gebhart/patrepeval huggingface dataset:
Disinfection with flash lamps. (2000)

The analysis of published and new data on a pulsed disinfection is presented. It allows the conclusion that the pulsed disinfection mechanism includes both germicidal action of UVC light and a rupture of bacteria due to thermal stress, caused primarily by all UV components of the light pulse. The role of simultaneous cooling and heating of bacteria during a flash lamp pulse has been estimated and a direct detection of such a mechanism is proposed. It is suggested that an optimum pulsed light source for disinfection must have as much percentile content of a broad UV spectrum and a high peak power as is technically justified. Two new applications for pharmaceutics and medicine are suggested.
The Use of Fura-2 Fluorescence to Monitor the Movement of Free Calcium Ions into the Matrix of Plant Mitochondria (Pisum sativum and Helianthus tuberosus) (1993)

Purified mitochondria isolated from pea (Pisum sativum L. cv Alaska) stems and Jerusalem artichoke (Helianthus tuberosus L. cv OB1) tubers were loaded with the acetoxymethyl ester of the fluorescent Ca2+ indicator fura-2. This made possible the continuous monitoring of free [Ca2+] in the matrix ([Ca2+]m) without affecting the apparent viability of the mitochondria. Pea stem mitochondria contained an initial [Ca2+]m of approximately 60 to 100 nM, whereas [Ca2+]m was severalfold higher (400-600 nM) in mitochondria of Jerusalem artichoke tubers. At low extramitochondrial Ca2+ concentrations ([greater than or equal to]100 nM), there was an energy-dependent membrane potential increase in [Ca2+]m; the final [Ca2+]m was phosphate-dependent in Jerusalem artichoke but was phosphate-independent in pea stem mitochondria. The data presented indicate that (a) there is no absolute requirement for phosphate in Ca2+ uptake; (b) plant mitochondria can accumulate external free Ca2+ by means of an electrophoretic Ca2+ uniporter with an apparent affinity for Ca2+ (Km approximately 150 nM) that is severalfold lower than that measured by conventional methods (isotopes and Ca2+-sensitive electrodes); and (c) [Ca2+]m is within the regulatory range of mammalian intramitochondrial dehydrogenases.
Studies of the interactions between the anticytokeratin 8 monoclonal antibody TS1, its antigen and its anti‐idiotypic antibody αTS1 (2003)

The monoclonal antibody TS1 against cytokeratin 8 and its antiidiotype alphaTS1 have been used for immunotargeting and therapy of carcinomas in experimental tumor model systems. The interaction surfaces between mab TS1, the cytokeratin 8 epitope, and its anti-idiotypic antibody, alphaTS1, were studied in detail in order to make future veneering of the interactions possible. The V-genes of TS1 and alphaTS1 were cloned and sequenced and the CDRs and the framework residues were identified. Amino acids participating in the interactions were identified following chemical modifications of residues in non-protected and protected molecules of cytokeratin 8, alphaTS1 and TS1. From the sequences, the three-dimensional structures were generated using computer modelling of the antibody variable regions. Several charged amino acid, histidine and tyrosine residues were displayed in the antibody surfaces implicated in the interactions and chemical modification confirmed the importance of these amino acids. The cytokeratin 8 epitope has previously been identified by Johansson et al. and it displays negatively charged amino acid residues which could be identified in the chemical modification. It was also revealed that the TS1 binding to cytokeratin 8 and alphaTS1 respectively are partly overlapping; a histidine identified in TS1 is probably involved only in the interaction with alphaTS1. Furthermore, the chemical modification demonstrated that exchanging aspartic-glutamic acids to asparagine-glutamine residues in TS1 increased the binding of TS1 to cytokeratin 8, indicating that there is at least one acidic amino acid that is an obstacle in the TS1-CK8 binding. The detailed assembly of the interaction surfaces will facilitate the future use of site directed mutagenesis to improve the TS1-CK8 association rate and the clearing of TS1 with alphaTS1 in vivo.
Ultrahigh Purification of Silane for Semiconductor Silicon (1975)

Monosilane was purified with a newly developed ion‐exchanged zeolite A, which sorbs phosphine in silane. The phosphine content of silane was determined from electrical resistivity of silicon which was obtained by decomposing silane. Two kinds of silicon samples were used for analysis, i.e., epitaxial films on silicon substrate, and single crystal rods. The electrical resistivity of the silicon rods of p‐type ranged between at room temperature, depending on conditions of purification. A surface barrier type solid‐state detector, fabricated from this silicon, was evaluated with x‐rays and conversion electrons from 207Bi, and showed satisfactory characteristics. Characteristics of the adsorption column were studied with a simulation column by the aid of gas‐chromatographic techniques. Optimum conditions were deduced for the operation of the adsorption column.
Application of Palladium-Mediated 18F-Fluorination to PET Radiotracer Development: Overcoming Hurdles to Translation (2013)

New chemistry methods for the synthesis of radiolabeled small molecules have the potential to impact clinical positron emission tomography (PET) imaging, if they can be successfully translated. However, progression of modern reactions from the stage of synthetic chemistry development to the preparation of radiotracer doses ready for use in human PET imaging is challenging and rare. Here we describe the process of and the successful translation of a modern palladium-mediated fluorination reaction to non-human primate (NHP) baboon PET imaging-an important milestone on the path to human PET imaging. The method, which transforms [(18)F]fluoride into an electrophilic fluorination reagent, provides access to aryl-(18)F bonds that would be challenging to synthesize via conventional radiochemistry methods.
PTEN controls tumor-induced angiogenesis (2001)

Mutations of the tumor suppressor PTEN, a phosphatase with specificity for 3-phosphorylated inositol phospholipids, accompany progression of brain tumors from benign to the most malignant forms. Tumor progression, particularly in aggressive and malignant tumors, is associated with the induction of angiogenesis, a process termed the angiogenic switch. Therefore, we tested whether PTEN regulates tumor progression by modulating angiogenesis. U87MG glioma cells stably reconstituted with PTEN cDNA were tested for growth in a nude mouse orthotopic brain tumor model. We observed that the reconstitution of wild-type PTEN had no effect on in vitro proliferation but dramatically decreased tumor growth in vivo and prolonged survival in mice implanted intracranially with these tumor cells. PTEN reconstitution diminished phosphorylation of AKT within the PTEN-reconstituted tumor, induced thrombospondin 1 expression, and suppressed angiogenic activity. These effects were not observed in tumors reconstituted with a lipid phosphatase inactive G129E mutant of PTEN, a result that provides evidence that the lipid phosphatase activity of PTEN regulates the angiogenic response in vivo. These data provide evidence that PTEN regulates tumor-induced angiogenesis and the progression of gliomas to a malignant phenotype via the regulation of phosphoinositide-dependent signals.
JSON Data Management in RDBMS (2019)

Being a simple semi-structured data model, JSON has been widely accepted as a simple way to store, query, modify, and exchange data among applications. In comparison with schema-oriented relational data model to store, query, and update application data, JSON data model has the advantage of being self-contained, free from schema evolution issues, and flexible enough to enable agile style development paradigm. Therefore, during the last 5 years, SQL/JSON standard has been established as foundation for managing JSON data in SQL standard and there have been JSON functionalities added into RDBMS products to support SQL/JSON standard to various degree. In this chapter, the authors will analyze the strength and weakness of using JSON as the data model to manage data for applications. For use cases where JSON data model is ideal, they present the design approaches to store, index, query, and update JSON in the kernel of RDBMS to support SQL/JSON standard defined operations effectively and efficiently.
Amino acid sequence analysis of the asparagine-288 region of the carbohydrate variants of human plasminogen (1983)

The amino acid sequences of the two major carbohydrate variants in the region of Asn288 have been determined. A peptide isolated from plasminogen variant 1, which contains a complex-type Asn288-linked oligosaccharide, was found to possess the amino acid sequence-Ser280-Ala-Gln-Thr-Pro-His-Thr-His-Asn(CHO)-Arg-Thr290-Pro-Glu-, in agreement with the previously published sequence [Sottrup-Jensen, L., Claeys, H., Zajdel, M., Petersen, T. E., & Magnusson, S. (1978) in Progress in Chemical Fibrinolysis and Thrombolysis (Davidson, J. F., Rowan, R. M., Samama, M. M., & Desnoyers, P. C., Eds.) Vol. 3, pp 191-209, Raven Press, New York]. A similar peptide isolated from plasminogen variant 2 did not contain oligosaccharide but possessed an amino acid sequence identical with the corresponding variant 1 peptide. Thus, the basis for the lack of the complex-type oligosaccharide in human plasminogen variant 2 does not reside in substitution of essential amino acid residues in the region of the Asn288-linked glycosylation site.
The repertoire for pattern recognition of pathogens by the innate immune system is defined by cooperation between Toll-like receptors (2000)

Toll-like receptors (TLRs) have been shown to participate in the recognition of pathogens by the innate immune system, but it is not clear how a restricted family of receptors has the capacity to recognize the wide spectrum of TLR stimuli known to exist. We report here that two members of the TLR family, TLR2 and TLR6, together coordinate macrophage activation by Gram-positive bacteria and the yeast cell-wall particle, zymosan. TLR6 and TLR2 both are recruited to the macrophage phagosome, where they recognize peptidoglycan, a Gram-positive pathogen component. By contrast, TLR2 recognizes another component, bacterial lipopeptide, without TLR6. The requirement for TLR cooperation is supported by the finding that TLR2 needs a partner to activate tumor necrosis factor-alpha production in macrophages. Dimerization of the cytoplasmic domain of TLR2 does not induce tumor necrosis factor-alpha production in macrophages, whereas similar dimerization of the TLR4 cytoplasmic domain does. We show that the cytoplasmic domain of TLR2 can form functional pairs with TLR6 or TLR1, and this interaction leads to cytokine induction. Thus, the cytoplasmic tails of TLRs are not functionally equivalent, with certain TLRs requiring assembly into heteromeric complexes, whereas others are active as homomeric complexes. Finally, we show that TLR6, TLR2, and TLR1 are recruited to macrophage phagosomes that contain IgG-coated erythrocytes that do not display microbial components. The data suggest that TLRs sample the contents of the phagosome independent of the nature of the contents, and can establish a combinatorial repertoire to discriminate among the large number of pathogen-associated molecular patterns found in nature.
Targeting of Cancer-Related Proteins with PNA Oligomers (2001)

Aberrant gene expression is characteristic to all cancer cells and pathophysiology in general. Selective inhibition of constitutively elevated expression of oncogenes provides an opportunity to hinder the proliferation of malignant cells. Small synthetic molecules that specifically interfere with transcription and/or translation have great potential as anticancer drugs. Currently first-generation antisense oligonucleotides are widely used to inhibit the oncogene expression. The second generation of antisense agents have been studied mainly in vitro. One of these agents, peptide nucleic acid (PNA) is an oligonucleotide mimic with a non-charged achiral polyamide backbone to which the nucleobases are linked. PNA oligomers bind tightly to complementary DNA or RNA and are very stable in biological fluids. PNA can inhibit transcription and translation of target genes by specifically hybridizing to DNA or mRNA. The in vitro experiments showing inhibition of target protein expression by PNA have been followed by the first successful applications of PNA as an antisense agent in cultured cells and also in vivo. Hopefully this will lead to a wider use of PNA in the studies of cancer biology and therapy.
Cardiorespiratory Fitness and the Incidence of Type 2 Diabetes (2003)

These results indicate that a low cardiorespiratory fitness level is an important risk factor for incidence of type 2 diabetes among Japanese men.
Lithium-Ion Transport in Nanocrystalline Spinel-Type Li[InxLiy]Br4 as Seen by Conductivity Spectroscopy and NMR (2020)

Currently, a variety of solid Li<sup>+</sup> conductors are being discussed that could potentially serve as electrolytes in all-solid-state Li-ion batteries and batteries using metallic Li as the anode. Besides oxides, sulfides and thioposphates, and also halogenides, such as Li<sub>3</sub>YBr<sub>6</sub>, belong to the group of such promising materials. Here, we report on the mechanosynthesis of ternary, nanocrystalline (defect-rich) Li[In <sub><i>x</i></sub> Li <sub><i>y</i></sub> ]Br<sub>4</sub>, which crystallizes with a spinel structure. We took advantage of a soft mechanochemical synthesis route that overcomes the limitations of classical solid-state routes, which usually require high temperatures to prepare the product. X-ray powder diffraction, combined with Rietveld analysis, was used to collect initial information about the crystal structure; it turned out that the lithium indium bromide prepared adopts cubic symmetry ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mstyle><mml:mtext>Fd</mml:mtext></mml:mstyle> <mml:mover><mml:mrow><mml:mn>3</mml:mn></mml:mrow> <mml:mo>¯</mml:mo></mml:mover> <mml:mstyle><mml:mtext>m</mml:mtext></mml:mstyle> </mml:math> ). The overall and electronic conductivity were examined via broadband conductivity spectroscopy and electrical polarization measurements. While electric modulus spectroscopy yielded information on long-range ion transport, <sup>7</sup>Li nuclear magnetic resonance (NMR) spin-lattice relaxation measurements revealed rapid, localized ionic hopping processes in the ternary bromide. Finally, we studied the influence of thermal treatment on overall conductivity, as the indium bromide might find applications in cells that are operated at high temperatures (330 K and above).
A Model of the Ventilatory Depressant Potency of Remifentanil in the Non–steady State (2003)

Remifentanil is a potent ventilatory depressant. Simulations demonstrated that remifentanil concentrations well tolerated in the steady state will cause a clinically significant hypoventilation following bolus administration, confirming the acute risk of bolus administration of fast-acting opioids in spontaneously breathing patients.
Anterograde Transneuronal Viral Tracing of Central Viscerosensory Pathways in Rats (2004)

Previous studies demonstrated that strain H129 of herpes simplex virus-1 undergoes anterograde transneuronal transport in mice and primates after peripheral or central injection. In this study, H129 was used in rats to identify CNS regions that receive relayed viscero-sensory inputs from the stomach wall. We also examined whether transneuronal viral transport in this model is exclusively anterograde. H129 or an established retrograde transneuronal viral tracer, pseudorabies virus (PRV), was injected into the ventral stomach wall in intact rats or in rats with previous subdiaphragmatic vagal sensory deafferentation. Rats were perfused with fixative 3-5 d later, and tissues were processed for immunocytochemical detection of transported virus. In intact rats, H129 was transported transneuronally via vagal and spinal viscerosensory neurons to postsynaptic target cells in the medullary dorsal vagal complex and thoracic dorsal horn, respectively, with subsequent transport to discrete regions of the medullary and pontine reticular formation, cerebellum, parabrachial nucleus, periaqueductal gray, thalamus, hypothalamus, amygdala, bed nucleus of the stria terminalis, and other central sites. Comparison of labeling patterns in intact and vagal deafferented rats indicated that H129 also produced first-order retrograde infection of autonomic neurons that project directly to virus injection sites, similar to PRV. Unlike PRV, however, H129 was not transported transneuronally in the retrograde direction from infected neurons to central sources of presynaptic input. We conclude that transneuronal transport of H129 occurs exclusively in the anterograde direction to reveal CNS regions that receive direct and relayed viscerosensory signals.
Fluorescence anisotropy assays implicate protein-protein interactions in regulating trp repressor DNA binding (1993)

The study of interactions between proteins and nucleic acids is central to the understanding of the control of genetic expression. Fluorescence anisotropy has been used to measure, in solution, the equilibrium binding profiles of a bacterial repressor protein, the tryptophan repressor (TR), to a fluorescently labeled oligonucleotide containing one of its target operator sequences. Investigation of the effects of changing concentrations of corepressor, operator DNA, and protein implicate TR oligomers in the regulation of DNA binding. These studies also demonstrate that the relatively straightforward technique of fluorescence anisotropy can be applied to the study of the interactions between proteins and nucleic acids. The fluorescence technique exhibits sufficient sensitivity to replace radioactive methods of detection in most cases. In addition, since it is a solution-based methodology, it offers a true equilibrium measure of the protein-nucleic acid equilibria, and the effects of changes in solution conditions such as salt and ligand concentration, pH, and temperature can be readily evaluated. Data acquisition is relatively simple and rapid, and the data are of sufficient quality for detailed thermodynamic analyses of complex systems. Given these attributes, fluorescence anisotropy will find multiple applications in the area of genetic regulation.
A Two-Year Trial of Oleic and Erucic Acids (“Lorenzo's Oil”) as Treatment for Adrenomyeloneuropathy (1993)

In this open trial we found no evidence of a clinically relevant benefit from dietary treatment with oleic and erucic acids ("Lorenzo's oil") in patients with adrenomyeloneuropathy.
An open-label, single-arm pilot study in patients with severe plaque-type psoriasis treated with an oral anti-inflammatory agent, apremilast (2008)

Apremilast demonstrated biological activity and improved psoriasis clinical efficacy scores in patients with severe plaque-type psoriasis. The majority of adverse events were mild in nature. Two adverse events (fatigue and dizziness) were judged by the investigator to be moderate and related to apremilast. In addition, there were no clinically-relevant abnormal laboratory test results in subjects treated with apremilast for 29 days.
Invertase beta-galactosidase hybrid proteins fail to be transported from the endoplasmic reticulum in Saccharomyces cerevisiae. (1984)

The yeast SUC2 gene codes for the secreted enzyme invertase. A series of 16 different-sized gene fusions have been constructed between this yeast gene and the Escherichia coli lacZ gene, which codes for the cytoplasmic enzyme beta-galactosidase. Various amounts of SUC2 NH2-terminal coding sequence have been fused in frame to a constant COOH-terminal coding segment of the lacZ gene, resulting in the synthesis of hybrid invertase-beta-galactosidase proteins in Saccharomyces cerevisiae. The hybrid proteins exhibit beta-galactosidase activity, and they are recognized specifically by antisera directed against either invertase or beta-galactosidase. Expression of beta-galactosidase activity is regulated in a manner similar to that observed for invertase activity expressed from a wild-type SUC2 gene: repressed in high-glucose medium and derepressed in low-glucose medium. Unlike wild-type invertase, however, the invertase-beta-galactosidase hybrid proteins are not secreted. Rather, they appear to remain trapped at a very early stage of secretory protein transit: insertion into the endoplasmic reticulum (ER). The hybrid proteins appear only to have undergone core glycosylation, an ER process, and do not receive the additional glycosyl modifications that take place in the Golgi complex. Even those hybrid proteins containing only a short segment of invertase sequences at the NH2 terminus are glycosylated, suggesting that no extensive folding of the invertase polypeptide is required before initiation of transmembrane transfer. beta-Galactosidase activity expressed by the SUC2-lacZ gene fusions cofractionates on Percoll density gradients with ER marker enzymes and not with other organelles. In addition, the hybrid proteins are not accessible to cell-surface labeling by 125I. Accumulation of the invertase-beta-galactosidase hybrid proteins within the ER does not appear to confer a growth-defective phenotype to yeast cells. In this location, however, the hybrid proteins and the beta-galactosidase activity they exhibit could provide a useful biochemical tag for yeast ER membranes.
Enhancing Stability of Camelid and Shark Single Domain Antibodies: An Overview (2017)

Single domain antibodies (sdAbs) are gaining a reputation as superior recognition elements as they combine the advantages of the specificity and affinity found in conventional antibodies with high stability and solubility. Melting temperatures (<i>T</i><sub>m</sub>s) of sdAbs cover a wide range from below 50 to over 80°C. Many sdAbs have been engineered to increase their <i>T</i><sub>m</sub>, making them stable until exposed to extreme temperatures. SdAbs derived from the variable heavy chains of camelid and shark heavy chain-only antibodies are termed VHH and VNAR, respectively, and generally exhibit some ability to refold and bind antigen after heat denaturation. This ability to refold varies from 0 to 100% and is a property dependent on both intrinsic factors of the sdAb and extrinsic conditions such as the sample buffer ionic strength, pH, and sdAb concentration. SdAbs have also been engineered to increase their solubility and refolding ability, which enable them to function even after exposure to temperatures that exceed their melting point. In addition, efforts to improve their stability at extreme pH and in the presence of chemical denaturants or proteases have been undertaken. Multiple routes have been employed to engineer sdAbs with these enhanced stabilities. The methods utilized to achieve these goals include grafting complementarity-determining regions onto stable frameworks, introduction of non-canonical disulfide bonds, random mutagenesis combined with stringent selection, point mutations such as inclusion of negative charges, and genetic fusions. Increases of up to 20°C have been realized, pushing the <i>T</i><sub>m</sub> of some sdAbs to over 90°C. Herein, we present an overview of the work done to stabilize sdAbs derived from camelids and sharks. Utilizing these various strategies sdAbs have been stabilized without significantly compromising their affinity, thereby providing superior reagents for detection, diagnostic, and therapeutic applications.