gebhart/patrepeval huggingface dataset:
Classification of tumor markers. (1996)

Since the discovery of the first tumor markers more than a century ago (Bence-Jones proteins), a vast array of molecules have been described as being associated with cancer. These are generally naturally occurring biomolecules with the exception of neo-antigens expressed in certain tumors induced by viruses. Tumor markers can be broadly classified into tumor specific antigens and tumor-associated markers. Most tumor markers were often heralded as highly tumor specific but subsequent studies demonstrated their presence in normal tissues of the adult or in various stages of ontogeny. As a result, very few tumor-specific antigens can be recognized. The idiotypes of immunoglobulins of B cell tumors and certain neo-antigens of virus induced tumors are two examples that are strictly tumor specific. The vast majority of tumor markers are in reality tumor-associated antigens and can be classified into two types based on their size. The low-molecular weight tumor markers (approximately < 1000 Daltons) include some nucleosides, lipid associated sialic acid, polyamines, pseudouridine, pigment derivatives, and other metabolites. The macromolecular tumor antigens are the most important sub-type useful in the clinical management of cancer patients. The large cancer antigens are either enzymes, growth factors, hormones, receptors, biological response modifiers, oncogenes and their products, or glycoconjugates which include glycoproteins and glycolipids. Collectively all the commercial tumor marker assays available to the oncologist for cancer patient management amount to an annual sales of > $1 billion world wide. The demonstrated clinical usefulness and commercial success of tumor markers have continued to fuel exciting research into the discovery and novel uses of new analytes.
The effects of vegetable oil properties on injection and combustion in two different diesel engines (1984)

Abstract Four different vegetable oils, each in at least 3 different stages of processing, have been characterized according to their physical and chemical properties, their injection and atomization characteristics, and their performance and combustion characteristics in both a direct‐injection and an indirect‐injection diesel engine. The injection and atomization characteristics of the vegetable oils are significantly different than those of petroleum‐derived diesel fuels, mainly as the result of their high viscosities. Heating the oils, however, results in spray characteristics more like those observed with diesel fuel. The 2 engine types demonstrated different sensitivities to the composition of the various oils. The combustion characteristics and the durability of the direct‐injection engine were affected by the oil composition. The indirect‐injection engine, however, was not greatly affected by composition. Two different preliminary specifications have been proposed: a stringent specification including compositional requirements for direct‐injection engines, and a less stringent specification for indirect‐injection engines. The specifications are discussed in terms of the data and the rationale used in their development. Some precautions concerning the application of the specifications are also presented.
Pacifastin-derived Peptides Target Tumors for Use in In Vivo Imaging (2018)

Although there are some obstacles to developing pacifastin-derived peptides for therapeutic activity, these optimized peptides have great promise for cancer imaging.
PATS: A Framework of Pattern-Aware Trajectory Search (2010)

In this paper, we develop a framework of trajectory search called pattern-aware trajectory search (abbreviated as PATS). Given a set of trajectories, potential regions are extracted first and potential regions are viewed as popular regions interested by users. Furthermore, potential regions are organized as a region transition graph where each vertex is a potential region and edges capture sequential travels of potential regions from a set of trajectories given. By exploring the concept of random walk, the attractiveness of a potential region is derived. In light of attractiveness of potential regions the attractiveness of a trajectory is formulated and PATS will return top-K trajectories according to their attractiveness. We evaluated our framework by a real GPS dataset. Experimental results show that PATS is able to retrieve trajectories interested by users.
Visualizing and Understanding Recurrent Networks (2015)

Recurrent Neural Networks (RNNs), and specifically a variant with Long Short-Term Memory (LSTM), are enjoying renewed interest as a result of successful applications in a wide range of machine learning problems that involve sequential data. However, while LSTMs provide exceptional results in practice, the source of their performance and their limitations remain rather poorly understood. Using character-level language models as an interpretable testbed, we aim to bridge this gap by providing an analysis of their representations, predictions and error types. In particular, our experiments reveal the existence of interpretable cells that keep track of long-range dependencies such as line lengths, quotes and brackets. Moreover, our comparative analysis with finite horizon n-gram models traces the source of the LSTM improvements to long-range structural dependencies. Finally, we provide analysis of the remaining errors and suggests areas for further study.
Interactions between endothelial cells and electrospun methacrylic terpolymer fibers for engineered vascular replacements (2009)

A compliant terpolymer made of hexylmethacrylate (HMA), methylmethacrylate (MMA), and methacrylic acid (MAA) intended for use in small diameter vascular graft applications has been developed. The mechanical properties and in vitro biostability of this terpolymer have been previously characterized. The goal of this investigation was to examine the interactions between endothelial cells and the new terpolymer and to evaluate endothelial cell function. Electrospinning was used to produce both oriented and random terpolymer fiber scaffolds. Smooth solution cast films and tissue culture polystyrene were used as negative and positive controls, respectively. Human blood outgrowth endothelial cells and human umbilical vein endothelial cells were incubated with the test and control samples and characterized with respect to initial cell attachment, proliferation, viability, and maintenance of the endothelial cell phenotype. It was found that the terpolymer is cytocompatible allowing endothelial cell growth, with random fibers being more effective in promoting enhanced cellular activities than oriented fibers. In addition, endothelial cells cultured on these substrates appeared to maintain their phenotype. The results from this study demonstrate that electrospun HMA:MMA:MAA terpolymer has the potential to be used successfully in fabricating small diameter blood vessel replacements.
Flow cytometry and in vitro analysis of human glioma–associated macrophages (2009)

The CD45(+)/CD11b(+) cells are the predominant inflammatory cell infiltrating human gliomas. Of this type, the CD45(bright)/CD11b(+) cells, a phenotype compatible with circulating macrophages in rodent models, and not microglia, are the most common. Their immunomarker profile is compatible with an immature antigen-presenting cell. They are present in primary glioma cultures but are lost in successive passages. Their role is enigmatic, and they may prove an important target for future glioma immunotherapy studies.
In vivo flow cytometer for real-time detection and quantification of circulating cells (2004)

An in vivo flow cytometer is developed that allows the real-time detection and quantification of circulating fluorescently labeled cells in live animals. A signal from a cell population of interest is recorded as the cells pass through a slit of light focused across a blood vessel. Confocal detection of the excited fluorescence allows continuous monitoring of labeled cells in the upper layers of scattering tissue, such as the skin. The device is used to characterize the in vivo kinetics of red and white blood cells circulating in the vasculatúre of the mouse ear. Potential applications in biology and medicine are discussed.
Targeted Nalmefene With Simple Medical Management in the Treatment of Heavy Drinkers: A Randomized Double‐Blind Placebo‐Controlled Multicenter Study (2007)

Nalmefene appears to be effective and safe in reducing heavy drinking, even when accompanied by minimal psychosocial support.
Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure (2008)

Inclusion of additional template(s) does not necessarily improve model quality, but there are distinct combinations of the two templates, which can be selected a priori, that tend to show improvement in model quality over the single template model. The benefit derived from the structural complementarity is dependent on the accuracy of the modeling alignment. The study helps to explain the observation that a careful selection of templates together with an accurate target:template alignment are necessary to the benefit from using multiple templates in comparative modeling and provides guidelines to maximize the benefit from using multiple templates. This enables formulation of simple template selection rules to rank targets of a protein family in the context of structural genomics.
The T‐region of Ti plasmids codes for an enzyme synthesizing indole‐3‐acetic acid (1984)

Gene 2 from the T region of Ti plasmids appears to be expressed both in eucaryotic and in procaryotic systems. In transformed plant cells it participates in auxin-controlled growth and differentiation, and in bacteria it is expressed into a defined protein of Mr 49000. We investigated the possibility that it codes for an enzyme involved in auxin biosynthesis. Only extracts from Escherichia coli cells expressing gene 2 hydrolyzed indole-3-acetamide into a substance which was unambiguously identified as indole-3-acetic acid. The same reaction was found in Agrobacteria containing gene 2, but not in strains lacking the gene. Extracts from tobacco crown gall cells, but not from non-transformed cells, showed the same enzyme activity, and the reaction product was also identified as indole-3-acetic acid. The results indicate that gene 2 of the T region, which participates in tumorous growth of plant cells, codes both in bacteria and in plants for an amidohydrolase involved in the biosynthesis of the plant hormone indole-3-acetic acid.
A Joint Coordinate System for the Clinical Description of Three-Dimensional Motions: Application to the Knee (1983)

The experimental study of joint kinematics in three dimensions requires the description and measurement of six motion components. An important aspect of any method of description is the ease with which it is communicated to those who use the data. This paper presents a joint coordinate system that provides a simple geometric description of the three-dimensional rotational and translational motion between two rigid bodies. The coordinate system is applied to the knee and related to the commonly used clinical terms for knee joint motion. A convenient characteristic of the coordinate system shared by spatial linkages is that large joint displacements are independent of the order in which the component translations and rotations occur.
Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells (2007)

Recent studies have suggested that, in ES cells, inactive genes encoding early developmental regulators possess bivalent histone modification domains and are therefore poised for activation. However, bivalent domains were not observed at typical tissue-specific genes. Here, we show that windows of unmethylated CpG dinucleotides and putative pioneer factor interactions mark enhancers for at least some tissue-specific genes in ES cells. The unmethylated windows expand in cells that express the gene and contract, disappear, or remain unchanged in nonexpressing tissues. However, in ES cells, they do not always coincide with common histone modifications. Genomic footprinting and chromatin immunoprecipitation demonstrated that transcription factor binding underlies the unmethylated windows at enhancers for the Ptcra and Alb1 genes. After stable integration of premethylated Ptcra enhancer constructs into the ES cell genome, the unmethylated windows readily appeared. In contrast, the premethylated constructs remained fully methylated and silent after introduction into Ptcra-expressing thymocytes. These findings provide initial functional support for a model in which pioneer factor interactions in ES cells promote the assembly of a chromatin structure that is permissive for subsequent activation, and in which differentiated tissues lack the machinery required for gene activation when these ES cell marks are absent. The enhancer marks may therefore represent important features of the pluripotent state.
Cytokines in Patients with Lung Cancer (2003)

Lung cancer is one of the most common malignant diseases and is amongst the leading causes of death. Cell-mediated immune response and cytokines could play an important role in antitumour immunity. The aim of the study was to evaluate the cytokines', tumour necrosis factor-alpha (TNF-alpha), interleukin-1beta (IL-1beta) and IL-6, releasing capacity in patients with lung carcinoma and benign lung disease. A group of 41 patients were tested for the production of TNF-alpha, IL-1beta and IL-6 in bronchoalveolar lavage (BAL) and blood. The levels of cytokines in the lung cancer patients were: (1) in BAL - IL-6, 173 +/- 85 pg/ml; TNF-alpha, 170 +/- 116 pg/ml; and IL-1beta, 473 +/- 440 pg/ml; (2) in the blood - IL-6, 197 +/- 53 pg/ml; TNF-alpha, 311 +/- 202 pg/ml; and IL-1beta, 915 +/- 239 pg/ml. Alveolar macrophages of the patients with a lung cancer secreted significantly more cytokines, IL-6 (P = 0.0004) and IL-1beta (P = 0.0047), than alveolar macrophages of the patients with a nonmalignant lung cancer. However, significantly lower levels of cytokine production by the BAL cells were found in patients with small cell lung cancer. This production decreased further in phase IV of nonsmall cell lung cancer.
<title>Virage image search engine: an open framework for image management</title> (1996)

Until recently, the management of large image databases has relied exclusively on manually entered alphanumeric annotations. Systems are beginning to emerge in both the research and commercial sectors based on 'content-based' image retrieval, a technique which explicitly manages image assets by directly representing their visual attributes. The Virage image search engine provides an open framework for building such systems. The Virage engine expresses visual features as image 'primitives.' Primitives can be very general (such as color, shape, or texture) or quite domain specific (face recognition, cancer cell detection, etc.). The basic philosophy underlying this architecture is a transformation from the data-rich representation of explicit image pixels to a compact, semantic-rich representation of visually salient characteristics. In practice, the design of such primitives is non-trivial, and is driven by a number of conflicting real-world constraints (e.g. computation time vs. accuracy). The virage engine provides an open framework for developers to 'plug-in' primitives to solve specific image management problems. The architecture has been designed to support both static images and video in a unified paradigm. The infrastructure provided by the Virage engine can be utilized to address high-level problems as well, such as automatic, unsupervised keyword assignment, or image classification.
Immunogenicity of pneumococcal revaccination in patients with chronic disease (1994)

<h3>Background:</h3> To prevent serious pneumococcal infections, 23-valent pneumococcal polysaccharide vaccine is recommended for individuals over 24 months of age with chronic predisposing diseases and for healthy older adults. This nonrandomized controlled study in rural Alaska assessed the immunogenicity of revaccination in adults. <h3>Methods:</h3> Twenty-six adults, 33 to 88 years of age, vaccinated a mean of 7.4 years before this study, were matched to 26 previously unvaccinated subjects by age, number of chronic diseases, sex, and ethnicity. One or more chronic diseases were validated in 62% of subjects (32 of 52). All received a first or second intramuscular dose of pneumococcal vaccine. Antibody levels were determined by radioimmunoassay for 12 pneumococcal capsular serotypes immediately before and 20 to 84 days after vaccination. <h3>Results:</h3> Six to 9 years after primary vaccination, over one third of serotype-specific antibody levels were below 500 ng of antibody nitrogen per milliliter, equal to the percentage in unvaccinated subjects of similar age. Antibody levels against all pneumococcal serotypes rose to similar levels after primary vaccination and revaccination, and 54% and 55%, respectively, of subjects who received primary vaccination and revaccination had at least a 1.4-fold increase in antibody levels. Only the antibody level for serotype 4 remained low. Neither gender nor age affected peak response. For those with chronic diseases, there was a trend toward fewer low antibody levels against three or more serotypes after revaccination (two subjects [13%]) than after primary vaccination (five subjects [31%]). <h3>Conclusions:</h3> Following the initial immunization of highrisk and elderly patients with pneumococcal polysaccharide, pneumococcal antibody levels appear to wane with time. Primary vaccination and revaccination 6 or more years after a first dose of pneumococcal vaccine stimulate comparable mean antibody levels. (Arch Intern Med. 1994;154:2209-2214)
Stimulus response coupling in the human neutrophil. II. Temporal analysis of changes in cytosolic calcium and calcium efflux. (1984)

The role of changes in cytosolic free calcium (Ca) in the activation sequence of the human neutrophil has been monitored by means of the fluorescent probe Quin2. "Complete" secretagogues such as the chemotactic peptide f-Met-Leu-Phe and aggregated IgG, as well as the "incomplete" secretagogue concanavalin A, elicited prompt rises in cytosolic Ca. The rise in cytosolic Ca was in all cases one of the earliest measurable events, consistent with the hypothesis that increments in cytosolic free Ca serve as a signal to activate subsequent physiological responses. The source of cytosolic Ca is principally intracellular, since removal of extracellular Ca had little effect on the rise in cytosolic Ca. Although increments in cytosolic Ca may be essential for neutrophil activation, they are evidently not sufficient; chemotactic levels of f-Met-Leu-Phe elicited optimal increments in cytosolic Ca without triggering degranulation, O-2 generation, and aggregation. Some other factor, associated with high levels of receptor occupancy, must be required for secretion. The tumor promoter phorbol myristate acetate was an exceptional stimulus, since it elicited degranulation, aggregation, and O-2 generation without triggering a rise in cytosolic Ca. Finally, an efflux of Ca is initiated which serves to maintain low intracellular levels of Ca.
Zileuton, a 5-lipoxygenase inhibitor in rheumatoid arthritis. (1992)

The effects of zileuton, a new 5-lipoxygenase inhibitor, on leukotriene generation and clinical response in rheumatoid arthritis (RA) was studied in a 4-week randomized double blind placebo controlled study at 2 academic rheumatology centers. Zileuton decreased the mean (+/- SEM) ionophore induced synthesis of leukotriene B4 at Week 1 by 70% from 191.2 +/- 28.5 to 57.5 +/- 17.0 ng/ml. A parallel suppression of all major 5-lipoxygenase pathway products was observed. An improvement in clinical variables was observed in the zileuton and placebo treated population. No unique toxicity was identified in this study. Zileuton inhibited 5-lipoxygenase in RA with a suggestion of clinical response with limited toxicity.
Evaluation of wet distillers composite for finishing ruminants. (1997)

Two trials evaluated the effect of a composite of feed ingredients formulated to be similar in nutrient composition to wet distillers byproducts on finishing performance of sheep and cattle. Trial 1 used 60 crossbred lambs (31 kg) assigned to one of four treatments: dry-rolled corn (DRC) control, dried distillers grains plus solubles, wet corn gluten feed (WCGF), and wet distillers grains composite (COMP1). The COMP1 consisted (DM basis) of 47.5 WCGF, 11.9% condensed distillers solubles, 30.5% corn gluten meal, 9.7% tallow, and .4% dicalcium phosphate and was fed at 40% of the diet DM. Lambs fed the COMP1 diet were 27% more efficient (P < .10) than lambs fed WCGF and 12% more efficient (P > .10) than lambs fed DRC. In Trial 2, 60 yearling crossbred steers (272 kg) were assigned to one of five treatments: DRC control, WCGF, wet distillers grains composite (COMP2), COMP2 minus tallow (-FAT), or COMP2 minus corn gluten meal (-CGM). the COMP2 consisted (DM basis) of 65.7% WCGF, 26.3% corn gluten meal, and 8.0% tallow and was fed at 40% of the diet DM. Steers fed COMP2 were more efficient (P < .10) than steers fed DRC or WCGF, and the steers fed -FAT and -CGM were intermediate to these three dietary treatments. A composite diet of WCGF, condensed distillers solubles, corn gluten meal, and tallow, formulated to be similar in nutrient composition to wet distillers byproducts, may improve feed efficiency compared with WCGF or DRC.
Breast cancer detection with sestamibi-Tc-99m and Tl-201 radionuclides in patients with non conclusive mammography. (1997)

Early diagnosis of breast cancer using breast examination, mammography and ultrasonography is highly accurate, but radiologically dense breast represent a challenge for the mammographic detection of early stage tumors. The aim of this study is to determine the clinical value of scintigraphic techniques in the early diagnosis of breast cancer when other methods give non-conclusive results. The study includes 160 women with clinical suspicion of breast cancer and non-conclusive findings in mammography, randomized either to scintigraphic scans with Sestamibi Tc 99m or Tl 201. Up to date, 64 women have been enrolled, 46 in Tl-201 and 18 in Sestamibi Tc 99m. Results obtained show 73% sensitivity and 94% specificity with Tl 201 and 77% sensitivity and 100% specificity with Sestamibi Tc 99m. In this group, diagnostic accuracy improves when the tumors are bigger than two centimetres in diameter or when they are palpable. These preliminary results show that scintigraphic breast examination seems useful when other diagnostic methods provide non-conclusive results.