gebhart/patrepeval huggingface dataset:
Regulation of MEF2 by Histone Deacetylase 4- and SIRT1 Deacetylase-Mediated Lysine Modifications (2005)

The class II deacetylase histone deacetylase 4 (HDAC4) negatively regulates the transcription factor MEF2. HDAC4 is believed to repress MEF2 transcriptional activity by binding to MEF2 and catalyzing local histone deacetylation. Here we report that HDAC4 also controls MEF2 by a novel SUMO E3 ligase activity. We show that HDAC4 interacts with the SUMO E2 conjugating enzyme Ubc9 and is itself sumoylated. The overexpression of HDAC4 leads to prominent MEF2 sumoylation in vivo, whereas recombinant HDAC4 stimulates MEF2 sumoylation in a reconstituted system in vitro. Importantly, HDAC4 promotes sumoylation on a lysine residue that is also subject to acetylation by a MEF2 coactivator, the acetyltransferase CBP, suggesting a possible interplay between acetylation and sumoylation in regulating MEF2 activity. Indeed, MEF2 acetylation is correlated with MEF2 activation and dynamically induced upon muscle cell differentiation, while sumoylation inhibits MEF2 transcriptional activity. Unexpectedly, we found that HDAC4 does not function as a MEF2 deacetylase. Instead, the NAD+-dependent deacetylase SIRT1 can potently induce MEF2 deacetylation. Our studies reveal a novel regulation of MEF2 transcriptional activity by two distinct classes of deacetylases that affect MEF2 sumoylation and acetylation.
ChemInform Abstract: PHOTOCHEMICAL SYNTHESIS OF BENZO(F)QUINOLINES (1978)

Abstract Z‐Methylthio‐benzoesäure (I) wird zum Carbinol (II) reduziert und dann mit hoher Ausbeute zum Aldehyd (IIIa) oxidiert wobei gleichzeitig geringe Mengen an dem Sulfoxid (IIIb) erhalten werden.
Egg-laying and locomotory screens with C. elegans yield a nematode-selective small molecule stimulator of neurotransmitter release (2022)

Nematode parasites of humans, livestock and crops dramatically impact human health and welfare. Alarmingly, parasitic nematodes of animals have rapidly evolved resistance to anthelmintic drugs, and traditional nematicides that protect crops are facing increasing restrictions because of poor phylogenetic selectivity. Here, we exploit multiple motor outputs of the model nematode C. elegans towards nematicide discovery. This work yielded multiple compounds that selectively kill and/or immobilize diverse nematode parasites. We focus on one compound that induces violent convulsions and paralysis that we call nementin. We find that nementin stimulates neuronal dense core vesicle release, which in turn enhances cholinergic signaling. Consequently, nementin synergistically enhances the potency of widely-used non-selective acetylcholinesterase (AChE) inhibitors, but in a nematode-selective manner. Nementin therefore has the potential to reduce the environmental impact of toxic AChE inhibitors that are used to control nematode infections and infestations.
Influence of Cold Rolling Reduction and Cross Rolling on Recrystallization Texture Formation in Electro Deposited Pure Iron with a Sharp and Homogeneous &lt;111&gt;//ND Fiber (2014)

The cold rolling and annealing texture formation has been investigated in electro deposited pure iron which has an extremely sharp and isotropic &lt;111&gt;//ND fiber. Regardless of cold rolling reduction, {111}&lt;112&gt; intensified texture is formed after cold rolling. Similar texture remains after recrystallization in 65% cold rolled material while {111}&lt;110&gt; type texture forms in 80% and 90% cold rolled ones. The recrystallized grains at the stage of 5% recrystallization have {111}&lt;112&gt; orientation in 65% cold rolled sheet, whereas {111}&lt;110&gt; is observed in 80% cold rolled one. From this aspect, it is considered that the nucleation orientation plays an important role in the recrystallization texture formation. In the meanwhile, the growth of the recrystallized nuclei is also supposed to affect the recrystallization texture formation. The nuclei with {111}&lt;112&gt; orientation in lightly cold rolled sheet are easier to consume the deformed matrix than they do in heavily cold rolled sheets because their frequency to encounter a deformed grain with nearly the same orientation is much smaller in lightly cold rolled specimen, which can result in a large mobility for growth. Cross cold rolling makes cold rolling texture rather homogeneous &lt;111&gt;//ND fiber, which gives rise to an almost homogeneous &lt;111&gt;//ND fiber after annealing.
Potent peptidic fusion inhibitors of influenza virus (2017)

Influenza therapeutics with new targets and mechanisms of action are urgently needed to combat potential pandemics, emerging viruses, and constantly mutating strains in circulation. We report here on the design and structural characterization of potent peptidic inhibitors of influenza hemagglutinin. The peptide design was based on complementarity-determining region loops of human broadly neutralizing antibodies against the hemagglutinin (FI6v3 and CR9114). The optimized peptides exhibit nanomolar affinity and neutralization against influenza A group 1 viruses, including the 2009 H1N1 pandemic and avian H5N1 strains. The peptide inhibitors bind to the highly conserved stem epitope and block the low pH-induced conformational rearrangements associated with membrane fusion. These peptidic compounds and their advantageous biological properties should accelerate the development of new small molecule- and peptide-based therapeutics against influenza virus.
Hardware Transactional Memory (2004)

This work shows how hardware transactional memory (HTM) can be implemented to support transactions of arbitrarily large size, while ensuring that small transactions run efficiently. Our implementation handles small transactions similar to Herlihy and Moss's scheme in that it holds tentative updates in a cache. Unlike their scheme, which uses a special fully associative cache, ours augments the ordinary processor cache and provides a mechanism to handle cache spills of uncommitted transactional data. Consequently, our scheme runs faster for small transactions while correctly handling transactions of arbitrarily large size. <br/>Although transactions are small in the common case, we argue that HTM should not restrict the size of transactions, because it complicates the programmer/compiler model and precludes some important programs from exploiting transactional memory. We show that the Linux 2.4.19 kernel can be automatically and efficiently “transactified” if boundless transactions can be supported. Our experimental results show that the largest transaction touches over 7000 64-byte cache lines, whereas 99.94\% of the transactions touch fewer than 64 cache lines. We further show that synchronized methods in Java can be easily compiled to our HTM scheme, thereby providing the advantages of nonblocking atomicity (including absence of deadlock) in a straightforward fashion. Our HTM scheme for boundless transactions uses an efficiently implementable hardware snapshot and the ordinary set-associative L2 cache extended with less than two bits per cache line. One of the bits tells whether the cached item is part of a transaction (as in the Herlihy-Moss scheme), and all the lines in an associative set share another bit telling whether a line has overflowed from the cache and is now stored in a special overflow area of main memory. We provide empirical results to show that our scheme does not adversely affect the processor pipeline or hinder speculative execution.
The Fragmentation of Alkoxychlorocarbenes in Hydrocarbon Solvents and in Low Temperature Argon Matrixes (2002)

Alkoxychlorocarbenes (ROCCl, R = benzyl, cyclohexyl, and 1-octyl) were generated from the corresponding diazirines in acetonitrile, dichloroethane, benzene, cyclohexane, and pentane solutions at 25 °C, and the fragmentations of these carbenes were examined. Formation of RCl (and alkenes when R = cyclohexyl or 1-octyl) occurred efficiently in all of the solvents. The rate constant for the fragmentation of PhCH2OCCl (determined by laser flash photolysis) was ∼105 s-1, and relatively independent of solvent. Photolysis of PhCH2OC(N2)Cl in Ar matrixes led to the carbene, PhCH2OCCl, as well as its primary fragmentation products, the benzyl and COCl radicals. A prominent product was also phenacyl chloride, PhCH2COCl, a formal rearrangement product of the carbene. Computational studies of the rearrangements and fragmentations of MeOCCl, EtOCCl, and PhCH2OCCl at the DFT and coupled cluster levels afforded transition states and energetics. These studies allowed us to identify several mechanistic pathways, including concerted and homolytic processes that are predicted to prevail in nonpolar solvents and matrixes as opposed to heterolytic (ionic) processes in polar solvents. The existence of cis and trans forms of R−OC−Cl, and their interconversion, are complicating factors that were considered computationally.
Search for R-parity-violating supersymmetry in events with four or more leptons in $ \sqrt{s}=7\;\mathrm{TeV} $ pp collisions with the ATLAS detector (2012)

A bstract A search for new phenomena in final states with four or more leptons (electrons or muons) is presented. The analysis is based on 4.7 fb −1 of $ \sqrt{s}=7\;\mathrm{TeV} $ proton-proton collisions delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in two signal regions: one that requires moderate values of missing transverse momentum and another that requires large effective mass. The results are interpreted in a simplified model of R -parity-violating supersymmetry in which a 95% CL exclusion region is set for charged wino masses up to 540 GeV. In an R -parity-violating MSUGRA/CMSSM model, values of m 1/2 up to 820 GeV are excluded for 10 &lt; tan β &lt; 40.
Aberrant High Expression of B Lymphocyte Chemokine (Blc/Cxcl13) by C11b+Cd11c+ Dendritic Cells in Murine Lupus and Preferential Chemotaxis of B1 Cells towards Blc (2001)

We observed here that the expression of B lymphocyte chemokine (BLC/CXCL13) was markedly enhanced in the thymus and kidney in aged (NZB x NZW)F1 (BWF1) mice developing lupus nephritis, but not in similarly aged NZB and NZW mice. BLC-positive cells were present in the cellular infiltrates in the target organs with a reticular pattern of staining. CD11b+CD11c+ dendritic cells were increased in the thymus and spleen in aged BWF1 mice and identified as the major cell source for BLC. CD4+ T cells as well as B cells were dramatically increased in the thymus in aged BWF1 mice, whereas no increase was observed in aged NZB and NZW mice. B1/B2 ratio in the thymus was significantly higher than those in the spleen and peripheral blood in aged BWF1 mice. Interestingly, BLC showed preferential chemotactic activity for B1 cells derived from several mouse strains, including nonautoimmune mice. Cell surface CXCR5 expression on B1 cells was significantly higher than that on B2 cells. Thus, aberrant high expression of BLC by myeloid dendritic cells in the target organs in aged BWF1 mice may play a pivotal role in breaking immune tolerance in the thymus and in recruiting autoantibody-producing B cells in the development of murine lupus.
Abatacept Limits Breach of Self-Tolerance in a Murine Model of Arthritis via Effects on the Generation of T Follicular Helper Cells (2010)

Abatacept modulates CD28-mediated T cell costimulation and is efficacious in the treatment of rheumatoid arthritis (RA). Its mechanism of action has not been fully elucidated but will likely reveal critical pathologic pathways in RA. We show that abatacept substantially modulated Ag-specific T and B cell responses in vivo. Ag-specific T cell proliferation was reduced, and the acquisition of an activated phenotype, characterized by upregulation of CD69, OX40, ICOS, and programmed death-1 and downregulation of CD62L, was suppressed. Furthermore, abatacept suppressed the production of inflammatory cytokines, such as IFN-gamma and IL-17. These effects were associated with a failure of Ag-specific T cells to acquire the CXCR5(+)ICOS(+) T follicular helper cell phenotype. This, in turn, led to a failure of these cells to enter B cell follicles, resulting in reduced specific Ab responses, despite normal B cell clonal expansion. To test the pathologic significance of this, we used a novel model of RA associated with breach of self-tolerance to self-Ag and demonstrated that abatacept prevented the emergence of self-reactivity. Thus, CD28-dependent signaling is required for optimal T follicular helper cell maturation and expansion, and its inhibition prevents loss of self-tolerance in a model of articular pathology. Thus, we provide a novel mode of action for abatacept with profound implications for its potential usefulness in early inflammatory arthropathies associated with autoantibody expression.
From 2 dimensions to 3rd dimension: Quantitative prediction of anterior chamber depth from anterior segment photographs via deep-learning (2023)

Anterior chamber depth (ACD) is a major risk factor of angle closure disease, and has been used in angle closure screening in various populations. However, ACD is measured from ocular biometer or anterior segment optical coherence tomography (AS-OCT), which are costly and may not be readily available in primary care and community settings. Thus, this proof-of-concept study aims to predict ACD from low-cost anterior segment photographs (ASPs) using deep-learning (DL). We included 2,311 pairs of ASPs and ACD measurements for algorithm development and validation, and 380 pairs for algorithm testing. We captured ASPs with a digital camera mounted on a slit-lamp biomicroscope. Anterior chamber depth was measured with ocular biometer (IOLMaster700 or Lenstar LS9000) in data used for algorithm development and validation, and with AS-OCT (Visante) in data used for testing. The DL algorithm was modified from the ResNet-50 architecture, and assessed using mean absolute error (MAE), coefficient-of-determination (R2), Bland-Altman plot and intraclass correlation coefficients (ICC). In validation, our algorithm predicted ACD with a MAE (standard deviation) of 0.18 (0.14) mm; R2 = 0.63. The MAE of predicted ACD was 0.18 (0.14) mm in eyes with open angles and 0.19 (0.14) mm in eyes with angle closure. The ICC between actual and predicted ACD measurements was 0.81 (95% CI 0.77, 0.84). In testing, our algorithm predicted ACD with a MAE of 0.23 (0.18) mm; R2 = 0.37. Saliency maps highlighted the pupil and its margin as the main structures used in ACD prediction. This study demonstrates the possibility of predicting ACD from ASPs via DL. This algorithm mimics an ocular biometer in making its prediction, and provides a foundation to predict other quantitative measurements that are relevant to angle closure screening.
Pilot Designs for Channel Estimation of OFDM Systems with Frequency-Dependent I/Q Imbalances (2009)

The advances in semiconductor downscaling have empowered communication devices with significantly enhanced signal processing capability, but with the side effect of larger device impairments. Among those impairments, the I/Q imbalance is a critical one as it causes intercarrier interferences in orthogonal frequency division multiplexing (OFDM) systems. The I/Q imbalances in general exist at both transmitter and receiver, and they can be frequency-dependent. They may vary over time (e.g. due to sudden changes in temperature or the dynamics of the cooperating/relaying users). Under such scenarios, estimation and compensation of the combined effect of the channel and I/Q imbalances are crucial. This paper presents efficient pilot designs for such tasks. The advantages of the proposed designs over the existing ones in terms of estimation performance and overhead efficiency are corroborated by analysis and simulation results.
Thermal dissociation of chemisorbed oxygen molecules on Ag(110): an investigation by scanning tunnelling microscopy (2002)

The thermal dissociation of oxygen molecules on A-(110) was studied by means of scanning tunnelling microscopy. At temperatures around 170 K a fraction of the molecules dissociate to form pairs of O atoms on the unreconstructed surface. The atoms lie in the trenches between the close-packed Ag rows; the intrapair distance is two lattice constants. The O atoms are very reactive with CO at temperatures as low as 70 K. The preferential orientation of the pairs in the [001] direction contrasts with the finding in a previous study (Hahn J R, Lee H J and Ho W 2000 Phys. Rev. Lett. 85 1914) that electron-induced dissociation exclusively leads to [110]-oriented pairs. The trajectories of thermal and electron-induced dissociations must therefore be different. In the temperature range of the dissociation, several additional oxygen features occur on the surface. These include unreacted O-2, molecules, the first nuclei of the added-row reconstruction, and two unidentified O-induced structures.
ChemInform Abstract: Synthesis of (‐)‐Oxetanocin. (1989)

Abstract The title compound (‐)‐oxetanocin (VIII) is synthesized starting from (‐)‐adenosine (I) as shown.
Water quality comprehensive evaluation method for large water distribution network based on clustering analysis Kui Chang, Jin Liang Gao, Wen Yan Wu and Yi Xing Yuan (2011)

In order to evaluate water quality for a large water distribution network comprehensively, a two-stage classification method was used and the clustering methods, self-organizing map (SOM), K-means method and fuzzy c-mean (FCM), were represented. With these clustering methods, the pipes of a large real water distribution network were divided into some groups considering one or more water quality indicators synchronously. The water quality indicators of residual chlorine, water age, THMs, TAAs, TOC and BDOC are used in this paper. Residual chlorine and water age are two main water quality indicators. THMs and TAAs can represents the disinfection byproducts information. And TOC and BDOC are used to represents biological stability. According to the clustering results, the status of water quality of the water network was analysed. The results showed that the classification of SOM could express the comprehensive water quality in a water distribution network (WDN) directly and vividly by high-dimension water quality indicator projection to a low dimensional topology grid and that two-stage classification method has higher efficiency in comparison to the traditional clustering method. Water quality comprehensive evaluation was of significance for locating water quality monitoring, water network rehabilitation and expansion.
Preventive Allergen-Specific Vaccination Against Allergy: Mission Possible? (2020)

Vaccines for infectious diseases have improved the life of the human species in a tremendous manner. The principle of vaccination is to establish <i>de novo</i> adaptive immune response consisting of antibody and T cell responses against pathogens which should defend the vaccinated person against future challenge with the culprit pathogen. The situation is completely different for immunoglobulin E (IgE)-associated allergy, an immunologically-mediated hypersensitivity which is already characterized by increased IgE antibody levels and T cell responses against <i>per se</i> innocuous antigens (i.e., allergens). Thus, allergic patients suffer from a deviated hyper-immunity against allergens leading to inflammation upon allergen contact. Paradoxically, vaccination with allergens, termed allergen-specific immunotherapy (AIT), induces a counter immune response based on the production of high levels of allergen-specific IgG antibodies and alterations of the adaptive cellular response, which reduce allergen-induced symptoms of allergic inflammation. AIT was even shown to prevent the progression of mild to severe forms of allergy. Consequently, AIT can be considered as a form of therapeutic vaccination. In this article we describe a strategy and possible road map for the use of an AIT approach for prophylactic vaccination against allergy which is based on new molecular allergy vaccines. This road map includes the use of AIT for secondary preventive vaccination to stop the progression of clinically silent allergic sensitization toward symptomatic allergy and ultimately the prevention of allergic sensitization by maternal vaccination and/or early primary preventive vaccination of children. Prophylactic allergy vaccination with molecular allergy vaccines may allow halting the allergy epidemics affecting almost 30% of the population as it has been achieved for vaccination against infectious diseases.
Calculation of the Cross-Section for the 1S→2P Transition of an Electron Bubble in Helium II (2006)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Wei Guo, Humphrey J. Maris; Calculation of the Cross‐Section for the 1S→2P Transition of an Electron Bubble in Helium II. AIP Conf. Proc. 7 September 2006; 850 (1): 165–166. https://doi.org/10.1063/1.2354653 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
RIG-I Mediates an Antiviral Response to Crimean-Congo Hemorrhagic Fever Virus (2015)

CCHFV is a tick-borne virus with a significant public health impact. In order for cells to respond to virus infection, they must recognize the virus as foreign and initiate antiviral signaling. To date, the receptors involved in immune recognition of CCHFV are not known. Here, we investigate and identify RIG-I as a receptor involved in initiating an antiviral response to CCHFV. This receptor initially was not expected to play a role in CCHFV recognition because of characteristics of the viral genome. These findings are important in understanding the antiviral response to CCHFV and support continued investigation into the spectrum of potential viruses recognized by RIG-I.
A Reduced-Order Modelfor Transient Analysis of Bladed Disk ForcedResponse (2005)

Abstract A method for predicting the vibratory response of bladed disks under high engine acceleration rates is developed. The method is based on the Fundamental Mistuning Model, an existing reduced order model for predicting the steady-state vibratory response. In addition, a criterion is developed for a critical engine acceleration rate, above which transient effects play a large role in the response. It is shown that military engines operate at acceleration rates above this critical value and therefore transient effects are important in practice.