gebhart/patrepeval huggingface dataset:
Adsorption ofMycoplasma pneumoniaeto Neuraminic Acid Receptors of Various Cells and Possible Role in Virulence (1968)

Monkey, rat, and chicken tracheal epithelial cells, as well as monkey, rat, guinea pig, and chicken erythrocytes, adsorbed firmly to colonies of Mycoplasma pneumoniae and M. gallisepticum. Colonies of M. pulmonis also adsorbed erythrocytes but with less avidity than M. pneumoniae or M. gallisepticum; unlike the latter organisms, M. pulmonis did not adsorb tracheal epithelial cells. Colonies of M. orale type 1 and M. orale type 3 adsorbed only chicken red cells. Other mycoplasma species tested, including four of human origin and one of animal origin, did not adsorb red cells or epithelial cells. M. pneumoniae and M. gallisepticum appeared to attach to erythrocytes or tracheal epithelial cells by neuraminic acid receptors on these cells, whereas M. orale types 1 and 3 and M. pulmonis seemed to utilize another type or other types of receptors. Pretreatment of red cells or tracheal epithelial cells with receptor-destroying enzyme, neuraminidase, or influenza B virus removed the adsorption receptors for M. pneumoniae. Similarly, pretreatment of M. pneumoniae colonies with neuraminic acid-containing materials prevented adsorption of erythrocytes or respiratory tract cells. The adsorption sites on M. pneumoniae were specifically blocked by homologous but not heterologous antisera. This property made it possible to study the nature of the mycoplasma adsorption sites by testing the capacity of different fractions of the organism to block the action of adsorption-inhibiting antibodies. Such studies suggested that the mycoplasma binding sites were probably lipid or lipoprotein in nature. The glycerophospholipid hapten was implicated as one such site, since this serologically active hapten blocked the action of hemadsorption-inhibiting antibodies in M. pneumoniae rabbit antiserum. The affinity of M. pneumoniae for respiratory tract epithelium, unique among the mycoplasmas that infect man, may play a role in virulence, since this type of attachment provides an unusual opportunity for peroxide, secreted by the organism, to attack the tissue cell membrane without being rapidly destroyed by catalase or peroxidase present in extracellular body fluids.
A CCR5-Dependent Novel Mechanism for Type 1 HIV gp120 Induced Loss of Macrophage Cell Surface CD4 (2001)

Type 1 HIV gp120 is especially effective in disrupting immune cell function because it is able to cause dysregulation of both infected and uninfected cells. We report a novel CCR5-dependent mechanism of gp120-induced CD4 loss from macrophages. An M-tropic gp120, using CCR5, is able to induce 70% loss of cell surface CD4 from macrophages within an hour. This cell surface CD4 loss is more substantial and rapid than the 20% loss observed with T-tropic gp120(IIIB) by 3 h. The rapid and substantial CD4 loss induced by M-tropic gp120 is not observed on macrophages homozygous for the ccr5Delta32 mutation, which fail to express cell surface CCR5. We have used confocal imaging to show that gp120 and CD4 are internalized together by a process resembling receptor-mediated endocytosis, and that both proteins enter HLA-DR containing compartments of the macrophage. We have also shown by semiquantitative RT-PCR that, in response to CD4 loss from the cell surface, mRNA for CD4 is up-regulated and the intracellular pool of CD4 increases. CCR5 mRNA levels are also increased. It is proposed that internalization of self and viral protein and increased pools of intracellular CD4 could modulate Ag presentation efficiencies and have implications for the induction and maintenance of both productive immune responses and self-tolerance.
Interactions during heat-induced gelation in a mixed system of soybean 7S and 11S globulins. (1986)

Heat-induced gelation and gel properties in a mixed system of soybean 7S and 11S globulins were studied. The gel hardness changed sigmoidally with the protein concentration and relative proportion of the globulins. The gel turbidity was decreased by the coexistence of 7S globulin. The gelling time was either retarded or shortened depending on the amount of 7S globulin. The 7S and 11S globulins interact noncovalently to form soluble aggregates consisting of both globulins in the course of gel formation. The extent of the interaction was affected by the proportions of the globulins. We conclude that such interactions may be the cause of various behaviors of gelation and gel properties observed here.
Quantification of Free Circulating Tumor DNA as a Diagnostic Marker for Breast Cancer (2008)

Quantification of circulating DNA by real-time PCR may be a good and simple tool for detection of breast cancer with a potential to clinical applicability together with other current methods used for monitoring the disease.
Heart rate variability as a biomarker for epilepsy seizure prediction (2017)

These results indicate that the HRV signal contains valuable information and can be a predictor for epilepsy seizure. Although our results in comparison with EEG ares a little bit weaker, the recording of ECG is much easier and faster than EEG. Also, our finding showed the results of this study are considerably better than recent research based on ECG (Tab. 1, Fig. 10, Ref. 17).
Surface generation and detection of phonons by picosecond light pulses (1986)

We report experiments in which picosecond light pulses are used to generate and detect very short stress pulses (coherent longitudinal phonons). We present a theory of the generation process, and describe how the spatial shape of the stress pulse is related to the optical, electronic, and acoustical properties of the material. The stress pulses are detected through a measurement of the changes they induce in the optical reflectivity of the sample surface. We describe the theory of this effect. We present experimental results we have obtained for a-${\mathrm{As}}_{2}$${\mathrm{Te}}_{3}$, a-Ge, a-${\mathrm{As}}_{2}$${\mathrm{Se}}_{3}$, and Ni.
Comparison of the efficiency, MTF and chromatic properties of four diffractive bifocal intraocular lens designs (2010)

The aim of this paper is to compare the properties of four different profiles which can be used as multifocal intraocular lens. The Hankel transform based on the theory of scalar diffraction is applied to a binary profile, a parabolic one, a parabolic profile with holes, and finally a sinusoidal one. This enables to study the various distributions of the diffractive efficiencies and the axial chromatism. The image quality is evaluated by means of simulations of the MTFs with Zemax. Finally we propose a new way to graphically synthesize all the properties of these lenses, using a radar graph.
Synthetic studies of the antitumor antibiotic streptonigrin. II. Synthesis of the C‐D ring portion of streptonigrin (1976)

Abstract Partial mclhylalion of gallopropiophenonc ( 4 ) followed by benzylation and base‐catalyzed condensation with ethyl acetate yielded 3‐(2‐benzyloxy‐3,4‐din]etlK&gt;xy)benzoyl‐2‐butanonc ( 6 ). Animation of the latter and subsequent base‐catalyzed cyclization with ethyl cyanoacetate gave 4‐(2‐benzyloxy‐3,4‐dimethoxy)phenyl‐5,6‐dimethyl‐2‐oxo‐1,2‐dihydropyridine ( 8 ). Removal of the 2‐oxo group of 8 through chlorination and dechlorination and stepwise conversion of the 5‐cyano and 2‐methyl groups into the 5‐amino and 2‐carboxylic acid groups, respectively, with introduction and removal of protecting groups at proper stages, yielded the C‐D ring moiety of the antitumor antibiotic streptonigrin.
Near Balance Drilling Benefits Addressed Through a Blowout Probability Model (2012)

Abstract Eni Near Balance Drilling (e-nbd™) is an innovative drilling process to maintain constant bottom hole annular pressure at all times while circulating, and to manage annular dynamic hydraulic pressure profile accordingly. The operational benefits of this process are measured on field operations through the enhancement of borehole quality, the reduction of NPT and the ability to reach targets otherwise inaccessible. e-nbd™ can improve drilling operations safety, especially by reducing the probability of the most significant threats, which is a blowout event. These benefits are not measurable on operations, unless having a huge number of statistical records. Nonetheless the probability of a complex event like a blowout can be effectively calculated through dedicated fault tree models. Eni drilling department has developed a replicable blowout probability model that is suitable for most of the current drilling and completion situations. This model is offering a high number of possible operating scenarios and detailed settings, in order to guarantee the accuracy of each analysis. This model has been used to address the benefits of e-nbd™, in order to compare analogous wells to be drill with or without e-nbd™. In both situations results were analysed to measure the overall impact on blowout probability and to further address the sensitivity to technical / non technical factors. By comparing two situations using a probabilistic fault tree, this paper shows that the key factors affecting a blowout probability are notably impacted by the use of e-nbd™. These key factors are not only technical, but also organizational and human.
Block-Based Hybrid Video Coding Using Motion-Compensated Long-Term Memory Prediction (1997)

: Our new approach extends the spatial displacement vector utilized in block-based hybrid video coding by a variable time delay permitting the use of more frames than the previously decoded one for motion compensation. The longterm memory covers the decoded frames of some seconds at the encoder&amp;apos;s as well as the decoder&amp;apos;s side. This scheme is well suited in cases of repetition in the sequence, e.g. a head is rotating back into its old position, or if the camera is shaking. However, transmission of the variable time delay requires additional bit-rate which may be prohibitive when the size of the long-term memory increases. Therefore, we control the bit-rate of the motion information by employing rate-constrained motion estimation. Simulation results are obtained by integrating long-term memory prediction into an H.263 codec. PSNR improvements up to 2 dB for the Foreman sequence and 1.5 dB for the Mother-Daughter sequence are demonstrated in comparison to the TMN-2.0 H.263 coder. 1. INTRO...
Triterpenoid 2,3-ketols, diols and their acetates: Preparation and conformation of the ring A (1989)

19β,28-Epoxy-18α-oleanane derivatives I-III were converted into hydroxy ketones IV, VIII and X , acetoxy ketones V, VII, IX and XI , diols and their mono- and diacetates XII-XXV . Seven of the eight possible isomeric 2,3-diol monoacetates were obtained. Conformation of the ring A in these compounds has been derived from the 1 H NMR and IR spectra. In 2β-acetoxy-3-ketone VII , 3α-hydroxy- and 3α-acetoxy-2-ketones VIII and IX , and in 2β,3α-diol monoacetates XVIII and XIX the ring A exists predominantly in a boat conformation.
Single-Turnover and Pre-Steady-State Kinetics of the Reaction of the Adenine Glycosylase MutY with Mismatch-Containing DNA Substrates (1998)

The DNA repair enzyme MutY plays an important role in the prevention of DNA mutations resulting from the presence of the oxidatively damaged lesion 7,8-dihydro-8-oxo-2'-deoxyguanosine (OG) in DNA by the removal of misincorporated adenine residues in OG:A mispairs. MutY also exhibits adenine glycosylase activity toward adenine in G:A and C:A mismatches, although the importance of this activity in vivo has not been established. We have investigated the kinetic properties of MutY's glycosylase activity with OG:A and G:A containing DNA duplexes. Our results indicate that MutY's processing of these two substrates is distinctly different. By using single-turnover experiments, the intrinsic rate for adenine removal by MutY from an OG:A substrate was found to be at least 6-fold faster than that from the corresponding G:A substrate. However, under conditions where [MutY] << [DNA], OG:A substrates are not quantitatively converted to product due to the inefficient turnover resulting from slow product release. In contrast, with a G:A substrate MutY's dissociation from the corresponding product is more facile, such that complete conversion of the substrate to product can be achieved under similar conditions. The kinetic results illustrate that the glycosylase reaction catalyzed by MutY has significant differences depending on the characteristics of the substrate. The lingering of MutY with the product of its reaction with OG:A mispairs may be biologically significant to prevent premature removal of OG. Thus, this approach is providing insight into factors that may be influencing the repair of damaged and mismatched DNA in vivo by base-excision repair glycosylases.
The Linkage of Innate to Adaptive Immunity via Maturing Dendritic Cells In Vivo Requires CD40 Ligation in Addition to Antigen Presentation and CD80/86 Costimulation (2004)

Dendritic cell (DC) maturation is an innate response that leads to adaptive immunity to coadministered proteins. To begin to identify underlying mechanisms in intact lymphoid tissues, we studied alpha-galactosylceramide. This glycolipid activates innate Valpha14(+) natural killer T cell (NKT) lymphocytes, which drive DC maturation and T cell responses to ovalbumin antigen. Hours after giving glycolipid i.v., tumor necrosis factor (TNF)-alpha and interferon (IFN)-gamma were released primarily by DCs. These cytokines induced rapid surface remodeling of DCs, including increased CD80/86 costimulatory molecules. Surprisingly, DCs from CD40(-/-) and CD40L(-/-) mice did not elicit CD4(+) and CD8(+) T cell immunity, even though the DCs exhibited presented ovalbumin on major histocompatibility complex class I and II products and expressed high levels of CD80/86. Likewise, an injection of TNF-alpha up-regulated CD80/86 on DCs, but CD40 was required for immunity. CD40 was needed for DC interleukin (IL)-12 production, but IL-12p40(-/-) mice generated normal ovalbumin-specific responses. Therefore, the link between innate and adaptive immunity via splenic DCs and innate NKT cells has several components under distinct controls: antigen presentation in the steady state, increases in costimulatory molecules dependent on inflammatory cytokines, and a distinct CD40/CD40L signal that functions together with antigen presentation ("signal one") and costimulation ("signal two") to generate functioning CD4(+) T helper cell 1 and CD8(+) cytolytic T lymphocytes.
A SERO-EPIDEMIOLOGICAL STUDY OF CONVENTIONAL INFECTIOUS AGENTS IN ALZHEIMER'S DISEASE (1987)

Serum antibody titres to Adenovirus, Chlamydia Group B, Coxiella burnettii, Cytomegalovirus, Herpes simplex virus, Influenza A, Influenza B, Measles and Mycoplasma pneumoniae were measured in 33 patients with a clinical diagnosis of Alzheimer's disease, and in 28 non-demented controls suffering from functional psychiatric disorders. No statistically significant differences were found between the patients and controls, and it is concluded that these agents play no role in the aetiology of Alzheimer's disease.
Recombinant Rat Surfactant-Associated Protein D Inhibits Human T Lymphocyte Proliferation and IL-2 Production (1998)

Components of the airspace-lining material may contribute to the local regulation of immune function within the lung. We report here that recombinant rat pulmonary surfactant-associated protein D (SP-D) inhibits the lectin- and anti-CD3-stimulated proliferation of human PBMCs. Inhibition was associated with a decreased production of IL-2, and the addition of human rIL-2 blocked the inhibitory action of SP-D. These effects were not inhibited by maltose, indicating that the inhibitory activity was not dependent upon the lectin activity of SP-D. Studies employing mutant SP-D lacking N-linked sugars or defective in multimerization further indicated that inhibition was not dependent upon cellular interactions with the N-linked oligosaccharide on SP-D or the oligomerization of trimeric SP-D subunits. Although a peptide containing an inverted DGR showed similar IL-2-dependent effects on anti-CD3-stimulated proliferation, deletion of the conserved DGRDGR sequence near the amino-terminal end of the collagen domain did not decrease the suppressive activity of SP-D. We hypothesize that SP-D can dampen lymphocyte responses to exogenous stimuli and protect the lung against collateral immune-mediated damage.
Drop Impact on Superheated Surfaces (2012)

At the impact of a liquid droplet on a smooth surface heated above the liquid's boiling point, the droplet either immediately boils when it contacts the surface ("contact boiling"), or without any surface contact forms a Leidenfrost vapor layer towards the hot surface and bounces back ("gentle film boiling"), or both forms the Leidenfrost layer and ejects tiny droplets upward ("spraying film boiling"). We experimentally determine conditions under which impact behaviors in each regime can be realized. We show that the dimensionless maximum spreading γ of impacting droplets on the heated surfaces in both gentle and spraying film boiling regimes shows a universal scaling with the Weber number We (γ~We(2/5)), which is much steeper than for the impact on nonheated (hydrophilic or hydrophobic) surfaces (γ~We(1/4)). We also interferometrically measure the vapor thickness under the droplet.
Video clip recognition using joint audio-visual processing model (2003)

The automatic recognition of video clips is an important capability with applications in broadcast monitoring for content theft and adherence to advertisement campaign. We present an approach for video clip recognition based on HMM and Gaussian mixture modeling for modeling video and audio streams respectively. The approach is used to model TV commercials. The recognition results of using single stream and joint models are compared The error rate of 0.01% is achieved when the joint audiovisual processing model is employed.
Mutational analysis of vaccinia DNA topoisomerase defines amino acid residues essential for covalent catalysis. (1994)

The eukaryotic family of type I DNA topoisomerases includes the nuclear type I enzymes and the enzymes encoded by vaccinia and other poxviruses. The small size of the vaccinia topoisomerase (314 amino acids as compared to 765-972 amino acids for the cellular enzymes) makes it likely that this protein constitutes the minimal functional unit of a eukaryotic type I enzyme and provides an opportunity for a comprehensive structure-function analysis through mutagenesis. Two protein subregions were targeted for mutagenesis in the present study. The role of the Ser-Lys-X-X-Tyr sequence present at the active site of all family members was examined by replacing each conserved residue with alanine. Alanine substitution at the active site Tyr abrogated topoisomerase activity. In contrast, mutations at Ser-270 and Lys-271 had no effect on enzyme activity. The region of the vaccinia topoisomerase from amino acids 126-142 (MFFIRFGKMKYLKENET) is highly conserved and contains a residue, Gly-132, shown previously to be essential. Twenty-nine different mutations were generated in this region, with at least one substitution at each position. Point mutations were identified at three positions, Arg-130, Tyr-136, and Leu-137, which either abrogated or severely reduced DNA relaxation. The effects on activity could be attributed to a defect in formation of the covalent intermediate. Alterations of 13 other amino acids, including conserved residues, had little or no effect on topoisomerase activity.
Hardware Support for Accelerating Data Movement in Server Platform (2007)

Data movement (memory copies) is a very common operation during network processing and application execution on servers. The performance of this operation is rather poor on today's microprocessors due to the following aspects: 1) Several long-latency memory accesses are involved because the source and/or the destination are typically in memory, 2) latency hiding techniques, such as out-of-order execution, hardware threading, and prefetching, are not very effective for bulk data movement, and 3) microprocessors move data at register (small) granularity. In this paper, we show this overhead of bulk data movement and propose the use of dedicated copy engines to minimize it. We present a detailed analysis of copy engine architectures along two dimensions: 1) on-die versus off-die and 2) synchronous versus asynchronous. These copy engine architectures are superior to traditional direct memory access (DMA) engines because they are tightly coupled to the core architecture and enable lower overhead communication and signaling. We describe the hardware support required to implement these copy engines and integrate them into server platforms. We perform a detailed case study to evaluate the performance of these copy engines. The evaluation is based on an execution-driven simulator, which was extended with detailed models of copy engines. Our simulation results show that copy engines are effective in reducing the bulk data movement overhead and, hence, hold significant promise for high-performance server platforms
Movable microstructures made by two-photon three-dimensional microfabrication (2003)

Movable microstructures were made by the use of two-photon three-dimensional (3D) microfabrication with submicron resolution beyond the diffraction limit of light. In our method, movable microstructures are fabricated by fast scanning a focal point through the inside of the liquid photopolymerizable resin. Therefore, unlike silicon micromachining, neither sacrificial layers nor supporting parts are needed to produce movable mechanism. Furthermore truly three-dimensional movable parts, which have not been produced by silicon micromachining, are easy to make. This method is useful to make complicated 3D microfluidic systems, which include various movable device. In our experiment, a micro gear with a shaft was successfully fabricated within 7 minutes. The rapid fabrication makes mass production of 3D MEMS possible.
Binary decision diagrams and beyond: enabling technologies for formal verification (1995)

Ordered Binary Decision Diagrams (OBDDs) have found widespread use in CAD applications such as formal verification, logic synthesis, and test generation. OBDDs represent Boolean functions in a form that is both canonical and compact for many practical cases. They can be generated and manipulated by efficient graph algorithms. Researchers have found that many tasks can be expressed as series of operations on Boolean functions, making them candidates for OBDD-based methods. The success of OBDDs has inspired efforts to improve their efficiency and to expand their range of applicability. Techniques have been discovered to make the representation more compact and to represent other classes of functions. This has led to improved performance on existing OBDD applications, as well as enabled new classes of problems to be solved. This paper provides an overview of the state of the art in graph-based function representations. We focus on several recent advances of particular importance for formal verification and other CAD applications.