gebhart/patrepeval huggingface dataset:
Targeted disruption of p70<sup>s6k</sup>defines its role in protein synthesis and rapamycin sensitivity (1998)

Here, we disrupted the p70 S6 kinase (p70(s6k)) gene in murine embryonic stem cells to determine the role of this kinase in cell growth, protein synthesis, and rapamycin sensitivity. p70(s6k-/-) cells proliferated at a slower rate than parental cells, suggesting that p70(s6k) has a positive influence on cell proliferation but is not essential. In addition, rapamycin inhibited proliferation of p70(s6k-/-) cells, indicating that other events inhibited by the drug, independent of p70(s6k), also are important for both cell proliferation and the action of rapamycin. In p70(s6k-/-) cells, which exhibited no ribosomal S6 phosphorylation, translation of mRNA encoding ribosomal proteins was not increased by serum nor specifically inhibited by rapamycin. In contrast, rapamycin inhibited phosphorylation of initiation factor 4E-binding protein 1 (4E-BP1), general mRNA translation, and overall protein synthesis in p70(s6k-/-) cells, indicating that these events proceed independently of p70(s6k) activity. This study localizes the function of p70(s6k) to ribosomal biogenesis by regulating ribosomal protein synthesis at the level of mRNA translation.
Digital computer arithmetic : design and implementation (1984)

Digital computer arithmetic: design and implementation , Digital computer arithmetic: design and implementation , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Fructose prevents hypoxic cell death in liver (1987)

Perfusion of livers from fasted rats with nitrogen-saturated buffer caused hepatocellular damage within 30 min. Lactate dehydrogenase (LDH) was released at maximal rates of approximately 300 U . g-1 . h-1 under these conditions, and virtually all cells in periportal and pericentral regions of the liver lobule were stained with trypan blue. Infusion of glucose, xylitol, sorbitol, or mannitol (20 mM) did not appreciably change the time course or extent of damage due to perfusion with nitrogen-saturated perfusate. However, fructose (20 mM) completely prevented damage assessed by LDH release, trypan blue uptake, and ultrastructural changes for at least 2 h of perfusion. Neither glucose, xylitol, sorbitol, nor mannitol (20 mM) increased lactate formation above basal levels during hypoxia. On the other hand, fructose (0.4-20 mM) caused a concentration-dependent increase in lactate formation that reached maximal rates of approximately 180 mumol . g-1 . h-1. The dose-dependent increase in glycolytic lactate production from fructose correlated well with cellular protection reflected by decreases in LDH release. ATP:ADP ratios were also increased from 0.4 to 1.8 in a dose-dependent manner by fructose. The results indicate that fructose protects the liver against hypoxic cell death by the glycolytic production of ATP in the absence of oxygen.
Exploiting Quasiperiodicity in Motion Correction of Free-Breathing Myocardial Perfusion MRI (2010)

Free-breathing image acquisition is desirable in first-pass gadolinium- enhanced magnetic resonance imaging (MRI), but the breathing movements hinder the direct automatic analysis of the myocardial perfusion and qualitative readout by visual tracking. Nonrigid registration can be used to compensate for these movements but needs to deal with local contrast and intensity changes with time. We propose an automatic registration scheme that exploits the quasiperiodicity of free breathing to decouple movement from intensity change. First, we identify and register a subset of the images corresponding to the same phase of the breathing cycle. This registration step deals with small differences caused by movement but maintains the full range of intensity change. The remaining images are then registered to synthetic references that are created as a linear combination of images belonging to the already registered subset. Because of the quasiperiodic respiratory movement, the subset images are distributed evenly over time and, therefore, the synthetic references exhibit intensities similar to their corresponding unregistered images. Thus, this second registration step needs to account only for the movement. Validation experiments were performed on data obtained from six patients, three slices per patient, and the automatically obtained perfusion profiles were compared with profiles obtained by manually segmenting the myocardium. The results show that our automatic approach is well suited to compensate for the free-breathing movement and that it achieves a significant improvement in the average Pearson correlation coefficient between manually and automatically obtained perfusion profiles before (0.87 +/- 0.18) and after (0.96 +/- 0.09) registration.
Role of Ebola Virus Secreted Glycoproteins and Virus-Like Particles in Activation of Human Macrophages (2005)

Ebola virus, a member of the family Filoviridae, causes one of the most severe forms of viral hemorrhagic fever. In the terminal stages of disease, symptoms progress to hypotension, coagulation disorders, and hemorrhages, and there is prominent involvement of the mononuclear phagocytic and reticuloendothelial systems. Cells of the mononuclear phagocytic system are primary target cells and producers of inflammatory mediators. Ebola virus efficiently produces four soluble glycoproteins during infection: sGP, delta peptide (Delta-peptide), GP(1), and GP(1,2Delta). While the presence of these glycoproteins has been confirmed in blood (sGP) and in vitro systems, it is hypothesized that they are of biological relevance in pathogenesis, particularly target cell activation. To gain insight into their function, we expressed the four soluble glycoproteins in mammalian cells and purified and characterized them. The role of the transmembrane glycoprotein in the context of virus-like particles was also investigated. Primary human macrophages were treated with glycoproteins and virus-like particles and subsequently tested for activation by detection of several critical proinflammatory cytokines (tumor necrosis factor alpha, interleukin-6 [IL-6], and IL-1 beta) and the chemokine IL-8. The presentation of the glycoprotein was determined to be critical since virus-like particles, but not soluble glycoproteins, induced high levels of activation. We propose that the presentation of GP(1,2) in the rigid form such as that observed on the surface of particles is critical for initiating a sufficient signal for the activation of primary target cells. The secreted glycoproteins do not appear to play any role in exogenous activation of these cells during Ebola virus infection.
Autophagy (2012)

Autophagy is a catabolic process that functions in recycling and degrading cellular proteins, and is also induced as an adaptive response to the increased metabolic demand upon nutrient starvation. However, the prosurvival role of autophagy in response to metabolic stress due to deprivation of glutamine, the most abundant nutrient for mammalian cells, is not well understood. Here, we demonstrated that when extracellular glutamine was withdrawn, autophagy provided cells with sub-mM concentrations of glutamine, which played a critical role in fostering cell metabolism. Moreover, we uncovered a previously unknown connection between metabolic responses to ATG5 deficiency and glutamine deprivation, and revealed that WT and atg5 (-/-) MEFs utilized both common and distinct metabolic pathways over time during glutamine deprivation. Although the early response of WT MEFs to glutamine deficiency was similar in many respects to the baseline metabolism of atg5 (-/-) MEFs, there was a concomitant decrease in the levels of essential amino acids and branched chain amino acid catabolites in WT MEFs after 6 h of glutamine withdrawal that distinguished them from the atg5 (-/-) MEFs. Metabolomic profiling, oxygen consumption and pathway focused quantitative RT-PCR analyses revealed that autophagy and glutamine utilization were reciprocally regulated to couple metabolic and transcriptional reprogramming. These findings provide key insights into the critical prosurvival role of autophagy in maintaining mitochondrial oxidative phosphorylation and cell growth during metabolic stress caused by glutamine deprivation.
Differential Oxidant Tolerance Determined by the Key Transcription Factor Yap1 Is Controlled by Levels of the Yap1-binding Protein, Ybp1 (2011)

The Saccharomyces cerevisiae transcription factor Yap1 is a central determinant of oxidative stress tolerance. This protein is found primarily in the cytoplasm in the absence of oxidative stress but, upon exposure to oxidants, rapidly translocates to the nucleus and activates expression of target genes. Although both diamide and H(2)O(2) have been used to impose oxidative stress on cells, these different oxidants trigger Yap1 nuclear localization in distinctly different ways. Diamide appears to oxidize particular cysteine residues on Yap1, leading to inhibition of association of Yap1 with the nuclear exportin Crm1. Crm1 would normally transport Yap1 out of the nucleus. H(2)O(2) activation of Yap1 nuclear localization requires the participation of the glutathione peroxidase Gpx3 and the Yap1-binding protein Ybp1. H(2)O(2) exposure triggers formation of a dual disulfide bonded Yap1 that is catalyzed by the presence of Gpx3 and Ybp1. In the current study, we have determined that two distinct pools of Yap1 exist in the cell. These pools are designated by the level of Ybp1. Ybp1 interacts directly with Yap1 and these proteins form a stable complex in vivo. Genetic and biochemical experiments indicate that Ybp1 is rate-limiting for Yap1 oxidative folding during H(2)O(2) stress. The fungal pathogen Candida glabrata expresses a protein homologous to Ybp1 called CgYbp1. Overproduction of CgYbp1 elevated H(2)O(2) tolerance in this pathogen indicating that the determinative role of Ybp1 in setting the level of H(2)O(2) resistance has been evolutionarily conserved.
&lt;title&gt;Dynamic correction of aberrations in focusing and deflection systems with shaped beams&lt;/title&gt; (1995)

In electron beam focusing and deflection systems, certain aberrations (such as deflection field curvature, astigmatism and distortion) can be `dynamically corrected', by applying appropriate focusing and stigmation fields corrections at each point in the deflection field. Such corrections are particularly important for large-area shaped-beam systems. In this paper, the question of which aberrations can be dynamically corrected is discussed, and the principle of applying dynamic corrections using dynamic focus coils and stigmators is summarized. The computation of the fields in magnetic and electrostatic stigmators is then described, and a unified aberration theory for handling electron lenses, deflectors, dynamic focus coils and stigmators is outlined. This theory has been implemented and incorporated in an optimization program. An example of the computer-aided design and optimization of a shaped beam system with dynamic corrections is presented. The results lead to the interesting conclusion that, as well as correcting field curvature and astigmatism, dynamic correction elements can also be used to significantly reduce the hybrid distortions of shaped beam systems, thereby largely eliminating pattern distortions and stitching errors.
Construction and application of plasmid- and transposon-based promoter-probe vectors for Streptomyces spp. that employ a Vibrio harveyi luciferase reporter cassette (1992)

Several versatile promoter-probe vectors have been constructed for Streptomyces strains which utilize the production of blue-green light as a measure of transcription activity. Three plasmid vectors (two high and one low copy number) and two transposons are described. The multicopy plasmids pRS1106 and pRS1108 contain a transcription terminator and multiple-cloning polylinker upstream of promoterless luciferase (lux) and neomycin resistance reporter genes. Plasmid pHI90 is similar in structure to the pRS vectors except that its single copy number is an advantage for regulation studies or situations in which overexpression is otherwise toxic to the cell. The two transposons carry a promoterless lux cassette cloned such that transposition into a target DNA and fusion to the target's transcription unit occur simultaneously. Tn5351 was created by inserting the luciferase genes near the right end of the viomycin resistance transposon Tn4563. Tn5353 carries the luciferase genes near the right end of a neomycin resistance transposon derived from Tn4556. The size of Tn5353 was minimized by deleting nonessential transposon sequences, making this element small enough to be cloned into phi C31 bacteriophages for efficient transposon delivery to target cells of Streptomyces strains. The two Tnlux transposons have been used to generate Streptomyces coelicolor morphological mutants and to monitor transcription from chromosomal promoters during development.
Immunohistochemistry of Estrogen and Progesterone Receptors Reconsidered (2005)

Paraffin sections or fine-needle aspiration smears from 5,993 cases of invasive mammary carcinomas were assessed immunohistochemically for estrogen receptor (ER; 1D5) and progesterone receptor (PR; 636) expression. Staining pattern and intensity were correlated with histologic subtypes and nuclear grades of tumors. Positive nuclear staining for ER and PR was observed in 75% and 55% of invasive carcinomas, respectively. In 92% of ER+ cases, diffuse and uniform staining of most tumor cells was observed. In the remaining 8%, a focal ER reaction was seen, usually because of inadequate fixation. In 21% of PR+ tumors, the reaction was heterogeneous or focal but unrelated to fixation. There were no ER-, PR+ tumors. All pure tubular, colloid, and infiltrating lobular carcinomas were ER+. All medullary, apocrine, and metaplastic and most high-nuclear-grade carcinomas were ER-. With monoclonal antibody 1D5 and antigen retrieval, immunohistochemical reaction for ER in breast cancer usually is an all-or-none phenomenon; therefore, quantitation of results is unnecessary. Despite antigen retrieval, inadequate fixation can cause false-negative results; evaluation of internal positive control samples is imperative. ER positivity and negativity are predictable in certain histologic types and nuclear grades of breast cancer. The reaction for PR can be heterogeneous or focal.
Systemic Hypertension and Age-Related Maculopathy in the Framingham Study (1986)

Analysis of data on 1,828 subjects from the Framingham Heart and Eye Studies shows a small and consistent significant association between age-related maculopathy and systemic hypertension. The association was found using blood pressure and medical history data collected both 25 years before the eye examination and concurrently with the eye examination. Prevalence of age-related maculopathy progressively increases with increasing duration of systemic hypertension. Previous epidemiologic studies of the association between systemic blood pressure and age-related maculopathy have produced conflicting results. The failure of some studies to detect an association may have resulted from inadequate sample sizes to detect the small relative risks and problems in determining the duration of the systemic hypertension.
A single dose of doxorubicin-functionalized bow-tie dendrimer cures mice bearing C-26 colon carcinomas (2006)

The antitumor effect of doxorubicin (DOX) conjugated to a biodegradable dendrimer was evaluated in mice bearing C-26 colon carcinomas. An asymmetric biodegradable polyester dendrimer containing 8-10 wt % DOX was prepared. The design of the dendrimer carrier optimized blood circulation time through size and molecular architecture, drug loading through multiple attachment sites, solubility through PEGylation, and drug release through the use of pH-sensitive hydrazone linkages. In culture, dendrimer-DOX was >10 times less toxic than free DOX toward C-26 colon carcinoma cells after exposure for 72 h. Upon i.v. administration to BALB/c mice with s.c. C-26 tumors, dendrimer-DOX was eliminated from the serum with a half-life of 16 +/- 1 h, and its tumor uptake was ninefold higher than i.v. administered free DOX at 48 h. In efficacy studies performed with BALB/c mice bearing s.c. C-26 tumors, a single i.v. injection of dendrimer-DOX at 20 mg/kg DOX equivalents 8 days after tumor implantation caused complete tumor regression and 100% survival of the mice over the 60-day experiment. No cures were achieved in tumor-implanted mice treated with free DOX at its maximum tolerated dose (6 mg/kg), drug-free dendrimer, or dendrimer-DOX in which the DOX was attached by means of a stable carbamate bond. The antitumor effect of dendrimer-DOX was similar to that of an equimolar dose of liposomal DOX (Doxil). The remarkable antitumor activity of dendrimer-DOX results from the ability of the dendrimer to favorably modulate the pharmacokinetics of attached DOX.
Adaptive streaming of audiovisual content using MPEG DASH (2012)

HTTP streaming has become a cost effective means for multimedia delivery nowadays. In this paper, we study the use of MPEG DASH standard to stream audiovisual content. We first describe a novel estimation method for connection throughput. Then, employing the extensibility feature of DASH syntax, we present a systematic method for selecting the best audio and video alternatives given the estimated throughput. The experiments show that our solution is stable to short-term fluctuations while responding quickly to large fluctuations.
Making improvements stick (2010)

Purpose Explains how to make organizational reforms last. Design/methodology/approach Describes the actions needed to move an organization from implementation to the point where improvements are fully embedded. Findings Highlights the importance of having a top‐level champion who supports and advocates change, gaining and maintaining stakeholder engagement, ensuring honest and timely communication, encouraging a long‐term focus on changing the behavior of the organization, supporting individuals with the capability to lead the improvement process, continuing to invest in building the internal capability of the organization and introducing robust financial and non‐financial incentives. Practical implications Stresses the need to allow people to comment constructively on reform. Social implications Details the impact of such social factors as ignorance, lethargy, committees and inflexibility in holding back improvements. Originality/value Emphasizes that improvement is more about people than about process.
Dual Composite Right/Left-Handed (D-CRLH) Transmission Line in GaAs MMIC Technology (2007)

A GaAs MMIC technology of the novel dual composite right/left-handed (D-CRLH) transmission line (TL) is presented. The D-CRLH is the dual of the conventional CRLH in the sense that it consists of an LC parallel-tank impedance and of an LC series-tank admittance. This topological duality results into dual properties. In contrast to the conventional CRLH TL which has LH operation at low-frequency and RH one at high-frequency, the D-LH TL exhibits its LH band at high frequencies and its RH band at low frequencies, a property that may be exploited in various kinds of component and antenna applications. The proposed D-CRLH prototype exhibits a DC to 2.9 GHz right-handed (RH) band and a 5.1 GHz to 6.9 GHz left-handed (LH) band. The results in this paper are obtained from full-wave analysis, and they will be followed next by experimental results
Targeting fibroblast-growth-factor-receptor-dependent signaling for cancer therapy (2011)

Strategies for targeting FGFR-signaling for cancer therapy are very promising, but need to be carefully developed based on the physiological roles of FGF signaling. Preventive measures may be necessary for protection from FGF-related side effects. Combined targeting of several receptor tyrosine kinases or combination with other therapies may be a useful way of avoiding or ameliorating side effects. FGF-related markers of prognosis and therapy response still need to be investigated.
Characterization of Extensive Genetic Alterations in Ductal Carcinoma In Situ by Fluorescence In Situ Hybridization and Molecular Analysis (1995)

This approach may give direction to future research aimed at precisely mapping loci altered in DCIS and help in understanding the biologic events associated with tumor progression or recurrence.
Cyberinfrastructure for e-Science (2005)

Here we describe the requirements of an e-Infrastructure to enable faster, better, and different scientific research capabilities. We use two application exemplars taken from the United Kingdom's e-Science Programme to illustrate these requirements and make the case for a service-oriented infrastructure. We provide a brief overview of the UK "plug-and-play composable services" vision and the role of semantics in such an e-Infrastructure.
Enteroglucagon, but not CCK, plays an important role in pancreatic hyperplasia after proximal small bowel resection (1994)

The present study was performed to examine the role played by pancreatotrophic factors, especially enteroglucagon and cholecystokinin (CCK), in the compensatory pancreatic hyperplasia observed after proximal small bowel resection (PSBR). Male Wistar rats were randomized into two groups, receiving either PSBR or transection (TRC). Five animals from each group were randomly selected for treatment with FK-480, a novel CCK antagonist. Four weeks after the operation, plasma levels of gastrin, CCK and enteroglucagon were measured. Pancreatic wet weight and protein, DNA, RNA and enzyme content were also determined. The wet weight and content of protein, DNA and RNA were significantly higher in PSBR rats than in TRC rats, regardless of whether they received FK-480. FK-480 had no suppressive effects on adaptive pancreatic growth after PSBR. Plasma enteroglucagon levels rose significantly in PSBR rats, and there were positive correlations between plasma enteroglucagon levels and pancreatic protein, DNA and RNA content. These findings demonstrated that plasma CCK was not the major trophic factor operating in the pancreas after PSBR, and showed that enteroglucagon plays an important role in the pancreatic hyperplasia that occurs after PSBR.
DC-DC Power Converter with digital PID controller (2011)

This paper presents an approach for an adaptive PID controller in order to improve the dynamic performance of DC-DC Power Converter. The control variables, namely the proportional constant (K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</sub> ) and integral constant (K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> ) are varied as a function of the uncompensated error voltage which results in improving the dynamic transient response of the power converter. The experimental results show that there is a reduction in overshoot/undershoot and settling time compared to the conventional PID.