gebhart/patrepeval huggingface dataset:
Phosphorylation of the Transcription Factor Forkhead Family Member FKHR by Protein Kinase B (1999)

Protein kinase B lies "downstream" of phosphatidylinositide (PtdIns) 3-kinase and is thought to mediate many of the intracellular actions of insulin and other growth factors. Here we show that FKHR, a human homologue of the DAF16 transcription factor in Caenorhabditis elegans, is rapidly phosphorylated by human protein kinase Balpha (PKBalpha) at Thr-24, Ser-256, and Ser-319 in vitro and at a much faster rate than BAD, which is thought to be a physiological substrate for PKB. The same three sites, which all lie in the canonical PKB consensus sequences (Arg-Xaa-Arg-Xaa-Xaa-(Ser/Thr)), became phosphorylated when FKHR was cotransfected with either PKB or PDK1 (an upstream activator of PKB). All three residues became phosphorylated when 293 cells were stimulated with insulin-like growth factor 1 (IGF-1). The IGF-1-induced phosphorylation was abolished by the PtdIns 3-kinase inhibitor wortmannin but not by PD 98059 (an inhibitor of the mitogen-activated protein kinase cascade) or by rapamycin. These results indicate that FKHR is a physiological substrate of PKB and that it may mediate some of the physiological effects of PKB on gene expression. DAF16 is known to be a component of a signaling pathway that has been partially dissected genetically and includes homologues of the insulin/IGF-1 receptor, PtdIns 3-kinase and PKB. The conservation of Thr-24, Ser-256, and Ser-319 and the sequences surrounding them in DAF16 therefore suggests that DAF16 is also a direct substrate for PKB in C. elegans.
DNA Handles for Single Molecule Experiments (2000)

We have worked out a procedure for covalent binding of DNA to polystyrene microspheres for optical tweezers experiments in aqueous buffer solutions. These new coupling procedures allow preparation of DNA-microspheres in advance and storage of these beads for months. The covalent coupling of the DNA fragments facilitates the investigation of short DNA fragments (<1000 bp) and the rotationally constraint fixation of individual DNA strands with force-measuring laser tweezers. DNA-protein interactions have been investigated and the mechanical properties of individual RecA-DNA filaments have been characterized. Furthermore, DNA handles were attached to proteins to enable future probing of individual single proteins.
Wirkung von Distamycin A und Netropsin auf normale und zellwandlose Zellen von Escherichia coli W1655F+ (1974)

Abstract Distamycin A and netropsin are basic oligopeptide antibiotics. Though the chemical structure of both antibiotics is very similar, the action on grampositive and gramnegative bacteria is quite different. Distamycin A acts only on grampositive bacteria, while netropsin inhibits grampositive as well as gramnegative bacteria. Our experiments with the normal rod form and the stable protoplast type L‐form of E. coli W1655F + have shown that distamycin A inhibits gramnegative bacteria to the same extent as netropsin, when wall‐less L‐form‐ells were used. The normal rod cells were inhibited by netropsin only. That means that the wall prevents the penetration of distamycin A as reported earlier for the macrolid antibiotics, actinomycin C and kirromycin.
A 5-Gbit/s CMOS Optical Receiver With Integrated Spatially Modulated Light Detector and Equalization (2010)

This paper presents an optical receiver with a monolithically integrated photodetector in 0.18-μm CMOS technology using a combination of spatially modulated light (SML) detection and an analog equalizer. A transimpedance amplifier employing negative Miller capacitance is introduced to increase its bandwidth without causing gain peaking. To provide sufficient reverse-bias voltage to the photodetector's p-n junction, the transimpedance amplifier is operated with a 3.3-V supply, while the rest of the circuit blocks is powered with a 1.8-V supply. The on-chip SML detector achieves a net responsivity of 0.052 A/W. Occupying a core area of 0.72 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , the fully integrated optical receiver achieves 4.25 and 5 Gbits/s with power consumption values of 144 and 183 mW, respectively.
Scanning Confocal Optical Microscopy and Magnetic Resonance on Single Defect Centers (1997)

The fluorescence of individual nitrogen-vacancy defect centers in diamond was observed with room-temperature scanning confocal optical microscopy. The centers were photostable, showing no detectable change in their fluorescence emission spectrum as a function of time. Magnetic resonance on single centers at room temperature was shown to be feasible. The magnetic resonance spectra revealed marked changes in zero-field splitting parameters among different centers. These changes were attributed to strain-induced differences in the symmetry of the centers.
Suppression of the breakthrough of human immunodeficiency virus type 1 (HIV-1) in cell culture by thiocarboxanilide derivatives when used individually or in combination with other HIV-1-specific inhibitors (i.e., TSAO derivatives). (1995)

Five structurally related thiophene and furane analogues of the oxathiin carboxanilide derivative NSC 615985 (UC84) (designated UC10, UC68, UC81, UC42, and UC16) were identified as potent inhibitors of HIV-1 replication in cell culture and HIV-1 reverse transcriptase activity. These compounds were markedly active against a series of mutant HIV-1 strains, containing the Leu-100-->Ile, Val-106-->Ala, Glu-138-->Lys, or Tyr-181-->Cys mutations in their reverse transcriptase. However, the thiocarboxanilide derivatives selected for mutations at amino acid positions 100 (Leu-->Ile), 101 (Lys-->Ile/Glu), 103 (Lys-->Thr/Asp) and 141 (Gly-->Glu) in the HIV-1 reverse transcriptase. The compounds completely suppressed HIV-1 replication and prevented the emergence of resistant virus strains when used at 1.3-6.6 microM--that is, 10- to 25-fold lower than the concentration required for nevirapine and bis(heteroaryl)piperazine (BHAP) U90152 to do so. If UC42 was combined with the [2',5'-bis-O-(tert-butyldimethylsilyl)-3'-spiro-5"-(4"-amino-1",2"- oxathiole-2",2"-dioxide)]-beta-D-pentofuranosyl (TSAO) derivative of N3-methylthymine (TSAO-m3T), virus breakthrough could be prevented for a much longer time, and at much lower concentrations, than if the compounds were used individually. Virus breakthrough could be suppressed for even longer, and at lower drug concentrations, if BHAP was added to the combination of UC42 with TSAO-m3T, which points to the feasibility of two- or three-drug combinations in preventing virus breakthrough and resistance development.
Iron Transport and Storage Proteins (1980)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Fair allocation of elastic traffic for a wireless base station (2003)

Increasingly deployed cellular wireless systems can often become the bottleneck of the network so the fair allocation of the capacity of a wireless base station becomes important. We present a simple allocation mechanism which distributes the capacity of a base station in a fair manner, and show how it can simply be extended to compensate for the losses on the air interface. Using partial or full compensation, it is possible to be fair not in allocations, but in user goodput. Through simulations we analyse the impact of i.i.d. and bursty losses and the effects of fully and semi-reliable ARQ protocols at the link layer.
Uniform Thin Films on Optical Fibers by Plasma-Enhanced Chemical Vapor Deposition: Fabrication, Mie Scattering Characterization, and Application to Microresonators (2018)

We demonstrate deposition of azimuthally uniform single- or multiple-layer thin films of silicon nitride and silica on fibers using plasma-enhanced chemical vapor deposition by continuously rotating the fibers during growth. Our fibers exhibit distinctive and uniform iridescence that strongly depends on coating configuration. We also report a non-invasive technique to measure refractive index and film thickness of coated fibers simultaneously based on Mie scattering. We found the films grown on fibers have very different characteristics from those grown on flat substrates. We deposit a 1-μm-thick SiN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> film on a spheroidal microrod resonator, which is shown numerically to push the guided fundamental mode into the silica core. We demonstrate a Q factor of 2.2 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> , indicating reasonably good thin film quality that could be further increased with improved process control. Our technique can be applied to coat whispering gallery mode microresonators with engineered (e.g., step, graded, or stratified) refractive index profiles, which are expected to enable many new applications.
Infant acute lymphoblastic leukaemia with t(11;19) (1990)

Seven cases of infant acute lymphoblastic leukaemia with t(11; 19) (q23; p13) are described. They are characterized by a high white cell count, organomegaly, early central nervous system (CNS) disease, and a poor prognosis. Blasts are usually of an immature early B-cell lineage although monocytoid features are present in some cases. The characteristics of infant acute leukaemia with t(11; 19) are very similar to those found with t(4; 11), and the presence of t(11; 19) may indicate the same poor prognosis.
Human tRNA-derived small RNAs in the global regulation of RNA silencing (2010)

Competition between mammalian RNAi-related gene silencing pathways is well documented. It is therefore important to identify all classes of small RNAs to determine their relationship with RNAi and how they affect each other functionally. Here, we identify two types of 5'-phosphate, 3'-hydroxylated human tRNA-derived small RNAs (tsRNAs). tsRNAs differ from microRNAs in being essentially restricted to the cytoplasm and in associating with Argonaute proteins, but not MOV10. The first type belongs to a previously predicted Dicer-dependent class of small RNAs that we find can modestly down-regulate target genes in trans. The 5' end of type II tsRNA was generated by RNaseZ cleavage downstream from a tRNA gene, while the 3' end resulted from transcription termination by RNA polymerase III. Consistent with their preferential association with the nonslicing Argonautes 3 and 4, canonical gene silencing activity was not observed for type II tsRNAs. The addition, however, of an oligonucleotide that was sense to the reporter gene, but antisense to an overexpressed version of the type II tsRNA, triggered robust, >80% gene silencing. This correlated with the redirection of the thus reconstituted fully duplexed double-stranded RNA into Argonaute 2, whereas Argonautes 3 and 4 were skewed toward less structured small RNAs, particularly single-strand RNAs. We observed that the modulation of tsRNA levels had minor effects on the abundance of microRNAs, but more pronounced changes in the silencing activities of both microRNAs and siRNAs. These findings support that tsRNAs are involved in the global control of small RNA silencing through differential Argonaute association, suggesting that small RNA-mediated gene regulation may be even more finely regulated than previously realized.
Using neoteric solvents in oil shale studies (2001)

Abstract The liquefaction, gasification, and other chemical modifications of oil shale are challenging goals of chemistry and chemical engineering. The use of new solvent systems, such as supercritical fluids and ionic liquids, represents new avenues in the search of environmentally benign technologies. Supercritical fluid extraction (SFE) with carbon dioxide is particularly effective for the isolation of substances of medium molecular weight and relatively low polarity. At elevated temperatures it is possible to unite the breaking chemical bonds in the kerogen organic matter and convert the former into oil with extraction using supercritical fluids. Quantitative and qualitative information obtained at different temperatures during SFE is providing some insight into the speciation of hydrocarbons in geological samples. Ionic liquids were studied as potential solvents for kerogen extraction. However, these chemical processes are favored at elevated temperatures up to the thermal degradation temperature of kerogen, 400 C. There were observed significant differences in the chemical composition of extracted oil and from the oil from the classical semicoking process of oil shale. An additional application would be a combination of the two methodsthe use of supercritical carbon dioxide to recover nonvolatile organic compounds from room-temperature ionic liquid without using organic solvents.
GCN4 -Based Expression System (pGES): Translationally Regulated Yeast Expression Vectors (2000)

The expression of foreign proteins in Saccharomyces cerevisiae is a powerful tool for basic research and the biotechnological industry. In spite of the potential of S. cerevisiae, only a few useful expression vectors have been developed for this yeast. These vectors are based on an increasing transcription rate in combination with an increase in gene dosage. Most vectors are maintained as plasmids, which forces growth of cultures on poor selective media. Expression of the yeast Gcn4 protein is regulated at the translational level and increases strongly under amino acid starvation. Because under these conditions protein synthesis in general ceases, it is conceivable that regulatory elements that control Gcn4 expression could support selective expression of foreign genes. We cloned DNA fragments residing upstream from the GCN4 coding sequence (including the 5' UTR) and ligated them to a cDNA that encodes the human serum albumin (HSA) gene. These GCN4 regulatory elements induced efficient HSA expression at the translational level under amino acid starvation. The GCN4/HSA cassette promoted efficient, inducible expression on either a multicopy or integrative plasmid. The integrated cassette induced a high level of HSA in dense cultures grown on rich media. Thus, the GCN4-based expression system (pGES) provides high protein quantities. pGES is the first expression vector to be induced at the translational level.
CD30 (Ki-1) molecule: a new cytokine receptor of the tumor necrosis factor receptor superfamily as a tool for diagnosis and immunotherapy (1995)

THE INITIAL description of the Ki-l monoclonal antibody (MoAb) in 1982,' there has been an overwhelming flood of information concerning the Hodgkm's disease @)associated molecule CD30. In a diagnostic point of view, the Ki-l antibody enabled in 1985' the identification of a new category of non-Hodgkn's lymphomas designated as Ki"D30 anaplastic large cell lymphoma (ALCL).'
The HELLS-join (2013)

Upcoming processors are combining different computing units in a tightly-coupled approach using a unified shared memory hierarchy. This tightly-coupled combination leads to novel properties with regard to cooperation and interaction. This paper demonstrates the advantages of those processors for a stream-join operator as an important data-intensive example. In detail, we propose our HELLS-Join approach employing all heterogeneous devices by outsourcing parts of the algorithm on the appropriate device. Our HELLS-Join performs better than CPU stream joins, allowing wider time windows, higher stream frequencies, and more streams to be joined as before.
Water-Soluble Two-Photon Absorbing Nitrosyl Complex for Light-Activated Therapy through Nitric Oxide Release (2008)

A water-soluble nitrosyl complex with large two-photon absorption was synthesized by incorporating a two-photon absorbing chromophore with tetra(ethylene glycol) units, into the Roussin's red salt. The nitrosyl complex exhibits quenched emission due to energy transfer from the two-photon chromophore to the Roussin's red salt. The nitric oxide (NO) release induced by one- or two-photon irradiation was detected by EPR spectroscopy with a chemical probe, the Fe(II)- N-(dithiocarbamoyl)- N-methyl- d-glucamine (Fe-MGD) complex. Increased one- or two-photon excited fluorescence, with a concomitant photochemical release of NO, was observed upon one- or two-photon light irradiation. With the observed light-dependent cytotoxicity against cancer cells of the water-soluble nitrosyl complex, it was demonstrated that two-photon-functionalized nitrosyl complexes can be effective NO donors for light-activated treatment.
IN test and simulation tool (2002)

This presentation addresses the reasons for developing the IN test and simulation tool, its role in the design and test process, and the benefits of using this tool.
De Novo Sequencing and Homology Searching (2011)

In proteomics, de novo sequencing is the process of deriving peptide sequences from tandem mass spectra without the assistance of a sequence database. Such analyses have traditionally been performed manually by human experts, and more recently by computer programs that have been developed because of the need for higher throughput. Although powerful, de novo sequencing often can only determine partially correct sequence tags because of imperfect tandem mass spectra. However, these sequence tags can then be searched in a sequence database to identify the exact or a homologous peptide. Homology searches are particularly useful for the study of organisms whose genomes have not been sequenced. This tutorial will present background important to understanding de novo sequencing, suggestions on how to do this manually, plus descriptions of computer algorithms used to automate this process and to subsequently carryout homology-based database searches. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 1).
“Sero-Switch” Adenovirus-Mediated In Vivo Gene Transfer: Circumvention of Anti-Adenovirus Humoral Immune Defenses Against Repeat Adenovirus Vector Administration by Changing the Adenovirus Serotype (1996)

Recombinant, replication-deficient adenovirus (Ad) vectors have been successfully used to transfer and express the normal human cystic fibrosis transmembrane conductance regulator (CFTR) cDNA in vivo in the respiratory epithelium of experimental animals and humans with cystic fibrosis (CF). Since Ad-directed gene expression wanes over time, repeat administration is necessary to achieve an effective treatment for CF. A major hurdle to such a strategy is the possibility that anti-Ad humoral immunity may prevent gene expression in individuals with pre-existing anti-Ad immunity or following repeat administration. One strategy to circumvent such a problem would be alternating the use of Ad vectors belonging to different subgroups. Neutralizing antibodies developed with the administration of one Ad serotype do not cross-react with an Ad belonging to a second serotype in a manner that blocks infection and gene expression. To test this hypothesis, an immunizing dose of wild-type Ad5 (subgroup C), Ad4 (subgroup E), or Ad30 (subgroup D) was administered intratracheally to experimental animals, followed by an intratracheal administration of a replication-deficient subgroup C-derived vector coding for marker genes (chloramphenicol acetyl transferase or beta-galactosidase) or for the normal human CFTR cDNA. As expected, studies with vectors coding for marker genes or for CFTR cDNA demonstrated that airway administration of a vector does not yield efficient gene transfer, if there has been prior recent airway administration of the same Ad subgroup. In contrast, effective expression from the second administration can be achieved with an adenovirus vector belonging to a subgroup different from the first adenovirus administered. These data support the paradigm of alternating Ad vectors derived from different subgroups as strategy to circumvent anti-Ad humoral immunity, thus permitting the use of Ad vectors as a means to treat the respiratory manifestations of CF.
Human immunodeficiency virus-specific cytotoxic responses of seropositive individuals: distinct types of effector cells mediate killing of targets expressing gag and env proteins (1989)

By using target cells that expressed isolated env, gag, p27nef, or p23vif molecules introduced by recombinant vaccinia viruses containing genes encoding these polypeptides, it was possible to identify env, gag, p27nef, and p23vif as cytolytic target antigens for freshly isolated blood cells from human immunodeficiency virus 1 (HIV-1) seropositive patients. Most of the patients tested (95%) manifested a specific cytotoxic activity against vaccinia virus-env-infected target cells. The env-specific cytotoxic activity was not restricted by the major histocompatibility complex and was not mediated by T lymphocytes, as shown by the absence of blocking effect with an anti-CD3 monoclonal antibody and by the inefficiency of CD3+, CD8+, or CD4+ and CD8+ depletion to reduce the cytotoxic activity against the env-expressing target cells. In the same conditions, the cytotoxic activity specific for gag was abrogated and gag major histocompatibility complex-restricted cytotoxic T lymphocytes were detected in 85% of the subjects tested. Therefore, in a HIV-1 seropositive subject, distinct types of effector cells mediate the lysis of target cells expressing gag and env proteins.
<title>Introduction to rugate filter technology</title> (1993)

Fundamental descriptive rugate filter parameters and concepts are shown. A simple rugate filter is derived from the Fourier analysis of a high/low refractive index pair used in a conventional non quarter-wave stack design. Progress in both design and fabrication is demonstrated by representative rugate filters which function in either the visible or infrared. Numerous examples are cited to show the utility of refractive index profile tailoring and the advantages of using this technology.
Lift-off metallization using poly(methyl methacrylate) exposed with a scanning tunneling microscope (1988)

The scanning tunneling microscope (STM) is a unique tool for ultrahigh resolution, ultralow voltage electron beam lithography. In a previous paper we described the formation of metallic patterns by a ‘‘contamination’’ process followed by sputter etching. Here we report the formation of 22-nm-wide metal lines by STM exposure of poly(methyl methacrylate) (PMMA) resist followed by liftoff. Resist exposure and liftoff have also been achieved with reverse polarity, where the electrons are emitted from the resist sample and accelerated towards the tip. Results include the first working device made with a STM, a thin-film resistor 2 μ long and 120 nm in width. In addition to lithographic applications, studying resists in this regime may offer new insights on the chemical process of resist exposure and the role played by secondary electrons in exposing resist. Our results indicate that PMMA only works as a negative resist for energies above 25 eV; below this value it appears that the electrons cannot cause sufficient crosslinking to render the resist insoluble in the usual solvents.