confluent cultures of 3T3-L1 fibroblasts were treated with or without bisphenol A (BPA) for 2 days and subsequently treated with insulin (INS) alone for 9 days. When BPA was absent during the first 2-day treatment period, the cultures contained 1.6 microg/microg DNA of triacylglycerol (TG), 202 mU/mg DNA of lipoprotein lipase (LPL) activity, and 462 nmol/min/mg DNA of glycerol-3-phosphate dehydrogenase (GPDH) activity. The presence of BPA during the same period caused a 150% increase in the TG content, a 60% increase in the LPL activity, and a 500% increase in the GPDH activity. Thus, BPA by itself can trigger 3T3-L1 fibroblasts to differentiate into adipocytes. Next, the confluent cultures were treated with BPA for 2 days and subsequently treated with a combination of INS and BPA for 9 days. The simultaneous presence of BPA with INS caused a 370% increase in the TG content, a 200% increase in the LPL activity, and a 225% increase in the GPDH activity compared with the cultures treated with INS alone. The amount of [(3)H]thymidine incorporated into DNA was lower in the cultures treated with INS in the presence of BPA than in those treated with INS alone, indicating that BPA has an anti-proliferative activity on 3T3-L1 cells. Taken together, our results indicate that BPA in combination with INS can accelerate the adipocyte conversion.
Calcium‐activated non‐selective cation channel in ventricular cells isolated from adult guinea‐pig hearts. (1988)

1. A class of Ca2+-activated non-selective cation channel was identified in ventricular cells, which were dissociated from adult guinea-pig hearts using collagenase. 2. Under cell-attached conditions the patch electrode filled with a Na+-rich solution recorded no obvious single-channel current at the resting membrane potential. Subsequent superfusion of the ventricular cell with a Na+-free Tyrode solution induced an inward-going single-channel current as well as contracture of the cell. Kinetics of this channel were not affected by varying the membrane potential. 3. Single-channel currents showing a conductance similar to those observed in the cell-attached patches were recorded in isolated inside-out membrane patches when the inner side of the membrane was exposed to a free Ca2+ concentration ([Ca2+]i) higher than 0.3 microM. The slope conductance of the channel was 14.8 +/- 2.9 pS (mean +/- S.D., n = 17) at 20-25 degrees C. 4. The reversal potential examined in the inside-out patch was about 0 mV irrespective of the Na+-rich, K+-rich, Li+-rich or Cs+-rich solutions on either side of the membrane, thereby indicating that the channel was almost equally permeable to these cations. 5. The open probability of the channel was increased by raising [Ca2+]i with the maximum value of 0.93 +/- 0.17 (n = 4) at about 10 microM [Ca2+]i. The dose-response relation was fitted to the saturation kinetics with a Hill coefficient of 3.0 and a half-maximum concentration of 1.2 microM [Ca2+]i. 6. The gating kinetics were complex; both the open and closed time histograms showed at least two exponential components with time constants of 3.8 +/- 1.3 ms and 140 +/- 110 ms for open time and 1.8 +/- 1.1 ms and 14.9 +/- 5.3 ms for closed time (n = 4) at 10 microM [Ca2+]i. Reduction of [Ca2+]i resulted in both a decrease of the time constant of the slow component in the open time histogram and an increase of the two time constants of the closed time histogram. 7. Contribution of the channel to the whole-cell current was discussed based on an estimation of the channel density, presumably about 0.04 approximately 0.4/microns 2. Maximum activation of the channel would produce 7.2 approximately 72 nS of membrane conductance, which would explain the reported magnitude of the Ca2+-mediated background conductance of the single myocyte. The channel may also contribute, at least in part, to the transient inward current which develops in Ca2+-overloaded cardiac cells.
An Automatic Annotation Tool for Virtual Anatomy (2007)

Visible Human Project (VHP) gains an increasingly concern all over the world since it was first initiated in the 90's due to the benefits it brings to medical research, education and training. With the precise visible human datasets, tailor-made applications can be developed for various purposes. In this paper, we propose a novel computing tool for annotating anatomical structures in virtual anatomy applications. Our automatic labeling algorithm can also be applied to other related applications, e.g. virtual acupuncture, which involves similar anatomic annotation requirements. A real-time interactive application which will automatically generate tissues labels was developed. The user can gain further description of a tissue by clicking on the corresponding label and also drag the labels to desired positions.
Diversifying Reply Suggestions Using a Matching-Conditional Variational Autoencoder (2019)

Budhaditya Deb, Peter Bailey, Milad Shokouhi. Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 2 (Industry Papers). 2019.
Activation Properties of Heterologously Expressed Mammalian TRPV2 (2007)

TRPV2 has been proposed as a potential pain target, in part due to its relatedness to the nociceptor TRPV1 and to its reported activation by noxious high temperatures (>52 degrees C). However, TRPV2 responses to heat as well as to the nonselective agonist 2-aminoethoxydiphenyl borate (2-APB) have not been universally reproduced in other laboratories, leading to debate about the activation properties of this channel. Here, we report the expression of rat, mouse, and human TRPV2 in HEK293 cells and the differential properties of their responses to heat and 2-APB. Expression of mouse or rat TRPV2 in HEK293 cells resulted in robust channel activation when induced by either temperature (>53 degrees C) or 2-APB. By contrast, expression of human TRPV2 did not lead to detectable activation by either of these stimuli. Human TRPV2 protein was expressed at levels comparable with those of rat TRPV2, exhibited similar surface localization and responded to a novelly identified TRPV2 agonist, Delta(9)-tetrahydrocannabinol, indicating that human TRPV2 is functionally expressed on the cell surface. Studies using deletion mutants and chimeras between rat and human TRPV2 indicated that both amino- and carboxyl-cytoplasmic termini of rat TRPV2 are important for responses to heat and 2-APB but can be supplied in trans to form an active channel. The present study not only confirms and extends previous reports demonstrating that rat and mouse TRPV2 respond to 2-APB and noxious heat but also indicates that further investigation will be required to elucidate TRPV2 activation and regulatory mechanisms.
MasterMotion (2002)

We present a wireless virtual reality system and MasterMotion, the full-body training application built with it. We combine realtime full-body optical motion capture with wireless audio/video broadcast, belt-worn electronics, and a lightweight head-mounted display (HMD), to provide a wide-area, untethered virtual environment system that allows exploration of new application areas.
Interleukin 6/Gp130–Dependent Pathways Are Protective During Chronic Liver Diseases (2003)

The contribution of the acute phase inducer interleukin 6 (IL-6) in the pathogenesis of liver diseases is yet unclear. Our analysis showed enhanced expression of IL-6 in livers derived from patients with acute and chronic liver diseases. Additionally, IL-6 plasma levels were significantly increased in patients with chronic liver diseases and showed an inverse correlation with biochemical markers of liver function and a positive correlation with inflammatory markers, signs of portal hypertension, and the degree of liver fibrosis. To prove the relevance of these clinical findings, we applied the tetrachlorcarbonide (CCl(4)) model to conditional knockout animals (Cre/loxP system) for gp130, the common signal transducer of IL-6 family cytokines. Cre recombinases were expressed through a hepatocyte (AlfpCre) and a ubiquitous (MxCre) control element. Gp130 deleted mice had a totally abolished STAT3 activation and acute phase response induction, but gp130 deletion had no effect on the degree of acute liver injury and subsequent hepatocyte proliferation. In contrast, during chronic liver injury induced by biweekly application of CCl(4), deletion of the gp130 receptor in nonparenchymal liver cells and not hepatocytes resulted in fibrosis progression. In conclusion, our experiments indicate an involvement of IL-6 in the pathogenesis of liver diseases and suggest a protective role of IL-6/gp130-dependent pathways in nonparenchymal liver cells during fibrosis progression in chronic liver diseases. (Hepatology 2003;38:218-229).
Scatter kernel estimation with an edge-spread function method for cone-beam computed tomography imaging (2008)

The clinical applications of kilovoltage x-ray cone-beam computed tomography (CBCT) have been compromised by the limited quality of CBCT images, which typically is due to a substantial scatter component in the projection data. In this paper, we describe an experimental method of deriving the scatter kernel of a CBCT imaging system. The estimated scatter kernel can be used to remove the scatter component from the CBCT projection images, thus improving the quality of the reconstructed image. The scattered radiation was approximated as depth-dependent, pencil-beam kernels, which were derived using an edge-spread function (ESF) method. The ESF geometry was achieved with a half-beam block created by a 3 mm thick lead sheet placed on a stack of slab solid-water phantoms. Measurements for ten water-equivalent thicknesses (WET) ranging from 0 cm to 41 cm were taken with (half-blocked) and without (unblocked) the lead sheet, and corresponding pencil-beam scatter kernels or point-spread functions (PSFs) were then derived without assuming any empirical trial function. The derived scatter kernels were verified with phantom studies. Scatter correction was then incorporated into the reconstruction process to improve image quality. For a 32 cm diameter cylinder phantom, the flatness of the reconstructed image was improved from 22% to 5%. When the method was applied to CBCT images for patients undergoing image-guided therapy of the pelvis and lung, the variation in selected regions of interest (ROIs) was reduced from >300 HU to <100 HU. We conclude that the scatter reduction technique utilizing the scatter kernel effectively suppresses the artifact caused by scatter in CBCT.
Free-Standing, Single-Monomer-Thick Two-Dimensional Polymers through Covalent Self-Assembly in Solution (2013)

The design and synthesis of two-dimensional (2D) polymers is a challenging task, hitherto achieved in solution only through the aid of a solid surface "template" or preorganization of the building blocks in a 2D confined space. We present a novel approach for synthesizing free-standing, covalently bonded, single-monomer-thick 2D polymers in solution without any preorganization of building blocks on solid surfaces or interfaces by employing shape-directed covalent self-assembly of rigid, disk-shaped building blocks having laterally predisposed reactive groups on their periphery. We demonstrate our strategy through a thiol-ene "click" reaction between (allyloxy)12CB[6], a cucurbit[6]uril (CB[6]) derivative with 12 laterally predisposed reactive alkene groups, and 1,2-ethanedithiol to synthesize a robust and readily transferable 2D polymer. We can take advantage of the high binding affinity of fully protonated spermine (positive charges on both ends) to CB[6] to keep each individual polymer sheet separated from one another by electrostatic repulsion during synthesis, obtaining, for the first-time ever, a single-monomer-thick 2D polymer in solution. The arrangement of CB[6] repeating units in the resulting 2D polymer has been characterized using gold nanoparticle labeling and scanning transmission electron microscopy. Furthermore, we have confirmed the generality of our synthetic approach by applying it to different monomers to generate 2D polymers. Novel 2D polymers, such as our CB[6] derived polymer, may be useful in selective transport, controlled drug delivery, and chemical sensing and may even serve as well-defined 2D scaffolds for ordered functionalization and platforms for bottom-up 3D construction.
Pipe-Torch: Pipeline-Based Distributed Deep Learning in a GPU Cluster with Heterogeneous Networking (2019)

Because training a deep neural network (DNN) takes arduous amounts of time and computation, often researchers expedite the training process via distributed parallel training on GPUs. On one hand, this lower computing-to-communication ratio makes traditional data parallelism difficult to scale, and traditional model parallelism leads to low GPU utilization. Both make it difficult to obtain a higher speedup. On the other hand, multi-GPU systems exhibit complex connectivity among GPUs. Overall, workload schedulers must consider hardware topology and workload communication requirements to allocate GPU resources for optimal execution time and improved utilization in GPU clusters with heterogeneous networking. Thus, in this paper, we introduce Pipe-torch, an improved pipeline-hybrid parallelism method (using both data and model parallelism) in a heterogeneous network environment. Ultimately, the framework's model partition algorithm aims to expedite pipeline-hybrid parallelism training between heterogeneous network-connected GPUs. Experiments with four different DNN models show that Pipetorch averages 1.4x speedup compared to data parallelism.
Network traffic anomalies detection and identification with flow monitoring (2008)

Network management and security is currently one of the most vibrant research areas, among which, research on detecting and identifying anomalies has attracted a lot of interest. Researchers are still struggling to find an effective and lightweight method for anomaly detection purpose. In this paper, we propose a simple, robust method that detects network anomalous traffic data based on flow monitoring. Our method works based on monitoring the four predefined metrics that capture the flow statistics of the network. In order to prove the power of the new method, we did build an application that detects network anomalies using our method. And the result of the experiments proves that by using the four simple metrics from the flow data, we do not only effectively detect but can also identify the network traffic anomalies.
ArF laser excited in a capacitively coupled discharge tube (1988)

Lasing in ArF was obtained with a longitudinal capacitively coupled high-voltage discharge. A laser energy of 15 μJ at 193-nm wavelength has been obtained by discharging a two-stage Marx generator with 60 pF capacitance and a voltage of 80 kV per stage into a discharge tube with a length of 35 cm and 2 mm inner diameter.