gebhart/patrepeval huggingface dataset:
Versatile Biosynthetic Engineering of Sialic Acid in Living Cells Using Synthetic Sialic Acid Analogues (2002)

Sialic acids are critical components of many glycoconjugates involved in biologically important ligand-receptor interactions. Quantitative and structural variations of sialic acid residues can profoundly affect specific cell-cell, pathogen-cell, or drug-cell interactions, but manipulation of sialic acids in mammalian cells has been technically limited. We describe the finding of a previously unrecognized and efficient uptake and incorporation of sialic acid analogues in mammalian cells. We added 16 synthetic sialic acid analogues carrying distinct C-1, C-5, or C-9 substitutions individually to cell cultures of which 10 were readily taken up and incorporated. Uptake of C-5- and C-9-substituted sialic acids resulted in the structural modification of up to 95% of sialic acids on the cell surface. Functionally, binding of murine sialic acid-binding immunoglobulin-like lectin-2 (Siglec-2, CD22) to cells increased after N-glycolylneuraminic acid treatment, whereas 9-iodo-N-acetylneuraminic acid abolished binding. Furthermore, susceptibility to infection by the B-lymphotropic papovavirus via a sialylated receptor was markedly enhanced following pretreatment of host cells with selected sialic acid analogues including 9-iodo-N-acetylneuraminic acid. This novel experimental strategy allows for an efficient biosynthetic engineering of surface sialylation in living cells. It is versatile, extending the repertoire of modification sites at least to C-9 and enables detailed structure-function studies of sialic acid-dependent ligand-receptor interactions in their native context.
Robust Scene Text Recognition with Automatic Rectification (2016)

Recognizing text in natural images is a challenging task with many unsolved problems. Different from those in documents, words in natural images often possess irregular shapes, which are caused by perspective distortion, curved character placement, etc. We propose RARE (Robust text recognizer with Automatic REctification), a recognition model that is robust to irregular text. RARE is a specially-designed deep neural network, which consists of a Spatial Transformer Network (STN) and a Sequence Recognition Network (SRN). In testing, an image is firstly rectified via a predicted Thin-Plate-Spline (TPS) transformation, into a more "readable" image for the following SRN, which recognizes text through a sequence recognition approach. We show that the model is able to recognize several types of irregular text, including perspective text and curved text. RARE is end-to-end trainable, requiring only images and associated text labels, making it convenient to train and deploy the model in practical systems. State-of-the-art or highly-competitive performance achieved on several benchmarks well demonstrates the effectiveness of the proposed model.
Quantitative analysis of tumor-derived methylated p16INK4a sequences in plasma, serum, and blood cells of hepatocellular carcinoma patients. (2003)

Quantification of epigenetic changes in peripheral blood by RTQ-MSP is useful for the detection and monitoring of HCC.
Proteus mirabilis Genes That Contribute to Pathogenesis of Urinary Tract Infection: Identification of 25 Signature-Tagged Mutants Attenuated at Least 100-Fold (2004)

Proteus mirabilis, a common cause of urinary tract infections (UTI) in individuals with functional or structural abnormalities or with long-term catheterization, forms bladder and kidney stones as a consequence of urease-mediated urea hydrolysis. Known virulence factors, besides urease, are hemolysin, fimbriae, metalloproteases, and flagella. In this study we utilized the CBA mouse model of ascending UTI to evaluate the colonization of mutants of P. mirabilis HI4320 that were generated by signature-tagged mutagenesis. By performing primary screening of 2088 P. mirabilis transposon mutants, we identified 502 mutants that ranged from slightly attenuated to unrecoverable. Secondary screening of these mutants revealed that 114 transposon mutants were reproducibly attenuated. Cochallenge of 84 of these single mutants with the parent strain in the mouse model resulted in identification of 37 consistently out-competed P. mirabilis transposon mutants, 25 of which were out-competed >100-fold for colonization of the bladder and/or kidneys by the parent strain. We determined the sequence flanking the site of transposon insertion in 29 attenuated mutants and identified genes affecting motility, iron acquisition, transcriptional regulation, phosphate transport, urease activity, cell surface structure, and key metabolic pathways as requirements for P. mirabilis infection of the urinary tract. Two mutations localized to a approximately 42-kb plasmid present in the parent strain, suggesting that the plasmid is important for colonization. Isolation of disrupted genes encoding proteins with homologies to known bacterial virulence factors, especially the urease accessory protein UreF and the disulfide formation protein DsbA, showed that the CBA mouse model and mutant pools are a reliable source of attenuated mutants with mutations in virulence genes.
Exact Design Techniques for Microwave Tem Filters. (1965)

A review is given of the exact theory of interdigital band-pass filters. Tables of self and mutual static capacitors are presented that allow the simplified design of Butterworth and Chebyshev interdigital filters for bandwidths of a few percent to 4:1 and greater. The design procedures developed make use of simple transformations performed on the static capacitance matrix of a parallel conductor array. Detailed design examples are given to illustrate the methods and techniques presented. A new type of filter-transformer consisting of multiple coaxial lines is described. Experimental results for a 3:1 bandwidth interdigital filter and a 3:1 bandwidth filter-transformer are presented. (Author)
Molecular analysis of resveratrol synthase (1988)

Resveratrol synthase (RS), a key enzyme in biosynthesis of stilbene-type phytoalexins, catalyzes the formation of resveratrol from coumaroyl-CoA and malonyl-CoA. Two cDNA clones, pGSC1 and pGSC2, have been isolated from cDNA libraries established with poly(A)-rich RNA from peanut (Arachis hypogaea) cell cultures specifically induced for RS. These cDNAs were used to identify two genomic clones (pGSG10 and pGSG11). Sequence analysis shows that the two clones overlap in a large stretch of nearly identical sequences, and that pGSG10 contains the 5' and pGSG11 the 3' end of RS genes. The sequences reveal a single intron, and the size of the predicted protein is 42.7 kDa, in close agreement with that observed in polyacrylamide gels (43 kDa). Chalcone synthase (CHS), a key enzyme of flavonoid biosynthesis, utilizes the same substrates as RS, but the product is different (naringenin chalcone). Comparison of RS with CHS consensus sequences shows that the two genes are related. Homology extends throughout the coding region, and the intron in RS is at the same position as a conserved intron in CHS. However, RS reveals a substantial number of amino acid differences to CHS in positions highly conserved in all CHS enzymes. It is proposed that the two proteins possess a common scaffold necessary for binding of the substrates and the type of enzyme reaction, and that the differences are responsible for the formation of different products.
[Cyclic nucleotides and membrane electrogenesis in cell differentiation in Neurospora crassa]. (1995)

Significance of membrane electrogenic system and cyclic nucleotides for developmental regulation in lower eukaryotes was studied in Neurospora crassa. Despite of their morphological uniformity, hyphal cells were differentiated by their electrophysiological parameters--membrane potential and input resistance. The cells maintained regulated electric communication through septal pores. Such electric communication allowed the apical "cell" to compensate the energy requirements for membrane transport by means of the electrogenic mechanism of proximal zone. The photoinduced gene expression related to differentiation of reproductive structures has been shown to be mediated via cAMP. The changes of electric parameters observed in illuminated hyphal cells were controlled by the same photoregulation mechanism but were not involved in direct control of photoinduced gene expression.
Effect of enhanced macrophage function on early wound healing. (1988)

Although the macrophage is important to wound healing, research has focused on its relationship to fibroblast and collagen synthesis. This study was designed to assess effects of enhanced macrophage function on early wound healing, before established collagen synthesis. Sprague-Dawley rats had dorsal incisions after one of three treatment regimens: (1) saline solution, 0.5 ml administered intravenously, (2) intravenous glucan, a macrophage stimulant, 20 mg; (3) topical glucan, 20 mg. Intravenous therapy was administered 24 hours before and after incision. Breaking strength was significantly increased (p less than 0.01) by both intravenous glucan (49.8 +/- 5.5 gm) and topical glucan (59.7 +/- 5.6 gm) on the fourth day after incision, compared with controls (22.0 +/- 2.6 gm). Similar results occurred on the seventh day after incision. Although formalin fixation significantly enhanced breaking strength in fresh control wounds (22.0 +/- 2.6 vs 39.5 +/- 2.2 gm), no increase occurred in wounds treated with intravenous glucan (49.8 +/- 5.0 vs 55.3 +/- 6.4 gm), indicating maximal cross-linking of collagen. Collagen synthesis, reflected by tritiated proline uptake, was no different in control versus glucan groups. Supernatants from control or glucan-activated macrophages were injected intraperitoneally or applied topically in the rat model. Activated supernatant, both intraperitoneal and topical, resulted in increased breaking strength on the fourth day after incision. Formalin fixation did not increase breaking strength in the activated supernatant groups. We conclude that enhanced macrophage function increases early wound breaking strength. This effect appears unrelated to collagen synthesis but may be related to increased cross-linking of collagen. Similar effects are seen with activated macrophage secretory products administered intraperitoneally or topically.
Involvement of retrovirus reverse transcriptase-associated RNase H in the initiation of strong-stop (+) DNA synthesis and the generation of the long terminal repeat (1984)

Reconstructed enzymatic reactions containing purified reverse transcriptase and defined analog substrates which mimic those purported to be natural substances for reverse transcription in vivo were employed to delineate the mechanism of strong-stop (+) DNA synthesis. Our analysis of this system has indicated that strong-stop (+) DNA synthesis is initiated after the introduction of a nick in the viral RNA genome between a polypurine sequence and an inverted repeat that represents the end of the long terminal repeat. Since inhibitors of the reverse transcriptase-associated RNase H activity prevent the introduction of the nick and the synthesis of strong-stop (+) DNA synthesis, it appears that this particular reverse transcriptase-associated enzymatic activity is responsible for the initiation of strong-stop (+) DNA. Our data also indicated that the RNase H activity creates a second nick in the viral RNA genome 11 nucleotides upstream from the strong-stop (+) DNA initiation site since the strong-stop (+) DNA synthesized in these reactions is covalently linked to an oligoribonucleotide 11 residues in length. Nucleotide sequence analysis of the oligoribonucleotide primer molecule indicated that a single homogenous oligomer was associated with strong-stop (+) DNA exhibiting the sequence rArGrGrGrArGrGrGrGrGrA. The oligoribonucleotide primer can be removed from strong-stop (+) DNA by the purified reverse transcriptase, which creates a nick at the junction between the primer and strong-stop (+) DNA. These data demonstrate that the initiation of strong-stop (+) DNA synthesis is mediated by RNase H and that the site of initiation is exactly at the end of the long terminal repeat, providing evidence for yet another function of this reverse transcriptase-associated enzymatic activity in the synthesis of retrovirus DNA.
Improvement of γ-ray energy resolution of LaBr3:Ce3+ scintillation detectors by Sr2+ and Ca2+ co-doping (2013)

Commercially available LaBr3:5% Ce3+ scintillators show with photomultiplier tube readout about 2.7% energy resolution for the detection of 662 keV γ-rays. Here we will show that by co-doping LaBr3:Ce3+ with Sr2+ or Ca2+ the resolution is improved to 2.0%. Such an improvement is attributed to a strong reduction of the scintillation light losses that are due to radiationless recombination of free electrons and holes during the earliest stages (1–10 ps) inside the high free charge carrier density parts of the ionization track.
IL‐12 and IL‐4 activate a CD39‐dependent intrinsic peripheral tolerance mechanism in CD8+ T cells (2016)

Immune responses to protein antigens involve CD4(+) and CD8(+) T cells, which follow distinct programs of differentiation. Naïve CD8 T cells rapidly develop cytotoxic T-cell (CTL) activity after T-cell receptor stimulation, and we have previously shown that this is accompanied by suppressive activity in the presence of specific cytokines, i.e. IL-12 and IL-4. Cytokine-induced CD8(+) regulatory T (Treg) cells are one of several Treg-cell phenotypes and are Foxp3(-) IL-10(+) with contact-dependent suppressive capacity. Here, we show they also express high level CD39, an ecto-nucleotidase that degrades extracellular ATP, and this contributes to their suppressive activity. CD39 expression was found to be upregulated on CD8(+) T cells during peripheral tolerance induction in vivo, accompanied by release of IL-12 and IL-10. CD39 was also upregulated during respiratory tolerance induction to inhaled allergen and on tumor-infiltrating CD8(+) T cells. Production of IL-10 and expression of CD39 by CD8(+) T cells was independently regulated, being respectively blocked by extracellular ATP and enhanced by an A2A adenosine receptor agonist. Our results suggest that any CTL can develop suppressive activity when exposed to specific cytokines in the absence of alarmins. Thus negative feedback controls CTL expansion under regulation from both nucleotide and cytokine environment within tissues.
A Phenomenological Approach to Analysis of Barite Sag in Drilling Muds (2007)

Abstract Barite sag is the undesirable fluctuation in drilling mud density that occurs due to downhole settling of the weighting agent. Barite sag causes problems such as differential sticking, lost circulation, and can lead to serious well control events. This paper describes a fundamental theoretical effort to describe dynamic sag in drilling muds by considering the behavior of a system of particles in a non-Newtonian Bingham fluid. A continuum mechanics based model of dynamic sag in an inclined annulus is presented in terms of the fluid and particle properties. The results of the model are used to understand the influence of typical oilfield variables in precipitating sag. The analysis presented in this paper represents one of the first modeling/computational efforts to predict sag using phenomenological models (rather than empirical correlations or observational rules of thumb).
Recovery of Pathogenic Measles Virus from Cloned cDNA (2000)

Reverse genetics technology so far established for measles virus (MeV) is based on the Edmonston strain, which was isolated several decades ago, has been passaged in nonlymphoid cell lines, and is no longer pathogenic in monkey models. On the other hand, MeVs isolated and passaged in the Epstein-Barr virus-transformed marmoset B-lymphoblastoid cell line B95a would retain their original pathogenicity (F. Kobune et al., J. Virol. 64:700-705, 1990). Here we have developed MeV reverse genetics systems based on the highly pathogenic IC-B strain isolated in B95a cells. Infectious viruses were successfully recovered from the cloned cDNA of IC-B strain by two different approaches. One was simple cotransfection of B95a cells, with three plasmids each encoding the nucleocapsid (N), phospho (P), or large (L) protein, respectively, and their expression was driven by the bacteriophage T7 RNA polymerase supplied by coinfecting recombinant vaccinia virus vTF7-3. The second approach was transfection with the L-encoding plasmid of a helper cell line constitutively expressing the MeV N and P proteins and the T7 polymerase (F. Radecke et al., EMBO J. 14:5773-5784, 1995) on which B95a cells were overlaid. Virus clones recovered by both methods possessed RNA genomes identical to that of the parental IC-B strain and were indistinguishable from the IC-B strain with respect to growth phenotypes in vitro and the clinical course and histopathology of experimentally infected cynomolgus monkeys. Thus, the systems developed here could be useful for studying viral gene functions in the context of the natural course of MeV pathogenesis.
Innate and adaptive immune responses in patients with pandemic influenza A(H1N1)pdm09 (2013)

Innate and adaptive immune responses play critical roles in the body's defense against viruses. We investigated the host immune response against the 2009 pandemic H1N1 influenza virus [A(H1N1)pdm09] in patients before and after anti-influenza therapy and found that the numbers of dendritic cells and T cells were significantly reduced compared with those of a healthy control group. In contrast, the frequency of natural killer, γδT and T regulatory (Treg) cells increased, and the concentrations of plasma interferon (IFN)-α/γ and interleukin (IL-15) were significantly higher than those of the control. Following therapy the frequency of γδT and Treg cells returned to normal; the counts of myeloid dendritic and plasmacytoid dendritic cells were still lower than the control, while the concentrations of IFN-α/γ and IL-15 remained high. We show that infection with A (H1N1)pdm09 was accompanied by changes in peripheral blood lymphocyte subgroups and cytokine profiles, leading to deleterious imbalances in innate and adaptive immunity.
Selective video encryption of distributed video coded bitstreams and multicast security over wireless networks (2006)

Here we discuss two security problems, video data encryption and multicast security, in wireless networks. Selective encryption is a technique that is used to minimize computational complexity or enable system functionality by only encrypting a portion of a compressed bitstream while still achieving reasonable security. For selective encryption to work, we need to rely not only on the beneficial effects of redundancy reduction, but also on the characteristics of the compression algorithm to concentrate important data representing the source in a relatively small fraction of the compressed bitstream. These important elements of the compressed data become candidates for selective encryption. In this thesis, we combine encryption and distributed video source coding to consider the choices of which types of bits are most effective for selective encryption of a video sequence that has been compressed using a distributed source coding method based on LDPC and Turbo codes. Instead of encrypting the entire video stream bit by bit, we encrypt only the highly sensitive bits. By combining the compression and encryption tasks and thus reducing the number of bits encrypted, we can achieve a reduction in system complexity. Secure multicast protocols are difficult to implement efficiently due to the dynamic nature of the multicast group and scarcity of bandwidth at the receiving and transmitting ends. Mobility is one of the most distinct features to be considered in a wireless network. Moving users onto the key tree causes extra key management resources even though they are still in service. To take care of frequent handoff between wireless access networks, it is necessary to reduce the number of rekeying messages and the size of the messages. In this dissertation, we design a key management tree such that neighbors on the key tree are also physical neighbors on the cellular network. By tracking the user location, we localize the delivery of rekeying messages to the users who need them. This lessens the amount of traffic in wireless and wired intervals of the network. The group key management scheme uses a pre-positioned secret sharing scheme.
Taxane-induced apoptosis decompresses blood vessels and lowers interstitial fluid pressure in solid tumors: clinical implications. (1999)

Elevated tumor interstitial fluid pressure (IFP) is partly responsible for the poor penetration and distribution of therapeutic agents in solid tumors. The etiology of tumor interstitial hypertension is poorly understood. We have postulated that the solid stress generated by tumor cells growing in a confined space compresses blood vessels and increases tumor microvascular pressure and IFP. To test the hypothesis that neoplastic cell loss would decompress blood vessels and lower IFP, we induced apoptosis in tumors with paclitaxel and docetaxel. Taxanes inhibited the growth of the murine mammary carcinoma (MCa-IV) and of the human soft tissue sarcoma (HSTS-26T). Taxanes induced apoptosis and reduced the density of intact neoplastic cells in both MCa-IV and HSTS-26T. To determine whether neoplastic cell loss decompressed blood vessels, we measured the diameter of tumor vessels in HSTS-26T tumors implanted in transparent dorsal skin fold chambers. At 48 and 96 h after paclitaxel, the diameter of tumor vessels was significantly increased. The increase in vascular diameters was associated with reductions in microvascular pressure and IFP. The changes in neoplastic cell density and IFP were also correlated. In the human glioblastoma U87, which is resistant to paclitaxel, the IFP and cellular density were not modified by paclitaxel treatment. Collectively, these results support the hypothesis that solid stress generated by neoplastic cell proliferation increases vascular resistance and IFP. The increase in vessel diameter induced by paclitaxel and docetaxel suggests that taxanes could improve tumor response by increasing the vascular surface area for delivery of therapeutic agents.
Antibacterial Compounds of Licorice against Upper Airway Respiratory Tract Pathogens. (2001)

The antibacterial activity of compounds obtained from licorice was measured against upper airway respiratory tract bacteria such as Streptococcus pyogenes, Kaemophilus irnfluenzae and Moraxella catarrhalis, Among the tested compounds, licoricidin exhibited the highest activity against all tested microorganisms with an MIC of 12.5, μg/mL. Three coumarin derivatives, glycyrol, glycyrin and glycycoumarin also showed antibacterial activ-ity.
Scientists in wonderland: A report on visualization applications in the CAVE virtual reality environment (1993)

The authors present the experiences at the Electronic Visualization Laboratory (EVL) in introducing computational scientists to the use of virtual reality as a research tool. They describe the virtual environment, the CAVE. They then describe several applications currently being developed at EVL using the CAVE and conclude with a discussion on possible research paths to follow in making virtual reality an effective tool for visualization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>