gebhart/patrepeval huggingface dataset:
Molecular spectroscopy and dynamics of intrinsically fluorescent proteins: Coral red (dsRed) and yellow (Citrine) (2000)

Gene expression of intrinsically fluorescent proteins in biological systems offers new noninvasive windows into cellular function, but optimization of these probes relies on understanding their molecular spectroscopy, dynamics, and structure. Here, the photophysics of red fluorescent protein (dsRed) from discosoma (coral), providing desired longer emission/absorption wavelengths, and an improved yellow fluorescent protein mutant (Citrine) (S65G/V68L/Q69 M/S72A/T203Y) for significant comparison, are characterized by using fluorescence correlation spectroscopy and time-correlated single-photon counting. dsRed fluorescence decays as a single exponential with a 3.65 +/- 0.07-ns time constant, indicating a single emitting state/species independent of pH 4.4-9.0, in contrast with Citrine. However, laser excitation drives reversible fluorescence flicker at 10(3)-10(4) Hz between dark and bright states with a constant partition fraction f(1) = 0.42 +/- 0.06 and quantum yield of approximately 3 x 10(-3). Unlike Citrine (pKa approximately 5.7), pH-dependent proton binding is negligible (pH 3. 9-11) in dsRed. Time-resolved anisotropy of dsRed reveals rapid depolarization (211 +/- 6 ps) plus slow rotational motion (53 +/- 8 ns), in contrast with a single rotational time (16 +/- 2 ns) for Citrine. The molecular dimensions, calculated from rotational and translational diffusion, indicate that dsRed is hydrodynamically 3.8 +/- 0.4 times larger than predicted for a monomer, which suggests an oligomer (possibly a tetramer) configuration even at approximately 10(-9) M. The fast depolarization is attributed to intraoligomer energy transfer between mobile nonparallel chromophores with the initial anisotropy implying a 24 +/- 3 degrees depolarization angle. Large two-photon excitation cross sections ( approximately 100 GM at 990 nm for dsRed and approximately 50 GM at 970 nm for Citrine), advantageous for two-photon-fluorescence imaging in cells, are measured.
Automobile Navigation: Where is it Going? (1987)

Automobile navigation systems based on dead reckoning, map matching, satellite positioning and other navigation technologies are under active development. ``Map intelligent'' systems achieve high relative accuracy by matching dead-reckoned paths with road geometry encoded in a digital map data base that may also serve other functions such as vehicle routing and geocoding. Satellite-based navigation systems achieve high absolute accuracy but require dead reckoning augmentation because of signal aberrations in the automotive environment. Future systems will probably include multiple navigation technologies. Issues influencing the design of future systems include safety concerns regarding the driver interface, and the future availability of comprehensive map data bases, real-time traffic data, and mobile data communication links necessary for on-board generation of optimum routes.
Decoherence limits to quantum computation using trapped ions (1997)

We investigate the problem of factorization of large numbers on a quantum computer which we imagine to be realized within a linear ion trap. We derive upper bounds on the size of the numbers that can be factorized on such a quantum computer. These upper bounds are independent of the power of the applied laser. We investigate two possible ways to implement qubits, in metastable optical transitions and in Zeeman sublevels of a stable ground state, and show that in both cases the numbers that can be factorized are not large enough to be of practical interest. We also investigate the effect of quantum error correction on our estimates and show that in realistic systems the impact of quantum error correction is much smaller than expected. Again no number of practical interest can be factorized.
Absence of an essential regulatory influence of the adenovirus E1B 19-kilodalton protein on viral growth and early gene expression in human diploid WI38, HeLa, and A549 cells (1994)

Mutations in the gene encoding the adenovirus (Ad) early region 1B 19-kDa protein (the 19K gene) result in multiple phenotypic effects upon infection of permissive human cells. It has been reported, for example, that Ad type 2 (Ad2) and Ad5 with mutations in the 19K gene (19K-defective mutants) have a marked growth advantage compared with wild-type virus in human diploid WI38 cells (E. White, B. Faha, and B. Stillman, Mol. Cell. Biol. 6:3763-3773, 1986), and it was proposed that this host range phenotype stems from the large increase in viral early gene expression reported to occur in the mutant-infected cells. These observations gave rise to the hypothesis that the 19-kDa protein (the 19K protein) normally functions as a negative regulator of Ad early gene expression and growth. We have tested this hypothesis and find that Ad5 and Ad12 wild-type viruses grow as efficiently as their respective 19K-defective mutants, in1 and dl337 and pm700 and in700, in WI38 and other human cell types. Neither the accumulation of E1A cytoplasmic mRNAs nor the synthesis of E1A and other viral early proteins in these cells is altered as a result of these mutations in the 19K gene, and we conclude that the 19K protein does not play an essential role in regulating viral early gene expression or viral growth in human cells.
Audiopad: A Tag-Based Interface For Musical Performance (2002)

We present Audiopad, an interface for musical performance that aims to combine the modularity of knob based controllers with the expressive character of multidimensional tracking interfaces. The performer's manipulations of physical pucks on a tabletop control a real-time synthesis process. The pucks are embedded with LC tags that the system tracks in two dimensions with a series of specially shaped antennae. The system projects graphical information on and around the pucks to give the performer sophisticated control over the synthesis process.
The mouse RANKL gene locus is defined by a broad pattern of histone H4 acetylation and regulated through distinct distal enhancers (2011)

RANKL is a stromal cell-derived tumor necrosis factor (TNF)-like factor that plays a primary role in osteoclast formation and function. Recent studies suggest that 1,25(OH)(2) D(3) induces Rankl expression via vitamin D receptor (VDR) interaction at several enhancers located up to 76 kb upstream of the gene's transcriptional start site (TSS). In the current studies, we explored these interactions further using ChIP-chip and RNA analysis. We confirm VDR and RXR binding to the five enhancers described previously and identify two additional sites, one located within the Rankl coding region. We also show that RNA polymerase II is recruited to these enhancers, most likely through transcription factors TBP, TFIIB, and TAF(II) 250. Interestingly, the recruitment of these factors leads to the production of RNA transcripts, although their role at present is unknown. We also discovered that histone H4 acetylation (H4ac) marks many upstream Rankl enhancers under basal conditions and that H4ac is increased upon 1,25(OH)(2) D(3) treatment. Surprisingly, the hormone also induces C/EBPβ binding across the Rankl locus. C/EBPβ binding correlates directly with increased H4ac activity following 1,25(OH)(2) D(3) treatment. Finally, elevated H4ac is restricted to an extended region located between two potential insulator sites occupied by CTCF and Rad21. These data suggest a mechanism whereby 1,25(OH)(2) D(3) functions via the VDR and C/EBPβ to upregulate Rankl expression.
GeoNet: Geometric Neural Network for Joint Depth and Surface Normal Estimation (2018)

In this paper, we propose Geometric Neural Network (GeoNet) to jointly predict depth and surface normal maps from a single image. Building on top of two-stream CNNs, our GeoNet incorporates geometric relation between depth and surface normal via the new depth-to-normal and normal-to-depth networks. Depth-to-normal network exploits the least square solution of surface normal from depth and improves its quality with a residual module. Normal-to-depth network, contrarily, refines the depth map based on the constraints from the surface normal through a kernel regression module, which has no parameter to learn. These two networks enforce the underlying model to efficiently predict depth and surface normal for high consistency and corresponding accuracy. Our experiments on NYU v2 dataset verify that our GeoNet is able to predict geometrically consistent depth and normal maps. It achieves top performance on surface normal estimation and is on par with state-of-the-art depth estimation methods.
Virus-induced polyclonal B cell activation improves protective CTL memoryvia retained CD27 expression on memory CTL (2005)

Different viruses elicit distinct phenotypes of memory cytotoxic T lymphocytes (CTL). This is reflected in differential expression of homing receptors and costimulatory molecules like CD27. Memory CTL retained CD27 following lymphocytic choriomeningitis virus (LCMV) infection, but not after immunization with recombinant vaccinia virus or tumor cells expressing LCMV glycoprotein. Stable CD27 expression on memory CTL required ligation by CD70 expressed on polyclonally activated B cells during the contraction phase. The functional consequence of CD27 expressed on virus-specific CTL was analyzed in CD27-deficient mice. LCMV infection of CD27(-/-) mice revealed that primary CTL activation and expansion as well as elimination of the virus were independent of CD27 expression. In contrast, ligation of CD27 on memory CTL upon secondary antigen encounter increased clonal expansion and improved protection against re-infection. This points to novel B cell-CTL interactions during viral infection and to a beneficial role of polyclonal B cell activation that represents a characteristic of murine LCMV, human immunodeficiency virus and human hepatitis B and C virus infection.
A New Nonhydrolytic Single-Precursor Approach to Surfactant-Capped Nanocrystals of Transition Metal Oxides (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA New Nonhydrolytic Single-Precursor Approach to Surfactant-Capped Nanocrystals of Transition Metal OxidesJörg Rockenberger, Erik C. Scher, and A. Paul AlivisatosView Author Information Department of Chemistry, Box 101 University of California, Berkeley, Berkeley California 94720 Cite this: J. Am. Chem. Soc. 1999, 121, 49, 11595–11596Publication Date (Web):November 24, 1999Publication History Received10 September 1999Published online24 November 1999Published inissue 1 December 1999https://pubs.acs.org/doi/10.1021/ja993280vhttps://doi.org/10.1021/ja993280vrapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views7246Altmetric-Citations652LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Metals,Nanocrystals,Nanoparticles,Oxides,Transmission electron microscopy Get e-Alerts
Escherichia coli DNA Topoisomerase III Is a Site-specific DNA Binding Protein That Binds Asymmetrically to Its Cleavage Site (1995)

The binding of DNA topoisomerase III (Topo III) to a single-stranded DNA substrate containing a strong cleavage site has been examined. The minimal substrate requirement for Topo III-catalyzed cleavage has been determined to consist of 7 bases; 6 bases 5' to the cleavage site and only 1 base 3' to the site. Nuclease P1 protection experiments indicate that the enzyme also binds to its substrate asymmetrically, protecting approximately 12 bases 5' to the cleavage site and only 2 bases 3' to the cleavage site. A catalytically inactive mutant of Topo III shows the same protection pattern as the active polypeptide, indicating that Topo III is a site-specific binding protein as well as a topoisomerase. Consistent with this view, an oligonucleotide containing a cleavage site is a more effective inhibitor and is bound more efficiently by Topo III than an oligonucleotide without a cleavage site.
Design, synthesis and biological evaluation of new molecules inhibiting epidermal growth factor receptor threonine790→ methionine790 mutant (2012)

A series of 5,8-dioxo-pyrimido[4,5-e][1,4]diazepine derivatives were designed and synthesized as new inhibitors against wild-type EGFR and a panel of mutants, including the clinical resistance related T790M mutants. One of the most potent compounds 2l inhibited all forms of EGFR evaluated with low nM IC50 values. It also strongly suppressed the proliferation of H1975 and HCC827 non-small cell lung cancer cells with IC50 values of 69 and 71 nM, respectively.
B-splines Algorithms for Solving Fredholm Linear Integro-Differential Equations (2004)

Algorithms using the second order of B -splines [B (x)] and the third order of B -splines [B,3(x)] are derived to solve 1' , 2nd and 3rd linear Fredholm integro-differential equations (F1DEs). These new procedures have all the useful properties of B -spline function and can be used comparatively greater computational ease and efficiency.The results of these algorithms are compared with the cubic spline function.Two numerical examples are given for conciliated the results of this method.
L-selectin and β7 integrin on donor CD4 T cells are required for the early migration to host mesenteric lymph nodes and acute colitis of graft-versus-host disease (2005)

The homing receptors L-selectin and alpha4beta7 integrin facilitate entry of T cells into the gut-associated organized lymphoid tissues such as the mesenteric lymph nodes and Peyer patches. We studied the impact of inactivation of genes encoding these receptors on the ability of purified donor CD4+ T cells to induce acute lethal graft-versus-host disease (GVHD) associated with severe colitis in irradiated major histocompatibility complex (MHC)-mismatched mice. Whereas lack of expression of a single receptor had no significant impact on the severity of colitis and GVHD, the lack of expression of both receptors markedly ameliorated colitis and early deaths observed with wild-type (WT) T cells. The changes in colitis and GVHD were reflected in a marked reduction in the early accumulation of donor T cells in the mesenteric lymph nodes and subsequently in the colon. The purified WT donor CD4+ T cells did not accumulate early in the Peyer patches and failed to induce acute injury to the small intestine. In conclusion, the combination of CD62L and beta7 integrin is required to induce acute colitis and facilitate entry of CD4+ donor T cells in the mesenteric nodes associated with lethal GVHD in allogeneic hosts.
Identification and molecular cloning of two new 30-kDa insulin-like growth factor binding proteins isolated from adult human serum (1991)

Three insulin-like growth factor binding proteins (IGFBP) with apparent molecular masses of 24, 28-30, and 30 kDa, nonreduced, have been isolated from human serum. The 15 NH2-terminal amino acids of the 24-kDa binding protein are identical with those of the 30-kDa BP. The apparent molecular mass of the latter is reduced to 24 kDa by N-glycanase, suggesting that the 30-kDa BP is the glycosylated form of the isolated 24-kDa BP. The complete amino acid sequences derived from the cloned cDNAs represent two new IGFBPs. They are tentatively termed IGFBP-4 and -5. The prepeptide sequences of BP-4 and -5 contain 27 and 21, the mature proteins 213 and 237 amino acids, respectively (Mr = 22,610 and 25,980). The NH2- and COOH-terminal thirds of BP-4 and -5 display pronounced homology to the other three human BPs. 16 of the 16-20 cysteines and 37 of the 213-289 amino acids (12.8-17.1%) are conserved in all five mature BPs. 10 amino acid positions located in the NH2-terminal region and shared by BP-1, -2, -3, and -5 are different in BP-4. These differences may account for the preferential affinity of BP-4 for IGF II. A most intriguing homology exists between the COOH-terminal quarter of the five IGFBPs, 10 repetitive domains of human thyroglobulin, a gastrointestinal tumor-associated antigen, and the invariant chain of the class II histocompatibility antigen. The cDNAs of five human IGFBPs are now available. They will allow their expression and production in sufficient quantities for in vivo studies to unravel their role in growth and metabolism.
Chemoenzymatic Synthesis of Fluorescent N‐Ras Lipopeptides and Their Use in Membrane Localization Studies in Vivo (1997)

Very small regions determine where lipoproteins accumulate in the cell. S-Farnesylated and S-palmitoylated N-Ras lipopeptides 1 accumulate specifically in the plasma membrane, as determined by investigations on fibroblast cells with fluorescence microscopy. (In the structure below the shaded circle symbolizes a fluorescent label). Peptides that were only S-farnesylated do not accumulate in the plasma membrane.
Applications of Silicon-Germanium Heterostructure Devices (2001)

The first book to deal with the design and optimization of transistors made from strained layers, Applications of Silicon-Germanium Heterostructure Devices combines three distinct topics-technology, device design and simulation, and applications-in a comprehensive way. Important aspects of the book include key technology issues for the growth of st
Tunable Single Mode Operation of Gas Lasers Using Intracavity Tilted Etalons (1969)

The use of a tilted solid etalon inside the resonator of a gas laser, for the purpose of obtaining a tunable single mode output from the laser, is described and analyzed. This technique is illustrated by single mode spectra and gain profiles obtained with various argon ion laser transitions.
Birth weight and body fat distribution in adolescent girls (1997)

In adolescent girls, the tendency to store fat on the trunk rather than the limbs, seems to be programmed by growth in fetal life, and is most evident in those who are overweight.
Nonviral Approach for Targeted Nucleic Acid Delivery (2012)

Despite their relatively lower efficiency, nonviral approaches are emerging as safer alternatives in gene therapy to viral vectors. Delivery of nucleic acids to the target site is an important factor for effective gene expression (plasmid DNA) or knockdown (siRNA) with minimal side effects. Direct deposition at the target site by physical methods, including ultrasound, electroporation and gene gun, is one approach for local delivery. For less accessible sites, the development of carriers that can home into the target tissue is required. Cationic peptides, lipoplexes, polyplexes and nanoplexes have been used as carriers for delivery of nucleic acids. Targeting ligands, such as cell targeting peptides, have also been applied to decorate delivery vehicles in order to enhance their efficacy. This review focuses on delivery strategies and recent progress in non-viral carriers and their modifications to improve their performance in targeting and transfection.
Nerves and nerve plexuses of the human vertebral column (1990)

The origin, distribution, and termination pattern of nerves supplying the vertebral column and its associated structures have been studied in the human fetus by means of an acetylcholinesterase whole-mount method. The vertebral column is surrounded by ventral and dorsal nerve plexuses which are interconnected. The ventral nerve plexus consists of the nerve plexus associated with the anterior longitudinal ligament. This longitudinally oriented nerve plexus has a bilateral supply from many small branches of the sympathetic trunk, rami communicantes, and perivascular nerve plexuses of segmental arteries. In the thoracic region, the ventral nerve plexus also is connected to the nerve plexuses of costovertebral joints. The dorsal nerve plexus is made up of the nerve plexus associated with the posterior longitudinal ligament. This nerve plexus is more irregular and receives contributions only from the sinu-vertebral nerves. The sinu-vertebral nerves originate from the rami communicantes and, in the cervical region, also from the nerve plexus of the vertebral artery. Thick and thin sinu-vertebral nerves are found. Most frequently three types of thick sinu-vertebral nerves are observed, i.e., ascending, descending, or dichotomizing ones. Finally, the distribution of the branches of the ventral and dorsal nerve plexuses and of the sinu-vertebral nerves is described.
Interferometry On Wolter X-Ray Optics: A Possible Approach (1989)

A novel interferometric approach for obtaining surface interferograms on Wolter-type optics is presented. A subaperture simulation experiment shows the data analysis steps required. A second, independent test basically confirms the simulation results. Splicing of the subaperture interferograms around the circumference is discussed.
VEGF via VEGF receptor-1 (Flt-1) mimics preeclamptic plasma in inhibiting uterine blood vessel relaxation in pregnancy: implications in the pathogenesis of preeclampsia. (1999)

Preeclampsia is a multisystem disorder characterized by hypertension and proteinuria. There is accumulating evidence that this is a disease of the endothelium, with an as-yet unidentified circulating factor, or factors, causing the observed alteration in vascular function. We previously reported that the function of myometrial vessels is altered on exposure to plasma from women with preeclampsia. Vascular endothelial growth factor (VEGF) is an angiogenic growth factor that acts via two high-affinity receptors (KDR and Flt-1), and its production is increased in preeclampsia. Here we report that VEGF and its Flt-1 receptor may play a pivotal role in the altered vascular function of preeclampsia. Myometrial resistance vessels were obtained at the time of cesarean section. Using the Mulvany wire myograph, the endothelium-dependent behavior of these vessels was studied. Incubation of vessels from pregnant women with VEGF resulted in a reduction of endothelium-dependent relaxation that mimicked the reduction induced by plasma from women with preeclampsia. The altered function that occurred upon exposure of vessels to VEGF or plasma from women with preeclampsia did not occur when plasma was incubated with antibodies to VEGF before vessel incubation. The presence of an anti-KDR receptor antibody had no effect on VEGF response. However, in the presence of an anti-Flt-1 receptor antibody, VEGF or plasma from women with preeclampsia no longer attenuated the endothelium-dependent relaxation (p < 0.05). The changes observed with VEGF and plasma from women with preeclampsia and their subsequent blockade with anti-VEGF antibody and anti-Flt-1 receptor antibody strongly suggest that VEGF acting through the Flt-1 receptor is pivotal in the pathogenesis of this disease.
The Jakinibs in systemic lupus erythematosus: progress and prospects (2018)

Inhibition of the JAK-STAT pathway is an attractive therapeutic option. The convenience of oral administration and lower production cost of the Jakinibs could replace the biological agents in the treatment hierarchy of autoimmune inflammatory diseases. Additional clinical data are needed; results of ongoing studies of the newer Jakinibs in cutaneous and non-life-threatening lupus are eagerly awaited.