gebhart/patrepeval huggingface dataset:
Cysteine Synthase Overexpression in Tobacco Confers Tolerance to Sulfur-Containing Environmental Pollutants (2001)

Cysteine (Cys) synthase [O-acetyl-L-Ser(thiol)-lyase, EC 4.2.99.8; CSase] is responsible for the final step in biosynthesis of Cys. Transgenic tobacco (Nicotiana tabacum; F(1)) plants with enhanced CSase activities in the cytosol and in the chloroplasts were generated by cross-fertilization of two transformants expressing cytosolic CSase or chloroplastic CSase. The F(1) transgenic plants were highly tolerant to toxic sulfur dioxide and sulfite. Upon fumigation with 0.1 microL L(-1) sulfur dioxide, the Cys and glutathione contents in leaves of F(1) plants were increased significantly, but not in leaves of non-transformed control plants. Furthermore, the leaves of F(1) plants exhibited the increased resistance to paraquat, a herbicide generating active oxygen species.
Targeted disambiguation of ad-hoc, homogeneous sets of named entities (2012)

In many entity extraction applications, the entities to be recognized are constrained to be from a list of "target entities". In many cases, these target entities are (i) ad-hoc, i.e., do not exist in a knowledge base and (ii) homogeneous (e.g., all the entities are IT companies). We study the following novel disambiguation problem in this unique setting: given the candidate mentions of all the target entities, determine which ones are true mentions of a target entity. Prior techniques only consider target entities present in a knowledge base and/or having a rich set of attributes. In this paper, we develop novel techniques that require no knowledge about the entities except their names. Our main insight is to leverage the homogeneity constraint and disambiguate the candidate mentions collectively across all documents. We propose a graph-based model, called MentionRank, for that purpose. Furthermore, if additional knowledge is available for some or all of the entities, our model can leverage it to further improve quality. Our experiments demonstrate the effectiveness of our model. To the best of our knowledge, this is the first work on targeted entity disambiguation for ad-hoc entities.
Follicular Homing T Helper (Th) Cells and the Th1/Th2 Paradigm (2000)

The Th1/Th2 paradigm is a cornerstone for our understanding of T cell responses ([1][1]). It conveniently subdivides T cell immune responses into those specialized for defense against intracellular pathogens including viruses and some bacteria (Th1), and a second for defense against large
Maize Phosphoenolpyruvate Carboxylase Involved in C4 Photosynthesis: Nucleotide Sequence Analysis of the 5' Flanking Region of the Gene1 (1989)

To clone the genomic DNA fragment containing the putative promoter region of the gene for phosphoenolpyruvate carboxylase [EC 4.1.1.31] involved in C4 photosynthesis (C4-type PEPC), maize genomic libraries were screened. On probing with a 384-bp fragment from the N-terminal coding region of the maize cDNA for C4-type PEPC, four EcoRI-fragments differing in the restriction map were cloned, reflecting the presence of a small gene family. Southern blot analyses were carried out on the genomic DNA and the cloned DNA fragments using several segments of the cDNA for C4-type PEPC as probes. The results indicated that the C4-type PEPC is encoded by a single gene and the cloned 7.0-kb fragment was derived from this gene. The transcription start site, as determined in a primer extension experiment, was located at about 4 kb downstream of the 5' end of the cloned fragment. The nucleotide sequence was determined for the region which extended about 1 kb upstream from the transcription start site and possible signal sequences related to gene expression were found, including four classes of direct repeats. The sequences of the corresponding regions of the other two cloned fragments (8.9 and 12.9 kb) which strongly hybridized with the 384-bp probe were very similar to each other, but they were quite different in the 5' upstream region from the sequence of the gene for C4-type PEPC.
Tetrodotoxin‐resistant impulses in single nociceptor nerve terminals in guinea‐pig cornea (1998)

1. Extracellular recording techniques have been used to study nerve impulses in single sensory nerve terminals in guinea-pig cornea isolated in vitro. 2. Nerve impulses occurred spontaneously and were evoked by electrical stimulation of the ciliary nerves. 3. The nerve impulses were identified as originating in polymodal receptors, mechano-receptors or 'cold' receptors. All three types are believed to be nociceptors. 4. Tetrodotoxin (TTX, 1 microM) blocked nerve impulses evoked by electrical stimulation of the ciliary nerves. However, ongoing and/or naturally evoked nerve impulses persisted in the presence of TTX in all three types of receptors. Lignocaine (lidocaine; 1 mM) blocked all electrical activity. 5. TTX-resistant sodium channels therefore play a major role in generating the action potentials that signal pain to the brain.
Directed Evolution of the Fatty-Acid Hydroxylase P450 BM-3 into an Indole-Hydroxylating Catalyst (2000)

The self-sufficient cytochrome P450 BM-3 enzyme from Bacillus megaterium catalyzes subterminal hydroxylation of saturated long-chain fatty acids and structurally related compounds. Since the primary structure of P450 BM-3 is homologous to that of mammalian P450 type II, it represents an excellent model for this family of enzymes. During studies on the directed evolution of P450 BM-3 into a medium-chain fatty-acid hydroxylase, several mutants, in particular the triple mutant Phe87Val, Leu188Gln, Ala74Gly, were observed to hydroxylate indole, producing indigo and indirubin at a catalytic efficiency of 1365 M(-1)s(-1) (kcat=2.73 s(-1) and Km=2.0 mM). Both products were unequivocally characterized by NMR and MS analysis. Wild-type P450 BM-3 is incapable to hydroxylate indole. These results demonstrate that an enzyme can be engineered to catalyze the transformation of substrates with structures widely divergent from those of its native substrate.
Hole-assisted lightguide fiber for large anomalous dispersion and low optical loss (2001)

Hole-assisted lightguide fiber (HALF) is a microstructured fiber comprising a material index profile for waveguiding and air holes for modifying optical properties. Anomalous dispersion larger than those of the conventional fibers can be realized without severe degradation in optical loss, because of low power fraction in the holes and structural simplicity. We investigate into the causes of the loss of the fabricated HALFs, and show that a GeO2-doped core, in addition to the low power fraction, is desirable for low loss. The fabricated HALF exhibits a loss as low as 0.41 dB/km and a large anomalous dispersion of +35 ps/nm/km at 1550 nm.
Reversible Daptomycin Tolerance of Adherent Staphylococci in an Implant Infection Model (2011)

Daptomycin (DAP) is bactericidal against methicillin-resistant Staphylococcus aureus (MRSA) in vitro, but it failed to eradicate MRSA in an experimental model of implant-associated infection. We therefore investigated various factors which could explain treatment failure by evaluating DAP activity, including the role of different cell wall components, adherence, biofilm, and calcium ions (Ca(2+)) in vitro and in vivo. In the tissue cage infection model, DAP was active only prophylactically and against low inocula. To identify the mechanisms of treatment failure, the in vitro activity of DAP against planktonic and adherent growing S. aureus and S. epidermidis mutants, differing in their capacity of biofilm formation and adherence, was determined. For planktonic staphylococci, the MIC was 0.625 μg/ml. For adherent staphylococci, DAP reduced biofilms at 30 μg/ml. However, it did not kill adherent bacteria up to 500 μg/ml, independent of biofilm biosynthesis (the ica mutant strain), nuclease (the nuc1/nuc2 mutant strain), LPXTG-anchored adhesin (the srtA mutant strain), autolysin (the atl mutant strain), or alanyl-LTA (the dltA mutant strain). Resistance of adherent staphylococci was not due to mutations of adherent bacteria, since staphylococci became DAP susceptible after detachment. Phenotypic tolerance was not explained by inactivation of DAP or inability of initial Ca(2+)-DAP complex formation. However, the addition of up to 100 mg/liter (2.5 mmol/liter) Ca(2+) gradually improved bactericidal activity toward adherent staphylococci in vitro and increased the prevention rate in the cage model from 40% to 60%. In summary, adherent staphylococci are resistant to DAP killing unless Ca(2+) is supplemented to physiologic concentrations.
Inhibition of tumor growth in vivo by hyaluronan oligomers (1998)

One of the critical events in tumor growth and metastasis is the interaction between tumor cells and host tissue stroma, mediated by different adhesion receptor repertoires in different tumor cell types. Several lines of evidence indicate that interaction between the hyaluronan receptor CD44, expressed on tumor cells, and host tissue stromal hyaluronan can enhance growth and invasiveness of certain tumors. Disruption of CD44-hyaluronan interaction by soluble recombinant CD44 has been shown to inhibit tumor formation by lymphoma and melanoma cells transfected with CD44. Since hyaluronan is a ubiquitous glycosaminoglycan polymer from which oligosaccharides of defined size can be readily purified, we tested the ability of hyaluronan oligomers to inhibit tumor formation by subcutaneously (s.c.) injected B16F10 melanoma cells. Our results indicate that hyaluronan oligomers injected at concentrations as low as 1 mg/ml can markedly inhibit B16F10 melanoma growth, providing a potentially attractive reagent for the control of local tumor development. Int. J. Cancer 77:396–401, 1998. © 1998 Wiley-Liss, Inc.
Highly Efficient Lipase-Catalyzed Kinetic Resolution of Chiral Amines (1994)

The lipase Candida antarctica catalyzes the enantioselective acetylation of chiral primary amines, kinetic resolution leading to an enantiomeric excess (ee) of 90–98%.
H 2 S Induces a Suspended Animation-Like State in Mice (2005)

Mammals normally maintain their core body temperature (CBT) despite changes in environmental temperature. Exceptions to this norm include suspended animation-like states such as hibernation, torpor, and estivation. These states are all characterized by marked decreases in metabolic rate, followed by a loss of homeothermic control in which the animal's CBT approaches that of the environment. We report that hydrogen sulfide can induce a suspended animation-like state in a nonhibernating species, the house mouse (Mus musculus). This state is readily reversible and does not appear to harm the animal. This suggests the possibility of inducing suspended animation-like states for medical applications.
Biogenesis of Ornithine Transcarbamylase in spf ash Mutant Mice: Two Cytoplasmic Precursors, One Mitochondrial Enzyme (1983)

Extracts of liver from hemizygous affected mice with the X-linked spfash mutation have 5 to 10 percent of normal ornithine transcarbamylase (OTC) activity, yet the homogeneous enzyme isolated from these extracts is identical to that in controls. The OTC messenger RNA from mutant livers programs the synthesis of two distinct OTC precursor polypeptides--one normal in size, the other distinctly elongated. Both precursors are imported and proteolytically processed by mitochondria, but only the normal one is assembled into active trimer. This novel phenotype may result from a mutation in the structural gene for OTC leading, primarily, to aberrant splicing of OTC messenger RNA and, secondarily, to formation of a structurally altered precursor whose posttranslational pathway is ultimately futile because its mature mitochondrial form is not capable of assembly and functional expression.
Biochemical Characterization of Osteo-Testicular Protein Tyrosine Phosphatase and Its Functional Significance in Rat Primary Osteoblasts (2000)

Rat osteo-testicular protein tyrosine phosphatase (OST-PTP), expressed in osteoblasts and testis, is a receptor-like transmembrane protein with two tandemly repeated phosphatase domains in the cytoplasmic region. In this report, we show that the first domain (CD1) is enzymatically active and appears to be influenced by the catalytically inactive second domain (CD2). The activity of CD1 is specific to phosphorylated tyrosine. Full-length OST-PTP protein expressed in COS cells has a molecular mass of approximately 185 kDa, and immunoprecipitates of this protein using OST-PTP-specific antisera show strong tyrosine phosphatase activity. Expression of OST-PTP mRNA in primary rat calvarial osteoblasts is temporally regulated, and peak expression is found at approximately day 15, which correlated well with the appearance of OST-PTP protein and its associated tyrosine phosphatase activity. Treatment of osteoblasts in culture with antisense oligonucleotides directed against the 5' untranslated region of OST-PTP results in abrogation of differentiation, confirming the functional importance of OST-PTP expression in osteoblast development.
The Physics of Solar Cells (2003)

Photons In, Electrons Out: Basic Principles of PV Electrons and Holes in Semiconductors Generation and Recombination Junctions Analysis of the p-n Junction Monocrystalline Solar Cells Thin Film Solar Cells Managing Light Over the Limit: Strategies for Higher Efficiency.
Retroviral transfer of CPP32beta gene into malignant gliomas in vitro and in vivo. (1998)

Malignant gliomas are highly aggressive neoplasms that are very resistant to current therapeutic approaches, including irradiation, chemotherapy, and immunotherapy. To improve the prognosis, it is absolutely essential to explore novel modalities of treatment. Recently, we have demonstrated that interleukin 1beta-converting enzyme (ICE), a mammalian homologue of the Caenorhabditis elegans cell death gene ced-3, induces apoptotic cell death in malignant glioma cells. To date, ICE and ICE-like proteases (the ICE family), such as Ich-1L, CPP32beta, Mch2alpha, and Mch3alpha, have been shown to mediate apoptosis in some cells. The purpose of this study is to determine whether the ICE gene family functions as a useful tool for the treatment of malignant glioma cells through induction of apoptosis. The transient transfection assays showed that CPP32beta and Mch2alpha genes induced apoptotic cell death in malignant glioma cells more effectively than did the ICE, Ich-1L, and Mch3alpha genes. To improve the efficiency of gene transfer into malignant glioma cells, we constructed the retroviral vectors containing the ICE gene family. The retroviral transfer of CPP32beta or Mch2alpha gene effectively induced apoptosis in malignant glioma cells in vitro. Furthermore, treatment of tumors grown in mice with retrovirus containing CPP32beta significantly inhibited growth of the tumors through induction of apoptosis. The retroviral transfer of CPP32beta or Mch2alpha, therefore, may be a novel and promising approach for the treatment of malignant glioma, an invariably fatal tumor.
DOWNREGULATION OF CONNEXIN 43 GENE EXPRESSION IN RAT HEART DURING INFLAMMATION. THE ROLE OF TUMOUR NECROSIS FACTOR (1999)

Gap junctions form channels that mediate the communication between adjacent cells. Alterations in gap junction function and/or expression are believed to contribute to cardiac dysfunction such as those observed in septic patients. The expression of connexin 43 (Cx43), the subunit component of the most abundant cardiac gap junction, was analysed in rat heart during inflammation induced by the administration of bacterial lipopolysaccharide (LPS). Cx43 mRNA levels were found to be dramatically (>50%) and rapidly (2 h) reduced in the heart after injection of LPS (1 mg/kg). To investigate the possible mechanism of the decrease in Cx43 expression during inflammation, the promoter region of this gene was cloned. The basal Cx43 promoter activity was observed within 224-134 bp of the transcriptional initiation site after transfection into a rat myoblast cell-line (H9c2). The Cx43 promoter activity was found to be reduced by incubation of the transfected cells with serum obtained from LPS-treated rats. Moreover, Cx43 promoter activity was also decreased upon incubation with tumour necrosis factor alpha. These results suggest that Cx43 expression in the heart can be modulated by circulating cytokines. These observations may have important implications in the depression of heart function observed in septic patients.
“Search and destroy” for methicillin-resistant Staphylococcus aureus in the intensive care unit: Should this now be the standard of care?* (2007)

Department of Surgery, Tufts-New England Medical Center, Tufts University School of Medicine, Boston, MA
Tandem Mass Tags:  A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS (2003)

A novel MS/MS-based analysis strategy using isotopomer labels, referred to as "tandem mass tags" (TMTs), for the accurate quantification of peptides and proteins is described. The new tags are designed to ensure that identical peptides labeled with different TMTs exactly comigrate in all separations. The tags require novel methods of quantification analysis using tandem mass spectrometry. The new tags and analysis methods allow peptides from different samples to be identified by their relative abundance with greater ease and accuracy than other methods. The new TMTs permit simultaneous determination of both the identity and relative abundances of peptide pairs using a collision induced dissociation (CID)-based analysis method. Relative abundance measurements made in the MS/MS mode using the new tags are accurate and sensitive. Compared to MS-mode measurements, a very high signal-to-noise ratio is achieved with MS/MS based detection. The new tags should be applicable to a wide variety of peptide isolation methods.
Adipose tissue angiogenesis1,2 (2004)

A review of adipose tissue angiogenesis includes the morphological and cytochemical development of adipose tissue vasculature and the concept of primitive fat organs. Spatial and temporal relationships between fetal vascular and fat cell development are discussed, including depot- and genetic-dependent arteriolar differentiation. The relationship between connective tissue deposition and elaboration of adipose tissue vasculature is discussed with respect to regulating adipocyte development in a depot-dependent manner. In vitro studies indicated that depot-dependent vascular traits may be attributable to intrinsic growth characteristics of adipose tissue endothelial cells. These studies indicate that adipogenesis may be regulated by factors that drive angiogenesis. Fundamental aspects of angiogenesis, including basement membrane breakdown, vasculogenesis, angiogenic remodeling, vessel stabilization, and vascular permeability were reviewed. Critical angiogenic factors include vascular endothelial growth factor (VEGF), VEGF receptors, angiopoietins (Ang), ephrins, matrix metalloproteinases, and the plasminogen enzymatic system. Vascular endothelial growth factor is the most critical factor because it initiates the formation of immature vessels and disruption of a single VEGF allele leads to embryonic lethality in mice. Expression of VEGF is influenced by hypoxia, insulin, growth factors, and several cytokines. Angiogenic factors secreted and/or produced by adipocytes or preadipocytes are discussed. Vascular endothelial growth factor expression and secretion by adipocytes is regulated by insulin and hypoxia, and is associated with adipose tissue accretion. Vascular endothelial growth factor accounts for most of the angiogenic activity of adipose tissue. The proposed role of leptin as an adipogenic factor is reviewed with respect to efficacy on various aspects of angiogenesis relative to other angiogenic factors. The VEGF and leptin genes are both hypoxia inducible, but potential links between VEGF and leptin gene expression have not been examined. Finally, several studies including a study of mice treated with antiangiogenic factors indicate that adipose tissue accretion can be controlled through the vasculature per se.
Survival of viruses on fresh produce, using MS2 as a surrogate for norovirus (2004)

Bacteriophage MS2 has been evaluated as a potential surrogate for noroviruses on fresh produce. Experimental results together with current knowledge of norovirus resistance and survival indicate that MS2 could be used as an effective surrogate in future evaluations.
Planar monopole folded into a compact structure for very‐low‐profile multiband mobile‐phone antenna (2002)

Abstract A planar monopole consisting of three branch strips and folded into a rectangular‐box‐like compact structure for very‐low‐profile GSM/DCS/PCS multiband mobile‐phone antennas is presented. The three branch strips are designed to operate as quarter‐wavelength structures at 900, 1800, and 1900 MHz, respectively, and the obtained impedance bandwidths cover the required bandwidths of the GSM band (890–960 MHz), the DCS band (1710–1880 MHz), and the PCS band (1850–1990 MHz). The proposed antenna has a compact size of 6.5 mm in height, 6 mm in width, and 25 mm in length, and can be mounted on top of a mobile phone with a small distance of 3 mm to the ground plane, resulting in a very low profile of 9.5 mm (less than 3% of the wavelength at 900 MHz) from ground for the proposed antenna in practical applications. © 2002 Wiley Periodicals, Inc. Microwave Opt Technol Lett 33: 22–25, 2002; DOI 10.1002/mop.10219
Autonomous conduct of indirect fire in interactive simulations (2002)

In the conduct of interactive computer simulations involving the combat of ground forces, it is frequently desirable to provide a capability to enable entities that can automatically emulate the actions of a particular group of participants from either side. This reduces the number of humans required to conduct the simulation. This capability is especially useful when special skills are required to interact in the roles concerned. To this end, an expert system could be constructed with the reasoning abilities necessary to simulate the cognitive contributions of its human counterpart. The construction of such an expert system for the purpose of simulating the conduct of indirect fires was the goal of this research. The result includes a working implementation of an autonomous simulated forward observer that is capable of issuing a standard call for indirect fire, and adjusting the "observed" fires in accordance with previously developed mission guidance.
Molecular characterization of a region of DNA associated with mutations at the agouti locus in the mouse. (1991)

Molecular characterization of a radiation-induced agouti (a)-locus mutation has resulted in the isolation of a segment of DNA that maps at or near the a locus on chromosome 2 in the mouse. This region of DNA is deleted in several radiation- or chemical-induced homozygous-lethal a-locus mutations and is associated with specific DNA structural alterations in two viable a-locus mutations. We propose that DNA probes from this region of chromosome 2 will be useful for ultimately characterizing the individual gene or genes associated with a-locus function.