gebhart/patrepeval huggingface dataset:
Genomic DNA Sequence, Expression, and Chromosomal Localization of the Human B1 Bradykinin Receptor Gene BDKRB1 (1996)

We have cloned and sequenced the human B1 bradykinin receptor gene (BDKRB1), which contains an uninterrupted coding exon. A putative promoter was identified by linking various lengths of the 5'-flanking region of the B1 receptor gene coding sequence to a CAT reporter and assaying for CAT activity. Deletion analysis showed that a 300-bp fragment in the promoter region is sufficient to direct the synthesis of the reporter and that an enhancer-like element is present between -1842 and -812. A genomic Southern blot using the B1 cDNA revealed that the receptor is encoded by a single-copy gene. The gene is located on chromosome 14q32.1-q32.2, in close proximity to the B2 receptor gene. Northern blot analysis identified a 1.7- to 1.8-kb mature mRNA transcript of the B1 receptor gene in the kidney and pancreas. A widespread tissue distribution of the B1 gene expression was identified by RT-PCR-Southern blot analysis using specific oligonucleotide probes.
Cloning and Expression of a Novel Hepatitis B Virus-binding Protein from HepG2 Cells (2001)

A direct involvement of the hepatitis B virus (HBV) preS1-(21-47) sequence in virus attachment to cell membrane receptor(s) and the presence on the plasma membranes of HepG2 cells of protein(s) with receptor activity for HBV have been suggested by many previous experiments. In this study, by using a tetravalent derivative of the preS1-(21-47) sequence, we have isolated by affinity chromatography from detergent-solubilized HepG2 plasma membranes a 44-kDa protein (HBV-binding protein; HBV-BP), which was found to closely correspond to the human squamous cell carcinoma antigen 1 (SCCA1), a member of the ovalbumin family of serine protease inhibitors. Comparison of SCCA1 sequence with the sequence of the corresponding HBV-BP cDNA, cloned by polymerase chain reaction starting from RNA poly(A)(+) fractions extracted from HepG2 cells, indicated the presence of only four nucleotide substitutions in the coding region, leading to three amino acid changes. Intact recombinant HBV-BP lacked inhibitory activity for serine proteases such as alpha-chymotrypsin and trypsin but inhibited with high potency cysteine proteases such as papain and cathepsin L. Direct binding experiments confirmed the interaction of recombinant HBV-BP with the HBV preS1 domain. HepG2 cells overexpressing HBV-BP after transfection of corresponding cDNA showed a virus binding capacity increased by 2 orders of magnitude compared with untransfected cells, while Chinese hamster ovary cells, which normally do not bind to HBV, acquired susceptibility to HBV binding after transfection. Native HBV particle entry was enhanced in transfected cells. Both recombinant HBV-BP and antibodies to recombinant HBV-BP blocked virus binding and internalization in transfected cells as well as in primary human hepatocytes in a dose-dependent manner. Our findings suggest that this protein plays a major role in HBV infection.
Superstructure-Enabled Anti-Fouling Membrane for Efficient Photothermal Distillation (2019)

Photothermal membrane distillation (MD) combining solar harvesting and heat localization is a rapidly emerging technology for water purification and desalination. However, state-of-the-art photothermal MD still suffers from several issues in membrane fouling, material instability, poor long-term performance, and complex synthesis. Herein, we demonstrate a multilevel-roughness membrane by immobilizing a nanoparticle-assembled superstructure on a nanofibrous membrane to obtain omniphobic surface wettability. The nanoparticle-assembled superstructure with abundant nano-/microchannels and low surface energy simultaneously captures solar energy, repels chemical/oil-based contaminants, and facilitates vapor flow. The unique mechanism based on the effects of the multilevel-roughness structure allows effective control of surface wettability, leading to a successful photothermal MD application, highlighted by highly efficient solar-thermal conversion, excellent antifouling behavior, and durability. A high clean water yield of 9.01 kg m–2 h–1 is obtained at a solar intensity of 10 kW m–2, corresponding to a solar-water efficiency of 66.8%. More importantly, when operating in complex feed-water conditions, including oil contaminated and high-saline solution, the speed of clean water generation still presents excellent stability over 48 h of consecutive operation, which significantly outperforms the commercial distillation membranes (typically 1 h). Multiple merits of efficient solar-thermal conversion and long-term stability, supported by techno-economic and scalability analyses, make the composite membrane promising for clean water generation from diverse contaminant mixtures in the solar-driven MD system.
Prutor: A System for Tutoring CS1 and Collecting Student Programs for Analysis (2016)

An introductory programming course (CS1) is an integral part of any undergraduate curriculum. Due to large number and diverse programming background of students, providing timely and personalised feedback to individual students is a challenging task for any CS1 instructor. The help provided by teaching assistants (typically senior students) is not sufficient as it suffers from unintentional bias and, most of the time, not quick enough. In this paper, we present Prutor, a tutoring system platform to conduct introductory programming courses. Prutor is a cloud-based web application that provides instant and useful feedback to students while solving programming problems. Prutor stores, at regular intervals, the snapshots of students' attempts to solve programming problems. These intermediate versions of the student programs provide the instructors (and data analysts) a view of the students' approach to solving programming problems. Since Prutor is accessible through any standard web browser, students do not need to worry about dependencies external to the programming course, viz. Operating Systems, Editors, Compilers, Compiler Options, etc.. This enables the students to focus on solving only the programming problems. Apart from the code snapshots at regular intervals, Prutor also collects other valuable data such as the time taken by the students to solve the problems, the number of compile and execution events, and the errors made. We have used this data in developing intelligent tools for giving feedback to students, some of which are described briefly in this paper. This system thus serves as a platform for tutoring as well as data collection for researchers.
Delay with network coding and feedback (2009)

We consider the problem of minimizing delay when broadcasting over erasure channels with feedback. A sender wishes to communicate the same set of mu messages to several receivers over separate erasure channels. The sender can broadcast a single message or a combination (encoding) of messages at each timestep. Receivers provide feedback as to whether the transmission was received. If at some time step a receiver cannot identify a new message, delay is incurred. Our notion of delay is motivated by real-time applications that request progressively refined input, such as the successive refinement of an image encoded using multiple description coding. Our setup is novel because it combines coding techniques with feedback information to the end of minimizing delay. It allows Theta(mu) benefits as compared to previous approaches for offline algorithms, while feedback allows online algorithms to achieve smaller delay than online algorithms without feedback. Our main complexity results are that the offline minimization problem is NP-hard when the sender only schedules single messages and that the general problem remains NP-hard even when coding is allowed. However we show that coding does offer delay and complexity gains over scheduling. We also discuss online heuristics and evaluate their performance through simulations.
Nanocrystals as Precursors for Flexible Functional Films (2005)

Nanocrystals – your flexible friends! The use of nanocrystals as precursors for the one-step formation of flexible functional films by using an air plasma is demonstrated. This treatment does not harm the photoluminescence of the individual nanocrystal building blocks but confers on them resilience to bending as well as acidic environments, hot solvents, annealing, and UV irradiation. The chemical accessibility and selective etching of the nanocrystals allows for micrometer-scale patterning of the film (see Figure).
Function, Activity, and Membrane Targeting of Cytosolic Phospholipase A2ζ in Mouse Lung Fibroblasts (2007)

Group IVA cytosolic phospholipase A(2) (cPLA(2)alpha) initiates eicosanoid production; however, this pathway is not completely ablated in cPLA(2)alpha(-/-) lung fibroblasts stimulated with A23187 or serum. cPLA(2)alpha(+/+) fibroblasts preferentially released arachidonic acid, but A23187-stimulated cPLA(2)alpha(-/-) fibroblasts nonspecifically released multiple fatty acids. Arachidonic acid release from cPLA(2) alpha(-/-) fibroblasts was inhibited by the cPLA(2)alpha inhibitors pyrrolidine-2 (IC(50), 0.03 microM) and Wyeth-1 (IC(50), 0.1 microM), implicating another C2 domain-containing group IV PLA(2). cPLA(2) alpha(-/-) fibroblasts contain cPLA(2)beta and cPLA(2)zeta but not cPLA(2)epsilon or cPLA(2)delta. Purified cPLA(2)zeta exhibited much higher lysophospholipase and PLA(2) activity than cPLA(2)beta and was potently inhibited by pyrrolidine-2 and Wyeth-1, which did not inhibit cPLA(2)beta. In contrast to cPLA(2)beta, cPLA(2)zeta expressed in Sf9 cells mediated A23187-induced arachidonic acid release, which was inhibited by pyrrolidine-2 and Wyeth-1. cPLA(2)zeta exhibits specific activity, inhibitor sensitivity, and low micromolar calcium dependence similar to cPLA(2)alpha and has been identified as the PLA(2) responsible for calcium-induced fatty acid release and prostaglandin E(2) production from cPLA(2) alpha(-/-) lung fibroblasts. In response to ionomycin, EGFP-cPLA(2)zeta translocated to ruffles and dynamic vesicular structures, whereas EGFP-cPLA(2)alpha translocated to the Golgi and endoplasmic reticulum, suggesting distinct mechanisms of regulation for the two enzymes.
Elafin is specifically inactivated by RgpB from Porphyromonas gingivalis by distinct proteolytic cleavage (2009)

Abstract Porphyromonas gingivalis, the major causative bacterium of periodontitis, contributes significantly to elevated proteolytic activity at periodontal pockets owing to the presence of both bacteria and host, predominantly neutrophil-derived, serine proteases. Normally the activity of the latter enzymes is tightly regulated by endogenous proteins, including elafin, a potent neutrophil elastase and proteinase 3 inhibitor released from epithelial cells at sites of inflammation. Here, we report that all three gingipains (HRgpA, RgpB, and Kgp) have the ability to degrade elafin, with RgpB being far more efficient than other gingipains. RgpB efficiently inactivates the inhibitory activity of elafin at subnanomolar concentrations through proteolysis limited to the Arg22-Cys23 peptide bond within the surface loop harboring the inhibitor active site. Notably, elafin resists inactivation by several Staphylococcus aureus-derived serine and cysteine proteases, confirming the high stability of this protein against proteolytic degradation. Therefore, we conclude that elafin inactivation by RgpB represents a specific pathogenic adaptation of P. gingivalis to disturb the protease-protease inhibitor balance in the infected gingival tissue. This contributes to enhanced degradation of host proteins and generation of a pool of peptides serving as nutrients for this asaccharolytic pathogen.
The transcriptome of Cryptosporidium oocysts and intracellular stages (2019)

Human cryptosporidiosis is caused primarily by two species of apicomplexan parasites, Cryptosporidium parvum and C. hominis. Although infection of cell monolayers with sporozoites does not support the complete parasite life cycle, the in vitro system is used to study the asexual phase of multiplication, which consists of two generations of merogony. To better understand host-parasite interaction and to gain insight into gene regulatory processes driving the complex life cycle of Cryptosporidium parasites, we analyzed the transcriptome of C. parvum in oocysts, sporozoites and infected cell monolayers 2-48 h post-infection. Analysis of RNA-Seq data from replicate oocyst, sporozoite and intracellular samples revealed significant differences between transcriptomes expressed outside and inside the host cell. Compared to the transcriptome found in the host cell, the oocyst transcriptome is less diverse. Biological processes significantly over-represented intracellularly relate to biosynthetic processes. Genes significantly overexpressed in oocysts show evidence of specialized functions not found in other Apicomplexa. A more comprehensive view of gene regulation during the Cryptosporidium life cycle will require the analysis of later time points during the infection, particularly of the poorly studied sexual phase of the life cycle.
Narrowband Interference Detection via Deep Learning (2023)

Due to the increased usage of spectrum caused by the exponential growth of wireless devices, detecting and avoiding interference has become an increasingly relevant problem to ensure uninterrupted wireless communications. In this paper, we focus our interest on detecting narrowband interference caused by signals that despite occupying a small portion of the spectrum only can cause significant harm to wireless systems, for example, in the case of interference with pilots and other signals that are used to equalize the effect of the channel or attain synchronization. Due to the small sizes of these signals, detection can be difficult due to their low energy footprint, while greatly impacting (or denying completely in some cases) network communications. We present a novel narrowband interference detection solution that utilizes convolutional neural networks (CNNs) to detect and locate these signals with high accuracy. To demonstrate the effectiveness of our solution, we have built a prototype that has been tested and validated on a real-world over-the-air large-scale wireless testbed. Our experimental results show that our solution is capable of detecting narrowband jamming attacks with an accuracy of up to 99%. Moreover, it is also able to detect multiple attacks affecting several frequencies at the same time even in the case of previously unseen attack patterns. Not only can our solution achieve a detection accuracy between 92% and 99%, but it does so by only adding an inference latency of 0.093ms.
Characteristics of low E a 193-nm chemical amplification resists (2006)

Polymers with methyl acetal ester moiety in the side chain as acid labile protecting group were synthesized and their thermal property, plasma stability and chemical amplification (CA) positive-tone resist characteristics were investigated. 2-Admantyloxymethyl (AdOM) groups in the copolymer indicated lower glass transition temperatures and higher thermal decomposition temperatures than those of 2-methyl-2-admantyl (MAd) groups in the copolymer. AdOM polymer film showed smooth surface roughness after Ar plasma exposure compared with MAd polymer film due to the high thermal stability. The activation energies (Ea) of these deprotection reactions were calculated from Arrhenius plots of these deprotection reaction rate constants. In the low post exposure bake (PEB) temperature region, the Ea of these resists decreased in the order MAd > AdOM. The low Ea methyl acetal resists displayed good thermal flow resist characteristics for contact holes printing. In addition, the low Ea methyl acetal resist achieved a wide exposure latitude of 8.1 % and depth of focus of 400 nm for printing 80 nm 1:1 dense line pattern using NSR-306C (NA 0.78, 2/3 annular). Furthermore, the 65 nm 1:1 dense lines using ASML XT1400 (NA 0.93, C-Quad) for low Ea methyl acetal resist pattern showed no tapered and no footing profiles and small roughness on the lines pattern sidewall was observed.
Simulation of MOS Circuits by Decision Diagrams (1985)

This paper describes a novel approach to switch-level simulation of MOS circuits. The circuit is first partitioned into connector-switch networks CSN [4]. Then each CSN is represented in terms of a decision diagram DD, which is particularly suitable for use in simulators. The advantages of DD's are that they are based on a solid theory and they permit fast evaluation of the network's response to any input vector. The CSN's are coupled through a 3-state automaton representing charge wells associated with transistor gates.
Assessment of celecoxib pharmacodynamics in pancreatic cancer (2006)

Cyclooxygenase-2 (COX-2) inhibitors are being developed as chemopreventive and anticancer agents. This study aimed to determine the biological effect of the COX-2 inhibitor celecoxib in pancreatic cancer as an early step to the further development of the agent in this disease. Eight patients scheduled for resection of an infiltrating adenocarcinoma of the pancreas were randomized to receive celecoxib at a dose of 400 mg twice daily or placebo for 5 to 15 days before the surgery. In addition, carcinomas from nine additional patients were xenografted in nude mice, expanded, and treated with vehicle or celecoxib for 28 days. Celecoxib markedly decreased the intra-tumor levels of prostaglandin E2 in patient carcinomas and in the heterotransplanted xenografts. However, this effect did not result in inhibition of cell proliferation or microvessel density (as assessed by Ki67 and CD31 staining). In addition, a panel of markers, including bcl-2, COX-1, COX-2, and VEGF, did not change with treatment in a significant manner. Furthermore, there was no evidence of antitumor effects in the xenografted carcinomas. In summary, celecoxib efficiently inhibited the synthesis of prostaglandin E2 both in pancreatic cancer surgical specimens and in xenografted carcinomas but did not exert evident antitumor, antiproliferative, or antiangiogenic effect as a single agent. The direct pancreatic cancer xenograft model proved to be a valuable tool for drug evaluation and biological studies and showed similar results to those observed in resected pancreatic cancer specimens.
Perfusion visualization and analysis for pulmonary embolism (2005)

Given the nature of pulmonary embolism (PE), timely and accurate diagnosis is critical. Contrast enhanced high-resolution CT images allow physicians to accurately identify segmental and sub-segmental emboli. However, it is also important to assess the effect of such emboli on the blood flow in the lungs. Expanding upon previous research, we propose a method for 3D visualization of lung perfusion. The proposed method allows users to examine perfusion throughout the entire lung volume at a single glance, with areas of diminished perfusion highlighted so that they are visible independent of the viewing location. This may be particularly valuable for better accuracy in assessing the extent of hemodynamic alterations resulting from pulmonary emboli. The method also facilitates user interaction and may help identify small peripheral sub-segmental emboli otherwise overlooked. 19 patients referred for possible PE were evaluated by CT following the administration of IV contrast media. An experienced thoracic radiologist assessed the 19 datasets with 17 diagnosed as being positive for PE with multiple emboli. Since anomalies in lung perfusion due to PE can alter the distribution of parenchymal densities, we analyzed features collected from histograms of the computed perfusion maps and demonstrate their potential usefulness as a preliminary test to suggest the presence of PE. These histogram features also offer the possibility of distinguishing distinct patterns associated with chronic PE and may even be useful for further characterization of changes in perfusion or overall density resulting from associated conditions such as pneumonia or diffuse lung disease.
Polarization holography for vortex retarders recording: laboratory demonstration (2015)

This paper will present a prototype of the first set of vortex retarders made of liquid crystal polymers recorded by polarization holography. Vortex retarders are birefringent plates characterized by a rotation of their fast axis. Liquid crystals possess birefringent properties and they are locally orientable. Their orientation is defined by the perpendicular to the local orientation of the recording field. Polarization holography is a purely optical recording method. It is based on the superimposition of coherent and differently polarized beams. It is used to shape the electric field pattern to enable the recording of vortex retarders. The paper details the mathematical model of the superimposition process. The recording setup is exposed; it is characterized by a nearly common path interferometer. Two sets of measurements allowing the prediction of the retarder's features are presented and compared. Finally, the experimentally recorded retarder is shown, its characteristics are investigated and compared to the predicted ones.
Classification of the symmetry of photoelectron dichroism broken by light (2020)

We investigate how the direction of polarized light can affect the dichroism pattern seen in angle-resolved photoemission spectroscopy. To this end, we prepared a sample composed of highly-oriented Bi(111) micro-crystals that macroscopically has infinite rotational and mirror symmetry of the point group $\rm{C}_{\infty\rm{v}}$ and examined whether the dichroism pattern retains the $\rm{C}_{\infty\rm{v}}$ symmetry under the stationary configuration of the light and sample. The direction of the light was imprinted in the pattern. Thereby, we apply group theory and classify the pattern with the configuration of light taken into account. We complete the classification by discussing the cases when the out-of-plane component of the polarization can be neglected, when the incidence angle is either 0$^{\circ}$ or 90$^{\circ}$, when the polarization is either elliptic or linear, and also when the sample is a crystal.
Skeletal Diversity via a Folding Pathway:  Synthesis of Indole Alkaloid-Like Skeletons (2004)

Inspired by the skeletal diversity of naturally occurring indole alkaloids and the rich potential of chemistry developed by Padwa and co-workers, we conceived a pathway entailing six modes of intramolecular reactions leading to indole alkaloid-like skeletons. In this context, an efficient folding pathway via a rhodium-catalyzed tandem cyclization-cycloaddition involving three of the modes has been developed (two of which are shown above) that affords densely functionalized compounds with three distinct skeletons in a stereocontrolled manner.
Onset of GaSb/GaAs quantum dot formation (2006)

Abstract We present cross‐sectional scanning tunneling microscopy results on GaSb nanostructures in GaAs, analyzing their shape, size and chemical composition. By comparing different quantum wells and quantum dot layers, grown both by metalorganic chemical vapor deposition and by molecular beam epitaxy, the onset of quantum dot evolution is studied. Quantum dots are found already after a deposition of 1 monolayer GaSb. Intermixing of the deposited GaSb with GaAs due to anion exchange as well as different effects of Sb segregation during overgrowth are demonstrated. (© 2006 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Preparation of a reduced graphene oxide/poly-l-glutathione nanocomposite for electrochemical detection of 4-aminophenol in orange juice samples (2015)

Schematic representation of the preparation of the RGO/P-<sc>l</sc>-GSH film.