gebhart/patrepeval huggingface dataset:
Quantum-assisted Helmholtz machines: A quantum–classical deep learning framework for industrial datasets in near-term devices (2018)

Machine learning has been presented as one of the key applications for near-term quantum technologies, given its high commercial value and wide range of applicability. In this work, we introduce the \textit{quantum-assisted Helmholtz machine:} a hybrid quantum-classical framework with the potential of tackling high-dimensional real-world machine learning datasets on continuous variables. Instead of using quantum computers only to assist deep learning, as previous approaches have suggested, we use deep learning to extract a low-dimensional binary representation of data, suitable for processing on relatively small quantum computers. Then, the quantum hardware and deep learning architecture work together to train an unsupervised generative model. We demonstrate this concept using 1644 quantum bits of a D-Wave 2000Q quantum device to model a sub-sampled version of the MNIST handwritten digit dataset with 16x16 continuous valued pixels. Although we illustrate this concept on a quantum annealer, adaptations to other quantum platforms, such as ion-trap technologies or superconducting gate-model architectures, could be explored within this flexible framework.
Molecular Cloning of Tomato Pectin Methylesterase Gene and its Expression in Rutgers, Ripening Inhibitor, Nonripening, and Never Ripe Tomato Fruits (1991)

We have purified pectin methylesterase (PME; EC 3.1.11) from mature green (MG) tomato (Lycopersicon esculentum Mill. cv Rutgers) pericarp to an apparent homogeneity, raised antibodies to the purified protein, and isolated a PME cDNA clone from a lambdagtll expression library constructed from MG pericarp poly(A)(+) RNA. Based on DNA sequencing, the PME cDNA clone isolated in the present study is different from that cloned earlier from cv Ailsa Craig (J Ray et al. [1989] Eur J Biochem 174:119-124). PME antibodies and the cDNA clone are used to determine changes in PME gene expression in developing fruits from normally ripening cv Rutgers and ripening-impaired mutants ripening inhibitor (rin), nonripening (nor), and never ripe (Nr). In Rutgers, PME mRNA is first detected in 15-day-old fruit, reaches a steady-state maximum between 30-day-old fruit and MG stage, and declines thereafter. PME activity is first detectable at day 10 and gradually increases until the turning stage. The increase in PME activity parallels an increase in PME protein; however, the levels of PME protein continue to increase beyond the turning stage while PME activity begins to decline. Patterns of PME gene expression in nor and Nr fruits are similar to the normally ripening cv Rutgers. However, the rin mutation has a considerable effect on PME gene expression in tomato fruits. PME RNA is not detectable in rin fruits older than 45 days and PME activity and protein begin showing a decline at the same time. Even though PME activity levels comparable to 25-day-old fruit were found in root tissue of normal plants, PME protein and mRNA are not detected in vegetative tissues using PME antibodies and cDNA as probes. Our data suggest that PME expression in tomato pericarp is highly regulated during fruit development and that mRNA synthesis and stability, protein stability, and delayed protein synthesis influence the level of PME activity in developing fruits.
The formation and function of extracellular enveloped vaccinia virus (2002)

Vaccinia virus produces four different types of virion from each infected cell called intracellular mature virus (IMV), intracellular enveloped virus (IEV), cell-associated enveloped virus (CEV) and extracellular enveloped virus (EEV). These virions have different abundance, structure, location and roles in the virus life-cycle. Here, the formation and function of these virions are considered with emphasis on the EEV form and its precursors, IEV and CEV. IMV is the most abundant form of virus and is retained in cells until lysis; it is a robust, stable virion and is well suited to transmit infection between hosts. IEV is formed by wrapping of IMV with intracellular membranes, and is an intermediate between IMV and CEV/EEV that enables efficient virus dissemination to the cell surface on microtubules. CEV induces the formation of actin tails that drive CEV particles away from the cell and is important for cell-to-cell spread. Lastly, EEV mediates the long-range dissemination of virus in cell culture and, probably, in vivo. Seven virus-encoded proteins have been identified that are components of IEV, and five of them are present in CEV or EEV. The roles of these proteins in virus morphogenesis and dissemination, and as targets for neutralizing antibody are reviewed. The production of several different virus particles in the VV replication cycle represents a coordinated strategy to exploit cell biology to promote virus spread and to aid virus evasion of antibody and complement.
Amplification and overexpression of the AKT2 oncogene in a subset of human pancreatic ductal adenocarcinomas (1998)

AKT2, an oncogene encoding a protein serine-threonine kinase implicated in phosphatidylinositol-3-OH kinase signaling, is amplified in some human ovarian and pancreatic carcinomas. We previously demonstrated that the tumorigenicity and invasiveness of pancreatic ductal adenocarcinoma (PDAC) cell lines with amplified AKT2 could be markedly reduced by transfection with antisense AKT2 constructs. To evaluate further the extent of AKT2 alterations in PDAC, DNA and immunohistochemical analyses were performed to assess amplification or overexpression of AKT2, respectively, in 72 PDACs. Thirty-five PDACs were subjected to Southern analyses, and AKT2 amplification was detected in seven tumors (20%). Forty-one formalin-fixed PDAC specimens were examined immunohistochemically with an anti-AKT2 monoclonal antibody, and moderate to intense staining was observed in eight tumors (20%). AKT2 immunostaining paralleled AKT2 genomic status in each of four cases in which both Southern and immunohistochemical analyses were performed. No obvious relationship was observed between AKT2 status and tumor TNM stage or grade. These observations suggest the utility of immunohistochemical analysis in assessing alterations of AKT2 in human cancers. Furthermore, the role played by the AKT2 kinase in the signaling pathways of various mitogenic growth factors implicated in the development of pancreatic cancer suggests that alteration of AKT2 may be an important component in the pathogenesis of a substantial subset of PDACs. Mol. Carcinog. 21:81–86, 1998. © 1998 Wiley-Liss, Inc.
Ethylene Suppresses Jasmonate-Induced Gene Expression in Nicotine Biosynthesis (2000)

In Nicotiana sylvestris, a set of nicotine biosynthesis genes were activated by exogenous application of methyl jasmonate, but the activation was effectively suppressed by simultaneous treatment with ethylene. When N. sylvestris transgenic hairy roots were treated with a natural ethylene precursor, the jasmonate-responsive expression of the promoter from a nicotine pathway enzyme gene was completely suppressed, and this suppressive effect was abolished when ethylene perception was blocked with silver cation. These and additional immunoblot results suggest that ethylene signal antagonizes jasmonate signal in nicotine biosynthesis.
ChemInform Abstract: Synthesis and Antiviral Activity of Benzopyran‐2‐one Derivatives. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
TRIMCyp expression in Old World primates Macaca nemestrina and Macaca fascicularis (2008)

Primates have evolved a variety of restriction factors that prevent retroviral replication. One such factor, TRIM5alpha, mediates a postentry restriction in many Old World primates. Among New World primates, Aotus trivirgatus exerts a similar early restriction mediated by TRIMCyp, a TRIM5-cyclophilin A (CypA) chimera resulting from a CypA retrotransposition between exons 7 and 8 of the TRIM5 gene. Macaca nemestrina do not express TRIM5alpha; therefore, we asked whether these animals and related Old World primates express TRIMCyp. RT-PCR of total RNA from M. nemestrina and Macaca fascicularis yielded three TRIMCyp amplification products, one of which is predicted to encode a TRIMCyp chimera containing a full-length CypA. Unlike A. trivirgatus, genomic sequencing of M. nemestrina and M. fascicularis identifies a CypA retrotransposition in the 3' untranslated region of the TRIM5 locus. There is approximately 78% homology between the predicted protein sequences of Old World and New World primate TRIMCyp, with most of the differences found in the TRIM5-derived sequence. Notably, exon 7 is absent from both M. nemestrina and M. fascicularis TRIMCyp. Neither M. nemestrina nor M. fascicularis TRIMCyp could restrict HIV-1 or simian immunodeficiency virus SIVmac in an in vitro infectivity assay. The discovery of TRIMCyp in both M. nemestrina and M. fascicularis indicates that TRIMCyp expression may be more common among Old World primates than previously believed. Convergent evolution of TRIMCyp in both Old World and New World primates suggests that TRIMCyp may have provided evolutionary advantages.
Volitional control of reflex cough (2012)

Multiple studies suggest a role for the cerebral cortex in the generation of reflex cough in awake humans. Reflex cough is preceded by detection of an urge to cough; strokes specifically within the cerebral cortex can affect parameters of reflex cough, and reflex cough can be voluntarily suppressed. However, it is not known to what extent healthy, awake humans can volitionally modulate the cough reflex, aside from suppression. The aims of this study were to determine whether conscious humans can volitionally modify their reflexive cough and, if so, to determine what parameters of the cough waveform and corresponding muscle activity can be modified. Twenty adults (18-40 yr, 4 men) volunteered for study participation and gave verbal and written informed consent. Participants were seated and outfitted with a facemask and pneumotacograph, and two surface EMG electrodes were positioned over expiratory muscles. Capsaicin (200 μM) was delivered via dosimeter and one-way (inspiratory) valve attached to a side port between the facemask and pneumotachograph. Cough airflow and surface EMG activity were recorded across tasks including 1) baseline, 2) small cough (cough smaller or softer than normal), 3) long cough (cough longer or louder than normal), and 4) not cough (alternative behavior). All participants coughed in response to 200 μM capsaicin and were able to modify the cough. Variables exhibiting changes include those related to the peak airflow during the expiratory phase. Results demonstrate that it is possible to volitionally modify cough motor output characteristics.
BENIGN PROSTATIC HYPERPLASIA Nutritional and botanical therapeutic options (1996)

Benign prostatic hyperplasia (BPH, benign prostatic hypertrophy), a non-malignant abnormal growth of the prostate gland, affects almost all men in some degree as they age and can cause a significant disruption of lifestyle due to urinary outflow obstructive and irritative symptoms. An accumulation of estrogen in the aging prostate, along with increased conversion of testosterone to its more active metabolite dihydrotestosterone (DHT) seems to induce this aberrant hyperplasia. Fatty acid deficiencies, zinc deficiency, and amino acid deficiencies may also contribute to the disease process. Numerous studies confirm the mechanisms and efficacy of Serenoa repens, Pygeum africanum, and Urtica dioca in reducing DHT conversion and/or binding to nuclear receptors, and reducing or relieving BPH symptoms. Usage of the amino acids alanine, glycine, and glutamic acid, alone and in combination with the above botanicals, has been proven to be effective at reducing symptomatology and prostate size. Pollen preparations, antifungals, zinc, and essential fatty acid supplementation may also be helpful. (Alt Med Rev 1996;1:18-25)
The Toll-like receptors and their role in septic shock (2003)

The Toll-like receptors (TLRs) are a class of pattern recognition molecules with unique functions in the innate and the acquired immune systems. The innate immune response has evolved as the immediate host defence system in response to foreign structures and it also serves to prime the adaptive immune response. As such, the TLRs set the tone and pace of the inflammatory response that follows initial contact with a microbial pathogen over the course of the following minutes, hours and days. Sepsis, a leading cause of death in critically ill patients worldwide, is defined as 'the systemic inflammatory response syndrome that occurs during infection' [1]; that is, sepsis is the orchestration of the events controlled by the gene products triggered by signals transduced through the TLRs. Through analysis of the human genome, ten TLRs have been identified, and several of them have been characterised with respect to their associated ligands. Following engagement of the cognate ligand to the ectodomain of each TLR, the assembly of intracellular homo- or heterodimers or multimers induces cell signalling. The receptors are variably expressed on different types of cells, such as neutrophils, dendritic cells, lymphocytes, endothelial cells etc. and can be up- and downregulated, blocked or triggered by mimetic substances. By controlling or modifying TLR responses, the trajectory of the entire septic process may be modified. This review covers the events responsible for TLR activation in detail, with an emphasis on possible points of pharmacological intervention.
Low-Energy Laser Irradiation Promotes Cellular Redox Activity (2005)

Low-energy visible light (LEVL) has been shown to stimulate cell functions. This is called "photobiostimulation" and has been used successfully over the last three decades for treating a range of conditions, including soft tissue injuries, severe wounds, chronic pain, and more. Nevertheless, the mechanism of photobiostimulative processes is still being debated. It is obvious that, in order to interact with the living cell, light has to be absorbed by intracellular chromophores. In a search for chromophores responsible for photobiostimulation, endogenous porphyrins, mitochondrial and membranal cytochromes, and flavoproteins were found to be suitable candidates. The above-mentioned chromophores are photosensitizers that generate reactive oxygen species (ROS) following irradiation. As the cellular redox state has a key role in maintaining the viability of the cell, changes in ROS may play a significant role in cell activation. In the present review, we summarize evidence demonstrating that various ROS and antioxidants are produced following LEVL illumination. We found that very little evidence for NO formation in illuminated non-vascular smooth muscle cells exists in the literature. We suggest that the change in the cellular redox state which plays a pivotal role in maintaining cellular activities leads to photobiostimulative processes.
10 W near-diffraction-limited peak pulsed powerfrom Al-free,0.98 µm-emitting phase-locked antiguided arrays (1997)

10 W peak-pulsed power emitted in a beam pattern 2×diffraction limit (DL) is obtained from a 40-element, 200 µm-aperture Al-free phase-locked antiguided array (λ = 0.98 µm). 60% of the power resides in the central lobe, and the external differential quantum efficiency is 54% for 1 mm-long optimised facet-coated devices.
Formulating a fluorogenic assay to evaluate S -adenosyl- L -methionine analogues as protein methyltransferasecofactors (2011)

Protein methyltransferases (PMTs) catalyze arginine and lysine methylation of diverse histone and nonhistone targets. These posttranslational modifications play essential roles in regulating multiple cellular events in an epigenetic manner. In the recent process of defining PMT targets, S-adenosyl-L-methionine (SAM) analogues have emerged as powerful small molecule probes to label and profile PMT targets. To examine efficiently the reactivity of PMTs and their variants on SAM analogues, we transformed a fluorogenic PMT assay into a ready high throughput screening (HTS) format. The reformulated fluorogenic assay is featured by its uncoupled but more robust character with the first step of accumulation of the commonly-shared reaction byproduct S-adenosyl-L-homocysteine (SAH), followed by SAH-hydrolase-mediated fluorogenic quantification. The HTS readiness and robustness of the assay were demonstrated by its excellent Z' values of 0.83-0.95 for the so-far-examined 8 human PMTs with SAM as a cofactor (PRMT1, PRMT3, CARM1, SUV39H2, SET7/9, SET8, G9a and GLP1). The fluorogenic assay was further implemented to screen the PMTs against five SAM analogues (allyl-SAM, propargyl-SAM, (E)-pent-2-en-4-ynyl-SAM (EnYn-SAM), (E)-hex-2-en-5-ynyl-SAM (Hey-SAM) and 4-propargyloxy-but-2-enyl-SAM (Pob-SAM)). Among the examined 8 × 5 pairs of PMTs and SAM analogues, native SUV39H2, G9a and GLP1 showed promiscuous activity on allyl-SAM. In contrast, the bulky SAM analogues, such as EnYn-SAM, Hey-SAM and Pob-SAM, are inert toward the panel of human PMTs. These findings therefore provide the useful structure-activity guidance to further evolve PMTs and SAM analogues for substrate labeling. The current assay format is ready to screen methyltransferase variants on structurally-diverse SAM analogues.
Space–time mapping and tiling: a helpful combination (2004)

Abstract Tiling is a well‐known technique for sequential compiler optimization, as well as for automatic program parallelization. However, in the context of parallelization, tiling should not be considered as a stand‐alone technique, but should be applied after a dedicated parallelization phase, in our case after space–time mapping . We show how tiling can benefit from space–time mapping, and we derive an algorithm for computing tiles which can minimize the number of communication startups, taking the number of physically available processors into account. We also present how the use of a simple cost model reduces real execution time. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Conformational Changes of Fibrinogen after Adsorption (2005)

The adsorption behavior of fibrinogen to two biomedical polyurethanes and a perfluorinated polymer has been investigated. Changes in the secondary structure of adsorbed fibrinogen were monitored using attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and sum frequency generation vibrational spectroscopy (SFG). SFG measurements were performed in the amide I range as well as in the C-H/N-H stretching range. Amide I signals from SFG demonstrate that fibrinogen has post-adsorption conformational changes that are dependent upon the polymer surface properties. For example, strong attenuation of the amide I and N-H stretching signals with increasing residence time was observed for fibrinogen adsorbed to poly(ether urethane) but not for the other two polymers. This change is not readily observed by ATR-FTIR. Differences in the observed spectral changes for fibrinogen adsorbed to each polymer are explained by different initial binding mechanisms and post-adsorption conformational changes.
460. Hydropyrimidines. Part III. Reduction of amino-pyrimidines (1964)

R. F. Evans, J. Chem. Soc., 1964, 2450 DOI: 10.1039/JR9640002450
The role of IL-23 in the immunopathogenesis of psoriasis (2010)

In just 10 years from its discovery in 2000, interleukin-23 has quickly moved from being recognized as a pro-inflammatory cytokine to a key player and potential therapeutic target in psoriasis.
Concordant Modulation of Neutralization Resistance and High Infectivity of the Primary Human Immunodeficiency Virus Type 1 MN Strain and Definition of a Potential gp41 Binding Site in gp120 (2002)

Efforts to develop a vaccine against human immunodeficiency virus type 1 (HIV-1) are complicated by resistance of virus to neutralization. The neutralization resistance phenotype of HIV-1 has been linked to high infectivity. We studied the mechanisms determining this phenotype using clones of the T-cell-line-adapted (TCLA) MN strain (MN-TCLA) and the neutralization-resistant, primary MN strain (MN-P). Mutations in the amino- and carboxy-terminal halves of gp120 and the carboxy terminus of gp41 contributed to the neutralization resistance, high-infectivity phenotype but depended upon sequences in the leucine zipper (LZ) domain of gp41. Among 23 clones constructed to map the contributing mutations, there was a very strong correlation between infectivity and neutralization resistance (R(2) = 0.81; P < 0.0001). Mutations that distinguished the gp120s of MN-P and MN-TCLA clones were clustered in or near the CD4 and coreceptor binding sites and in regions distant from those binding sites. To test the hypothesis that some of these distant mutations may interact with gp41, we determined which of them contributed to high infectivity and whether those mutations modulated gp120-gp41 association in the context of MN-P LZ sequences. In one clone, six mutations in the amino terminus of gp120, at least four of which clustered closely on the inner domain, modulated infectivity. This clone had a gp120-gp41 association phenotype like MN-P: in comparison to MN-TCLA, spontaneous dissociation was low, and dissociation induced by soluble CD4 binding was high. These results identify a region of the gp120 inner domain that may be a binding site for gp41. Our studies clarify mechanisms of primary virus neutralization resistance.
Autoantibodies that bind glomeruli: Cross‐reactivity with bacterial antigen (2005)

This study suggests that both DNA-binding and non-DNA-binding antibodies in SLE may be elicited by the same bacterial antigens.
Chloride Binding Regulates the Schiff Base pK in Gecko P521 Cone-Type Visual Pigment (1999)

The binding of chloride is known to shift the absorption spectrum of most long-wavelength-absorbing cone-type visual pigments roughly 30 nm to the red. We determined that the chloride binding constant for this color shift in the gecko P521 visual pigment is 0.4 mM at pH 6.0. We found an additional effect of chloride on the P521 pigment: the apparent pKa of the Schiff base in P521 is greatly increased as the chloride concentration is increased. The apparent Schiff base pKa shifts from 8.4 for the chloride-free form to >10.4 for the chloride-bound form. We show that this shift is due to chloride binding to the pigment, not to the screening of the membrane surface charges by chloride ions. We also found that at high pH, the absorption maximum of the chloride-free pigment shifts from 495 to 475 nm. We suggest that the chloride-dependent shift of the apparent Schiff base pKa is due to the deprotonation of a residue in the chloride binding site with a pKa of ca. 8.5, roughly that of the Schiff base in the absence of chloride. The deprotonation of this site results in the formation of the 475 nm pigment and a 100-fold decrease in the pigment's ability to bind chloride. Increasing the concentration of chloride results in the stabilization of the protonated state of this residue in the chloride binding site and thus increased chloride binding with an accompanying increase in the Schiff base pK.