gebhart/patrepeval huggingface dataset:
Caenorhabditis elegans AF4/FMR2 Family Homolog affl-2 Regulates Heat-Shock-Induced Gene Expression (2020)

To mitigate the deleterious effects of temperature increases on cellular organization and proteotoxicity, organisms have developed mechanisms to respond to heat stress. In eukaryotes, HSF1 is the master regulator of the heat shock transcriptional response, but the heat shock response pathway is not yet fully understood. From a forward genetic screen for suppressors of heat-shock-induced gene expression in <i>Caenorhabditis elegans</i>, we found a new allele of <i>hsf-1</i> that alters its DNA-binding domain, and we found three additional alleles of <i>sup-45</i>, a previously molecularly uncharacterized genetic locus. We identified <i>sup-45</i> as one of the two hitherto unknown <i>C. elegans</i> orthologs of the human AF4/FMR2 family proteins, which are involved in regulation of transcriptional elongation rate. We thus renamed <i>sup-45</i> as <i>affl-2</i> (AF4/FMR2-Like). Through RNA-seq, we demonstrated that <i>affl-2</i> mutants are deficient in heat-shock-induced transcription. Additionally, <i>affl-2</i> mutants have herniated intestines, while worms lacking its sole paralog (<i>affl-1</i>) appear wild type. AFFL-2 is a broadly expressed nuclear protein, and nuclear localization of AFFL-2 is necessary for its role in heat shock response. <i>affl-2</i> and its paralog are not essential for proper HSF-1 expression and localization after heat shock, which suggests that <i>affl-2</i> may function downstream of, or parallel to, <i>hsf-1</i> Our characterization of <i>affl-2</i> provides insights into the regulation of heat-shock-induced gene expression to protect against heat stress.
Range Expansion for Wireless Power Transfer: A Joint Beamforming and Waveform Architecture. (2020)

Far-field Wireless Power Transfer (WPT) has emerged as a viable power source for Internet of Things (IoT) and Wireless Sensor Network (WSN). Expansion of the power transfer range is an important challenge to enable the design of efficient networks of small autonomous devices and drive the massive numbers of devices using a single wireless power source. Several signal design strategies have been proposed and verified to maximize the output DC power at the receiver under a transmit power constraint. In this paper, we study channel-adaptive beamforming and waveform to expand the power transfer range as well as output DC power performance. To that end, we have designed, prototyped a far-field WPT system and established a WPT testbed in a realistic indoor environment. The experiments have been conducted in a variety of wireless channel conditions in an indoor office environment with various distances. The measurement data have been fitted using simple analytical model to analyze the output DC power and achievable range improvement depending on the signal design schemes and the number of tones and antennas. The model shows a clear relationship between signal design versus output DC power and achievable range, and enables to predict the achievable power transfer range for given transmit power constraint and target received DC power. Results highlight the significant benefit of a channel-adaptive joint beamforming and waveform architecture to expand the power transfer range.
Production of Monoclonal Antibodies to Listeria monocytogenes and Their Application To Determine the Virulence of Isolates from Channel Catfish (1999)

We produced monoclonal antibodies (MAbs) to the extracellular proteins of Listeria monocytogenes EGD grown in Chelex-treated improved minimal medium. Ten of the positive hybridomas generated were chosen for further characterization. Seven of the MAbs reacted with a protein having a molecular mass of 60 kDa. These MAbs inhibited listeriolysin (LLO)-mediated hemolysis, and two of them were specific for LLO and none of the other thiol-activated toxins tested. In an enzyme-linked immunosorbent assay and Western blot analysis, five of the anti-LLO MAbs reacted with ivanolysin from Listeria ivanovii. Three of the 10 MAbs reacted with a 29-kDa protein on Western blots and neutralized the phosphatidylcholine-specific phospholipase C (PC-PLC) activity of L. monocytogenes. These three anti-PC-PLC MAbs did not react with phospholipases from five different gram-positive bacteria. However, the anti-PC-PLC MAbs recognized a 27-kDa extracellular protein from L. ivanovii and neutralized sphingomyelinase activity in a hemolysis test that demonstrates the antigenic relatedness of listerial phospholipases. These data indicate that listerial thiol-activated toxins possess species-specific epitopes and share group-specific epitopes. This is the first description of MAbs that neutralize listerial PC-PLC, and the data suggest that there is antigenic similarity between L. monocytogenes PC-PLC and L. ivanovii sphingomyelinase. The reactions of the MAbs with catfish isolates of L. monocytogenes suggested that some of the isolates examined lack the LLO and/or PC-PLC required for pathogenicity. The MAbs described here differentiated some catfish isolates from previously described type strain-pathogenic isolates and could be useful for detecting and determining the virulence of L. monocytogenes in food and clinical samples and for detecting L. ivanovii in veterinary clinical samples.
Experimental investigation of fractional sampling in IEEE802.11a WLAN system (2008)

In the IEEE802.11a WLAN standard, orthogonal frequency division multiplexing (OFDM) modulation is employed. Diversity techniques are usually utilized to overcome fading channels in OFDM systems. Furthermore, a diversity technique with one antenna is desirable because the form factor of the terminal is important. Fractional sampling (FS) scheme is one of the diversity techniques with a single antenna. Through FS, it is possible to separate multipath components and obtain diversity gain in OFDM communication. However, an experimental investigation of FS has not been carried out. In this paper, the FS scheme on a IEEE802.11a WLAN system is evaluated through an experiment. Especially, the BER performances with line-of-sight (LOS) and non-LOS (NLOS) situations are compared. Numerical results through the experiment indicate that the FS can achieve path diversity.
Studies on Electron Beam Transport in a Linear Induction Accelerator for Free Electron Laser Application (2021)

Project of submillimeter free electron laser (FEL) is developed at BINP in collaboration with IAP [1] . The FEL scheme is based on a high current electron beam (E e = 5−20 MeV, I b = 1−2 kA, τ= 160−200 ns) generated at the new linear induction accelerator (LIA) [2] , [3] . According to our theoretical analysis, such beam allows us to generate coherent pulses of submm-radiation in the frequency range 0.3-1 THz. The radiation power in such scheme can reach a sub-megawatt level and the energy content up to ~100 J.
Quality adaptive trained filters for compression artifacts removal (2008)

A compression artifacts removal algorithm that is adaptive to the artifact visibility level of the input video signal is proposed. The artifact visibility is determined per frame by the ratio of the accumulated gradient on the block edges to that of the remaining area. The filtering of each video frame is optimized using a least mean square mechanism which trains on pairs of target images and decompressed images of similar quality as the input frame. Experimental results show that the proposed approach outperforms several methods in coding artifact reduction.
Large-scale testing of a sandwich shaft-sealing system at the Mont Terri rock laboratory (2021)

Abstract. Shaft-sealing systems for nuclear waste repositories are constructed to limit fluid inflow from the adjacent rock during the early stage after closure of the repository and to delay the release of possibly contaminated fluids from the repository at later stages. Current German concepts of shaft seals contain the hydraulic sandwich sealing system as a component of the lower seal in host rock (Kudla and Herold, 2021). The KIT-developed sandwich sealing system consists of alternating sealing segments (DS) of bentonite and equipotential segments (ES) that are characterized by a high hydraulic conductivity. Within the ES, fluid is evenly distributed over the cross section of the seal. Water bypassing the seal via the excavation-damaged zone or penetrating the seal inhomogeneously is contained, and a more homogeneous hydration and swelling of the DS is obtained. The functionality of such a system was proven in laboratory and semi-technical-scale experiments (Schuhmann et al., 2009). After a joint international pre-project (Emmerich et al., 2019) dedicated to the planning of a large-scale in situ test that demonstrates the feasibility and effectiveness of the sandwich shaft-sealing system in interaction with the host rock, the large-scale experiment was launched at the Mont Terri rock laboratory in July 2019 with partners from Germany, Switzerland, Spain, UK, and Canada. It consists of two experimental shafts of 1.18 m diameter and 10–12.6 m depth, constructed using a core drilling technique with a custom-made drill rig in a new niche in the sandy facies of the Opalinus Clay. The seal in shaft 1 consists of four DS (calcigel) of 1 m thickness and five ES (fine-grained quartz sand), each 30 cm thick (Fig. 1). Shaft sinking began in August 2020 and was completed in November 2020. In the following months, the sealing system and instrumentation of shaft 1 were installed. The sealing system is saturated from a pressure chamber located at the shaft bottom via an inclined lateral feeding borehole. Hydration of the system started in May 2021. Shaft 2 will host a slightly modified system emplaced 1–1.5 years later, in order to integrate experience obtained during the early operation phase of shaft 1. In contrast to shaft 1, the excavation-damaged zone around shaft 2 will have had time to develop. The seals and the surrounding rock are intensely monitored. Measurements in the rock (geophysics, pore pressure, and total stress) were started between August 2019 and March 2020. Characterization of the excavation-damaged zone along the wall of shaft 1 was performed by geophysical and surface packer measurements prior to seal emplacement. Measurements inside the shaft comprise water content, relative humidity, and temperature, pore pressure, stress, and displacements. The in situ work is backed by laboratory testing and model simulation. Data and experience obtained to date will be presented. The sandwich experiment is funded by the German Federal Ministry for Economic Affairs and Energy under contract 02E11799.
Soluble biomarkers in osteoarthritis - current status and future prospects? (2012)

There is an acute need for reliable soluble biomarkers that can facilitate earlier diagnosis of osteoarthritis (OA), inform the prognosis and monitor and predict the responses of patients to therapeutic interventions. The number of biomarkers that have been validated and qualified is relatively small. This article summarises the current state of play in the field of OA soluble biomarkers. It discusses the barriers that prevent biomarkers from achieving their full potential and provides some perspectives for basic researchers and clinicians. © Touch Medical Media 2012.
A Novel Battery Charger for Automotive Applications (2006)

In this paper, a new power electronics topology is introduced for battery pulse charging. The topology is based on a bidirectional isolated Cuk converter. The charging method provides positive and negative current and resting periods. This charging method results in less generated heat and longer battery life cycle. Different operating modes of the system and its small signal analysis are presented. The small signal system has been modeled using MATLAB. Simulation results are also provided to validate the mathematical analysis
Iridium Oxide-reduced Graphene Oxide Nanohybrid Thin Film Modified Screen-printed Electrodes as Disposable Electrochemical Paper Microfluidic pH Sensors (2016)

A facile, controllable, inexpensive and green electrochemical synthesis of IrO2-graphene nanohybrid thin films is developed to fabricate an easy-to-use integrated paper microfluidic electrochemical pH sensor for resource-limited settings. Taking advantages from both pH meters and strips, the pH sensing platform is composed of hydrophobic barrier-patterned paper micropad (µPAD) using polydimethylsiloxane (PDMS), screen-printed electrode (SPE) modified with IrO2-graphene films and molded acrylonitrile butadiene styrene (ABS) plastic holder. Repetitive cathodic potential cycling was employed for graphene oxide (GO) reduction which can completely remove electrochemically unstable oxygenated groups and generate a 2D defect-free homogeneous graphene thin film with excellent stability and electronic properties. A uniform and smooth IrO2 film in nanoscale grain size is anodically electrodeposited onto the graphene film, without any observable cracks. The resulting IrO2-RGO electrode showed slightly super-Nernstian responses from pH 2-12 in Britton-Robinson (B-R) buffers with good linearity, small hysteresis, low response time and reproducibility in different buffers, as well as low sensitivities to different interfering ionic species and dissolved oxygen. A simple portable digital pH meter is fabricated, whose signal is measured with a multimeter, using high input-impedance operational amplifier and consumer batteries. The pH values measured with the portable electrochemical paper-microfluidic pH sensors were consistent with those measured using a commercial laboratory pH meter with a glass electrode.
Super-miniaturized dielectric-metallic resonator antennas (2015)

A super-miniaturized resonator antenna is presented in this paper. Miniaturization is achieved by designing a new antenna configuration and applying high permittivity materials. The antenna size is smaller than λ/10, while stable radiation patterns as well as low cross polarization levels over the impedance bandwidth are observed. The proposed approach is very suitable for designing compact antennas which are desirable for many modern wireless communications and sensing systems.
Surface Deposition Method; A Novel Protein Immobilization Procedure on a Sensor Surface (2000)

A novel immobilization method, surface deposition method, for a membrane-binding protein on the solid surfaces of the sensor is described. We focused on the hydrophobicity of a membrane-binding region of a membrane-binding protein for this immobilization method. The surface deposition method consists of two steps; the first step is the protein adsorption on support surfaces by electrostatic interaction, and the second step is the deposition of the hydrophobic region of a membrane-binding protein onto the surfaces. The surface deposition method can immobilize a protein on solid surfaces under milder conditions than typical protein immobilization methods such as cross-linking and covalent binding. We also constructed a novel amperometric glucose sensing system employing membrane-binding PQQ glucose dehydrogenase using the surface deposition method.
Next-Science: A Novel Antimicrobial Agent that Inhibits Biofilm Development by Escherichia coli Clinical Isolates on Urinary Tract Catheters (2017)

Catheter-associated urinary tract infections (CAUTI) constitute about 40% of health-care associated infections in the United States. It is estimated that about 15% to 25% of hospitalized patients receive a urethral catheter at some point during hospitalization predisposing them to the development of CAUTI. Pathogenic bacteria colonize the surface of the catheter and develop highly resistant structures termed biofilms which protect them from the effects of diverse antibiotics. Escherichia coli are among the main causative agents of CAUTI. Due to the emergence of antibiotic resistant strains, it is critical to develop new novel antimicrobial agents. We recently showed that a novel anti-biofilm agent, Next Science, inhibited biofilm development by wound pathogens. In this study, we tried to determine if treating urinary tract catheters (UTC) with NS prevents the development if E. coli biofilms.
Three types of UTCs were cut into small pieces that were treated with NS. Biofilm development by an E. coli laboratory strain and several E. coli clinical isolates on treated and untreated pieces was accomplished using the microtiter plate assay. Biofilms developed on inner and outer surfaces of the catheters were quantified by determining the number of microorganisms (colony forming units) on each piece and visualized using confocal laser scanning microscopy (CLSM).
In comparison with untreated catheters, all three types of NS-treated catheters prevented biofilm development by tested E. coli strains. In addition, CLSM demonstrated the presence of E. coli biofilms on the inner and outer surfaces of the untreated but not treated catheters. Our results suggest that NS is a novel antimicrobial treatment to prevent biofilm development by pathogenic E. coli strains on UTCs.
Unveiling the mechanism of improved capacity retention in Pmn21 Li2FeSiO4 cathode by cobalt substitution (2019)

Substitution of cobalt in Li<sub>2</sub>FeSiO<sub>4</sub> improves capacity retention by facilitating phase transformation and forming beneficial cathode-electrolyte interfacial layer.
Development of an algorithm for detection of fatal cardiac arrhythmia for implantable cardioverter-defibrillator using a self-organizing map (2006)

In this study, we have introduced the pattern classifier using the self-organizing map (SOM) for detecting fatal cardiac arrhythmia in implantable cardioverter-defibrillators (ICDs). The SOM has learned patterns of sinus rhythm, ventricular fibrillation and ventricular tachycardia with the feature vectors extracted from electrocardiogram and right ventricular volume measured during an arrhythmia induction experiment of a dog. After learning, neurons of the SOM were labeled by using the k-Nearest Neighbor method. It was shown that the accuracy of the proposed method was higher than other competitive methods applied to the same test data.
Helicobacter pylori Biofilm Formation Is Differentially Affected by Common Culture Conditions, and Proteins Play a Central Role in the Biofilm Matrix (2018)

The concept of <i>Helicobacter pylori</i> biofilm formation is relatively new. To help provide a foundation for future biofilm studies, we characterized the biofilm formation ability of a common <i>H. pylori</i> lab strain, G27. The goal of this study was to evaluate biofilm formation by G27 in response to common culture conditions and to explore the biofilm matrix. Our results indicate that while various types of growth media did not dramatically affect biofilm formation, surface selection had a significant effect on the final biofilm mass. Furthermore, enzymatic assays and confocal microscopy revealed that proteins appear to be the primary structural component of the <i>H. pylori</i> extracellular matrix; extracellular DNA (eDNA) and polysaccharides were also present but appear to play a secondary role. Finally, we found that two well-characterized antibiofilm cationic peptides differentially affected early and late-stage biofilms. Together these results provide interesting avenues for future investigations that will seek to understand <i>H. pylori</i> biofilm formation.<b>IMPORTANCE</b> The study of <i>H. pylori</i> biofilm formation is still in its infancy. As such, there is great variability in how biofilm assays are performed across labs. While several groups have begun to investigate factors that influence <i>H. pylori</i> biofilm formation, it is not yet understood how <i>H. pylori</i> biofilm formation may vary based on commonly used conditions. These inconsistencies lead to difficulties in interpretation and comparison between studies. Here, we set out to characterize biofilm formation by a commonly available lab strain, G27. Our findings provide novel insight into optimal biofilm conditions, the biofilm matrix, and possible mechanisms to block or disrupt biofilm formation.
Gonococcal ribosomes as skin test antigens. II. Precision Of the Method, Attempts To Identify The Ribosomal Antigen, and Correlation with The Macrophage Migration Inhibition test. (1976)

Gonococcal crude ribosome preparation was found to be specific and sensitive when used to elicit delayed hypersensitivity reactions in sensitized guinea-pigs. Gonococcal crude ribosomes possess the ability to react with humoral antibody in sensitized animals; thus, ribosomes may be of value as an antigen in a sero-diagnostic test for gonorrhoea. Ribosomal protein or RNA, or gonococcal cell components including protoplasm, cell walls, and pilin, were less reactive than intact ribosomes. The ribosome preparation was used in an in vitro correlate of delayed hypersensitivity, suggesting that the human immune response in gonorrhoea might be studied using the crude ribosome in in vitro experiments with human peripheral lymphocytes.
Qualifying Bulk Metallic Glass Gear Materials for Spacecraft Applications (2018)

NASA is evaluating bulk metallic glass (BMG) gears for extreme environment (cryogenic) applications; e.g., Europa Lander. The main purpose of this report is to recommend a quality assurance (QA) protocol for the production of consistent and reliable gear castings. Currently, there are two, separate manufacturers involved; Materion Corporation produces re-melt stock and Visser Precision Cast, Inc. produces BMG castings. Division of the existing alloy specifications document into material supplier-specific documents is proposed. Until a composition-based specification is established, processability- and performance-based methodologies may be an option during manufacturing development. It is recommended that each of the documents has a distinct focus; the processing behavior of crystalline feedstock, and the mechanical behavior of amorphous castings. The report addresses the gray area in QA testing between these materials suppliers by outlining an equitable division of responsibilities. The use of a number of dedicated reference dies to produce witness materials for physical and mechanical property evaluation is strongly recommended. Allocation of QA tests between screen testing of gear castings, and formal testing of witness materials, including cryogenic properties, is also proposed. The most effective suite of tests for both physical and mechanical property determination are down-selected from available national and international standards. The contents of this report create a solid basis for selection of QA tests, thereby setting the stage for negotiations between the materials suppliers and the customer.This technical paper:a) provides recommendations to advance materials specifications document JPL D-56223,Rev. A from draft to preliminary status;b) proposes division of the current document into two supplier-specific documents;c) separates testing methods by ingots/castings and witness materials;d) classifies test methodology based on processability and performance;e) assembles candidate ASTM specifications for screen testing and formal testing;f) identifies standard tests compatible with evaluation of BMG flexspline gears;g) suggests division of responsibilities for processability and performance testing; andh) addresses the QA gray area between production of ingots and castings.The report recommends that:a) processability- and performance-based QA methods might be used in lieu ofcompositional specifications during manufacturing development only;b) reference dies be designed for acceptance and qualification castings;c) witness materials provide physical and mechanical property data;d) formal testing be conducted at ambient and cryogenic temperatures; ande) processing/properties be correlated with compositional variations.