gebhart/patrepeval huggingface dataset:
Development and Implementation of a Discourse Model for Newspaper Texts (1995)

In this paper, we will focus on the development, implementation, and evolution of a discourse model which is used to computationally instantiate a discourse structure in individual texts. This discourse model was developed for use in a Text Structuring module that recognizes discourse-level structure within a large-scale information retrieval system, DR-LINK (Liddy Myaeng, 1993). The Text Structurer produces an enriched representation of each document by computationally decomposing it into smaller, conceptually labelled components. This delineation of the discourse-level organization of each document’s contents facilitates retrieval of those documents which convey the appropriate discourse semantics that are responsive to the user’s query. The recognition of the existence of text-type models derives from research in discourse linguistics which has shown that writers who repeatedly produce texts of a particular type are influenced by the schema of that texttype and, when writing, consider not only the specific content they wish to convey but also what the usual structure is for that type of text based on the purpose it is intended to serve (Jones, 1983). As a result, texts of particular type evidence the schema that exists in the minds of those who produce the texts. These schema can be delineated, and as such provide models of their respective text-types which are of use in automatically structuring texts. A text schema explicates a discernible, predictable structure, the global schematic structure that is filled with different meaning in each particular example of that text-type (van Dijk, 1980). Among the text-types for which schemas or models have been developed are: folk-tales (Propp, 1958), newspaper articles (van Dijk, 1980), arguments (Cohen, 1987), historical journal articles (Tibbo, 1989), editorials (Alvarado, 1990), empirical abstracts (Liddy, 1991), theoretical abstracts (Francis & Liddy, 1991).
Disconnections in US and EU Agricultural Policy and Trade Negotiations: A Transaction Cost Politics Approach (2011)

This article investigates aspects of the institutions and decision making processes in the United States and the European Union that affect the coordination of domestic farm programs and trade negotiations for agriculture in each entity. We explore how current institutions and processes contribute to a level of incoherence - or lack of coordination - between domestic farm programs and trade negotiations in the United States. Constructs from transaction cost politics with an emphasis on the decision to delegate authority from the principal to an agent are used to understand how institutional processes affect the coordination of domestic legislation.
Introduction (2010)

As both questions and quip suggest, "literary history," or writing the history of literature, now seems a problematic form, both unavoidable and beyond our competence. The "now" in this sentence, and the fact that all three quotations in my epigraph are from twentieth- to twenty-first-century critics, speak to the fact that the enterprise has come to seem more elusive and contested even as it has become more sophisticated and self-conscious. The late nineteenth-century certainties of Edmund Gosse, John Morley, and George Saintsbury seem positively naïve after the successive challenges of new criticism, deconstruction, structuralism, new historicism, and cultural materialism, not to mention the strong paradigms created by Harold Bloom (the anxiety of influence) and Jerome McGann (Romantic ideology). Hardly surprising, then, that the goal of a new and complete literary history, while attractive, appears unachievable. This book takes a step back from the construction of such an inclusive, teleological narrative. Instead, it concentrates on a fairly narrow slice of time, 1770 to 1820, and considers the interest within that period in the writing of histories of literary history. In the half century on which I focus, the production of "literary history" has been both understudied and misunderstood. Interest has been shut off by the standard modern assumption that for contemporaries its goal was simply the formation of a transcendent canon, a register of enduring works of "original Genius of a high order."2KeywordsLiterary CriticismLiterary HistoryLiterary CultureEnglish PoetryTrace AttackThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Six-fold speed-up of Smith–Waterman sequence database searches using parallel processing on common microprocessors (2000)

A fast implementation of the Smith-Waterman sequence-alignment algorithm using Single-Instruction, Multiple-Data (SIMD) technology is presented. This implementation is based on the MultiMedia eXtensions (MMX) and Streaming SIMD Extensions (SSE) technology that is embedded in Intel's latest microprocessors. Similar technology exists also in other modern microprocessors. Six-fold speed-up relative to the fastest previously known Smith-Waterman implementation on the same hardware was achieved by an optimized 8-way parallel processing approach. A speed of more than 150 million cell updates per second was obtained on a single Intel Pentium III 500 MHz microprocessor. This is probably the fastest implementation of this algorithm on a single general-purpose microprocessor described to date.
siRNA Specific Delivery System for Targeting Dendritic Cells (2010)

siRNA therapy offers immense potential for clinical application. Under physiological conditions, however, siRNA was demonstrated to have a short half-life. Additionally, it may also cause ubiquitous gene silencing as it does not possess a tissue-specific homing mechanism. Thus, the rate-limiting step in the emergence of siRNA as a potential therapeutic agent is the current lack of a safe and tissue- or cell-specific in vivo delivery system. Herein, we propose a novel, cell-specific method for the in vivo delivery of siRNA to dendritic cells (DCs) with the purpose of inducing immune modulation. CD40 siRNA was incorporated within the interior of 86 nm liposomes, which were decorated with surface-bound mAb NLDC-145 as a targeting mechanism. The siRNA encapsulation efficiency was determined to be approximately 7%. CD40 siRNA immunoliposomes (CD40 siILs) were able to specifically bind to DCs and silence CD40 expression in vitro. Furthermore, in vitro CD40-silenced DCs significantly inhibited the proliferation of alloreactive T cells in an MLR. Upon in vivo administration, siIL-encapsulated, Cy3-labeled siRNA exhibited moderate uptake by the liver at an early time point following administration with greater accumulation in the spleen at a later time point. In contrast, naked siRNA primarily accumulated in the kidney immediately after administration and circulated out in a short time period. To address in vivo gene silencing and immune modulation, mice were simultaneously immunized with KLH and subcutaneously injected with DC-specific CD40 siILs, siILs containing negative control siRNA, naked CD40 siRNA, or PBS. A second injection of CD40 siILs, or control treatments, followed 24 h later. Flow cytometry, reverse transcriptase PCR, and quantitative real-time PCR analysis of CD11c(+) DCs from mice treated with CD40 siILs demonstrated reduced expression of CD40, in comparison with control groups. CD11c(-) cells were also analyzed by flow cytometry, but no differences were observed between treatment groups. Furthermore, CD40 siIL-treated mice were found to have an increased proportion of Treg cells (CD4(+)CD25(+) FoxP3(+)), and DCs cells from these mice were able to inhibit T cell proliferation in an antigen-specific recall response. In summary, CD40 siILs were shown to specifically target and deliver CD40 siRNA to DCs, significantly reducing CD40 expression and resulting in DC-mediated immune modulation as well as generation of Treg cells. These findings highlight the therapeutic potential for siRNA-based and DC-mediated immunotherapy in the clinic. To the best of our knowledge, this is the first study to use siILs for targeted delivery of siRNA to DCs and for immune modulation.
The role of polymer nanosurface roughness and submicron pores in improving bladder urothelial cell density and inhibiting calcium oxalate stone formation (2009)

Synthetic polymers have been proposed for replacing resected cancerous bladder tissue. However, conventional (or nanosmooth) polymers used in such applications (such as poly(ether) urethane (PU) and poly-lactic-co-glycolic acid (PLGA)) often fail clinically due to poor bladder tissue regeneration, low cytocompatibility properties, and excessive calcium stone formation. For the successful reconstruction of bladder tissue, polymer surfaces should be modified to combat these common problems. Along these lines, implementing nanoscale surface features that mimic the natural roughness of bladder tissue on polymer surfaces can promote appropriate cell growth, accelerate bladder tissue regeneration and inhibit bladder calcium stone formation. To test this hypothesis, in this study, the cytocompatibility properties of both a non-biodegradable polymer (PU) and a biodegradable polymer (PLGA) were investigated after etching in chemicals (HNO(3) and NaOH, respectively) to create nanoscale surface features. After chemical etching, PU possessed submicron sized pores and numerous nanometer surface features while PLGA possessed few pores and large amounts of nanometer surface roughness. Results from this study strongly supported the assertion that nanometer scale surface roughness produced on PU and PLGA promoted the density of urothelial cells (cells that line the interior of the bladder), with the greatest urothelial cell densities observed on nanorough PLGA. In addition, compared to respective conventional polymers, the results provided evidence that nanorough PU and PLGA inhibited calcium oxalate stone formation; submicron pored nanorough PU inhibited calcium oxalate stone formation the most. Thus, results from the present study suggest the importance of nanometer topographical cues for designing better materials for bladder tissue engineering applications.
The Impact of Zr Substitution on the Structure, Electrochemical Performance and Thermal Stability of Li[Ni1/3Mn1/3−zCo1/3Zrz]O2 (2011)

Li[Ni1/3Mn1/3− z Co1/3Zrz ]O2 (0 ≤ z ≤ 0.1) samples were prepared from hydroxide precursors. The hydroxide precursors were heated with Li2CO3 at 900°C to prepare the oxides. X-ray diffraction results suggest that single phase samples can be prepared for 0 ≤ z ≤ 0.02. Chemical analysis using atomic absorption spectroscopy showed that the samples had some excess Li. Rietveld refinements of X-ray diffraction data show that Zr substitution for Mn does not induce substantial cation mixing in the Li layer. Electrochemical studies of single phase samples, Li[Ni1/3Mn1/3− z Co1/3Zrz ]O2 (0 ≤ z ≤0.02), show a small reduction in capacity and no advantage in capacity retention as Zr is substituted for Mn. The impact of Zr substitution on the thermal stability of the Li[Ni1/3Mn1/3− z Co1/3Zrz ]O2 samples was studied via accelerating rate calorimetry. The accelerating rate calorimetry results show that the substitution of Zr into the layered structure of Li[Ni1/3Mn1/3− z Co1/3Zrz ]O2 does not improve the thermal stability of the samples.
Normal telomere length and chromosomal end capping in poly(ADP-ribose) polymerase–deficient mice and primary cells despite increased chromosomal instability (2001)

Poly(ADP-ribose) polymerase (PARP)-1, a detector of single-strand breaks, plays a key role in the cellular response to DNA damage. PARP-1-deficient mice are hypersensitive to genotoxic agents and display genomic instability due to a DNA repair defect in the base excision repair pathway. A previous report suggested that PARP-1-deficient mice also had a severe telomeric dysfunction consisting of telomere shortening and increased end-to-end fusions (d'Adda di Fagagna, F., M.P. Hande, W.-M. Tong, P.M. Lansdorp, Z.-Q. Wang, and S.P. Jackson. 1999. NAT: Genet. 23:76-80). In contrast to that, and using a panoply of techniques, including quantitative telomeric (Q)-FISH, we did not find significant differences in telomere length between wild-type and PARP-1(-/)- littermate mice or PARP-1(-/)- primary cells. Similarly, there were no differences in the length of the G-strand overhang. Q-FISH and spectral karyotyping analyses of primary PARP-1(-/)- cells showed a frequency of 2 end-to-end fusions per 100 metaphases, much lower than that described previously (d'Adda di Fagagna et al., 1999). This low frequency of end-to-end fusions in PARP-1(-/)- primary cells is accordant with the absence of severe proliferative defects in PARP-1(-/)- mice. The results presented here indicate that PARP-1 does not play a major role in regulating telomere length or in telomeric end capping, and the chromosomal instability of PARP-1(-/)- primary cells can be explained by the repair defect associated to PARP-1 deficiency. Finally, no interaction between PARP-1 and the telomerase reverse transcriptase subunit, Tert, was found using the two-hybrid assay.
Antibody Fragments and Their Purification by Protein L Affinity Chromatography (2015)

Antibodies and related proteins comprise one of the largest and fastest-growing classes of protein pharmaceuticals. A majority of such molecules are monoclonal antibodies; however, many new entities are antibody fragments. Due to their structural, physiological, and pharmacological properties, antibody fragments offer new biopharmaceutical opportunities. In the case of recombinant full-length antibodies with suitable Fc regions, two or three column purification processes centered around Protein A affinity chromatography have proven to be fast, efficient, robust, cost-effective, and scalable. Most antibody fragments lack Fc and suitable affinity for Protein A. Adapting proven antibody purification processes to antibody fragments demands different affinity chromatography. Such technology must offer the unit operation advantages noted above, and be suitable for most of the many different types of antibody fragments. Protein L affinity chromatography appears to fulfill these criteria—suggesting its consideration as a key unit operation in antibody fragment processing.
An acid-sensing ion channel that detects ischemic pain (2005)

Ischemic pain occurs when there is insufficient blood flow for the metabolic needs of an organ. The pain of a heart attack is the prototypical example. Multiple compounds released from ischemic muscle likely contribute to this pain by acting on sensory neurons that innervate muscle. One such compound is lactic acid. Here, we show that ASIC3 (acid-sensing ion channel #3) has the appropriate expression pattern and physical properties to be the detector of this lactic acid. In rats, it is expressed only in sensory neurons and then only on a minority (approximately 40%) of these. Nevertheless, it is expressed at extremely high levels on virtually all dorsal root ganglion sensory neurons that innervate the heart. It is extraordinarily sensitive to protons (Hill slope 4, half-activating pH 6.7), allowing it to readily respond to the small changes in extracellular pH (from 7.4 to 7.0) that occur during muscle ischemia. Moreover, both extracellular lactate and extracellular ATP increase the sensitivity of ASIC3 to protons. This final property makes ASIC3 a "coincidence detector" of three molecules that appear during ischemia, thereby allowing it to better detect acidosis caused by ischemia than other forms of systemic acidosis such as hypercapnia.
Quantum information processing: cryptography, computation, and teleportation (1996)

Present information technology is based on the laws of classical physics. However, advances in quantum physics have stimulated interest in its potential impact on such technology. This article is an introductory review of three aspects of quantum information processing, cryptography, computation, and teleportation. The author serves up hors d'oeuvres on the relevant parts of quantum physics and the sorts of quantum systems which might form the building blocks for quantum processors. Quantum cryptography utilizes states of individual quantum systems for the transfer of conventional classical bits of information. The impossibility of measuring quantum systems without disturbing them guarantees the detection of eavesdropping and hence secure information transfer is possible. In a sense, teleportation is the inverse of cryptography, using more robust classical bits to faithfully transfer a quantum state through a noisy environment. Quantum computation utilizes the evolving quantum state of a complex system, which consists of many interacting individuals. If such a machine could be built, it would be capable of solving some problems which are intractable on any conventional computer; he illustrates this with Shor's (see Proc. 35th IEEE Symposium on Foundations of Computer Science, p.124, 1994) quantum factoring algorithm. Details are given of the current experimental achievements, proposals, and prospects for the future and of the patents granted to date.
The Activin-binding Protein Follistatin is Expressed in Developing Murine Molar and Induces Odontoblast-like Cell Differentiation in vitro (1997)

It has recently been shown that mice deficient in activin-beta A subunits and follistatin exhibit major defects in dentition. To increase understanding of the roles played by these molecules during tooth development, we determined the temporospatial expression of activin-beta A subunit and follistatin messenger RNA and their corresponding proteins in developing murine molars (between day E 14 and 2 days after birth). The effects of recombinant human activin A and its binding protein follistatin on odontoblast differentiation were also studied in cultures of dental papillae (DP) isolated from the mandibular first molars of E-17-day mice. In situ hybridization indicated that transcripts for activin-beta A subunit were abundant in pre-odontoblasts at the tips of forming cusps prior to odontoblast terminal differentiation, and transcripts for follistatin in overlying inner enamel epithelial cells (pre-ameloblasts). Pre-odontoblasts were also weakly immunoreactive in relation to activin-beta A subunit, pre-ameloblasts in relation to follistatin. When follistatin was added at different concentrations to a DP culture model (2-14 nmol/DP) together with heparin at constant concentration, differentiation of odontoblast-like cells was induced, as evidenced by polarization and deposition of extracellular matrix in vitro, to extents depending on the follistatin concentration. In contrast, the addition of activin A (2 nmol/DP) had no effect on the differentiation parameters studied. These findings suggest that the activin-follistatin system regulates odontoblast differentiation during tooth development. In particular, we suggest that binding of endogenous activin A by follistatin may allow odontoblast terminal differentiation to occur.
Molecular cloning of a novel membrane-type matrix metalloproteinase from a human breast carcinoma. (1996)

A new member of the matrix metalloproteinase (MMP) family of enzymes has been cloned from a human breast carcinoma cDNA library. The isolated cDNA contains an open reading frame 1554 bp long, encoding a polypeptide of 518 amino acids. The predicted amino acid sequence displays a similar domain organization as the remaining MMPs, including a prodomain with the activation locus, the zinc-binding site, and the hemopexin domain. In addition, it contains a C-terminal extension, rich in hydrophobic residues and similar in size to those present in the different membrane-type MMPs (MT-MMPs) identified to date. On the basis of these structural characteristics, this novel MMP has been tentatively called MT4-MMP, because it represents the fourth member of this subclass of MMPs characterized mainly by the occurrence of putative transmembrane domain in their amino acid sequences. MT4-MMP also contains a nine-residue insertion between the propeptide and the catalytic domain, which is a common feature of MT-MMPs and stromelysin-3. This amino acid sequence insertion ends with the consensus sequence R-X-R/K-R, which seems to be essential in the activation of these proteinases by furin. Northern blot analysis of polyadenylated RNAs isolated from a variety of human tissues revealed that the MT4-MMP gene (MMP-17) is expressed mainly in the brain, leukocytes, the colon, the ovary, and the testis. The expression of MT4-MMP in leukocytes together with its putative membrane localization suggest that this enzyme could be involved in the activation of membrane-bound precursors of growth factors or inflammatory mediators such as tumor necrosis factor-alpha. In addition, MT4-MMP transcripts were detected in all breast carcinomas, as well as in all breast cancer cell lines analyzed in the present work. On the basis of these expression data in breast tumors, a potential role for human MT4-MMP in the tumoral process is also suggested.
Efficient key distribution for slow computing devices: achieving fast over the air activation for wireless systems (2002)

Any system which contains some form of cryptographic authentication, confidentiality and/or identification requires the provisioning of a secure key generation and distribution capability. The key distribution mechanism for wireless cellular systems, such as IS-95 CDMA, IS-136 TDMA and IS-91 Analog, has recently been investigated by the Telephone Industry Association's standards working groups. There are several requirements that a cellular key provisioning system must satisfy; however, the current approaches for such generation and distribution are in general inadequate. As with any commercial application, the system must satisfy cost (e.g., efficiency by all parties, minimal specialized equipment, etc.), convenience and most of all security requirements. The cellular system requirements, however, are much more constraining than most environments since the customers' cellular phones have minimal computational capabilities and the authenticated setup protocol is generally performed with the user and carrier never meeting face to face. Moreover, the cellular phone companies are also insisting, for business competition needs, that the key distribution and generation mechanism is as convenient and transparent to the user (customer) as possible. We propose a cryptographically secure approach for such generation and distribution which will satisfy the phone industries' needs as well as the needs of other applications using slow devices.
Nuclear PTEN Controls DNA Repair and Sensitivity to Genotoxic Stress (2013)

Loss of function of the phosphatase and tensin homolog deleted on chromosome 10 (PTEN) tumor suppressor gene is associated with many human cancers. In the cytoplasm, PTEN antagonizes the phosphatidylinositol 3-kinase (PI3K) signaling pathway. PTEN also accumulates in the nucleus, where its function remains poorly understood. We demonstrate that SUMOylation (SUMO, small ubiquitin-like modifier) of PTEN controls its nuclear localization. In cells exposed to genotoxic stress, SUMO-PTEN was rapidly excluded from the nucleus dependent on the protein kinase ataxia telangiectasia mutated (ATM). Cells lacking nuclear PTEN were hypersensitive to DNA damage, whereas PTEN-deficient cells were susceptible to killing by a combination of genotoxic stress and a small-molecule PI3K inhibitor both in vitro and in vivo. Our findings may have implications for individualized therapy for patients with PTEN-deficient tumors.
Telomeres and Their Synthesis (1990)

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