gebhart/patrepeval huggingface dataset:
Cytokine Expression in the Presence or Absence of Late Airway Responses After Antigen Challenge of Sensitized Rats (1996)

To assess whether Th-2 cytokines are involved in the late airway response (LR) after antigen challenge, we evaluated cytokine mRNA expression in the lungs of two strains of rats before and 8 h after saline or antigen challenge: Brown Norway (BN) rats, high IgE producers that develop LR after antigen challenge and Sprague-Dawley (SD) rats, low IgE producers that develop little LR and no increased airway responsiveness after antigen challenge. Rats were sensitized with ovalbumin (OA) and 14 days later, lungs were obtained before or after OA challenge and measurement of lung physiology for 8 h. Lung tissue was either fixed for in situ hybridization or frozen for evaluation of mRNA expression by reverse transcription-polymerase chain reaction (RT-PCR). We examined mRNA expression for interleukin-4 (IL-4), and IL-5 (Th-2 cytokines) and IL-2 and interferon gamma (IFN-gamma, Th-1 cytokines). In situ hybridization showed that cells expressing IL-4 and -5 mRNA were increased in the airways of the lungs of BN rats after OA challenge (P < 0.05) and that cells expressing mRNA for IFN-gamma and IL-2 were higher in SD than in BN rats after antigen challenge (P < 0.05). Results from PCR showed that prior to antigen challenge, BN rats expressed in their lungs mRNA for IL-4 and -5 and SD rats expressed very little mRNA for IL-5 only. After antigen challenge most BN and SD rats expressed mRNA for IL-4 and -5 but expression of mRNA for IL-2 and IFN-gamma was only found in SD rats. In conclusion, rats that develop a LR after antigen challenge preferentially increase Th-2 cytokine expression in their lungs whereas those without LRs preferentially express Th-1 cytokines. Our results support the role of Th-2 cytokines in the LR and asthma.
Flea beetle (Chrysomelidae: Alticinae) species composition and abundance in different cruciferous oilseed crops and the potential for a trap crop system (2014)

Flea beetles are significant insect pests of cruciferous oilseed crops in northern Europe. A two-year small-scale field experiment was performed to determine the species complex and abundance of flea beetles (Chrysomelidae: Alticinae) associated with eight cruciferous oilseed plants: Brassica juncea (L.) Czern., Brassica napus L. var. oleifera subvar. annua, Brassica nigra (L.) Koch, Brassica rapa L. var. oleifera subvar. annua, Camelina sativa (L.) Crantz, Eruca sativa Mill., Raphanus sativus L. spp. oleifera (DC) Metzg. and Sinapis alba L. Their relative attractiveness to flea beetles was compared to assess their potential for use within a trap crop system for spring oilseed rape. Adults of six species of flea beetles were found on the test plants. Phyllotreta undulata Kutsch. was the most abundant species followed by Phyllotreta nigripes (Fabr.), Phyllotreta nemorum L. and Phyllotreta vittata (=striolata) (Fabr.), while Phyllotreta atra (Fabr.) and Chaetocnema concinna Marsh. were occasionally present. The species composition of flea beetles on seven of the investigated plant species was fairly similar but differed significantly on C. sativa. The flea beetle species discriminated between the tested host plants, with a general gradient in attraction from E. sativa > B. juncea > B. nigra > R. sativus > S. alba > B. rapa > B. napus through to C. sativa. Brassica juncea and B. nigra developed faster and at early growth stages were more attractive to overwintered adult flea beetles than B. napus and therefore had potential as trap plants to protect spring rape. R. sativus and E. sativa, despite their development rate being slower than B. napus were also more attractive to flea beetles. Thus, further experiments with a complex of attractive early season and late-season plant species (multiple trap crops) should be undertaken.
Role of Grounded Liquid Collectors in Precise Patterning of Electrospun Nanofiber Mats (2017)

Liquid collectors are applicable as ground collectors in electrospinning, which fabricates complex nanofiber architectures. However, the influence of the electrical properties of liquid collectors on the controlled deposition of electrospun nanofiber mats has received little attention. Here, we prepare two types of liquid collectors (electrolyte solutions and dielectric liquids) and newly scrutinize their roles in the patterning of electrospun nanofiber mats in experiments and in numerical simulations. By simulating the concentrations of the electric fields around the liquid collectors, we indirectly evaluated the patternability of the collectors. The patternability trends were verified by the patterning of nanofiber mats on line-array-shaped liquid collectors fabricated by electrospinning. The deposition accuracy of the electrolyte solution collector was very high, equivalent to that of a conventional metal collector even at low salt concentrations (e.g., 0.01 M KCl). However, the nanofiber mats fabricated by electrospinning with the dielectric liquid collector showed retarded patternability.
Dependent advice (2009)

Many aspects for runtime monitoring are history-based: they contain pieces of advice that execute conditionally, based on the observed execution history. History-based aspects are notorious for causing high runtime overhead. Compilers can apply powerful optimizations to history-based aspects using domain knowledge. Unfortunately, current aspect languages like AspectJ impede optimizations, as they provide no means to express this domain knowledge.
Logo Matching for Document Image Retrieval (2009)

Graphics detection and recognition are fundamental research problems in document image analysis and retrieval. As one of the most pervasive graphical elements in business and government documents, logos may enable immediate identification of organizational entities and serve extensively as a declaration of a document's source and ownership. In this work, we developed an automatic logo-based document image retrieval system that handles: (1) Logo detection and segmentation by boosting a cascade of classifiers across multiple image scales; and (2) Logo matching using translation, scale, and rotation invariant shape descriptors and matching algorithms. Our approach is segmentation free and layout independent and we address logo retrieval in an unconstrained setting of 2D feature point matching. Finally, we quantitatively evaluate the effectiveness of our approach using large collections of real-world complex document images.
Regional Differentiation of Retinoic Acid-Induced Human Pluripotent Embryonic Carcinoma Stem Cell Neurons (2011)

The NTERA2 cl D1 (NT2) cell line, derived from human teratocarcinoma, exhibits similar properties as embryonic stem (ES) cells or very early neuroepithelial progenitors. NT2 cells can be induced to become postmitotic central nervous system neurons (NT2N) with retinoic acid. Although neurons derived from pluripotent cells, such as NT2N, have been characterized for their neurotransmitter phenotypes, their potential suitability as a donor source for neural transplantation also depends on their ability to respond to localized environmental cues from a specific region of the CNS. Therefore, our study aimed to characterize the regional transcription factors that define the rostocaudal and dorsoventral identity of NT2N derived from a monolayer differentiation paradigm using quantitative PCR (qPCR). Purified NT2N mainly expressed both GABAergic and glutamatergic phenotypes and were electrically active but did not form functional synapses. The presence of immature astrocytes and possible radial glial cells was noted. The NT2N expressed a regional transcription factor code consistent with forebrain, hindbrain and spinal cord neural progenitors but showed minimal expression of midbrain phenotypes. In the dorsoventral plane NT2N expressed both dorsal and ventral neural progenitors. Of major interest was that even under the influence of retinoic acid, a known caudalization factor, the NT2N population maintained a rostral phenotype subpopulation which expressed cortical regional transcription factors. It is proposed that understanding the regional differentiation bias of neurons derived from pluripotent stem cells will facilitate their successful integration into existing neuronal networks within the CNS.
Physician economic efficiency--a new factor in credentialing. (1991)

"Economic credentialing"--the use of economic indicators in evaluating physicians for the purposes of staff appointment and reappointment--is a controversial new development in the ongoing struggle to control hospital costs while maintaining quality patient care. This article describes the concept of economic credentialing, discusses some of the legal considerations raised by the use of economic criteria in the credentialing process, and presents the findings of a recent study of the utilization of economic credentialing in hospitals today.
Evaluation of Hydroxyethyl Esters of Mefenamic Acid and Diclofenac as Prodrugs (1997)

Hydroxyethyl esters of diclofenac and mefenamic acid were prepared with the aim of obtaining enzymatically labile prodrugs, and their stability was evaluated in aqueous buffer solutions of pH 7.4, 1 N HCl, and also in human plasma. The hydrolytic degradation of diclofenac ester in aqueous buffer solutions was slow, as shown by t1/2 values greater than 22 hr, while rapid enzymatic hydrolysis occurred in the plasma (t1/2 = 1.12 hr). However, the mefenamic acid ester showed a relatively higher stability in buffer solutions (t1/2 greater than 38 hr at pH 10) as well as in the plasma (t1/2 = 7.28 hr) compared with the diclofenac ester. Therefore, the mefenamic acid ester would not be considered suitable as a prodrug.
Solving the minimum-cost satisfiability problem using SAT based branch-and-bound search (2006)

Boolean Satisfiability (SAT) has seen many successful applications in various fields, such as Electronic Design Automation (EDA) and Artificial Intelligence (AI). However, in some cases it may be required/preferable to use variations of the general SAT problem. In this paper we consider one important variation, the Minimum-Cost Satisfiability Problem (MinCostSAT). MinCostSAT is a SAT problem which minimizes the cost of the satisfying assignment. MinCostSAT has various applications, e.g. Automatic Test Pattern Generation (ATPG), FPGA Routing, AI Planning, etc. This problem has been tackled before - first by covering algorithms, e.g. scherzo [3], and more recently by SAT based algorithms, e.g. bsolo [16]. However the SAT algorithms they are based on are not the current generation of highly efficient solvers. The solvers in this generation, e.g. Chaff [20], MiniSat [5] etc., incorporate several new advances, e.g. two literal watching based Boolean Constraint Propagation, that have delivered order of magnitude speedups. We first point out the challenges in using this class of solvers for the MinCostSAT problem and then present techniques to overcome these challenges. The resulting solver MinCostChaff shows order of magnitude improvement over several current best known branch-and-bound solvers for a large class of problems, ranging from Minimum Test Pattern Generation, Bounded Model Checking in EDA to Graph Coloring and Planning in AI.
Structure and expression of the Kas12 gene encoding a beta-ketoacyl-acyl carrier protein synthase I isozyme from barley. (1992)

The beta-ketoacyl-acyl carrier protein (ACP) synthase I in the plant fatty acid synthetase catalyzes the condensations of acetate units to a growing acyl-ACP leading to the synthesis of palmitoyl-ACP. Barley chloroplasts contain three cerulenin sensitive beta-ketoacyl-ACP synthase I isoforms, alpha 2, alpha beta, and beta 2. The Kas12 gene encoding the beta 2 isozyme has been isolated and sequenced. The gene spans 3.8 kilobases and contains seven exons separated by six intervening sequences varying from 75 to 1008 base pairs in length. The mosaic gene structure is different compared with that of the beta-ketoacyl synthase in the multifunctional rat and goose fatty acid synthetases. Southern blot analyses of genomic DNA from barley, wheat, and the barley-wheat chromosome addition lines indicate that Kas12 is a single copy gene located on chromosome 2. Primer extension analyses identified four transcription start sites located 168-171 nucleotides upstream from the translation initiation codon. The Kas12 promoter lacks an appropriately positioned TATA box and contains a GC-rich region including two GC elements similar to the Sp1 transcription factor-binding site. In this regard Kas12 closely resembles a set of ubiquitously expressed eucaryotic genes. In accord with this deduction, polymerase chain reaction analysis showed that the Kas12 transcript is present in barley roots, germinating embryos, developing kernels, and leaves.
CA 19-9 ELISA test: a new method for studying mucus changes in tears (1998)

Impression cytology can be regarded as a valuable method for obtaining samples of glycoconjugates of mucin. The decrease of sialylated chains observed with this method confirms the hypothesis that some quantitative changes in the tear film may be encountered in ocular surface disorders.
SceneNet: Understanding Real World Indoor Scenes With Synthetic Data (2015)

Scene understanding is a prerequisite to many high level tasks for any automated intelligent machine operating in real world environments. Recent attempts with supervised learning have shown promise in this direction but also highlighted the need for enormous quantity of supervised data --- performance increases in proportion to the amount of data used. However, this quickly becomes prohibitive when considering the manual labour needed to collect such data. In this work, we focus our attention on depth based semantic per-pixel labelling as a scene understanding problem and show the potential of computer graphics to generate virtually unlimited labelled data from synthetic 3D scenes. By carefully synthesizing training data with appropriate noise models we show comparable performance to state-of-the-art RGBD systems on NYUv2 dataset despite using only depth data as input and set a benchmark on depth-based segmentation on SUN RGB-D dataset. Additionally, we offer a route to generating synthesized frame or video data, and understanding of different factors influencing performance gains.
2.5 Gb/s CMOS preamplifier for low-cost fiber-optic receivers (2010)

This paper reports an optical preamplifier intended for low-cost fiber-optic receivers. The preamplifier is based on a resistive shunt-feedback topology, is power-optimized and employs two different frequency compensation techniques, phantom zeros and shunt-peaking. The circuit is designed in a 1.8 V 0.18 μm CMOS technology. Experimental results report a transresistance of 58 dBΩ and a bandwidth of 1.5 GHz, respectively. Eye diagrams obtained at 2.5 Gb/s show a total jitter of 18 ps and a bit error rate (BER) of 10−12 when the input current amplitude (Iin) is equal to or higher than 8.5 μA. Higher bit rates up to 3 Gb/s also have been tested achieving a BER of 10−12 when Iin ≥9.5 μA. The power consumption and die active area are 23.7 mW and 0.017 mm2, respectively.
Allocating Progressive Injury Liability among Successive Insurance Policies (1997)

Environmental damage and toxic exposure cases often involve injuries that occur over a number of years, known as "progressive injuries."'One recent case, for example, involved the cleanup of an industrial site that had been continuously polluted by oil seepage from the nineteenth century until the 1980s. 2Asbestos exposure cases are another common example; decades of exposure may precede the first manifestation of any symptoms of asbestos-related diseases. 3 Progressive injuries frequently occur over time periods in which a liable party had insurance coverage under several different insurance policies, often provided by a number of insurance companies. 4 In most of these cases, it is both scientifically and administratively impossible to allocate to each policy the liability ' B.
Antitumor vaccination of prostate cancer patients elicits PD-1/PD-L1 regulated antigen-specific immune responses (2016)

We have previously reported that tumor antigen-specific DNA vaccination in mice led to an increase in IFNγ-secreting T cells and an increase in tumor expression of PD-L1. Further, we demonstrated that increasing the encoded antigen's MHC-binding affinity led to increased PD-1 expression on antigen-specific CD8(+) T cells. Together these phenomena provided resistance to antitumor immunization that was abrogated with PD-1/PD-L1 blockade. We consequently sought to determine whether similar regulation occurred in human patients following antitumor immunization. Using clinical samples from prostate cancer patients who were previously immunized with a DNA vaccine, we analyzed changes in checkpoint receptor expression on antigen-specific CD8(+) T cells, the effect of PD-1 blockade on elicited immune responses, and for changes in checkpoint ligand expression on patients' circulating tumor cells (CTCs). We observed no significant changes in T-cell expression of PD-1 or other checkpoint receptors, but antigen-specific immune responses were detected and/or augmented with PD-1 blockade as detected by IFNγ and granzyme B secretion or trans vivo DTH testing. Moreover, PD-L1 expression was increased on CTCs following vaccination, and this PD-L1 upregulation was associated with the development of sustained T-cell immunity and longer progression-free survival. Finally, similar results were observed with patients treated with sipuleucel-T, another vaccine targeting the same prostate antigen. These findings provide in-human rationale for combining anticancer vaccines with PD-1 blocking antibodies, particularly for the treatment of prostate cancer, a disease for which vaccines have demonstrated benefit and yet PD-1 inhibitors have shown little clinical benefit to date as monotherapies.
Modeling and discovering human behavior from smartphone sensing life-log data for identification purpose (2015)

Abstract Today, personal data is becoming a new economic asset. Personal data which generated from our smartphone can be used for many purposes such as identification, recommendation system, and etc. The purposes of our research are to discover human behavior based on their smartphone life log data and to build behavior model which can be used for human identification. In this research, we have collected user personal data from 37 students for 2 months which consist of 19 kinds of data sensors. There is still no ideal platform that can collects user personal data continuously and without data loss. The data which collected from user’s smartphone have various situations such as the data came from multiple sensors and multiple source information which sometimes one or more data does not available. We have developed a new approach to building human behavior model which can deal with those situations. Furthermore, we evaluate our approach and present the details in this paper.
Disulfide-bonded discontinuous epitopes on the glycoprotein of vesicular stomatitis virus (New Jersey serotype) (1992)

Intrachain disulfide bonds between paired cysteines in the glycoprotein (G) of vesicular stomatitis virus (VSV) are required for the recognition of discontinuous epitopes by specific monoclonal antibodies (MAbs) (W. Keil and R. R. Wagner, Virology 170:392-407, 1989). Cleavage by Staphylococcus aureus V8 protease of the 517-amino-acid VSV-New Jersey G protein, limited to the glutamic acid at residue 110, resulted in a protein (designated GV8) with greatly retarded migration by polyacrylamide gel electrophoresis (PAGE) under nonreducing conditions. By Western blot (immunoblot) analysis, protein GV8 was found to lose discontinuous epitope IV, which maps within the first 193 NH2-terminal amino acids. These data, coupled with those obtained by PAGE migration of a vector-expressed, truncated protein (G1-193) under reducing and nonreducing conditions, lead us to postulate the existence of a major loop structure within the first 193 NH2-terminal amino acids of the G protein, possibly anchored by a disulfide bond between cysteine 108 and cysteine 169, encompassing epitope IV. Site-directed mutants in which 10 of the 12 cysteines were individually converted to serines in vaccinia virus-based vectors expressing these single-site mutant G proteins were also constructed, each of which was then tested by immunoprecipitation for its capacity to recognize epitope-specific MAbs. These results showed that mutations in NH2-terminal cysteines 130, 174, and, to a lesser extent, 193 all resulted in the loss of neutralization epitope VIII. A mutation at NH2-terminal cysteine 130 also resulted in the loss of neutralization epitope VII, as did a mutation at cysteine 108 to a lesser extent. Both epitopes VII and VIII disappeared when mutations were made in COOH-distal cysteine 235, 240, or 273, the general map locations of epitopes VII and VIII. These studies also reveal that distal, as well as proximal, cysteine residues markedly influence the disulfide-bond secondary structure, which ostensibly determines the conformational structure of the VSV-New Jersey G protein required for presentation of the major discontinuous epitopes recognized by neutralizing MAbs.
<title>Hybrid boundary-based and region-based deformable models for biomedical image segmentation</title> (1994)

The problem of segmenting an image into visually sensible regions has received considerable attention. Recent techniques based on deformable models show particular promise for this problem because they produce smooth closed object boundaries. These techniques can be broadly classified into two categories: boundary-based deformable models, and region-based deformable models. Both of these approaches have distinct advantages and disadvantages. In this paper, we introduce a hybrid deformable modeling technique which combines the advantages of both approaches and avoids some of their disadvantages. This is accomplished by first minimizing a region-based functional to obtain initial edge strength estimates. Smooth closed object boundaries are then obtained by minimizing a boundary-based functional which is attracted to the initial edge locations. In this paper, we discuss the theoretical advantages of this hybrid approach over existing image segmentation methods and show how this technique can be effectively implemented and used for the segmentation of 2D biomedical images.