gebhart/patrepeval huggingface dataset:
Enzymatic assays for native plasmin, plasminogen and plasminogen activators in bovine milk (2001)

Rapid and sensitive assays for plasmin, plasminogen and plasminogen activators (PA) were developed and applied to bovine milk. The reaction medium was clarified by addition of a dissolving agent after hydrolysis of a fluorescent substrate specific for plasmin. This final step enabled the use of larger sample amount with higher substrate concentration than other methods, and avoided previous sample preparation. The use of 4 g gelatin/l in buffers preserved plasmin activity, thus avoiding risks of overestimation of the assays results. Sensitivity, detection level, repeatability and analysis run time of plasmin and plasminogen assay were improved over previous enzymatic methods with synthetic substrates. The PA assay was assessed by measuring conversion of exogenous plasminogen into plasmin. A new kinetic approach was used to enable the direct determination of global PA activities on raw milk samples without interference from indigenous plasmin.
A PC-based MPEG compressed data decoder (1995)

A PC-based MPEG compressed data decoder card is presented. The decoder serves as a PC add-on card and is capable of decoding MPEG compressed data from compact discs (CD) for display on PC monitors. The MPEG decoder is able to accept both MPEG1 audio packets and MPEG1 video packets which conform to the ISO/MPEG1 system and video bitstreams respectively.
Gastric carcinoma: the Helicobacter pylori trail. (1995)

Gastric carcinoma is the world's overall second most common cancer. Besides obvious environmental factors, recent epidemiological studies and a better knowledge of Helicobacter Pylori biological properties revealed that the microorganism is involved in the first steps of gastric carcinogenesis as proposed by the Correa model (from normal gastric tissue through superficial gastritis, multifocal atrophic gastritis, intestinal metaplasia and dysplasia to carcinoma). Significant correlation between the prevalence of H. pylori infection and incidence of gastric carcinoma (mainly the intestinal type) in various geographical areas has been reported. The high prevalence of HP in pre-neoplastic states and in cases of early gastric cancer indicates the infection would precede the development of gastric cancer. HP-related chronic inflammation of gastric mucosa with increased mucosal cell proliferation, deficit in local ascorbic acid concentration, topical ammonia toxicity are putative mechanisms that overexpose a weakened gastric mucosa to environmental carcinogens.
A New System for Stringent, High-Titer Vesicular Stomatitis Virus G Protein-Pseudotyped Retrovirus Vector Induction by Introduction of Cre Recombinase into Stable Prepackaging Cell Lines (1998)

We report here on stable prepackaging cell lines which can be converted into packaging cell lines for high-titer vesicular stomatitis virus G protein (VSV-G)-pseudotyped retrovirus vectors by the introduction of Cre recombinase-expressing adenovirus. The generated prepackaging cell lines constitutively express the gag-pol genes and contain an inducible transcriptional unit for the VSV-G gene. From this unit, the introduced Cre recombinase excised both a neomycin resistance (Neo(r)) gene and a poly(A) signal flanked by a tandem pair of loxP sequences and induced transcription of the VSV-G gene from the same promoter as had been used for Neo(r) expression. By inserting an mRNA-destabilizing signal into the 3' untranslated region of the Neo(r) gene to reduce the amount of Neo(r) transcript, we were able efficiently to select the clones capable of inducing VSV-G at high levels. Without the introduction of Cre recombinase, these cell lines produce neither VSV-G nor any detectable infectious virus at all, even after the transduction of a murine leukemia virus-based retrovirus vector encoding beta-galactosidase. They reproducibly produced high-titer virus stocks of VSV-G-pseudotyped retrovirus (1.0 x 10(6) infectious units/ml) from 3 days after the introduction of Cre recombinase. We also present evidence that VSV-G-producing cells are still fully susceptible to transduction by VSV-G pseudotypes. However, in this vector-producing system, which regulates VSV-G pseudotype production in an all-or-none manner, the integration of vector DNA into packaging cell lines would be minimized. We further show that heparin significantly inhibits retransduction of VSV-G pseudotypes in the culture fluids of packaging cell lines, leading to a two- to fourfold increase in the yield of the pseudotypes after induction. This vector-producing system was very stable and should be advantageous in human gene therapy.
Recent advances in immunostimulatory CpG oligonucleotides. (2003)

The vertebrate immune system has evolved a mechanism to detect CpG motifs within microbial DNA (CpG DNA). Synthetic oligonucleotides containing CpG motifs (CpG ODNs) are potent immunomodulatory molecules and outstanding vaccine adjuvants. A number of recent findings have greatly improved our understanding of the biology of CpG DNA, and the immunological effects of CpG DNA are now recognized to be distinct in mouse and human. The plasmacytoid dendritic cell (PDC) was identified to play a pivotal role in mediating CpG-induced immune responses. So far, the B-cell is the only other immune cell subset in humans besides the PDC, equipped with the toll-like receptor-9 to detect CpG motifs. The information on these two prime CpG-sensitive cells has allowed the identification of novel CpG ODNs with distinct functional activity. Together with exciting contributions from animal studies, the way seems to be paved for the successful clinical development of this novel class of molecular therapeutics.
Phagocytic activity of monocytes in patients with breast cancer at different clinical stages (2001)

Background: Disruption of the balance between apoptosis and proliferation is considered to be an important factor in the development and progression of tumor. In this study we determined the in vivo cell kinetics along the spectrum of apparently normal epithelium, hyperplasia, preinvasive lesions and invasive carcinoma, in breast tissues affected by fibrocystic changes in which preinvasive and/or invasive lesions developed, as a model of breast carcinogenesis. Materials and method: A total of 32 areas of apparently normal epithelium and 135 ductal proliferative and neoplastic lesions were studied. More than one epithelial lesion per case was analyzed. The apoptotic index (AI) and the proliferative index (PI) were expressed as the percentage of TUNEL (TdT-mediated dUTP-nick end-labelling) and Ki-67 positive cells, respectively. The proliferative/apoptotic index (P/A) was calculated for each case. Results: Statistical analysis demonstrated significant differences among the tissue groups for both indices (P < 0.0001). The Als and PIs were significantly higher in hyperplasia than in apparently normal epithelium (P = 0.04 and P = 0.0005, respectively), in atypical hyperplasia than in hyperplasia (P = 0.01 and P = 0.04, respectively) and in invasive carcinoma than in in situ carcinoma (P = 0.0001 and P < 0.0001, respectively). The two indices were similar in atypical hyperplasia and in in situ carcinoma. The P/A index increased significantly from normal epithelium to hyperplasia (P = 0.01) and from preinvasive lesions to invasive carcinoma (P = 0.04), whereas it was decreased (NS) from hyperplasia to preinvasive lesions. A strong positive correlation between the Als and the Pls was found (r = 0.83; P < 0.0001).
THE HEMALOG D WHITE CELL DIFFERENTIAL SYSTEM (1974)

The Hemalog D system performs automated differential white cell counts utilizing principles of cytochemistry, electro-optical measurement and signal logic processing. Using 0.4 ml of anticoagulated whole blood and an automated continuous flow staining technique, the system is designed to process a new sample each minute. The decision logic classifies individual cells by size and intensity of staining as they flow through detectors designed to measure light loss and light scattering simultaneously. With this system, 10,000 cells/ sample are classified in less than 1 min. Alcian Blue identifies basophils when used in the presence of quaternary ammonium salts and other counterions. Monocytes are the only cells stained in an esterase method using α-naphthol butyrate at pH 6.1 with hexazonium pararosanilin as coupler. This unstable diazonium is produced on stream continuously from stable components. Size and peroxidase staining serve to classify the remaining cells. Lymphocytes and large mononuclear cells are unstained, neutrophils have moderate peroxidase activity, while eosinophils stain very strongly. Threshold detection logic for light scattering and absorption differentiate the neutrophils, eosinophils and lymphocytes. The distribution of peroxidase activity in neutrophils serves as an index of maturity of these cells. The clinical evaluation of this index is reported elsewhere. Results are reported as percentage and as cells per cubic millimeter. A total white blood cell count is also reported and the pattern of cell measurements for 10,000 cells is provided as a picture with diagnostic information content. Advantages of this system in rapid screening result from improved precision of automation, the processing of large numbers of cells and the saving of labor. Precision also makes the acquisition of sequential data on single patients more meaningful and diagnostically valuable.
Synthesis of i- and g-Line Sensitive Photoacid Generators and Their Application to Photopolymer Systems (2003)

We synthesized a series of i- and g-line sensitive non-ionic photoacid generators (PAGs). Photolysis and catalytic properties of the PAGs were examined. Photoreactivity of the PAGs was evaluated using UV-vis spectroscopy. The PAGs were used for photocrosslinking of epoxy-based polymers. The PAGs were also applied to positive-type photoresist materials. Sensitivity profile of the photoresists containing PAGs was affected not only by the photosensitivity of PAGs but also by the acidity of the generated acid. Post-exposure delay of the photoresists was dependent on the molecular size of the generated acid.
Use of polymerase chain reaction for diagnosis of picornavirus infection in subjects with and without respiratory symptoms (1993)

Rhinoviruses and enteroviruses are the major members of the picornavirus genus that cause human disease. We compared the polymerase chain reaction and viral culture for the identification of picornaviruses in nasal aspirates from children during episodes of respiratory symptoms and when asymptomatic and from asymptomatic adults. One hundred eight children, aged 9 to 11 years, completed a year-long study. Within 24 to 48 h of a report of respiratory symptoms, a nasal aspirate was taken in the home. Nasal aspirates were also taken from 65 of the children and from 33 normal adults when they had been free of respiratory symptoms for at least 2 weeks. Picornaviruses were isolated by culture for three passages in Ohio HeLa cells in rolling tubes at 33 degrees C and pH 7.0. For the polymerase chain reaction, duplicate 50-microliters samples were amplified with conserved primers from the 5' noncoding region. Picornaviruses generated approximately 380-bp bands in agarose gel electrophoresis; the specificity of these bands was confirmed by filter hybridization with a conserved internal probe. Picornaviruses were isolated by culture in 47 (46 rhinoviruses) of 292 symptomatic episodes (16%), whereas the polymerase chain reaction identified picornavirus genomic material in 146 episodes (50%), including all but one of the culture-positive episodes. As for asymptomatic samples, eight (12%) children and two (4%) adults were positive by the polymerase chain reaction, whereas only one child's specimen was positive by culture. This polymerase chain reaction assay represents a clear advance in the identification of picornavirus infection, with a detection rate threefold greater than the virus culture method.
Optimal smoothing schedules for real-time streams (extended abstract) (2000)

We consider the problem of smoothing real-time streams (such as video streams), where the goal is to reproduce a variable-bandwidth stream remotely, while minimizing bandwidth cost, space overhead, and playback delay. We focus on lossy schedules, where some bytes may be dropped due to limited bandwidth or space. We present the following results. First, we determine the optimal tradeoff between buffer space, queuing delay, and link bandwidth for lossy smoothing schedules. Specifically, this means that if one of these parameters is under our control, we can precisely calculate the optimal value which minimizes data loss while avoiding resource wastage. The tradeoff is accomplished by a simple generic algorithm, that allows one some freedom in choosing which data to discard. This algorithm is very easy to implement both at the server and at the client, and it enjoys the nice property that only the server decides which data to discard, and the client needs only to reconstruct the stream.
Cro regulatory protein specified by bacteriophage lambda. Structure, DNA-binding, and repression of RNA synthesis. (1977)

The Cro protein specified by bacteriophage lambda is a repressor of the genes expressed early in phage development and is required for a normal late stage of lytic growth. We have purified Cro protein to virtual homogeneity and analyzed its structure and properties as a DNA-binding protein and repressor of RNA synthesis. To confirm that the protein is the product of the cro gene, we have also shown that a missense mutation in the cro gene leads to a product that is more temperature- and salt-sensitive in its DNA-binding property. As purified, Cro protein is a dimer of identical subunits of molecular weight 8600. The purified protein binds to lambda-DNA carrying the specific binding sites (operators oL and oR) with an estimated dissociation constant of 10(-10) M to 10(-11) M; there is also weaker binding to other sites on DNA, as found for other DNA-binding regulatory proteins. In a purified transcription system, the Cro protein is an effective and specific repressor of RNA synthesis from the N and cro genes; thus Cro is an autorepressor which regulates its own synthesis. A comparison of the properties of the two lambda repressor proteins, cI and Cro, indicates that cI is a "strong repressor" specialized for complete turnoff of lytic functions needed for the maintenance of lysogeny, whereas Cro is a "weak repressor" specialized for a gradual turnoff of early viral genes that potentiates the late stage of lytic development.
Connecting automatic generation control and economic dispatch from an optimization view (2014)

Automatic generation control (AGC) regulates mechanical power generation in response to load changes through local measurements. Its main objective is to maintain system frequency and keep energy balanced within each control area so as to maintain the scheduled net interchanges between control areas. The scheduled interchanges as well as some other factors of AGC are determined at a slower time scale by considering a centralized economic dispatch (ED) problem among different generators. However, how to make AGC more economically efficient is less studied. In this paper, we study the connections between AGC and ED by reverse engineering AGC from an optimization view, and then we propose a distributed approach to slightly modify the conventional AGC to improve its economic efficiency by incorporating ED into the AGC automatically and dynamically.
Phase reconstruction from multiple coil data using a virtual reference coil (2013)

The proposed virtual reference coil method determines a phase distribution for each coil from which an optimal phase map can be obtained.
Expanded polyglutamine peptides disrupt EGF receptor signaling and glutamate transporter expression in Drosophila (2005)

Huntington's disease (HD) is a late onset heritable neurodegenerative disorder caused by expansion of a polyglutamine (polyQ) sequence in the protein huntingtin (Htt). Transgenic models in mice have suggested that the motor and cognitive deficits associated to this disease are triggered by extended neuronal and possibly glial dysfunction, whereas neuronal death occurs late and selectively. Here, we provide in vivo evidence that expanded polyQ peptides antagonize epidermal growth factor receptor (EGFR) signaling in Drosophila glia. We targeted the expression of the polyQ-containing domain of Htt or an extended polyQ peptide alone in a subset of Drosophila glial cells, where the only fly glutamate transporter, dEAAT1, is detected. This resulted in formation of nuclear inclusions, progressive decrease in dEAAT1 transcription and shortened adult lifespan, but no significant glial cell death. We observed that brain expression of dEAAT1 is normally sustained by the EGFR-Ras-extracellular signal-regulated kinase (ERK) signaling pathway, suggesting that polyQ could act by antagonizing this pathway. We found that the presence of polyQ peptides indeed abolished dEAAT1 upregulation by constitutively active EGFR and potently inhibited EGFR-mediated ERK activation in fly glial cells. Long polyQ also limited the effect of activated EGFR on Drosophila eye development. Our results further indicate that the polyQ acts at an upstream step in the pathway, situated between EGFR and ERK activation. This suggests that disruption of EGFR signaling and ensuing glial cell dysfunction could play a direct role in the pathogenesis of HD and other polyQ diseases in humans.
An alternatively spliced cadherin-11 enhances human breast cancer cell invasion. (2002)

Although reduced levels of the epithelial cell adhesion molecule E-cadherin are often associated with poorly differentiated breast cancers, recent studies show that expression of other cadherins such as N-cadherin, P-cadherin, and the mesenchymal cadherin-11 is actually elevated in invasive breast cancers and cell lines. Cadherin-11 is unique among cadherins in that it exists as two alternatively spliced forms that are expressed together in the same cell. We now show that expression of wild-type cadherin-11, with or without coexpression of the COOH-terminal truncated splice variant, promotes epithelial differentiation of the cadherin-negative SKBR3 cell line. Exogenous wild-type cadherin-11 association with and membrane recruitment of beta-catenin and p120 are unaffected by coexpression of the truncated variant. Cadherin-11-expressing cells exhibit modest changes in cell proliferation and no change in anchorage-independent growth. However, coexpression of wild-type cadherin-11 and the splice variant promotes a dramatic increase in the ability of SKBR3 cells and E-cadherin-positive MCF7 cells to traverse Matrigel-coated filters. Biochemical studies indicate that the truncated variant may be secreted from the cell and/or enter a detergent-insoluble compartment. These data suggest that the presence of the cadherin-11 splice variant promotes invasion of cadherin-11-positive breast cancer cells.
α-DNA VI: comparative study of α- and β-anomeric oligodeoxyribonucleotides in hybridization to mRNA and in cell free translation inhibition (1987)

alpha and beta-anomeric d(G2T12G2) oligodeoxyribonucleotides were compared for their hybridization to rA12: the observed melting temperatures are 27 degrees C for beta-oligodeoxyribonucleotide/RNA hybrid and 53 degrees C for alpha-oligodeoxyribonucleotide/RNA. alpha-oligonucleotides with the four bases, complementary to natural mRNAs, were synthesized for the first time, labeled at their 5'-end with [32P] and used as probes in Northern blot experiments. In spite of these higher affinities for their target RNA's, they were unable to block translation of natural or synthetic mRNA's in rabbit reticulocyte lysate. We have studied the RNase H activity on model rA12:alpha- or beta-d(G2T12G2) hybrids or on mRNA:alpha- or beta-oligonucleotides hybrids. Specific hybridization protects RNA strech when using alpha-oligonucleotides but not beta-oligonucleotides. Thus, our results show the inability of RNase H to degrade RNA in alpha-oligodeoxyribonucleotides:RNA duplexes.
Rapid Detection of Point Mutations by Fluorescence Resonance Energy Transfer and Probe Melting Curves in Candida Species (2000)

The LightCycler technique offers standardized, fast, sensitive, and reproducible detection of point mutations in different Candida spp.
Extracellular release of the ‘differentiation enhancing factor’, a HMG1 protein type, is an early step in murine erythroleukemia cell differentiation (1995)

Differentiation enhancing factor (DEF) is a 29 kDa protein expressed in murine erythroleukemia (MEL) cells and active in promoting a significant increase in the rate of hexamethylenebisacetamide induced differentiation of these cells. The factor was recently shown to possess an amino acid sequence identical to that reported for one of the HMG1 proteins, designated as 'amphoterin' on the basis of its highly dipolar sequence. In the present study, we have expressed DEF cDNA in an E. coli strain and found that the recombinant protein has functional properties identical to those observed with native DEF. Furthermore, we demonstrate that, following MEL cell stimulation with the chemical inducer, DEF is secreted in large amounts in the extracellular medium. In fact, the N-terminal sequence and the partial amino acid sequence of tryptic peptides from the secreted protein correspond to those of DEF isolated from the soluble fraction of resting MEL cells. These results are indicative for an extracellular localization as the site of action of DEF and suggest a novel function for proteins belonging to the HMG1 family. Finally, the early decay of DEF mRNA, in chemical induced MEL cells, support the hypothesis that the involvement of the enhancing factor occurs and is completed in the early phases of cell differentiation.
Clonal breadth of the HIV-1-specific T-cell receptor repertoire in vivo as determined by subtractive analysis (2005)

Given the potentially crucial role of T-cell receptor breadth for viral recognition and avoidance of escape, this subepitopic analysis of CTL may offer an important measure of cellular immunity for pathogenesis and vaccine studies.
Important Therapeutic Targets in Chronic Myelogenous Leukemia (2007)

Understanding the pathophysiology of CML and mechanisms of resistance has produced effective targeted strategies for imatinib-resistant CML.
Optical Coherence Tomography—Enhanced Microlaryngoscopy: Preliminary Report of a Noncontact Optical Coherence Tomography System Integrated with a Surgical Microscope (2008)

Optical coherence tomography is able to produce high-resolution images of vocal fold mucosa to a maximum depth of 1.6 mm. It may be used in the diagnosis of VF lesions, particularly early squamous cell carcinoma, in which OCT can show disruption of the basement membrane. Mounting the OCT device directly onto the operating microscope allows hands-free noncontact OCT imaging and simultaneous conventional microscopic visualization of the VFs. However, the lateral resolution of the OCT microscope system is 50 microm, in contrast to the conventional handheld probe system (10 microm). Although such images at this resolution are still useful clinically, improved resolution would enhance the system's performance, potentially enabling real-time OCT-guided microsurgery of the larynx.