gebhart/patrepeval huggingface dataset:
Collaborative computing: a toolset for student motivation in esl courses (2011)

The concern of educational leaders for finding ways to motivate students to achieve learning goals is addressed in this problem based learning (PBL). Much research on education and teaching English as a Second Language (ESL) addresses the need for effective instructional approaches to engage and motivate students with a view to enhancing learning. Specifically, this project focused on building understanding how collaborative computing may be used with recommended teaching approaches in ESL courses to enhance student engagement and motivation. This was done with a view to incorporating a new component into the NDU ESL syllabus which may become effective when all stakeholders participate in its formation.
To learn more about how students may be engaged and motivated in ESL courses, an extensive Knowledge and Information Search was conducted. The views of NDU students and teachers pertaining to ESL courses within a blended milieu utilizing computer networking are also considered. This was achieved through the administration of two surveys based on the themes emerging from the Knowledge and Information Search. The survey was distributed to ENL 110 students and teachers at NDU. The data obtained from the survey was analyzed, and the project culminated in recommendations for using computing in ESL classes at NDU with a view to enhancing student engagement and motivation. 
Project findings suggested teachers can and should work toward enhancing motivation through their approaches and student-centered classes. The findings from the Knowledge and Information Search suggested well-designed use of technology can enhance student engagement and motivation in a way that is conducive to learning, and provide for more flexible, student-centered, collaborative, and personalized learning plans if used appropriately. Computer technology can facilitate such approaches by providing a platform for interaction, discussion, immediate and clear feedback, and flexibility. Findings based on the surveys indicate students and teachers were positive about the proposed approaches and their perceptions of collaborative computing were positive. Therefore, recommendations were made to the Department of English, Translation, and Education at NDU for implementing and sustaining an online component with collaborative applications for feedback and literary narratives as part of the ESL curriculum.
Functional Activity of the Fanconi Anemia Protein FAA Requires FAC Binding and Nuclear Localization (1998)

Fanconi anemia (FA) is an autosomal recessive disease characterized by genomic instability, cancer susceptibility, and cellular hypersensitivity to DNA-cross-linking agents. Eight complementation groups of FA (FA-A through FA-H) have been identified. Two FA genes, corresponding to complementation groups FA-A and FA-C, have been cloned, but the functions of the encoded FAA and FAC proteins remain unknown. We have recently demonstrated that FAA and FAC interact to form a nuclear complex. In this study, we have analyzed a series of mutant forms of the FAA protein with respect to functional activity, FAC binding, and nuclear localization. Mutation or deletion of the amino-terminal nuclear localization signal (NLS) of FAA results in loss of functional activity, loss of FAC binding, and cytoplasmic retention of FAA. Replacement of the NLS sequence with a heterologous NLS sequence, derived from the simian virus 40 T antigen, results in nuclear localization but does not rescue functional activity or FAC binding. Nuclear localization of the FAA protein is therefore necessary but not sufficient for FAA function. Mutant forms of FAA which fail to bind to FAC also fail to promote the nuclear accumulation of FAC. In addition, wild-type FAC promotes the accumulation of wild-type FAA in the nucleus. Our results suggest that FAA and FAC perform a concerted function in the cell nucleus, required for the maintenance of chromosomal stability.
Fullerene-based polymer grid triodes (1997)

We report the fabrication of polymer grid triodes (PGTs) using C60 as the semiconducting medium. The structure, a self-assembling porous conducting polyaniline network placed between two semiconducting layers of C60, and sandwiched between two metal electrodes, demonstrates the I–V characteristics of a three terminal device in which the current is controlled by the grid potential. As a result of the higher mobilities of the fullerenes compared to those of conjugated polymers, the fullerene devices offer some performance advantages; the operating voltages are less than 5 V with current densities exceeding 1 mA/cm2. By fabricating devices with different grid densities, it is shown that the grid exhibits a strong influence on the I–V characteristics for high grid densities, and a correspondingly low influence for low densities, in agreement with theory. The I–V characteristics of the C60 PGTs are well described by an effective diode model, similar to that used for vacuum triodes.
A Convenient Synthesis of Methyl (Z)-1-Carbamoyl-2-ethenylcyclopropanecarboxylate and (Z)-1-Carbamoyl-2-ethenylcyclopropanecarboxylic Acid (1994)

Abstract A simple method for the preparation of the title compounds via the reaction of dimethyl 2-ethenylcyclopropane-1,1-dicarboxylate with 6M ammonia in methanol is described.
Identification of two different surface epitopes of human ovarian epithelial carcinomas by monoclonal antibodies. (1985)

Monoclonal antibodies (Mabs) against human ovarian mucinous and serous carcinoma were obtained by the Mab technique. Their reactivities against human tumors were tested by indirect immunofluorescence. One of the Mabs, named 4C7, derived from the spleen cells of mice immunized with mucinous carcinoma line OVA-1, reacted to ovarian mucinous carcinoma, endometrioid carcinoma, and mesonephroid carcinoma but did not react to ovarian serous carcinoma. Another Mab, 3C2, obtained from the spleen cells of mice immunized with serous carcinoma line HOC-21, reacted to serous carcinoma and endometrioid carcinoma of ovary, but never reacted to mucinous carcinoma or mesonephroid carcinoma. Neither of the Mabs reacted to other types of ovarian carcinomas such as undifferentiated carcinoma, dysgerminoma, endodermal sinus tumor, and malignant teratoma of ovary, and also did not react to any benign ovarian tumors or other normal human tissues. Both Mabs 3C2 and 4C7 had no reactivity to carcinoma of other organs such as stomach, colon, lung, lymphoid system, and kidney and also did not react to human lymphocytic or carcinoembryonic antigen as confirmed by using many human cell lines and surgically resected samples. Since the cross-reactivities of these Mabs were limited within the ovarian epithelial carcinomas, it is suggested that two distinct epitopes are expressed on the ovarian epithelial carcinomas. One epitope, identified by Mab 4C7, is expressed only on mucinous carcinoma, endometrioid carcinoma, and mesonephroid carcinoma, while the epitope, identified by Mab 3C2, appears only on serous and endometrioid carcinoma.
Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut (2004)

The mechanism to maintain homeostasis of the gut microbiota remains largely unknown despite its critical role in the body defense. In the intestines of mice with deficiency of activation-induced cytidine deaminase (AID), the absence of hypermutated IgA is partially compensated for by the presence of large amounts of unmutated IgM and normal expression levels of defensins and angiogenins. We show here a predominant and persistent expansion of segmented filamentous bacteria throughout the small intestine of AID(-/-) mice. Reconstitution of lamina propria IgA production in AID(-/-) mice recovered the normal composition of gut flora and abolished the local and systemic activation of the immune system. The results indicate that secretions of IgAs rather than innate defense peptides are critical to regulation of commensal bacterial flora and that the segmented filamentous bacteria antigens are strong stimuli of the mucosal immune system.
Structural analysis of class II major histocompatibility complex proteins. (1992)

Numerous studies have contributed much data that, taken together, provide considerable insight into the structural features of class II molecules. The putative peptide-binding region has been modeled from the crystal structure of the class I molecule HLA-A2. Mutational analyses and peptide-binding studies support this model. Direct structural studies have established features of the noncovalent association of the alpha and beta chains of class II molecules, and detergents and phospholipids have been shown to affect class II protein structure and/or peptide-binding capacity. Spectroscopic studies have revealed dynamic features of class II molecules in solution, and suggest differences in the overall structures of class I and II molecules that may reflect differences in function.
Cancer therapy and p53 (1995)

Apoptosis is now recognized as an important process in tissue homeostasis. In malignancy, mutations in apoptotic programs may promote tumor progression as well as reduce the efficacy of cancer therapy. Recent studies identify the product of the p53 tumor-suppressor gene as an important regulator of apoptosis in tumor cells. At the same time, clinical studies implicate p53 mutations in pleiotropic resistance to cytotoxic cancer therapy. Together, these observations suggest that inactivation of p53 promotes resistance to anticancer agents by attenuating apoptosis. This view identifies p53 as a potential drug target and suggests several strategies for therapeutic intervention.
Biomarkers for Itch and Disease Severity in Atopic Dermatitis (2011)

Atopic dermatitis (AD) is a common allergic disease and constitutes a huge social and economic burden for the whole country. AD usually heralds other allergic diseases, such as asthma and allergic rhinitis. The pathogenesis of AD remains to be studied but generally includes abnormal skin barrier and aberrant cutaneous immune responses. Biomarkers are important in monitoring disease severity, prognosis and treatment responses. With the investigation and robust knowledge on AD pathophysiology, more and more biomarkers are being explored. Aberrant cutaneous inflammation is associated with Th2 polarization, chemokine upregulation in Langerhans cells and keratinocytes, IgE production by B cells, and degranulation of mast cells and eosinophils, subsequently leading to changes in the levels of cell-specific biomarkers in blood or urine. Furthermore, skin barrier abnormalities, including increased transepidermal water loss and decreased skin hydration, are biomarkers for severity and itch intensity in AD. Cross-talk between skin barrier abnormalities and aberrant immune responses is evidenced by epidermal abnormalities enhancing the release of keratinocyte-derived cytokines and chemokines, including CC chemokine ligand (CCL) 17, CCL27 and thymic stromal lymphopoietin, resulting in modulation of skin immune responses. The pathophysiology of itch in AD remains unclear. The subjective nature of itch makes biomarkers to estimate its intensity crucial in AD patients. Pruritus results from the activation of small nerve endings in the skin by noxious mediators, including neuropeptides, proinflammatory cytokines and prostaglandins, all of which might serve as potential biomarkers for itch. Recently, IL-31 and gastrin-releasing peptide have been reported to be involved in the development of itch, making the estimation of itch intensity a future reality. With the enormous amount of research in immunology, skin physiology and neurology in AD, more biomarkers in AD and its itch will be found in the near future.
Characterization of Candidate Live Oral Salmonella typhi Vaccine Strains Harboring Defined Mutations in aroA , aroC , and htrA (1999)

The properties of two candidate Salmonella typhi-based live oral typhoid vaccine strains, BRD691 (S. typhi Ty2 harboring mutations in aroA and aroC) and BRD1116 (S. typhi Ty2 harboring mutations in aroA, aroC, and htrA), were compared in a number of in vitro and in vivo assays. BRD1116 exhibited an increased susceptibility to oxidative stress compared with BRD691, but both strains were equally resistant to heat shock. Both strains showed a similar ability to invade Caco-2 and HT-29 epithelial cells and U937 macrophage-like cells, but BRD1116 was less efficient at surviving in epithelial cells than BRD691. BRD1116 and BRD691 were equally susceptible to intracellular killing within U937 cells. Similar findings were demonstrated in vivo, with BRD1116 being less able to survive and translocate to secondary sites of infection when inoculated into the lumen of human intestinal xenografts in SCID mice. However, translocation of BRD1116 to spleens and livers in SCID mice occurred as efficiently as that of BRD691 when inoculated intraperitonally. The ability of BRD1116 to increase the secretion of interleukin-8 following infection of HT-29 epithelial cells was comparable to that of BRD691. Therefore, loss of the HtrA protease in S. typhi does not seem to alter its ability to invade epithelial cells or macrophages or to induce proinflammatory cytokines such as IL-8 but significantly reduces intracellular survival in human intestinal epithelial cells in vitro and in vivo.
Effect of &Beta;-Sitosterol, a Plant Sterol, on Growth, Protein Phosphatase 2A, and Phospholipase D in LNCaP Cells (2000)

Previous work from this laboratory suggests an activation of the sphingomyelin cycle as a mechanism for growth inhibition with the incorporation of beta-sitosterol (SIT) into human prostate cancer LNCaP cells. In the present study we examined two key enzymes that have been shown to play a role in the sphingomyelin cycle. Dietary sterols (SIT and cholesterol) were compared for their effect on LNCaP cell growth, phospholipase D (PLD) activity, and protein phosphatase 2A (PP 2A) activity and expression. PP 2A has been suggested as a direct in vitro target of ceramide action on cell growth and apoptosis. Ceramide also inhibits phorbol myristate acetate-stimulated PLD. SIT (16 microM) increased PP 2A activity by 50% compared with cholesterol treatment in LNCaP prostate cells; however, SIT did not alter protein levels of PP 2A. There was an increase in PLD activity in the presence of phorbol myristate acetate in cells supplemented with 16 microM SIT compared with those supplemented with cholesterol after five days of treatment. The present study suggests that the activation of PP 2A added support to the role of the activation of the sphingomyelin cycle by SIT treatment. However, the increase in PLD activity, which was modest but significant, with SIT supplementation suggests that this pathway may be modulated by other mechanisms. This includes the incorporation of SIT into cell membranes that may alter fluidity and, thus, influence the activation of membrane-bound enzymes such as PLD.
Synthetic peptides homologous to prion protein residues 106-147 form amyloid-like fibrils in vitro. (1993)

Gerstmann-Sträussler-Scheinker disease (GSS) is a prion-related encephalopathy pathologically characterized by massive deposition of prion protein (PrP) amyloid in the central nervous system. The major component of amyloid fibrils isolated from patients of the Indiana kindred of GSS (GSS-Ik) is an 11-kDa fragment of PrP spanning residues 58 to approximately 150. These patients carry a missense mutation of the PRNP gene, causing a Phe-->Ser substitution at codon 198. We investigated fibrillogenesis in vitro by using synthetic peptides homologous to consecutive segments of GSS-Ik amyloid protein (residues 57-64, 89-106, 106-126, and 127-147) as well as peptides from the PrP region with the GSS-Ik mutation (residues 191-205 and 181-205, both wild type and mutant). Peptide PrP-(106-126) formed straight fibrils similar to those extracted from GSS brains, whereas peptide PrP-(127-147) formed twisted fibrils resembling scrapie-associated fibrils isolated from subjects with transmissible spongiform encephalopathies. Congo red staining and x-ray fibril diffraction showed that both straight and twisted fibrils had tinctorial and conformational properties of native amyloid. Conversely, the other peptides did not form amyloid-like fibrils under similar conditions. These findings suggest that the sequence spanning residues 106-147 of PrP is central to amyloid fibril formation in GSS and related encephalopathies.
Tunable Nonlinear Activation Functions for Optical Neural Networks (2020)

We introduce an electro-optic hardware platform for realizing optical nonlin earities and demonstrate that, as a nonlinear activation function, it can substantially improve the classification performance of optical neural networks.
Elastic Scaling for Data Stream Processing (2014)

This article addresses the profitability problem associated with auto-parallelization of general-purpose distributed data stream processing applications. Auto-parallelization involves locating regions in the application's data flow graph that can be replicated at run-time to apply data partitioning, in order to achieve scale. In order to make auto-parallelization effective in practice, the profitability question needs to be answered: How many parallel channels provide the best throughput? The answer to this question changes depending on the workload dynamics and resource availability at run-time. In this article, we propose an elastic auto-parallelization solution that can dynamically adjust the number of channels used to achieve high throughput without unnecessarily wasting resources. Most importantly, our solution can handle partitioned stateful operators via run-time state migration, which is fully transparent to the application developers. We provide an implementation and evaluation of the system on an industrial-strength data stream processing platform to validate our solution.
Three dimensional spot beam scanning method for proton conformation radiation therapy. (1983)

In order to fully utilize the excellent dose distribution of heavy charged particles for radiation therapy a 3-D spot beam scanning method for proton conformation therapy has been developed. It is effective in reducing the dose to normal tissues compared with the ordinary beam scattering method or the 2-D spot beam scanning method. Hopefully, it will also be useful for heavy charged particle therapy in the future.
Variable immunoreactivity of D-dimer preparations for monoclonal antibody DD-3B6/22 (1995)

The monoclonal antibody DD-3B6/22, which is specific for crosslinked fibrin breakdown products, is used clinically in the diagnosis and monitoring of certain thrombotic conditions and has potential as a delivery agent for in vivo clot localisation. Laboratory preparations of D-dimer are used as reference standards in DD-3B6/22 assay systems. In this study, four D-dimer preparations, produced using a standardised method, were presented to the monoclonal antibody, DD-3B6/22 in different antigenic formats and immunoreactivity was assessed using a variety of methods. The results show a variability in reactivity of the D-dimer samples to DD-3B6/22; one preparation (QUT2) was immunoreactive only when immobilised on a surface and not when in solution. The implications of variable immunorecognition of target antigens are discussed with regard to diagnostic standards and in vivo clot localisation.
High-throughput oxidation screen of antibody–drug conjugates by analytical protein A chromatography following IdeS digest (2018)

A novel high-throughput method for an interchain cysteine-linked ADC oxidation screens during formulation development was developed.
Simultaneous wide-field imaging and spectroscopy of localized fluorophores (2004)

A method that combines fluorescence imaging and spectroscopy of single molecules at room temperature is presented. This approach allows us to identify a number of imaged molecules unequivocally by simultaneously recording their fluorescence emission spectra. Furthermore, their spectral characteristics not only allow us to separate different fluorescent labels quantitatively and qualitatively but also provide information on the microenvironment of the molecules. This new method was successfully tested on a system of yellow-green and red fluorescent 20-nm latex beads, and its usefulness in studies of biological systems was illustrated for a preparation of combined binary ratio labeling-fluorescence in situ hybridization-stained mouse chromosomes.
ENSEMBLE COMPETITIVE LEARNING NEURAL NETWORKS WITH REDUCED INPUT DIMENSION (1995)

Conventional neural networks utilize all the dimensions of the original input patterns for training and classification. However, a particular attribute of the input patterns does not necessarily contribute to classification and may even cause misclassification in certain cases. A new ensemble competitive learning method using the reduced input dimension is proposed. In contrast to the previous ensemble neural networks which adjust learning parameters, the proposed method takes advantage of the information in each dimension of the input patterns. Since the degree of contribution of each attribute to classification is not known beforehand, the different input data sets with one dimension reduced are presented to multiple neural networks. The classification information from each competitive learning neural network is then combined to make a final decision for classification. In order to improve classification accuracy, the ambiguous output neurons are eliminated which cannot be assigned to any class after training. We use three consensus schemes to judge the classification using ensemble neural networks. The experimental results with remote sensing and speech data indicate the improved performance of the proposed method.
Detection of cancer‐specific epigenomic changes in biofluids: Powerful tools in biomarker discovery and application (2012)

The genetic and epigenetic material originating from tumour that can be found in body fluids of individuals with cancer harbours tumour-specific alterations and represents an attractive target for biomarker discovery. Epigenetic changes (DNA methylation, histone modifications and non-coding RNAs) are present ubiquitously in virtually all types of human malignancies and may appear in early cancer development, and thus they provide particularly attractive markers with broad applications in diagnostics. In addition, because changes in the epigenome may constitute a signature of specific exposure to certain risk factors, they have the potential to serve as highly specific biomarkers for risk assessment. While reliable detection of cancer-specific epigenetic changes has proven to be technically challenging, a substantial progress has been made in developing the methodologies that allow an efficient and sensitive detection of epigenomic changes using the material originating from body fluids. In this review we discuss the application of epigenomics as a tool for biomarker research, with the focus on the analysis of DNA methylation in biofluids.
Inferring and visualizing social networks on internet relay chat (2004)

Internet relay chat is a system that allows groups of people to collaborate and chat from anywhere in the world. Clearly defined by several RFC documents, it is arguably the most standard real-time chat system currently in use. This work describes a method of inferring the social network of a group of IRC users in a channel. An IRC bot is used to monitor a channel and perform a heuristic analysis of events to create a mathematical approximation of the social network. From this, the bot can produce a visualization of the inferred social network on demand. These visualizations reveal the structure of the social network, highlighting connectivity, clustering and strengths of relationships between users. Animated output allows viewers to see the evolution of the social network over time. Some novel ideas for future work are discussed, showing other useful applications of this system.