gebhart/patrepeval huggingface dataset:
Topological Data analysis of Ion Migration Mechanism (2023)

Topological data analysis based on persistent homology has been applied to the molecular dynamics simulation for the fast ion-conducting phase (α-phase) of AgI to show its effectiveness on the ion migration mechanism analysis. Time-averaged persistence diagrams of α-AgI, which quantitatively record the shape and size of the ring structures in the given atomic configurations, clearly showed the emergence of the four-membered rings formed by two Ag and two I ions at high temperatures. They were identified as common structures during the Ag ion migration. The averaged potential energy change due to the deformation of the four-membered ring during Ag migration agrees well with the activation energy calculated from the conductivity Arrhenius plot. The concerted motion of two Ag ions via the four-membered ring was also successfully extracted from molecular dynamics simulations by our approach, providing new insight into the specific mechanism of the concerted motion.
Localization of Xenobiotic-responsive Element Binding Protein in Rat Hepatocyte Nuclei After Methylcholanthrene Administration as Revealed by In Situ Southwestern Hybridization (1998)

Xenobiotic-responsive element binding protein (XRE-BP), a heterodimer of aryl hydrocarbon receptor (AhR) and its nuclear translocator (Arnt), regulates the transcription of cytochrome P-450 1A1 gene (CYP1A1) through XRE in response to xenobiotic inducers. For a better understanding of the regulatory mechanism of CYP1A1 through XRE, localization of XRE-BP was examined in liver sections or isolated hepatocyte nuclei from control and 3-methylcholanthrene (MC)-treated rats by in situ Southwestern hybridization, using synthetic XRE as a probe, and was observed by confocal laser scanning microscopy and electron microscopy. Gel mobility shift assay and competitive binding assay showed specificity of the synthetic XRE probe. XRE-BP was exclusively localized in hepatocyte nuclei in liver sections from animals 3 hr after MC injection, whereas the protein was absent in hepatocyte cytoplasm in MC-treated animals and in hepatocyte nuclei and cytoplasm in control animals. In isolated hepatocyte nuclei, XRE-BP began to accumulate in the central region between 0.5 and 3 hr, showed a peak between 3 and 6 hr, decreased gradually between 6 and 72 hr, and disappeared at 72 hr after MC injection. The protein was scarce in peripheral and nucleolar regions of the nucleus. Therefore, XRE-BP is formed in the nuclei of hepatocytes after MC stimulation. In addition, XRE-BP was found in isolated hepatocyte nuclei from control animals after preincubation with cytoplasmic lysate from MC-treated animals, although the protein was absent in the nuclei before the preincubation. These findings strongly suggest that AhR translocates from hepatocyte cytoplasm to the nucleus and forms XRE-BP in the nucleus after MC stimulation.
Filter Design for Signal Processing Using MATLAB and Mathematica (2000)

From the Publisher:
A complete up-to-date reference for advanced analog and digital IIR filter design rooted in elliptic functions. Revolutionary in approach, this book opens up completely new vistas in basic analog and digital IIR filter design--regardless of the technology. By introducing exceptionally elegant and creative mathematical stratagems (e.g., accurate replacement of Jacobi elliptic functions by functions comprising polynomials, square roots, and logarithms), optimization routines carried out with symbolic analysis by Mathematica, and the advance filter design software of MATLAB, it shows readers how to design many types of filters that cannot be designed using conventional techniques. The filter design algorithms can be directly programed in any language or environment such as Visual BASIC, Visual C, Maple, DERIVE, or MathCAD. Signals; Systems; Transforms; Classical Analog Filter Design; Advanced Analog Filter Design Case Studies; Advanced Analog Filter Design Algorithms; Multi-criteria Optimization of Analog Filter Designs; Classical Digital Filter Design; Advanced Digital Filter Design Case Studies; Advanced Digital Filter Design Algorithms; Multi-criteria Optimization of Digital Filter Designs; Elliptic Functions; Elliptic Rational Function.
Emulator of first- and second-order polarization-mode dispersion (2002)

Contrary to approaches which try to mimic a standard fiber as closely as possible, the emulator presented here gives constant (but user adjustable) values for differential group delay (DGD) and ratio of first- to second-order polarization-mode dispersion (PMD). Once it is set, the ratio is conserved while the DGD can be easily varied within a range of 0-300 ps. This allows to investigate the low-probability events of large DGD and second-order PMD important for system outage.
Hepatotoxicity of antirheumatic drugs. (1990)

The central role of the liver in drug metabolism makes it vulnerable to toxic injury. Drug induced liver injury may mimic any of the naturally occurring liver diseases. The rheumatic diseases themselves may have liver disease associated with them, making it especially difficult to recognize hepatotoxicity. Nevertheless, hepatotoxicity has been reported with most of the drugs used to treat the rheumatic diseases. Because the reactions may be fatal, it is important to recognize hepatotoxicity. The current drug development process does not and cannot identify drugs with a low incidence of hepatotoxicity. Therefore, it is necessary for physicians to be aware of the potential of any drug to cause liver injury. Serious hepatotoxicity, however, can usually be prevented by awareness and appropriate monitoring. Most of the nonsteroidal antiinflammatory drugs, azathioprine and dantrolene should be monitored at monthly intervals for the first 6 months of therapy. Methotrexate should be monitored indefinitely. It remains unrealistic to expect premarketing studies to identify hepatotoxicity and, thus, surveillance is needed for all newly marketed drugs.
A scientific approach to estimate the safe depth of burial of submarine pipelines against wave forces for different marine soil conditions (2013)

Submarine pipelines encounter significant wave forces in shallow coastal waters due to the action of waves. In order to reduce such forces (also to protect the pipe against anchors and dropped objects) they are buried below the seabed. The wave force variation due to burial depends on the engineering characteristics of the sub soil like hydraulic conductivity and porosity, apart from the design environmental conditions. For a given wave condition, in certain type of soil, the wave force can reduce drastically with increased burial and in certain other type of soil, it may not. It is hence essential to understand how the wave forces vary in soils of different hydraulic conductivity. Based on physical model study, the wave forces on the buried pipeline model is assessed for a wide range of wave conditions, for different burial depths and for four types of cohesion-less soils, covering hydraulic conductivity in the range of 0.286 to 1.84 mm/s. It is found that for all the four soil types, the horizontal wave force reduces with increase in depth of burial, whereas the vertical force is high for half buried condition. Among the soils, well graded one is better for half buried case, since the least vertical force is experienced for this situation. It is found that uniformly graded and low hydraulic conductivity soil attracts the maximum vertical force for half buried case. A case study analysis is carried out and is reported. The results of this study are useful for submarine buried pipeline design.
SCREEN, PHONE, AND VOICE USER INTERFACES (1991)

Office principles often have multiple ways to complete typical tasks. For example, scheduling can be done on a paper calendar, electronically, by phone store-and-forward, etc. Each of the ways has unique user-interface characteristics and limitations, as well as a set of economic costs and benefits. We recently completed a study where 18 users compared traditional screen-based, phone-based, and voice-activated interfaces to calendar facilities. The voice-activated and phone-based user interfaces showed the highest level of usability among the comparison set, showing significantly smaller times to complete tasks and assistance requirements than screen-based facilities. With respect to preference 75% percent of the users prefered using a voice-activated or phone-based system for the typical calendaring task of signing out of the office, while only 5% stated a preference for a screen-based system.
Role of serotonin neurons in the induction of levodopa‐ and graft‐induced dyskinesias in Parkinson's disease (2010)

Recent studies in animal models of Parkinson's disease (PD) have provided evidence that dopamine released from spared serotonin afferents can act as a trigger of dyskinetic movements induced by repetitive, low doses of levodopa. Serotonin neurons have the capacity to store and release dopamine synthesized from systemically administered levodopa. However, because of the lack of any autoregulatory feedback control, dopamine released from serotonin terminals results in excessive swings in extracellular dopamine levels after peripheral administration of levodopa. Such "dysregulated" release of levodopa-derived dopamine is likely to be responsible for the appearance of the abnormal movements in levodopa-primed animals. This mechanism may also play a role in the development of graft-induced dyskinesias in patients that receive fetal neuron transplants, possibly due to the inclusion of serotonin neurons in the grafted ventral midbrain tissue, which contribute to maintain dopamine receptors of the denervated striatum in a supersensitive state.
Evanescent wave acceleration of electrons from 0.2-c to 0.95-c (1994)

Accelerators for electrons with velocities between 0.2c and 0.95c will be presented.The accelerators use evanescent waves as the accelerating electric field.The source for the evanescent waves will be electromagnetic waves (1 m and 10.5 cm wavelengths) incident at the interface of two materials with different indices of refraction.,Continuous phase matching between the electrons and the evanescent wave is possible.Alternatively a non-phase matching accelerator is possible and experimentally easier to build.Accelerator lengths range from 1 to 5 meters for fields at 0.56 MV/m and from 0.2 to 1 meter for fields at 5.6 MV/m.
ULTRAVIOLET-INDUCED GENETIC RECOMBINATION IN A PARTIALLY DIPLOID STRAIN OF ESCHERICHIA COLI (1968)

UNDERSTANDING the mechanism of genetic recombination is of prime concern to biologists. Breakage-reunion-type recombination events account for most, if not all, recombinant structures in bacteriophages h (MESELSON and WEIGLE 1961 ; KELLENBERGER, ZICHICHI and WEIGLE 1961; MESELSON 1964) and T4 (TOMIZAWA and ANRAKU 1964,1965; ANRAKU and TOMIZAWA 1965a, b; TOMIZAWA, ANRAKU and IWAMA 1966). These studies have also revealed the nature of some of the steps intermediate to recombinant formation. The genetic systems available in Escherichia coli K-12 are unusual in that they off er opportunities to study both reciprocal and nonreciprocal recombination events. Genetic ( TOMIZAWA 1960) and isotopic labeling ( OPPENHEIM and RILEY 1966) experiments have revealed some aspects of the recombination process following conjugal transfer of donor genetic material to recipient strains. However, problems concerned with replication of the donor chromosome during conjugation and vegetative chromosome replication in the recipient (CURTIS 1966) make complete analysis of recombination events following conjugation difficult. Therefore, it was decided to investigate recombination events in a partially diploid strain of E. coli K-12 (CURTISS 1962, 1964) in order to eliminate problems concerned with gene transfer. LEDERBERG, LEDERBERG, ZINDER and LIVELY (1951) and BECKHORN (see DEMEREC, WITKIN, BECKHORN, VISCONTI, FLINT, CAHN, COON, DOLLINGER, POWELL and SCHWARTZ 1951) showed that small doses of UV (ultraviolet light, 2537 A) would induce haploidization in partially diploid strains of E. coli K-12, but they did not study the kinetics of the process, since all surviving colonies still contained partially diploid cells. UV is known to stimulate genetic recombination in phage (JACOB and WOLLMAN 1955; HERSHEY 1958; LEVINE and CURTIS 196l), in E. coliK-12 (JACOB and WOLLMAN 1961), in yeast (ROMAN and JACOB 1958), and in the phage P22-Salmonella typhimurium transduction system (GAREN and ZINDER 1955). Thus, it was felt that the use of UV to stimulate genetic recombination in a partially diploid strain of E. coli K-12 ( CURTISS 1964) would provide a closed system, not involving gene transfer, with which meaningful results could be obtained. This communication reports findings on UV-induced haploidization, on recombination leading to homozygosity
Prospects and Future Directions of Self-Healing Fiber-Reinforced Composite Materials (2020)

In this paper, the anticipated challenges and future applications of self-healing composite materials are outlined. The progress made, from the classical literature to the most recent approaches, is summarized as follows: general history of current self-healing engineering materials, self-healing of structural composite materials, and self-healing under extreme conditions. Finally, the next stage of research on self-healing composites is discussed.
RECOVERY OF CARDIAC ISCHEMIC INSULT AFTER STANDARD HYPOTHERMIC STORAGE VERSUS PRESERVATION WITH PEG-HB (2000)

INTRODUCTION: Preservation of the heart for transplantation following infusion of cardioplegia and extirpation of a cardiac allograft represents an ischemic insult to the myocardiocytes. This ischemic insult may to a loss of function in the transplanted heart. Hypothermic perfusion preservation with an oxygen hemoglobin carrying solution may avert ischemic injury and lead to improved recovery of cardiac function. The purpose of this study was to compare cardiac function after 8 hrs of continuous hypothermic perfusion with a PEG-Hemoglobin(Hb) solution to hearts preserved by 4 hrs of hypothermic ischemic storage. Non-preserved hearts serve as functional controls. METHODS: The hearts of 28 anesthetized and intubated NZW rabbits were harvested after cold cardioplegic arrest. Group I(n=10) hearts were perfused with a PEG-Hb solution at 20C and 30 mmHg for 8 hours. PO2 was maintained ± 500mm Hg. Group II(n=10) hearts were preserved by cold ischemic storage for 4 hours at 4C. Group III(n=8) were tested immediately after harvest. LV function was measured in the non-working state at 15 min, 1hr, and 2 hrs after transfer to a standard crystalloid Langendorff circuit. RESULTS: Developed LV pressure at 0.5cc LV volume was greater in Group I (75.7±10.3mmHg) than Group II (49.1±5.4mmHg, p = .04) and similar to Group III (69.41±5.1mmHg, p=.6) Maximum-dp/dT at 0.5 cc LV volume was greater in Group I s(−610.6±68.4mmHg/sec) than Group II (−354.8±49.1mmHg/sec, p=.01) and trended toward superiority over Group III(−456.2±44.1mmHg/sec, p=.09). Maximum +dp/dT at 0.5cc LV volume was greater in Group I (964.9±156.6mmHg/sec) than both Group II (428.4±54.9mmHg/sec, p=.004) and Group III(514.6±48.9mmHg/sec, p=.02).FigureCONCLUSIONS: Continuous perfusion preservation of rabbit hearts for 8 hrs with PEG-Hb solution at 30 mmHg and 20 C yields left ventricular function that is superior to 4 hrs of ischemic hypochermic storage. Furthermore, return of cardiac function after perfusion preservation using this PEG-Hb solution may be superior to that obtained in freshly arrested hearts. These data suggest there may occur some recovery of myocardial function during perfusion preservation with this PEG-Hb solution after the ischemic insult of carioplegic arrest. Continuous perfusion preservation using this PEG-Hb solutioon deserves further investigation in large animal transplant models.
NTRK rearrangements in a subset of NF1-related malignant peripheral nerve sheath tumors as novel actionable target (2022)

Contains fulltext : 291288.pdf (Publisher’s version ) (Open Access)
Computational identification of HCV neutralizing antibodies with a common HCDR3 disulfide bond motif in the antibody repertoires of infected individuals (2022)

Despite recent success in hepatitis C virus (HCV) treatment using antivirals, an HCV vaccine is still needed to prevent reinfections in treated patients, to avert the emergence of drug-resistant strains, and to provide protection for people with no access to the antiviral therapeutics. The early production of broadly neutralizing antibodies (bNAbs) associates with HCV clearance. Several potent bNAbs bind a conserved HCV glycoprotein E2 epitope using an unusual heavy chain complementarity determining region 3 (HCDR3) containing an intra-loop disulfide bond. Isolation of additional structurally-homologous bNAbs would facilitate the recognition of key determinants of such bNAbs and guide rational vaccine design. Here we report the identification of new antibodies containing an HCDR3 disulfide bond motif using computational screening with the Rosetta software. Using the newly-discovered and already-known members of this antibody family, we review the required HCDR3 amino acid composition and propose determinants for the bent versus straight HCDR3 loop conformation observed in these antibodies.
Mechanistic insights into catalytic CO2 hydrogenation using Mn(i)-complexes with pendant oxygen ligands (2018)

Hydrogenation of CO2 to formic acid catalysed by Mn(<sc>i</sc>)-complexes with pendant oxygen ligands.
Forced periodic operations of a chemical reactor for methanol synthesis – the search for the best scenario based on Nonlinear Frequency Response Method. Part I Single input modulations (2021)

<strong>Abstract</strong> In this two-part paper a comprehensive study of the potential to improve performance criteria of a methanol synthesis reactor through forced periodical operations is presented. The study uses the Nonlinear Frequency Response method, a powerful analytical and approximate tool which gives an answer whether and under which conditions certain periodic operation would lead to improvement of process performance. To demonstrate the method, isothermal and isobaric methanol synthesis in a lab-scale CSTR is considered. In Part I, the analysis is performed for single input modulations. Partial pressures of each reactant in the feed stream and the total inlet volumetric flow-rate are considered as possible modulated inputs. The results show that modulations of single inputs essentially do not provide potential for significant improvements. In Part II, the study will be extended to analysis of periodic operations with simultaneous modulations of two inputs and conditions offering significant performance enhancements will be identified.
Abstract 5492: Preclinical study of the PARP inhibitor ABT-888 in metastatic prostate cancer (2011)

Abstract Background: Despite recent advances in androgen deprivation therapy, chemotherapy and immunotherapy, metastatic prostate cancers (mPCa) eventually become resistant to these treatments through further mutations. Cancer cells often diminish their DNA repair pathways to obtain high mutation rates. We aimed to develop a therapeutic approach that directly targets cells with high mutation rates and explored the therapeutic potential of PARP inhibitor, ABT-888 (kindly provided by Abbott) in mPCa preclinical models. Methods and Results: Meta-analysis of 5 published prostate cancer gene expression profiles with total of 53 metastatic samples and 183 primary samples were performed with oncomine 4.1. BRCA1 was among genes significantly over expressed in mPCa. Inhibiting BRCA1 expression with shRNA in Lncap (intact PTEN) and PC3 (loss of PTEN) cells, however, did not lead to synthetic lethality when ABT-888 (up to 10uM) were added in the in vitro cytotoxicity assays. When ABT-888 was combined with DNA damaging chemotherapy agents, synergies in cell killing were observed with 100nM of ABT-888 and 10nM SN38, an active metabolite of topoisomerase I inhibitor CPT-11. Such synergies were observed at higher dose levels with Temazolomide (1uM) and ABT-888 (1uM). The enhanced cell killing correlated well with inhibition of PAR and increased formation of DNA double strand breaks. No synergies with ABT888 were observed with topoisomerase II inhibitor (etoposide and mitoxantrone) or platinums in the WST-1 cytotoxicity assays. The CPT-11 and ABT888 combination was then tested in PC3 mouse xenografts with 4 treatment groups: vehicle control, ABT-888, CPT-11, and ABT-888 plus CPT-11. ABT-888 was given by oral gavages at 12.5mg/kg on days 1-5 of each 21 day cycle; whereas CPT-11 was given by intraperitoneal injection at 60mg/kg on days 1 and 5 of each 21 day cycle. Compared to vehicle control, ABT-888 by itself had no anti-tumor activities. The inhibition of tumor growth by CPT-11 was further enhanced when it was combined with ABT-888. More than 30% tumor volume shrinkage was observed in 4 of the 8 xenografts after 2 cycles of treatments with ABT-888 and CPT-11. These anti-tumor effects, however, were not sustainable beyond treatment cycles. Conclusion: ABT-888 enhanced the anti-tumor activities of CPT-11. The dose and schedule of this combination will be modified and its anti-tumor activities will be compared with docetaxel in future pre-clinical studies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5492. doi:10.1158/1538-7445.AM2011-5492
Sun heated surfaces are an environmental hazard for young children (2019)

Heat contact type burn injuries from sun heated surfaces commonly affect children ⩽2 years of age during the summer months, and the majority of these injuries occur around the home environment. They are preventable injuries, and this information should be used for prevention and education materials for parents and healthcare providers, who reside in hot, sunny climates.
Crack-arrest behavior in SEN wide plates of low-upper-shelf base metal tested under nonisothermal conditions: WP-2 series (1990)

The Heavy-Section Steel Technology (HSST) Program at the Oak Ridge National Laboratory under the sponsorship of the Nuclear Regulatory Commission is conducting analytical and experimental studies aimed at understanding the circumstances that would initiate the growth of an existing crack in a reactor pressure vessel (RPV) and the conditions leading to arrest of a propagating crack. Objectives of these studies are to determine (1) if the material will exhibit crack-arrest behavior when the driving force on a crack exceeds the ASME limit, (2) the relationship between K{sub Ia} and temperature, and (3) the interaction of fracture modes (arrest, stable crack growth, unstable crack growth, and tensile instability) when arrest occurs at high temperatures. In meeting these objectives, crack-arrest data are being developed over an expanded temperature range through tests involving large thermally shocked cylinders, pressurized thermally shocked vessels, and wide-plate specimens. The wide-plate specimens provide the opportunity for a significant number of data points to be obtained at relatively affordable costs. These tests are designed to provide fracture-toughness measurements approaching or above the onset of the Charpy upper-shelf regime in a rising toughness region and with an increasing driving force. This document discusses test methodology and results. 23 refs., 92 figs., 25 tabs.