gebhart/patrepeval huggingface dataset:
Catalytic consumption of nitric oxide by 12/15- lipoxygenase: Inhibition of monocyte soluble guanylate cyclase activation (2001)

12/15-Lipoxygenase (LOX) activity is elevated in vascular diseases associated with impaired nitric oxide (( small middle dot)NO) bioactivity, such as hypertension and atherosclerosis. In this study, primary porcine monocytes expressing 12/15-LOX, rat A10 smooth muscle cells transfected with murine 12/15-LOX, and purified porcine 12/15-LOX all consumed *NO in the presence of lipid substrate. Suppression of LOX diene conjugation by *NO was also found, although the lipid product profile was unchanged. *NO consumption by porcine monocytes was inhibited by the LOX inhibitor, eicosatetraynoic acid. Rates of arachidonate (AA)- or linoleate (LA)-dependent *NO depletion by porcine monocytes (2.68 +/- 0.03 nmol x min(-1) x 10(6) cells(-1) and 1.5 +/- 0.25 nmol x min(-1) x 10(6) cells(-1), respectively) were several-fold greater than rates of *NO generation by cytokine-activated macrophages (0.1-0.2 nmol x min(-1) x 10(6) cells(-1)) and LA-dependent *NO consumption by primary porcine monocytes inhibited *NO activation of soluble guanylate cyclase. These data indicate that catalytic *NO consumption by 12/15-LOX modulates monocyte *NO signaling and suggest that LOXs may contribute to vascular dysfunction not only by the bioactivity of their lipid products, but also by serving as catalytic sinks for *NO in the vasculature.
VLSI architectures for video signal processing (1995)

The paper presents an overview on architectures for VLSI implementations of video compression schemes as specified by standardization committees of the ITU and ISO, focussing on programmable architectures. Programmable video signal processors are classified and specified as homogeneous and heterogeneous processor architectures. Heterogeneous processors outperform homogeneous processors due to adaptation to the requirements of special subtasks by dedicated modules. The majority of heterogeneous processors incorporate dedicated modules for high performance subtasks of high regularity like DCT and block matching. By normalization to a fictive 1.0 micron CMOS process typical linear relationships between silicon area and throughput rate have been determined for the different architectural styles. This relationship indicates a figure of merit for silicon efficiency.
Interleukin‐6 and its receptor in cancer (2007)

Interleukin-6 (IL-6) plays a major role in the response to injury or infection and is involved in the immune response, inflammation, and hematopoiesis. Its deregulation impacts numerous disease states, including many types of cancer. Consequently, modulating IL-6 may be an innovative therapeutic strategy in several diseases. A review of relevant published literature regarding IL-6 and its receptor was performed. In addition, a review of the relevance of this cytokine system to human illness, particularly in cancer, was undertaken. IL-6 is a pleiotropic cytokine that is involved in the physiology of virtually every organ system. Aberrant expression of this cytokine has been implicated in diverse human illnesses, most notably inflammatory and autoimmune disorders, coronary artery and neurologic disease, gestational problems, and neoplasms. In cancer, high levels of circulating IL-6 are observed in almost every type of tumor studied and predict a poor outcome. Furthermore, elevated IL-6 levels are associated strongly with several of the striking phenotypic features of cancer. Several molecules have been developed recently that target the biologic function of IL-6. Early results in the clinic suggest that this strategy may have a significant salutary impact on diverse tumors. The field of cytokine research has yielded a deep understanding of the fundamental role of IL-6 and its receptor in health and disease. Therapeutic targeting of IL-6 and its receptor in cancer has strong biologic rationale, and there is preliminary evidence suggesting that targeting of the IL-6 system may be beneficial in the treatment of cancer.
ADADELTA: An Adaptive Learning Rate Method (2012)

We present a novel per-dimension learning rate method for gradient descent called ADADELTA. The method dynamically adapts over time using only first order information and has minimal computational overhead beyond vanilla stochastic gradient descent. The method requires no manual tuning of a learning rate and appears robust to noisy gradient information, different model architecture choices, various data modalities and selection of hyperparameters. We show promising results compared to other methods on the MNIST digit classification task using a single machine and on a large scale voice dataset in a distributed cluster environment.
Age-Dependent and Task-Related Morphological Changes in the Brain and The Mushroom Bodies of The Ant Camponotus Floridanus (1996)

Based on a brief description of the general brain morphology of Camponotus floridanus, development of the brain is examined in ants of different ages (pupa to 10 months). During this period, brain volume increases by approximately 20 % while the antennal lobes and the mushroom body neuropile show a more substantial growth, almost doubling their volume. In addition to the age-dependent changes, the volume of the mushroom body neuropile also increases as a consequence of behavioural activity associated with brood care and foraging. Foraging activity may lead to a more than 50 % additional increase in mushroom body neuropile volume. It is unlikely that the growth of mushroom body neuropile results from cell proliferation because no neurogenesis could be observed in adult ant brains.
Human c-fms proto-oncogene: comparative analysis with an abnormal allele. (1985)

The organization of the human c-fms proto-oncogene has been determined and compared with an abnormal allele. The human v-fms homologous genetic sequences are dispersed discontinuously and colinearly with the viral oncogene over a DNA region of ca. 32 kilobase pairs. The abnormal c-fms locus contains a small deletion in its 3' portion. DNA sequencing analysis indicated that it was 426 base pairs in size and located in close proximity to a putative c-fms exon.
A Probabilistic Approach for Concurrent Map Acquisition and Localization for Mobile Robots (1997)

This paper addresses the problem of building large-scale geometric maps of indoor environments with mobile robots. It poses the map building problem as a constrained, probabilistic maximum-likelihood estimation problem. It then devises a practical algorithm for generating the most likely map from data, along with the most likely path taken by the robot. Experimental results in cyclic environments of size up to 80 by 25 meter illustrate the appropriateness of the approach. y These authors are affiliated with the Institut fur Informatik III, Universat Bonn, Germany The research was financially supported by Daimler Benz Research, Germany. Keywords: autonomous robots, Baum-Welch, mobile robots, navigation, localization, mapping, positioning, probabilistic algorithms, robot mapping A Probabilistic Approach for Concurrent Map Acquisition and Localization 1 1 Introduction Over the last two decades or so, the problem of acquiring maps in large-scale indoor environments has received con...
Homa: An Efficient Topology and Route Management Approach in SD-WAN Overlays (2020)

This paper presents an efficient topology and route management approach in Software-Defined Wide Area Networks (SD-WAN). Traditional WANs suffer from low utilization and lack of global view of the network. Therefore, during failures, topology/service/traffic changes, or new policy requirements, the system does not always converge to the global optimal state. Using Software Defined Networking architectures in WANs provides the opportunity to design WANs with higher fault tolerance, scalability, and manageability. We exploit the correlation matrix derived from monitoring system between the virtual links to infer the underlying route topology and propose a route update approach that minimizes the total route update cost on all flows. We formulate the problem as an integer linear programming optimization problem and provide a centralized control approach that minimizes the total cost while satisfying the quality of service (QoS) on all flows. Experimental results on real network topologies demonstrate the effectiveness of the proposed approach in terms of disruption cost and average disrupted flows.
An electrochemical peptide-based biosensing platform for HIV detection (2009)

We have fabricated a potentially generalizable electrochemical peptide-based (E-PB) sensor for the detection of HIV anti-p24 antibodies. The E-PB sensor is sensitive, specific and fares well even when challenged in a realistically complex medium such as human urine proxy.
Xavier Le Roy (2013)

Chris Sharp describes his initiation into Xavier Le Roy’s ‘Retrospective?, arguing that his vulnerability as an artist, as well as the agency allowed to audiences in his performances, makes Le Roy ‘the ignorant choreographer’.
Change in chronic anorexic patients (2009)

In an attempt to explore the possible factors that contribute to psychic growth, development, change and recovery in anorexic patients, it seems essential to return to the important mental processes that begin during infancy. I am suggesting here that the types of internal conflict and mental dysfunctioning that inhibits the anorexic patient from being able to ‘take‐in’ from another, and obstructs the possibility of recovery, can to some extent be explained by a failure in their early containment. By using clinical and theoretical material I will attempt to demonstrate that a recovery from such developmental failure is integral in enabling some degree of psychic and behavioural change in the anorexic patient.
Method for the Purification of Tissue DNA Suitable for PCR After Fixation with Bouinʼs Fluid (1997)

Paraffin-embedded tissues are often the only available material to perform polymerase chain reaction (PCR)-based analysis in various medical purposes. Unfortunately, the use in many countries of acid fixatives such as Bouin's fluid limits the use of such a material for molecular analysis. This article reports the methodological details of a DNA purification technique from Bouin-fixed and paraffin-embedded samples based on a double washing, in an alcohol then in an aqueous medium, of the DNA, which enables PCR reactions from this material. Comparison of the results with those obtained by organic solvent purification of DNA from frozen tissue fragments showed excellent reproducibility in terms of detection of an amplification product on agarose gel. However, differences between the methods were quite frequently seen in the allelic typing profile of microsatellite sequences (CA repeats), either as neo-alleles or by the loss of normal alleles in the fixed materials that constitute a limitation in using DNA from Bouin-fixed tissue as a substrate for fine allelotyping.
Substrate Specificity of Human Collagenase 3 Assessed Using a Phage-displayed Peptide Library (2000)

The substrate specificity of human collagenase 3 (MMP-13), a member of the matrix metalloproteinase family, is investigated using a phage-displayed random hexapeptide library containing 2 x 10(8) independent recombinants. A total of 35 phage clones that express a peptide sequence that can be hydrolyzed by the recombinant catalytic domain of human collagenase 3 are identified. The translated DNA sequence of these clones reveals highly conserved putative P1, P2, P3 and P1', P2', and P3' subsites of the peptide substrates. Kinetic analysis of synthetic peptide substrates made from human collagenase 3 selected phage clones reveals that some of the substrates are highly active and selective. The most active substrate, 2, 4-dinitrophenyl-GPLGMRGL-NH(2) (CP), has a k(cat)/K(m) value of 4.22 x 10(6) m(-)(1) s(-)(1) for hydrolysis by collagenase 3. CP was synthesized as a consensus sequence deduced from the preferred subsites of the aligned 35 phage clones. Peptide substrate CP is 1300-, 11-, and 820-fold selective for human collagenase 3 over the MMPs stromelysin-1, gelatinase B, and collagenase 1, respectively. In addition, cleavage of CP is 37-fold faster than peptide NF derived from the major MMP-processing site in aggrecan. Phage display screening also selected five substrate sequences that share sequence homology with a major MMP cleavage sequence in aggrecan and seven substrate sequences that share sequence homology with the primary collagenase cleavage site of human type II collagen. In addition, putative cleavage sites similar to the consensus sequence are found in human type IV collagen. These findings support previous observations that human collagenase 3 can degrade aggrecan, type II and type IV collagens.
Fibroblast Activation Protein in Remodeling Tissues (2012)

Tissue remodeling is critical during development and wound healing. It also characterizes a number of pathologic conditions, including chronic inflammation, fibrosis and cancer. It is well appreciated that reactive stromal cells play critical roles in these settings. However, understanding of the mechanisms involved in the differentiation of reactive stromal cells and their biologic activities has been hampered by the fact that they are generated from diverse progenitors, and by their phenotypic and function heterogeneity. Furthermore, molecular markers that are expressed by all reactive stromal cells and that distinguish them from all other cell types have been lacking. Fibroblast activation protein (FAP) is a serine protease that was originally discovered as a cell surface protein expressed on astrocytomas and sarcomas. Over the last two decades, FAP has attracted increasing attention as a selective marker of carcinoma-associated fibroblasts (CAFs) and more broadly, of activated fibroblasts in tissues undergoing remodeling of their extracellular matrix (ECM) due to chronic inflammation, fibrosis or wound healing. Herein we review the evidence that FAP is indeed a robust and selective marker for reactive mesenchymal stromal cells associated with pathophysiologic tissue remodeling. We also review recent insights obtained using FAP as a tool to define the relationship between subpopulations of reactive stromal cells in various settings of tissue remodeling. Furthermore, we review recent genetic and pharmacologic data indicating that FAP and FAP-expressing cells play important roles in such conditions. Finally, we discuss the potential risks and therapeutic benefits of targeting FAP and FAP-expressing cells, as well as approaches to do so.
Pinpoint: problem determination in large, dynamic Internet services (2003)

Traditional problem determination techniques rely on static dependency models that are difficult to generate accurately in today's large, distributed, and dynamic application environments such as e-commerce systems. We present a dynamic analysis methodology that automates problem determination in these environments by 1) coarse-grained tagging of numerous real client requests as they travel through the system and 2) using data mining techniques to correlate the believed failures and successes of these requests to determine which components are most likely to be at fault. To validate our methodology, we have implemented Pinpoint, a framework for root cause analysis on the J2EE platform that requires no knowledge of the application components. Pinpoint consists of three parts: a communications layer that traces client requests, a failure detector that uses traffic-sniffing and middleware instrumentation, and a data analysis engine. We evaluate Pinpoint by injecting faults into various application components and show that Pinpoint identifies the faulty components with high accuracy and produces few false-positives.
Mutant of Escherichia coli K-12 Defective in d -Glucosamine Biosynthesis (1971)

A mutant was isolated from a derivative of Escherichia coli K-12 after mutagenesis with N-methyl-N'-nitro-N-nitrosoguanidine. This mutant contained normal levels of 2-amino-2-deoxy-d-glucose-6-phosphate ketol-isomerase (deaminating) (EC 5.3.1.10), but no detectable activity of l-glutamine:d-fructose-6-phosphate amino-transferase (EC 2.6.1.16). It required either N-acetyl-d-glucosamine or d-glucosamine for growth, and went into rapid lysis when the supply of these compounds was exhausted. In medium containing 11% sucrose, the cells were converted into spheroplasts in the absence of d-glucosamine.
Fast and scalable layer four switching (1998)

In Layer Four switching, the route and resources allocated to a packet are determined by the destination address as well as other header fields of the packet such as source address, TCP and UDP port numbers. Layer Four switching unifies firewall processing, RSVP style resource reservation filters, QoS Routing, and normal unicast and multicast forwarding into a single framework. In this framework, the forwarding database of a router consists of a potentially large number of filters on key header fields. A given packet header can match multiple filters, so each filter is given a cost, and the packet is forwarded using the least cost matching filter.In this paper, we describe two new algorithms for solving the least cost matching filter problem at high speeds. Our first algorithm is based on a grid-of-tries construction and works optimally for processing filters consisting of two prefix fields (such as destination-source filters) using linear space. Our second algorithm, cross-producting, provides fast lookup times for arbitrary filters but potentially requires large storage. We describe a combination scheme that combines the advantages of both schemes. The combination scheme can be optimized to handle pure destination prefix filters in 4 memory accesses, destination-source filters in 8 memory accesses worst case, and all other filters in 11 memory accesses in the typical case.
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function (2010)

GeneMANIA (http://www.genemania.org) is a flexible, user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data. GeneMANIA also reports weights that indicate the predictive value of each selected data set for the query. Six organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Homo sapiens and Saccharomyces cerevisiae) and hundreds of data sets have been collected from GEO, BioGRID, Pathway Commons and I2D, as well as organism-specific functional genomics data sets. Users can select arbitrary subsets of the data sets associated with an organism to perform their analyses and can upload their own data sets to analyze. The GeneMANIA algorithm performs as well or better than other gene function prediction methods on yeast and mouse benchmarks. The high accuracy of the GeneMANIA prediction algorithm, an intuitive user interface and large database make GeneMANIA a useful tool for any biologist.
Symbolic probabilistic inference in belief networks (1990)

The Symbolic Probabilistic Inference (SPI) Algorithm [D'Ambrosio, 1989] provides an efficient framework for resolving general queries on a belief network. It applies the concept of dependency-directed backward search to probabilistic inference, and is incremental with respect to both queries and observations. Unlike most belief network algorithms, SPI is goal directed, performing only those calculations that are required to respond to queries. The directed graph of the underlying belief network is used to develop a tree structure for recursive query processing. This allows effective caching of intermediate results and significant opportunities for parallel computation. A simple preprocessing step ensures that, given the search tree, the algorithm will include no unnecessary distributions. The preprocessing step eliminates dimensions from the intermediate results and prunes the search path.
A HYBRID APPROACH TO MUSICAL NOTE ONSET DETECTION (2002)

ABSTRACT Common problems with current methods of musical note onsetdetection are detection of fast passages of musical audio, detectionof all onsets within a passage with a strong dynamic range anddetection of onsets of varying types, such as multi-instrumentalmusic. We present a method that uses a subband decompositionapproach to onset detection. An energy-based detector is used onthe upper subbands to detect strong transient events. This yieldsprecision in the time resolution of the onsets, but does not detectsofter or weaker onsets. A frequency based distance measure isformulated for use with the lower subbands, improving detectionaccuracy of softer onsets.We also present a method for improving the detection func-tion, by using a smoothed difference metric. Finally, we show thatthe detection threshold may be set automatically from analysis ofthe statistics of the detection function, with results comparable inmost places to manual setting of thresholds. 1. BACKGROUND Note onset detection aims to ﬁnd the start of musical events fromthe audio signal itself. It is an essential component of many largersystems such as automatic musical transcription schemes, non-linear time scaling [1], and many new audio effects and editingtools, such as ’beat detective’[2] from Digidesign. It is also com-mon for many synthesis applications to require isolation of the at-tack portions of notes.Despite some proposed solutions, it remains an unsolved, andoften over-simpliﬁed, problem. Traditional methods such as highfrequency detection rely on theassumption that allnote onsets con-tain high frequency energy [3]. The assumption that, for most in-struments, a note will contain more high frequency energy at itsonset is fair to make. However, in the case of real world audioexamples where there may be high notes with considerable highfrequency energy at their onset in the same region as low noteswith weak high frequency energy, the lower notes become almostimpossible to detect from the detection function. This work ad-dresses this problem directly.If we consider the nature of musical signals, there is a range ofdifferent types of instrument onsets. Figure 1 shows short sectionsof signals from a guitar and a violin. The guitar is a string in-strument that is played percussively, leading to ’hard’ note onsets,appearing as wide-band noise in the spectogram. For this type ofinstrument, high frequency content is a useful detection method.However, the violin in this ﬁgure is an example of a bowed stringinstrument, with a ’soft’ onset. The strings are excited because ofthe stick-slip caused by the friction of the bow. In this case, thenotes are being excited constantly, hence there is little, or no, de-cay. Here, the change in frequency content, particularly at lowerfrequencies, is our best guide to note onsets. Most everyday musi-cal signals contain a range of hard and soft onsets.Figure 1: