gebhart/patrepeval huggingface dataset:
Physical association of the cytoplasmic domain of CD2 with the tyrosine kinases p56lck and p59fyn (1993)

In T lymphocytes, CD2 forms part of a loosely associated membrane complex which includes the T cell receptor (TcR) for antigen, the CD3 subunits, CD4 or CD8, CD5 and the protein tyrosine kinases p56lck and p59fyn. The interaction of CD2 with tyrosine kinases in this complex provides a possible mechanism for transmembrane signal transduction by CD2. We have investigated whether the interaction of CD2 with the kinases is dependent on other known members of the complex, or whether an independent association can be observed. Using in vitro kinase assays with immune complexes precipitated from cell lysates, we demonstrate that CD2 can associate with p56lck and p59fyn in a rat thymoma line that does not express CD4 or CD8, and in a TcR-negative Jurkat cell line. In TcR-positive Jurkat cells that express rat CD2, interaction of CD2 with p56lck and p59fyn was clearly seen, but it was absent in cells where the cytoplasmic tail of CD2 is truncated, indicating that the interactions are mediated by the cytoplasmic region of CD2. Furthermore, using cells expressing CD2 molecules with partial truncations in the cytoplasmic domain, we show that the association of CD2 with p56lck is progressively lost as the cytoplasmic domain is shortened, and that the capacity of the mutants to associate with p56lck correlates with their capacity to transduce transmembrane signals.
Light‐Driven Conformational Switch of i‐Motif DNA (2007)

Making the switch: A photoinduced DNA conformational switch between the i-motif and random-coil structures has been achieved by combination with a reversible photoirradiated pH-jump system (see picture; MGCB: malachite green carbinol base, MG: malachite green). Multiple cycling of this switch has also been demonstrated.
Pulsed time-of-flight laser range finder techniques for fast, high precision measurement applications (2004)

This thesis describes the development of high bandwidth (~1 GHz) TOF (time-of-flight) laser range finder techniques for industrial measurement applications in the measurement range of zero to a few dozen metres to diffusely reflecting targets. The main goal has been to improve single-shot precision to mm-level in order to shorten the measurement result acquisition time. A TOF laser range finder consists of a laser transmitter, one or two receivers and timing discriminators, and a time measuring unit. In order to improve single-shot precision the slew-rate of the measurement pulse should be increased, so the optical pulse of the laser transmitter should be narrower and more powerful and the bandwidth of the receiver should be higher without increasing the noise level too much. In the transmitter usually avalanche transistors are used for generating the short (3–10 ns) and powerful (20–100 A) current pulses for the semiconductor laser. Several avalanche transistor types were compared and the optimization of the switching circuit was studied. It was shown that as high as 130 A current pulses are achievable using commercially available surface mount avalanche
Organic Phosphorus Compounds (1976)

The present invention relates to new organic phosphorus containing compounds which have been found to have surface active properties. The present compounds are new phosphinic acids of alkylated benzene hydrocarbons and amine derivatives or salts thereof. They may be generally represented by...
Neural adhesion molecules L1 and CHL1 are survival factors for motoneurons (2005)

Many neurotrophic factors with survival activity for motoneurons in vivo were first identified using cultures of purified embryonic motoneurons. The L1 neural cell adhesion molecule has multiple roles in brain development. We showed by in situ hybridization and RT-PCR that L1 mRNA was expressed at significant levels in motoneurons of embryonic and postnatal spinal cord. We therefore cultured purified motoneurons from E14 rat embryos in the absence of trophic factors but with L1-Fc and CHL1-Fc fusion proteins. L1-Fc prevented the death of approximately half of the motoneurons that were saved by BDNF in a dose-dependent manner (EC50 = 10 pM). CHL1-Fc saved the same number of motoneurons as did L1-Fc, whereas P0-Fc had little neurotrophic activity at the same concentrations. Survival induced by L1 and CHL1 was completely inhibited by 20 microM LY294002 and PD98059, indicating that both MEK and PI3K pathways are required for signaling by these molecules. L1 can signal in other cell types through the FGF receptor FGFR1. In cultures of motoneurons, effects of suboptimal concentrations of L1 and suboptimal concentrations of FGF-2 were additive, but the effects of optimal concentrations of FGF-2 (50 ng/ml) were not further increased in the presence of L1-Fc. Thus, in this system, too, FGF and L1 may use similar signaling pathways.
Investigation of spectral conversion of d(TTAGGG) 4 and d(TTAGGG) 13 upon potassium titration by a G-quadruplex recognizer BMVC molecule (2007)

We have introduced a G-quadruplex-binding ligand, 3,6-bis(1-methyl-4-vinylpyridinium)carbazole diiodide (BMVC), to verify the major structure of d(T2AG3)4 (H24) in potassium solution and examine the structural conversion of H24 in sodium solution upon potassium titration. The studies of circular dichroism, induced circular dichroism, spectral titration and gel competition have allowed us to determine the binding mode and binding ratio of BMVC to the H24 in solution and eliminate the parallel form as the major G-quadruplex structure. Although the mixed-type form could not be eliminated as a main component, the basket and chair forms are more likely the main components of H24 in potassium solution. In addition, the circular dichroism spectra and the job plots reveal that a longer telomeric sequence d(T2AG3)13 (H78) could form two units of G4 structure both in sodium or potassium solutions. Of particular interest is that no appreciable change on the induced circular dichroism spectra of BMVC is found during the change of the circular dichroism patterns of H24 upon potassium titration. Considering similar spectral conversion detected for H24 and a long sequence H78 together with the G4 structure stabilized by BMVC, it is therefore unlikely that the rapid spectral conversion of H24 and H78 is due to structural change between different types of the G4 structures. With reference to the circular dichroism spectra of d(GAA)7 and d(GAAA)5, we suggest that the spectral conversion of H24 upon potassium titration is attributed to fast ion exchange resulting in different loop base interaction and various hydrogen bonding effects.
Application of quadrature mirror filtering to the coding of monochrome and color images (2005)

In this paper an efficient method for subband coding of color images is presented. The basic approach is to transfer an RGB picture into YIQ components where each component is decomposed separately into several narrow bands. The higher band signals corresponding to the Y component are retained and coded separately, while the higher bands associated with I, and Q components are discarded. Furthermore, the low band signals are coded using a DPCM coding scheme. Our simulation results show that, by using such a coding scheme, good quality pictures can be reconstructed at low transmission rates.
Plasmodium falciparum AARP1, a giant protein containing repeated motifs rich in asparagine and aspartate residues, is associated with the infected erythrocyte membrane (1997)

During Plasmodium falciparum asexual intraerythrocytic development, the host's cell plasma membrane is modified by the insertion of parasite proteins. One or more of these modifications mediate the cytoadherence of infected erythrocytes to host vascular endothelium. However, these surface antigens can be the target of cytophilic antibodies which promote phagocytosis of the infected erythrocyte. It has been proposed that antibodies directed to epitopes rich in asparagine play an important role in this process, which has promoted efforts to isolate the corresponding gene(s). We describe here P. falciparum asparagine- and aspartate-rich protein 1 (PfAARP1), a new giant (circa 700-kDa) protein associated with the infected erythrocyte membrane which is rich in asparagine and aspartate residues due to the presence of nine blocks of repeats. Topology analysis predicts that PfAARP1 has multiple transmembrane domains and at least five external loops. Human antibodies immunopurified against a sequence composed exclusively of asparagine and aspartate amino acids derived from PfAARP1 label the surface of the infected erythrocyte, demonstrating that such motifs are exposed. Interestingly, external loop 4 of PfAARP1 contains repetitions of these residues, and their possible role as a target of cytophilic antibodies is discussed.
Effective reversal of warfarin-induced excessive anticoagulation with low dose vitamin K1. (1992)

Reversal of the anticoagulant effect of warfarin in patients with no active haemorrhage can be achieved by administration of intravenous vitamin K1. Currently recommended doses of intravenous vitamin K1, for this purpose often result in subsequent difficulties in anticoagulation. We observed the response to low dose intravenous vitamin K1 in patients requiring reversal of anticoagulant therapy. Ten consecutive patients received 1 mg and 21 further patients received 0.5 mg of intravenous vitamin K1. In 50% of the patients who received 1 mg of vitamin K1 the INR (International Normalised Ratio) fell below 2 at 24 h whereas in patients who received 0.5 mg the INR fell below 5.5 in all subjects after 24 h and in none did it fall below 2.0. No patient had any thrombotic or haemorrhagic complications and no difficulty was encountered in re-establishing anticoagulant control after 24 h. We recommend 0.5 mg of vitamin K1 as an effective and convenient method of predictable and fine control of oral anticoagulant therapy.
Orphan G protein–coupled receptor GPR56 plays a role in cell transformation and tumorigenesis involving the cell adhesion pathway (2007)

GPR56 is an orphan G protein - coupled receptor, mutations of which have recently been associated with bilateral frontoparietal polymicrogyria, a rare neurologic disease that has implications in brain development. However, no phenotype beyond central nervous system has yet been described for the GPR56-null mutations despite abundant GPR56 expression in many non - central nervous system adult tissues. In the present study, we show that higher GPR56 expression is correlated with the cellular transformation phenotypes of several cancer tissues compared with their normal counterparts, implying a potential oncogenic function. RNA interference-mediated GPR56 silencing results in apoptosis induction and reduced anchorage-independent growth of cancer cells via increased anoikis, whereas cDNA overexpression resulted in increased foci formation in mouse fibroblast NIH3T3 cell line. When GPR56 silencing was induced in vivo in several xenograft tumor models, significant tumor responses (including regression) were observed, suggesting the potential of targeting GPR56 in the development of tumor therapies. The expression profiling of GPR56-silenced A2058 melanoma cell line revealed several genes whose expression was affected by GPR56 silencing, particularly those in the integrin-mediated signaling and cell adhesion pathways. The potential role of GPR56 in cancer cell adhesion was further confirmed by the observation that GPR56 silencing also reduced cell adhesion to the extracellular matrix, which is consistent with the observed increase in anoikis and reduction in anchorage-independent growth phenotypes. The oncogenic potential and apparent absence of physiologic defects in adult human tissues lacking GPR56, as well as the targetable nature of G protein - coupled receptor by small molecule or antibody, make GPR56 an attractive drug target for the development of cancer therapies.
Diversity of Cl− Channels (2005)

Cl(-) channels are widely found anion pores that are regulated by a variety of signals and that play various roles. On the basis of molecular biologic findings, ligand-gated Cl(-) channels in synapses, cystic fibrosis transmembrane conductors (CFTRs) and ClC channel types have been established, followed by bestrophin and possibly by tweety, which encode Ca(2+)-activated Cl(-) channels. The ClC family has been shown to possess a variety of functions, including stabilization of membrane potential, excitation, cell-volume regulation, fluid transport, protein degradation in endosomal vesicles and possibly cell growth. The molecular structure of Cl(-) channel types varies from 1 to 12 transmembrane segments. By means of computer-based prediction, functional Cl(-) channels have been synthesized artificially, revealing that many possible ion pores are hidden in channel, transporter or unidentified hydrophobic membrane proteins. Thus, novel Cl(-)-conducting pores may be occasionally discovered, and evidence from molecular biologic studies will clarify their physiologic and pathophysiologic roles.
28.2: Stereoscopic Near to Eye Display using a Single Microdisplay (2007)

Abstract A binocular Near to Eye Displays (NED) offering stereoscopic images is technically very challenging to realize. Already in a biocular system, there are many issues related to health and wellbeing although both eyes get an identical image. The virtual reality display (VRD), based on planar waveguide, offers an opportunity to realize a stereoscopic, ergonomically superior NED, if it is based on a single optical system offering images for both eyes. In this paper it is discussed how frame sequential stereoscopic images can be shown using a planar waveguide based NED. This system has only a single microdisplay and single image formation optics. The illumination of the LCD in this stereoscopic application differs from the biocular one. It is essential that the diffractive planar waveguide has very asymmetric grating profiles. An example of a design of a planar waveguide based optical engine is shown.
Mutant Thermotoga neapolitana DNA polymerase I: altered catalytic properties for non-templated nucleotide addition and incorporation of correct nucleotides (2002)

Thermotoga neapolitana (Tne) DNA polymerase belongs to the DNA polymerase I (Pol I) family. The O-helix region of these polymerases is involved in dNTP binding and also plays a role in binding primer-template during DNA synthesis. Here we report that mutations in the O-helix region of Tne DNA polymerase (Arg722 to His, Tyr or Lys) almost completely abolished the enzyme's ability to catalyze the template-independent addition of a single base at the 3'-end of newly synthesized DNA in vitro. The mutations did not significantly affect the DNA polymerase catalytic activity and reduced base misinsertions 5- to 50-fold. The same Arg722 mutations dramatically increased the ability of the enzyme's 3'-->5' exonuclease to remove mispaired 3' bases in a primer extension assay. These mutant DNA polymerases can be used to accurately amplify target DNA in vitro for gene cloning and genotyping analysis.
Roles of partly unfolded conformations in macromolecular self‐assembly (2001)

From genes to cells there are many steps of hierarchical increments in building up complex frameworks that provide intricate networks of macromolecular interactions, through which cellular activities such as gene expression, signal processing, energy transduction and material conversion are dynamically organized and regulated. The self-assembly of macromolecules into large complexes is one such important step, but this process is by no means a simple aggregation of macromolecules with predefined, rigid complementary structures. In many cases the component molecules undergo either domain rearrangements or folding of disordered portions, which occurs only following binding to their correct partners. The partial disorder is used in some cases to prevent spontaneous assembly at inappropriate times or locations. It is also often used for finely tuning the equilibrium and activation energy of reversible binding. In other cases, such as protein translocation across membranes, an unfolded terminus appears to be the prerequisite for the process as an initiation signal, as well as the physical necessity to be taken into narrow channels. Self-assembly processes of viruses and bacterial flagella are typical examples where the induced folding of disordered chains plays a key role in regulating the addition of new components to a growing assembly. Various aspects of mechanistic roles of natively unfolded conformations of proteins are overviewed and discussed in this short review.
ROCK PHYSICS OF GEOPRESSURE AND PREDICTION OF ABNORMAL PORE FLUID PRESSURES USING SEISMIC DATA (2002)

Summary Various physical processes cause anomalous pressures of underground fluids in a petroleum province. We quantify the effect on seismic properties caused by the common mechanisms of overpressure generation such as (kerogen-to-oil and oil-to-gas conversion) disequilibrium compaction. Fluid pressure due to kerogen-to-oil conversion in sourcerock shale significantly reduces the seismic velocities and enhances the anisotropy. Attenuation and attenuation anisotropy are also strongly affected, thus further enhancing the seismic visibility of overpressure in the shale. In deeply buried reservoirs, oil-to-gas cracking may increase the fluid pressure to reach the lithostatic pressure, and the seismic velocities decrease significantly when only a small fraction of oil in a closed reservoir is converted to gas.
Advancing Deepwater Kick Detection (2014)

Abstract Numerous developments in automation have made the modern mobile offshore drilling unit a marvel of engineering achievement and a model of efficiency. Yet, even with the surge in advancements, kick detection, which can be comparatively elementary for a fixed drilling unit, has proven significantly more difficult to master on a vessel which subject to wave motion and currents. A lack of consensus on universal standards and regulations have left kick detection largely ignored. But further, the lack of innovation has been coupled with drilling in greater water depths which are subject to the use of longer risers with greater volume and weight. Thus, in addition to the complications of dynamic environments are the material requirements to properly intervene during an influx event. Operators and shipyards have kept pace with these material issues by designing larger, smarter vessels with greater capacities and better controls systems to cope with the complexities of drilling in deepwater environments. Despite the best efforts and ballooning costs, influx events continue to occur because an operating envelope and a universal philosophy for deepwater kick detection have yet to be established. With the primary driver for deepwater and ultra-deepwater drilling being to access the most productive formations possible, a recipe is formed such that a slight variation between formation pressure and fluid pressure has the potential to draw a significant hydrocarbon volume into the well bore. When well control procedures are initiated, a series of checks take place which, though proven and reliable for detecting kicks, consume valuable response time and potentially aggravate the initial problem. After an influx has been confirmed, remedial work often takes days and sometimes weeks to recondition the well for drilling. Whether in terms of personnel, equipment, facility, environment, or finance, the risk presented to the drilling operation by influx and loss events is substantial. Therefore, an advanced approach should be adopted which views kick/loss detection as a safety critical measurement and incorporates a modern, control system based design philosophy with established methods to overcome shortcomings. This paper will describe experiences, challenges, and approaches to solving the problems related to creating an advanced early kick detection system suitable for floating mobile offshore drilling units. Necessary components, operational considerations, and design limitations will be discussed. Additionally, a discussion will offered on the current state of regulatory requirements related to kick detection and considerations for future standards.
The high binding affinity of phosphorothioate-modified oligomers for Ff gene 5 protein is moderated by the addition of C-5 propyne or 2'-O-methyl modifications (2002)

One of the problems that hamper the use of antisense DNAs as effective drugs is the non-specific binding of chemically-modified oligonucleotides to cellular proteins. We previously showed that the affinity of a model ssDNA-binding protein, the Ff gene 5 protein (g5p), was >300-fold higher for phosphorothioate-modified DNA (S-DNA) than for unmodified dA(36), consistent with the propensity of S-DNA to bind indiscriminately to proteins. The current work shows that g5p binding is also sensitive to sugar and pyrimidine modifications used in antisense oligomers. Binding affinities of g5p for 10 36mer oligomers were quantitated using solution circular dichroism measurements. The oligomers contained C-5-propyne (prC), 2'-O-methyl (2'-O-Me) or 2'-OH (RNA) groups, alone or combined with the phosphorothioate modification. In agreement with reported increases in antisense activity, the addition of prC or 2'-O-Me modifications substantially reduced the affinity of oligomers for g5p by approximately 2-fold compared with the same DNA oligomer sequences containing only phosphorothioate linkages. That is, such modifications moderated the propensity of the phosphorothioate group to bind tightly to the g5p. The Ff g5p could be a useful model protein for assessing non-specific binding effects of antisense oligomer modifications.
Analysis of high impedance faults using fractal techniques (1996)

Phase currents and voltages in a distribution power system change with a certain degree of chaos when high impedance faults (HIFs) occur. This paper describes application of the concepts of fractal geometry to analyze chaotic properties of high impedance faults. Root-mean-square rather that instantaneous values of currents are used for characterization of temporal system behavior; this results in relatively short time-series available for analysis. An algorithm is presented for pattern recognition and detection of HIFs; it is based on techniques suited for analysis of relatively small data sets. Examples are given to illustrate the ability of this approach to discriminate between faults and other transients in a power system.
Anti‐metastatic and Anti‐invasive Effects of Polymeric Arg‐Gly‐Asp (RGD) Peptide, Poly(RGD), and Its Analogues (1990)

We have investigated the anti-metastatic and anti-invasive activities of polypeptide analogues based on the Arg-Gly-Asp (RGD) adhesive signal in fibronectin, poly(RGD), poly(RGDS)[Arg-Gly-Asp-Ser] and poly(RGDT)[Arg-Gly-Asp-Thr]. These polypeptides containing repetitive RGD sequences were able to inhibit experimental and spontaneous lung metastases of B16-BL6 cells more effectively than the corresponding monomer peptides. In the spontaneous metastasis model, multiple i.v. administrations of these polymeric peptides before or after surgical excision of the primary tumor resulted in a significant reduction of lung tumor colonies. However, there was no significant difference in ability to inhibit spontaneous lung metastasis among poly(RGD), poly(RGDS) and poly(RGDT), although the carboxy-terminal amino acid residue (i.e., Xaa in -RGDXaa-) has been shown to play an important role in the expression of cell adhesive character. The treatment with poly(RGD) substantially prolonged the survival time for mice injected s.c. with B16-BL6 melanoma as compared with the untreated control. We also found that the polypeptides were potently able to inhibit the invasion and migration of tumor cells in vitro. Since these polypeptide analogues showed no antigenicity in the host and had no toxic effect on tumor cells in vitro, they may be potentially useful in the prevention of cancer metastasis.