gebhart/patrepeval huggingface dataset:
Content-based image retrieval at the end of the early years (2000)

Presents a review of 200 references in content-based image retrieval. The paper starts with discussing the working conditions of content-based retrieval: patterns of use, types of pictures, the role of semantics, and the sensory gap. Subsequent sections discuss computational steps for image retrieval systems. Step one of the review is image processing for retrieval sorted by color, texture, and local geometry. Features for retrieval are discussed next, sorted by: accumulative and global features, salient points, object and shape features, signs, and structural combinations thereof. Similarity of pictures and objects in pictures is reviewed for each of the feature types, in close connection to the types and means of feedback the user of the systems is capable of giving by interaction. We briefly discuss aspects of system engineering: databases, system architecture, and evaluation. In the concluding section, we present our view on: the driving force of the field, the heritage from computer vision, the influence on computer vision, the role of similarity and of interaction, the need for databases, the problem of evaluation, and the role of the semantic gap.
Terahertz Pulsed Spectroscopy of Human Basal Cell Carcinoma (2006)

Good contrast is seen between normal tissue and regions of tumor in terahertz pulsed imaging of basal cell carcinoma (BCC). To date, the source of contrast at terahertz frequencies is not well understood. In this paper we present results of a spectroscopy study comparing the terahertz properties (absorption coefficient and refractive index) of excised normal human skin and BCC. Both the absorption coefficient and refractive index were higher for skin that contained BCC. The difference was statistically significant over the range 0.2 to 2.0 THz (6.6 cm(-1) to 66.6 cm(-1)) for absorption coefficient and 0.25 to 0.90 THz (8.3 cm(-1) to 30 cm(-1)) for refractive index. The maximum difference for absorption was at 0.5 THz(16.7 cm(-1)). These changes are consistent with higher water content. These results account for the contrast seen in terahertz images of BCC and explain why parameters relating to the reflected terahertz pulse provide information about the lateral spread of the tumor. Knowing the properties of the tissue over the terahertz frequency range will enable the use of mathematical models to improve understanding of the terahertz response of normal and diseased tissue.
Predestination: Where Do You Want to Go Today? (2007)

Mobile computers have the potential to provide a new array of location-based services to drivers as they travel around. The predestination algorithm predicts a driver's destination based on both general trends, such as the likelihood that people will choose various types of destinations, and personalized data such as a list of previously visited locations. We designed the algorithm to run on a vehicle's navigation system and learn a driver's habits based on logged GPS measurements. Predictions about destination can be an important component of ubiquitous computing, and we hope that such predictions might one day enhance the provision of information and services to people as they move through the world
VT-ASOS: Holistic system software customization for many cores (2008)

VT-ASOS is a framework for holistic and continuous customization of system software on HPC systems. The framework leverages paravirtualization technology. VT-ASOS extends the Xen hypervisor with interfaces, mechanisms, and policies for supporting application-specific resource management schemes on many-core systems, while retaining the advantages of virtualization, including protection, performance isolation, and fault tolerance. We outline the VTASOS framework and present results from a preliminary prototype, which enables static customization of scheduler parameters and runtime adaptation of parallel virtual machines.
Ranking and Matchmaking (2006)

Online game modes are gradually becoming the standard for console games, rather than an added bonus. But how do you get the right players playing against the right people, close enough in skill to be challenging, but not so difficult as to be frustrating?
Web image retrieval re-ranking with relevance model (2004)

Web image retrieval is a challenging task that requires efforts from image processing, link structure analysis, and Web text retrieval. Since content-based image retrieval is still considered very difficult, most current large-scale Web image search engines exploit text and link structure to "understand" the content of the Web images. However, local text information, such as caption, filenames and adjacent text, is not always reliable and informative. Therefore, global information should be taken into account when a Web image retrieval system makes relevance judgment. We propose a re-ranking method to improve Web image retrieval by reordering the images retrieved from an image search engine. The re-ranking process is based on a relevance model, which is a probabilistic model that evaluates the relevance of the HTML document linking to the image, and assigns a probability of relevance. The experiment results showed that the re-ranked image retrieval achieved better performance than original Web image retrieval, suggesting the effectiveness of the re-ranking method. The relevance model is learned from the Internet without preparing any training data and independent of the underlying algorithm of the image search engines. The re-ranking process should be applicable to any image search engines with little effort.
AN ALTERNATIVE STRATEGY FOR NON‐LINEAR INVERSION OF SEISMIC WAVEFORMS1 (1991)

A bstract A common example of a large‐scale non‐linear inverse problem is the inversion of seismic waveforms. Techniques used to solve this type of problem usually involve finding the minimum of some misfit function between observations and theoretical predictions. As the size of the problem increases, techniques requiring the inversion of large matrices become very cumbersome. Considerable storage and computational effort are required to perform the inversion and to avoid stability problems. Consequently methods which do not require any large‐scale matrix inversion have proved to be very popular. Currently, descent type algorithms are in widespread use. Usually at each iteration a descent direction is derived from the gradient of the misfit function and an improvement is made to an existing model based on this, and perhaps previous descent directions. A common feature in nearly all geophysically relevant problems is the existence of separate parameter types in the inversion, i.e. unknowns of different dimension and character. However, this fundamental difference in parameter types is not reflected in the inversion algorithms used. Usually gradient methods either mix parameter types together and take little notice of the individual character or assume some knowledge of their relative importance within the inversion process. We propose a new strategy for the non‐linear inversion of multi‐offset reflection data. The paper is entirely theoretical and its aim is to show how a technique which has been applied in reflection tomography and to the inversion of arrival times for 3D structure, may be used in the waveform case. Specifically we show how to extend the algorithm presented by Tarantola to incorporate the subspace scheme. The proposed strategy involves no large‐scale matrix inversion but pays particular attention to different parameter types in the inversion. We use the formulae of Tarantola to state the problem as one of optimization and derive the same descent vectors. The new technique splits the descent vector so that each part depends on a different parameter type, and proceeds to minimize the misfit function within the sub‐space defined by these individual descent vectors. In this way, optimal use is made of the descent vector components, i.e. one finds the combination which produces the greatest reduction in the misfit function based on a local linearization of the problem within the subspace. This is not the case with other gradient methods. By solving a linearized problem in the chosen subspace, at each iteration one need only invert a small well‐conditioned matrix (the projection of the full Hessian on to the subspace). The method is a hybrid between gradient and matrix inversion methods. The proposed algorithm requires the same gradient vectors to be determined as in the algorithm of Tarantola, although its primary aim is to make better use of those calculations in minimizing the objective function.
The Role of the Leukocyte Adhesion Molecules VLA-4, LFA-1, and Mac-1 in Allergic Airway Responses in the Rat (1994)

Chronic airway inflammation is involved in the pathogenesis of asthma. The leukocyte adhesion molecules VLA-4 of the beta 1 integrin family, and LFA-1 and Mac-1 of the beta 2 family have a demonstrated role in leukocyte-endothelial adherence and may play a role in airway inflammation in asthma. We studied the effects of blocking VLA-4 (CD49d/CD29) and both LFA-1 (CD11a/CD18) and Mac-1 (CD11b/CD18) airway responses and inflammation in rats. BN rats were sensitized with ovalbumin (OA) subcutaneously and were challenged 14 d later with aerosolized OA. Twelve rats were treated prior to challenge with anti-rat VLA-4 monoclonal antibody (mAb), 10 rats received both anti-LFA-1 and anti-Mac-1 mAb, and 14 rats received a control mAb. The pulmonary resistance (RL) was measured for 8 h after challenge. The inflammatory response was evaluated by bronchoalveolar lavage (BAL) and by measuring the lung and airway inflammatory cells retrieved by enzymative dispersion. The early response was significantly decreased in both the anti-VLA-4 group (131% baseline RL) and the anti-LFA-1/Mac-1 group (118%; p < 0.05) compared with the control group (202%). The late response was also significantly decreased in both the anti-VLA-4 (3.7) and anti-LFA-1/Mac-1 (2.6) groups compared with the control group (19.7). The significant differences in bronchoalveolar lavage were a decrease in neutrophils in the LFA-1/Mac-1 group and an increase in macrophages in the anti-VLA-4 group.(ABSTRACT TRUNCATED AT 250 WORDS)
Localization of two epitopes of apolipoprotein A-I that are exposed on human high density lipoproteins using monoclonal antibodies and synthetic peptides. (1988)

To understand the structure of apolipoprotein A-I, we have used an immunochemical approach and identified specific regions of apoA-I that may be exposed on the apoprotein as it exists on high density lipoprotein (HDL). Twelve mouse monoclonal antibodies specific for human apoA-I were generated from six fusions. Thirteen synthetic peptides of between 5 and 16 amino acid residues in length, which span the amino-terminal two-thirds of apoA-I, were tested for their ability to react with each of the 12 antibodies. In a competitive solid-phase radioimmunoassay, a synthetic peptide, which represented residues 1-15 of mature apoA-I, inhibited the binding of antibody AI-16 to immobilized HDL. Similarly, a synthetic peptide, which represented residues 90-105 of apoA-I, inhibited the binding of antibody AI-18 to immobilized HDL. Using systematic changes in the size and sequence of the oligopeptides, the limits and essential amino acid residues of these epitopes were defined. Comparisons of the slopes of the competition curves obtained with immunoreactive peptides, isolated apoA-I, and HDL verified that these two regions of apoA-I are exposed on the surface of apoA-I as it exists on native HDL.
Feedback Regulation of Nitrate Influx in Barley Roots by Nitrate, Nitrite, and Ammonium (1993)

The short-lived radiotracer 13N was used to study feedback regulation of nitrate influx through the inducible high-affinity transport system of barley (Hordeum vulgare L. cv Steptoe) roots. Both wild-type plants and the mutant line Az12:Az70 (genotype nar1a;nar7w), which is deficient in the NADH-specific and NAD(P)H-bispecific nitrate reductases (R.L. Warner, R.C. Huffaker [1989] Plant Physiol 91: 947-953) showed strong feedback inhibition of nitrate influx within approximately 5 d of exposure to 100 fmu]M nitrate. The result with the mutant, in which the flux of nitrogen into reduced products is greatly reduced, indicated that nitrate itself was capable of exercising feedback regulation upon its own influx. This conclusion was supported by the observation that feedback in wild-type plants occurred in both the presence and absence of L-methionine sulfoximine, an inhibitor of ammonium assimilation. Nitrite and ammonium were also found to be capable of exerting feedback inhibition upon nitrate influx, although it was not determined whether these ions themselves or subsequent metabolites were responsible for the effect. It is suggested that feed-back regulation of nitrate influx is potentially mediated through several nitrogen pools, including that of nitrate itself.
[Fluorescence in Situ Hybridization for Detecting Molecular Cytogenetic Abnormalities of Chronic Lymphocytic Leukemia]. (2020)

FISH can greatly increase the detection rate of molecular cytogenetic abnormalities in CLL patients, which, as a powerful supplement to the conventional cytogenetics, can be applied for the clinical staging and prognosis evaluation of CLL patients.
Progression of primary pneumonic plague: A mouse model of infection, pathology, and bacterial transcriptional activity (2005)

Although pneumonic plague is the deadliest manifestation of disease caused by the bacterium Yersinia pestis, there is surprisingly little information on the cellular and molecular mechanisms responsible for Y. pestis-triggered pathology in the lung. Therefore, to understand the progression of this unique disease, we characterized an intranasal mouse model of primary pneumonic plague. Mice succumbed to a purulent multifocal severe exudative bronchopneumonia that closely resembles the disease observed in humans. Analyses revealed a strikingly biphasic syndrome, in which the infection begins with an antiinflammatory state in the first 24-36 h that rapidly progresses to a highly proinflammatory state by 48 h and death by 3 days. To assess the adaptation of Y. pestis to a mammalian environment, we used DNA microarray technology to analyze the transcriptional responses of the bacteria during interaction with the mouse lung. Included among the genes up-regulated in vivo are those comprising the yop-ysc type III secretion system and genes contained within the chromosomal pigmentation locus, validating the use of this technology to identify loci essential to the virulence of Y. pestis.
Activated Raf-1 causes growth arrest in human small cell lung cancer cells. (1998)

Small cell lung cancer (SCLC) accounts for 25% of all lung cancers, and is almost uniformly fatal. Unlike other lung cancers, ras mutations have not been reported in SCLC, suggesting that activation of ras-associated signal transduction pathways such as the raf-MEK mitogen-activated protein kinases (MAPK) are associated with biological consequences that are unique from other cancers. The biological effects of raf activation in small cell lung cancer cells was determined by transfecting NCI-H209 or NCI-H510 SCLC cells with a gene encoding a fusion protein consisting of an oncogenic form of human Raf-1 and the hormone binding domain of the estrogen receptor (DeltaRaf-1:ER), which can be activated with estradiol. DeltaRaf-1:ER activation resulted in phosphorylation of MAPK. Activation of this pathway caused a dramatic loss of soft agar cloning ability, suppression of growth capacity, associated with cell accumulation in G1 and G2, and S phase depletion. Raf activation in these SCLC cells was accompanied by a marked induction of the cyclin-dependent kinase (cdk) inhibitor p27(kip1), and a decrease in cdk2 protein kinase activities. Each of these events can be inhibited by pretreatment with the MEK inhibitor PD098059. These data demonstrate that MAPK activation by DeltaRaf-1:ER can activate growth inhibitory pathways leading to cell cycle arrest. These data suggest that raf/MEK/ MAPK pathway activation, rather than inhibition, may be a therapeutic target in SCLC and other neuroendocrine tumors.
Mechanisms of Antigenic Variation in Borrelia hermsii and African Trypanosomes (1995)

Several pathogenic microorganisms, ranging from viruses to protozoa, evade the mammalian immune response by periodically changing the molecular constituents on their surface, a phenomenon called antigenic variation(1). Two pathogens particularly adept at using this strategy are Borrelia hermsii, a prokaryotic spirochete that causes relapsing fever in the western United States and Canada(2), and African trypanosomes, eukaryotic protozoan parasites that cause sleeping sickness in Africa(3). B. hermsii is transmitted by ticks and African trypanosomes by tsetse flies.
The Yeast Deletion Collection: A Decade of Functional Genomics (2014)

The yeast deletion collections comprise >21,000 mutant strains that carry precise start-to-stop deletions of ∼6000 open reading frames. This collection includes heterozygous and homozygous diploids, and haploids of both MAT A: and MATα mating types. The yeast deletion collection, or yeast knockout (YKO) set, represents the first and only complete, systematically constructed deletion collection available for any organism. Conceived during the Saccharomyces cerevisiae sequencing project, work on the project began in 1998 and was completed in 2002. The YKO strains have been used in numerous laboratories in >1000 genome-wide screens. This landmark genome project has inspired development of numerous genome-wide technologies in organisms from yeast to man. Notable spinoff technologies include synthetic genetic array and HIPHOP chemogenomics. In this retrospective, we briefly describe the yeast deletion project and some of its most noteworthy biological contributions and the impact that these collections have had on the yeast research community and on genomics in general.
Colloidal macromolecular phenomena. Part II. Novel microcrystals of polymers (1967)

Abstract Colloidal microcrystalline cellulose, introduced in 1961, now is a successful commercial product with growing world‐wide markets. This paper describes some major findings of our continuing research to convert fibrous or fiber‐forming polymer systems into new colloidal microcrystalline physical states without going through a homogeneous molecular solution phase. Several novel microcrystalline colloidal products from the following natural and/or synthetic polymeric raw materials are described and compared for the first time: cellulose, amylose, collagen, nylon, and chrysotile mineral silicates. Many previously unpublished electron micrographs are presented. These products demonstrate a new and growing field of colloidal microcrystalline polymer science. They open up increasing opportunities for new polymer products based on the original concept, namely, the unhinging of polymer microcrystals from their natural or synthetic network and then by appropriate mechanical energy, releasing them as discrete, submicron colloidal polymer microcrystals dispersed in various liquid media to form unique gel systems, or reaggregated in the dry state to form porous colloidal particles.
The Emerging Concept of Vascular Remodeling (1994)

The vessel wall is an active, integrated organ composed of endothelial, smooth-muscle, and fibroblast cells coupled to each other in a complex autocrine-paracrine set of interactions. The vasculature is capable of sensing changes within its milieu, integrating these signals by intercellular communication, and changing itself through the local production of mediators that influence structure as well as function. Vascular remodeling is an active process of structural alteration that involves changes in at least four cellular processes -- cell growth, cell death, cell migration, and production or degradation of extracellular matrix -- and is dependent on a dynamic interaction between locally . . .
Experimental Evaluation of Real-Time Mechanical Formation Classification using Drill String Vibration Measurements (2012)

Abstract A drill bit creates a hole in subsurface formations by applying weight on bit and rotary speed. The bit is the first segment of the bottom hole assembly (BHA) and the drill string which contacts formation. Today it is possible to monitor drilling parameters such as weight on bit, rotary speed of drill string, azimuthal and inclination angles of the well using downhole sensors. An additional set of parameters recorded and monitored downhole near the bit is the vibration of the drill string as a consequence of the interaction between bit and different formations drilled. Dependent on formation characteristics such as the uniaxial compressive strength of rock, axial vibration is expected to change when the bit contacts formation with changing mechanical properties. Therefore, in case of using drill bits with similar characteristics, recognizing different layers of formation in real-time is expected to be possible if the axial vibration is monitored. Experiments, using a fully automated laboratory scale drilling rig, the CDC miniRig, were performed. A vibration sensor sub is attached to the drill string above the bit. Concrete cubes with uniform strength as well as layered bonded cubes with different strength were drilled using different ranges of weight on bit and rotational speed. Higher order frequency moments were calculated and used for evaluation of the drilled concrete cubes. The cubes were built with different compressive strength and quantified by uniaxial compressive strength measurements prior to the test. The results of the experiments showed good correspondence with the expected behavior and allowed to differentiate the individual layers of concrete of different strength. The means to identify layers of rock based on vibration analysis are described in this paper. Necessary next steps to translate these results to more complex rocks are presented.
Relative Roles of CD90 and c‐Kit to the Regenerative Efficacy of Cardiosphere‐Derived Cells in Humans and in a Mouse Model of Myocardial Infarction (2014)

The majority population of CDCs (CD105(+)/CD90(-)/c-kit(-)) constitutes the active fraction, both in terms of therapeutic efficacy and in the ability to undergo cardiomyogenic differentiation. The c-kit(+) fraction is neither necessary for, nor contributory to, the regenerative efficacy of CDCs.