gebhart/patrepeval huggingface dataset:
A novel aspect of calpain activation (1998)

Calpain, a Ca2+-dependent biomodulator, alters the properties of substrate proteins by cleaving them at a limited number of specific sites. Recent studies of the structure-function relationship of calpain and X-ray analysis of its Ca2+-binding domain have revealed hitherto unknown features of the regulation of calpain activity. A novel dissociation/autolysis mechanism for the activation of calpain at the membrane is proposed, which incorporates recent findings from structure-function studies of calpain, and its implications are discussed.
Improving Referring Expression Grounding with Cross-modal Attention-guided Erasing (2019)

Referring expression grounding aims at locating certain objects or persons in an image with a referring expression, where the key challenge is to comprehend and align various types of information from visual and textual domain, such as visual attributes, location and interactions with surrounding regions. Although the attention mechanism has been successfully applied for cross-modal alignments, previous attention models focus on only the most dominant features of both modalities, and neglect the fact that there could be multiple comprehensive textual-visual correspondences between images and referring expressions. To tackle this issue, we design a novel cross-modal attention-guided erasing approach, where we discard the most dominant information from either textual or visual domains to generate difficult training samples online, and to drive the model to discover complementary textual-visual correspondences. Extensive experiments demonstrate the effectiveness of our proposed method, which achieves state-of-the-art performance on three referring expression grounding datasets.
D-amino acid aminotransferase of Bacillus sphaericus. Enzymologic and spectrometric properties. (1975)

D-Amino acid aminotransferase, purified to homogeneity and crystallized from Bacillus sphaericus, has a molecular weight of about 60,000 and consists of two subunits identical in molecular weight (30,000). The enzyme exhibits absorption maxima at 280, 330, and 415 nm, which are independent of the pH (5.5 to 10.0), and contains 2 mol of pyridoxal 5'-phosphate per mol of enzyme. One of the pyridoxal-5'-P, absorbing at 415 nm, is bound in an aldimine linkage to the epsilon-amino group of a lysine residue of the protein, and is released by incubation with phenylhydrazine to yield the catalytically inactive form. The inactive form, which is reactivated by addition of pyridoxal 5'phosphate, still has a 330 nm peak and contains 1 mol of pyridoxal 5'-phosphate. Therefore, this form is regarded as a semiapoenzyme. The holoenzyme shows negative circular dichroic bands at 330 and 415 nm. D-Amino acid aminotransferase catalyzes alpha transamination of various D-amino acids and alpha-keto acids. D-Alanine, D-alpha-aminobutyrate and D-glutamate, and alpha-ketoglutarate, pyruvate, and alpha-ketobutyrate are the preferred amino donors and acceptors, respectively. The enzyme activity is significantly affected by both the carbonyl and sulfhydryl reagents. The Michaelis constants are as follows: D-alanine (1.3 and 4.2 mM with alpha-ketobutyrate and alpha-ketoglutarate, respictively), alpha-ketobutyrate (14 mM withD-alanine), alpha-ketoglutarate (3.4 mM with D-alanine), pyridoxal 5'-phosphate (2.3 muM) and pyridoxamine 5'-phosphate (25 muM).
Molecular Cloning and Disease Association of Hepatitis G Virus: A Transfusion-Transmissible Agent (1996)

An RNA virus, designated hepatitis G virus (HGV), was identified from the plasma of a patient with chronic hepatitis. Extension from an immunoreactive complementary DNA clone yielded the entire genome (9392 nucleotides) encoding a polyprotein of 2873 amino acids. The virus is closely related to GB virus C (GBV-C) and distantly related to hepatitis C virus, GBV-A, and GBV-B. HGV was associated with acute and chronic hepatitis. Persistent viremia was detected for up to 9 years in patients with hepatitis. The virus is transfusion-transmissible. It has a global distribution and is present within the volunteer blood donor population in the United States.
Pressure-induced gastric accommodation studied with a new distension paradigm. Abnormally low accommodation rate in patients with functional dyspepsia (2005)

This new barostat paradigm allowed detailed analysis of short-term pressure-induced accommodation in man. Impaired gastric distension-induced accommodation is a novel abnormality in FD.
Consistency Analysis and Improvement of Vision-aided Inertial Navigation (2013)

In this paper, we study estimator inconsistency in vision-aided inertial navigation systems (VINS) from the standpoint of system's observability. We postulate that a leading cause of inconsistency is the gain of spurious information along unobservable directions, which results in smaller uncertainties, larger estimation errors, and divergence. We develop an observability constrained VINS (OC-VINS), which explicitly enforces the unobservable directions of the system, hence preventing spurious information gain and reducing inconsistency. This framework is applicable to several variants of the VINS problem such as visual simultaneous localization and mapping (V-SLAM), as well as visual-inertial odometry using the multi-state constraint Kalman filter (MSC-KF). Our analysis, along with the proposed method to reduce inconsistency, are extensively validated with simulation trials and real-world experimentation.
The Sensor Fish: Measuring Fish Passage in Severe Hydraulic Conditions (2003)

This article describes PNNL's efforts to develop the Sensor Fish, a waterproof sensor package that travels thru the turbines of spillways of hydroelectric dam to collect pressure and acceleration data on the conditions experienced by live salmon smolts during dam passage. Sensor Fish development is sponsored by the DOE Advanced Hydropower Turbine Survival Program. The article also gave two recent examples of Sensor Fish use: turbine passage at a McNary Kaplan turbine and spill passage in topspill at Rock Island Dam.
Renal nerves in the pathogenesis of hypertension in experimental animals and humans (1983)

Efferent renal innervation is composed of postganglionic sympathetic fibers to the renal arterioles, juxtaglomerular apparatus, and renal tubules. Increased efferent renal sympathetic nerve activity results in increased renal vascular resistance, renin release, and sodium retention. These responses from enhanced renal sympathetic activity contribute to normal cardiovascular homeostasis but could also facilitate the development of hypertension by shifting the arterial pressure-renal sodium excretion curve to the right. Accordingly, interruption of the renal nerves should prevent the development of hypertension in animal models in which increased sympathetic nervous system activity has been implicated. Renal denervation delays the development of hypertension and results in greater sodium excretion in the Okamoto and New Zealand spontaneously hypertensive rat and in the DOCA-salt-treated rat, suggesting that these responses are due, at least in part, to loss of efferent renal nerve activity. Similar sympathetically mediated renal vasoconstriction has been implicated in the pathogenesis of early essential hypertension in man. Recent studies indicate that the kidney is a sensory organ with mechano-receptive and chemoreceptive afferent renal nerves involved in renorenal and cardiovascular regulation. Renal denervation in established one-kidney one-clip and two-kidney one-clip Goldblatt hypertension in the rat and chronic coarctation in the dog results in an attenuation of the hypertension. The depressor effect of renal denervation in these models is not due to change in renin activity or sodium excretion but is associated with decreased activity of the sympathetic nervous system. These findings suggest that the afferent renal nerves contribute to the pathogenesis of renovascular hypertension by enhancing the activity of the sympathetic nervous system. The role of the afferent renal nerves in renovascular hypertension in humans warrants further study.
Acid-catalyzed cracking of paraffinic hydrocarbons. 3. Evidence for the protonated cyclopropane mechanism from hydrocracking/hydroisomerization experiments (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAcid-catalyzed cracking of paraffinic hydrocarbons. 3. Evidence for the protonated cyclopropane mechanism from hydrocracking/hydroisomerization experimentsS. Tiong SieCite this: Ind. Eng. Chem. Res. 1993, 32, 3, 403–408Publication Date (Print):March 1, 1993Publication History Published online1 May 2002Published inissue 1 March 1993https://pubs.acs.org/doi/10.1021/ie00015a002https://doi.org/10.1021/ie00015a002research-articleACS PublicationsRequest reuse permissionsArticle Views806Altmetric-Citations83LEARN 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
The effect of 3D widget representation and simulated surface constraints on interaction in virtual environments (2002)

The paper reports empirical results from two studies of effective user interaction in immersive virtual environments. The use of 2D interaction techniques in 3D environments has received increased attention recently. We introduce two new concepts to the previous techniques: the use of 3D widget representations; and the imposition of simulated surface constraints. The studies were identical in terms of treatments, but differed in the tasks performed by subjects. In both studies, we compared the use of two-dimensional (2D) versus three-dimensional (3D) interface widget representations, as well as the effect of imposing simulated surface constraints on precise manipulation tasks. The first study entailed a drag-and-drop task, while the second study looked at a slider-bar task. We empirically show that using 3D widget representations can have mixed results on user performance. Furthermore, we show that simulated surface constraints can improve user performance on typical interaction tasks in the absence of a physical manipulation surface. Finally, based on these results, we make some recommendations to aid interface designers in constructing effective interfaces for virtual environments.
Postinfarct Cytokine Therapy Regenerates Cardiac Tissue and Improves Left Ventricular Function (2006)

We systematically investigated the comparative efficacy of three different cytokine regimens, administered after a reperfused myocardial infarction, in regenerating cardiac tissue and improving left ventricular (LV) function. Wild-type (WT) mice underwent a 30-minute coronary occlusion followed by reperfusion and received vehicle, granulocyte colony-stimulating factor (G-CSF)+Flt-3 ligand (FL), G-CSF+stem cell factor (SCF), or G-CSF alone starting 4 hours after reperfusion. In separate experiments, chimeric mice generated by reconstitution of radioablated WT mice with bone marrow from enhanced green fluorescent protein (EGFP) transgenic mice underwent identical protocols. Mice were euthanized 5 weeks later. Echocardiographically, LV function was improved in G-CSF+FL- and G-CSF+SCF-treated but not in G-CSF-treated mice, whereas LV end-diastolic dimensions were smaller in all three groups. Morphometrically, cytokine-treated hearts had smaller LV diameter and volume. Numerous EGFP-positive cardiomyocytes, capillaries, and arterioles were noted in the infarcted region in cytokine-treated chimeric mice treated with G-CSF+FL or G-CSF+SCF, but the numbers were much smaller in G-CSF-treated mice. G-CSF+FL therapy mobilized bone marrow-derived cells exhibiting increased expression of surface antigens (CD62L and CD11a) that facilitate homing. We conclude that postinfarct cytokine therapy with G-CSF+FL or G-CSF+SCF limits adverse LV remodeling and improves LV performance by promoting cardiac regeneration and probably also by exerting other beneficial actions unrelated to regeneration, and that G-CSF alone is less effective.
Biomarkers of Lung Inflammation in Recreational Joggers Exposed to Ozone (1996)

Humans exhibit an acute inflammatory response in the lungs after controlled laboratory exposure to ozone. The present study was designed to test whether biomarkers of inflammation are detectable in humans exposed to ozone and associated copollutants under natural conditions outdoors. Bronchoscopy with bronchoalveolar lavage (BAL) was carried out on 19 normal volunteer joggers from Governors Island, NY, who exercised in the afternoon during the 1992 summer (S1) season. Fifteen subjects were retested during the following, low ozone, winter season (W). The BAL protocol involved an initial instillation of 20 ml saline followed by four sequential 50-ml saline washes carried out in both the right middle lobe and the lingula. The eight 50-ml samples were pooled as the 'alveolar' sample. Analyses performed on the alveolar lavage samples included cell differentials, release of IL-8, TNF-alpha, and reactive oxygen species (ROS) by pooled cells, and levels of IL-8, protein, LDH, fibronectin, alpha1-antitrypsin (alpha1-AT), complement fragment 3a (C3a), and prostaglandin E2 (PGE2) in lavage fluids. Release of ROS by stimulated BAL cells was lower in S1 than in W (p = 0.03). In contrast, LDH levels in BAL fluids were 2-fold higher in S1 than in W (p = 0.02), as were IL-8 (p = 0.12) and PGE2 (p = 0.06). These results suggest a possible ongoing inflammatory response in the lungs of recreational joggers exposed to ozone and associated copollutants during the summer months.
Characterization of a functional NF-kappa B site in the human interleukin 1 beta promoter: evidence for a positive autoregulatory loop. (1993)

The -300 region of the interleukin 1 beta (IL-1 beta) promoter contains a functional NF-kappa B binding site composed of the decamer sequence 5'-GGGAAAATCC-3'. Probes representing the -300 region or the NF-kappa B site alone interacted with NF-kappa B proteins present in phorbol myristate acetate-, lipopolysaccharide-, or Sendai virus-induced myeloid cell extracts as well as recombinant NFKB1 (p50) and RelA (p65); furthermore, NF-kappa B protein-DNA complex formation was dissociated in vitro by the addition of recombinant I kappa B alpha. Mutation of the NF-kappa B site in the context of the IL-1 beta promoter reduced the responsiveness of the IL-1 beta promoter to various inducers, including phorbol ester, Sendai virus, poly(rI-rC), and IL-1 beta. A 4.4-kb IL-1 beta promoter fragment linked to a chloramphenicol acetyltransferase reporter gene was also preferentially inducible by coexpression of individual NF-kappa B subunits compared with a mutated IL-1 beta promoter fragment. When multiple copies of the IL-1 beta NF-kappa B site were linked to an enhancerless simian virus 40 promoter, this element was able to mediate phorbol ester- or lipopolysaccharide-inducible gene expression. In cotransfection experiments, RelA (p65) and c-Rel (p85) were identified as the main subunits responsible for the activation of the IL-1 beta NF-kappa B site; also, combinations of NFKB1 (p50) and RelA (p65) or c-Rel and RelA were strong transcriptional activators of reporter gene activity. The presence of a functional NF-kappa B binding site in the IL-1 beta promoter suggests that IL-1 positively autoregulates its own synthesis, since IL-1 is a strong inducer of NF-kappa B binding activity. Thus, the IL-1 beta gene may be considered as an important additional member of the family of cytokine genes regulated in part by the NF-kappa B/rel family of transcription factors.
Genome sequence surveys of Brachiola algerae and Edhazardia aedis reveal microsporidia with low gene densities (2008)

Our results demonstrate that microsporidian genome architecture varies greatly between microsporidia. Much of the genome size difference could be accounted for by non-coding material, such as intergenic spaces and retrotransposons, and this suggests that the forces dictating genome size may vary across the phylum.
Molecular analysis of the methylprednisolone-mediated inhibition of NK-cell function: evidence for different susceptibility of IL-2– versus IL-15–activated NK cells (2007)

Steroids have been shown to inhibit the function of fresh or IL-2-activated natural killer (NK) cells. Since IL-15 plays a key role in NK-cell development and function, we comparatively analyzed the effects of methylprednisolone on IL-2- or IL-15-cultured NK cells. Methylprednisolone inhibited the surface expression of the major activating receptors NKp30 and NKp44 in both conditions, whereas NK-cell proliferation and survival were sharply impaired only in IL-2-cultured NK cells. Accordingly, methylprednisolone inhibited Tyr phosphorylation of STAT1, STAT3, and STAT5 in IL-2-cultured NK cells but only marginally in IL-15-cultured NK cells, whereas JAK3 was inhibited under both conditions. Also, the NK cytotoxicity was similarly impaired in IL-2- or IL-15-cultured NK cells. This effect strictly correlated with the inhibition of ERK1/2 Tyr phosphorylation, perforin release, and cytotoxicity in a redirected killing assay against the FcRgamma(+) P815 target cells upon cross-linking of NKp46, NKG2D, or 2B4 receptors. In contrast, in the case of CD16, inhibition of ERK1/2 Tyr phosphorylation, perforin release, and cytotoxicity were not impaired. Our study suggests a different ability of IL-15-cultured NK cells to survive to steroid treatment, thus offering interesting clues for a correct NK-cell cytokine conditioning in adoptive immunotherapy.
Modulation of natural killer cell antitumor activity by the aryl hydrocarbon receptor (2013)

The aryl hydrocarbon receptor (AhR) has become increasingly recognized for its role in the differentiation and activity of immune cell subsets; however, its role in regulating the activity of natural killer (NK) cells has not been described. Here, we show that AhR expression is induced in murine NK cells upon cytokine stimulation. We show that in the absence of AhR, NK cells have reduced cytolytic activity and reduced capacity to control RMA-S tumor formation in vivo, despite having normal development and maturation markers. Although AhR was first identified to bind the xenobiotic compound dioxin, AhR is now known to bind a variety of natural exogenous (e.g., dietary) and endogenous ligands. We show that activation of AhR with an endogenous tryptophan derivative, 6-formylindolo[3,2-b]carbazole, potentiates NK cell IFN-γ production and cytolytic activity. Further, administration of 6-formylindolo[3,2-b]carbazole in vivo enhances NK cell control of tumors in an NK cell- and AhR-dependent manner. Finally, similar effects on NK cell potency occur with AhR dietary ligands, potentially explaining the numerous associations that have been observed in the past between diet and NK cell function. Our studies introduce AhR as another regulator of NK cell activity in vivo.
Specificity of G protein beta and gamma subunit interactions. (1992)

Multiple heterotrimeric guanine nucleotide binding protein (G protein) subunits have evolved to couple a large variety of receptors to intracellular effectors. G protein beta gamma subunits are essential for efficient coupling of alpha subunits to receptors, and they are also important for modulation of effectors. Several different beta and gamma subunits exist, but it is not known whether all possible combinations of beta and gamma can form functional dimers. To answer this question, we have compared the ability of in vitro translated beta 1, beta 2, and beta 3 to form dimers with either gamma 1 or gamma 2. Dimerization was monitored by gel filtration, resistance to tryptic digestion, and chemical cross-linking. The results indicate that beta 1 binds both gamma subunits, beta 2 binds only gamma 2, and beta 3 will bind neither gamma 1 or gamma 2. Hence, the occurrence of beta gamma dimers may be partially regulated by the ability of the subunits to associate. Specificity of dimerization might allow cells to co-express multiple beta and gamma subunits while maintaining efficient and specific signal transduction.
Fas and its ligand in a general mechanism of T-cell-mediated cytotoxicity. (1994)

To investigate the mechanisms of T-cell-mediated cytotoxicity, we estimated the involvement of apoptosis-inducing Fas molecule on the target cells and its ligand on the effector cells. When redirected by ConA or anti-CD3 monoclonal antibody, a CD4+ T-cell clone, BK1, could lyse the target cells expressing wild-type Fas molecule but not those expressing death signaling-deficient mutants. This indicates the involvement of Fas-mediated signal transduction in the target cell lysis by BK1. Anti-CD3-activated but not resting BK1 expressed Fas ligand as detected by binding of a soluble Fas-Ig fusion protein, and the BK1-mediated cytotoxicity was blocked by the addition of Fas-Ig, implicating the inducible Fas ligand in the BK1 cytotoxicity. Ability to exert the Fas-mediated cytotoxicity was not confined to BK1, but splenic CD4+ T cells and, to a lesser extent, CD8+ T cells could also exert the Fas-dependent target cell lysis. This indicates that the Fas-mediated target cell lytic pathway can be generally involved in the T-cell-mediated cytotoxicity. Interestingly, CD4+ T cells prepared from gld/gld mice did not mediate the Fas-mediated cytotoxicity, indicating defective expression of functional Fas ligand in gld mice.
Epigenetic targets in hematological malignancies: combination therapies with HDACis and demethylating agents (2007)

Chromatin modeling in DNA is fundamental to gene expression, DNA repair and replication. Methylation of promoter regions of tumor-suppressor genes and histone deacetylation leads to gene silencing and transcriptionally repressive chromatin. Histone deacetylase inhibitors and hypomethylating agents allow upregulation of proapoptotic genes and downregulation of antiapoptotic genes, and show significant single-agent anticancer activity, predominantly in cutaneous T-cell lymphoma and myelodysplasia, respectively. Combinations of these drugs are being employed in clinical trials to target multiple biological pathways, with the hope of synergistic pharmacodynamics. Preclinical studies of combinations of these agents with chemotherapy, monoclonal antibodies and small-molecule inhibitors are ongoing and demonstrate synergy in multiple hematological cancers, raising the prospect of future treatment for these diseases having a multitargeted approach.