gebhart/patrepeval huggingface dataset:
Rosiglitazone Treatment Prevents Mitochondrial Dysfunction in Mutant Huntingtin-expressing Cells (2008)

Peroxisome proliferator-activated receptor-gamma (PPARgamma) is a member of the PPAR family of transcription factors. Synthetic PPARgamma agonists are used as oral anti-hyperglycemic drugs for the treatment of non-insulin-dependent diabetes. However, emerging evidence indicates that PPARgamma activators can also prevent or attenuate neurodegeneration. Given these previous findings, the focus of this report is on the potential neuroprotective role of PPARgamma activation in preventing the loss of mitochondrial function in Huntington disease (HD). For these studies we used striatal cells that express wild-type (STHdh(Q7/Q7)) or mutant (STHdh(Q111/Q111)) huntingtin protein at physiological levels. Treatment of mutant cells with thapsigargin resulted in a significant decrease in mitochondrial calcium uptake, an increase in reactive oxygen species production, and a significant decrease in mitochondrial membrane potential. PPARgamma activation by rosiglitazone prevented the mitochondrial dysfunction and oxidative stress that occurred when mutant striatal cells were challenged with pathological increases in calcium. The beneficial effects of rosiglitazone were likely mediated by activation of PPARgamma, as all protective effects were prevented by the PPARgamma antagonist GW9662. Additionally, the PPARgamma signaling pathway was significantly impaired in the mutant striatal cells with decreases in PPARgamma expression and reduced PPARgamma transcriptional activity. Treatment with rosiglitazone increased mitochondrial mass levels, suggesting a role for the PPARgamma pathway in mitochondrial function in striatal cells. Altogether, this evidence indicates that PPARgamma activation by rosiglitazone attenuates mitochondrial dysfunction in mutant huntingtin-expressing striatal cells, and this could be an important therapeutic avenue to ameliorate the mitochondrial dysfunction that occurs in HD.
Study on Halide Ions Selectivity of Industrial Grade Anion Exchange Resin Auchlite A-378 (2014)

The thermodynamic approach was applied to predict the trend selectivity of industrial grade anion exchange resin Auchlite A-378 in chloride form towards iodide and bromide ions in the solution. The study was conducted by performing the Clˉ/Iˉ and Clˉ/Brˉ uni-univalent ion exchange reactions under gradually increasing temperature conditions. The thermodynamic equilibrium constants K values were used to calculate the enthalpies of the two uni-univalent ion exchange reactions. It was observed that the K values for Clˉ/Iˉ ion exchange reaction were higher than Clˉ/Brˉ exchange reaction under identical experimental conditions. Also the enthalpy values for the two uni-univalent ion exchange reactions were calculated as -39.51 and -18.38 kJ/mol respectively. The high K and low enthalpy values obtained for Clˉ/Iˉ ion exchange reaction is responsible for higher selectivity of the resin towards iodide ions as compared to that towards bromide ions, when both the ions are present in the same solution.
Internal entry of ribosomes on a tricistronic mRNA encoded by infectious bronchitis virus (1992)

mRNA3 specified by the coronavirus infectious bronchitis virus appears to be functionally tricistronic, having the capacity to encode three small proteins (3a, 3b, and 3c) from separate open reading frames (ORFs). The mechanism by which this can occur was investigated through in vitro translation studies using synthetic mRNAs containing the 3a, 3b, and 3c ORFs, and the results suggest that translation of the most distal of the three ORFs, that for 3c, is mediated by an unconventional, cap-independent mechanism involving internal initiation. This conclusion is based on several observations. A synthetic mRNA whose peculiar 5' end structure prevents translation of the 5'-proximal ORFs (3a and 3b) directs the synthesis of 3c normally. Translation of 3c, unlike that of 3a and 3b, was insensitive to the presence of the 5' cap analog 7-methyl-GTP, and it was unaffected by alteration of the sequence contexts for initiation on the 3a and 3b ORFs. Finally, an mRNA in which the 3a/b/c infectious bronchitis virus coding region was placed downstream of the influenza A virus nucleocapsid protein gene directed the efficient synthesis of 3c as well as nucleocapsid protein, whereas initiation at 3a and 3b could not be detected. Expression of the 3c ORF from this mRNA, however, was abolished when the 3a and 3b coding region was deleted, indicating that 3c initiation is dependent on upstream sequence elements which together may serve as a ribosomal internal entry site similar to those described for picornaviruses.
CASPER: Embedding Power Estimation and Hardware-Controlled Power Management in a Cycle-Accurate Micro-Architecture Simulation Platform for Many-Core Multi-Threading Heterogeneous Processors (2012)

Despite the promising performance improvement observed in emerging many-core architectures in high performance processors, high power consumption prohibitively affects their use and marketability in the low-energy sectors, such as embedded processors, network processors and application specific instruction processors (ASIPs). While most chip architects design power-efficient processors by finding an optimal power-performance balance in their design, some use sophisticated on-chip autonomous power management units, which dynamically reduce the voltage or frequencies of idle cores and hence extend battery life and reduce operating costs. For large scale designs of many-core processors, a holistic approach integrating both these techniques at different levels of abstraction can potentially achieve maximal power savings. In this paper we present CASPER, a robust instruction trace driven cycle-accurate many-core multi-threading micro-architecture simulation platform where we have incorporated power estimation models of a wide variety of tunable many-core micro-architectural design parameters, thus enabling processor architects to explore a sufficiently large design space and achieve power-efficient designs. Additionally CASPER is designed to accommodate cycle-accurate models of hardware controlled power management units, enabling architects to experiment with and evaluate different autonomous power-saving mechanisms to study the run-time power-performance trade-offs in embedded many-core processors. We have implemented two such techniques in CASPER–Chipwide Dynamic Voltage and Frequency Scaling, and Performance Aware Core-Specific Frequency Scaling, which show average power savings of 35.9% and 26.2% on a baseline 4-core SPARC based architecture respectively. This power saving data accounts for the power consumption of the power management units themselves. The CASPER simulation platform also provides users with complete support of SPARCV9 instruction set enabling them to run a full operating system software stack, and hence a wide variety of benchmarking applications.
Abrogation of gamma interferon-induced inhibition of Ehrlichia chaffeensis infection in human monocytes with iron-transferrin (1994)

Ehrlichia chaffeensis is an obligate intracellular bacterium which infects cells of the macrophage/monocyte lineage. To test whether gamma interferon (IFN-gamma) inhibits infection of monocytes with E. chaffeensis, human peripheral blood monocytes were incubated with recombinant human IFN-gamma for 3 h and then exposed to E. chaffeensis. With 2,000 U of IFN-gamma per ml, maximal inhibition of infection by E. chaffeensis was observed. THP-1 cells, a human monocyte cell line, pretreated with phorbol myristic acetate or not pretreated, were incubated with various concentrations of IFN-gamma. Maximum inhibition was obtained at 1,000 U of IFN-gamma per ml with phorbol myristic acetate-treated THP-1 cells. However, nontreated cells did not achieve a similar level of anti-ehrlichial activity even with 10,000 U of IFN-gamma per ml. IFN-gamma given within 6 h postinfection was effective in inhibiting E. chaffeensis. Nitric oxide production was not demonstrated in the monocyte medium incubated with IFN-gamma and E. chaffeensis. None of the reactive oxygen intermediate scavengers tested blocked the IFN-gamma-induced anti-ehrlichial activity. Deferoxamine, an intracellular iron chelator, at 15 microM completely inhibited the survival of E. chaffeensis. Iron-saturated transferrin at 1.67 mg/ml completely reversed the IFN-gamma-induced ehrlichial killing. These results indicate that (i) E. chaffeensis is sensitive to intracytoplasmic iron depletion, (ii) E. chaffeensis is sensitive to IFN-gamma-induced killing, and (iii) the anti-ehrlichial activity induced in human monocytes by IFN-gamma is mediated by limitation of available cytoplasmic iron and is not due to the generation of reactive oxygen intermediates or nitric oxide.
Electro-Absorption-Based Fast Photonic Integrated Circuit Sources for Next Network Capacity Scaling [Invited] (2012)

Increasing component speed, throughput and efficiency inevitably leads to optoelectronic transmitters and receivers of more complexity, larger footprint, consumption and cost. Monolithic integration is known to help in solving these problems typical of discrete components. However, lowering of the cost, consumption and material usage must preserve high modulation performance especially while increasing the data rate. These issues are addressed by our new photonic integrated circuit technology on indium phosphide. The demonstrated laser transmitter circuits rely on electro-absorption modulators, one of the smallest and most energy-efficient electro-optic converters. By improving old and creating new component classes, this approach is expected to reduce dramatically their environmental footprint.
Effect of Cosmic Rays on Computer Memories (1979)

A method is developed for evaluating the effects of cosmic rays on computer memories and is applied to some typical memory devices. The sea-level flux of cosmic-ray particles is reviewed and the interaction of each type of particle with silicon is estimated, with emphasis on processes that produce bursts of charge. These charge pulses are then related to typical computer large-scale integrated circuit components and cosmic-ray-induced errors are estimated. The effects of shielding (such as building ceilings and walls), altitude, and solar cycle are estimated. Cosmic-ray nucleons and muons can cause errors in current memories at a level of marginal significance, and there may be a very significant effect in the next generation of computer memory circuitry. Error rates increase rapidly with altitude, which may be used for testing to make electronic devices less sensitive to cosmic rays.
Building Social Life Networks. (2013)

The availability of enormous volumes of heterogeneous Cyber-Physical-Social (CPS) data streams allow design and implementation of networks to connect people with essential life resources. We call these networks Social Life Networks (SLNs). We are developing concepts, technology, and infrastructure to design and build these networks. SLNs will be helpful in addressing several essential societal problems in everyday life as well as during abnormal situations. A person needs to be connected to appropriate resources under the given situations and her own persona and context. Situations should be detected by using heterogeneous data streams. We are building a software framework for situation recognition and determining persona and personal context to connect people to resources efficiently, effectively, and promptly. We present our research in situation recognition, EventShop, persona building, and making connections using a few example scenarios.
Re-evaluation of a subsurface injection experiment for testing flow and transport models (1995)

The current preferred method for disposal of low-level radioactive waste (LLW) at the Hanford Site is to vitrify the wastes so they can be stored in a near-surface, shallow-land burial facility (Shord 1995). Pacific Northwest Laboratory (PNL) managed the PNL Vitrification Technology Development (PVTD) Project to assist Westinghouse Hanford Company (WHC) in designing and assessing the performance of a disposal facility for the vitrified LLW. Vadose zone flow and transport models are recognized as necessary tools for baseline risk assessments of stored waste forms. The objective of the Controlled Field Testing task of the PVTD Project is to perform and analyze field experiments to demonstrate the appropriateness of conceptual models for the performance assessment. The most convincing way to demonstrate appropriateness is to show that the model can reproduce the movement of water and contaminants in the field. Before expensive new experiments are initiated, an injection experiment conducted at the Hanford Site in 1980 (designated the ``Sisson and the Lu experiment``) should be completely analyzed and understood. Briefly, in that test, a solution containing multiple tracers was injected at a single point into the subsurface sediments. The resulting spread of the water and tracers was monitored in wells surrounding the injection point. Given the advances in knowledge, computational capabilities, and models over the last 15 years, it is important to re-analyze the data before proceeding to other experiments and history-matching exercises.
Native Lignin<sup>1</sup> I. Its Isolation and Methylation (1939)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNative Lignin1 I. Its Isolation and MethylationF. E. BraunsCite this: J. Am. Chem. Soc. 1939, 61, 8, 2120–2127Publication Date (Print):August 1, 1939Publication History Published online1 May 2002Published inissue 1 August 1939https://pubs.acs.org/doi/10.1021/ja01877a043https://doi.org/10.1021/ja01877a043research-articleACS PublicationsRequest reuse permissionsArticle Views585Altmetric-Citations98LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Deep Neural Network Based Video Source Recognition (2020)

To enable network service providers to better allocate network resources, a variety of traffic identification algorithms have been developed, but few new features with stronger differentiation power are reported, causing unsatisfactory False Positive Rate (FPR) performance in existing methods. To deal with this issue, this paper presents a new method for recognizing streaming video sources in encrypted tunnels based on deep learning (DL). A modified Kolmogorov-Smirnov Discretization (MKSD) algorithm that produces a continuously differentiable histogram curve, is developed to train a deep neural network (DNN) model for optimal histogram bin placement. Experimental validation with simulated real network complexity (traffic combinations in encrypted VPN tunnels) demonstrates that the MKSD algorithm can improve True Positive Rate (TPR) for system identification, while reducing FPR. Compared with existing methods, the proposed method shows higher identification accuracy of video sources in single and multi-stream scenarios.
Fabrication of a Mixed Matrix Membrane with in Situ Synthesized Quaternized Polyethylenimine Nanoparticles for Dye Purification and Reuse (2015)

A facile and novel method for the fabrication of mixed matrix membranes (MMMs) has been developed, i.e., in situ synthesis of quaternized polyethylenimine (QPEI) soft nanoparticles (SNPs) followed by quaternization with bromoethane in poly(ether sulfone) (PES) casting solution. The resulting composite membranes were constructed via phase inversion method. The influences of SNPs on the morphology and performance of the hybrid membranes were systematically investigated by scanning electron microscopy, dynamic water contact angle, antifouling measurement, etc. The composite membranes exhibited a thin top layer and porous finger-like structure, which were greatly affected by in situ synthesized SNPs. Contact angle and water uptake measurements indicated that the hydrophilicity of hybrid membranes markedly improved in contrast with that of unfilled membrane. Meanwhile, the water flux of the membranes significantly enhanced due to the incorporation of SNPs. The ion-exchange capacity (IEC) value could achieve as high as 0.72 mmol g–1 with an initial PEI content of 1.5 wt %. The salts rejection of MMMs followed the order: MgCl2 > MgSO4 > Na2SO4 > NaCl, confirming that the hybrid membranes were positively charged. Meanwhile, the fouling parameters demonstrated that the composite membranes exhibited a preferable antifouling property. The newly developed membranes demonstrated an impressive prospect for the dye purification due to the high rejection of reactive dyes with a high permeation flux, as well as low multivalent ions retention. The possible separation mechanism of dyes and salts for composite membranes influenced by synthesized SNPs was also proposed in this study.
Beta-lactam antibiotic decreases acquisition of and motivation to respond for cocaine, but not sweet food, in C57Bl/6 mice (2011)

No medication is approved to treat cocaine addiction, but mounting evidence suggests that glutamate-directed approaches may reduce cocaine dependence and relapse. We tested the hypotheses that the glutamate transporter subtype 1 activator, ceftriaxone, disrupts acquisition of cocaine self-administration, motivation to self-administer cocaine, and conditioned place preference in mice. Repeated ceftriaxone (200 mg/kg) reduced the ability of mice to acquire cocaine and the motivation to self-administer cocaine after successful acquisition without affecting acquisition of or motivation for sweet food. Repeated ceftriaxone had no effect on cocaine-conditioned place preference. These results suggest that a β-lactam antibiotic reduces the direct reinforcing strength of cocaine without producing nonspecific deficits in conditioned learning processes.
Indoleamine 2,3-dioxygenase is a novel prognostic indicator for endometrial cancer (2006)

Indoleamine 2,3-dioxygenase (IDO) is a tryptophan-catabolising enzyme inducing immune tolerance. The present study aimed to investigate IDO expression and its prognostic significance in endometrial cancer. Indoleamine 2,3-dioxygenase expression in endometrial cancer tissues (n = 80) was immunohistochemically scored as four groups (IDO-, 1+, 2+, and 3+). The high IDO expression (IDO2+ or 3+) in tumour cells was found in 37 (46.3%) of the 80 cases, and was positively correlated with surgical stage, myometrial invasion, lymph-vascular space involvement, and lymph node metastasis, but not with the histological grade. Patients with high IDO expression had significantly impaired overall survival and progression-free survival (PFS) (P = 0.002 and P = 0.001, respectively) compared to patients with no or weak expression of IDO (IDO- or 1+). The 5-year PFS for IDO-/1+, 2+, and 3+ were 97.7, 72.9, and 36.4%, respectively. Even in patients with early-stage disease (International Federation of Gynecology and Obstetrics I/II, n = 64), the PFS for IDO2+/3+ was significantly poor (P = 0.001) compared to that for IDO-/1+. On multivariate analysis, IDO expression was an independent prognostic factor for PFS (P = 0.020). These results indicated that the high IDO expression was involved in the progression of endometrial cancer and correlated with the impaired clinical outcome, suggesting that IDO is a novel and reliable prognostic indicator for endometrial cancer.
A side-reaction in the SPPS of Trp-containing peptides (1999)

Syntheses of several Trp-containing peptides on a Wang solid support afforded significant amounts of a side-product. 1H-NMR and MS data showed that an unexpected alkylation by the linker has occurred on the indole nucleus. This was observed whatever the scavenger used, and whatever the position of the Trp residue in the sequence, unless it was in the C-terminal position.
Wirkstoffdesign (2009)

Dieses für den deutschen Raum einzigartige Lehrbuch richtet sich an Studenten der Pharmazie, Chemie und Biowissenschaften, aber auch an Quereinsteiger in Forschungs- und Entwicklungsabteilungen der Ph
PI3K Signaling Pathway Activation Predicts Class I PI3K Inhibitor GDC-0941 Sensitivity in AML. (2009)

Abstract Abstract 1057 Poster Board I-79 The PI3K-Akt signal transduction pathway plays a key role in the pathogenesis of many human cancers. In AML malignancy, deregulation of upstream receptor tyrosine kinases such as FLT3, c-Kit, and c-FMS or mutations in K-Ras, N-Ras, B-Raf and CEBPA genes lead to activation of PI3K-Akt signaling to promote cell survival and cell growth. A highly selective Class I PI3K inhibitor, GDC-0941, provides exciting therapeutic opportunities for targeting this pathway in AML. Here we show that GDC-0941 significantly inhibits the viability of the majority of a large panel of AML cell lines tested in vitro (80% or 19/24) at a concentration of < 1 uM. Because not all AML cell lines responded to GDC-0941, we show that PI3K-Akt pathway activation, evidenced by basal pAkt level, can serve as a potential predictive biomarker for GDC-0941 in AML in that sensitive cell lines displayed higher level of pAkt relative to resistant cell lines. Consistently, GDC-0941 treatment leads to decreased pAkt, and therefore the down-regulation of this important pro-survival signaling. Our further analysis shows that GDC-0941 treatment can induce apoptosis and/or cell cycle arrest. We also obtained fresh AML tumor samples to test whether GDC-0941 can similarly induces apoptosis in blast cells and showed that GDC-0941 treatment results in a down-regulation of pAkt level and increased apoptosis. Other PD biomarkers such as phospho-BAD level and Bim expression are both consistent with the observed apoptotic responses. Furthermore, the mammalian target of rapamycin complex 1 (mTORC1) inhibitor, rapamycin, synergizes with GDC-0941 to produce an increased amount of apoptosis in several AML cell lines tested. This is likely due to the fact that long-term treatment with rapamycin induces the sensitivity of the PI3K –Akt signaling pathway by releasing the negative feedback loop of mTORC1-S6K-IRS1/2 module. Importantly, in some AML cell lines we observe synergies between GDC-0941 and AraC. Interestingly, while AraC alone does not induce apoptosis in AML cell lines with PTEN loss or mutation, the synergy between AraC and GDC-0941 comes from increased apoptotic response, suggesting that GDC-0941 can synergize with chemo agents that induces S/G2 cell cycle arrest. Together, our preclinical data suggest that GDC-0941 may be used as a targeted therapy in AML patients as a single agent or in combination with other chemotherapies in clinic. Disclosures: Ma: Genentech Inc.: Employment. Du:Genentech, Inc.: Employment, Equity Ownership. Sun:Genentech Inc.: Employment. Shi:Genentech, Inc.: Employment, Equity Ownership. Friedman:Genentech Inc.: Employment. Dornan:Genentech, Inc.: Employment, Equity Ownership. Ebens:Genentech, Inc.: Employment, Equity Ownership, Patents & Royalties.
Chemical Kinetics is Turing Universal (1997)

We show that digital logic can be implemented in the chemical kinetics of homogeneous solutions: We explicitly construct logic gates and show that arbitrarily large circuits can be made from them. This proves that a subset of the constructions available to life has universal (Turing) computational power.