gebhart/patrepeval huggingface dataset:
A natural genetic code expansion cassette enables transmissible biosynthesis and genetic encoding of pyrrolysine (2007)

Pyrrolysine has entered natural genetic codes by the translation of UAG, a canonical stop codon. UAG translation as pyrrolysine requires the pylT gene product, an amber-decoding tRNA(Pyl) that is aminoacylated with pyrrolysine by the pyrrolysyl-tRNA synthetase produced from the pylS gene. The pylTS genes form a gene cluster with pylBCD, whose functions have not been investigated. The pylTSBCD gene order is maintained not only in methanogenic Archaea but also in a distantly related Gram-positive Bacterium, indicating past horizontal gene transfer of all five genes. Here we show that lateral transfer of pylTSBCD introduces biosynthesis and genetic encoding of pyrrolysine into a naïve organism. PylS-based assays demonstrated that pyrrolysine was biosynthesized in Escherichia coli expressing pylBCD from Methanosarcina acetivorans. Production of pyrrolysine did not require tRNA(Pyl) or PylS. However, when pylTSBCD were coexpressed with mtmB1, encoding the methanogen monomethylamine methyltransferase, UAG was translated as pyrrolysine to produce recombinant monomethylamine methyltransferase. Expression of pylTSBCD also suppressed an amber codon introduced into the E. coli uidA gene. Strains lacking one of the pylBCD genes did not produce pyrrolysine or translate UAG as pyrrolysine. These results indicated that pylBCD gene products biosynthesize pyrrolysine using metabolites common to Bacteria and Archaea and, furthermore, that the pyl gene cluster represents a "genetic code expansion cassette," previously unprecedented in natural organisms, whose transfer allows an existing codon to be translated as a novel endogenously synthesized free amino acid. Analogous cassettes may have served similar functions for other amino acids during the evolutionary expansion of the canonical genetic code.
New ouabain-conjugated peptide found from phage displayed peptide library*1 (2004)

It is important that the results not only obtain distinctive OCP, but also supply valuable experimental data in detection of ouabain and therapy in hypertension.
Electrical Contact Resistance of Bismuth Telluride Nanowires (2006)

With increasing miniaturization in microelectronics, one of the challenges to maintaining device performance is the management of excess heat. The room-temperature thermoelectric efficiencies of bismuth telluride (BiTe) compounds are the highest reported for any material. Therefore, BiTe nanowires are interesting as building blocks of thermoelectric circuits that can be used for heat management. Further improvements in nanoscale thermoelectrics may lead to new applications such as nanoscale room temperature coolers and generators, and uncooled bolometers. The exploitation of the thermoelectric properties of devices based on nanowires of thermoelectric materials requires good electrical contacts between the nanowires and metal electrodes and this is the subject of the present report. We present a study of the contact resistance and methods for controlling its value in individual bismuth telluride nanowires. The wires are fabricated by employing a two step method. First, dense arrays of 200-nm bismuth telluride nanowires are prepared by a nonlithographic fabrication technique consisting of the pressure injection of an alumina template with molten bismuth telluride. In the second step, individual nanowires are removed from the template by etching the alumina. The two step method has the advantage that, as we will show, some of the nanowires' properties can be characterized by performing measurements on the arrays. In our investigations, we employed a simple device consisting of attaching a bismuth telluride nanowire to two gold planar electrodes. We find that the contact resistance has the potential of being non-ohmic and therefore lead to non-equilibrium
Effect of coalescence energy release on the temporal shape evolution of nanoparticles (2001)

The driving force for coalescence of two nanoparticles is the reduction in free energy through a reduction in surface area. The resulting particle also has a lower total potential energy, which through conservation of energy can lead to a significant increase in particle temperature. In a growth process particle heating competes with heat transfer to the cooler carrier gas. In this paper we develop a model that illustrates that this temperature increase can be extremely important and should be accounted for when modeling collision/coalescence processes. Our calculations indicate that the heat release associated with particle coalescence may reduce the coalescence time by as much as a few orders of magnitude. This is especially true for the final stages of exponential surface area decay toward sphericity, which becomes much faster and qualitatively explains the fact that primary particles of only a few nanometers in diameter are of spherical shape. We develop in this analysis a dimensionless ``coalescence heating number,'' which can be used to assess if the exothermic nature of coalescence should be accounted for under a given set of conditions. We also show that a simple coalescence model, which includes the temperature effect, closely follows our prior molecular dynamics calculations for silicon nanoparticles sintering. This analysis also explains a set of experimental results for alumina nanoparticle production, previously unexplainable by classical methods. Finally, we see that lower gas pressures result in lower gas-phase heat transfer, which in turn results in larger primary particles.
Noninferiority of IncobotulinumtoxinA, Free from Complexing Proteins, Compared with Another Botulinum Toxin Type A in the Treatment of Glabellar Frown Lines (2010)

IncobotulinumtoxinA is equally as effective as onabotulinumtoxinA in the treatment of glabellar frown lines. Both preparations were well tolerated.
IM means business (2002)

Instant messaging (IM), no longer just a facet of teenage life, now speeds everything from naval operations to customer service. IM is moving from computers and laptops to cellphones, PDAs, and other devices. Through its prosaic "buddy list," a continuously updated window that shows who among your family, friends, or colleagues are online and available, IM connects you to your inner circle in ways that phones and e-mail can't. What will make IM more than just the next hot idea to come and go is a single key feature called presence. In essence, this is a protocol to tell the world that you're available on a particular device. Outside IM, presence is being built into collaboration tools, word processors, e-mail directories, and even online games. Being always available has its drawbacks, of course. All too often, work and other obligations spill over into our private time. Many find the prospect of co-workers and even family always being able to contact us daunting. Concentration can be shattered; questions that seem important to the questioner may not be so to you. If usability researchers and application developers get it wrong, presence will be a burden, instead of a benefit. If they get it right, though, if they can deliver the right amount of your availability to the right set of people, IM can become the main way we initiate contact with the people we communicate with most often. indeed, those now-primary forms of communication, the telephone and e-mail, will either have presence built into them, or take a back seat to IM.
Effect of Liposomal Model Membrane Composition on Immunogenicity (1978)

We have examined the effect of composition on the immunogenicity in mice of liposomal model membranes sensitized with dinitrophenyl-epsilon-aminocaproyl-phosphatidylethanolamine (DNP-Cap-PE) derivatives. Neither cholesterol content nor incorporation of exogenous charged amphiphile (dicetylphosphate, stearylamine) exerted a significant influence on the in vivo anti-DNP response as measured by the appearance of direct plaque-forming cells in the spleen. Similarly, the nature of the fatty acids (saturated vs unsaturated) present in DNP-Cap-PE had no effect. In contrast, the nonpolar region of the basic phospholipids comprising the liposomal bilayers played an important role as revealed by a comparative study of model membranes prepared with beef sphingomyelin (SM), egg phosphatidylcholine (PC), and synthetic distearoyl-, dimyristoyl-, dilauroyl-, and dioleoyl-phosphatidylcholines (DSPC, DMPC, DLPC, DOPC). Thus, liposomes with a large content of phospholipids possessing a high transition temperature (e.g., beef SM, DSPC) were more immunogenic than those containing phospholipids of low transition temperature (e.g., egg PC, DOPC). This correlation held for both unsonicated and sonicated liposomes. These findings may have a bearing on the phenomenon of membrane-localized antigen expression.
Genetic screen for modifiers of the rough eye phenotype resulting from overexpression of the notch antagonist hairless in drosophila (2002)

Hairless was identified as antagonist in the Notch signaling pathway based on genetic interactions. Molecularly, Hairless inhibits Notch target gene activation by directly binding to the Notch signal transducer Su(H). Additional functional domains apart from the Su(H) binding domain, however, suggest additional roles for the Hairless protein. To further our understanding of Hairless functions, we have performed a genetic screen for modifiers of a rough eye phenotype caused by overexpression of Hairless during eye development. A number of enhancers were identified that comprise mutations in components of Notch- and EGFR-signaling pathways, some unknown genes and the gene rugose. Mutant alleles of rugose display manifold genetic interactions with mutants in Notch and EGFR signaling pathway components. Accordingly, the rugose eye phenotype is rescued by Hairless and enhanced by Delta. Molecularly, interactions might occur at the protein level because rugose appears not to be a direct transcriptional target of Notch.
The continuing evolution of intelligence for telecommunications power plants (2002)

The author discusses the development of the T1E1.6 Standard which will provide standard, inexpensive intra power plant messaging for telecommunication power systems. The implementation of this standard, once it is developed, will result in intelligent power components being connected by a simple twisted pair. The user will merely add on the particular power component-whether that component be a rectifier, an engine/alternator, a battery, an inverter, a ringing plant, etc.-to the system and plug it into the network for autoconfiguration.
The Use of Recombinant Human Bone Morphogenetic Protein 2 (rhBMP-2) to Promote Spinal Fusion in a Nonhuman Primate Anterior Interbody Fusion Model (1999)

This study was able to document the efficacy of rhBMP-2 with an absorbable collagen sponge carrier and a cortical dowel allograft to promote anterior interbody fusion in a nonhuman primate model at a dose of 0.4 mg per implant site (1.5 mg/mL concentration). The late of new bone formation and fusion with the use of rhBMP-2 and cortical dowel allograft appears to be far superior to that of autogenous cancellous iliac crest graft with cortical dowel allograft.
Synthesis of 2,2-Disubstituted Pyrrolidine-4-carboxylic Acid Derivatives and Their Incorporation into β-Peptide Oligomers (2005)

[reaction: see text] We have recently shown that members of a new class of beta-peptides, containing 2,2-disubstituted pyrrolidine-4-carboxylic acid residues, display discrete conformational preferences despite the impossibility of internal hydrogen bonding (Huck et al. J. Am. Chem. Soc. 2003, 125, 9035). Here we describe the synthesis of a variety of 2,2-disubstituted pyrrolidine-4-carboxylic derivatives that bear a diverse set of side chains and protecting groups suitable for oligomer synthesis. In addition, we discuss coupling methods for construction of oligomers in solution and on solid phase. Non-hydrogen bonded foldamers such as those generated from 2,2-disubstituted pyrrolidine-4-carboxylic acids may be useful in biomedical applications because the low intrinsic polarity of their backbones may promote bioavailability.
Coronary Aging in HIV‐Infected Patients (2009)

Increased vascular age is frequent among HIV-infected patients and appears to be associated with CD4+ cell count. If these findings were to be confirmed in prospective trials, a positive response to ART with an increase in CD4+ cell count may become a marker of increased risk of atherosclerosis development.
A strategy for making synthetic peptide vaccines. (1992)

We have determined the H-2 class II allele-specific amino acid motif of the agretope (the site of contact between the peptide antigen and the major histocompatibility complex) for a synthetic peptide composed of residues 43-58 of pigeon cytochrome c (p43-58). Residues 46 and 54 functioned as the agretope, and residues 50 and 52 functioned as the epitope (the site for contact between the peptide antigen and the T-cell antigen receptor). In general, agretopes and epitopes function independently. Thus, substitution of amino acids in the epitope does not significantly affect binding of the peptide antigen to a class II molecule. On the basis of these findings, synthetic peptide vaccines against influenza Aichi (H3N2) virus were prepared by introducing seven residues of the influenza virus hemagglutinin into the frame component residues 43-46 and 54-58 of p43-58 analogues including the agretopes for Ak or Ab previously determined on the p43-58 segment. These peptide vaccines induced both helper T-cell responses and production of antibodies that were specific for influenza Aichi hemagglutinin but not for the major histocompatibility complex binding frame in mice bearing Ak or Ab. The antibodies produced neutralize the infectivity of influenza Aichi in vitro. The present findings should provide a basis for preparing potent peptide vaccines that function without producing side effects.
TFE3: a helix-loop-helix protein that activates transcription through the immunoglobulin enhancer muE3 motif. (1990)

The muE3 motif within the immunoglobulin heavy-chain enhancer is required for full enhancer activity and is known to bind one, or perhaps a family, of related ubiquitous nuclear proteins. Here, we present the isolation of a cDNA that encodes an apparently novel microE3-binding protein designated TFE3. The major open reading frame of the cDNA predicts a protein of 59 kD, with a leucine zipper situated adjacent to an myc-related motif that has been proposed to assume a helix-loop-helix structure. Both of these motifs have been shown (for other proteins) to facilitate protein-protein interactions and DNA binding. Expression of the cDNA in 3T3 cells stimulates transcription from an artificial promoter consisting of four muE3 sites linked to a TATA box and also augments transcription of a reporter gene when it is linked to multiple copies of a particular heavy-chain enhancer subfragment but not when it is linked to the intact enhancer. Using GAL4 fusion proteins, we mapped a strong transcription activation domain within TFE3 that is distinct from the leucine zipper and helix-loop-helix motifs and includes a potential negative amphipathic helix. Like the other muE3-binding proteins detected in nuclear extracts, in vitro-synthesized TFE3 also binds to the USF/MLTF site found in the adenovirus major late promoter.
Notch ligand-bearing thymic epithelial cells initiate and sustain Notch signaling in thymocytes independently of T cell receptor signaling (2001)

Thymic epithelial cells are specialized to play essential roles at multiple stages of T cell development in the thymus, yet the molecular basis of this specialization is largely unknown. Recently, the Notch family of transmembrane proteins has been implicated in thymocyte development. Such proteins interact with cell surface proteins of the Delta-like and Jagged families. It is known that Notch ligands are expressed intrathymically, and that Notch signaling is regulated by Notch ligands expressed on either the same or third-party cells. However, functional analysis of Notch ligand expression, and elucidation of the mechanism of Notch ligand signaling in thymocyte development, are unclear. Here, we find that Notch ligand expression in the thymus is compartmentalized, with MHC class II(+) thymic epithelium, but not thymocytes nor dendritic cells, expressing Jagged-1, Jagged-2 and Delta-like-1. We also provide evidence that contact with Notch ligands on thymic epithelium is necessary to activate and sustain Notch signaling in thymocytes, and that this can occur independently of positive selection induction. Our data suggest that Notch ligand expression by thymic epithelium may partly explain the specialization of these cells in supporting thymocyte development, by regulating Notch activation via an inductive signaling mechanism independently of signaling leading to positive selection.
Smart Windows for Automobiles (1990)

&lt;div class="htmlview paragraph"&gt;Influenced both by styling considerations and by the aerodynamic benefits possible using flush glazing, car designers are making increasing use of glazing on automobiles. This leads to higher throughput of solar radiation into the car. Solar heat load will thus become a greater problem given that fuel efficiency requirements limit increase in the size of vehicle air-conditioners. Driver discomfort will increase due to the absence of shade, and greenhouse effects will become more serious. This leads to opportunities for energy-efficient glazing in vehicles. Smart windows - windows whose luminous and solar transmission vary dynamically to suit changing climatic conditions - have a potential application as energy-efficient automobile glazing. A variety of chromogenic technologies have been proposed. These include liquid crystal (LC) technology such as encapsulated LC devices consisting of small liquid crystal droplets encapsulated in a polymer matrix. Electrochromic (EC) technology - where transmittance changes under applied electric field or current - is also proposed for energy efficient glazing. A variety of designs are possible including laminate constructions formed from two glass substrates that sandwich an electrochromically active medium, and all solid-state devices fabricated by deposition of electrochromic thin films onto a single glass substrate. This paper reviews how publicly announced chromogenic technologies match automotive window needs and applications. Construction and performance of smart window designs currently under development are described. World-wide activity in this area is reviewed. Various chromogenic and nonchromogenic technologies are compared in terms of how they meet the performance, safety, and environmental resilience required of automotive glazing.&lt;/div&gt;
The repair of full-thickness articular cartilage defects. Immune responses to reparative tissue formed by allogeneic growth plate chondrocyte implants. (1991)

Growth plate cartilage cultivated in vitro was attached with a fibrin clot to a full-thickness articular cartilage defect on knee joints in allogeneic New Zealand rabbits. The healing of the defects was assessed by gross examination, light microscopy, and immunologic analysis for 24 weeks. Immunologic assessment of cell-mediated immunity, cytotoxicity of a humoral antibody by a 51chromium release assay, and immunofluorescence studies were carried out. During the first two weeks following grafting, healing was excellent in 11 of the 17 defects. From three to 24 weeks, 11 of 42 defects examined had good results. Host lymphocytes had accumulated around the allograft at two to 12 weeks. Most of the implanted cartilage grown in vitro died and was replaced by fibrous tissue. The immunologic studies suggested that the implanted cartilage began to degenerate two to three weeks after implantation partially because of a humoral immune response but more importantly because of cell-mediated cytotoxicity.
Gene expression profiling-based prediction of response of colon carcinoma cells to 5-fluorouracil and camptothecin. (2003)

5-Fluorouracil (5-FU) is the most common chemotherapeutic agent used in the treatment of colorectal cancer, yet objective response rates are low. Recently, camptothecin (CPT) has emerged as an effective alternative therapy. Decisive means to determine treatment, based on the likelihood of response to each of these agents, could greatly enhance the management of this disease. Here, the ability of cDNA microarray-generated basal gene expression profiles to predict apoptotic response to 5-FU and CPT was determined in a panel of 30 colon carcinoma cell lines. Genes whose basal level of expression correlated significantly with 5-FU- and CPT-induced apoptosis were selected, and their predictive power was assessed using a "leave one out" jackknife cross-validation strategy. Selection of the 50 genes best correlated with 5-FU-induced apoptosis, but not 50 randomly selected genes, significantly predicted response to this agent. Importantly, this gene expression profiling approach predicted response more effectively than four previously established determinants of 5-FU response: thymidylate synthase and thymidine phosphorylase activity; and p53 and mismatch repair status. Furthermore, reanalysis of the database demonstrated that selection of the 149 genes best correlated with CPT-induced apoptosis maximally and significantly predicted response to this agent. These studies demonstrate that the basal gene expression profile of colon cancer cells can be used to predict and distinguish response to multiple chemotherapeutic agents and establish the potential of this methodology as a means by which rational decisions regarding choice of therapy can be approached.
A Sensitive New Prenatal Test for Sickle-Cell Anemia (1982)

METHODS for prenatal diagnosis of sickle-cell anemia are improving rapidly.1 Initially the diagnostic procedure required fetal blood sampling, but new techniques for restriction-endonuclease analysis of DNA now permit the use of amniocentesis. A polymorphic HpaI site, present in 70 per cent of the American black population, was first used to diagnose the sickle mutation in the β-globin gene by linkage analysis.2 Recently the enzyme DdeI was shown to detect the sickle mutation directly in all cases.3 , 4 A drawback of the DdeI assay is that the amniotic cells must be cultured to provide a sufficient amount of DNA . . .
Information-Theoretic Feature Selection in Microarray Data Using Variable Complementarity (2008)

The paper presents an original filter approach for effective feature selection in microarray data characterized by a large number of input variables and a few samples. The approach is based on the use of a new information-theoretic selection, the double input symmetrical relevance (DISR), which relies on a measure of variable complementarity. This measure evaluates the additional information that a set of variables provides about the output with respect to the sum of each single variable contribution. We show that a variable selection approach based on DISR can be formulated as a quadratic optimization problem: the dispersion sum problem (DSP). To solve this problem, we use a strategy based on backward elimination and sequential replacement (BESR). The combination of BESR and the DISR criterion is compared in theoretical and experimental terms to recently proposed information-theoretic criteria. Experimental results on a synthetic dataset as well as on a set of eleven microarray classification tasks show that the proposed technique is competitive with existing filter selection methods.