gebhart/patrepeval huggingface dataset:
System Design and Advanced Receiver Techniques for MBMS Broadcast Services (2006)

Raptor codes have been recently standardized by 3GPP to be used in the application layer. These codes are very efficient and perform sufficiently close to the so-called ideal fountain code on the block-erasure channel. However, for real applications, a simple receiver enhancement called permeable layer receiver can be done, which provides huge performance gains. Standard Raptor decoding algorithms have to be revised and new efficient decoding algorithms need to be introduced. In this work we present a practical and efficient implementation of the Raptor decoder for permeable layer receiver. We show that, not only we achieve huge performance gains, but we achieve them at an affordable (low) decoding complexity. Complexity and decoding performance simulation results are presented for the download delivery and video broadcasting.
Stimulation of extracellular matrix components in the normal brain by invading glioma cells (1998)

Malignant gliomas are characterized by an extensive invasion of tumor cells into the normal brain parenchyma. A substantial amount of data indicates that cell movement in general is regulated by specific interactions between extracellular matrix components and specific cell-surface receptors. In the present work, multicellular spheroids from 4 human glioma cell lines (U-373Mg, A-172Mg, U-251Mg and HF-66) were confronted with normal rat brain cell aggregates in vitro, which resulted in a progressive invasion of tumor cells into the brain aggregates. The co-cultures were then sectioned and immuno-stained for specific extracellular matrix components (laminin, fibronectin and collagen type IV) and for specific cell-surface receptors which bind to these components (integrins beta1, beta4, alpha3, alpha6). In addition, flow-cytometric measurements and Northern blot analyses showed expression of several different integrins within the cell lines. The alpha3 subunit was expressed strongly in all cell lines. Whereas the beta1 subunit was expressed weakly in exponentially growing monolayer cultures, it showed a pronounced expression in multicellular spheroids, indicating that the integrin expression may vary depending on the micro-environment within a tumor. Furthermore, normal brain tissue was able to produce laminin when confronted with the glioma cells, which also was observed for fibronectin and collagen type IV. The relevance of our observations to the in vivo situation was investigated further by immuno-staining 5 human glioma biopsy samples for laminin. In some areas of the tumors, specific deposits of laminin were observed. In conclusion, we have shown that normal brain tissue has the ability to produce extracellular matrix components, such as laminin, collagen type IV and fibronectin, when confronted with invading glioma cells. Our results show that the glioma cells express specific integrins which can interact with these extracellular matrix components. Such interactions may facilitate tumor cell migration and invasion.
Hepatocyte Cocultures with Endothelial Cells and Fibroblasts on Micropatterned Fibrous Mats to Promote Liver-Specific Functions and Capillary Formation Capabilities (2014)

The maintenance of hepatocyte phenotype and functions remains as a great challenge in the generation of functional liver tissue and in vitro model for drug metabolism studies. The use of hepatocyte coculture systems plays essential roles in the establishment of cell-cell and cell-extracellular matrix communications similar to native liver tissues. In the current study, micropatterned electrospun fibrous mats were created to load hepatocytes, fibroblasts, and endothelial cells (ECs), which were precisely assembled to establish their spatially controlled coculture for mimicking the in vivo structure of hepatic lobules. Hepatocytes formed compact polyhedral spheroids with an average diameter of 80-100 μm, reorganized actin filaments in the cell-cell contact regions, and well-developed bile canaliculi. Compared with hepatocytes cultured alone, the coculture of hepatocytes with either fibroblasts or ECs led to significantly higher albumin secretion, urea synthesis and cytochrome P-450 expression, which were dramatically improved by the coculture of hepatocytes with both fibroblasts and ECs. The cocultured ECs well spread on patterned regions with little organized filamentous actin, and significantly higher densities and deeper penetration into patterned scaffolds were determined for ECs after coculture with fibroblasts and hepatocytes compared with those after cultured alone or coculture with either fibroblasts or hepatocytes. A Matrigel overlay assay showed that the capabilities of ECs to form capillary tubes were significantly enhanced by micropatterned coculture with fibroblasts and hepatocytes. Thus, the coculture of hepatocytes, fibroblasts, and ECs on micropatterned fibrous mats helps both hepatocytes in the maintenance of hepatic functions and ECs in the formation of capillary-like structures. It is suggested that the micropatterned coculture model described here not only provides functional hepatic tissues for predictions of drug metabolism profiles, but also will enable investigations on more complex and physiological cell-cell communications.
Applications of a Rapid Endospore Viability Assay for Monitoring UV Inactivation and Characterizing Arctic Ice Cores (2006)

We have developed a rapid endospore viability assay (EVA) in which endospore germination serves as an indicator for viability and applied it to (i) monitor UV inactivation of endospores as a function of dose and (ii) determine the proportion of viable endospores in arctic ice cores (Greenland Ice Sheet Project 2 [GISP2] cores; 94 m). EVA is based on the detection of dipicolinic acid (DPA), which is released from endospores during germination. DPA concentrations were determined using the terbium ion (Tb3+)-DPA luminescence assay, and germination was induced by L-alanine addition. The concentrations of germinable endospores were determined by comparison to a standard curve. Parallel EVA and phase-contrast microscopy experiments to determine the percentage of germinable spores yielded comparable results (54.3% +/- 3.8% and 48.9% +/- 4.5%, respectively), while only 27.8% +/- 7.6% of spores produced CFU. EVA was applied to monitor the inactivation of spore suspensions as a function of UV dose, yielding reproducible correlations between EVA and CFU inactivation data. The 90% inactivation doses were 2,773 J/m2, 3,947 J/m2, and 1,322 J/m2 for EVA, phase-contrast microscopy, and CFU reduction, respectively. Finally, EVA was applied to quantify germinable and total endospore concentrations in two GISP2 ice cores. The first ice core contained 295 +/- 19 germinable spores/ml and 369 +/- 36 total spores/ml (i.e., the percentage of germinable endospores was 79.9% +/- 9.3%), and the second core contained 131 +/- 4 germinable spores/ml and 162 +/- 17 total spores/ml (i.e., the percentage of germinable endospores was 80.9% +/- 8.8%), whereas only 2 CFU/ml were detected by culturing.
The apoptosis/autophagy paradox: autophagic vacuolization before apoptotic death (2005)

Autophagic cell death is morphologically characterized by an accumulation of autophagic vacuoles. Here, we show that inactivation of LAMP2 by RNA interference or by homologous recombination leads to autophagic vacuolization in nutrient-depleted cells. Cells that lack LAMP2 expression showed an enhanced accumulation of vacuoles carrying the marker LC3, yet a decreased colocalization of LC3 and lysosomes, suggesting that the fusion between autophagic vacuoles and lysosomes was inhibited. While a fraction of mitochondria from starved LAMP2-expressing cells colocalized with lysosomal markers, within autophagolysosomes, no such colocalization was found on removal of LAMP2 from the experimental system. Of note, LAMP1 depletion had no such effects and did not aggravate the phenotype induced by LAMP2-specific small interfering RNA. Serum and amino acid-starved LAMP2-negative cells exhibited an accumulation of autophagic vacuoles and then succumbed to cell death with hallmarks of apoptosis such as loss of the mitochondrial transmembrane potential, caspase activation and chromatin condensation. While caspase inhibition retarded cell death, it had no protective effect on mitochondria. Stabilization of mitochondria by overexpression of Bcl-2 or the mitochondrion-targeted cytomegalovirus protein vMIA, however, blocked all signs of apoptosis. Neither caspase inhibition nor mitochondrial stabilization antagonized autophagic vacuolization in LAMP2-deficient cells. Altogether, these data indicate that accumulation of autophagic vacuoles can precede apoptotic cell death. These findings argue against the clear-cut distinction between type 1 (apoptotic) and type 2 (autophagic) cell death.
Perinatal cannabinoid exposure: Effects on hepatic cytochrome P‐450 and plasma protein levels in male mice (1986)

Maternal exposure to the major psychoactive delta 9-tetrahydrocannabinol (THC), or to the nonpsychoactive cannabinol (CBN) or cannabidiol (CBD) on day 12 of gestation, or on day 1 postpartum, affected the concentrations of hepatic cytochromes P-450 in adult male offspring. Levels of P-450 were significantly increased in adult males prenatally exposed to cannabinoids, but were reduced after postnatal exposure. The response to exogenous testosterone was also differentially affected by perinatal cannabinoid exposure, with reduced plasma androgen in males prenatally exposed to THC, but increased levels of hormone in mice exposed postnatally to THC or CBN. There was a concomitant decrease in plasma albumin and increased gamma-globulin in adult males postnatally exposed to CBN. Beta-globulin levels were also significantly increased in adult males exposed to cannabichromene (CBC) on day 1 postpartum. Cannabinoid exposure during perinatal periods of development exert effects on hepatic function, plasma androgen levels, and on the immune system. These effects may reflect the ability of perinatal cannabinoid exposure to interfere with androgen-mediated processes of differentiation.
Phenology-Based Vegetation Index Differencing for Mapping of Rubber Plantations Using Landsat OLI Data (2015)

Accurate and up-to-date mapping and monitoring of rubber plantations is challenging. In this study, we presented a simple method for rapidly and accurately mapping rubber plantations in the Xishuangbanna region of southwest China using phenology-based vegetation index differencing. Temporal profiles of the Normalized Difference Vegetation Index (NDVI), Enhanced Vegetation Index (EVI), Atmospherically Resistant Vegetation Index (ARVI), Normalized Difference Moisture Index (NDMI), and Tasselled Cap Greenness (TCG) for rubber trees, natural forests and croplands were constructed using 11 Landsat 8 OLI images acquired within one year. These vegetation index time series accurately demonstrated the unique seasonal phenological dynamics of rubber trees. Two distinct phenological phases (i.e., defoliation and foliation) of rubber trees were clearly distinguishable from natural forests and croplands. Rubber trees undergo a brief defoliation-foliation process between late December and mid-March. Therefore, vegetation index differencing between the nearly complete defoliation (leaf-off) and full foliation (leaf flushing) phases was used to delineate rubber plantations within fragmented tropical mountainous landscapes. The method presented herein greatly improved rubber plantation classification accuracy. Overall classification accuracies derived from the differences of the five vegetation indices varied from 92% to 96% with corresponding kappa coefficients of 0.84–0.92. These results demonstrate the promising potential of phenology-based vegetation index differencing for mapping and monitoring rubber expansion at the regional scale.
Longman Grammar of Spoken and Written English (2000)

Introduction Since its publication in 1985, the outstanding 1,800-page Comprehensive Grammar of the English Language, by Randolph Quirk, Sidney Greenbaum, Geoffrey Leech, and Jan Svartvik, has been the definitive description of the grammar of English and an in-. dispensable reference for any research in the analysis or generation of English that attempts serious coverage of the syntactic phenomena of the language. The new Longman Grammar of Spoken and Written English, by Douglas Biber, Stig Johansson, Geoffrey Leech, Susan Conrad, and Edward Finegan, is an important complement to the earlier work, extending and sometimes revising the descriptions of Quirk et al., by means of an extensive corpus analysis by the five authors and their research assistants. Now, the bookshelf of any researcher in English linguistics is incomplete without both volumes. Like Quirk et al. (hereafter CGEL), Biber and his colleagues attempt a detailed description of all the syntactic phenomena of English. But
Using fuzzy ontology for query refinement in a personalized abstract search engine (2002)

Recommending alternate queries during information seeking activities is an important feature in a Web-based search engine because users often do not know the exact terms to locate the information relevant to their interests. This paper describes an approach to construct automatically a fuzzy ontology that can be used to refine a user's query. The method has been incorporated in a domain-specific search engine namely Personalized Abstract Search Services (PASS). Preliminary results suggest that the basic approaches adopted as well as the technique developed for practical use are intuitively promising.
The requirements of recording and using provenance in e- Science experiments (2005)

Abstract. In e-Science experiments, it is vital to record the experimental process for later use such as in interpreting results, verifying that the correct process took place or tracing where data came from. The process that led to some data is called the provenance of that data, and a provenance architecture is the software architecture for a system that will provide the necessary functionality to record, store and use process documentation to determine the provenance of data items. However, there has been little principled analysis of what is actually required of a provenance architecture, so it is impossible to determine the functionality they would ideally support. In this paper, we present use cases for a provenance architecture from current experiments in biology, chemistry, physics and computer science, and analyse the use cases to determine the technical requirements of a generic, application-independent architecture. We propose an architecture that meets these requirements and evaluate a preliminary implementation by attempting to realise two of the use cases. 1.
Adding to the standards (2005)

Graeme Prior has been a senior administator of one of the world's leading aged care organisations since leaving an accounting position in 1992. Now he believes all of our numbers are up in the queue to play our part in improving the system. The responsibility, indeed the spirit, must come from within, he says.
Space-Time Bit-Interleaved Coded Modulation for OFDM Systems (2004)

Space-time coding techniques significantly improve transmission efficiency in radio channels by using multiple transmit and/or receive antennas and coordination of the signaling over these antennas. Bit-interleaved coded modulation gives good diversity gains with higher order modulation schemes using well-known binary convolutional codes on a single transmit and receive antenna link. By using orthogonal frequency division multiplexing (OFDM), wideband transmission can be achieved over frequency-selective fading radio channels without adaptive equalizers. In this correspondence, we combine these three ideas into a family of flexible space-time coding methods. The pairwise error probability is analyzed based on the correlated fading assumption. Near-optimum iterative decoders are evaluated by means of simulations for slowly varying wireless channels. Theoretical evaluation of the achievable degree of diversity is also presented. Significant performance gains over the wireless local area network (LAN) 802.11a standard system are reported.
Crosslinking by advanced glycation end products increases the stiffness of the collagen network in human articular cartilage: A possible mechanism through which age is a risk factor for osteoarthritis (2002)

Increasing cartilage AGE crosslinking by in vitro incubation with threose resulted in increased stiffness of the collagen network. Increased stiffness by AGE crosslinking may contribute to the age-related failure of the collagen network in human articular cartilage to resist damage. Thus, the age-related accumulation of AGE crosslinks presents a putative molecular mechanism whereby age is a predisposing factor for the development of OA.
A rapid bioluminescence assay for measuring myeloperoxidase activity in human plasma (2015)

Myeloperoxidase (MPO) is a circulating cardiovascular disease (CVD) biomarker used to estimate clinical risk and patient prognosis. Current enzyme-linked immunosorbent assays (ELISA) for MPO concentration are costly and time-intensive. Here we report a novel bioluminescence assay, designated MPO activity on a polymer surface (MAPS), for measuring MPO activity in human plasma samples using the bioluminescent substrate L-012. The method delivers a result in under an hour and is resistant to confounding effects from endogenous MPO inhibitors. In a pilot clinical study, we compared MAPS and two clinical ELISAs using 72 plasma samples from cardiac catheterization patients. Results from parallel MAPS and ELISAs were concordant within 2±11 μg l(-1) MPO with similar uncertainty and reproducibility. Results between parallel MAPS and ELISA were in better agreement than those between independent ELISAs. MAPS may provide an inexpensive and rapid assay for determining MPO activity in plasma samples from patients with CVD or potentially other immune and inflammatory disorders.
The Design of the Borealis Stream Processing Engine (2005)

Borealis is a second-generation distributed stream processing engine that is being developed at Brandeis University, Brown University, and MIT. Borealis inherits core stream processing functionality from Aurora [14] and distribution functionality from Medusa [51]. Borealis modifies and extends both systems in non-trivial and critical ways to provide advanced capabilities that are commonly required by newly-emerging stream processing applications. In this paper, we outline the basic design and functionality of Borealis. Through sample real-world applications, we motivate the need for dynamically revising query results and modifying query specifications. We then describe how Borealis addresses these challenges through an innovative set of features, including revision records, time travel, and control lines. Finally, we present a highly flexible and scalable QoS-based optimization model that operates across server and sensor networks and a new fault-tolerance model with flexible consistency-availability trade-offs.
Cocaine and Other Stimulants (1988)

SENSATIONALISM and shifting acceptance of drug use have influenced much of what has been written about cocaine. This review attempts a reasoned psychiatric appraisal of the prototypical abused psychomotor stimulants, cocaine and the amphetamines. We review the historical and epidemiologic features of the recent upsurge in cocaine abuse, summarize clinical psychiatric observations about stimulant abuse and emerging treatment approaches, and describe new perceptions of the biologic nature of stimulant addiction. Because emergency medical treatment of stimulant overdose and medical complications of cocaine and amphetamine abuse have been reviewed recently,1 2 3 4 we have excluded these topics.Recent History and EpidemiologySeven years . . .
Evidence based guidelines for complex regional pain syndrome type 1 (2010)

Based on the literature identified and the extent of evidence found for therapeutic interventions for CRPS-I, we conclude that further research is needed into each of the therapeutic modalities discussed in the guidelines.
A Novel Adenovirus Type 6 (Ad6)-Based Hepatitis C Virus Vector That Overcomes Preexisting Anti-Ad5 Immunity and Induces Potent and Broad Cellular Immune Responses in Rhesus Macaques (2006)

Success in resolving hepatitis C virus (HCV) infection has been correlated to vigorous, multispecific, and sustained CD8(+) T-cell response in humans and chimpanzees. The efficacy of inducing T-cell-mediated immunity by recombinant serotype 5 adenovirus vector has been proven in many animal models of infectious diseases, but its immunogenicity can be negatively influenced by preexisting immunity against the vector itself. To evaluate the less prevalent adenovirus serotype 6 (Ad6) as an alternative vector for and HCV vaccine development, we have generated serotype 5 and 6 adenoviral vectors directing expression of the nonstructural region of HCV (MRKAd5-NSmut and MRKAd6-NSmut). Immunogenicity studies in mice showed that the two vectors induced comparable T-cell responses but that only MRKAd6-NSmut was not suppressed in the presence of anti-Ad5 immunity. In contrast, preexisting anti-Ad5 immunity dramatically blunted the immunogenicity of the serotype 5-based HCV vector. Furthermore, MRKAd6-NSmut showed equivalent potency, breadth, and longevity of HCV-specific T-cell responses in rhesus macaques as the corresponding Ad5-based vector over a wide range of doses and was capable of boosting DNA-primed animals even if administered at low doses. These data support the use of the MRKAd6-NSmut for anti-HCV immunotherapy and, more generally, for the Ad6 serotype as a better genetic vaccine vehicle than Ad5.
Polylysine and CVIM Sequences of K-RasB Dictate Specificity of Prenylation and Confer Resistance to Benzodiazepine Peptidomimetic in Vitro (1995)

BZA-5B, a benzodiazepine peptidomimetic, inhibits CAAX farnesyltransferase (FTase) and blocks attachment of farnesyl groups to oncogenic and wild-type H-Ras in animal cells. This compound slows the growth of cells transformed with oncogenic H-Ras at concentrations that do not affect the growth of nontransformed cells. This finding suggested that nontransformed cells may produce a form of Ras whose prenylation is resistant to BZA-5B. In the current studies, we found that FTase had a 50-fold higher affinity for K-RasB than for H-Ras in vitro. Farnesylation of K-RasB was inhibited by BZA-2B, the active form of BZA-5B, but only at concentrations that were 8-fold higher than those that inhibited farnesylation of H-Ras. K-RasB, but not H-Ras, was also a substrate for CAAX geranylgeranyltransferase-1 (GGTase-1), and its affinity for the enzyme was equal to that of Rap1B, an authentic leucine-terminated substrate for GGTase-1. Inhibition of the geranylgeranylation of K-RasB occurred only at high concentrations of BZA-2B. All of these properties of K-RasB were traced to the combined effects of its COOH-terminal CVIM sequence and the adjacent polylysine sequence, neither of which is present in H-Ras. These studies provide a potential explanation for the resistance of nontransformed cells to growth inhibition by BZA-5B. Inasmuch as the majority of Ras-related human cancers contain oncogenic versions of K-RasB rather than H-Ras, the current data suggest that in vitro studies of FTase inhibitors with potential anti-cancer activity should use authentic K-RasB as a substrate.
Altered Cardiovascular Variability in Obstructive Sleep Apnea (1998)

Cardiovascular variability is altered in patients with OSA. This alteration is evident even in the absence of hypertension, heart failure, or other disease states and may be linked to the severity of OSA. Abnormalities in cardiovascular variability may be implicated in the subsequent development of overt cardiovascular disease in patients with OSA.