gebhart/patrepeval huggingface dataset:
High-Affinity IgG Antibodies Develop Naturally in Ig-Knockout Rats Carrying Germline Human IgH/Igκ/Igλ Loci Bearing the Rat CH Region (2013)

Mice transgenic for human Ig loci are an invaluable resource for the production of human Abs. However, such mice often do not yield human mAbs as effectively as conventional mice yield mouse mAbs. Suboptimal efficacy in delivery of human Abs might reflect imperfect interaction between the human membrane IgH chains and the mouse cellular signaling machinery. To obviate this problem, in this study we generated a humanized rat strain (OmniRat) carrying a chimeric human/rat IgH locus (comprising 22 human V(H)s, all human D and J(H) segments in natural configuration linked to the rat C(H) locus) together with fully human IgL loci (12 Vκs linked to Jκ-Cκ and 16 Vλs linked to Jλ-Cλ). The endogenous Ig loci were silenced using designer zinc finger nucleases. Breeding to homozygosity resulted in a novel transgenic rat line exclusively producing chimeric Abs with human idiotypes. B cell recovery was indistinguishable from wild-type animals, and human V(D)J transcripts were highly diverse. Following immunization, the OmniRat strain performed as efficiently as did normal rats in yielding high-affinity serum IgG. mAbs, comprising fully human variable regions with subnanomolar Ag affinity and carrying extensive somatic mutations, are readily obtainable, similarly to conventional mAbs from normal rats.
Bioactive silicon structure fabrication through nanoetching techniques (1995)

A microporous film of silicon is shown to induce hydroxyapatite growth both on itself and on neighboring areas of bulk silicon (e.g. see figure). This indicates that silicon could be developed as an active biomaterial, which has encouraging implications for the use of VLSI technology in, for example, invasive sensing and biosensing and other electronic prosthetic devices magnified image .
Biologic properties and nucleotide sequence analysis of human papillomavirus type 51 (1991)

Human papillomaviruses (HPVs) may be grouped according to the site from which they are isolated and the disease with which they are associated. We recently identified and cloned HPV type 51 (HPV-51) from a low-grade precancerous lesion (G. Nuovo, E. DeVilliers, R. Levine, S. Silverstein, and C. Crum. J. Virol. 62:1452-1455, 1988). Molecular epidemiologic analysis of cervical lesions, including condylomata and low- and high-grade precancers, revealed that HPV-51 was present in about 5% of the samples we examined. We have now determined the complete nucleotide sequence of this virus and compared it with other sequenced HPVs. Our analysis reveals that the 7,808-bp genome is composed of eight open reading frames which are encoded on the same strand and that this virus is most closely related to HPV-31. Sequence comparisons place this virus in the group of high-risk viruses (those with an increased risk of progressing to malignancy) along with HPV-16, -18, -31, and -33. Morphologic transformation experiments demonstrated that HPV-51 had transformation potential and that transformed cells contained RNAs homologous to E6 and E7.
Low-overhead, low-complexity [burst] synchronization for OFDM (2002)

A rapid synchronization method is presented for an OFDM system using either a continuous transmission or a burst operation over a time-varying, fading channel. It will acquire the signal and provide channel estimation upon the receipt of just one training sequence of two symbols in the presence of unknown symbol and frame timing, large carrier and sampling frequency offsets, and very low SNRs, while maintaining low latency and low complexity. It can then track the signal with the same algorithms. Digital TV and wireless LAN are used as examples.
The bonding of CO to metal surfaces (2000)

The atom and symmetry specific properties of x-ray emission spectroscopy have been applied to the investigation of CO adsorbed on Ni(100) and Cu(100) surfaces. In comparison to ab initio electronic structure calculations, obtained in density functional theory, we develop a consistent electronic structure model of CO adsorption on transition and noble metals and extend to a conceptual model of the surface chemical bond. A strong CO–substrate interaction is found, characterized by significant hybridization of the initial CO orbitals and the metal bands. In the π system an allylic configuration is found as the result of orbital mixing between the CO 1π, 2π* and the metal dπ-band which is manifested experimentally in the observation of an oxygen lone-pair state. In the σ system experimental evidence of equally strong orbital mixing has been found. Energetically, the adsorbate–substrate complex is stabilized by the π-interaction but is destabilized by the σ-interaction. Furthermore, the internal C–O bond carried by the π-interaction is weakened upon adsorption, which is opposite for the internal C–O σ bond that is strengthened. The equilibrium properties of CO adsorbed on these metals are found to be the direct result of the balance between the σ- and π-interactions; both in terms of the total energy and the local bond properties.
Gene targeting of ErbB3 using a Cre‐mediated unidirectional DNA inversion strategy (2006)

Recombinase-mediated unidirectional DNA inversion and transcriptional arrest is a promising strategy for high throughput conditional mutagenesis in the mouse. Banks of mouse embryonic stem cells with defined, transcriptionally silent insertions that can be activated by Cre recombinase would take advantage of existing transgenic Cre lines to rapidly produce hundreds of lineage specific and temporally controlled knockout mice for each gene, thereby introducing significant parallelism to functional gene annotation. However, the extent to which this strategy results in effective gene knockout has not been established. To test the feasibility of this strategy we targeted ErbB3, a member of the ErbB family of tyrosine kinase receptors, using this strategy. Insertion of a reversed "flipflox" vector consisting of a gene inactivation cassette (GI) and an internal ribosome entry site (IRES)-GFP reporter into intron 1 of ErbB3 was transcriptionally silent and did not affect ErbB3 expression. Crosses with ubiquitous and lineage specific Cre recombinase expressing lines permanently inverted the inserted GI cassette and blocked ErbB3 expression. Unidirectional DNA inversion by in vivo recombination is an effective strategy for targeted or ubiquitous gene knockout.
Predicting the QRS complex and detecting small changes using principal component analysis (2007)

In this paper, a new method for QRS complex analysis and estimation based on principal component analysis (PCA) and polynomial fitting techniques is presented. Multi-channel ECG signals were recorded and QRS complexes were obtained from every channel and aligned perfectly in matrices. For every channel, the covariance matrix was calculated from the QRS complex data matrix of many heartbeats. Then the corresponding eigenvectors and eigenvalues were calculated and reconstruction parameter vectors were computed by expansion of every beat in terms of the principal eigenvectors. These parameter vectors show short-term fluctuations that have to be discriminated from abrupt changes or long-term trends that might indicate diseases. For this purpose, first-order poly-fit methods were applied to the elements of the reconstruction parameter vectors. In healthy volunteers, subsequent QRS complexes were estimated by calculating the corresponding reconstruction parameter vectors derived from these functions. The similarity, absolute error and RMS error between the original and predicted QRS complexes were measured. Based on this work, thresholds can be defined for changes in the parameter vectors that indicate diseases.
Human anelloviruses: diverse, omnipresent and commensal members of the virome (2020)

Anelloviruses are small, single stranded circular DNA viruses. They are extremely diverse and have not been associated with any disease so far. Strikingly, these small entities infect most probably the complete human population, and there are no convincing examples demonstrating viral clearance from infected individuals. The main transmission could be via fecal-oral or airway route, as infections occur at an early age. However, due to the lack of an appropriate culture system, the virus-host interactions remain enigmatic. Anelloviruses are obviously mysterious viruses, and their impact on human life is not yet known, but, with no evidence of a disease association, a potential beneficial effect on human health should also be investigated.
The inflammasome in lung diseases (2012)

Inflammation, the process aimed at restoring homeostasis after an insult, can be more damaging than the insult itself if uncontrolled, excessive, or prolonged. The inflammasome is an intracellular multimeric protein complex that regulates the maturation and release of proinflammatory cytokines of the IL-1 family in response to pathogens and endogenous danger signals. Growing evidence indicates that the inflammasome plays a key role in the pathogenesis of acute and chronic respiratory diseases. The inflammasome can be activated by the pathogens that account for the most prevalent infectious diseases of the respiratory tract, such as influenza A virus, Streptococcus pneumoniae, Pseudomonas aeruginosa, and Mycobacterium tuberculosis. The inflammasome also plays a role in the chronic inflammation of the airways of patients with asthma and chronic obstructive pulmonary disease, as well as in the initiation and progression of the inflammatory process in pulmonary fibrosis. The aim of this review is to summarize the most relevant points of inflammasome activation in lung diseases.
The Chemistry and Biological Effects of Flavonoids and Phenolic Acidsa (1998)

Flavonoids and phenolic acids are widely distributed in higher plants and form part of the human diet. Recent interest in these substances has been stimulated by the potential health benefits arising from the antioxidant activity of these polyphenolic compounds. This review outlines the basic chemistry, biosynthesis, and structure-activity relationships of these compounds with respect to their antioxidant activity. Although there is considerable in vitro evidence establishing antioxidant activity for polyphenolics found in the diet, there are few studies in humans on the absorption and bioavailability of these compounds. The possible in vivo antioxidant effects of the flavonoids is even less well understood. For example, controlled human intervention studies with beverages, such as red wine, that are rich in polyphenolic compounds, have yielded conflicting results. Our own work and that of others suggests that the final effects of such beverages may be a balance between the well-described prooxidant effects of alcohol and its metabolism and the antioxidant effects of the polyphenolic constituents. There is a need for further studies to increase our understanding of the absorption and in vivo biological effects of this family of compounds.
Carbohydrate-Based Micelle Clusters Which Enhance Hydrophobic Drug Bioavailability by Up to 1 Order of Magnitude (2006)

Amphiphilic chitosan-based polymers (Mw < 20 kDa) self-assemble in aqueous media at low micromolar concentrations to give previously unknown micellar clusters of 100-300 nm in size. Micellar clusters comprise smaller 10-30 nm aggregates, and the nanopolarity/drug incorporation efficiency of their hydrophobic domains can be tailored by varying the degree of lipidic derivatization and molecular weight of the carbohydrate. The extent of drug incorporation by these novel micellar clusters is 1 order of magnitude higher than is seen with triblock copolymers, with molar polymer/drug ratios of 1:48 to 1:67. On intravenous injection, the pharmacodynamic activity of a carbohydrate propofol formulation is increased by 1 order of magnitude when compared to a commercial emulsion formulation, and on topical ocular application of a carbohydrate prednisolone formulation, initial drug aqueous humor levels are similar to those found with a 10-fold dose of prednisolone suspension.
Doping dependent NH3 sensing of indium oxide nanowires (2003)

NH 3 gas sensing properties of In2O3 nanowires were carefully studied. Change of conductance in opposite directions was observed with different nanowire sensors. We suggest that this differential response is caused by various doping concentrations in the semiconducting In2O3 nanowires. In addition, we have also investigated a “gate-screening effect” exhibited in our nanowire chemical sensors at high NH3 concentrations, which is induced by adsorbed NH3 molecules working as charge traps. Both the doping-dependent response and the gate-screening effect will be especially valuable and helpful for understanding the detailed sensing mechanism of semiconducting metal oxide materials.
Influence of polarization on the properties of GaN based FET structures (2003)

GaN is the first highly polar semiconductor used in field effect transistors. Polarization charge dipoles are an essential part contributing to the device performance. Especially at the surface such charges may influence stability and large signal characteristics. Switching transients in output current of AlGaN/GaN-FETs related to charge storage effects are discussed and related to the polar nature of this material system. Alternative structures not suffering of the surface charge problem are introduced, namely an InGaN-channel FET and a AlGaN/GaN-double barrier structure. For realization doping screening of the polarization field is applied as main tool. (© 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
LASER (TWO‐QUANTUM) PHOTOLYSIS OF POLYNUCLEOTIDES AND NUCLEOPROTEINS: QUANTITATIVE PROCESSING OF RESULTS (1990)

The paper offers and substantiates a technique for quantitative processing of the photochemical reactions in polynucleotides, nucleoproteins and their components caused by the action of powerful ultraviolet laser pulse radiation.
The Myeloid-Lymphoid Initiating Cell (ML-IC) Assay Assesses the Fate of Multipotent Human Progenitors In Vitro (1999)

Abstract Hematopoietic stem cells (HSC) are cells with self-renewing multilineage differentiation potential. Although engraftment in xenogeneic recipients can be used to measure human HSC, these assays do not allow assessment of individual progenitors. We developed an in vitro assay that allows the identification of a single human bone marrow progenitor closely related to HSC, which we termed “Myeloid-Lymphoid Initiating Cell,” or ML-IC, because it is capable of generating multiple secondary progenitors that can reinitiate long-term myeloid and lymphoid hematopoiesis in vitro. The assay is done in contact with murine AFT024 fetal liver stromal cells and with Flt3-Ligand, stem cell factor, and interleukin-7. In this assay, 0.2% to 1.7% of Lin−/34+/DRdim cells could generate 1 to 3 long-term culture initiating cells (LTC-IC) as well as 1 to 4 NK-IC after 4 to 6 weeks. In addition, this assay measures contribution of net-progenitor conservation and net-progenitor proliferation over time, providing insight in the fate of individual LTC-IC and NK-IC. This assay will prove useful to enumerate the number of very primitive human progenitors with multilineage differentiation potential, as well as to evaluate future ex vivo culture conditions.
Phosphodiesterase-IV Inhibitors: Novel Therapeutics for the Treatment of Inflammatory Diseases (1995)

The identification and characterization of the multiple isoforms of the phosphodiesterase enzyme has generated considerable interest in the preparation of selective inhibitors of these isozymes. Phosphodiesterase-IV (PDE-IV) is a cyclic AMP-specific phosphodiesterase which has been shown to play an important role in the regulation of inflammatory and immune cell activation. Thus, it has been proposed that selective PDE-IV inhibitors may be useful for the treatment of inflammatory diseases. A diversity of structural types have been reported as selective PDE-IV inhibitors. Molecular modeling studies have played an important role in the discovery of these agents. An analysis of the structure-activity relationships (SAR) of novel inhibitors and their associated in vitro and in vivo profiles will be discussed.
How functional foods play critical roles in human health (2012)

How do functional foods affect human health? To answer this question it is important to understand what happens when food is digested and taken up by the gastrointestinal (GI) tract. The gut is a selective nutrient absorption system and the most important signal transduction and information exchange system within the body. It acts as a signal transducer, a neuroendocrine sensor, and an immunological recognition and presentation system. It is also a complex information exchange system comprising a number of signaling networks involving GI cells and cells immobilized in organs or transported in blood. The bioactivity of functional foods in vivo may be due to their effects on such networks, but this raises the question of what signaling pathways are used by non-nutrients that cannot be absorbed by the gut. The purpose of this review is to describe intestinal nutrient transportation, identify a number of widely expressed receptors and signal transduction pathways, and outline our current understanding of the mechanisms involved in health and disease. At the end of the review, a method for developing a cell communication network is described. This network is convenient for investigating the effects of oral administration of experimental medicines, drugs, or functional foods on cytokines of interest. Because cytokines and chemokines are transported via the circulatory system, a simple 2–3 mL blood sample from a volunteer is a rich source of information. This method may become the gold standard for evaluating the effects of functional foods or medicines in vivo.
Oncogenic kinase NPM/ALK induces through STAT3 expression of immunosuppressive protein CD274 (PD-L1, B7-H1) (2008)

The mechanisms of malignant cell transformation caused by the oncogenic, chimeric nucleophosmin (NPM)/anaplastic lymphoma kinase (ALK) remain only partially understood, with most of the previous studies focusing mainly on the impact of NPM/ALK on cell survival and proliferation. Here we report that the NPM/ALK-carrying T cell lymphoma (ALK+TCL) cells strongly express the immunosuppressive cell-surface protein CD274 (PD-L1, B7-H1), as determined on the mRNA and protein level. The CD274 expression is strictly dependent on the expression and enzymatic activity of NPM/ALK, as demonstrated by inhibition of the NPM/ALK function in ALK+TCL cells by the small molecule ALK inhibitor CEP-14083 and by documenting CD274 expression in IL-3-depleted BaF3 cells transfected with the wild-type NPM/ALK, but not the kinase-inactive NPM/ALK K210R mutant or empty vector alone. NPM/ALK induces CD274 expression by activating its key signal transmitter, transcription factor STAT3. STAT3 binds to the CD274 gene promoter in vitro and in vivo, as shown in the gel electromobility shift and chromatin immunoprecipitation assays, and is required for the PD-L1 gene expression, as demonstrated by siRNA-mediated STAT3 depletion. These findings identify an additional cell-transforming property of NPM/ALK and describe a direct link between an oncoprotein and an immunosuppressive cell-surface protein. These results also provide an additional rationale to therapeutically target NPM/ALK and STAT3 in ALK+TCL. Finally, they suggest that future immunotherapeutic protocols for this type of lymphoma may need to include the inhibition of NPM/ALK and STAT3 to achieve optimal clinical efficacy.
Large-aperture chirped volume Bragg grating based fiber CPA system (2007)

A fiber chirped pulse amplification system at 1558 nm was demonstrated using a large-aperture volume Bragg grating stretcher and compressor made of Photo-Thermal-Refractive (PTR) glass. Such PTR glass based gratings represent a new type of pulse stretching and compressing devices which are compact, monolithic and optically efficient. Furthermore, since PTR glass technology enables volume gratings with transverse apertures which are large, homogeneous and scalable, it also enables high pulse energies and powers far exceeding those achievable with other existing compact pulse-compression technologies. Additionally, reciprocity of chirped gratings with respect to stretching and compression also enables to address a long-standing problem in CPA system design of stretcher-compressor dispersion mismatch.
Protein Secretion Systems in Gram-Negative Bacteria (2006)

Protein export systems are present in all living organisms, including gram-negative bacteria and the eukaryotic organelles that derived from them (Table 1). In contrast to other organisms, however, gram-negative bacteria contain numerous, apparently independent systems for exporting proteins, including at least eight types that mediate export across or insertion into the inner cytoplasmic membrane and another eight that specifically mediate export across or insertion into the outer lipopolysaccharide-containing membrane.
Integration of heterologous genes in several yeast species using vectors containing a -derived rDNA-targeting element (2003)

A method that has been successfully used to generate recombinant Hansenula polymorpha strains by transformation with rDNA-targeting vectors was applied in the present study to a range of alternative yeast hosts, using vectors with an H. polymorpha-derived integration sequence. The dimorphic yeast Arxula adeninivorans, which is currently being assessed for heterologous gene expression, was the main focus of the study. As in H. polymorpha, it was possible to co-integrate more than a single plasmid carrying an expressible gene. Additionally, the vectors were examined in two further species, Pichia stipitis and Saccharomyces cerevisiae. Based on these results the design of a 'universal' fungal vector appears to be feasible.
ChemInform Abstract: APPLICATION OF ALLYLISOTHIOCYANATE IN THE SYNTHESIS OF 3‐ALLYL‐2‐THIOHYDANTOINS FROM AMINO ACIDS AND IN DEGRADATION OF PROTEINS (1974)

Abstract 3‐Allyl‐2‐thiohydantoine lassen sich durch Umsetzung von AHYÜSOIIUOCyHHHI mit Aminosäuren wie Alu, Gly, lle, Leu, Asp, Trp, V211, Phe.