gebhart/patrepeval huggingface dataset:
Alignment of U3 region sequences of mammalian type C viruses: identification of highly conserved motifs and implications for enhancer design (1990)

We aligned published sequences for the U3 region of 35 type C mammalian retroviruses. The alignment reveals that certain sequence motifs within the U3 region are strikingly conserved. A number of these motifs correspond to previously identified sites. In particular, we found that the enhancer region of most of the viruses examined contains a binding site for leukemia virus factor b, a viral corelike element, the consensus motif for nuclear factor 1, and the glucocorticoid response element. Most viruses containing more than one copy of enhancer sequences include these binding sites in both copies of the repeat. We consider this set of binding sites to constitute a framework for the enhancers of this set of viruses. Other highly conserved motifs in the U3 region include the retrovirus inverted repeat sequence, a negative regulatory element, and the CCAAT and TATA boxes. In addition, we identified two novel motifs in the promoter region that were exceptionally highly conserved but have not been previously described.
Fusion from without directed by human immunodeficiency virus particles (1994)

Fusion from without is the process through which particles of some enveloped viruses can direct fusion of target cells in the absence of viral replication. We demonstrate here that human immunodeficiency virus (HIV) particles can efficiently promote fusion from without. Using HeLa-CD4 cells carrying a Tat-inducible lacZ gene, we observed syncytia as early as 6 h after exposure to HIV particles, before HIV gene expression could be detected. Efficient syncytium formation could be obtained when cells were treated with zidovudine, which prevented HIV replication and expression but not cell-cell fusion. Fusion was also observed when cells were exposed to particles of a replication-defective HIV integrase mutant. Fusion from without by HIV particles could be blocked by a monoclonal antibody specific for the V3 loop of the HIV-1 envelope glycoprotein and by soluble CD4. This mechanism of cytopathicity, which can involve cells that do not actively replicate HIV and can be directed by replication-defective particles, could participate in the pathogenicity of the CD4 cell depletion that characterizes HIV infection.
A Class of Nonconvex Penalties Preserving Overall Convexity in Optimization-Based Mean Filtering (2016)

ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> mean filtering is a conventional, optimization based method to estimate the positions of jumps in a piecewise constant signal perturbed by additive noise. In this method, the ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> norm penalizes sparsity of the first-order derivative of the signal. Theoretical results, however, show that in some situations, which can occur frequently in practice, even when the jump amplitudes tend to ∞, the conventional method identifies false change points. This issue, which is referred to as the stair-casing problem herein, restricts practical importance of ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> mean filtering. In this paper, sparsity is penalized more tightly than the ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> norm by exploiting a certain class of nonconvex functions, while the strict convexity of the consequent optimization problem is preserved. This results in a higher performance in detecting change points. To theoretically justify the performance improvements over ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> mean filtering, deterministic and stochastic sufficient conditions for exact change point recovery are derived. In particular, theoretical results show that in the stair-casing problem, our approach might be able to exclude the false change points, while ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> mean filtering may fail. A number of numerical simulations assist to show superiority of our method over ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> mean filtering and another state-of-the-art algorithm that promotes sparsity tighter than the ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> norm. Specifically, it is shown that our approach can consistently detect change points when the jump amplitudes become sufficiently large, while the two other competitors cannot.
Panobinostat in combination with azacitidine reduces the frequency of TNFR2+ regulatory T cells in acute myeloid leukemia patients. (P2048) (2013)

Abstract Panobinostat (LBH) and azacitidine (Aza) are currently being evaluated in the therapy of AML. The effect of this drug combination on T cells, particularly on regulatory T cells (Tregs) has not been previously investigated. The presence of Tregs in AML is detrimental, as these cells suppress anti-tumor immunity. Tregs expressing Tumor Necrosis Factor Receptor 2 (TNFR2) are associated with maximal immune suppressor activity. Here, we investigated the combined effect of LBH and Aza on effector T cells (Teff), and TNFR2+ and TNFR2- Tregs in newly diagnosed AML patients. Patients were treated with Aza on days 1-5 for each 28-day cycle combined with 7 doses of LBH on days 5-19. T cells within peripheral blood (PB) and bone marrow (BM) were analyzed via flow cytometry, at baseline and at the end of cycle 1 (EOC1). Specifically, TNFR2+ Tregs were present at high levels within patient PB when compared to controls and were significantly reduced by EOC1 of treatment. Interestingly, only patients who responded to treatment had this reduction in their BM. Mechanistic studies adding LBH alone or with Aza to PB cells during T cell activation in vitro indicated LBH might primarily drive the reduction in Tregs. Concomitant with Treg reduction, IFNγ and IL2 production by CD4 Teff and the ratio of CD4 Teff to TNFR2+ Tregs were enhanced by EOC1 in the BM of responder, but not non-responder patients. AML patients who responded to Aza and LBH treatment have a beneficial immunological outcome.
Antigen Identification Using SEREX (2013)

Serological analysis of recombinant cDNA expression libraries (SEREX) allows systematic identification of antigens recognized by the spontaneous autoantibody repertoire of patients with cancer and autoimmune disease. SEREX is based on screening of lambda phage expression libraries constructed from diseased tissue with the autologous patient's serum. This chapter provides the key protocols for SEREX immunoscreening and for downstream validation of autoantigens.
Comparing transverse momentum balance of b jet pairs in pp and PbPb collisions at $\sqrt{s_\mathrm{NN}} =$ 5.02 TeVC (2018)

The transverse momentum balance of pairs of back-to-back b quark jets in PbPb and pp collisions recorded with the CMS detector at the LHC is reported. The center-of-mass energy in both collision systems is 5.02 TeV per nucleon pair. Compared to the pp collision baseline, b quark jets have a larger imbalance in the most central PbPb collisions, as expected from the jet quenching effect. The data are also compared to the corresponding measurement with inclusive dijets. In the most central collisions, the imbalance of b quark dijets is comparable to that of inclusive dijets.
Pattern Dependence of Data Distortion in Slow-Light Elements (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Slow light has been proposed as a potential solution to all-optically tunable delay line. However, a slow-light element may degrade data quality in an optical communication system while decreasing group velocity of optical pulses. In this paper, pattern dependence of signal distortion is identified as a main reason for data degradation, which is caused by narrow-band amplitude and phase responses of the slow-light elements. We define figure of merit involving pulse delay and data degradation to optimize slow-light devices. It is shown that the pattern dependence can be reduced by detuning slow-light devices away from the signal carrier frequency, which allows using narrow-band slow-light techniques to increase normalized delay up to 0.8, with <formula formulatype="inline"><tex>$Q$</tex></formula> improvement of 2 dB. </para>
Generic Relevance of Counter Charges for Cation-Based Nanoscale Resistive Switching Memories (2013)

Resistive switching memories (ReRAMs) are the major candidates for replacing the state-of-the-art memory technology in future nanoelectronics. These nonvolatile memory cells are based on nanoionic redox processes and offer prospects for high scalability, ultrafast write and read access, and low power consumption. The interfacial electrochemical reactions of oxidation and reduction of ions necessarily needed for resistive switching result inevitably in nonequilibrium states, which play a fundamental role in the processes involved during device operation. We report on nonequilibrium states in SiO2-based ReRAMs being induced during the resistance transition. It is demonstrated that the formation of metallic cations proceeds in parallel to reduction of moisture, supplied by the ambient. The latter results in the formation of an electromotive force in the range of up to 600 mV. The outcome of the study highlights the hitherto overlooked necessity of a counter charge/reaction to keep the charge electroneutrality in cation-transporting thin films, making it hard to analyze and compare experimental results under different ambient conditions such as water partial pressure. Together with the dependence of the electromotive force on the ambient, these results contribute to the microscopic understanding of the resistive switching phenomena in cation-based ReRAMs.
Antibiotika aus Basidiomyceten, 28. Hydroxystrobilurin D, ein antifungisches Antibiotikum aus Kulturen von Mycena sanguinolenta (Agaricales) (1988)

Abstract Aus Kulturen des Blätterpilzes Mycena sanguinolenta wird das antifungische Hydroxystrobilurin D ( 3 ) isoliert. Seine Strukturaufklärung beruht auf spektroskopischen Untersuchungen sowie auf der Thermolyse zum Biphenylderivat 6 , das sich säurekatalysiert in das 2 H ‐1,5‐Benzodioxepin‐Derivat 7 umwandelt. 7 gestattet die Festlegung der Substituentenanordnung am Benzolring und die Bestimmung der absoluten Konfiguration nach Horeau. Die biologischen Eigenschaften von 3 werden diskutiert.
The diverse role of Pdr12 in resistance to weak organic acids (2014)

Resistance to weak organic acids is important relative to both weak organic acid preservatives and the development of inhibitor tolerant yeast as industrial production organisms. The ABC transporter Pdr12 is important for resistance to sorbic and propionic acid, but its role in tolerance to other weak organic acids with industrial relevance is not well established. In this study, yeast strains with altered expression of PDR12 and/or CMK1, a protein kinase associated with post-transcriptional negative regulation of Pdr12, were exposed to seven weak organic acids: acetic, formic, glycolic, lactic, propionic, sorbic and levulinic acid. These are widely used as preservatives, present in lignocellulosic hydrolysates or attractive as chemical precursors. Overexpression of PDR12 increased tolerance to acids with longer chain length, such as sorbic, propionic and levulinic acid, whereas deletion of PDR12 increased tolerance to the shorter acetic and formic acid. The viability of all strains decreased dramatically in acetic or propionic acid, but the Δpdr12 strains recovered more rapidly than other strains in acetic acid. Furthermore, our results indicated that Cmk1 plays a role in weak organic acid tolerance, beyond its role in regulation of Pdr12, since deletion of both Cmk1 and Pdr12 resulted in different responses to exposure to acids than were explained by deletion of Pdr12 alone.
“Bicontinuous Cubic” Liquid Crystalline Materials from Discotic Molecules: A Special Effect of Paraffinic Side Chains with Ionic Liquid Pendants (2009)

Triphenylene (TP) derivatives bearing appropriate paraffinic side chains with imidazolium ion-based ionic liquid (IL) pendants were unveiled to display a phase diagram with liquid crystalline (LC) mesophases of bicontinuous cubic (Cub(bi)) and hexagonal columnar (Col(h)) geometries. While their phase transition behaviors are highly dependent on the length of the side chains and the size of the ionic liquid pendants, TPs with hexadecyl side chains exclusively form a Cub(bi) LC assembly over an extremely wide temperature range of approximately 200 degrees C from room temperature when the anions of the IL pendants are relatively small. Wide-angle X-ray diffraction analysis suggested that the Cub(bi) LC mesophase contains pi-stacked columnar TP arrays with a plane-to-plane separation of approximately 3.5 A. Consistently, upon laser flash photolysis, it showed a transient microwave conductivity comparable to that of a Col(h) LC reference.
VoDEx: a Python library for time annotation and management of volumetric functional imaging data (2023)

Summary: In functional imaging studies, accurately synchronizing the time course of experimental manipulations and stimulus presentations with resulting imaging data is crucial for analysis. Current software tools lack such functionality, requiring manual processing of the experimental and imaging data, which is error-prone and potentially non-reproducible. We present VoDEx, an open-source Python library that streamlines the data management and analysis of functional imaging data. VoDEx synchronizes the experimental timeline and events (eg. presented stimuli, recorded behavior) with imaging data. VoDEx provides tools for logging and storing the timeline annotation, and enables retrieval of imaging data based on specific time-based and manipulation-based experimental conditions. Availability and Implementation: VoDEx is an open-source Python library and can be installed via the "pip install" command. It is released under a BSD license, and its source code is publicly accessible on GitHub https://github.com/LemonJust/vodex. A graphical interface is available as a napari-vodex plugin, which can be installed through the napari plugins menu or using "pip install." The source code for the napari plugin is available on GitHub https://github.com/LemonJust/napari-vodex.
Relationship of Endo-β-D-Mannanase Activity and Cell Wall Hydrolysis in Tomato Endosperm to Germination Rates (1997)

The endosperm tissue enclosing the radicle tip (endosperm cap) governs radicle emergence in tomato (Lycopersicon esculentum Mill.) seeds. Weakening of the endosperm cap has been attributed to hydrolysis of its mannan-rich cell walls by endo-[beta]-D-mannanase. To test this hypothesis, we measured mannanase activity in tomato endosperm caps from seeds allowed to imbibe under conditions of varying germination rates. Over a range of suboptimal temperatures, mannanase activity prior to radicle emergence increased in accordance with accumulated thermal time. Reduced water potential delayed or prevented radicle emergence but enhanced mannanase activity in the endosperm caps. Abscisic acid did not prevent the initial increase in mannanase activity, although radicle emergence was markedly delayed. Sugar composition and percent mannose (Man) content of endosperm cap cell walls did not change prior to radicle emergence under any condition. Man, glucose, and other sugars were released into the incubation solution by endosperm caps isolated from intact seeds during imbibition. Pregerminative release of Man was suppressed and the release of glucose was enhanced when seeds were incubated in osmoticum or abscisic acid; the opposite occurred in the presence of gibberellin. Thus, whereas sugar release patterns were sensitive to environmental and hormonal factors affecting germination, neither assayable endo-[beta]-D-mannanase activity nor changes in cell wall sugar composition of endosperm caps correlated well with tomato seed germination rates under all conditions.
Investigation of the Role of TNF-α Converting Enzyme (TACE) in the Inhibition of Cell Surface and Soluble TNF-α Production by Acute Ethanol Exposure (2012)

Toll-like receptors (TLRs) play a fundamental role in the immune system by detecting pathogen associated molecular patterns (PAMPs) to sense host infection. Ethanol at doses relevant for humans inhibits the pathogen induced cytokine response mediated through TLRs. The current study was designed to investigate the mechanisms of this effect by determining whether ethanol inhibits TLR3 and TLR4 mediated TNF-α secretion through inhibition of transcription factor activation or post-transcriptional effects. In NF-κB reporter mice, activation of NF-κB in vivo by LPS was inhibited by ethanol (LPS alone yielded 170,000±35,300 arbitrary units of light emission; LPS plus ethanol yielded 56,120±16880, p = 0.04). Inhibition of protein synthesis by cycloheximide revealed that poly I:C- or LPS-induced secreted TNF-α is synthesized de novo, not released from cellular stores. Using real time RT-PCR, we found inhibition of LPS and poly I:C induced TNF-α gene transcription by ethanol. Using an inhibitor of tumor necrosis factor alpha converting enzyme (TACE), we found that shedding caused by TACE is a prerequisite for TNF-α release after pathogen challenge. Flow cytometry was used to investigate if ethanol decreases TNF-α secretion by inhibition of TACE. In cells treated with LPS, ethanol decreased both TNF-α cell surface expression and secretion. For example, 4.69±0.60% of untreated cells were positive for cell surface TNF-α, LPS increased this to 25.18±0.85%, which was inhibited by ethanol (86.8 mM) to 14.29±0.39% and increased by a TACE inhibitor to 57.88±0.62%. In contrast, cells treated with poly I:C had decreased secretion of TNF-α but not cell surface expression. There was some evidence for inhibition of TACE by ethanol in the case of LPS, but decreased TNF-α gene expression seems to be the major mechanism of ethanol action in this system.
Supplementary Figure 1 from Metformin-Mediated Bambi Expression in Hepatic Stellate Cells Induces Prosurvival Wnt/β-Catenin Signaling (2023)

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Extraction and physicochemical characterization of a new polysaccharide obtained from the fresh fruits of abelmoschus esculentus. (2011)

This paper is the first multi-scale characterization of the fluidize-dried gum extracted from the fresh fruits of the plant Abelmoschus esculentus. It describes the physical, thermal, sorptional and functional properties of this natural gum. Elemental analysis, scanning electron microscopy (SEM), particle size analysis, X-ray powder diffraction (XPRD), thermo-gravimetric analysis (TGA), differential scanning calorimetry (DSC), fourier transmittance infra red (FT-IR), and nuclear magnetic resonance (NMR) spectroscopy were used to characterize the gum sample. Abelmoschus Esculentus Gum (AEG) had a glass transition temperature (Tg) of 70°C and no melting peak. It showed a 14.91% loss in weight at 195°C. X-ray diffractogram showed numerous broad halos for AEG. Elemental analysis showed that AEG contains 39.5, 7.3, 51.8, and 1.4% carbon, hydrogen, oxygen and nitrogen respectively. The results obtained in this study established the fundamental characteristics of AEG and suggests its potential application in the food, cosmetic and pharmaceutical sectors.
Radioprotective Gene Therapy: Current Status and Future Goals (2008)

This chapter contains sections titled: Introduction Organ-specific radiation protection: oral cavity/oropharynx MnSOD-PL treatment reduces pulmonary irradiation damage MnSOD-PL gene therapy down-modulates marrow cell migration to the lungs MnSOD-PL systemic administration for radiation protection from TBI Summary and future directions References
Targeted therapies for killing tumor cells (2001)

In this issue of PNAS, Su et al. (1) present evidence that transfection and expression of the mda-7 gene in human pancreatic cancer cells combined with antisense inhibition of expression of a mutant K-ras gene results in tumor cell growth suppression and induction of apoptosis. They show that both of these treatments are required for this effect and also indicate that these treatments should not affect normal cells having wild-type K-ras. These results suggest translating the laboratory findings into the clinic as a new rational approach for this deadly disease. How can this translation take place, what are the potential problems, and can this approach be applied to other types of cancer?
Immediate Hypersensitivity Elicits Renin Release from Cardiac Mast Cells (2007)

Our findings disclose that immediate-type hypersensitivity elicits renin release from mast cells, activating a local renin-angiotensin system, thereby promoting norepinephrine release. As renin is stored in human heart mast cells, allergic reactions could initiate renin release, leading to local angiotensin formation and hyperadrenergic dysfunction.
Parallel-type coherent multistage interference canceller with multiple-antenna reception in DS-CDMA reverse link (2002)

This paper proposes a new parallel-type coherent multistage interference canceller (COMSIC) coupled with multiple-antenna reception (MA-COMSIC) and evaluates the capacity increase in a multipath fading channel in the DS-CDMA reverse link, in order to improve further the channel estimation accuracy and increase the space diversity effect. Simulation results show that the MA-COMSIC with a two block-wise antenna configuration, in which each block has 3 antennas (we denote as (B, D) = (2, 3)), achieved a lower required transmit E/sub b//N/sub 0/ than that with (B, D) = (1, 6) except for extreme cases such as when the number of simultaneous users K exceeds 120 corresponding to K/Pg = 250% (where Pg is the processing gain of 48 = 16/spl times/3). Consequently, even when K = 120, the increase in the required transmit E/sub b//N/sub 0/ of MA-COMSIC with (B, D) = (2, 3) from that in a single-user case is only 1.0 dB owing to the significant improvement in the channel estimation accompanied by the diversity effect. We also elucidate that even when the angle spread among constituent waves in the same path is /spl sigma//sub /spl Lambda/S/ = 5 degrees, the loss of the required transmit E/sub b//N/sub 0/ with (B, D) = (2, 3) for the ideal fading correlation case is suppressed to within 0.5 dB.
Determination of the parton distribution functions of the proton from ATLAS measurements of differential W± and Z boson production in association with jets (2021)

A bstract This article presents a new set of proton parton distribution functions, ATLASepWZVjet20, produced in an analysis at next-to-next-to-leading order in QCD. The new data sets considered are the measurements of W + and W − boson and Z boson production in association with jets in pp collisions at $$ \sqrt{s} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:mi>s</mml:mi> </mml:msqrt> </mml:math> = 8 TeV performed by the ATLAS experiment at the LHC with integrated luminosities of 20 . 2 fb − 1 and 19 . 9 fb − 1 , respectively. The analysis also considers the ATLAS measurements of differential W ± and Z boson production at $$ \sqrt{s} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:mi>s</mml:mi> </mml:msqrt> </mml:math> = 7 TeV with an integrated luminosity of 4 . 6 fb − 1 and deep-inelastic-scattering data from e ± p collisions at the HERA accelerator. An improved determination of the sea-quark densities at high Bjorken x is shown, while confirming a strange-quark density similar in size to the up- and down-sea-quark densities in the range x ≲ 0 . 02 found by previous ATLAS analyses.