gebhart/patrepeval huggingface dataset:
Two-photon absorption induced transmission changes in ZnSe interference filters (1988)

We observe two-photon absorption (2PA) of picosecond, 0.6-μm, 0.3-nJ pulses in a 0.4-μm film of ZnSe. We use high-frequency-modulation phase-sensitive detection to be near the shot-noise limit combined with a low-frequency pulse-delay modulation to discriminate against large thermal nohlinearities. This dual-modulation technique, combined with the field enhancement produced by placing the film in a resonant cavity, permits observation of 2PA and other fast nonlinearities by using pulses having peak powers of the order of 1 W.
Innate gamma/delta T-cells during HIV infection: Terra relatively Incognita in novel vaccination strategies? (2011)

Despite a long-lasting global effort, the Holy Grail quest for a protective vaccine, able to confer prevention to HIV infection, did not reach the hoped for results, nor seems able to do so in the near future. Since mucosal surfaces of the host serve as the main entry point for HIV, it seems now logical to switch from a systemic to a localized view of events, in order to reveal critical steps useful in designing new and different vaccination strategies. In this context, the recent description of the very early phases of infection, from the eclipse to the viremia peak phase, seems to define a point-of-no-return threshold after which the main HIV infection steps, i.e. the massive destruction of the CD4+CCR5+ cell pool, the destruction of the mucosal physical barrier, and the establishment of reservoir sanctuaries, have already been accomplished. Nevertheless, the underlying mechanisms, the timing, and the consequences of evasion mechanisms exploited by HIV are still under scrutiny. Innate immunity, as part of a rapid lymphoid stress surveillance system, is known to play a central role in host responses to many infectious agents. In particular, Vγ9Vδ2 T-cells are able to quickly respond to danger signals without the need for classical major histocompatibility complex presentation, and may act as a bridge between innate and acquired arms of immune response, being able to kill infected/transformed cells, release antimicrobial soluble factors, and increase the deployment of other innate and acquired responses. Many experimental evidences suggest a direct role of circulating Vγ9Vδ2 T-cells during HIV disease. They may exert a direct anti-HIV role by secreting chemokines competing for HIV entry coreceptors as well as other soluble antiviral factors, and by killing infected cells by cytotoxic natural killer-like mechanisms. Moreover, they were found progressively depleted and anergic in advanced stages of HIV disease, this effect being directly linked to uncontrolled HIV replication. Scarce evidences are available on the involvement of mucosal gamma/delta T-cells during the early phases of HIV infection. In particular, the relative cause/effect links between HIV infection, destruction of the mucosal physical barrier, nonspecific activation of the immune system, and mucosal innate cell activation and effector functions, are still not completely defined. In order to attain an effective manipulation of innate immune cells, aiming at the induction of an effective adaptive immunity against HIV, any information on the role of mucosal antiviral factors and innate immune cells will be very important. The aim of this review is to summarize the information on the role of gamma/delta T-cells during HIV infection, from the general circulating population to mucosal sites, in order to better describe areas deserving increased attention. In particular, strategies enhancing gamma/delta T-cell functions may open the possibility to formulate new immunotherapeutic regimens, which could impact the improvement of immune control of HIV disease.
Thermodynamic Evaluation of Ligand Binding in the Plant-like Phosphoethanolamine Methyltransferases of the Parasitic Nematode Haemonchus contortus (2011)

Nematodes are a major cause of disease and the discovery of new pathways not found in hosts is critical for development of therapeutic targets. Previous studies suggest that Caenorhabditis elegans synthesizes phosphocholine via two S-adenosylmethionine (AdoMet)-dependent phosphoethanolamine methyltransferases (PMT). Here we examine two PMT from the parasitic nematode Haemonchus contortus. Sequence analysis suggests that HcPMT1 contains a methyltransferase domain in the N-terminal half of the protein and that HcPMT2 encodes a C-terminal methyltransferase domain, as in the C. elegans proteins. Kinetic analysis demonstrates that HcPMT1 catalyzes the conversion of phosphoethanolamine to phosphomonomethylethanolamine (pMME) and that HcPMT2 methylates pMME to phosphodimethylethanolamine (pDME) and pDME to phosphocholine. The IC(50) values for miltefosine, sinefungin, amodiaquine, diphenhydramine, and tacrine suggest differences in the active sites of these two enzymes. To examine the interaction of AdoMet and S-adenosylhomocysteine (AdoCys), isothermal titration calorimetry confirmed the presence of a single binding site in each enzyme. Binding of AdoMet and AdoCys is tight (K(d) ∼2-25 μm) over a range of temperatures (5-25 °C) and NaCl concentrations (0.05-0.5 m). Heat capacity changes for AdoMet and AdoCys binding suggests that each HcPMT differs in interaction surface area. Nonlinear van't Hoff plots also indicate a possible conformational change upon AdoMet/AdoCys binding. Functional analysis of the PMT from a parasitic nematode provides new insights on inhibitor and AdoMet/AdoCys binding to these enzymes.
Context-Aware Security for 6G Wireless The Role of Physical Layer Security (2021)

Sixth generation systems are expected to face new security challenges, while opening up new frontiers towards context awareness in the wireless edge. The workhorse behind this projected technological leap will be a whole new set of sensing capabilities predicted for 6G devices, in addition to the ability to achieve high precision localization. The combination of these enhanced traits can give rise to a new breed of context-aware security protocols, following the quality of security (QoSec) paradigm. In this framework, physical layer security solutions emerge as competitive candidates for low complexity, low-delay and low-footprint, adaptive, flexible and context aware security schemes, leveraging the physical layer of the communications in genuinely cross-layer protocols, for the first time.
Expression and characterization of a truncated murine Fc gamma receptor. (1988)

We have isolated a recombinant secreted Fc gamma R beta molecule by deletion of the transmembrane and cytoplasmic domains encoding sequence from a Fc gamma R beta 1 cDNA clone, and insertion of the truncated cDNA into a eukaryotic expression vector, pcEXV-3. To express and amplify the production of the truncated Fc gamma R beta molecule, we transfected the truncated cDNA plasmid into a dihydrofolate reductase-minus CHO cell line along with a dhfr minigene, and amplified the gene products with methotrexate. The resulting cell line secretes 2-3 micrograms/ml/24 h of truncated Fc gamma R beta, which can be readily purified by affinity chromatography on IgG-Sepharose. The truncated Fc gamma R beta has a Mr of 31-33,000 on SDS-PAGE and is glycosylated. N-glycosidase F cleavage reduces the Mr to 19,000, consistent with the size of the truncated product, 176 amino acid residues. There are two disulfide bonds in the protein. Binding of immune complexes formed between DNP20BSA and anti-DNP mAbs reveals better binding of IgG1 aggregates than that of IgG2b and IgG2a aggregates. The binding of the immune complexes was somewhat better at more acidic pH, in contrast to previous experiments with binding of purified Fc gamma R to immune complex-coated beads. We were surprised to observe that the truncated Fc gamma R beta did not react with the anti-Fc gamma R mAb 6B7C. Previous work had shown that 6B7C reacts with Fc gamma R on immunoblots, fails to bind to the surface of resting B cells and peritoneal macrophages, but does bind to macrophage cell lines and LPS-stimulated B cells. We show, by binding of mAb 6B7C to a peptide conjugate, that the 6B7C epitope lies within residues 169-183 of the intact Fc gamma R beta, which is just outside the plasma membrane. The availability of the truncated Fc gamma R beta in microgram quantities should facilitate further analysis of structure and function of these receptors.
Detoxification of an Alkylating Drug, N,N-Bis(2-chloroethyl)-p-aminophenylbutyric Acid (Chlorambucil), in Human Gastric Juice and Saliva (1998)

N,N-Bis(2-chloroethyl)-p-aminophenylbutyric acid (chlorambucil, 1) is an orally administered drug widely used in the chemotherapy of chronic lymphocytic leukemia. It is converted in gastric juice into three stable metabolites, which were characterized as N,N-bis(2-hydroxyethyl)-p-aminophenylbutyric acid (4), N-(2-hydroxyethyl)-N-[2-(thiocyano)ethyl]-p-aminophenylbutyric+ ++ acid (5), and N,N-bis[2-(thiocyano)ethyl]-p-aminophenylbutyric acid (6). 4 is the product of chloroambucil hydrolysis, while 5 and 6 are results of the reaction of 1 with saliva-derived thiocyanate ion. The destabilizing effect of low gastric oxonium ion concentration on 1 is also demonstrated.
Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection (2018)

The synthetic tumors and somatic structural variant detection leaderboards remain available as a community benchmarking resource, and BAMSurgeon is available at https://github.com/adamewing/bamsurgeon .
Prospective Evaluation of Trunk Range of Motion in Adolescents With Idiopathic Scoliosis Undergoing Spinal Fusion Surgery (2002)

Whereas range of motion was reduced in the fused regions of the spine, it was also reduced in unfused regions. The lack of compensatory increase in motion at unfused regions contradicts current theory and suggests early postoperative range of motion therapy to facilitate motion in unfused regions.
ChemInform Abstract: SYNTHETIC STUDIES ON HISTRIONICOTOXINS PART 1, A STEREOCONTROLLED SYNTHESIS OF (+‐)‐PERHYDROHISTRIONICOTOXIN (1975)

Abstract 2‐Nitro‐cyclohexanonketal (I) addiert Methylacrylat in Gegenwart basischer Katalysatoren zum Addukt (II), aus dem die homologe Säure (III) hergestellt wird.
TONIC: A timing database for VLSI design (2002)

A unified timing database for VLSI (very large scale integration) design is presented. The approach has been successfully used for the design of a three million transistor microprocessor. The database and timing methodology are oriented towards, but not restricted to, the top-down design style. Emphasis is placed upon integration with other timing tools such as circuit simulators, logic synthesis tools, and static timing analyzers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Tyrosine phosphorylations in vivo associated with v-fms transformation. (1988)

The role of tyrosine-specific phosphorylation in v-fms-mediated transformation was examined by immunoblotting techniques together with a high-affinity antibody that is specific for phosphotyrosine. This antiphosphotyrosine antibody detected phosphorylated tyrosine residues on the gp140v-fms molecule, but not gP180v-fms or gp120v-fms, in v-fms-transformed cells. This antibody also identified a number of cellular proteins that were either newly phosphorylated on tyrosine residues or showed enhanced phosphorylation on tyrosine residues as a result of v-fms transformation. However, the substrates of the v-fms-induced tyrosine kinase activity were not the characterized pp60v-src substrates. The phosphorylation of some of these cellular proteins and of the gp140fms molecule was found to correlate with the ability of v-fms/c-fms hybrids to transform cells. In addition, immunoblotting with the phosphotyrosine antibody allowed a comparison to be made of the substrates phosphorylated on tyrosine residues in various transformed cell lines. This study indicates that the pattern of tyrosine phosphorylation in v-fms-transformed cells is strikingly similar to that in v-sis-transformed cells.
Fungi that Infect Humans (2017)

Fungi must meet four criteria to infect humans: growth at human body temperatures, circumvention or penetration of surface barriers, lysis and absorption of tissue, and resistance to immune defenses, including elevated body temperatures. Morphogenesis between small round, detachable cells and long, connected cells is the mechanism by which fungi solve problems of locomotion around or through host barriers. Secretion of lytic enzymes, and uptake systems for the released nutrients, are necessary if a fungus is to nutritionally utilize human tissue. Last, the potent human immune system evolved in the interaction with potential fungal pathogens, so few fungi meet all four conditions for a healthy human host. Paradoxically, the advances of modern medicine have made millions of people newly susceptible to fungal infections by disrupting immune defenses. This article explores how different members of four fungal phyla use different strategies to fulfill the four criteria to infect humans: the Entomophthorales, the Mucorales, the Ascomycota, and the Basidiomycota. Unique traits confer human pathogenic potential on various important members of these phyla: pathogenic Onygenales comprising thermal dimorphs such as <i>Histoplasma</i> and <i>Coccidioides</i>; the <i>Cryptococcus</i> spp. that infect immunocompromised as well as healthy humans; and important pathogens of immunocompromised patients-<i>Candida</i>, <i>Pneumocystis</i>, and <i>Aspergillus</i> spp. Also discussed are agents of neglected tropical diseases important in global health such as mycetoma and paracoccidiomycosis and common pathogens rarely implicated in serious illness such as dermatophytes. Commensalism is considered, as well as parasitism, in shaping genomes and physiological systems of hosts and fungi during evolution.
Stacked Spatio-Temporal Graph Convolutional Networks for Action\n Segmentation (2018)

We propose novel Stacked Spatio-Temporal Graph Convolutional Networks\n(Stacked-STGCN) for action segmentation, i.e., predicting and localizing a\nsequence of actions over long videos. We extend the Spatio-Temporal Graph\nConvolutional Network (STGCN) originally proposed for skeleton-based action\nrecognition to enable nodes with different characteristics (e.g., scene, actor,\nobject, action, etc.), feature descriptors with varied lengths, and arbitrary\ntemporal edge connections to account for large graph deformation commonly\nassociated with complex activities. We further introduce the stacked hourglass\narchitecture to STGCN to leverage the advantages of an encoder-decoder design\nfor improved generalization performance and localization accuracy. We explore\nvarious descriptors such as frame-level VGG, segment-level I3D, RCNN-based\nobject, etc. as node descriptors to enable action segmentation based on joint\ninference over comprehensive contextual information. We show results on CAD120\n(which provides pre-computed node features and edge weights for fair\nperformance comparison across algorithms) as well as a more complex real-world\nactivity dataset, Charades. Our Stacked-STGCN in general achieves 4.0%\nperformance improvement over the best reported results in F1 score on CAD120\nand 1.3% in mAP on Charades using VGG features.\n
Substrate-Specific Heterogeneous Catalysis of CeO2 by Entropic Effects via Multiple Interactions (2014)

Achieving complete substrate specificity through multiple interactions like an enzyme is one of the ultimate goals in catalytic studies. Herein, we demonstrate that multiple interactions between the CeO2 surface and substrates are the origin of substrate-specific hydration of nitriles in water by CeO2, which is exclusively applicable to the nitriles with a heteroatom (N or O) adjacent to the α-carbon of the CN group but is not applicable to the other nitriles. Kinetic studies reveal that CeO2 reduces the entropic barrier (TΔS‡) for the reaction of the former reactive substrate, leading to 107-fold rate enhancement compared with the latter substrate. Density functional theory (DFT) calculations confirmed multiple interaction of the reactive substrate with CeO2, as well as preferable approximation and alignment of the nitrile group of the substrate to the active OH group on CeO2 surface. This can lead to the reduction of the entropic barrier. This is the first example of an entropy-driven substrate-specific catalysis of a nonporous metal oxide surface, which will provide a new design strategy for enzyme-inspired synthetic catalysts.
Carbohydrate-Based Macrolides Prepared via a Convergent Ring Closing Metathesis Approach:  In Search for Novel Antibiotics (2007)

An efficient convergent approach has been developed for the construction of novel, nonnatural polysubstituted carbohydrate-based macrolides. A key step in the synthesis is the formation of the macrocyclic ring via a ring-closing metathesis reaction. The obtained macrolide analogues have been screened for biological activity against gram-positive and gram-negative bacteria, yeasts, and molds.
3-D Integration of 10-GHz Filter and CMOS Receiver Front-End (2007)

A 10-GHz filter/receiver module is implemented in a novel 3-D integration technique suitable for RF and microwave circuits. The receiver designed and fabricated in a commercial 0.18-mum CMOS process is integrated with embedded passive components fabricated on a high-resistivity Si substrate using a recently developed self-aligned wafer-level integration technology. Integration with the filter is achieved through bonding a high-Q evanescent-mode cavity filter onto the silicon wafer using screen printable conductive epoxy. With adjustment of the input matching of the receiver integrated circuit by the embedded passives fabricated on the Si substrate, the return loss, conversion gain, and noise figure of the front-end receiver are improved. At RF frequency of 10.3 GHz and with an IF frequency of 50 MHz, the integrated front-end system achieves a conversion gain of 19 dB, and an overall noise figure of 10 dB. A fully integrated filter/receiver on an Si substrate that operates at microwave frequencies is demonstrated.
Expression of fully and under-glycosylated forms of MUC1 mucin in gastric carcinoma (1998)

The membrane-bound MUC1 mucin is expressed in normal mucosas and the aberrant expression of its under-glycosylated forms has been reported in carcinomas from different sites. Several studies have provided conflicting evidence regarding the relationship between MUC1 expression and outcome in cancer patients. In this study, we investigated the immunohistochemical expression of MUC1 epitopes, using 2 monoclonal antibodies (MAbs): HMFG1, which reacts with the fully glycosylated MUC1, was studied in 73 gastric carcinomas; and SM3, which recognises an under-glycosylated form of MUC1, was studied in 180 cases. HMFG1 stained the antrum foveolar cells and the body glands of normal gastric mucosa, whereas SM3 reactivity was restricted to the perinuclear region of some foveolar cells. Type I intestinal metaplasia exhibited down-regulation of MUC1 expression using both MAbs. Every gastric carcinoma was stained with HMFG1 and 80% with SM3. High levels of expression of HMFG1 were associated with lymphatic invasion, nodal metastatization, and advanced pTNM staging. The expression of SM3 was associated with the histologic (solid) type of carcinoma, expanding growth pattern, wall penetration, lymphatic invasion and age of the patients. Despite a trend for a poor outcome in patients with tumours (over)expressing MUC1 mucin, the survival of the patients evaluated by univariate and multivariate analysis was not significantly associated with the levels of expression of HMFG1 or with the expression of the SM3 epitope. We conclude that (a) MUC1 expression, namely of the SM3 cancer-associated epitope, is significantly associated with several aspects of gastric cancer development and progression; and (b) MUC1 expression should not be used as a prognostic marker in patients with gastric carcinoma.
Magnetic-resonance-imaging–coupled broadband near-infrared tomography system for small animal brain studies (2005)

A novel magnetic-resonance-coupled broadband near-infrared (NIR) tomography system for small animal brain studies is described. Several features of the image formation approach are new in NIR tomography and represent major advances in the path to recovering high-resolution hemoglobin and oxygen saturation images of tissue. The NIR data were broadband and continuous wave and were used along with a second-derivative-based estimation of the path length from water absorption. The path length estimation from water was then used along with the attenuation spectrum to recover absorption and reduced scattering coefficient images at multiple wavelengths and then to recover images of total hemoglobin and oxygen saturation. Going beyond these basics of NIR tomography, software has been developed to allow inclusion of structures derived from MR imaging (MRI) for the external and internal tissue boundaries, thereby improving the accuracy and spatial resolution of the properties in each tissue type. The system has been validated in both tissue-simulating phantoms, with 10% accuracy observed, and in a rat cranium imaging experiment. The latter experiment used variation in inspired oxygen (FiO2) to vary the observed hemoglobin and oxygen saturation images. Quantitative agreement was observed between the changes in deoxyhemoglobin values derived from NIR and the changes predicted with blood-oxygen-level-dependent (BOLD) MRI. This system represents the initial stage in what will likely be a larger role for NIR tomography, coupled to MRI, and illustrates that the technological challenges of using continuous-wave broadband data and inclusion of a priori structural information can be met with careful phantom studies.
Quantitative visualization of combustion species in a plane (1982)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text George Kychakoff, Robert D. Howe, Ronald K. Hanson, and James C. McDaniel, "Quantitative visualization of combustion species in a plane," Appl. Opt. 21, 3225-3227 (1982) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Classification of crystalline topological insulators and superconductors with point group symmetries (2019)

Crystalline topological phases have recently attracted a lot of experimental and theoretical attention. Key advances include the complete elementary band representation analyses of crystalline matter by symmetry indicators and the discovery of higher-order hinge and corner states. However, current classification schemes of such phases are either implicit or limited in scope. We present a scheme for the explicit classification of crystalline topological insulators and superconductors. These phases are protected by crystallographic point group symmetries and are characterized by bulk topological invariants. The classification paradigm generalizes the Clifford algebra extension process of each Altland-Zirnbauer symmetry class and utilizes algebras which incorporate the point group symmetry. Explicit results for all point group symmetries of three-dimensional crystals are presented as well as for all symmorphic layer groups of two-dimensional crystals. We discuss future extensions for treatment of magnetic crystals and defected or higher-dimensional systems as well as weak and fragile invariants.