gebhart/patrepeval huggingface dataset:
Novel indolizine compounds as potent inhibitors of phosphodiesterase IV (PDE4): structure–activity relationship (2010)

A series of novel indolizine 2-oxoacetamides were designed and synthesized as PDE4 inhibitors. Preliminary SAR of this new class of compounds revealed key structural features required for high potency. Compounds 1ab and 2a are among the most potent inhibitors of PDE4 with low single nM IC50. Cellular activity was demonstrated by the inhibition of TNFα production from human PBMC with IC50 ranging from 14 to 72 nM. Docking analyses suggest the OH group in 1ab enhance the binding via an H-bond interaction with the PDE4 enzyme.
Antibody-mediated autoimmune myocarditis depends on genetically determined target organ sensitivity. (1995)

Injury to cardiac myocytes often leads to the production of anti-myosin antibodies. While these antibodies are a marker of myocardial injury, their contribution to pathogenesis in diseases such as autoimmune myocarditis or rheumatic fever is much less clear. We demonstrate in this report that monoclonal anti-myosin antibodies can mediate myocarditis in a susceptible mouse strain. Additionally, we show disease susceptibility depends on the presence of myosin or a myosin-like molecule in cardiac extracellular matrix. This study demonstrates that susceptibility to autoimmune heart disease depends not only on the activation of self-reactive lymphocytes but also on genetically determined target organ sensitivity to autoantibodies.
Structure and Activity Associated with Multiple Forms ofSchizosaccharomyces pombe DNA Polymerase δ (2000)

DNA polymerase delta (Pol delta) isolated from Schizosaccharomyces pombe (sp) consists of at least four subunits, Pol3, Cdc1, Cdc27, and Cdm1. We have reconstituted the four-subunit complex by simultaneously expressing these polypeptides in baculovirus-infected insect cells. The properties of the purified cloned spPol delta were identical to the native spPol delta isolated from S. pombe cells. In addition, we also isolated a three-subunit complex containing Pol3, Cdc1, and Cdm1. Both three- and four-subunit complexes required replication factor C and proliferating cell nuclear antigen for DNA replication. However, in the presence of low levels of polymerase complexes, the three-subunit complex was less efficient than the four-subunit complex in supporting DNA replication. The inefficient synthesis of DNA by the three-subunit complex can be remedied by the addition of Cdc27, the subunit missing in the three-subunit complex. Gel filtration analysis demonstrated that the three-subunit complex is a monomer of the heterotrimer (Pol3, Cdc1, and Cdm1) and that the four-subunit complex is a dimer of the heterotetramer (Pol3, Cdc1, Cdc27, and Cdm1), similar to the structure of native spPol delta. We have further shown that Cdc1 and Cdc27 interact to form a heterodimeric complex. Gel filtration studies indicate that the structure of this complex is dimeric. These observations suggest that the Cdc27 subunit may play an important role contributing to the dimerization of Pol delta.
DSASync: Managing End-to-End Connections in Dynamic Spectrum Access Wireless LANs (2012)

Wireless LANs (WLANs) have been widely deployed as edge access networks that provide the important service of Internet access to wireless devices. Therefore, performance of end-to-end connections to/from such WLANs is of great importance. The advent of Dynamic Spectrum Access (DSA) technology is expected to play a key role in improving wireless communication. With DSA capability, WLANs opportunistically access licensed channels in order to improve spectrum-usage efficiency and provide better network performance. In this paper, we identify the key issues that impact end-to-end connection performance when a DSA-enabled WLAN is integrated with the wired cloud. We propose a new network management framework, called DSASync, to mitigate the identified performance issues. DSASync achieves this objective by managing the connections at the transport layer as a third-party supervisor and targets both TCP streams and UDP flows. DSASync requires no modifications to the network infrastructure or the existing network stack and protocols while ensuring transport protocol (TCP or UDP) semantics to be obeyed. It mainly consists of a combination of buffering and traffic-shaping algorithms to minimize the adverse side-effects of DSA on active connections. DSASync is evaluated using a prototype implementation and deployment in a testbed. The results show significant improvement in end-to-end connection performance, with substantial gains on QoS metrics like goodput, delay, and jitter. Thus, DSASync is a promising step toward applying DSA technology in consumer WLANs.
Self-cloning of the Catalase Gene in Environmental Isolates Improves Their Colony-forming Abilities on Agar Media (2023)

Hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) inhibits microbial growth at a specific concentration. However, we previously isolated two environmental bacterial strains that exhibited sensitivity to a lower H<sub>2</sub>O<sub>2</sub> concentration in agar plates. Putative catalase genes, which degrade H<sub>2</sub>O<sub>2</sub>, were detected in their genomes. We herein elucidated the characteristics of these putative genes and their products using a self-cloning technique. The products of the cloned genes were identified as functional catalases. The up-regulation of their expression increased the colony-forming ability of host cells under H<sub>2</sub>O<sub>2</sub> pressure. The present results demonstrated high sensitivity to H<sub>2</sub>O<sub>2</sub> even in microbes possessing functional catalase genes.
Characterization of proliferating cell nuclear antigen recognized by autoantibodies in lupus sera. (1984)

A nuclear antigen associated with cell proliferation (proliferating cell nuclear antigen [PCNA]) and blast transformation is recognized by autoantibodies in the sera of some patients with systemic lupus erythematosus. Using this autoantibody as a reagent, PCNA was purified 120-fold by ammonium sulfate fractionation, DEAE chromatography, and Sephadex G200 gel filtration. The antigenicity of PCNA was sensitive to trypsin but resistant to ribonuclease and deoxyribonuclease, suggesting that the antigenic determinant resided in protein and not nucleic acids. PCNA was inactivated at 56 degrees C for 30 min. Isoelectrophoretic focusing showed that the pI was 4.8. Analysis of immunoprecipitates on polyacrylamide gels showed the presence of IgG heavy and light chains and a single polypeptide band of 33,000 mol wt. This polypeptide band was the reactive antigen in immunoblotting (Western transfer) assays.
Epidemiological and Virological Characteristics of 2 Subgroups of Hepatitis B Virus Genotype C (2005)

HBV genotype C can be differentiated into 2 subgroups--namely, genotype Ce and genotype Cs--that have different epidemiological distributions and virological characteristics.
Influence of microfibrillated cellulose fractions on the rheology of water suspensions : Colloidal interactions and viscoelastic properties (2018)

Influence of microfibrillated cellulose fractions on the rheology of water suspensions : Colloidal interactions and viscoelastic properties
Improved biomarker performance for the detection of hepatocellular carcinoma by inclusion of clinical parameters (2012)

We have previously identified several biomarkers of hepatocellular carcinoma (HCC). The levels of three of these biomarkers were analyzed individually and in combination with the currently used marker, alpha fetoprotein (AFP), for the ability to distinguish between a diagnosis of cirrhosis (n=113) and HCC (n=164). We have utilized several novel biostatistical tools, along with the inclusion of clinical factors such as age and gender, to determine if improved algorithms could be used to increase the probability of cancer detection. Using several of these methods, we are able to detect HCC in the background of cirrhosis with an AUC of at least 0.95. The use of clinical factors in combination with biomarker values to detect HCC is discussed.
Lack of Association ofHelicobacter pyloriSeroprevalence and Gastric Cancer in a Population with Low Gastric Cancer Incidence (1995)

In contrast to previous results, these data do not provide evidence that the contribution of H. pylori infection to the carcinogenesis of gastric cancer is of major significance in a population with low gastric cancer rates and with high socioeconomic status.
Chattanooga SmartBus Project Final Phase II Evaluation Report (2008)

This report presents the results of Phase II of the national evaluation of the Chattanooga Area Regional Transportation Authority’s (CARTA’s) SmartBus Project. The Smartbus Project is a comprehensive transit ITS program for the city of Chattanooga, Tennessee. It involves deployment of a wide array of transit ITS technologies including: data warehousing and reporting software to accumulate data from different CARTA applications and provide reports to support CARTA operations; new operations management software to support fixed-route scheduling and demand response scheduling and dispatch; ticket vending machines for the Incline Railway; a remote diagnostics maintenance system; various on-board systems (mobile data computers, computer-aided dispatch / automated vehicle location software, a covert alarm, automated passenger counters, and a next stop automated announcement system); and new fareboxes, a revenue management system, and a multi-modal transit/parking smart card electronic fare payment system. The goal of the evaluation is to determine the impacts of these technologies in performing daily functions such as operations, scheduling, service planning, and maintenance, and to gather and document any lessons learned by the project team throughout the process of the deployment and operation of the technologies. This report discusses impacts to date of the technologies that have been in place for at least 1 year. It is important to note that the full impacts of many of the technologies are not expected to be realized until the onboard systems are in place and integrated with the existing technologies, and that those later impacts will be documented in the Phase III report. The evaluation involved a series of interviews with various CARTA staff, as well as gathering data on various performance measures including transit ridership, on-time performance, and on the road failures. The results of the study indicate that the ticket vending machines for the Incline Railway have helped CARTA access to make better business decisions about the Incline service; the data warehousing and reporting software has allowed for more rapid preparation of a variety of reports, has resulted in efficiencies in operations, and has made it possible to answer complex business decisions more quickly; the fixed route scheduling software has allowed CARTA to provide the same level of service with lower operating costs; and the paratransit scheduling and dispatch management software has increased efficiency in terms of passengers per vehicle-hour while it has not reduced the time required to issue invoices or improved the on-time performance.
Defibrillation Thresholds For Single And Successive Biphasic Shocks (2005)

To determine the effect of varying the separation between two successive biphasic shocks given over different lead configurations, defibrillation thresholds (DFTs) were obtained in six animals for separations ranging from 0.2 to 125 ms, and were compared with results from a previous study for each of the two biphasic shocks alone[l]. The optimal separation between two successive biphasic shocks is either short (510 ms) or long (between 75 and 125 ms) with improved defibrillation efficacy over either single shock by itself. There is a marked rise in the DFT at a delay of 50 ms, to a value much greater than a single shock alone.
Compress-and-Forward via Multilevel Coding (2019)

We investigate the performance of discrete (coded) modulations in the full-duplex compress-and-forward relay channel using multilevel coding. We numerically analyze the rates assigned to component binary codes of all levels. LDPC codes are used as the component binary codes to provide error protection. The compression at the relay is done via a scalar quantizer whose output is mapped to a codeword through LDPC codes. A compound Tanner graphical model and information exchange algorithm are described for the joint decoding of both messages sent from the source and relay. Simulation results show that the performance of the proposed system based on multilevel coding is better than that based on BICM, and is separated from the SNR threshold of the known compress-and-forward achievable rate by two factors consisting approximately of the sum of the shaping gain (due to the scalar quantization) and the separation of the LDPC code implementation from AWGN capacity.
Material design of negative-tone polyphenol resist for EUV and EB lithography (2007)

In order to enable design of a negative-tone polyphenol resist using polarity-change reaction, five resist compounds (3M6C-MBSA-BLs) with different number of functional group of &ggr;-hydroxycarboxyl acid were prepared and evaluated by EB lithography. The resist using mono-protected compound (3M6C-MBSA-BL1a) showed 40-nm hp resolution at an improved dose of 52 &mgr;C/cm<sup>2</sup> probably due to removal of a non-protected polyphenol while the sensitivity of the resist using a compound of protected ratio of 1.1 on average with distribution of different protected ratio was 72 &mgr;C/cm<sup>2</sup>. For evaluation of the di-protected compound based resist, a di-protected polyphenol was synthesized by a newly developed synthetic route of 3-steps reaction, which is well-suited for mass production. The resist using di-protected compound (3M6C-MBSA-BL2b) also showed 40-nm hp resolution at a dose of 40 &mgr;C/cm<sup>2</sup>, which was faster than that of mono-protected resist. Fundamental EUV lithographic evaluation of the resist using 3M6C-MBSA-BL2b by an EUV open frame exposure tool (EUVES-7000) gave its estimated optimum sensitivity of 7 mJ/cm<sup>2</sup> and a proof of fine development behavior without any swelling.
Microsatellite instability and mutational analysis of transforming growth factor β receptor type II gene (TGFBR2) in sporadic ovarian cancer (2001)

These findings suggest that: (1) MSI (both conventional and mononucleotide) is infrequent in ovarian cancer and (2) inactivation of the MSH2, MLH1, and MSH6 mismatch repair genes and TGFBR2 gene mutations do not play a major role in ovarian cancer tumorigenesis. The spurious TGFBR2 frameshift mutations detected by sequencing after conventional PCR underline the importance of confirming putative mutations in repetitive sequences by alternative methods.
Examining the Treatment Efficacy of PEERS in Japan: Improving Social Skills Among Adolescents with Autism Spectrum Disorder (2019)

This study examines the efficacy of the Japanese version of the Program for the Education and Enrichment of Relational Skills (PEERS), which focuses on improving social functioning through making friends and maintaining good relationships for adolescents with autism spectrum disorder (ASD) without intellectual disabilities. Originally developed in the United States, PEERS is one of the few evidence-based social skills training programs for youth with ASD. The present study shows that with linguistic and cultural modifications, PEERS is effective in improving social functioning for adolescents with ASD in Japan. Positive results were found specifically in the areas of socialization, communication, knowledge of social skills, autistic mannerisms, and behavioral and emotional problems. In addition, most treatment gains were maintained at a 3-month follow-up assessment. These findings suggest that the Japanese version of PEERS is beneficial across multiple socio-emotional and behavioral domains for adolescents with ASD.
Effect of Converter Topology on the Specific Energy Consumption of Alkaline Water Electrolyzers (2018)

Water electrolysis will be used to produce renewable hydrogen for energy storage and Power-to-X applications in the future renewable-energy-based energy systems. Therefore, the energy efficiency of hydrogen production will probably become a major issue. In this study, the effect of practical supply power converters on the specific energy consumption of megawatt (MW)-scale alkaline electrolyzers is studied and compared with an ideal dc power supply. The current quality and the stack specific energy consumption are studied in the case of traditional thyristor rectifiers and a transistor-based converter. The stack specific energy consumption is analyzed based on the simulated current waveforms and the electrical equivalent circuit of the electrolyzer stack. It is found that the transistor-based converter offers up to 14% lower electrolyzer stack specific energy consumption than the 6-pulse thyristor rectifier and up to 9.2% lower electrolyzer stack specific energy consumption than the 12-pulse thyristor rectifier as the current varies between 5000 and 1000 A. The simulated change in the stack specific energy consumption of the MW-scale alkaline water electrolyzer outweighs the losses occurring in the rectifiers. Further, selection of the ac voltage level may have a more adverse effect on the stack specific energy consumption with the thyristor rectifier topologies compared with the transistor-based topologies.
Dual chamber pacing mode in an atrial antitachycardia pacing device without a ventricular lead – A necessary evil (2015)

We present a case of a single chamber atrial pacemaker implanted for sinus node dysfunction and treatment of macroreentrant atrial tachycardias with atrial antitachycardia pacing. The patient presented with sustained atrial tachycardia above the detection rate, however, the device was unable to detect the tachycardia and did not deliver the programmed therapy. We discuss the nuances of the atrial tachyarrhythmia detection algorithms, and the programming strategies to maximize detection of atrial arrhythmias in a single chamber atrial pacemaker.
Mach-Zehnder recording systems for pulsed power diagnostics (2012)

Fiber-optic transmission and recording systems, based on Mach-Zehnder modulators, have been developed and installed at the National Ignition Facility (NIF), and are being developed for other pulsed-power facilities such as the Z accelerator at Sandia, with different requirements. We present the design and performance characteristics for the mature analog links, based on the system developed for the Gamma Reaction History diagnostic at the OMEGA laser and at NIF. For a single detector channel, two Mach-Zehnders are used to provide high dynamic range at the full recording bandwidth with no gaps in the coverage. We present laboratory and shot data to estimate upper limits on the radiation effects as they impact recorded data quality. Finally, we will assess the technology readiness level for mature and developing implementations of Mach-Zehnder links for these environments.
Toward Quantitative Measurements of Enzyme Kinetics by Dissolution Dynamic Nuclear Polarization (2014)

Dissolution dynamic nuclear polarization (D-DNP) experiments enabled us to study the kinetics of the enzymatic phosphorylation reaction of glucose to form glucose-6-phosphate (G6P) by hexokinase (HK), with or without the presence of an excess of G6P, which is known to be an inhibitor of the enzyme. Against all expectations, our observations demonstrate that the phosphorylation of both α and β glucose anomers occurs with comparable kinetics. The catalytic constant of the reaction was estimated based on a simple kinetic model tailored for hyperpolarized systems.
The capsule of Cryptococcus neoformans modulates phagosomal pH through its acid-base properties (2018)

Abstract Phagosomal acidification is a critical cellular mechanism for the inhibition and killing of ingested microbes by phagocytic cells. The acidic environment activates microbicidal proteins and creates an unfavorable environment for the growth of many microbes. Consequently, numerous pathogenic microbes have developed strategies for countering phagosomal acidification through various mechanisms that include interference with phagosome maturation. The human pathogenic fungus Cryptococcus neoformans resides in acidic phagosome after macrophage ingestion that actually provides a favorable environment for replication since the fungus replicates faster at acidic pH. We hypothesized that the glucuronic acid residues in the capsular polysaccharide had the capacity to affect phagosome acidity through their acid-base properties. A ratiometric fluorescence comparison of imaged phagosomes containing C. neoformans to those containing beads showed that the latter were significantly more acidic. Similarly, phagosomes containing non-encapsulated C. neoformans cells were more acidic than those containing encapsulated cells. Acid-base titrations of isolated C. neoformans polysaccharide revealed that it behaves as a weak acid with maximal buffering capacity around pH 4-5. We interpret these results as indicating that the glucuronic acid residues in the C. neoformans capsular polysaccharide can buffer phagosomal acidification. Interference with phagosomal acidification represents a new function for the cryptococcal capsule in virulence and suggests the importance of considering the acid-base properties of microbial capsules in the host-microbe interaction for other microbes with charged residues in their capsules. Importance Cryptococcus neoformans is the causative agent of cryptococcosis, a devastating fungal disease that affects thousands of individuals worldwide. This fungus has the capacity to survive inside phagocytic cells, which contributes to persistence of infection and dissemination. One of the major mechanisms of host phagocytes is to acidify the phagosomal compartment after ingestion of microbes. This study shows that the capsule of C. neoformans can interfere with full phagosomal acidification by serving as a buffer.
Correction: Corrigendum: Identification and evolution of a plant cell wall specific glycoprotein glycosyl transferase, ExAD (2017)

This corrects the article DOI: 10.1038/srep45341.