gebhart/patrepeval huggingface dataset:
Role of CCN2/CTGF in the proliferation of <i>Mastomys</i> enterochromaffin-like cells and gastric carcinoid development (2006)

Mastomys enterochromaffin-like (ECL) cell proliferation is initially gastrin driven, but once neoplasia develops, cells become gastrin autonomous. We hypothesized that CCN2 (CTGF), a mitogenic growth factor, may regulate ECL cell proliferation. A Mastomys GeneChip database was examined (dCHIP) to identify CCN2 expression levels. CCN2 in normal and tumor ECL cell preparations obtained using FACS (100 nM acridine orange) was examined by real-time PCR. CCN2 protein was identified in mucosal and ECL cell preparations by immunohistochemistry. Short-term cultured cells were stimulated with either CCN2 or CCN2 + EGF, and proliferation was measured (MTT assay). The ERK1/2 inhibitor PD-98059 (0.1-100 microM) was assessed in terms of CCN2 (1 ng/ml)-mediated proliferation and ERK1/2 phosphorylation. CCN2 transcript and protein was then examined in clinical gastric carcinoids. The ccn2 transcript was upregulated in tumor samples compared with the normal mucosa (+2.36-fold, P < 0.01). PCR demonstrated that ccn2 was not expressed in FACS-prepared (>98% pure) normal ECL cells but was elevated in tumor ECL cell fractions (41.3 +/- 10.7-fold). Immunostaining of the Mastomys gastric mucosa and FACS preparations confirmed that CCN2 protein was present in ECL tumors but not in normal ECL cells. Neither CCN2 nor CCN2 + EGF stimulated normal ECL cell proliferation. CCN2 stimulated tumor proliferation (EC50 approximately 0.01 ng/ml); EGF significantly augmented (P < 0.01) CCN2-induced tumor cell proliferation (EC50 = 20 pg/ml). PD-98059 inhibited CCN2-induced proliferation (-12 +/- 3%, P < 0.05) and ERK1/2 phosphorylation (-34 +/- 5%, P < 0.05) in tumor cells. In clinical samples, both CCN2 transcript and protein were elevated in gastrin-autonomous carcinoids (P < 0.02) compared with the normal mucosa. In conclusion, CCN2 may be a proliferative regulator of Mastomys ECL neoplastic proliferation once these cells become autonomous of gastrin regulation. Identification of CCN2 in gastric carcinoid tissue may be useful both as an indicator of ECL cell transformation and may define gastrin autonomy, a criteria of gastric carcinoid malignancy.
A Study in Public School Excellence for Minority Students. (1980)

Although an effective therapy for prion disease has not yet been established, many advances have been made toward understanding its pathogenesis, which has facilitated research into therapeutics for the disease. Several compounds, including flupirtine, quinacrine, pentosan polysulfate, and doxycycline, have recently been used on a trial basis for patients with prion disease. Concomitantly, several lead antiprion compounds, including compound B (compB), IND series, and anle138b, have been discovered. However, clinical trials are still far from yielding significantly beneficial results, and the findings of lead compound studies in animals have highlighted new challenges. These efforts have highlighted areas that need improvement or further exploration to achieve more effective therapies. In this work, we review recent advances in prion-related therapeutic research and discuss basic scientific issues to be resolved for meaningful medical intervention of prion disease.
The Meaning of Memory Safety (2018)

We give a rigorous characterization of what it means for a programming language to be memory safe, capturing the intuition that memory safety supports local reasoning about state. We formalize this principle in two ways. First, we show how a small memory-safe language validates a noninterference property: a program can neither affect nor be affected by unreachable parts of the state. Second, we extend separation logic, a proof system for heap-manipulating programs, with a “memory-safe variant” of its frame rule. The new rule is stronger because it applies even when parts of the program are buggy or malicious, but also weaker because it demands a stricter form of separation between parts of the program state. We also consider a number of pragmatically motivated variations on memory safety and the reasoning principles they support. As an application of our characterization, we evaluate the security of a previously proposed dynamic monitor for memory safety of heap-allocated data.
NX-1207: a novel investigational drug for the treatment of benign prostatic hyperplasia (2010)

In four US clinical trials to date, NX-1207 has shown evidence of symptomatic improvement substantially better than currently approved BPH medications with no significant safety issues. Larger Phase III trials are ongoing to further confirm the efficacy, safety and tolerability for this minimally invasive, anesthetic free, clinic-based treatment for BPH.
The outcome of T‐cell costimulation through intercellular adhesion molecule‐1 differs from costimulation through leucocyte function‐associated antigen‐1 (2003)

Optimal T-cell activation requires both an antigen-specific and a costimulatory signal. The outcome of T-cell activation can be influenced by the nature of the costimulatory signal the T cell receives. We recently demonstrated the ability of stimulation through intercellular adhesion molecule-1 (ICAM-1), resident on the T-cell surface, to provide a second signal for T-cell activation, and have extended that work here to begin an examination of the functional outcome of this set of signals. Costimulation through ICAM-1 resulted in a greater percentage of cells having undergone more than three divisions when compared to costimulation through leucocyte function-associated antigen-1 (LFA-1). Costimulation through ICAM-1 also had an effect similar to costimulation through CD28 in its ability to down-regulate the cyclin dependent kinase inhibitor p27kip1. Costimulation through ICAM-1 provided greater protection from apoptosis than costimulation through LFA-1, especially in cells having divided more than three times. This was supported by the ability of costimulation through ICAM-1 to up-regulate the anti-apoptotic protein Bcl-2. Finally, costimulation through ICAM-1 or CD28 produced a greater number of T cells with a memory phenotype than costimulation through LFA-1.
Toxicity of Deepwater Horizon Source Oil and the Chemical Dispersant, Corexit® 9500, to Coral Larvae (2013)

Acute catastrophic events can cause significant damage to marine environments in a short time period and may have devastating long-term impacts. In April 2010 the BP-operated Deepwater Horizon (DWH) offshore oil rig exploded, releasing an estimated 760 million liters of crude oil into the Gulf of Mexico. This study examines the potential effects of oil spill exposure on coral larvae of the Florida Keys. Larvae of the brooding coral, Porites astreoides, and the broadcast spawning coral, Montastraea faveolata, were exposed to multiple concentrations of BP Horizon source oil (crude, weathered and WAF), oil in combination with the dispersant Corexit® 9500 (CEWAF), and dispersant alone, and analyzed for behavior, settlement, and survival. Settlement and survival of P. astreoides and M. faveolata larvae decreased with increasing concentrations of WAF, CEWAF and Corexit® 9500, however the degree of the response varied by species and solution. P. astreoides larvae experienced decreased settlement and survival following exposure to 0.62 ppm source oil, while M. faveolata larvae were negatively impacted by 0.65, 1.34 and 1.5 ppm, suggesting that P. astreoides larvae may be more tolerant to WAF exposure than M. faveolata larvae. Exposure to medium and high concentrations of CEWAF (4.28/18.56 and 30.99/35.76 ppm) and dispersant Corexit® 9500 (50 and 100 ppm), significantly decreased larval settlement and survival for both species. Furthermore, exposure to Corexit® 9500 resulted in settlement failure and complete larval mortality after exposure to 50 and 100 ppm for M. faveolata and 100 ppm for P. astreoides. These results indicate that exposure of coral larvae to oil spill related contaminants, particularly the dispersant Corexit® 9500, has the potential to negatively impact coral settlement and survival, thereby affecting the resilience and recovery of coral reefs following exposure to oil and dispersants.
<i>MACROD2</i> overexpression mediates estrogen independent growth and tamoxifen resistance in breast cancers (2014)

Tamoxifen is effective for treating estrogen receptor-alpha (ER) positive breast cancers. However, few molecular mediators of tamoxifen resistance have been elucidated. Here we describe a previously unidentified gene, MACROD2 that confers tamoxifen resistance and estrogen independent growth. We found MACROD2 is amplified and overexpressed in metastatic tamoxifen-resistant tumors. Transgene overexpression of MACROD2 in breast cancer cell lines results in tamoxifen resistance, whereas RNAi-mediated gene knock down reverses this phenotype. MACROD2 overexpression also leads to estrogen independent growth in xenograft assays. Mechanistically, MACROD2 increases p300 binding to estrogen response elements in a subset of ER regulated genes. Primary breast cancers and matched metastases demonstrate MACROD2 expression can change with disease evolution, and increased expression and amplification of MACROD2 in primary tumors is associated with worse overall survival. These studies establish MACROD2 as a key mediator of estrogen independent growth and tamoxifen resistance, as well as a potential novel target for diagnostics and therapy.
What’s in a name? First use of the term ‘allergy’ (2013)

Abstract In the course of the last few years a number of facts have been collected which belong to the domain of Immunology but fit poorly into its framework. They are the findings of supersensitivity in the immunized organism. These two terms clash with each other. Do we not regards an organism as immune if it is protected against the disease, is not attacked by it a second time? How can this organism at the same time be supersensitive to the same disease? . . . these two terms contradict each other; their union is a forced one. In fact, the concept of immunity has been carried on since a time when supersensitivity was unknown . . . What we need is a new generalized term, which prejudices nothing but expresses the change in condition, which an animal experiences after contact with any organic poison, be it animate or inanimate. The vaccinated person behaves towards vaccine lymph, the syphilitic towards the virus of syphilis, the tuberculous patient towards tuberculin, the person injected with serum towards this serum, in a different manner from him who has not previously been in contact with such an agent. Yet he is not insensitive to it. We can only say of him that his power to react has undergone a change. For this general concept of a changed reactivity I propose the term Allergy. ‘Allos’ implies deviation from the original state, from the behaviour of the normal individual, as it is used in the words Allorhythmia, Alloptropism. The vaccinated, the tuberculous, the individual injected with serum becomes allergic towards the corresponding foreign substance. A foreign substance, which by one or more application stimulates the organism to a change in reaction is an Allergen.
Textured growth of highly coercive L10 ordered FePt thin films on single crystalline and amorphous substrates (2004)

FePt films have been prepared by pulsed laser deposition at a temperature of 800 °C onto (001) oriented single crystalline (MgO, SrTiO3) as well as amorphous substrates (Si3N4, glass) with and without a (001) textured MgO buffer layer. Although all films have been prepared under identical conditions, significant differences in coercivity are observed. Very high values of up to 5.6 T have been measured for the epitaxial films, while on the amorphous substrates the coercivities range between 0.8 and 2.0 T. We analyze whether changes in intrinsic or extrinsic properties due to a modified microstructure are responsible for these differences.
A computer-aided diagnostic system to characterize CT focal liver lesions: design and optimization of a neural network classifier (2003)

In this paper, a computer-aided diagnostic (CAD) system for the classification of hepatic lesions from computed tomography (CT) images is presented. Regions of interest (ROIs) taken from nonenhanced CT images of normal liver, hepatic cysts, hemangiomas, and hepatocellular carcinomas have been used as input to the system. The proposed system consists of two modules: the feature extraction and the classification modules. The feature extraction module calculates the average gray level and 48 texture characteristics, which are derived from the spatial gray-level co-occurrence matrices, obtained from the ROIs. The classifier module consists of three sequentially placed feed-forward neural networks (NNs). The first NN classifies into normal or pathological liver regions. The pathological liver regions are characterized by the second NN as cyst or "other disease." The third NN classifies "other disease" into hemangioma or hepatocellular carcinoma. Three feature selection techniques have been applied to each individual NN: the sequential forward selection, the sequential floating forward selection, and a genetic algorithm for feature selection. The comparative study of the above dimensionality reduction methods shows that genetic algorithms result in lower dimension feature vectors and improved classification performance.
Data markets in the cloud (2011)

Cloud-computing is transforming many aspects of data management. Most recently, the cloud is seeing the emergence of digital markets for data and associated services. We observe that our community has a lot to offer in building successful cloud-based data markets. We outline some of the key challenges that such markets face and discuss the associated research problems that our community can help solve.
Incentives for Regionalization of Water Supply Infrastructure (1990)

Regionalization of water supply entails an agreement between two or more previously independent water suppliers wherein regionalization offers each something more than they could obtain alone. Regionalization can offer different types of benefits to any number of water service components for a particular utility. Once the relative benefits of regionalization are recognized, there must be an equitable sharing of those benefits among the cooperating water suppliers for regionalization to successfully occur.
A Theory of Quantum Superluminal Communication (2004)

The implications of quantum nonlocality are briefly reviewed. It is shown that the collapse of the wave function requires the existence of a preferred Lorentz frame. This opens the first door to quantum superluminal communication (QSC). A theory of QSC is deeply analyzed. We demonstrate that the combination of the collapse of the wave function and the consciousness of the observer will permit the observer to distinguish nonorthogonal states under some condition. This provides a principle for realizing QSC. A practical QSC scheme is given based upon the QSC principle. Some evidence of the existence of QSC is also discussed. Besides, a new space-time transformation for QSC is analyzed, and two ways to measure the preferred Lorentz frame are given.
Uptake and incorporation of saturated and unsaturated fatty acids into macrophage lipids and their effect upon macrophage adhesion and phagocytosis (1990)

Murine thioglycollate-elicited peritoneal macrophages were cultured in the presence of a variety of fatty acids added as complexes with bovine serum albumin. All fatty acids tested were taken up readily by the cells and both neutral and phospholipid fractions were enriched with the fatty acid provided in the medium. This generated a range of cells enriched in saturated, monounsaturated or polyunsaturated fatty acids, including n-3 acids of fish oil origin. Saturated fatty acid enrichment enhanced macrophage adhesion to both tissue culture plastic and bacterial plastic compared with enrichment with polyunsaturated fatty acids. Macrophages enriched with the saturated fatty acids myristate or palmitate showed decreases of 28% and 21% respectively in their ability to phagocytose unopsonized zymosan particles. Those enriched with polyunsaturated fatty acids showed 25-55% enhancement of phagocytic capacity. The greatest rate of uptake was with arachidonate-enriched cells. Phagocytic rate was highly correlated with the saturated/unsaturated fatty acid ratio, percentage of polyunsaturated fatty acid and index of unsaturation, except for macrophages enriched with fish-oil-derived fatty acids; they showed lower phagocytic activity than expected on the basis of their degree of unsaturation. These results suggest that membrane fluidity is important in determining macrophage adhesion and phagocytic activity. However, in the case of phagocytosis, this effect may be partially overcome if the cells are enriched with fish-oil-derived fatty acids. Thus it may be possible to modulate the activity of cells of the immune system, and so an immune response, by dietary lipid manipulation.
Analysis and Environmental Fate of Air Force Distillate and High Density Fuels (1981)

Five high density fuels (RJ-4, RJ-5, RJ-6, JP-9, and JP-10) and three distillate fuels were analyzed by capillary column gas chromatography (GC). The major components of the distillate fuels were identified by gas chromatography- mass spectrometry (GC-MS). The molecular weight of the isomers of the high density fuel components were also determined, but the structures of only a few components were assigned by comparing the GC retention times with authentic samples. The concentration and identity of the major water-soluble fuel components were also identified. The volatilization rates of the water-soluble components of JP-4, JP-8, and JP-9 were measured by preparing solutions of the fuel components in water, stirring at three stirring rates, and measuring the rate of decrease of the concentration of each component by GC as a function of time. The water-soluble components of JP-4 were photolyzed for 21 days in sunlight in deionized water, natural seawater, and water from a local pond. The distribution of the fuel components was estimated, using the method recently proposed by Mackay and Patterson. The alkanes should partition almost entirely into the atmosphere, the monoaromatics should be in both the air and water, and the naphthalene should partition into the water and the sediment phases. Adsorption of the alkanes and monoaromatics should not be a major environmental fate. It is recommended that the rate of dissolution in water and evaporation of the pure fuels be studied in detail because they may be the rate-limiting transport processes.
TNF-alpha up-regulates renal MIF expression in rat crescentic glomerulonephritis. (1997)

This study demonstrates for the first time that TNF-alpha up-regulates local MIF expression by both infiltrating macrophages and resident kidney cells in rat crescentic glomerulonephritis. In addition, TNF-alpha regulates systemic MIF production. Thus, TNF-alpha, together with MIF, may play a pathological role in immunologically induced renal disease.
Differences in insect resistance between tomato species endemic to the Galapagos Islands (2013)

Our results suggest that S. galapagense and S. cheesmaniae might be morphotypes rather than two species and that their co-existence is likely the result of selective pressure.
The Cytoplasmic Heme-binding Protein (PhuS) from the Heme Uptake System of Pseudomonas aeruginosa Is an Intracellular Heme-trafficking Protein to the δ-Regioselective Heme Oxygenase (2006)

The uptake and utilization of heme as an iron source is a receptor-mediated process in bacterial pathogens and involves a number of proteins required for internalization and degradation of heme. In the following report we provide the first in-depth spectroscopic and functional characterization of a cytoplasmic heme-binding protein PhuS from the opportunistic pathogen Pseudomonas aeruginosa. Spectroscopic characterization of the heme-PhuS complex at neutral pH indicates that the heme is predominantly six-coordinate low spin. However, the resonance Raman spectra and global fit analysis of the UV-visible spectra show that at all pH values between 6 and 10 three distinct species are present to varying degrees. The distribution of the heme across multiple spin states and coordination number highlights the flexibility of the heme environment. We provide further evidence that the cytoplasmic heme-binding proteins, contrary to previous reports, are not heme oxygenases. The degradation of the heme-PhuS complex in the presence of a reducing agent is a result of H2O2 formed by direct reduction of molecular oxygen and does not yield biliverdin. In contrast, the heme-PhuS complex is an intracellular heme trafficking protein that specifically transfers heme to the previously characterized iron-regulated heme oxygenase pa-HO. Surface plasmon resonance experiments confirm that the transfer of heme is driven by a specific protein-protein interaction. This data taken together with the spectroscopic characterization is consistent with a protein that functions to shuttle heme within the cell.
Storage of cellular 5′ mRNA caps in P bodies for viral cap-snatching (2008)

The minus strand and ambisense segmented RNA viruses include multiple important human pathogens and are divided into three families, the Orthomyxoviridae, the Bunyaviridae, and the Arenaviridae. These viruses all initiate viral transcription through the process of "cap-snatching," which involves the acquisition of capped 5' oligonucleotides from cellular mRNA. Hantaviruses are emerging pathogenic viruses of the Bunyaviridae family that replicate in the cytoplasm of infected cells. Cellular mRNAs can be actively translated in polysomes or physically sequestered in cytoplasmic processing bodies (P bodies) where they are degraded or stored for subsequent translation. Here we show that the hantavirus nucleocapsid protein binds with high affinity to the 5' cap of cellular mRNAs, protecting the 5' cap from degradation. We also show that the hantavirus nucleocapsid protein accumulates in P bodies, where it sequesters protected 5' caps. P bodies then serve as a pool of primers during the initiation of viral mRNA synthesis by the viral polymerase. We propose that minus strand segmented viruses replicating in the cytoplasm have co-opted the normal degradation machinery of P bodies for storage of cellular caps. Our data also indicate that modification of the cap-snatching model is warranted to include a role for the nucleocapsid protein in cap acquisition and storage.
Feature-Based Deep Neural Networks for Short-Term Prediction of WiFi Channel Occupancy Rate (2021)

Spectrum occupancy prediction is a key enabling technology to facilitate a proactive resource allocation for dynamic spectrum management systems. This work focuses on the prediction of duty cycle (DC) metric that reflects spectrum usage (in the time domain). The spectrum usage is typically measured on a shorter time scale than needed for prediction. Hence, data thinning is required and we apply block averaging. However, averaging operation results in flattening the DC data and losing essential features to assist deep neural network (DNN) to predict the spectrum usage. To improve DC prediction after block averaging, a feature-based deep learning framework is proposed. Namely, long short-term memory (LSTM) and gated recurrent unit (GRU) are selected and enhanced by using features of the data, such as the variance of DC data in addition to DC data themself. The proposed model is capable of proactively predicting the spectrum usage by capturing complex relationships among various input features for the measured spectrum, thus providing higher prediction accuracy with an average improvement of 5% in RMSE compared with traditional models. Moreover, to have a better understanding of the proposed model, we quantify the effect of input features on the predicted spectrum usage values. Based on the most significant input features, a simpler and more efficient model is proposed to estimate DC with similar accuracy to when using all features.