gebhart/patrepeval huggingface dataset:
A Plan Recognition Model for Subdialogues in Conversations (1987)

Previous plan‐based models of dialogue understanding have been unable to account for many types of subdialogues present in naturally occurring conversations. One reason for this is that the models have not clearly differentiated between the varoius ways that an utterance can relate to a plan structure representing a topic. In this paper we present a plan‐based theory that allows a wide variety of utterance‐plan relationships. We introduce a set of discourse plans, each one corresponding to a particular way that an utterance can relate to a discourse topic, and distinguish such plans from the set of plans that are actually used to model the topics. By incorporating knowledge about discourse into a plan‐based framework, we can account for a wide variety of subdialogues while maintaining the computational advantages of the plan‐based approach.
A Collagen-Remodeling Gene Signature Regulated by TGF-β Signaling Is Associated with Metastasis and Poor Survival in Serous Ovarian Cancer (2013)

Our findings suggest that collagen-remodeling genes regulated by TGF-β1 signaling promote metastasis and contribute to poor OS in patients with serous ovarian cancer. Our 10-gene signature has both predictive value and biologic relevance and thus may be useful as a therapeutic target.
PTS files Chapter 11 (2006)

Subtitle: Second-largest autohauler joins Allied Holdings in bankruptcy as automakers close plans [i.e. plants], cut jobs.
Scanning Electron Microscopy of Eggshells of Contemporary Reptiles (1986)

Eggshells of contemporary turtles and squamate reptiles (lizards, snakes, and the tuatara) are either flexible or rigid, and usually are composed of both a fibrous shell membrane and an overlying calcareous layer. The calcareous layer of turtle eggs is calcium carbonate in the form of aragonite, whereas the crystalline material of squamate eggs generally is calcite. Both rigid and flexible shells of turtle eggs are composed of individual building blocks or shell units. Shell units of rigid shells abut tightly, and few pores penetrate the calcareous layer. In contrast, flexible shells exhibit large numbers of spaces or pores in the crystalline material. Rigid eggshells of squamates are characterized by interlocking columns of calcareous material that yield a compact, non-compliant matrix. Pores are presumed to penetrate the crystalline layer but have yet to be described in such eggshells. Flexible-shelled eggs laid by squamates exhibit the greatest variability in gross morphology of all reptilian eggs examined to date. The crystalline layer may occur as a thin, relatively unstructured crust overlying the shell membrane or may exhibit protrusions or nodes of variable morphology. In some cases, the crystalline material exists as widely dispersed aggregates separated by uncalcified areas. Pores as distinct structural entities similar to the pores of turtle eggshells do not occur, but holes and pore-like structures, as well as cracks and fissures, presumably provide for transport of gases and water between eggs and their environment.
A potential role for RNA interference in controlling the activity of the human LINE-1 retrotransposon (2005)

Long interspersed nuclear elements (LINE-1 or L1) comprise 17% of the human genome, although only 80-100 L1s are considered retrotransposition-competent (RC-L1). Despite their small number, RC-L1s are still potential hazards to genome integrity through insertional mutagenesis, unequal recombination and chromosome rearrangements. In this study, we provide several lines of evidence that the LINE-1 retrotransposon is susceptible to RNA interference (RNAi). First, double-stranded RNA (dsRNA) generated in vitro from an L1 template is converted into functional short interfering RNA (siRNA) by DICER, the RNase III enzyme that initiates RNAi in human cells. Second, pooled siRNA from in vitro cleavage of L1 dsRNA, as well as synthetic L1 siRNA, targeting the 5'-UTR leads to sequence-specific mRNA degradation of an L1 fusion transcript. Finally, both synthetic and pooled siRNA suppressed retrotransposition from a highly active RC-L1 clone in cell culture assay. Our report is the first to demonstrate that a human transposable element is subjected to RNAi.
Renal and Cardiovascular Protection in Type 2 Diabetes Mellitus (2002)

Aggressive treatment of hypertension is effective in reducing both microvascular and macrovascular complications in type 2 diabetes, and target BP less than 130/85 or 130/80 mmHg are now recommended. Inhibition of renin angiotensin aldosterone system (RAAS) plays an essential role in the treatment of hypertension and diabetes-related complications. Studies focusing on renal end-points suggest that angiotensin-converting enzyme inhibitors (ACE-I) are more effective than other traditional agents in reducing the onset of clinical proteinuria in both type 1 and type 2 diabetic patients with incipient nephropathy, mainly in normotensive ones (secondary prevention). However, several small trials in type 2 diabetic patients with overt nephropathy (tertiary prevention) failed to demonstrate a specific renoprotective role for ACE-I, at variance with type 1 diabetes. Three recent large trials address the question of whether angiotensin II receptor blockers (ARB) prevent the development of clinical proteinuria or delay the progression of nephropathy in type 2 diabetes. The IRMA study showed that irbesartan is more effective than conventional therapy in preventing the development of clinical proteinuria and in favoring the regression to normoalbuminuria for comparable BP control in patients with incipient nephropathy. The IDNT and RENAAL trials showed that ARB are more effective than traditional antihypertensive therapies in reducing progression toward end-stage renal failure (ESRF) in type 2 diabetic patients with overt nephropathy independently of changes in BP. Moreover, a reduction in hospitalizations for heart failure was demonstrated for ARB-treated patients compared with placebo. Furthermore, the LIFE study showed that losartan is more effective than conventional therapy in reducing cardiovascular morbidity and mortality in a cohort of diabetic patients with hypertension and left ventricular hypertrophy. In conclusion, ARB seem to be effective in both preventing renal damage and reducing progression toward ESRF in type 2 diabetic patients. Thus, the guidelines for the prevention and treatment of diabetic nephropathy are now changed. In type 1 diabetes ACE-I are the first-choice drug; in type 2 diabetes, ARB are considered first-choice drugs in secondary prevention as well as ACE-I and have been now elected the unique first-choice drug in tertiary prevention of ESRF. Finally, ARB should be considered as the first-choice drug in cardiovascular prevention too, as well as ACE-I.
In vivo characterization of the first acyl-CoA Δ6-desaturase from a member of the plant kingdom, the microalga Ostreococcus tauri (2005)

Genomic DNA of Ostreococcus tauri, a fully sequenced marine unicellular alga from the phytoplankton, was used to amplify a gene coding for a typical front-end desaturase involved in polyunsaturated fatty acid biosynthesis. Heterologous expression in Saccharomyces cerevisiae revealed very high desaturation activity with Delta6-regioselectivity. Short-time kinetic experiments showed that the desaturase product was detected in the acyl-CoA pool 5 min after addition of the exogenous substrate to the yeast medium and long before its appearance in the total fatty acids. When this desaturase was co-expressed with the acyl-CoA Delta6-elongase from Physcomitrella patens and the lipid-linked Delta5-desaturase from Phaeodactylum tricornutum, high proportions of arachidonic or eicosapentaenoic acid were obtained, because nearly all of the Delta6-desaturated products were elongated. Furthermore, the product/educt ratios calculated in each glycerolipid for the Delta6-desaturase or for the acyl-CoA Delta6-elongase were in about the same range, whereas this ratio showed a very uneven profile in the case of the lipid-linked Delta5-desaturase. Finally, a sequence-based comparison of all the functionally characterized Delta6-desaturases showed that this enzyme was not related to any previously described sequence. Altogether, our data suggest that this desaturase from O. tauri is an acyl-CoA Delta6-desaturase, the first one cloned from a photosynthetically active organism.
Gossypol Induced Apoptosis in the Human Promyelocytic Leukemia Cell Line HL 60. (1999)

In human promyelocytic leukemia cell line HL60, apoptosis was induced by treatment with gossypol that is an inhibitor of protein kinase C. Gossypol acetic acid was added to HL 60 cells at 50, 100, 150 and 200 microM concentrations for six hours. Morphological features of apoptosis as well as internucleosomal DNA fragmentation were evaluated by light microscope, agarose gel electrophoresis and spectrofluorometric quantitation. Our results indicated that with the effective concentrations of gossypol (50 and 100 microM), apoptosis was induced in HL 60 cells.
Quinone Methides Tethered to Naphthalene Diimides as Selective G-Quadruplex Alkylating Agents (2009)

We have developed novel G-quadruplex (G-4) ligand/alkylating hybrid structures, tethering the naphthalene diimide moiety to quaternary ammonium salts of Mannich bases, as quinone-methide precursors, activatable by mild thermal digestion (40 degrees C). The bis-substituted naphthalene diimides were efficiently synthesized, and their reactivity as activatable bis-alkylating agents was investigated in the presence of thiols and amines in aqueous buffered solutions. The electrophilic intermediate, quinone-methide, involved in the alkylation process was trapped, in the presence of ethyl vinyl ether, in a hetero Diels-Alder [4 + 2] cycloaddition reaction, yielding a substituted 2-ethoxychroman. The DNA recognition and alkylation properties of these new derivatives were investigated by gel electrophoresis, circular dichroism, and enzymatic assays. The alkylation process occurred preferentially on the G-4 structure in comparison to other DNA conformations. By dissecting reversible recognition and alkylation events, we found that the reversible process is a prerequisite to DNA alkylation, which in turn reinforces the G-quadruplex structural rearrangement.
Functional compatibility between isoform α and β of type II DNA topoisomerase (2004)

DNA topoisomerase II (topo II) plays a crucial role in controlling the conformation of both DNA and whole chromosomes. This activity is essential for several cellular events such as DNA replication, transcription, chromosome condensation and segregation. In mammals, two genes code for isoforms of topo II, termed alpha and beta. They are similar in primary structure and have almost identical catalytic properties in vitro. We transfected HeLa cells with small interfering RNAs (siRNAs) targeted against either topo IIalpha or IIbeta, and succeeded in knocking down the expression of the corresponding protein. Chromosomes were condensed and aligned at metaphase in topo IIalpha-knockdown cells. Although some lagging chromosomes were observed, they were still segregated at anaphase despite the absence of topo IIalpha. When both topo IIalpha and topo IIbeta were removed, the segregation of chromosomes was severely arrested, suggesting that topo IIbeta could partially substitute for topo IIalpha. Double-knockdown experiments also revealed that topo II was required for shortening of the chromosome axis.
JAK-STAT Signaling Mediates Gangliosides-induced Inflammatory Responses in Brain Microglial Cells (2002)

Neuronal cell membranes are particularly rich in gangliosides, which play important roles in brain physiology and pathology. Previously, we reported that gangliosides could act as microglial activators and are thus likely to participate in many neuronal diseases. In the present study we provide evidence that JAK-STAT inflammatory signaling mediates gangliosides-stimulated microglial activation. Both in rat primary microglia and murine BV2 microglial cells, gangliosides stimulated nuclear factor binding to GAS/ISRE elements, which are known to be STAT-binding sites. Consistent with this, gangliosides rapidly activated JAK1 and JAK2 and induced phosphorylation of STAT1 and STAT3. In addition, gangliosides increased transcription of the inflammation-associated genes inducible nitric-oxide synthase, ICAM-1, and MCP-1, which are reported to contain STAT-binding elements in their promoter regions. AG490, a JAK inhibitor, reduced induction of these genes, nuclear factor binding activity, and activation of STAT1 and -3 in gangliosides-treated microglia. AG490 also inhibited gangliosides-induced release of nitric oxide, an inflammation hallmark. Furthermore, AG490 markedly reduced activation of ERK1/2 MAPK, indicating that ERKs act downstream of JAK-STAT signaling during microglial activation. However, AG490 did not affect activation of p38 MAPK. We also report that the sialic acid residues present on gangliosides may be one of the essential components in activation of JAK-STAT signaling. The present study indicates that JAK-STAT signaling is an early event in gangliosides-induced brain inflammatory responses.
Oncostatin M as a Potent Mitogen for AIDS-Kaposi's Sarcoma-Derived Cells (1992)

Oncostatin M, a cytokine produced by activated lymphoid cells, regulates the growth and differentiation of a number of tumor and normal cells. In contrast to its effects on normal endothelial and aortic smooth muscle cell cultures, Oncostatin M was a potent mitogen for cells derived from acquired immunodeficiency syndrome-related Kaposi's sarcoma (AIDS-KS). After exposure to Oncostatin M, AIDS-KS cells assumed a spindle morphology, had an increased ability to proliferate in soft agar, and secreted increased amounts of interleukin-6. Oncostatin M RNA and immunoreactive Oncostatin M protein were found in AIDS-KS-derived cell isolates. These results suggest that Oncostatin M may play a role in the pathogenesis of AIDS-KS.
Prostate Cancer, Version 2.2014 (2014)

Prostate cancer has surpassed lung cancer as the most common cancer in men in the United States. The NCCN Guidelines for Prostate Cancer provide multidisciplinary recommendations on the clinical management of patients with prostate cancer based on clinical evidence and expert consensus. NCCN Panel guidance on treatment decisions for patients with localized disease is represented in this version. Significant updates for early disease include distinction between active surveillance and observation, a new section on principles of imaging, and revisions to radiation recommendations. The full version of these guidelines, including treatment of patients with advanced disease, can be found online at the NCCN website.
A Method for the Selection of Human Embryonic Stem Cell Sublines with High Replating Efficiency After Single‐Cell Dissociation (2006)

Human embryonic stem cells (hESCs) exhibit pluripotency and indefinite proliferation and are a potential source of cells for transplantation therapies and drug discovery. These applications will require large amounts of hESCs. However, hESCs are difficult to culture and maintain at larger scales, in part because of their low resistance to dissociation during passaging. To circumvent this, we developed a simple and easy method for establishing hESC sublines tolerant of complete dissociation. These cells exhibit high replating efficiency and also high cloning efficiency, and they maintain their ability to differentiate into the three germ layers. Several sublines have no detectable abnormalities in their karyotypes, and they retained their characteristics under feeder-free culture conditions and after freeze-thawing. Thus, these hESC sublines would be valuable for hESC applications.
<title>Similarity indexing: algorithms and performance</title> (1996)

Efficient indexing support is essential to allow content-based image and video databases using similarity-based retrieval to scale to large databases (tens of thousands up to millions of images). In this paper, we take an in depth look at this problem. One of the major difficulties in solving this problem is the high dimension (6-100) of the feature vectors that are used to represent objects. We provide an overview of the work in computational geometry on this problem and highlight the results we found are most useful in practice, including the use of approximate nearest neighbor algorithms. We also present a variant of the optimized k-d tree we call the VAM k-d tree, and provide algorithms to create an optimized R-tree we call the VAMSplit R-tree. We found that the VAMSplit R-tree provided better overall performance than all competing structures we tested for main memory and secondary memory applications. We observed large improvements in performance relative to the R*-tree and SS-tree in secondary memory applications, and modest improvements relative to optimized k-d tree variants.
In vitro and in vivo Release of Soluble erbB‐2 Protein from Human Carcinoma Cells (1990)

An enzyme-linked immunosorbent assay (ELISA) was developed to measure soluble erbB-2 protein in culture supernatants of various human cell lines and sera of patients suffering from recurrent breast carcinoma. Soluble erbB-2 protein was demonstrated in culture supernatants of cell lines that expressed high levels of erbB-2 protein as shown by western blot analysis of cell lysates. Increased levels of the protein, 40- to 190-fold higher than in healthy controls, were demonstrated in sera of 3 out of 12 patients with breast carcinomas. On immunohistological study of tumor tissues from 9 patients, high immune reaction with the anti-erbB-2 protein antibody was observed in 2 cases. These were two of the three patients who had elevated levels of erbB-2 protein in serum (a sample was not available from the third patient). These results raise the possibility that soluble erbB-2 protein level in serum can be used as an indicator for spread of carcinomas that overexpress erbB-2 protein.
Singapore No Pushover for NZ Consultants (1993)

Opportunities exist for New Zealand consultancies in the Singaporean market, especially in environmental engineering and heavy mechanical and electrical engineering. Singapore is a good centre for investment as it has a stable government, an excellent and continuously improving infrastructure and a geographical location central to the other rapidly developing Asian nations. The best course would be for both to get into joint ventures with locally established consultancies for particular projects with the Singaporean consultancy providing the Professional Engineeing services and making the relevant Authority submissions.
Identification of the Retinoic Acid-inducible All-trans-retinoic Acid 4-Hydroxylase (1996)

Retinoic acid (RA) metabolites of vitamin A are key regulators of gene expression involved in embryonic development and maintenance of epithelial tissues. The cellular effects of RA are dependent upon the complement of nuclear receptors expressed (RARs and RXRs), which transduce retinoid signals into transcriptional regulation, the presence of cellular retinoid-binding proteins (CRABP and CRBP), which may be involved in RA metabolism, and the activity of RA metabolizing enzymes. We have been using the zebrafish as a model to study these processes. To identify genes regulated by RA during exogenous RA exposure, we utilized mRNA differential display. We describe the isolation and characterization of a cDNA, P450RAI, encoding a novel member of the cytochrome P450 family. mRNA transcripts for P450RAI are expressed normally during gastrulation, and in a defined pattern in epithelial cells of the regenerating caudal fin in response to exogenous RA. In COS-1 cells transfected with the P450RAI cDNA, all-trans-RA is rapidly metabolized to more polar metabolites. We have identified 4-oxo-RA and 4-OH-RA as major metabolic products of this enzyme. P450RAI represents the first enzymatic component of RA metabolism to be isolated and characterized at the molecular level and provides key insight into regulation of retinoid homeostasis.
Cytotoxic T Lymphocytes Specific for a Nonpolymorphic Proteinase 3 Peptide Preferentially Inhibit Chronic Myeloid Leukemia Colony-Forming Units (1997)

We previously showed that a peptide (PR1) derived from the primary granule enzyme proteinase 3 induced peptide specific cytotoxic T lymphocytes (CTL) in a normal HLA-A2.1+ individual. These CTL showed HLA-restricted cytotoxicity to myeloid leukemias (which overexpress proteinase 3). To further investigate their antileukemic potential, we studied the ability of PR1-specific CTL, derived from two HLA-A2.1+ normal individuals, to inhibit colony-forming unit granulocyte-macrophage (CFU-GM) from normal and leukemic individuals. CTL from 20 day PR1 peptide-pulsed lymphocyte cultures showed 89% to 98% HLA-A2.1-restricted colony inhibition of chronic myeloid leukemia targets. Colony formation in normal HLA-A2.1+ bone marrow or HLA-A2.1- CML cells was not inhibited. Sequencing of the exon encoding PR1 showed that colony inhibition was not caused by polymorphic differences in proteinase 3 between effectors and targets. Analysis by flow cytometry showed that proteinase 3 was overexpressed in the leukemia targets compared with normal marrow targets (median channel fluorescence 1,399 v 298, P = .009). These results show that PR1-specific allogeneic T cells preferentially inhibit leukemic CFU-GM based on overexpression of proteinase 3, and that proteinase 3-specific CTL could be used for leukemia-specific adoptive immunotherapy.
Molecular cloning, expression, and DNA sequence analysis of the gene that encodes the 16-kilodalton outer membrane lipoprotein of Serpulina hyodysenteriae (1993)

The gene (smpA) that encodes the 16-kDa outer membrane lipoprotein of Serpulina hyodysenteriae was cloned in Escherichia coli, and its primary structure was determined by nucleotide sequencing. The putative open reading frame encodes a prolipoprotein of 16.8 kDa which in its fully acylated and cleaved form is 15.1 kDa. Analysis of the N-terminal amino acid sequence derived from the DNA sequence revealed the presence of a signal sequence and a putative acylation and signal peptidase II cleavage site (Phe-Ala-Val-Ser-Cys). In E. coli, processing of the prolipoprotein was less efficient than that observed in S. hyodysenteriae, and globomycin, an inhibitor of signal peptidase II, inhibited cleavage of the lipoprotein expressed in E. coli but did not inhibit cleavage in S. hyodysenteriae.
The theory and characteristics of an efficient surface wave launcher (surfatron) producing long plasma columns (1979)

Long plasma columns, in many instances preferable to the positive columns of DC discharges, can be obtained by means of a UHF surface wave propagating along the column. This is possible through the use of a novel wave-launching structure, called a surfatron. The launcher is compact and located on the outside of the dielectric tube containing the plasma. The surfatron is described and analysed in terms of an equivalent circuit theory. Guidelines for its design and operation are given.