gebhart/patrepeval huggingface dataset:
Abstract 2530: Bcl-2 and Bcl-xL dual inhibitor, ABT-737, circumvents JNK mediated upregulation of anti-apoptotic molecules in cisplatin treated non-small cell lung cancer models (2015)

Abstract Introduction; Non-small cell lung cancer (NSCLC), which does not have druggable driver oncogene, is treated with cytotoxic chemotherapy, but clinical outcome is suboptimal. Cisplatin is still one of the most commonly used drugs for the treatment of NSCLC, and, however, there are limitations of the therapeutic effect because of the multiple resistance mechanisms. In particular, elevated level of anti-apoptotic proteins (Bcl-2, Bcl-xL, Mcl-1) triggered by cisplatin-induced DNA damage response correlate with the drug resistance. In this study, we investigated synergic effects of combined treatment with cisplatin and dual inhibitor of Bcl-2/Bcl-xL, ABT-737, in NSCLC models. Materials and Methods; H460 and A549 NSCLC cells, and LSL K-Ras G12D mouse model were used. Protein expression was evaluated by immunoblotting and cytotoxicity was measured by FACS followed by annexin-V and PI staining. LSL Kras G12D mouse were inhaled 5 × 107 PFU AdCre virus at 8 weeks after birth and, in 24 weeks after inhalation, were taken microCT, randomized into 4 groups, and then treated with ABT-737 (50mg/kg, i.p., daily) and/or cisplatin (5 mg/kg, i.p., weekly) for two weeks. Results; There was a dose dependent phosphorylation of JNK, which is most prominent between 6 to 24hr after cisplatin treatment. Expression of anti-apoptotic molecules, Bcl-2, Bcl-w, Bcl-xL, and Mcl-1 were increased by cisplatin treatment in a dose and time dependent manner. JNK specific activator, anisomycin, increased mRNA level of anti-apoptotic molecules. ABT-737 displaced BCL-xL to the cytoplasm and aggregated Bak. Furthermore, ABT-737 released cytochrome C from mitochondria to the cytoplasm. ABT-737 itself showed cytotoxic effects and combination of ABT-737 potentiates cytotoxic effects of cisplatin with strong synergism. Combination of ABT-737 with cisplatin treatment induced significant tumor regression in 2 weeks in LSL K-ras G12D mouse model when compared those treated with single agents or vehicle. Conclusion; Combination of ABT-737 with cisplatin showed synergistic cytotoxic effects and anti-tumor activities in NSCLC preclinical models. These findings suggest that clinical trials using combination with ABT-737 and cisplatin may be beneficial in advanced NSCLC patients. Citation Format: Eun Young KIM, Arum Kim, Yoon Soo Chang. Bcl-2 and Bcl-xL dual inhibitor, ABT-737, circumvents JNK mediated upregulation of anti-apoptotic molecules in cisplatin treated non-small cell lung cancer models. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2530. doi:10.1158/1538-7445.AM2015-2530
Inhibition of Japanese encephalitis virus infection by nitric oxide: antiviral effect of nitric oxide on RNA virus replication (1997)

The antiviral effects of nitric oxide (NO) on Japanese encephalitis virus (JEV), a member of the family Flaviviridae, were investigated in this study. In vitro, inhibition of replication of JEV in gamma interferon-activated RAW 264.7 murine macrophages was correlated to cellular NO production. When cocultured with infected murine neuroblastoma N18 cells, gamma interferon-activated RAW 264.7 cells also efficiently hindered JEV replication in contiguous bystanders, and this anti-JEV effect could be reversed by an NO synthase (NOS) inhibitor, N-monomethyl-L-arginine acetate. In vivo, the mortality rate increased as the NOS activity of JEV-infected mice was inhibited by its competitive inhibitor, N-nitro-L-arginine methyl ester. Moreover, when an organic donor, S-nitro-N-acetylpenicillamine (SNAP), was used, the NO-mediated antiviral effect was also observed in primarily JEV-infected N18, human neuronal NT-2, and BHK-21 cells, as well as in persistently JEV-infected C2-2 cells. These data reaffirm that NO has an effective and broad-spectrum antimicrobial activity against diversified intracellular pathogens. Interestingly, the antiviral effect of NO was not enhanced by treatment of N18 cells with SNAP prior to JEV infection, a measure which has been shown to greatly increase the antiviral effect of NO in infection by vesicular stomatitis virus. From biochemical analysis of the impact of NO on JEV replication in cell culture, NO was found to profoundly inhibit viral RNA synthesis, viral protein accumulation, and virus release from infected cells. The results herein thus suggest that NO may play a crucial role in the innate immunity of the host to restrict the initial stage of JEV infection in the central nervous system.
Improving recognition accuracy on CVSD speech under mismatched conditions (2003)

Abstract: Emerging technology in mobile communications is seeing increasingly high acceptance as a preferred choice for last-mile communication. There have been a wide range of techniques to achieve signal compression to suit to the smaller bandwidths available on mobile communication channels; but speech recognition methods have seen success mostly only in controlled speech environments. However, designing of speech recognition systems for mobile communications is crucial in order to provide voice enabled command and control and for applications like Mobile Voice Commerce. Continuously Variable Slope Delta (CVSD) modulation, a technique for low bitrate coding of speech, has been in use particularly in military wireless environments for over 30 years, and is now also adopted by BlueTooth. CVSD is particularly suitable for Internet and mobile environments due to its robustness against transmission errors, and simplicity of implementation and the absence of a need for synchronization. In this paper, we study some characteristics of the CVSD speech in the context of robust recognition of compressed speech, and present two methods of improving the recognition accuracy in Automatic Speech Recognition (ASR) systems. We study the characteristics of the features extracted for ASR and how they relate to the corresponding features computed from Pulse Coded Modulation (PCM) speech and apply this relation to correct the CVSD features to improve recognition accuracy. Secondly we show that the ASR done on bit-streams directly, gives a good recognition accuracy and when combined with our approach gives a better accuracy. Key-words: CVSD, bitstream, speech recognition, corrected MFCC estimation
Bio3d: an R package for the comparative analysis of protein structures (2006)

The bio3d package is distributed with full source code as a platform-independent R package under a GPL2 license from: http://mccammon.ucsd.edu/~bgrant/bio3d/
The optimum mean-square estimate for decoding binary block codes (1974)

By the use of abstract Fourier analysis on groups, the optimum mean-square-error decoding rule is developed for a fixed block code. The optimum one-to-one coding role to be used with this optimum decoder is derived, and a procedure for simultaneous optimization over both encoding and decoding rules is given. It is shown that there is a linear encoding rule which is optimum. A system which implements the optimum decoding rule is outlined. The major difference between this work and others involving coding for mean-square error is that the decoding rule developed here is a mapping from binary <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</tex> -tuples directly into the real numbers with the optimization being over all possible mappings into the real numbers. As such the system developed here replaces both the error-correction and digital-to-analog conversion components used in most numerical data transmission systems.
HIV-1感染高危人群中HIV DNA的测定及CD 8 细胞群的改变 (1995)

为了寻找 HIV-1感染早期诊断的指标, 我们追踪检测了 HIV-1(-)及 HIV-1(+)的同性恋男子及 AIDS 病人的病毒学和免疫学的特点。在同性恋的高危人群中,38例病人HIV-1抗体反复测定(ELISA.WB)均为阴性,但 PCR 检测的结果表明13%的病人发现了 HIV-1的 gag.LTR.和 env 的基因序列,外周血淋巴细胞(PBL)培养分离 HIV-1
Bioreactor Production of Secondary Metabolites from Cell Cultures of Periwinkle and Sandalwood (2009)

A bench-top bioreactor allowing continuous extraction of secondary metabolites is designed for Catharanthus roseus L. (G.) Don (periwinkle) and Santalum album L. (sandalwood) plant cell suspensions. Periwinkle cell cultures are exposed to biotic elicitors (Aspergillus niger, crude chitin) and abiotic elicitors (mannitol, methyl jasmonate) to induce alkaloid production. Whereas most of the biotic elicitors are effective when added on day 15 of culture, the abiotic elicitors are effective when added on day 20. The use of trans-cinnamic acid, an inhibitor of phenylalanine ammonia lyase (PAL) activity, results in significant increase in the alkaloid production of periwinkle cell cultures. Exposure of the cells to mannitol-induced osmotic stress produced marked increment in the total alkaloid production. When biotic and abiotic stress treatments are applied sequentially, an additive effect in alkaloid accumulation is observed. Although no essential oils are detected, secondary metabolites in the form of phenolics are produced by the sandalwood cell cultures in the bioreactor environment. The use of morphologic modification such as organ cultures and transformed cultures is believed to be required for both production and storage of essential oil constituents in sandalwood. The present chapter demonstrates that periwinkle and sandalwood cell suspensions could be developed and successfully cultured in a modified air-lift bioreactor. The exploitation of variant cell strains and biotransformation of added precursors can certainly improve the use of periwinkle and sandalwood cell cultures for the bioproduction of desired compounds.
Inherited DNA lesions determine G1 duration in the next cell cycle (2017)

Replication stress is a major source of DNA damage and an important driver of cancer development. Replication intermediates that occur upon mild forms of replication stress frequently escape cell cycle checkpoints and can be transmitted through mitosis into the next cell cycle. The consequences of such inherited DNA lesions for cell fate and survival are poorly understood. By using time-lapse microscopy and quantitative image-based cytometry to simultaneously monitor inherited DNA lesions marked by the genome caretaker protein 53BP1 and cell cycle progression, we show that inheritance of 53BP1-marked lesions from the previous S-phase is associated with a prolonged G1 duration in the next cell cycle. These results suggest that cell-to-cell variation in S-phase commitment is determined, at least partially, by the amount of replication-born inherited DNA damage in individual cells. We further show that loss of the tumor suppressor protein p53 overrides replication stress-induced G1 prolongation and allows S-phase entry with excessive amounts of inherited DNA lesions. Thus, replication stress and p53 loss may synergize during cancer development by promoting cell cycle re-entry with unrepaired mutagenic DNA lesions originating from the previous cell cycle.
Alignment-stabilized interference filter-tuned external-cavity quantum cascade laser (2014)

A passively alignment-stabilized external cavity quantum cascade laser (EC-QCL) employing a "cat's eye"-type retroreflector and an ultra-narrowband transmissive interference filter for wavelength selection is demonstrated and experimentally investigated. Compared with conventional grating-tuned ECQCLs, the setup is nearly two orders of magnitude more stable against misalignment of the components, and spectral fluctuation is reduced by one order of magnitude, allowing for a simultaneously lightweight and fail-safe construction, suitable for applications outdoors and in space. It also allows for a substantially greater level of miniaturization and cost reduction. These advantages fit in well with the general properties of modern QCLs in the promise to deliver useful and affordable mid-infrared-light sources for a variety of spectroscopic and imaging applications.
Oncogenic H‐Ras and PI3K signaling can inhibit E‐cadherin‐dependent apoptosis and promote cell survival after photodynamic therapy in mouse keratinocytes (2008)

Maintenance of E-cadherin mediated cell-cell contacts is often required for the survival of epithelial cells and tissues. Here we report that oncogenic activation of H-Ras in murine keratinocytes can prevent cell death induced by immunological disruption of E-cadherin adhesion. A similar situation was observed in cells showing constitutive activation of the p110 alpha catalytic subunit of class IA PI3K. This protective effect is associated with beta-catenin-dependent transcription and with activation of survival factor Akt/PKB. In addition, we induced cell death by employing photodynamic therapy, using Zn-phthalocyanine as a photosensitizer that targets E-cadherin adhesion complexes. We have found that cell death based on this photodynamic action is also bypassed in cells showing constitutive activation of H-Ras and p110 alpha. Taken together, these results indicate that H-Ras/PI3K/Akt signaling plays a key role in cell survival mediated by E-cadherin cell-cell contacts.
Herpes Simplex Virus Type 1 Immediate-Early Protein Vmw110 Induces the Proteasome-Dependent Degradation of the Catalytic Subunit of DNA-Dependent Protein Kinase (1999)

Herpes simplex virus type 1 (HSV-1) infection causes the active degradation of the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs), and this process is reliant on the expression of the HSV-1 immediate-early protein Vmw110. In this study we investigated in more detail the mechanism by which the degradation occurs, the domains of Vmw110 which are required, and whether Vmw110 is by itself sufficient for the effect. We found that proteasome inhibitors prevented the degradation of DNA-PKcs, indicating the involvement of a proteasome pathway. Furthermore, the continued activity of DNA-PK during infection in the presence of these inhibitors indicated that Vmw110 does not directly alter the enzyme activity of DNA-PKcs prior to its degradation in a normal infection. Indeed, Vmw110 was found to bind to neither the catalytic nor Ku subunits of DNA-PK. Using mutant Vmw110 viruses we show that the RING finger domain of Vmw110 is essential for the induced degradation of DNA-PKcs but that the ability of Vmw110 to bind to a cellular ubiquitin-specific protease (HAUSP) is not required. When expressed in the absence of other viral proteins, Vmw110 was sufficient to cause the degradation of DNA-PKcs, indicating that the effect on the stability of DNA-PKcs was a direct consequence of Vmw110 activity and not an indirect Vmw110-dependent effect of virus infection. Finally, the Vmw110-induced degradation of DNA-PKcs and loss in DNA-PK activity appears to be beneficial to HSV-1 infection, as virus replication was more efficient in cells lacking DNA-PKcs, especially at low multiplicities of infection.
Event Detection in Water Distribution Systems from Multivariate Water Quality Time Series (2012)

In this study, a general framework integrating a data-driven estimation model with sequential probability updating is suggested for detecting quality faults in water distribution systems from multivariate water quality time series. The method utilizes artificial neural networks (ANNs) for studying the interplay between multivariate water quality parameters and detecting possible outliers. The analysis is followed by updating the probability of an event, initially assumed rare, by recursively applying Bayes' rule. The model is assessed through correlation coefficient (R(2)), mean squared error (MSE), confusion matrices, receiver operating characteristic (ROC) curves, and true and false positive rates (TPR and FPR). The product of the suggested methodology consists of alarms indicating a possible contamination event based on single and multiple water quality parameters. The methodology was developed and tested on real data attained from a water utility.
The 9- <i>cis</i> -epoxycarotenoid cleavage reaction is the key regulatory step of abscisic acid biosynthesis in water-stressed bean (1999)

Abscisic acid (ABA), a cleavage product of carotenoids, is involved in stress responses in plants. A well known response of plants to water stress is accumulation of ABA, which is caused by de novo synthesis. The limiting step of ABA biosynthesis in plants is presumably the cleavage of 9-cis-epoxycarotenoids, the first committed step of ABA biosynthesis. This step generates the C(15) intermediate xanthoxin and C(25)-apocarotenoids. A cDNA, PvNCED1, was cloned from wilted bean (Phaseolus vulgaris L.) leaves. The 2, 398-bp full-length PvNCED1 has an ORF of 615 aa and encodes a 68-kDa protein. The PvNCED1 protein is imported into chloroplasts, where it is associated with the thylakoids. The recombinant protein PvNCED1 catalyzes the cleavage of 9-cis-violaxanthin and 9'-cis-neoxanthin, so that the enzyme is referred to as 9-cis-epoxycarotenoid dioxygenase. When detached bean leaves were water stressed, ABA accumulation was preceded by large increases in PvNCED1 mRNA and protein levels. Conversely, rehydration of stressed leaves caused a rapid decrease in PvNCED1 mRNA, protein, and ABA levels. In bean roots, a similar correlation among PvNCED1 mRNA, protein, and ABA levels was observed. However, the ABA content was much less than in leaves, presumably because of the much smaller carotenoid precursor pool in roots than in leaves. At 7 degrees C, PvNCED1 mRNA and ABA were slowly induced by water stress, but, at 2 degrees C, neither accumulated. The results provide evidence that drought-induced ABA biosynthesis is regulated by the 9-cis-epoxycarotenoid cleavage reaction and that this reaction takes place in the thylakoids, where the carotenoid substrate is located.
Role of vitamin D in cardiovascular disease. (2010)

There is increasing evidence for health benefits accomplished by activated vitamin D through interaction with the vitamin D receptor (VDR) that go beyond calcium and bone homeostasis and regulation of parathyroid hormone (PTH) secretion. Treatment with vitamin D receptor agonists (VDRAs) is associated with reduced mortality in (pre)dialysis patients. Interestingly, these relations are independent of PTH levels and calcium x phosphorus product. This suggests the presence of biological functions of vitamin D that are independent of its interaction with the parathyroid glands. Because chronic kidney disease leads to increased cardiovascular mortality, mechanisms in which VDRAs can influence cardiovascular disease are discussed. These mechanisms comprise the potential ameliorating effects of VDRAs on atherosclerosis, arterial media calcification, cardiac hypertrophy, the renin-angiotensin system and thrombosis. Moreover, treatment strategies with VDRAs are discussed together with several recent observational studies. Treatment advice consists of correction of 25(OH) vitamin D deficiency, low-dose calcitriol in patients with secondary hyperparathyroidism, and activated vitamin D analogues may be indicated when higher doses are needed to suppress PTH secretion. New insights into biological and clinical effects of VDRAs may broaden the patient group that may benefit from VDRA treatment to patients with creatinine clearances in the 30 to 60 ml/min range.
Metabolism of dibenzothiophene by a Beijerinckia species (1977)

Beijerinckia B8/36 when grown with succinate in the presence of dibenzothiophene, accumulated (+)-cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene and dibenzothiophene-5-oxide in the culture medium. Each metabolite was isolated in crystalline form and characterized by a variety of chemical techniques, cis-Naphthalene dihydrodiol dehydrogenase, isolated from Pseudomonas putida, oxidized (+)-cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene to a compound that was tentatively identified as 1,2-dihydroxydibenzothiophene. The same product was formed when crude cell extracts of the parent strain of Beijerinckia oxidized (+)-cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene under anaerobic conditions. Further metabolism of 1,2-dihydroxydibenzothiophene by heat-treated cell extracts led to the formation of 4[2-(3-hydroxy)-thionaphthenyl]-2-oxo-3-butenoic acid. The latter compound was metabolized by crude cell extracts to 3-hydroxy-2-formylthionaphthene. Further degradation of this metabolite was not observed.
On the origin of charge-density waves in select layered transition-metal dichalcogenides (2011)

The occurrence of charge-density waves in three selected layered transition-metal dichalcogenides-1T-TaS(2), 2H-TaSe(2) and 1T-TiSe(2)-is discussed from an experimentalist's point of view with a particular focus on the implications of recent angle-resolved photoelectron spectroscopy results. The basic models behind charge-density-wave formation in low-dimensional solids are recapitulated, the experimental and theoretical results for the three selected compounds are reviewed, and their band structures and spectral weight distributions in the commensurate charge-density-wave phases are calculated using an empirical tight-binding model. It is explored whether the origin of charge-density waves in the layered transition-metal dichalcogenides can be understood in a unified way on the basis of a few measured and calculated parameters characterizing the interacting electron-lattice system. It is found that the predictions of the standard mean-field model agree only semi-quantitatively with the experimental data and that there is not one generally dominant factor driving charge-density-wave formation in this family of layer compounds. The need for further experimental and theoretical scrutiny is emphasized.
Scaling in MPEG-2 decoding loop with mixed processing (2002)

MPEG-2 decoding with internal resolution scaling degrades video quality particularly for interlaced video with high vertical activities. Previously known methods apply the same algorithm to each picture without utilizing the observation that errors in different types of pictures (I, P, or B) contribute differently to the total degradation. We propose a solution that mixes highand low-complexity algorithms to ensure that more critical pictures are processed with higher quality thereby increasing the overall video quality. Simulation results confirm that such an approach yields a better trade-off between quality and complexity than simply applying a single high- or low-complexity algorithm to all pictures.
Modulation waveforms for second-harmonic detection with tunable diode lasers (1986)

Second-harmonic signals of the Lorentzian absorption line at the line center are calculated for various modulation waveforms. The suppression efficiency of fine-pitch étalon fringe signals by those modulation waveforms is discussed. It is found that there are several modulation waveforms that give larger absorption signals and suppress fine-pitch fringe signals more efficiently than does the sinusoidal waveform. The dependence of the efficiency of the fringe-signal suppression on different jitter waveforms is also calculated.
Ontology Summit 2018 Communiqué: Contexts in context (2018)

It is generally agreed that the interpretation of information, in any form, is context-dependent. The goal of the recent Ontology Summit 2018 was to explore the various relationships spanning ontology and context. This article is the end product of the summit and associated symposium. It describes motivation for creating explicit, formal context specifications, and discusses approaches for finding, understanding and formalizing context. We present this work and associated materials with the goal to foster the research and development of approaches to contexts and to drive towards context-aware solutions which can be incorporated into both knowledge engineering processes and ontology design best practices.