gebhart/patrepeval huggingface dataset:
Topic Detection and Tracking Pilot Study Final Report (2018)

Topic Detection and Tracking (TDT) is a DARPA-sponsored initiative to investigate the state of the art in finding and following new events in a stream of broadcast news stories. The TDT problem consists of three major tasks: (1) segmenting a stream of data, especially recognized speech, into distinct stories; (2) identifying those news stories that are the first to discuss a new event occurring in the news; and (3) given a small number of sample news stories about an event, finding all following stories in the stream. The TDT Pilot Study ran from September 1996 through October 1997. The primary participants were DARPA, Carnegie Mellon University, Dragon Systems, and the University of Massachusetts at Amherst. This report summarizes the findings of the pilot study. The TDT work continues in a new project involving larger training and test corpora, more active participants, and a more broadly defined notion of “topic” than was used in the pilot study. The following individuals participated in the research reported. James Allan, UMass Brian Archibald, CMU Doug Beeferman, CMU Adam Berger, CMU Ralf Brown, CMU Jaime Carbonell, CMU Ira Carp, Dragon Bruce Croft, UMass, George Doddington, DARPA Larry Gillick, Dragon Alex Hauptmann, CMU John Lafferty, CMU Victor Lavrenko, UMass Xin Liu, CMU Steve Lowe, Dragon Paul van Mulbregt, Dragon Ron Papka, UMass Thomas Pierce, CMU Jay Ponte, UMass Mike Scudder, UMass Charles Wayne, DARPA Jon Yamron, Dragon Yiming Yang, CMU
Hybrid retrieval from the unified web (2007)

The goal of Semantic Web initiative is to make the semantics of Web content accessible to machines. The Semantic Web has been evolving into a web of data separate from the existing HTML web. Our work focuses on establishing and exploiting connections between the two webs, especially hyperlink connections from the HTML web pages to the Semantic Web nodes, so as to enhance both data and document retrieval. We propose the Unified Web model to integrate the two webs, and a hybrid query language to retrieve data and documents from the Unified Web. Specifically, the query language amalgamates graph-based reasoning over RDF with keyword-based search.
Rhs elements of Escherichia coli: a family of genetic composites each encoding a large mosaic protein (1994)

The Rhs family comprises a set of composite elements found in the chromosomes of many natural Escherichia coli strains. Five Rhs elements occur in strain K-12. The most prominent Rhs component is a giant core open reading frame (core ORF) whose features are suggestive of a cell surface ligand-binding protein. This hypothetical protein contains a peptide motif, xxGxxxRYxYDxxGRL(I or T)xxxx, that is repeated 28 times. A similar repeated motif is found in a Bacillus subtilis wall-associated protein. The Rhs core ORFs consist of two distinct parts: a large N-terminal core that is conserved in all Rhs elements, and a smaller C-terminus that is highly variable. Distinctive G+C contents of Rhs components indicate that the elements have a recent origin outside the E. coli species, and that they are composites assembled from segments with very different evolutionary histories. The Rhs cores fall into three sub-families that are mutually more than 20% divergent. Downstream of the core ORF is a second, much shorter ORF. Like the adjacent core extension, these are highly variable. In most examples, the hypothetical product of this ORF has a candidate signal sequence for transport across the cytoplasmic membrane. Another Rhs component, the 1.3 kb H-rpt, has features typical of insertion sequences. Structures homologous to H-rpt have been detected in other bacterial genera, such as Vibrio and Salmonella, where they are associated with loci that determine O-antigen variation.
Xanthomonas campestris pv. campestris gum Mutants: Effects on Xanthan Biosynthesis and Plant Virulence (1998)

Xanthan is an industrially important exopolysaccharide produced by the phytopathogenic, gram-negative bacterium Xanthomonas campestris pv. campestris. It is composed of polymerized pentasaccharide repeating units which are assembled by the sequential addition of glucose-1-phosphate, glucose, mannose, glucuronic acid, and mannose on a polyprenol phosphate carrier (L. Ielpi, R. O. Couso, and M. A. Dankert, J. Bacteriol. 175:2490-2500, 1993). A cluster of 12 genes in a region designated xpsI or gum has been suggested to encode proteins involved in the synthesis and polymerization of the lipid intermediate. However, no experimental evidence supporting this suggestion has been published. In this work, from the biochemical analysis of a defined set of X. campestris gum mutants, we report experimental data for assigning functions to the products of the gum genes. We also show that the first step in the assembly of the lipid-linked intermediate is severely affected by the combination of certain gum and non-gum mutations. In addition, we provide evidence that the C-terminal domain of the gumD gene product is sufficient for its glucosyl-1-phosphate transferase activity. Finally, we found that alterations in the later stages of xanthan biosynthesis reduce the aggressiveness of X. campestris against the plant.
Large document, small screen (2008)

We present a three degree-of-freedom control designed for viewing large documents and images on a mobile device equipped with a camera. Tracking natural features detected in the camera's field of view, we can roughly estimate the motion of the device, using the results to scroll and zoom the current document. Central to our implementation is the manner by which we amplify the motion, allowing the user to scroll through large portions of the document with minimal hand movement. Then, using a Hidden Markov Model, we determine when the user is scrolling, zooming, or some combination of the two, thus providing smoother, more fluid control. We demonstrate a prototype of our 3DOF control that can easily navigate documents that are many times larger than the display area, and show how it might be incorporated into a larger document retrieval application.
Multiprotocol lambda switching: combining MPLS traffic engineering control with optical crossconnects (2001)

This article describes an approach to the design of control planes for optical crossconnects which leverages existing control plane techniques developed for MPLS traffic engineering. The proposed approach combines recent advances in MPLS traffic engineering control plane constructs with OXC technology to provide a framework for real-time provisioning of optical channels, foster development and deployment of a new class of OXCs, and allow the use of uniform semantics for network management and operations control in hybrid networks consisting of OXCs and label switching routers. The proposed approach is particularly advantageous for OXCs intended for data-centric optical internetworking systems.
Characterization of a peptide alpha-amidation activity from rat anterior pituitary. (1984)

A secretory granule associated enzymatic activity from the rat anterior pituitary that can convert the synthetic peptide D-Tyr-Val-Gly into D-Tyr-Val-NH2 is described. Due to the presence of inhibitory activity in the cytosol and rough endoplasmic reticulum/Golgi apparatus fractions, the alpha-amidation activity is barely detectable in crude rat anterior pituitary homogenates. The alpha-amidation activity was primarily soluble, displayed a pH optimum of about 7.0, and showed a requirement for molecular oxygen. The activity was stimulated 7-fold by the addition of optimal concentrations of copper. Of the cofactors tested, only reduced ascorbate produced a severalfold stimulation of activity. Studies with varied D-Tyr-Val-Gly or varied monoiodo-D-Tyr-Val-Gly demonstrate Michaelis Menten kinetics with indistinguishable kinetic constants for both peptides. Upon addition of ascorbate, the apparent Km and Vmax for the synthetic substrate, as estimated from Lineweaver-Burk and Eadie-Hofstee plots, increased by 30- and 60-fold, respectively. Several alpha-melanotropin- and gamma-melanotropin-related peptides with COOH-terminal glycine residues were effective competitive inhibitors of the reaction while the corresponding alpha-amidated peptides were very poor inhibitors. The rat anterior pituitary alpha-amidation activity appears to be very similar to the alpha-amidation activity in rat intermediate and neural pituitary, and mouse anterior pituitary tumor cells.
Electrically induced light scattering from anisotropic gels (1990)

Anisotropic gels were produced by photopolymerization of an oriented liquid-crystalline (LC) mixture containing LC diacrylates and conventional LC molecules. Gels produced in this way were clear and did not give rise to excess scattering of light. Upon application of an electric field across the gel, the system turned translucent. Light scattered by the gel was found to be highly dependent on the direction of polarization and wavelength of the incident light.
Thioredoxin-independent Regulation of Metabolism by the α-Arrestin Proteins (2009)

Thioredoxin-interacting protein (Txnip), originally characterized as an inhibitor of thioredoxin, is now known to be a critical regulator of glucose metabolism in vivo. Txnip is a member of the alpha-arrestin protein family; the alpha-arrestins are related to the classical beta-arrestins and visual arrestins. Txnip is the only alpha-arrestin known to bind thioredoxin, and it is not known whether the metabolic effects of Txnip are related to its ability to bind thioredoxin or related to conserved alpha-arrestin function. Here we show that wild type Txnip and Txnip C247S, a Txnip mutant that does not bind thioredoxin in vitro, both inhibit glucose uptake in mature adipocytes and in primary skin fibroblasts. Furthermore, we show that Txnip C247S does not bind thioredoxin in cells, using thiol alkylation to trap the Txnip-thioredoxin complex. Because Txnip function was independent of thioredoxin binding, we tested whether inhibition of glucose uptake was conserved in the related alpha-arrestins Arrdc4 and Arrdc3. Both Txnip and Arrdc4 inhibited glucose uptake and lactate output, while Arrdc3 had no effect. Structure-function analysis indicated that Txnip and Arrdc4 inhibit glucose uptake independent of the C-terminal WW-domain binding motifs, recently identified as important in yeast alpha-arrestins. Instead, regulation of glucose uptake was intrinsic to the arrestin domains themselves. These data demonstrate that Txnip regulates cellular metabolism independent of its binding to thioredoxin and reveal the arrestin domains as crucial structural elements in metabolic functions of alpha-arrestin proteins.
S1 nuclease sensitivity of a double-stranded telomeric DNA sequence (1987)

We examined structural properties of poly d(C4A2).d(T2G4), the telomeric DNA sequence of the ciliated protozoan Tetrahymena. Under conditions of high negative supercoiling, poly d(C4A2).d(T2G4) inserted in a circular plasmid vector was preferentially sensitive to digestion with S1 nuclease. Only the C4A2 strand was sensitive to first-strand S1 cutting, with a markedly skewed pattern of hypersensitive sites in tracts of either 46 or 7 tandem repeats. Linear poly d(C4A2).(T2G4) showed no preferential S1 sensitivity, no circular dichroism spectra indicative of a Z-DNA conformation, no unusual Tm, and no unusual migration in polyacrylamide gel electrophoresis. The S1 nuclease sensitivity properties are consistent with a model proposed previously for supercoiled poly d(CT).d(AG) (Pulleyblank et al., Cell 42:271-280, 1985), consisting of a double-stranded, protonated, right-handed underwound helix. We propose that this structure is shared by related telomeric sequences and may play a role in their biological recognition.
Urodilatin binds to and activates renal receptors for atrial natriuretic peptide. (1993)

Urodilatin is a recently described member of the atrial natriuretic peptide family, thought possibly to be synthesized in the kidney. To determine if urodilatin binding sites are present in rat and human kidney, we evaluated the effect of urodilatin on iodine-125-labeled atrial natriuretic peptide (ANP) (100 pM) binding to tissue sections using an in situ autoradiographic technique. 125I-ANP binding occurred primarily in glomeruli and medullary structures of both rat and human kidney. Increasing concentrations of urodilatin yielded a monophasic displacement of 125I-ANP binding with an IC50 of 4.2 nM, a value nearly identical to that achieved with unlabeled ANP (7.2 nM). In additional experiments, rat glomeruli and inner medullary collecting duct cells were isolated and incubated in vitro with either ANP or urodilatin (10(-11) to 10(-6) M) and cyclic guanosine-3',5'-monophosphate accumulation measured by radioimmunoassay. Dose-response curves for the two peptides were superimposable in each tissue; at 10(-6) M, ANP generated 613 +/- 41 and urodilatin 603 +/- 55 fmol cyclic guanosine monophosphate per 10 minutes per milligram protein in inner medullary collecting duct cells (p = NS). Thus, urodilatin is as effective as ANP in displacing 125I-ANP binding to both rat and human renal tissue and in generating cyclic guanosine monophosphate in renal target cells in the rat, suggesting that its physiological effects may occur through the same receptors and signaling pathways that mediate the actions of ANP.
Long‐Term Study of Oral Testosterone Undecanoate in Hypogonadal Males (1978)

Thirty‐four hypogonadal male patients were given testosterone undecanoate (TU) orally for 8 months in a dosage of from 40 to 160 mg/day. Before the start of, and during, the study the patients were interviewed about their libido and their sexual, physical and mental activities, and plasma levels of testosterone (T), 5α‐dihydrotestosterone (DHT), oestradiol (Oe 2 ), FSH, and LH were measured by radioimmunoassays simultaneously. Prostate gland was palpated regularly and a routine laboratory screening programme was also performed. All patients reported a marked increase in libido and sexual, physical and/or mental activities and preferred TU over injectable preparations. Circulating T, DHT and Oe 2 rose significantly in all 34 patients and the levels remained stable throughout the whole study. The mean plasma FSH and LH levels in the hypergonadotrophic patients were significantly lowered, but remained above the upper normal limit. In the hypogonadotrophic patients, mean plasma FSH levels increased, but not significantly, while mean LH levels remained unchanged. Neither changes in the size and consistency of the prostate gland, nor abnormal values during the routine laboratory screening programme were observed.
Dynamics of Cell Surface Molecules During T Cell Recognition (2003)

Recognition of foreign antigens by T lymphocytes is a very important component of vertebrate immunity-vital to the clearance of pathogenic organisms and particular viruses and necessary, indirectly, for the production of high affinity antibodies. T cell recognition is mediated by the systematic scanning of cell surfaces by T cells, which collectively express many antigen receptors. When the appropriate antigenic peptide bound to a molecule of the major histocompatibility complex is found-even in minute quantities-a series of elaborate cell-surface molecule and internal rearrangements take place. The sequence of events and the development of techniques required to observe these events have significantly enhanced our understanding of T cell recognition and may find application in other systems of transient cell:cell interactions as well.
Ewing Tumor: Tumor Biology and Clinical Applications (2001)

The Ewing tumor family includes classical Ewing's sarcoma of bone and soft tissues, peripheral primitive neuroectodermal tumors (pPNET), Askin tumor, and other less frequent variants. This group of tumors is defined by the consistent presence of chromosomal translocations resulting in gene fusions between EWS gene and a member of the ETS family of transcription factors, mainly FLI1 and ERG. Analogous fusions are seen in other solid developmental tumors, like desmoplastic small round cell tumor. These fusions, which are consistently present and tumor-specific, control transcription of several target genes, largely unknown but critical to cell proliferation and differentiation. Therefore, gene fusions are useful to diagnose and classify small round cell tumors, have prognostic significance, are probably useful to detect micrometastasis and monitor minimal residual disease, and are potential therapeutic targets. Secondary molecular alterations, which include mutations of cell cycle regulatory genes, are not tumor-specific but are related to progression and may have prognostic value. The Ewing tumor family represents a paradigm of the application of the knowledge of biology of neoplasia to the clinical management of patients.
Low-Cost Acoustic Array for Small UAV Detection and Tracking (2008)

This paper describes a low-cost acoustic array designed to locate and track small unmanned aerial vehicles (UAVs). The goal of this project was to create an inexpensive array with dynamically placed microphones that could detect and locate broadband sources in the far-field through algorithms for array calibration and beamforming. Experiments performed using remote controlled airplanes in an open field demonstrated favorable results.
Humanized mouse model supports development, function, and tissue residency of human natural killer cells (2017)

Immunodeficient mice reconstituted with a human immune system represent a promising tool for translational research as they may allow modeling and therapy of human diseases in vivo. However, insufficient development and function of human natural killer (NK) cells and T cell subsets limit the applicability of humanized mice for studying cancer biology and therapy. Here, we describe a human interleukin 15 (<i>IL15</i>) and human signal regulatory protein alpha (<i>SIRPA</i>) knock-in mouse on a <i>Rag2<sup>-/-</sup> Il2rg<sup>-/-</sup></i> background (SRG-15). Transplantation of human hematopoietic stem and progenitor cells into SRG-15 mice dramatically improved the development and functional maturation of circulating and tissue-resident human NK and CD8<sup>+</sup> T cells and promoted the development of tissue-resident innate lymphoid cell (ILC) subsets. Profiling of human NK cell subsets by mass cytometry revealed a highly similar expression pattern of killer inhibitory receptors and other candidate molecules in NK cell subpopulations between SRG-15 mice and humans. In contrast to nonobese diabetic severe combined immunodeficient <i>Il2rg</i><sup>-/-</sup> (NSG) mice, human NK cells in SRG-15 mice did not require preactivation but infiltrated a Burkitt's lymphoma xenograft and efficiently inhibited tumor growth following treatment with the therapeutic antibody rituximab. Our humanized mouse model may thus be useful for preclinical testing of novel human NK cell-targeted and combinatory cancer immunotherapies and for studying how they elicit human antitumor immune responses in vivo.
Shade trees (1984)

Shading is an important part of computer imagery, but shaders have been based on fixed models to which all surfaces must conform. As computer imagery becomes more sophisticated, surfaces have more complex shading characteristics and thus require a less rigid shading model. This paper presents a flexible tree-structured shading model that can represent a wide range of shading characteristics. The model provides an easy means for specifying complex shading characteristics. It is also efficient because it can tailor the shading calculations to each type of surface .
Ablation of transplanted HTLV-I tax-transformed tumors in mice by antisense inhibition of NF-kappa B (1993)

In our report "Ablation of transplanted HTLV-I tax-transformed tumors in mice by antisense inhibition of NF-κB" (11 Dec., p. 1792), note 11 (p. 1795), in which the sequence of the oligodeoxynucleotides (ODNs) selected for antisense inhibition of NF-κB was described, was incorrect. We accidentally listed human NF-κB target sequences [S. M. Ruben et al., Science 251, 1490 (1991)] rather than mouse-specific sequences [for p65, G. P. Nolan et al., Cell 64, 961 (1991); forp50, S. Gosh et al., ibid. 62, 1019 (1990)]. The note should have read, "The ODNs [oligodeoxy nucleotides] for p50 NF-KB were antisense 5′-TCGTCTGCCATGGTGAAGAT- 3′ and sense 5 ′-ATCTTCACCATGGCAGACGA-3′. The corresponding ODNs for p65 were antisense 5′-AAACAGATCGTCCATGGTCA- 3′ and sense 5′-TGACCATGGACGATCTGTTT- 3′." The ODNs used for tax inhibition of mouse cells were correctly stated in the text. We regret any confusion this error may have caused.
Role of CXC Chemokine Receptor 3 Pathway in Renal Ischemic Injury (2006)

Chemokines play a major role in the recruitment of leukocytes in inflammation and in the regulation of T helper 1 (Th1)/Th2 immune responses. These mechanisms have been recognized to be important in the pathogenesis of renal ischemia-reperfusion (I/R) injury. The interaction of the CXC chemokine receptor 3 (CXCR3) receptor with its ligands is a key pathogenic pathway in promoting inflammation and in enhancing Th1 immune responses. After the induction of ischemia in the mouse model of renal ischemia, an increase in intrarenal expression of CXCR3 and its ligands was observed. Compared with the wild-type (WT) mice, CXCR3-deficient mice (CXCR3-/-) had significantly lower serum creatinine levels, better survival rate, and significantly less acute tubular necrosis and cellular infiltrates. In the kidney, intracellular staining of infiltrating cells that were recovered from kidneys revealed a lower percentage of CD4+IFN-gamma+ cells in the CXCR3-/- mice compared with the WT mice. Furthermore, adoptive transfer of WT CD3+ cells into CXCR3-/- mice before induction of I/R injury abrogated the protection of CXCR3-/- mice from I/R injury. It is concluded that CXCR3 plays an important role in orchestrating the recruitment of Th1 cells to the ischemic kidney and in mediating I/R injury and therefore may serve as a novel target for the therapy of I/R injury.
Primary structure of theompFgene that codes for a major outer membrane protein ofEscherichia coliK-12 (1982)

The nucleotide sequence of the ompF gene coding for a major outer membrane protein of Escherichia coli K-12 has been determined and the amino acid sequence of the OmpF protein was deduced from it. The OmpF protein contains 340 amino acid residues, and is produced from a precursor having 22 extra amino acid residues, the signal peptide, at the amino terminus. The expected secondary structure of the OmpF protein had a high beta-sheet content with a low alpha-helix content. The promoter region and the transcription termination region of the ompF gene had a significantly high AT content, while the AT content of the coding region was about the same as the average AT content of the E. coli chromosome. Following the termination codon, a typical rho-independent transcription termination signal was observed. The codon usage in the ompF gene was highly nonrandom; the codons preferably utilized are those recognized by the most abundant species of isoaccepting tRNAs or those, among synonymous codons recognized by the same tRNA, that can interact more properly with the anticodon.