gebhart/patrepeval huggingface dataset:
Human Cytomegaloviruses Expressing Yellow Fluorescent Fusion Proteins - Characterization and Use in Antiviral Screening (2010)

Recombinant viruses labelled with fluorescent proteins are useful tools in molecular virology with multiple applications (e.g., studies on intracellular trafficking, protein localization, or gene activity). We generated by homologous recombination three recombinant cytomegaloviruses carrying the enhanced yellow fluorescent protein (EYFP) fused with the viral proteins IE-2, ppUL32 (pp150), and ppUL83 (pp65). In growth kinetics, the three viruses behaved all like wild type, even at low multiplicity of infection (MOI). The expression of all three fusion proteins was detected, and their respective localizations were the same as for the unmodified proteins in wild-type virus-infected cells. We established the in vivo measurement of fluorescence intensity and used the recombinant viruses to measure inhibition of viral replication by neutralizing antibodies or antiviral substances. The use of these viruses in a pilot screen based on fluorescence intensity and high-content analysis identified cellular kinase inhibitors that block viral replication. In summary, these viruses with individually EYFP-tagged proteins will be useful to study antiviral substances and the dynamics of viral infection in cell culture.
Structure of a heparin-dependent complex of Hedgehog and Ihog (2006)

Hedgehog (Hh) signaling molecules mediate key tissue-patterning events during animal development, and inappropriate activation of Hh signaling in adults has been associated with human cancers. Recently, a conserved family of type I integral membrane proteins required for normal response to the Hh signal was discovered. One member of this family, Ihog (interference hedgehog), functions upstream or at the level of Patched (Ptc), but how Ihog participates in Hh signaling remains unclear. Here, we show that heparin binding induces Ihog dimerization and is required to mediate high-affinity interactions between Ihog and Hh. We also present crystal structures of a Hh-binding fragment of Ihog, both alone and complexed with Hh. Heparin is not well ordered in these structures, but a basic cleft in the first FNIII domain of Ihog (IhogFn1) is shown by mutagenesis to mediate heparin binding. These results establish that Hh directly binds Ihog and provide the first demonstration of a specific role for heparin in Hh responsiveness.
Supporting wilderness search and rescue using a camera‐equipped mini UAV (2007)

Abstract Wilderness Search and Rescue (WiSAR) entails searching over large regions in often rugged remote areas. Because of the large regions and potentially limited mobility of ground searchers, WiSAR is an ideal application for using small (human‐packable) unmanned aerial vehicles (UAVs) to provide aerial imagery of the search region. This paper presents a brief analysis of the WiSAR problem with emphasis on practical aspects of visual‐based aerial search. As part of this analysis, we present and analyze a generalized contour search algorithm, and relate this search to existing coverage searches. Extending beyond laboratory analysis, lessons from field trials with search and rescue personnel indicated the immediate need to improve two aspects of UAV‐enabled search: How video information is presented to searchers and how UAV technology is integrated into existing WiSAR teams. In response to the first need, three computer vision algorithms for improving video display presentation are compared; results indicate that constructing temporally localized image mosaics is more useful than stabilizing video imagery. In response to the second need, a goal‐directed task analysis of the WiSAR domain was conducted and combined with field observations to identify operational paradigms and field tactics for coordinating the UAV operator, the payload operator, the mission manager, and ground searchers. © 2008 Wiley Periodicals, Inc.
AlN HTCC super miniaturized millimeterwave transceiver MCMs, the novel structure for the high reliability, the high performance and the mass productivity (2003)

NEC has developed a novel structure of millimeterwave multi-chip-modules (MCMs) for the radiocommunications systems based on the aluminum nitride (AlN) high temperature cofired ceramic (HTCC). This package has the LCC and a waveguide I/O structure. We realized both excellent electrical performance and high reliability with more than 10-years of MTTF, for 1.37 inch/spl times/1.37 inch size of the super miniaturized and extremely simplified structure.
<i>In situ</i>transmission electron microscopy imaging of grain growth in a platinum nanobridge induced by electric current annealing (2011)

We report an in situ transmission electron microscopy (TEM) imaging of grain growth in a Pt nanobridge induced by a high electric current density. The change in morphology at the nanoscale was recorded in real time together with the electrical characterization of the Pt nanobridge. We find a drop in the differential resistance as the voltage across the bridge is increased; TEM inspection shows that this coincides with thermally induced grain growth, indicating that a reduction of grain boundary scattering is the cause of the resistance decrease.
Inhibition of ICE-Related Proteases (Caspases) and Nuclear Apoptosis by Phenylarsine Oxide (1997)

Biochemical analyses of nuclear apoptosis in vitro have revealed the existence of multiple active interleukin-1beta-converting enzyme-related proteases (caspases) with distinct substrate recognition properties in extracts of preapoptotic chicken DU249 cells (S/M extracts). Previously we demonstrated that the activity of a caspase that cleaves lamins is required for the disintegration of nuclei in the late stages of apoptosis, despite the presence of a second active caspase that cleaves poly(ADP-ribose) polymerase (PARP). One simple explanation for this observation was that the lamin-cleaving caspase is sufficient to drive the nuclear events of apoptotic execution. Here, we report that phenylarsine oxide (PAO) inhibits the protease activities of recombinant human caspases as well as endogenous chicken caspases that are active in S/M extracts. PAO at 100 microM blocks the morphological changes of nuclear apoptosis in vitro and internucleosomal DNA fragmentation in S/M extracts without interfering with PARP or lamin A cleavage. Thus, lamin cleavage is not sufficient to drive the changes in nuclear morphology characteristic of apoptosis. Affinity labeling with YV(bio)KD-aomk shows that the degree of sensitivity to PAO differs among active caspases in S/M extracts. These results suggest that a PAO-sensitive caspase that is distinct from the PARP- or lamin-cleaving enzymes is required for the initiation of apoptotic morphological changes and for the activation of endonuclease(s). Taken together, our results suggest that two or more caspases are required for proteolytic events that are essential for the initiation and completion of nuclear apoptotic changes. The observation that PAO is an inhibitor of caspases and nuclear apoptotic events should be useful for the biochemical dissection of apoptosis in vitro and in vivo.
Reaction of Human Monoclonal Antibodies to SARS-CoV-2 Proteins With Tissue Antigens: Implications for Autoimmune Diseases (2021)

We sought to determine whether immune reactivity occurs between anti-SARS-CoV-2 protein antibodies and human tissue antigens, and whether molecular mimicry between COVID-19 viral proteins and human tissues could be the cause. We applied both human monoclonal anti-SARS-Cov-2 antibodies (spike protein, nucleoprotein) and rabbit polyclonal anti-SARS-Cov-2 antibodies (envelope protein, membrane protein) to 55 different tissue antigens. We found that SARS-CoV-2 antibodies had reactions with 28 out of 55 tissue antigens, representing a diversity of tissue groups that included barrier proteins, gastrointestinal, thyroid and neural tissues, and more. We also did selective epitope mapping using BLAST and showed similarities and homology between spike, nucleoprotein, and many other SARS-CoV-2 proteins with the human tissue antigens mitochondria M2, F-actin and TPO. This extensive immune cross-reactivity between SARS-CoV-2 antibodies and different antigen groups may play a role in the multi-system disease process of COVID-19, influence the severity of the disease, precipitate the onset of autoimmunity in susceptible subgroups, and potentially exacerbate autoimmunity in subjects that have pre-existing autoimmune diseases. Very recently, human monoclonal antibodies were approved for use on patients with COVID-19. The human monoclonal antibodies used in this study are almost identical with these approved antibodies. Thus, our results can establish the potential risk for autoimmunity and multi-system disorders with COVID-19 that may come from cross-reactivity between our own human tissues and this dreaded virus, and thus ensure that the badly-needed vaccines and treatments being developed for it are truly safe to use against this disease.
Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products (2014)

Metagenomics is a valuable tool for the study of microbial communities but has been limited by the difficulty of "binning" the resulting sequences into groups corresponding to the individual species and strains that constitute the community. Moreover, there are presently no methods to track the flow of mobile DNA elements such as plasmids through communities or to determine which of these are co-localized within the same cell. We address these limitations by applying Hi-C, a technology originally designed for the study of three-dimensional genome structure in eukaryotes, to measure the cellular co-localization of DNA sequences. We leveraged Hi-C data generated from a simple synthetic metagenome sample to accurately cluster metagenome assembly contigs into groups that contain nearly complete genomes of each species. The Hi-C data also reliably associated plasmids with the chromosomes of their host and with each other. We further demonstrated that Hi-C data provides a long-range signal of strain-specific genotypes, indicating such data may be useful for high-resolution genotyping of microbial populations. Our work demonstrates that Hi-C sequencing data provide valuable information for metagenome analyses that are not currently obtainable by other methods. This metagenomic Hi-C method could facilitate future studies of the fine-scale population structure of microbes, as well as studies of how antibiotic resistance plasmids (or other genetic elements) mobilize in microbial communities. The method is not limited to microbiology; the genetic architecture of other heterogeneous populations of cells could also be studied with this technique.
One-Pot Synthesis of Mo<sup>0</sup> Dinitrogen Complexes Possessing Monodentate and Multidentate Phosphine Ligands (2012)

Mo(0) dinitrogen complexes bearing electron-rich mono- and bidentate phosphines can be synthesized in good yields from inexpensive and readily accessible MoCl(5) via a one-step mild reduction with Mg metal. trans-[(N(2))(2)Mo(PMePh(2))(PPh(CH(2)CH(2)PPh(2))(2))] can also be obtained via this strategy. However, in the presence of tri- and tetradentate ligands that are sterically restrictive, the analogous reduction leads to either (η(6)-arene) formation or [Mo(multidentate phosphine)(m)](n) oligomer complexes that have no dinitrogen ligands. One such η(6)-arene complex, where the Mo(0) center is ligated by 1,1,1-tris(diphenylphosphinomethyl)ethane, was isolated and characterized via X-ray crystallography.
Measuring Unilateral Otolith Function Via the Otolith-ocular Response and the Subjective Visual Vertical (2001)

In the present study, attention is directed to the unilateral response of the otolith system to static and dynamic tilt, as reflected by subjective estimation of the visual vertical (oculogravic perception). Measurements were performed with a variable radius rotary chair, which permits controlled modulation of the centripetal, or radial, acceleration. By limiting the radius, i.e. eccentric displacement of the head by 3.5 cm during constant-velocity rotation about the earth-vertical axis, adequate unilateral stimulation of the otolith organ--predominantly the utricle--is generated, without involving the semicircular canals. This paradigm has been employed to measure the unilateral utriculo-ocular response. In contrast to the otolith-ocular response (OOR), the subjective visual vertical (SVV) reflects the processing of otolithic information in the higher brain centres (thalamus, vestibular cortex). Exploitation of these two complementary approaches provides useful information for both experimental and clinical scientists. The findings also reveal that centripetal acceleratory stimulation during constant angular velocity with the subject centred on axis is sufficient to localize peripheral otolith dysfunction by means of SVV estimation. This represents a novel test of otolith function that can be easily integrated into routine clinical testing.
Optimality of beamforming in fading MIMO multiple access channels (2009)

We consider the sum capacity of a multi-input multi-output (MIMO) multiple access channel (MAC) where the receiver has the perfect channel state information (CSI), while the transmitters have either no or partial CSI. When the transmitters have partial CSI, it is in the form of either the covariance matrix of the channel or the mean matrix of the channel. For the covariance feedback case, we mainly consider physical models that result in single-sided correlation structures. For the mean feedback case, we consider physical models that result in in-phase received signals. Under these assumptions, we analyze the MIMO-MAC from three different viewpoints. First, we consider a finite-sized system. We show that the optimum transmit directions of each user are the eigenvectors of its own channel covariance and mean feedback matrices, in the covariance and mean feedback models, respectively. Also, we find the conditions under which beamforming is optimal for all users. Second, in the covariance feedback case, we prove that the region where beamforming is optimal for all users gets larger with the addition of new users into the system. In the mean feedback case, we show through simulations that this is not necessarily true. Third, we consider the asymptotic case where the number of users is large. We show that in both no and partial CSI cases, beamforming is asymptotically optimal. In particular, in the case of no CSI, we show that a simple form of beamforming, which may be characterized as an arbitrary antenna selection scheme, achieves the sum capacity. In the case of partial CSI, we show that beamforming in the direction of the strongest eigenvector of the channel feedback matrix achieves the sum capacity. Finally, we generalize our covariance feedback results to double-sided correlation structures in the Appendix.
Diffuse glioma growth: a guerilla war (2007)

In contrast to almost all other brain tumors, diffuse gliomas infiltrate extensively in the neuropil. This growth pattern is a major factor in therapeutic failure. Diffuse infiltrative glioma cells show some similarities with guerilla warriors. Histopathologically, the tumor cells tend to invade individually or in small groups in between the dense network of neuronal and glial cell processes. Meanwhile, in large areas of diffuse gliomas the tumor cells abuse pre-existent "supply lines" for oxygen and nutrients rather than constructing their own. Radiological visualization of the invasive front of diffuse gliomas is difficult. Although the knowledge about migration of (tumor)cells is rapidly increasing, the exact molecular mechanisms underlying infiltration of glioma cells in the neuropil have not yet been elucidated. As the efficacy of conventional methods to fight diffuse infiltrative glioma cells is limited, a more targeted ("search & destroy") tactic may be needed for these tumors. Hopefully, the study of original human glioma tissue and of genotypically and phenotypically relevant glioma models will soon provide information about the Achilles heel of diffuse infiltrative glioma cells that can be used for more effective therapeutic strategies.
Immunotoxins to the murine transferrin receptor: intracavitary therapy of mice bearing syngeneic peritoneal tumors. (1987)

Two rat monoclonal antibodies to the murine transferrin receptor (TFR) were each conjugated to recombinant ricin toxin A chain (rRTA). The monoclonal antibodies, R17 217 and YE1/9.9, bound to partially overlapping antigenic determinants on the murine TFR that were distinct from the transferrin binding site. Immunotoxins R17 217-rRTA and YE1/9.9-rRTA were potent cytotoxins for mouse cell lines in vitro. Animal toxicity studies showed that they were 10 to 20 times more toxic to mice than were control immunotoxins, including the anti-human-TFR immunotoxin 454A12-rRTA. The mouse toxicity of i.p. injected R17 217-rRTA could be partially blocked by the i.p. or i.v. administration of unconjugated R17 217 monoclonal antibody. I.p. but not i.v. administration of antimouse-TFR immunotoxins prolonged the survival of mice given implants of syngeneic peritoneal P388D1 lymphoid tumors. The anti-mouse-TFR immunotoxins killed at least 99.9% of the P388D1 tumor cells in vivo. In addition, i.p. treatment with immunotoxin R17 217-rRTA was able to prolong the survival of mice given an implant of a murine ovarian teratocarcinoma. The results show that anti-TFR immunotoxins can be efficacious in homologous species when the tumor is confined to a specific body cavity and immunotoxin can be delivered into that cavity.
Preparation and reactions of steroidal cross-conjugated 3-nitrones (1982)

Treatment of the N-methylnitrone (1b) of dichlorisone acetate (E–Z-mixture) with toluene-p-sulphonyl chloride in pyridine in the presence of water gave dichlorisone acetate (1a)(88%). In the presence of hydrogen sulphide, however, the nitrone was deoxygenated to give the corresponding imine (1c), which on prolonged reaction with hydrogen sulphide in pyridine afforded the corresponding 1,4-diene-3-thione (1d). Similarly prepared were the unstable imines (2d), (3c), and (4c), which were smoothly converted into the corresponding thiones (2e), (3d), and (4d), respectively. In the absence of strong nucleophiles, dichlorisone acetate nitrone (1b) was treated with toluene-p-sulphonyl chloride in pyridine to give the corresponding trienimine (1g)(45%). Under similar conditions, however, prednisolone-21-propionate nitrone (3b) gave the 2-p-tolylsulphonyloxy-derivative (3e) as the major product. Separate treatment of both Z- and E-isomers of dehydrotestosterone acetate nitrone [(2b) and (2c)] afforded, in both cases, the 2-p-tolylsulphonyloxy-derivative (2g)(25%), whereas betamethasone nitrone (4b) gave a mixture of the 2-p-tolylsulphonyloxy-dienimine (4f) and the trienimine (4h) in low yield.
Simple procedure for measuring neutrophil chemiluminescence (1981)

A simple method is described whereby measurement of neutrophil chemiluminescence was performed at variable reaction temperatures even though the scintillation counting chamber was refrigerated.
A Comprehensive Gold Standard for the Enron Organizational Hierarchy (2012)

Many researchers have attempted to predict the Enron corporate hierarchy from the data. This work, however, has been hampered by a lack of data. We present a new, large, and freely available gold-standard hierarchy. Using our new gold standard, we show that a simple lower bound for social network-based systems outperforms an upper bound on the approach taken by current NLP systems. 1
Molecular cloning of the gene for bilirubin oxidase from Myrothecium verrucaria and its expression in yeast. (1993)

Myrothecium verrucaria bilirubin oxidase (EC 1.3.3.5) is an enzyme catalyzing the oxidation of bilirubin to biliverdin and other substrates. We have purified bilirubin oxidase from the medium of M. verrucaria and determined its partial amino acid sequence and isolated cDNA fragment amplified by polymerase chain reaction using oligonucleotide primers designed on the basis of the partial amino acid sequence. The gene for bilirubin oxidase has been cloned from a genomic library using the cDNA fragment as a probe. The gene encodes a precursor of bilirubin oxidase consisting of 572 amino acid residues, which comprises the prepro-region of 38 amino acid residues and the mature enzyme of 534 amino acid residues containing one cysteine. Five introns were found within the coding region. Sequence comparison of bilirubin oxidase with other blue copper proteins (laccase, ascorbate oxidase, human ceruloplasmin, plastocyanin, and azurin) revealed the presence of four domains corresponding to potential copper ligands. We have expressed this bilirubin oxidase gene in Saccharomyces cerevisiae under the repressible acid phosphatase promotor and found an active recombinant bilirubin oxidase, establishing the functional identity of the gene.
Regulation of Catechol-O-Methyltransferase Expression in Human Myometrial Cells (2006)

Catechol-O-methyltransferase expression may be regulated in the myometrium to control the local action of estrogen. Low levels of catechol-O-methyltransferase in the myometrium would result in an accumulation of 2-hydroxyestrogen and may antagonize the local effect of estrogen. High levels of catechol-O-methyltransferase in the myometrium would result in lower levels of 2-hydroxyestrogen and may increase sensitivity to estrogen.
REVIEWS OF BOOKS (1949)

REVIEWS OF BOOKS Get access EARLY CHAMBER MUSIC. By Ruth Halle Rowen. ( King's Crown Press, New York, 1949. Pp. 188.) G. S. DICKINSON G. S. DICKINSON Search for other works by this author on: Oxford Academic Google Scholar The Musical Quarterly, Volume XXXV, Issue 4, October 1949, Pages 638–640, https://doi.org/10.1093/mq/XXXV.4.638 Published: 01 October 1949
Near-contact Hydrodynamics of Two Viscous Drops (1989)

The hydrodynamic force resisting the relative motion of two drops moving along their line‐of‐centers is determined for Stokes flow conditions. The drops are assumed to be in near‐contact and to have sufficiently high interfacial tension that they remain spherical. The squeeze flow in the narrow gap between the drops is analyzed using lubrication theory, and the flow within the drops near the axis of symmetry is analyzed using a boundary integral technique. The two flows are coupled through the nonzero tangential stress and velocity at the interface.Depending on the ratio of drop viscosity to that of the continuous phase, and also on the ratio of the distance between the drops to their reduced radius, three possible flow situations arise, corresponding to nearly rigid drops, drops with partially mobile interfaces, and drops with fully mobile interfaces. The results for the resistance functions are in good agreement with an earlier series solution using bispherical coordinates. The new results for near‐cont...