gebhart/patrepeval huggingface dataset:
Gain-of-function <i>CCR4</i> mutations in adult T cell leukemia/lymphoma (2014)

Adult T cell leukemia/lymphoma (ATLL) is an aggressive malignancy caused by human T cell lymphotropic virus type-I (HTLV-I) without curative treatment at present. To illuminate the pathogenesis of ATLL we performed whole transcriptome sequencing of purified ATLL patient samples and discovered recurrent somatic mutations in CCR4, encoding CC chemokine receptor 4. CCR4 mutations were detected in 14/53 ATLL samples (26%) and consisted exclusively of nonsense or frameshift mutations that truncated the coding region at C329, Q330, or Y331 in the carboxy terminus. Functionally, the CCR4-Q330 nonsense isoform was gain-of-function because it increased cell migration toward the CCR4 ligands CCL17 and CCL22, in part by impairing receptor internalization. This mutant enhanced PI(3) kinase/AKT activation after receptor engagement by CCL22 in ATLL cells and conferred a growth advantage in long-term in vitro cultures. These findings implicate somatic gain-of-function CCR4 mutations in the pathogenesis of ATLL and suggest that inhibition of CCR4 signaling might have therapeutic potential in this refractory malignancy.
Differential Regulation of a Hyperthermophilic α-Amylase with a Novel (Ca,Zn) Two-metal Center by Zinc (2003)

The crystal structure of the alpha-amylase from the hyperthermophilic archaeon Pyrococcus woesei was solved in the presence of three inhibitors: acarbose, Tris, and zinc. In the absence of exogenous metals, this alpha-amylase bound 1 and 4 molar eq of zinc and calcium, respectively. The structure reveals a novel, activating, two-metal (Ca,Zn)-binding site and a second inhibitory zinc-binding site that is found in the -1 sugar-binding pocket within the active site. The data resolve the apparent paradox between the zinc requirement for catalytic activity and its strong inhibitory effect when added in molar excess. They provide a rationale as to why this alpha-amylase, in contrast to commercially available alpha-amylases, does not require the addition of metal ions for full catalytic activity, suggesting it as an ideal target to maximize the efficiency of industrial processes like liquefaction of starch.
Evaluation of the Digene Hybrid Capture II Assay with the Rapid Capture System for Detection of<i>Chlamydia trachomatis</i>and<i>Neisseria gonorrhoeae</i> (2002)

Screening for chlamydial and gonococcal infection has been strongly recommended for all sexually active women under the age of 26. Advances in the ability to detect infection by nucleic acid detection techniques have improved access to screening methods in routine clinical practices. To meet the increasing demand for testing, a high-throughput system is desirable. We evaluated the performance of the Hybrid Capture 2 CT/GC (HC2) assay with the Digene Rapid Capture System (HC2-RCS). The results of HC2-RCS for endocervical samples from 330 women were compared to those of culture and the COBAS Amplicor PCR. For detection of chlamydial infection, HC2-RCS had a sensitivity and a specificity similar to those of PCR (P > 0.5) and an improved sensitivity compared to that of culture (P = 0.007). For identification of gonococcal infections, all assays performed similarly (P > 0.5). The performance of HC2-RCS was also compared to that of the manual HC2 format (HC2-M) with these samples and with 911 endocervical samples collected previously. The performance of HC2-RCS was equivalent to that of HC2-M; the overall concordance rates for the detection of chlamydia and gonorrhea were 99.7% (kappa = 0.97) and 99.8% (kappa = 0.97), respectively. When the HC2 assay was performed with a semiautomated system application designed for high throughput, it demonstrated high sensitivity and a high specificity for detection of both Chlamydia trachomatis and Neisseria gonorrhoeae.
3-D scene data recovery using omnidirectional multibaseline stereo (1996)

A traditional approach to extracting geometric information from a large scene is to compute multiple 3-D depth maps from stereo pairs or direct range finders, and then to merge the 3-D data. However, the resulting merged depth maps may be subject to merging errors if the relative poses between depth maps are not known exactly. In addition, the 3-D data may also have to be resampled before merging, which adds additional complexity and potential sources of errors. This paper provides a means of directly extracting 3-D data covering a very wide field of view, thus by-passing the need for numerous depth map merging. In our work, cylindrical images are first composited from sequences of images taken while the camera is rotated 360/spl deg/ about a vertical axis. By taking such image panoramas at different camera locations, we can recover 3-D data of the scene using a set of simple techniques: feature tracking, an 8-point structure from motion algorithm, and multibaseline stereo. We also investigate the effect of median filtering on the recovered 3-D point distributions, and show the results of our approach applied to both synthetic and real scenes.
Pharmacokinetic antagonism of (+)-methamphetamine discrimination by a low-affinity monoclonal anti-methamphetamine antibody (2002)

Animals were trained to discriminate 5 or 10 mg/kg cocaine (rats), or 3 mg/kg (+)-amphetamine (pigeons) from saline, after which dose-response curves were determined for (+)-methamphetamine and other drugs before and after administration of a (+)-methamphetamine-specific monoclonal antibody (K(D) =250 nM). In rats trained to discriminate 10 mg/kg cocaine from saline, intravenous (+)-methamphetamine was about three times more potent as a discriminative stimulus than intraperitoneal (+)-methamphetamine. Also in these rats, intraperitoneal (+)-methamphetamine and (+)-amphetamine were about equipotent as discriminative stimuli, and were about three times more potent than intraperitoneal cocaine. In pigeons trained to discriminate 3 mg/kg intramuscular (i.m.) (+)-amphetamine from saline, (+)-methamphetamine and (+)-amphetamine were nearly equipotent, while cocaine was slightly less potent. In rats trained to discriminate 5 or 10 mg/kg cocaine from saline, intravenous administration of 1 g/kg of the antibody shifted both intravenous and intraperitoneal dose-response curves for (+)-methamphetamine discrimination approximately threefold to the right at 1 or 4 days after administration of the antibody. In pigeons trained to discriminate 3 mg/kg intramuscular (+)-amphetamine from saline, a similar shift of the (+)-methamphetamine dose-response curve to the right also lasted for 4-7 days. However, the antibody did not affect the (+)-amphetamine dose-response curve (pigeons), or the cocaine (rats) dose-response curve. The data show that a low affinity anti-(+)-methamphetamine-specific antibody can produce a specific antagonism of an effect of (+)-methamphetamine that is closely associated with its abuse.
Massive MIMO real-time channel measurements and theoretic TDD downlink throughput predictions (2016)

This paper is the first to evaluate the realistic performance of Massive MIMO using real-time channel measurements conducted at 3.51GHz. Our testbed consists of 64 National Instruments Universal Software Radio Peripheral Reconfigurable Input and Output (NI USRP RIO) software defined radios (SDRs) with 128 dipole antennas at the Base Station (BS) side, and 6 USRPs configured as 12 single-antenna User Equipment (UE) nodes. The system operates in a Time Division Duplex (TDD) fashion with a Long Term Evolution (LTE) like Physical Layer framework which, when fully deployed, will enable instantaneous throughput measurements on the Uplink (UL) and Downlink (DL) according to a user-defined frame schedule. In this paper we present real-time UL channel measurements at all BS antenna ports simultaneously, which allows the temporal characteristics of the Massive MIMO channel to be recorded. Eigen-beamforming precoding and a Received Bit-level Mutual Information Rate (RBIR) abstraction simulator are then used to predict the theoretic DL performance. We quantify the co-located Massive MIMO throughput for differing numbers of BS antennas (i.e. 32, 64 and 112 elements) and UE locations for an indoor environment.
STAT-1 Knockout Mice as a Model for Wild-Type Sudan Virus (SUDV) (2021)

Currently there is no FDA-licensed vaccine or therapeutic against Sudan ebolavirus (SUDV) infections. The largest ever reported 2014-2016 West Africa outbreak, as well as the 2021 outbreak in the Democratic Republic of Congo, highlight the critical need for countermeasures against filovirus infections. A well-characterized small animal model that is susceptible to wild-type filoviruses would greatly add to the screening of antivirals and vaccines. Here, we infected signal transducer and activator of transcription-1 knock out (STAT-1 KO) mice with five different wildtype filoviruses to determine susceptibility. SUDV and Marburg virus (MARV) were the most virulent, and caused 100% or 80% lethality, respectively. Zaire ebolavirus (EBOV), Bundibugyo ebolavirus (BDBV), and Taï Forest ebolavirus (TAFV) caused 40%, 20%, and no mortality, respectively. Further characterization of SUDV in STAT-1 KO mice demonstrated lethality down to 3.1 × 10<sup>1</sup> pfu. Viral genomic material was detectable in serum as early as 1 to 2 days post-challenge. The onset of viremia was closely followed by significant changes in total white blood cells and proportion of neutrophils and lymphocytes, as well as by an influx of neutrophils in the liver and spleen. Concomitant significant fluctuations in blood glucose, albumin, globulin, and alanine aminotransferase were also noted, altogether consistent with other models of filovirus infection. Finally, favipiravir treatment fully protected STAT-1 KO mice from lethal SUDV challenge, suggesting that this may be an appropriate small animal model to screen anti-SUDV countermeasures.
The First Subcomponent of Complement, C1q, Triggers the Production of IL-8, IL-6, and Monocyte Chemoattractant Peptide-1 by Human Umbilical Vein Endothelial Cells (1998)

We and others have demonstrated previously the occurrence of cC1qR/CaR, a receptor for the collagen-like stalks of complement component C1q, on endothelial cells. In the present study we investigated whether binding of C1q to endothelial cells resulted in enhancement of cytokine or chemokine production. HUVEC produced 82 +/- 91 pg/ml of IL-8, 79 +/- 113 pg/ml of IL-6, and 503 +/- 221 pg/ml of monocyte chemoattractant peptide-1 (MCP-1) under basal conditions. Incubation with C1q resulted in a time- and dose-dependent up-regulation of IL-8 (1012 +/- 43 pg/ml), IL-6 (392 +/- 20 pg/ml), and MCP-1 (2450 +/- 101 pg/ml). This production is dependent on de novo protein synthesis, as demonstrated by the detection of specific mRNA after C1q stimulation, and inhibition of peptide production in the presence of cycloheximide. The production of all factors was inhibited (69 +/- 7%) by the collagenous fragments of C1q, while the C1q globular heads only induced 13 +/- 11% inhibition. When HUVEC were incubated with C1q in the presence of aggregated IgM, enhanced production of IL-8 (2500 +/- 422 pg/ml), IL-6 (997 +/- 21 pg/ml), and MCP-1 (5343 +/- 302 pg/ml) was found. Furthermore, F(ab')2 anti-calreticulin partially inhibited the production of IL-8, confirming at least the involvement of cC1qR/CaR. These experiments suggest that in an inflammatory response C1q not only is able to activate the complement pathway, but when presented in a proper fashion also might induce the production of factors that contribute to acute phase responses and recruitment of inflammatory cells.
A nitric oxide synthase inhibitor reduces inflammation, down-regulates inflammatory cytokines and enhances interleukin-10 production in carrageenin-induced oedema in mice. (1994)

Mice injected in the footpad with carrageenin developed local inflammation which peaked at 48 hr. This delayed-type footpad swelling was significantly reduced in mice injected intraperitoneally (i.p.) with a specific nitric oxide (NO) synthase inhibitor, L-NGmonomethyl-arginine (L-NMMA). The draining lymph node (DLN) cells from mice injected 48 hr previously with carrageenin produced significantly higher levels of proliferation and interleukin-1 (IL-1), IL-2, IL-6 and interferon-gamma (IFN-gamma), but less IL-10, compared to cells from saline-injected controls, when stimulated with concanavalin A (Con A) in vitro. Treatment of the carrageenin-injected mice with L-NMMA had little effect on the proliferative response of the DLN cells, but significantly reduced the production of IL-1, IL-2, IL-6 and IFN-gamma, and increased the secretion of IL-10. These data demonstrate that NO plays a significant role in local inflammation and the pattern of cytokines induced in this model.
Preparation of Triangular Silver Nanoplates and its Application in Printed Electronics (2015)

Conductive ink for inkjet printing has attracted considerable interest for the preparation of advanced electronic circuits. However, high silver content and multiple printing are necessary in order to acquire better conductivity when using spherical silver nanoparticles. In order to reduce manufacturing cost, triangular silver nanoplates were prepared by modified solvothermal method and used for conductive ink. During sintering process of prtinted patterns, the tips of triangular nanoplates were first melted and turned round for high energy of tips. The resistivity of inkjet printed line is 7.6×10 -6 Ω·cm when using triangular nanoplates ink with 10 percent content, while it is necessary to use more than 15 percent content for spherical nanoparticles. This is because surface contact between nanoplates can provide more paths for electron transmission relative to spherical nanoparticles.
Efficient and secure document similarity search cloud utilizing mapreduce (2015)

Document similarity has important real life applications such as finding duplicate web sites and identifying plagiarism. While the basic techniques such as k-similarity algorithms have been long known, overwhelming amount of data, being collected such as in big data setting, calls for novel algorithms to find highly similar documents in reasonably short amount of time. In particular, pairwise comparison of documents sharing a common feature, necessitates prohibitively high storage and computation power. The wide spread availability of cloud computing provides users easy access to high storage and processing power. Furthermore, outsourcing their data to the cloud guarantees reliability and availability for their data while privacy and security concerns are not always properly addressed. This leads to the problem of protecting the privacy of sensitive data against adversaries including the cloud operator. Generally, traditional document similarity algorithms tend to compare all the documents in a data set sharing same terms (words) with query document. In our work, we propose a new filtering technique that works on plaintext data, which decreases the number of comparisons between the query set and the search set to find highly similar documents. The technique, referred as ZOLIP algorithm, is efficient and scalable, but does not provide security. We also design and implement three secure similarity search algorithms for text documents, namely Secure Sketch Search, Secure Minhash Search and Secure ZOLIP. The first algorithm utilizes locality sensitive hashing techniques and cosine similarity. While the second algorithm uses the Minhash Algorithm, the last one uses the encrypted ZOLIP Signature, which is the secure version of the ZOLIP algorithm. We utilize the Hadoop distributed file system and the MapReduce parallel programming model to scale our techniques to big data setting. Our experimental results on real data show that some of the proposed methods perform better than the previous work in the literature in terms of the number of joins, and therefore, speed.
From Molecular Weight And Nmr Relaxation To Viscosity: An Innovative Approach For Heavy Oil Viscosity Estimation For Real-Time Applications (2010)

Vertical and lateral viscosity variations in heavy oil reservoirs must be accurately understood for proper reserve assessment, well placement, reservoir simulation and well-test interpretation. Well-logs must be used to determine viscosity trends in the absence of a-priori information or direct viscosity measurements. This paper introduces a novel approach to estimate in-situ heavy oil viscosity using triple-combo and NMR logs. Three components, each with a distinct characteristic NMR relaxation time range and a specific molecular weight, are used to define the heavy oil phase. An empirical transform, built from a database of live oil samples collected in heavy oil reservoirs, is used to compute macroscopic viscosity from the relative volume fractions of the constituents. Case histories presented demonstrate the utility of the methodology in complex carbonate environments. The results clearly show that proper characterization of a heavy oil reservoir requires viscosity information, and interpretations based solely on mobility may have limited success. The case histories also highlight that actual viscosity distributions in heavy oil reservoirs can be quite different from the simple models often used to describe them.
Unsupervised identification of synonymous query intent templates for attribute intents (2013)

Among all web search queries there is an important subset of queries containing entity mentions. In these queries, it is observed that users are most interested in requesting some attribute of an entity, such as "Obama age" for the intent of age, which we refer to as the attribute intent. In this work we address the problem of identifying synonymous query intent templates for the attribute intent. For example, "how old is [Person]" and "[Person]'s age" are both synonymous templates for the age intent. Successful identification of the synonymous query intent templates not only can improve the performance of all existing query annotation approaches, but also could benefit applications such as instant answers and intent-based query suggestion. In this work we propose a clustering framework with multiple kernel functions to identify synonymous query intent templates for a set of canonical templates jointly. Furthermore, signals from multiple sources of information are integrated into a kernel function between templates, where the weights of these signals are tuned in an unsupervised manner. We have conducted extensive experiments across multiple domains in FreeBase, and results demonstrate the effectiveness of our clustering framework for finding synonymous query intent templates for attribute intents.
Conjugated polymer nanoparticles for small interfering RNA delivery (2011)

Loosely aggregated conjugated polymer nanoparticles (CPNs) were used as nontoxic and efficient small interfering RNA (siRNA) delivery vehicles with delivery visualization. A significant down regulation (94%) of a target gene was achieved by transfection of HeLa cells with the CPNs/siRNA complexes, supporting CPN as a promising siRNA delivery carrier.
Dynamic Models for Torque Converter Equipped Vehicles (1982)

<div class="htmlview paragraph">A dynamic model for the coupled engine-torque converter-vehicle system was developed to allow mathematical analysis and performance prediction for engine or powertrain controls in torque converter equipped vehicles.</div> <div class="htmlview paragraph">The principal contribution of this work is the derivation and justification of a static nonlinear terminal model of the torque converter. This model, when approximated, allows simple coupling of available engine, geartrain, and vehicle models.</div> <div class="htmlview paragraph">The resulting differential equations provide a reasonably simple, physically justified model for engine and vehicle behavior when driven by large signal variations in either engine net torque output or vehicle load.</div>
The Hummingbird minipositioner-providing three-axis motion at 50 g's with low reactions (2003)

The Hummingbird minipositioner is a three-axis servo-mechanism designed to provide fast and accurate positioning of a low-mass probe tip on or above a nearly planar object. Peak XYZ accelerations in excess of 500 m/s/sup 2/ (50 g) are obtained, with positioning resolution under 1 mu m and a workspace of 13 by 13 by 1 mm. The system weighs 950 g and is nearly reactionless during X-Y motion to simplify integration with large-area positioners. The design of the dynamically balanced five-bar linkage assembly and the Z-actuator is presented, along with data on in-plane linkage resonances (shown to be >1 kHz) and the torque cancellation effectiveness. A typical incremental move of 5 mm with 50 g peak acceleration and a move time of 8 ms is also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A comparison of random forest and its Gini importance with standard chemometric methods for the feature selection and classification of spectral data (2009)

The Gini importance of the random forest provided superior means for measuring feature relevance on spectral data, but - on an optimal subset of features - the regularized classifiers might be preferable over the random forest classifier, in spite of their limitation to model linear dependencies only. A feature selection based on Gini importance, however, may precede a regularized linear classification to identify this optimal subset of features, and to earn a double benefit of both dimensionality reduction and the elimination of noise from the classification task.
Bromocriptine: a novel approach to the treatment of type 2 diabetes. (2000)

Bromocriptine improves glycemic control and glucose tolerance in obese type 2 diabetic patients. Both reductions in fasting and postprandial plasma glucose levels appear to contribute to the improvement in glucose tolerance. The bromocriptine-induced improvement in glycemic control is associated with enhanced maximally stimulated insulin-mediated glucose disposal.
A high performance CMOS process for submicron 16 Mb EPROM (2003)

A high-performance and reliable 0.6 mu m CMOS process has been developed for the fabrication of next-generation 16-Mb density high-speed electrically programmable ROMs (EPROMs). The key process technologies are: (a) less than 0.2- mu m bird's beak isolation; (b) high-performance n/p channel LDD (lightly doped drain) transistors; (c) thin reliable interpoly dielectrics; (d) cold end processing using RTA (rapid thermal annealing) for both glass reflow and n/sup +/,p/sup +/ junction activation; and (e) less than 4.5- mu m/sup 2/ cell area (for practical die size) with fast writing speed, sufficient read current, and soft write endurance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>