gebhart/patrepeval huggingface dataset:
Regulation in Vitro of Metallothionein Gene Binding Factors (1987)

Mouse nuclear factors that bind to an upstream metal regulatory element of the mouse metallothionein-I gene have been identified by DNA footprinting and oligonucleotide band shift assays. The formation of complexes at this site can be activated 20- to 40-fold by the vitro addition of ionic cadmium. The activation reaction is rapid, reversible by a metal chelator, and may involve multiple proteins. These results suggest that the initial step in cadmium detoxification is an interaction between the metal and nuclear DNA-binding factors leading to an increase in metallothionein gene transcription. The ability to observe metal activation in vitro makes this a powerful system to study the biochemistry of eukaryotic gene regulation.
Enrichment of Early Fetal‐Liver Hemopoietic Stem Cellsof the Rat Using Monoclonal Antibodies Against theTransferrin Receptor, Thy‐1, and MRC‐Oχ82 (1995)

Fetal livers from inbred rat fetuses at 14 days' gestation were dispersed into a single-cell suspension by physical disruption and collagenase digestion. Pluripotent stem cells were characterized and partially purified by a combination of monoclonal antibodies. These included CD71 (anti-transferrin receptor, MRC-OX26, used for rosetting), Cdw90 (anti-Thy-1, MRC-OX7), and the newly described MRC-OX82 (reacting with myeloiid cells in peritoneal exudate), employed in FACS sorting. Enrichment was monitored by long-term reconstitution of lethally irradiated congenic rats genetically distinguishable from the donor by an allelomorphic variant of the CD45 cell-surface antigen. At intervals from 3 months to 1 year, lymph-node cells and peritoneal exudate cells were biopsied for analysis by two-color flow cytometry--one color to determine donor origin, the other to identify Th cell (CD4+), Tc cell (CD8+), B cell (sIg+ or CD45RC+), neutrophil (OX82+ or OX43-), and macrophage (OX43+) compartments. The degree of chimaerism was taken as the read out of stem-cell activity. No significant differentials between lymph-node and peritoneal exudate chimaerisms were detected in any of the recipients; therefore, the enrichment procedure revealed only pluripotent cells, not stem cells of restricted potency. All recovered stem-cell activity was in the OX26(CD71)-negative, OX7(CDw90)-positive, OX82-positive fraction. In the optimum case, an enrichment of very roughly 200-fold in cell-for-cell activity was obtained. Rat bone-marrow colony-forming units in the spleen (CFUs-12) were found to lack the surface antigens recognized by the monoclonal antibodies CD53 (MRC-OX44), MRC-OX39, MRC-OX59, and 144.2.15. These would provide a strategy for their enrichment by depletion.
Ellagic acid embryoprotection in vitro: Distribution and effects on DNA adduct formation (1993)

Ellagic acid (EA) is a naturally occurring plant phenol that was recently demonstrated to protect cultured rat embryos from the embryotoxic effects of N-methyl-N-nitrosourea (MNU). The teratogenic mechanism of action of MNU, as well as other methylating agents, is debated: both cell death and mutation have been proposed. In some model systems, EA has been reported to selectively decrease the mutagenic DNA adduct O6-methylguanine (O6MG) when compared to the cytotoxic DNA adduct N7-methylguanine (N7MG). The present study was initiated to determine 1) the distribution of 14C-EA and 3H-MNU in the rat whole embryo culture model system and 2) the effects of EA on MNU-induced DNA adduct formation in this model system. 14C-EA (50 microM for 2 hr, known embryoprotective concentration; no MNU added) was used to demonstrate access of EA to the embryo within the 2 hr exposure period. The majority of EA (99.5%) remained in the media while tissue concentrations of 57.0 and 47.9 pmol/mg were attained in the yolk sacs and embryos, respectively. Similarly, MNU (75 microM for 1 hr, known effective concentration; no EA added) was distributed between the media, yolk sacs, and embryos at 99.7%, 73.7 and 112.9 pmol/mg, respectively. When non-radiolabeled EA (50 microM for 2 hr) was used to protect embryos prior to exposure to 3H-MNU (75 microM for 1 hr), the distribution of MNU in the model system was unchanged.(ABSTRACT TRUNCATED AT 250 WORDS)
Fiberoptic Confocal Microscopy Using a 1.55-$\mu$m Fiber Laser for Multimodal Biophotonics Applications (2008)

We have experimentally demonstrated a fiberoptic confocal microscope using a 1.55-mum laser source. A compact and efficient Er-doped fiber laser source and conventional single-mode fiber components were used to construct a near-infrared fiberoptic confocal microscope system with 3-D scanning capability. A broadband 1.55-mum light source was used to reduce fringe patterns and interferences that occur when a highly coherent source is used. Our system showed a lateral resolution as high as 1.1 mum with a 60times objective lens, which is close to the theoretical limit. The system can be used in various multimodal biophotonics platforms including precise 3D imaging, biosensing, and laser tissue ablation due to its high water absorption characteristics while maintaining low thermomechanical and self-focusing damage from high-power lasers.
Image subband coding using arithmetic coded trellis coded quantization (1995)

A method is presented for encoding memoryless sources using trellis coded quantization (TCQ) with uniform thresholds. The trellis symbols are entropy-coded using arithmetic coding. The performance of the arithmetic coded uniform threshold TCQ, for encoding the family of generalized Gaussian densities, is compared with uniform threshold quantization (UTQ) and the Shannon lower bound (SLB). At high rates, the method performs within 0.5 dB of the rate-distortion bound for the family of generalized Gaussian densities. A simple modification of the uniform codebook is shown to result in improved performance at low bit rates. The arithmetic and trellis coding method is used for encoding image subbands. Coding results for monochrome images are presented and compared with other results in the literature. Working C code that implements arithmetic coded uniform threshold TCQ can be obtained using anonymous ftp.
Genomic Cloning and Expression of Three Murine UDP-galactose: β-N-Acetylglucosamine β1,3-Galactosyltransferase Genes (1998)

Based on the detection of expressed sequence tags that are similar to known galactosyltransferase sequences, we have isolated three novel UDP-galactose:beta-N-acetylglucosamine beta1, 3-galactosyltransferase (beta3GalT) genes from a mouse genomic library. The three genes, named beta3GalT-I, -II, and -III, encode type II transmembrane proteins of 326, 422, and 331 amino acids, respectively. The three proteins constitute a distinct subfamily as they do not share any sequence identity with other eucaryotic galactosyltransferases. Also, the entire protein-coding region of the three beta3GalT genes was contained in a single exon, which contrasts with the genomic organization of the beta1,4- and alpha1, 3-galactosyltransferase genes. The three beta3GalT genes were mainly expressed in brain tissue. The expression of the full-length murine genes as recombinant baculoviruses in insect cells revealed that the beta3GalT enzymes share the same acceptor specificity for beta-linked GlcNAc, although they differ in their Km for this acceptor and the donor UDP-Gal. The identification of beta3GalT genes emphasizes the structural diversity present in the galactosyltransferase gene family.
Antibody biomarker discovery through in vitro directed evolution of consensus recognition epitopes (2013)

To enable discovery of serum antibodies indicative of disease and simultaneously develop reagents suitable for diagnosis, in vitro directed evolution was applied to identify consensus peptides recognized by patients' serum antibodies. Bacterial cell-displayed peptide libraries were quantitatively screened for binders to serum antibodies from patients with celiac disease (CD), using cell-sorting instrumentation to identify two distinct consensus epitope families specific to CD patients (PEQ and (E)/DxFV(Y)/FQ). Evolution of the (E)/DxFV(Y)/FQ consensus epitope identified a celiac-specific epitope, distinct from the two CD hallmark antigens tissue transglutaminase-2 and deamidated gliadin, exhibiting 71% sensitivity and 99% specificity (n = 231). Expansion of the first-generation PEQ consensus epitope via in vitro evolution yielded octapeptides QPEQAFPE and PFPEQxFP that identified ω- and γ-gliadins, and their deamidated forms, as immunodominant B-cell epitopes in wheat and related cereal proteins. The evolved octapeptides, but not first-generation peptides, discriminated one-way blinded CD and non-CD sera (n = 78) with exceptional accuracy, yielding 100% sensitivity and 98% specificity. Because this method, termed antibody diagnostics via evolution of peptides, does not require prior knowledge of pathobiology, it may be broadly useful for de novo discovery of antibody biomarkers and reagents for their detection.
Temperature dependent characteristics of bulk GaN Schottky rectifiers on free-standing GaN substrates (2004)

The performance of Schottky rectifiers fabricated with dielectric overlap edge termination on epitaxial layers grown on a free-standing GaN template is reported. The power figure-of-merit (VB)2/RON where VB is the reverse breakdown voltage and RON is the on-state resistance was 11.5 MW cm−2. The forward turn-on voltage was ∼3.5 V at 25 °C, with an on-state resistance of ∼5×10−3 Ω cm2. The reverse recovery time was ⩽50 ns in switching from forward bias to reverse bias. The reverse breakdown showed a temperature coefficient of −0.45 V/C.
Structure and Function of Heterotrimeric G Proteins in Plants (2001)

Heterotrimeric G proteins are mediators that transmit the external signals via receptor molecules to effector molecules. The G proteins consist of three different subunits: alpha, beta, and gamma subunits. The cDNAs or genes for all the alpha, beta, and gamma subunits have been isolated from many plant species, which has contributed to great progress in the study of the structure and function of the G proteins in plants. In addition, rice plants lacking the alpha subunit were generated by the antisense method and a rice mutant, Daikoku d1, was found to have mutation in the alpha-subunit gene. Both plants show abnormal morphology such as dwarfism, dark green leaf, and small round seed. The findings revealed that the G proteins are functional molecules regulating some body plans in plants. There is evidence that the plant G proteins participate at least in signaling of gibberellin at low concentrations. In this review, we summarize the currently known information on the structure of plant heterotrimeric G proteins and discuss the possible functions of the G proteins in plants.
Clot Removal Therapy by Aspiration and Extraction for Acute Embolic Carotid Occlusion (2006)

Balloon guide catheter-assisted clot removal therapy for embolic ICA occlusion may provide a high recanalization rate and good clinical outcome in patients with anatomic crossflow.
Inhibition of endothelial cell proliferation by Notch1 signaling is mediated by repressing MAPK and PI3K/Akt pathways and requires MAML1 (2006)

The requirement for Notch signaling in vasculogenesis and angiogenesis is well documented. In a previous study, we showed that activation of the Notch pathway in endothelial cells induces differentiation-associated growth arrest; however, the underlying mechanism remains to be elucidated. Here, we show that activation of the Notch pathway by either stimulation of cell surface Notch receptors with crosslinked soluble delta-like 4 (sDll4)/Jagged1 (sJag1) or constitutive expression of the Notch1 intracellular domain (N(IC)) suppresses endothelial cell proliferation. This suppression is mediated by the mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3-kinase (PI3K)/Akt pathways. Following Notch1 activation, both pathways were suppressed in endothelial cells, and alterations in MAPK or PI3K/Akt pathway activity reversed Notch1-induced growth inhibition. Furthermore, we found the effect of Notch1 on endothelial cells to require Mastermind-like (MAML). Overexpression of a dominant-negative mutant of MAML1 antagonized the effects of activated Notch1 on the MAPK and PI3K/Akt pathways. Ectopic expression of Hairy/Enhancer of Split 1 (HES1) consistently reproduced the inhibitory effect of N(IC) on endothelial cell proliferation. Together, our data demonstrate that the Notch/MAML-HES signaling cascade can regulate both MAPK and PI3K/Akt pathways, which suggests a molecular mechanism for the inhibitory effect of Notch signaling on endothelial cell proliferation.
Posttransplantation function of hearts preserved with fluorochemical emulsion. (1994)

This study was designed to determine whether the novel perfluoroperhydrophenanthrene-egg yolk phospholipid emulsion, APE-LM, was an effective oxygen carrier for long-term hypothermic heart preservation. We postulated that hearts preserved with APE-LM would be well oxygenated during 24-hour preservation and that reperfusion of such hearts with blood would not produce functional or metabolic evidence of myocardial ischemia. Four groups of rabbit hearts were studied (n = 7 per group): fresh controls: nonpreserved, nontransplanted hearts; surgical controls: fresh hearts transplanted heterotopically for 75 minutes before explant and study for 4 hours as isolated working hearts perfused at 37 degrees C; crystalloid-preserved: hearts preserved with crystalloid medium, followed by transplantation and isolated heart perfusion; APE-LM-preserved: hearts treated as those in the crystalloid-preserved group, but preservation was with medium containing APE-LM emulsion (10 ml/dl). Preservation was with continuous coronary perfusion at 18 mm Hg pressure, 12 degrees C, and oxygen tension 838 +/- 11 mm Hg. During preservation, APE-LM hearts had significantly higher pyruvate consumption, and correspondingly higher oxygen consumption, than that of crystalloid hearts. No significant differences were found among fresh controls, surgical controls, and APE-LM-preserved hearts with respect to contractile or output function, oxygen consumption and efficiency indexes, or lactate production during in vitro perfusion. Left ventricular peak systolic pressure and peak rate of pressure development were significantly lower for crystalloid-preserved hearts than for fresh and surgical controls. Left ventricular end-diastolic pressure of crystalloid-preserved hearts was higher than that of the other three groups. The data indicate that rabbit hearts in this model were well preserved with APE-LM and that this emulsion produced better recovery of function than did crystalloid preservation, possibly as a consequence of the high oxygen delivery by the fluorocarbon during preservation.
Identification and characterization of the niddamycin polyketide synthase genes from Streptomyces caelestis (1997)

The genes encoding the polyketide synthase (PKS) portion of the niddamycin biosynthetic pathway were isolated from a library of Streptomyces caelestis NRRL-2821 chromosomal DNA. Analysis of 40 kb of DNA revealed the presence of five large open reading frames (ORFs) encoding the seven modular sets of enzymatic activities required for the synthesis of a 16-membered lactone ring. The enzymatic motifs identified within each module were consistent with those predicted from the structure of niddamycin. Disruption of the second ORF of the PKS coding region eliminated niddamycin production, demonstrating that the cloned genes are involved in the biosynthesis of this compound.
High performance 0.1- mu m room temperature Si MOSFETs (2003)

The design and implementation of 0.15- mu m-channel N-MOSFETs with very high current drive and good short channel behavior at room temperature are discussed. Measured subthreshold characteristics show a slope of 84 mV/dec and a shift for 75 mV for Delta V/sub ds/=1 V. A peak g/sub m/ of 570 mS/mm was recorded, leading to a unity-current-gain cutoff frequency (f/sub T/) of 89 GHz. Key process steps include the formation of 40-AA gate oxides and sub-500-AA junctions. Vertical doping engineering was used to minimize doping at the surface and beneath the junctions, while maintaining good turn-off characteristics.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Lipid transfer proteins (nsLTPs) from barley and maize leaves are potent inhibitors of bacterial and fungal plant pathogens (1993)

Four homogeneous proteins (Cw18, Cw20, Cw21, Cw22) were isolated from etiolated barley leaves by extraction of the insoluble pellet from a Tris-HCl (pH 7.5) homogenate with 1.5 M LiCl and fractionation by reverse-phase high-performance liquid chromatography. All 4 proteins inhibited growth of the pathogen Clavibacter michiganensis subsp. sepedonicus (EC50s = 1-3 x 10(-7) M) and had closely related N-terminal amino acid sequences. The complete amino acid sequences of proteins Cw18 and Cw21 were determined and found to be homologous to previously described, non-specific lipid transfer proteins from plants (32-62% identical positions). The proteins also inhibited growth of the bacterial pathogen Pseudomonas solanacearum (EC50s = 3-6 x 10(-7) M) and the fungus Fusarium solani (EC50s = 3-20 x 10(-6) M). A homologous protein from maize leaves (Cw41) was purified in a similar manner and also found to have inhibitory properties. A synergistic effect against the fungus was observed when protein Cw21 was combined with thionins. A defense role for non-specific lipid transfer proteins from plants is proposed.
Detection of volatile vapors emitted from explosives with a handheld ion mobility spectrometer (2001)

Abstract Vapor detection of plastic explosives is difficult because of the low vapor pressures of explosive components (i.e. RDX and PETN) present in the complex elastomeric matrix. To facilitate vapor detection of plastic explosives, detection agents (taggants) with higher vapor pressures can be added to bulk explosives during manufacture. This paper investigates the detection of two of these taggants, ethyleneglycol dinitrate (EGDN) and 2,3‐dimethyl‐2,3‐dinitrobutane (DMNB), using a handheld ion mobility spectrometer. These two taggants were detected both from neat vapor sources as well as from bulk explosives (nitroglycerin (NG)‐dynamite and C‐4 tagged with DMNB). EGDN was detected from NG‐dynamite as EGDN·NO 3 − at a reduced mobility value of 1.45 cm 2 V −1 s −1 with detection limits estimated to be about 10 ppb v . DMNB was identified from tagged C‐4 as both negative and positive ions with reduced mobility values of 1.33 cm 2 V −1 s −1 for DMNB·NO 2 − and 1.44 cm 2 V −1 s −1 for DMNB·NH 4 + . Positive ions for cyclohexanone were also apparent in the spectra from tagged C‐4 producing three additional peaks. © 2001 John Wiley &amp; Sons, Inc. Field Analyt Chem Technol 5: 215–221, 2001
Porcine Proinsulin: Characterization and Amino Acid Sequence (1968)

Proinsulin in nearly homogeneous form has been isolated from a preparation of porcine insulin. A molecular weight close to 9100 was calculated from the amino acid composition and from sedimentation-equilibrium studies. Through the action of trypsin this single-chain protein is transformed to desalanine insulin by cleavage of a polypeptide chain connecting the carboxy-terminus of the B chain to the amino-terminus of the A chain of insulin. The amino acid sequence of this connecting peptide was found to be Arg-Arg-Glu-Ala-Gln-Asn-Pro-Gln-Ala-Gly-Ala-Val-Glu-Leu-Gly-Gly-Gly-Leu-Gly-Gly-Leu-Gln-Ala-Leu-Ala-Leu-Glu-Gly-Pro-Pro-Gln-Lys-Arg.
Apoptosis of nur77/N10-transgenic thymocytes involves the Fas/Fas ligand pathway. (1996)

The orphan nuclear receptor Nur77/N10 has recently been demonstrated to be involved in apoptosis of T cell hybridomas. We report here that chronic expression of Nur77/N10 in thymocytes of transgenic mice results in a dramatic reduction of CD4+CD8+ double-positive as well as CD4+CD8- and CD4-CD8+ single-positive cell populations due to an early onset of apoptosis. CD4-CD8- double-negative and CD25+ precursor cells, however, are unaffected. Moreover, nur77/N10-transgenic thymocytes show increased expression of Fas ligand (FasL), while the levels of the Fas receptor (Fas) are not increased. The mouse spontaneous mutant gld (generalized lymphoproliferative disease) carries a point mutation in the extracellular domain of the FasL gene that abolishes the ability of FasL to bind to Fas. Thymuses from nur77/N10-transgenic mice on a gld/gld background have increased cellularity and an almost normal profile of thymocyte subpopulations. Our results demonstrate that one pathway of apoptosis triggered by Nur77/N10 in double-positive thymocytes occurs through the upregulation of FasL expression resulting in increased signaling through Fas.
CAD/CAM imaging in dentistry. (1991)

CAD/CAM (computer-assisted design/computer assisted manufacturing), although devised 20 years ago, has only been available for routine dental practice for 2 years. As a supplement to the conventional methods for making dental prostheses, CAD/CAM will have profound effects on the dental profession. CAD/CAM will improve versatility, accuracy, and cost effectiveness and will be a part of routine dental practice by the beginning of the 21st century.
Tumor antigen–specific CD8 T cells infiltrating the tumor express high levels of PD-1 and are functionally impaired (2009)

Tumor antigen-specific T cells are found within melanomas, yet tumors continue to grow. Although the tumor microenvironment is thought to influence the suppression of tumor-reactive T cells, the underlying mechanisms for this T-cell dysfunction are not clear. Here, we report that the majority of tumor infiltrating T lymphocytes (TIL), including MART-1/Melan-A melanoma antigen-specific CD8 T cells, predominantly expressed PD-1, in contrast to T cells in normal tissues and peripheral blood T lymphocytes (PBL). PD-1(+) TIL expressed CTLA-4 and Ki-67, markers that were not expressed by PD-1(-) TIL and T cells in the normal tissues and PBL. Moreover, PD-1(+) TIL were primarily HLA-DR(+) and CD127(-), in contrast to PD-1(-) TIL. Effector cytokine production by PD-1(+) TIL was impaired compared with PD-1(-) TIL and PBL. Collectively, the phenotypic and functional characterizations of TIL revealed a significantly higher frequency and level of PD-1 expression on TIL compared with normal tissue T-cell infiltrates and PBL, and PD-1 expression correlated with an exhausted phenotype and impaired effector function. These findings suggest that the tumor microenvironment can lead to up-regulation of PD-1 on tumor-reactive T cells and contribute to impaired antitumor immune responses.
On-line LDA: Adaptive Topic Models for Mining Text Streams with Applications to Topic Detection and Tracking (2008)

This paper presents Online Topic Model (OLDA), a topic model that automatically captures the thematic patterns and identifies emerging topics of text streams and their changes over time. Our approach allows the topic modeling framework, specifically the Latent Dirichlet Allocation (LDA) model, to work in an online fashion such that it incrementally builds an up-to-date model (mixture of topics per document and mixture of words per topic) when a new document (or a set of documents) appears. A solution based on the Empirical Bayes method is proposed. The idea is to incrementally update the current model according to the information inferred from the new stream of data with no need to access previous data. The dynamics of the proposed approach also provide an efficient mean to track the topics over time and detect the emerging topics in real time. Our method is evaluated both qualitatively and quantitatively using benchmark datasets. In our experiments, the OLDA has discovered interesting patterns by just analyzing a fraction of data at a time. Our tests also prove the ability of OLDA to align the topics across the epochs with which the evolution of the topics over time is captured. The OLDA is also comparable to, and sometimes better than, the original LDA in predicting the likelihood of unseen documents.