gebhart/patrepeval huggingface dataset:
Sensitivity‐encoded (SENSE) proton echo‐planar spectroscopic imaging (PEPSI) in the human brain (2007)

Magnetic resonance spectroscopic imaging (MRSI) provides spatially resolved metabolite information that is invaluable for both neuroscience studies and clinical applications. However, lengthy data acquisition times, which are a result of time-consuming phase encoding, represent a major challenge for MRSI. Fast MRSI pulse sequences that use echo-planar readout gradients, such as proton echo-planar spectroscopic imaging (PEPSI), are capable of fast spectral-spatial encoding and thus enable acceleration of image acquisition times. Combining PEPSI with recent advances in parallel MRI utilizing RF coil arrays can further accelerate MRSI data acquisition. Here we investigate the feasibility of ultrafast spectroscopic imaging at high field (3T and 4T) by combining PEPSI with sensitivity-encoded (SENSE) MRI using eight-channel head coil arrays. We show that the acquisition of single-average SENSE-PEPSI data at a short TE (15 ms) can be accelerated to 32 s or less, depending on the field strength, to obtain metabolic images of choline (Cho), creatine (Cre), N-acetyl-aspartate (NAA), and J-coupled metabolites (e.g., glutamate (Glu) and inositol (Ino)) with acceptable spectral quality and localization. The experimentally measured reductions in signal-to-noise ratio (SNR) and Cramer-Rao lower bounds (CRLBs) of metabolite resonances were well explained by both the g-factor and reduced measurement times. Thus, this technology is a promising means of reducing the scan times of 3D acquisitions and time-resolved 2D measurements.
Modulation of NF-κB Activity and Apoptosis in Chronic Lymphocytic Leukemia B Cells (2000)

Chronic lymphocytic leukemia (CLL) is an indolent malignancy of CD5+ B lymphocytes. CLL cells express CD40, a key regulator of B cell proliferation, differentiation, and survival. In nonmalignant B cells, CD40 ligation results in nuclear translocation and activation of NF-kappaB proteins. Based on observations that in some CLL cases, the tumor cells express both CD40 and its ligand, CD154 (CD40 ligand), we proposed a model for CLL pathogenesis due to CD40 ligation within the tumor. To evaluate this issue, we used freshly isolated CLL B cells to examine constitutive and inducible NF-kappaB activity by electrophoretic mobility shift assay. We consistently observed high levels of nuclear NF-kappaB-binding activity in unstimulated CLL B cells relative to that detected in nonmalignant human B cells. In each case examined, CD40 ligation further augmented NF-kappaB activity and prolonged CLL cell survival in vitro. The principle NF-kappaB proteins in stimulated CLL cells appear to be quite similar to those in nonmalignant human B cells and include p50, p65, and c-Rel. In a CD154-positive case, blocking CD154 engagement by mAb to CD154 resulted in inhibition of NF-kappaB activity in the CLL cells. The addition of anti-CD154 mAb resulted in accelerated CLL cell death to a similar degree as was observed in cells exposed to dexamethasone. These data indicate that CD40 engagement has a profound influence on NF-kappaB activity and survival in CLL B cells, and are consistent with a role for CD154-expressing T and B cells in CLL pathogenesis. The data support the development of novel therapies based on blocking the CD154-CD40 interaction in CLL.
Workload-aware database monitoring and consolidation (2011)

In most enterprises, databases are deployed on dedicated database servers. Often, these servers are underutilized much of the time. For example, in traces from almost 200 production servers from different organizations, we see an average CPU utilization of less than 4%. This unused capacity can be potentially harnessed to consolidate multiple databases on fewer machines, reducing hardware and operational costs. Virtual machine (VM) technology is one popular way to approach this problem. However, as we demonstrate in this paper, VMs fail to adequately support database consolidation, because databases place a unique and challenging set of demands on hardware resources, which are not well-suited to the assumptions made by VM-based consolidation.
Lymphocyte subset and cellular immune responses to a brief experimental stressor. (1992)

To evaluate effects of acute mental stress on aspects of cellular immunity, lymphocyte populations and phytohemagglutinin (PHA)-stimulated T-cell mitogenesis were measured in 33 healthy young men, both before and immediately following subjects' performance of a frustrating, 21-minute laboratory task (Stroop test). Relative to baseline evaluations, post-task measurements showed a significant reduction in mitogenesis and alterations in various circulating lymphocyte populations; the latter included a diminished T-helper/T-suppressor cell ratio and an elevation in the number of natural killer cells. Eleven subjects assigned to a control (unstressed) condition exhibited no changes in lymphocyte populations, but did show an increase in T-cell proliferation, compared with pretask measurements.
Phase I Trial of a Pathotropic Retroviral Vector Expressing a Cytocidal Cyclin G1 Construct (Rexin-G) in Patients With Advanced Pancreatic Cancer (2008)

Rexin-G is a pathotropic retroviral vector displaying a von Willebrand factor-targeting motif and expressing a dominant negative cyclin G1 gene. We undertook a phase I trial of intravenous (i.v.) administration of Rexin-G in patients with gemcitabine refractory, metastatic pancreatic adenocarcinoma. Twelve patients were treated. Dose escalation was performed from a dose of 1 x 10(11) colony forming units (CFU) per cycle to 6 x 10(11) CFU per cycle. The treatment was well tolerated. One dose-limiting toxicity (DLT) at dose level 2 (1.5 x 10(11) CFU per cycle) was observed, consisting of grade 3 transaminitis. There was no detection of replication-competent virus in patients' peripheral blood mononuclear cells (PBMCs) or viral integration in DNA obtained from PBMCs, and no development of neutralizing antibodies. No evidence of antitumor activity was observed. The best objective response was progressive disease in 11 of the 12 study patients, while 1 patient showed radiographically stable disease with clinical deterioration and increase in the CA19.9 tumor marker. Median time to progression was 32 days. The median duration of survival of the study patients was 3.5 months from treatment initiation. Rexin-G is well tolerated in doses up to 6 x 10(11) CFU in patients with recurrent pancreatic cancer, but there was no evidence of clinical antitumor activity.
Tethered ligand agonist peptides. Structural requirements for thrombin receptor activation reveal mechanism of proteolytic unmasking of agonist function. (1992)

The human platelet thrombin receptor is activated when thrombin cleaves its receptor's amino-terminal extension to reveal a new amino terminus that functions as a tethered peptide ligand. Exactly how this "agonist peptide domain" remains cryptic within the uncleaved receptor and becomes functional after receptor cleavage is unknown. In this report we define the structural features of the thrombin receptor's agonist peptide domain important for receptor activation. Studies with mutant thrombin receptors have suggested that agonist peptide domain residues 2-6 contained determinants critical for receptor activation, and the synthetic peptide SFLLR-NH2 representing the 1st 5 amino-terminal residues of the agonist peptide domain was sufficient to specify agonist activity. Acetylating or removing the agonist peptide's amino-terminal ammonium group greatly attenuated agonist activity. Agonist peptide residue Phe2 was vital for agonist function; residues Leu4 and Arg5 individually played less important roles. These structure-function relationships held for both platelet activation and activation of the cloned receptor expressed in transfected mammalian cells. Our studies suggest that structures at the extreme amino terminus of the thrombin receptor's agonist peptide domain, in particular the free ammonium group of Ser1 and the phenyl ring of Phe2, are critical for receptor activation and that the agonist function of this domain is expressed when receptor proteolysis unmasks such determinants. In addition to revealing details of the thrombin receptor's proteolytic triggering mechanism, these studies open avenues to the development of drugs targeting the thrombin receptor and to further definition for the role of the thrombin receptor in cellular regulation.
T-cell antigen receptor (TCR)-α/β heterodimer formation is a prerequisite for association of CD3-ζ2 into functionally competent TCR·CD3 complexes (1989)

In order to study the relationship between assembly, surface expression, and signal transduction of the alpha/beta T-cell antigen receptor-CD3 complex (TCR.CD3), a series of T-cell mutants with a partial block in assembly of the complex was generated. By chemical mutagenesis, we produced somatic cell variants of the human T-leukemia cell line, HPB-ALL, which expressed low amounts of TCR.CD3 complexes on their surface. RNA and protein analyses demonstrated that most variants synthesized normal amounts of the individual members of the complex, i.e. TCR-alpha, TCR-beta, CD3-gamma, -delta, -epsilon, and -zeta. In these variants, less than 10% of the TCR.CD3 complexes inside the cell contained the CD3-zeta 2 homodimer due to an intrinsic deficiency in the formation of the TCR-alpha/beta heterodimer. The low level of assembly of CD3-zeta 2 into the TCR.CD3 complex and an additional decrease in the rate of export of the TCR.CD3 complex from the endoplasmic reticulum explained the low level of expression of alpha/beta receptors on the surface of these mutants. Only cells with the complete set of subunits of the TCR.CD3 complex on their surface were capable of transducing CD3-mediated signals. The results presented in this paper indicate that TCR-alpha/beta heterodimer formation is an obligatory requirement for assemblage of CD3-zeta 2 into a functionally competent TCR.CD3 complex.
Recursive Recurrent Nets with Attention Modeling for OCR in the Wild (2016)

We present recursive recurrent neural networks with attention modeling (R2AM) for lexicon-free optical character recognition in natural scene images. The primary advantages of the proposed method are: (1) use of recursive convolutional neural networks (CNNs), which allow for parametrically efficient and effective image feature extraction, (2) an implicitly learned character-level language model, embodied in a recurrent neural network which avoids the need to use N-grams, and (3) the use of a soft-attention mechanism, allowing the model to selectively exploit image features in a coordinated way, and allowing for end-to-end training within a standard backpropagation framework. We validate our method with state-of-the-art performance on challenging benchmark datasets: Street View Text, IIIT5k, ICDAR and Synth90k.
Saponin and sapogenol. XXXV. Chemical constituents of astragali radix, the root of Astragalus membranaceus Bunge. (2). Astragalosides I,II and IV, acetylastragaloside I and isoastragalosides I and II. (1983)

Twelve triterpene-oligoglycosides were isolated from the glycosidic constituents of Astragali Radix, the root of Korean Astragalus membranaceus BUNGE. (Leguminosae). They were acetylastragaloside I (3), isoastragalosides I (5) and II (7), astragalosides I (4, major), II (6), III, IV (8), V, VI and VII, which contain a 9, 19-cyclolanostane cycloastragenol (1) as the aglycone, and astragaloside VIII and soyasaponin I (9), which possess an oleanene-type aglycone, soyasapogenol B. By means of chemical degradations, which included a selective cleavage method for the glucuronide linkage, and 13C-NMR examinations, the structure of astragaloside IV was elucidated as 3-O-β-D-xylopyranosyl-6-O-β-D-glucopyranosylcycloastragenol (8). In addition, the structures of five acetyl derivatives of 8 : acetylastragaloside I, astragaloside I, isoastragaloside I, astragaloside II and isoastragaloside II, were elucidated as 3-O-β-(2', 3', 4'-tri-O-acetyl)-D-xylopyranosyl- (3), 3-O-β-(2', 3'-di-O-acetyl)-D-xylopyranosyl- (4), 3-O-β-(2', 4'-di-O-acetyl)-D-xylopyranosyl- (5), 3-O-β-(2'-O-acetyl)-D-xylopyranosyl- (6) and 3-O-β-(3'-O-acetyl)-D-xylopyranosyl-6-O-β-D-glucopyranosylcycloastragenol (7), respectively.
Identification of extractable growth factors from small intestinal submucosa (1997)

When implanted as a biomaterial for tissue replacement, selected submucosal layers of porcine small intestine induce site-specific tissue remodeling. Small intestinal submucosa (SIS), as isolated, is primarily an acellular extracellular matrix material. In an attempt to discover the components of small intestinal submucosa which are able to induce this tissue remodeling, the material was extracted and extracts were tested for the ability to stimulate Swiss 3T3 fibroblasts to synthesize DNA and proliferate. Each of the four different extracts of small intestinal submucosa had measurable cell-stimulating activity when analyzed in both a whole cell proliferation assay (alamarBlue dye reduction) and a DNA synthesis assay ([3H]-thymidine incorporation). Proteins extracted from SIS with 2 M urea induced activity profiles in the two assays which were very similar to the activity profiles of basic fibroblast growth factor (FGF-2) in the assays. As well, the changes in cell morphology in response to the extracted proteins mimicked the changes induced by FGF-2. Neutralization experiments with specific antibodies to this growth factor confirmed the presence of FGF-2 and indicated that it was responsible for 60% of the fibroblast-stimulating activity of the urea extract of small intestinal submucosa. Western blot analysis with a monoclonal antibody specific for FGF-2 detected a reactive doublet at approximately 19 kDa and further confirmed the presence of FGF-2. Cell stimulating activity of proteins extracted from SIS with 4 M guanidine was neutralized by an antibody specific for transforming growth factor beta (TGF beta). Changes in the morphology of the fibroblasts exposed to this extract were nearly identical to changes induced by TGF beta. Although no reactive protein band was detected at 25 kDa in nonreduced western blot analysis, several bands were reactive at higher molecular weight. The identity of this TGF beta-related component of small intestinal submucosa is unknown. Identification of FGF-2 and TGF beta-related activities in SIS, two growth factors known to significantly affect critical processes of tissue development and differentiation, provides the opportunity to further elucidate the mechanisms by which this extracellular matrix biomaterial modulates wound healing and tissue remodeling.
Epigenetic Down-Regulation of ARF Expression Is a Selection Step in Immortalization of Human Fibroblasts by c-Myc (2007)

The transcription factor c-Myc is implicated in the pathogenesis of many cancers. Among the multiple functions of c-Myc, activation of hTert and other genes involved in cellular life span contributes to its role as an oncogene. However, the ability of c-Myc to directly immortalize human cells remains controversial. We show here that overexpression of c-Myc reproducibly immortalizes freshly isolated human foreskin fibroblasts. c-Myc-immortalized cells displayed no gross karyotypic abnormalities but consisted of an oligoclonal population, suggesting that additional events cooperated to achieve immortalization. Levels of p53 and p16 were increased, but both p53-dependent DNA damage response and growth arrest in response to p16 overexpression remained intact. A marked decrease in expression of the tumor suppressor ARF occurred in several independently established c-Myc-immortalized cell lines. Methylation-specific PCR showed that the ARF gene was methylated in immortalized but not early-passage c-Myc cells, whereas p16 was unmethylated in both cell populations. Restoration of ARF expression by treatment with a demethylating agent or overexpression by a retroviral vector coincided with inhibition of proliferation and senescence of c-Myc-immortalized cells. Our findings predict that epigenetic events play a significant role in human tumors that express high levels of c-Myc.
Vaginal administration of estradiol: effects of dose, preparation and timing on plasma estradiol levels (2014)

Low-dose vaginal estrogen appears to be an effective strategy for managing women whose symptoms result from vulvovaginal atrophy. These regimens limit but do not completely eliminate systemic absorption. Low-doses regimens should be preferred clinically to intermediate- or high-dose methods.
<title>Four-channel multimode wavelength-division-demultiplexer (WDM) system based on surface-normal volume holographic gratings and substrate-guided waves</title> (1998)

We demonstrate a four channel integrated wavelength division multiplexer (WDM) and demultiplexer (WDDM) based on volume holographic gratings and substrate-guided waves at near IR wavelengths. The four operating wavelengths are centered at 750, 780, 810 and 840 nm respectively. The WDM and WDDM are demonstrated using 50/125 multimode fibers. The channel-to- channel crosstalk level is measured to be less than -40 dB. The system insertion losses are -23 dB, -21 dB, -20 dB, -22 dB respectively for 750 nm, 780 nm, 810 nm and 840 nm.
Unipolar Signal Modification as a Guide for Lesion Creation During Radiofrequency Application in the Left Atrium (2013)

Unipolar signal modification is a useful end point for radiofrequency energy delivery in patients with paroxysmal atrial fibrillation who undergo PVI and leads to a substantial midterm sinus rhythm maintenance rate.
Discovery of Ubiquinones-1, -2, -3, and -4 and the Nature of Biosynthetic Isoprenylation* (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiscovery of Ubiquinones-1, -2, -3, and -4 and the Nature of Biosynthetic Isoprenylation*G. Doyle Daves, Jr., R. F. Muraca, J. S. Whittick, Palle Friis, and Karl FolkersCite this: Biochemistry 1967, 6, 9, 2861–2866Publication Date (Print):September 1, 1967Publication History Published online1 May 2002Published inissue 1 September 1967https://pubs.acs.org/doi/10.1021/bi00861a029https://doi.org/10.1021/bi00861a029research-articleACS PublicationsRequest reuse permissionsArticle Views56Altmetric-Citations36LEARN 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
ADP-Glucose Pyrophosphorylase-Deficient Pea Embryos Reveal Specific Transcriptional and Metabolic Changes of Carbon-Nitrogen Metabolism and Stress Responses (2008)

We present a comprehensive analysis of ADP-glucose pyrophosphorylase (AGP)-repressed pea (Pisum sativum) seeds using transcript and metabolite profiling to monitor the effects that reduced carbon flow into starch has on carbon-nitrogen metabolism and related pathways. Changed patterns of transcripts and metabolites suggest that AGP repression causes sugar accumulation and stimulates carbohydrate oxidation via glycolysis, tricarboxylic acid cycle, and mitochondrial respiration. Enhanced provision of precursors such as acetyl-coenzyme A and organic acids apparently support other pathways and activate amino acid and storage protein biosynthesis as well as pathways fed by cytosolic acetyl-coenzyme A, such as cysteine biosynthesis and fatty acid elongation/metabolism. As a consequence, the resulting higher nitrogen (N) demand depletes transient N storage pools, specifically asparagine and arginine, and leads to N limitation. Moreover, increased sugar accumulation appears to stimulate cytokinin-mediated cell proliferation pathways. In addition, the deregulation of starch biosynthesis resulted in indirect changes, such as increased mitochondrial metabolism and osmotic stress. The combined effect of these changes is an enhanced generation of reactive oxygen species coupled with an up-regulation of energy-dissipating, reactive oxygen species protection, and defense genes. Transcriptional activation of mitogen-activated protein kinase pathways and oxylipin synthesis indicates an additional activation of stress signaling pathways. AGP-repressed embryos contain higher levels of jasmonate derivatives; however, this increase is preferentially in nonactive forms. The results suggest that, although metabolic/osmotic alterations in iAGP pea seeds result in multiple stress responses, pea seeds have effective mechanisms to circumvent stress signaling under conditions in which excessive stress responses and/or cellular damage could prematurely initiate senescence or apoptosis.
Identification of Novel Extracellular Signal-Regulated Kinase Docking Domain Inhibitors (2005)

The extracellular signal regulated kinase (ERK1 and ERK2) signal transduction pathways play a critical role in cell proliferation. Hyperactivation of the ERK proteins either through increased expression of membrane-bound growth factor receptors or genetic mutations of upstream proteins is thought to be involved in the pathogenesis of many human cancers. Thus, targeted inhibition of ERK signaling is viewed as a potential approach to prevent cancer cell proliferation. Currently, no specific inhibitors of the ERK proteins exist. Moreover, most kinase inhibitors lack specificity because they target the ATP binding region, which is well conserved among the protein kinase families. Taking advantage of recently identified ERK docking domains, which are reported to facilitate substrate protein interactions, we have used computer-aided drug design (CADD) to identify novel small molecular weight ERK inhibitors. Following a CADD screen of over 800 000 molecules, 80 potential compounds were selected and tested for activity in biological assays. Several compounds inhibited ERK-specific phosphorylation of ribosomal S6 kinase-1 (Rsk-1) or the ternary complex factor Elk-1 (TCF/Elk-1), both of which are involved in promoting cell proliferation. Active compounds showed a dose-dependent reduction in the proliferation of several cancer cell lines as measured by colony survival assays. Direct binding between the active compounds and ERK2 was indicated by fluorescence quenching. These active compounds may serve as lead candidates for development of novel specific inhibitors of ERK-substrate interactions involved in cell proliferation.