gebhart/patrepeval huggingface dataset:
Detection of C−Si Covalent Bond in CH3 Adsorbate Formed by Chemical Reaction of CH3MgBr and H:Si(111) (2003)

High-resolution electron energy loss spectroscopy (HREELS) yielded evidence for the formation of single covalent bonds between Si(111) surface atoms and CH(3) groups from the reaction of CH(3)MgBr and hydrogen-terminated H:Si(111)(1 x 1). The vibration at 678 cm(-)(1), assigned to the C-Si bond, was isolated within the spectrum of CH(3) on deuterium-terminated D:Si(111)(1 x 1). The CH(3) groups were thermally stable at temperatures below 600 K. The C-Si bonds are essential for enhancing the usefulness of alkyl moieties, which will lead to a new prospective technology of nanoscale fabrication and biochemical application.
Quadruplex DNA: sequence, topology and structure (2006)

G-quadruplexes are higher-order DNA and RNA structures formed from G-rich sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential quadruplex sequences have been identified in G-rich eukaryotic telomeres, and more recently in non-telomeric genomic DNA, e.g. in nuclease-hypersensitive promoter regions. The natural role and biological validation of these structures is starting to be explored, and there is particular interest in them as targets for therapeutic intervention. This survey focuses on the folding and structural features on quadruplexes formed from telomeric and non-telomeric DNA sequences, and examines fundamental aspects of topology and the emerging relationships with sequence. Emphasis is placed on information from the high-resolution methods of X-ray crystallography and NMR, and their scope and current limitations are discussed. Such information, together with biological insights, will be important for the discovery of drugs targeting quadruplexes from particular genes.
EARLY AND DIFFERENTIAL INDUCTION OF ERKs IN LIVER AFTER BURN. (1998)

Dept. of Surgery, The University of Texas Medical Branch and Shriners Hospitals for Children, Galveston, TX 77550.
Towards context-aware face recognition (2005)

In this paper, we focus on the use of context-aware, collaborative filtering, machine-learning techniques that leverage automatically sensed and inferred contextual metadata together with computer vision analysis of image content to make accurate predictions about the human subjects depicted in cameraphone photos. We apply Sparse-Factor Analysis (SFA) to both the contextual metadata gathered in the MMM2 system and the results of PCA (Principal Components Analysis) of the photo content to achieve a 60% face recognition accuracy of people depicted in our cameraphone photos, which is 40% better than media analysis alone. In short, we use context-aware media analysis to solve the face recognition problem for cameraphone photos.
Extra-mitochondrial localisation of frataxin and its association with IscU1 during enterocyte-like differentiation of the human colon adenocarcinoma cell line Caco-2 (2005)

Friedreich's ataxia is a recessive neurodegenerative disease due to insufficient expression of the mitochondrial protein frataxin. Although it has been shown that frataxin is involved in the control of intracellular iron metabolism, by interfering with the mitochondrial biosynthesis of proteins with iron/sulphur (Fe/S) clusters its role has not been well established. We studied frataxin protein and mRNA expression and localisation during cellular differentiation. We used the human colon adenocarcinoma cell line Caco-2, as it is considered a good model for intestinal epithelial differentiation and the study of intestinal iron metabolism. Here we report that the protein, but not the mRNA frataxin levels, increase during the enterocyte-like differentiation of Caco-2 cells, as well as in in-vivo-differentiated enterocytes at the upper half of the crypt-villus axis. Furthermore, subcellular fractionation and double immunostaining, followed by confocal analysis, reveal that frataxin localisation changes during Caco-2 cell differentiation. In particular, we found an extramitochondrial localisation of frataxin in differentiated cells. Finally, we demonstrate a physical interaction between extramitochondrial frataxin and IscU1, a cytoplasmic isoform of the human Fe/S cluster assembly machinery. Based on our data, we postulate that frataxin could be involved in the biosynthesis of iron-sulphur proteins not only within the mitochondria, but also in the extramitochondrial compartment. These findings might be of relevance for the understanding of both the pathogenesis of Friedreich's ataxia and the basic mechanism of Fe/S cluster biosynthesis.
Amplification of cellular oncogenes: A predictor of clinical outcome in human cancer (1990)

Increased dosage of cellular oncogenes resulting from amplification of DNA is a frequent genetic abnormality of tumor cells and the study of oncogene amplification has been paradigmatic for the usefulness of molecular genetic research in clinical oncology. Certain types of human tumors carry an amplified cellular oncogene at frequencies of up to 50-60%. Human neuroblastoma has been prototypic for the importance of oncogene amplification in tumorigenesis, and evidence is emerging that amplification may be an early event involved in a more malignant form of this cancer. It is unclear at which stage amplification plays a role in other cancers. Amplification of cellular oncogenes is a good predictor of clinical outcome in some human malignancies.
CD14+,CD16+ blood monocytes and joint inflammation in rheumatoid arthritis (2002)

These results indicate that the maturation of blood monocytes into tissue-infiltrative CD16+ cells before entry into the joint, induced by cytokine spillover from the inflamed joint, may contribute to the persistent joint inflammation of RA.
Focused ion beam nano-structuring of photonic Bragg gratings in $Al_2O_3$ waveguides (2007)

Focused ion beam (FIB) etching is receiving increasing attention for the fabrication of active integrated optical components such as waveguide amplifiers and lasers. Si-technology compatible low-loss $Al_2O_3$ channel waveguides grown on thermally oxidized silicon substrates have been reported recently. We used FIB milling for reflection grating definition on Al2O3 channel and ridge waveguides. Structural optimization has been achieved by experimentally adjusting FIB patterning parameters such as ion current, dwell time, loop repetitions, scanning strategy, and applying a top metal layer for reducing charging effects and sidewall definition improvement. Optical properties of these devices are currently being studied.
Hydroformylation of bisolefinic amine derivatives catalyzed by cobalt and rhodium (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydroformylation of bisolefinic amine derivatives catalyzed by cobalt and rhodiumMichael E. Garst and David LuktonCite this: J. Org. Chem. 1981, 46, 22, 4433–4438Publication Date (Print):October 1, 1981Publication History Published online1 May 2002Published inissue 1 October 1981https://pubs.acs.org/doi/10.1021/jo00335a022https://doi.org/10.1021/jo00335a022research-articleACS PublicationsRequest reuse permissionsArticle Views686Altmetric-Citations26LEARN 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-Alertsclose Get e-Alerts
Chaperone Properties of Bacterial Elongation Factor EF-Tu (1998)

Elongation factor Tu (EF-Tu) is involved in the binding and transport of the appropriate codon-specified aminoacyl-tRNA to the aminoacyl site of the ribosome. We report herewith that the Escherichia coli EF-Tu interacts with unfolded and denatured proteins as do molecular chaperones that are involved in protein folding and protein renaturation after stress. EF-Tu promotes the functional folding of citrate synthase and alpha-glucosidase after urea denaturation. It prevents the aggregation of citrate synthase under heat shock conditions, and it forms stable complexes with several unfolded proteins such as reduced carboxymethyl alpha-lactalbumin and unfolded bovine pancreatic trypsin inhibitor. The EF-Tu.GDP complex is much more active than EF-Tu.GTP in stimulating protein renaturation. These chaperone-like functions of EF-Tu occur at concentrations that are at least 20-fold lower than the cellular concentration of this factor. These results suggest that EF-Tu, in addition to its function in translation elongation, might be implicated in protein folding and protection from stress.
Universal Optimal Transmission of Light Through Disordered Materials (2008)

We experimentally demonstrate increased diffuse transmission of light through strongly scattering materials. Wave front shaping is used to selectively couple light to the open transport eigenchannels, specific solutions of Maxwell's equations which the sample transmits fully, resulting in an increase of up to 44% in the total angle-integrated transmission compared to the case where plane waves are incident. The results for each of several hundreds of experimental runs are in excellent quantitative agreement with random matrix theory. From our measurements we conclude that with perfectly shaped wave fronts the transmission of a disordered sample tends to a universal value of 2/3, regardless of the thickness.
Drilling Nanopores in Graphene with Clusters: A Molecular Dynamics Study (2012)

Using molecular dynamics simulation with empirical potentials, we show that energetic cluster ion beam is a powerful tool to drill nanopores in graphene, which have been proved to possess the potential applications in nanopore-based single-molecule detection and analysis such as DNA sequencing. Two types of clusters are considered, and different cluster size and incident energies are used to simulate the impact events. Our results demonstrate that by choosing suitable cluster species and controlling its energy, a nanopore with expected size and quality could be created in a graphene sheet. Furthermore, suspended carbon chains could be formed at the edge of the nanopore via adjusting the ion energy, which provided a feasible way to decorate the nanopore with chemical methods such as adsorption of large molecules or foreign atoms for biosensing applications.
Competitive PCR to detect eIF4E gene amplification in head and neck cancer (1999)

Overexpression and associated gene amplification of elF4E were present in HNSCC but not in benign tissue. Gene amplification of elF4E may be an important mechanism for elF4E overexpression.
Antioxidant Properties of an Endogenous Thiol: Alpha-lipoic Acid, Useful in the Prevention of Cardiovascular Diseases (2009)

In the past few years, a growing interest has been given to the possible antioxidant functions of a natural acid, synthesized in human tissues: alpha-lipoic acid (ALA). Both the oxidized (disulfide) and reduced (dithiol: dihydrolipoic acid, DHLA) forms of ALA show antioxidant properties. ALA administered in the diet accumulates in tissues, and a substantial part is converted to DHLA via a lipoamide dehydrogenase. Commercial ALA is usually a racemic mixture of the R and S forms. Chemical studies have indicated that ALA scavenges hydroxyl radicals, hypochlorous acid, and singlet oxygen. ALA exerts antioxidant effects in biological systems not only through direct ROS quenching but also via transition metal chelation. ALA has been shown to possess a number of beneficial effects both in the prevention and treatment of diabetes in experimental conditions. ALA presents beneficial effects in the management of symptomatic diabetic neuropathy and has been used in this context in Germany for more than 30 years. In cardiovascular disease, dietary supplementation with ALA has been successfully employed in a variety of in vivo models: ischemia-reperfusion, heart failure, and hypertension. More mechanistic and human in vivo studies are needed to determine whether optimizing the dietary intake of ALA can help to decrease cardiovascular diseases. A more complete understanding of cellular biochemical events that influence oxidative damage is required to guide future therapeutic advances.
Interferon-alpha and -gamma expression in the rat testis. (1995)

Interferon-alpha (IFN alpha), -beta, and -gamma are well known for their antiviral, antiproliferative, and immunoregulatory activities. Although several studies suggest an involvement of IFNs in the spermatogenic process, nothing is known about the possible production of these molecules within the testis. Moreover, the antiviral capabilities of testicular cells have not yet been explored despite their importance in the context of sexually transmissible diseases. Using reverse transcription-polymerase chain reaction, a cytopathic inhibition micromethod assay, and an enzyme-linked immunosorbent assay, the present study demonstrates for the first time that IFN alpha and -gamma are produced by testicular cells. IFN alpha protein and corresponding messenger RNA are expressed by peritubular, Sertoli, and germ cells. In vitro, IFN alpha production by Sertoli cells, peritubular cells, and early spermatids was inducible by the Sendai virus, whereas pachytene spermatocyte IFN alpha production was not triggered by this virus. Of all the testicular cell types tested, Sertoli cells by far produced the highest concentrations of IFN alpha/beta, followed by peritubular cells. Both IFN gamma messenger RNA and IFN gamma protein were found in early spermatids, but, in contrast, were not produced by peritubular cells, Sertoli cells, or pachytene spermatocytes. In conclusion, our study establishes the cellular distribution of IFNs within the seminiferous tubules and provides the basis for research into the possible involvement of IFNs in regulation of the spermatogenic process. To the best of our knowledge, our results afford the first insight on how the testicular antiviral defense system is organized.
Water-Soluble Organocatalysts for Hydrazone and Oxime Formation (2013)

The formation of oximes and hydrazones is widely used in chemistry and biology as a molecular conjugation strategy for achieving ligation, attachment, and bioconjugation. However, the relatively slow rate of reaction has hindered its utility. Here, we report that simple, commercially available anthranilic acids and aminobenzoic acids act as superior catalysts for hydrazone and oxime formation, speeding the reaction considerably over the traditional aniline-catalyzed reaction at neutral pH. This efficient nucleophilic catalysis, involving catalyst-imine intermediates, allows rapid hydrazone/oxime formation even with relatively low concentrations of the two reactants. The most efficient catalysts are found to be 5-methoxyanthranilic acid and 3,5-diaminobenzoic acid; we find that they can enhance rates by factors of as much as 1-2 orders of magnitude over the aniline-catalyzed reaction. Evidence based on a range of differently substituted arylamines suggests that the ortho-carboxylate group in the anthranilate catalysts serves to aid in intramolecular proton transfer during imine and hydrazone formation.
A methodology for the computation of an upper bound on noise current spectrum of CMOS switching activity (2003)

Currents injected by CMOS digital circuit blocks into the power grid and into the substrate of a system-on-a-chip may affect reliability and performance of other sensitive circuit blocks. To verify the correct operation of the system, an upper bound for the spectrum of the noise current has to be provided with respect to all possible transitions of the circuit inputs. The number of input transitions is exponential in the number of circuit inputs. In this paper, we present a novel approach for the computation of the upper bound that avoids the untractable exhaustive exploration of the entire space. Its computational complexity is indeed linear in the number of gates. Our approach requires CMOS standard cell libraries to be characterized for injected noise current. In this paper, we also present an approach for this characterization of CMOS standard cells. Experimental results have proven the accuracy of both the algorithm and the noise current models used for the library characterization.
Differentiation of Mesenchymal Stem Cells Transplanted to a Rabbit Degenerative Disc Model (2005)

MSCs transplanted to degenerative discs in rabbits proliferated and differentiated into cells expressing some of the major phenotypic characteristics of nucleus pulposus cells, suggesting that these MSCs may have undergone site-dependent differentiation. Further studies are needed to evaluate their functional role.
An efficient signature scheme based on quadratic equations (1984)

Electronic messages, documents and checks must be authenticated by digital signatures which are not forgeable even by their recipients. The RSA system can generate and verify such signatures, but each message requires hundreds of high precision modular multiplications which can be implemented efficiently only on special purpose hardware. In this paper we propose a new signature scheme which can be easily implemented in software on microprocessors: signature generation requires one modular multiplication and one modular division, signature verification requires three modular multiplications, and the key size is comparable to that of the RSA system. The new scheme is based on the quadratic equation m = s21 + ks22 (mod n), where m is the message, s1 and s2 are the signature, and k and n are the publicly known key. While we cannot prove that the security of the scheme is equivalent to factoring, all the known methods for solving this quadratic equation for arbitrary k require the extraction of square roots modulo n or the solution of similar problems which are at least as hard as factoring. A novel property of the new scheme is that legitimate users can choose k in such a way that they can sign messages even without knowing the factorization of n, and thus everyone can use the same modulus if no one knows its factorization.
Digital Component Separator for future W-CDMA-LINC Transmitters implemented on an FPGA (2005)

Abstract. This paper presents the implementation of a Digital-Component-Separator (DCS) for a LINC-transmitter (linear amplification using nonlinear components) on an FPGA (field programmable gate array). It investigates and estimates the bandwidth requirements for such a LINC system. The influence of bandwidth limitations on a digitally based LINC-transmitter for W-CDMA utilization is studied by simulations. Furthermore a LINC transmitter is proposed which employs a flexible image-reject- or a direct up-conversion-architecture for transmission of single or combined multi-carrier/channel W-CDMA signals using the phase-modulation approach. The sampling frequency can be chosen at a value up to 32 times (122.88MHz) the symbol rate of the W-CDMA chip rate of 3.84Mbits/s. Measurement results for a LINC transmitter are presented and discussed.
CD28-B7 interactions allow the induction of CD8+ cytotoxic T lymphocytes in the absence of exogenous help. (1993)

The activation requirements for the generation of CD8+ cytotoxic T cells (CTL) are poorly understood. Here we demonstrate that in the absence of exogenous help, a CD28-B7 interaction is necessary and sufficient for generation of class I major histocompatibility complex-specific CTL. Costimulation is required only during the inductive phase of the response, and not during the effector phase. Transfection of the CD28 counter receptor, B7, into nonstimulatory P815 cells confers the ability to elicit P815-specific CTL, and this response can be inhibited by anti-CD28 Fab or by the chimeric B7-binding protein CTLA4Ig. Anti-CD28 monoclonal antibody (mAb) can provide a costimulatory signal to CD8+ T cells when the costimulatory capacity of splenic stimulators is destroyed by chemical fixation. CD28-mediated signaling provokes the release of interleukin 2 (IL-2) from the CD8+ CTL precursors, as anti-CD28 mAb could be substituted for by the addition of IL-2, and an anti-IL-2 mAb can block the generation of anti-CD28-induced CTL. CD4+ cells are not involved in the costimulatory response in the systems examined. We conclude that CD8+ T cell activation requires two signals: an antigen-specific signal mediated by the T cell receptor, and an additional antigen nonspecific signal provided via a CD28-B7 interaction.
Preclinical screening of anti‐HER2 nanobodies for molecular imaging of breast cancer (2011)

Accurate determination of tumor human epidermal growth factor receptor 2 (HER2)-status in breast cancer patients is possible via noninvasive imaging, provided adequate tracers are used. In this study, we describe the generation of a panel of 38 nanobodies, small HER2-binding fragments that are derived from heavy-chain-only antibodies raised in an immunized dromedary. In search of a lead compound, a subset of nanobodies was biochemically characterized in depth and preclinically tested for use as tracers for imaging of xenografted tumors. The selected compound, 2Rs15d, was found to be stable and to interact specifically with HER2 recombinant protein and HER2-expressing cells in ELISA, surface plasmon resonance, flow cytometry, and radioligand binding studies with low nanomolar affinities, and did not compete with anti-HER2 therapeutic antibodies trastuzumab and pertuzumab. Single-photon-emission computed tomography (SPECT) imaging quantification and biodistribution analyses showed that (99m)Tc-labeled 2Rs15d has a high tumor uptake in 2 HER2(+) tumor models, fast blood clearance, low accumulation in nontarget organs except kidneys, and high concomitant tumor-to-blood and tumor-to-muscle ratios at 1 h after intravenous injection. These values were dramatically lower for an irrelevant control (99m)Tc-nanobody and for (99m)Tc-2Rs15d targeting a HER2(-) tumor.