gebhart/patrepeval huggingface dataset:
Replication-Independent Long-Distance Trafficking by Viral RNAs in <i>Nicotiana benthamiana</i> (2007)

Viruses with separately encapsidated genomes could have their genomes introduced into different leaves of a plant, thus necessitating long-distance trafficking of the viral RNAs for successful infection. To examine this possibility, individual or combinations of genome segments from the tripartite Brome mosaic virus (BMV) were transiently expressed in leaves of Nicotiana benthamiana plants using engineered Agrobacterium tumefaciens. BMV RNA3 was found to traffic from the initial site of expression to other leaves of the plant, as detected by RNA gel blot analyses and also by the expression of an endoplasmic reticulum-targeted green fluorescent protein. When RNA3 trafficked into leaves containing the BMV replication enzymes, RNA replication, transcription, and virion production were observed. RNA3 trafficking occurred even when it did not encode the movement or capsid proteins. However, coexpression of the movement protein increased the trafficking of BMV RNAs. BMV RNA1 and RNA2 could also traffic throughout the plant, but less efficiently than RNA3. All three BMV RNAs trafficked bidirectionally to sink leaves near the apical meristem as well as to the source leaves at the bottom of the stem, suggesting that trafficking used the phloem. These results demonstrate that BMV RNAs can use a replication-independent mechanism to traffic in N. benthamiana.
Interferon-Alpha Promotes Th1 Response and Epithelial Apoptosis via Inflammasome Activation in Human Intestinal Mucosa (2016)

By using an ex vivo model, we show an interindividual heterogeneity of IFN alpha effects. We show that IFN alpha is able to disrupt both epithelial and immune homeostasis in the human intestine, by activation of an innate immunity platform, the inflammasome, which drives a Th1 response and leads to epithelial barrier disruption.
Composite materials with enhanced dimensionless Young’s modulus and desired Poisson’s ratio (2015)

Abstract We have designed a new type of composite materials which not only has a Young’s modulus much larger than the Voigt limit, but also is always nearly isotropic. Moreover, its Poisson’s ratio can be designed at a desired value, e.g. positive, or negative, or zero. We have also demonstrated that structural hierarchy can help to enhance the stiffness of this type of composite materials. The results obtained in this paper provide a very useful insight into the development of new functional materials and structures.
Involvement of Arabidopsis Clock-Associated Pseudo-Response Regulators in Diurnal Oscillations of Gene Expression in the Presence of Environmental Time Cues (2008)

In plants, the circadian clock is implicated in the biological system that generates diurnal oscillations in cellular and physiological activities. The circadian clock must be synchronized (or entrained) to local time by environmental time cues, such as light/dark and/or hot/cold cycles. In Arabidopsis thaliana, although a number of clock-associated components have been uncovered over the last decade, the clock-associated elements that are involved in entrainment to environmental time cues are largely unknown. In this regard, we have been characterizing one core group of clock components that together control the pace of the central oscillator, including PSEUDO-RESPONSE REGULATOR9 (PRR9), PRR7, PRR5 and TIMING OF CAB2 EXPRESSION 1 (TOC1; or PRR1). The primary aim of this study is to clarify whether these PRR members are implicated in entrainment of the circadian clock to environmental time cues. For this purpose, the diurnal oscillation profiles of clock-controlled genes in the presence of environmental time cues were determined in a set of prr mutants, including a prr9 prr7 prr5 toc1 quadruple mutant. As an extreme phenotype, the prr9-10 prr7-11 prr5-11 toc1-2 quadruple mutant showed an arrhythmia phenotype even under light/dark and hot/cold cycles. In contrast, a cca1-1 lhy-11 toc1-2 triple mutant maintained robust oscillations in the presence of these environmental time cues, although their phases were markedly affected. Based on these results, we propose that the clock components PRR9, PRR7 and PRR5 together might represent elements necessary for the circadian clock to entrain properly to local time in response to light/dark and hot/cold cycles in natural habitats.
Plasma Levels of Adiponectin, a Novel Adipocyte‐Derived Hormone, in Sleep Apnea<sup>**</sup> (2005)

Plasma adiponectin levels are elevated in otherwise healthy subjects with OSA. Therefore, low adiponectin is unlikely to explain the association between OSA and cardiovascular disease.
Debittering and nutritional upgrading of enzymic casein hydrolysates (1981)

Abstract Commercially‐available proteolytic enzymes were used to prepare casein hydrolysates. Treatment of the hydrolysates with activated carbon resulted in the elimination of the bitter taste which developed during the course of hydrolysis. However, the debittering step was accompanied by a selective loss of tryptophan (63%), phenylalanine (36%) and arginine (30%). Consequently, the activated‐carbon‐treated hydrolysates exhibited poor nutritional quality in rat feeding studies. Supplementation of the treated hydrolysates with the proper amounts of tryptophan and phenylalanine greatly improved their nutritional quality. A simulated milk formula based on a partially debittered hydrolysate, resulted in a product of reasonably good nutritive value. The study demonstrates that an optimum balance between debittering by activated carbon and supplementation with tryptophan and phenylalanine is feasible. This will permit the production of casein hydrolysates of acceptable taste and of high nutritive quality.
Novel phase‐locked loop with digital control techniques (1990)

Abstract Recently, a number of digital phase‐locked loops (DPLL) have been studied. In the usual DPLLs, a divider is added to the output so that the discontinuous and sudden variations in the frequency and phase adjustment by digital operations can be averaged and smoothed. Hence, in the usual DPLLs, an internal clock oscillator with its frequency several tens times the input frequency is needed. This requirement places a certain limit in the input frequency by the maximum operating frequency of the digital logic circuit if the DPLL is used for a high input frequency. This paper proposes a phase‐locked loop (DC‐PLL) in which no divider is used and a clock frequency is almost equal to that of the input signal used for digital control. The free running frequency of the loop is equal to the clock frequency. The waveform of the clock signal is transformed to a saw‐toothed signal and the content of the reversible counter is transformed to a dc signal by a D‐A converter. These two signals are injected simultaneously to the voltage comparator so that the comparator outputs at the moment the former exceeds the latter. This is the output signal of the system. By the phase control signal, the content of the reversible counter varies and the output dc level of the D‐A converter also varies. At the same time, the phase of the output signal changes so that the phase control is accomplished. The characteristics of the proposed phase‐locked loop are confirmed to be identical to those of the conventional DPLL in which a divider is used.
Current Directions in the Auricular Vagus Nerve Stimulation II – An Engineering Perspective (2019)

Electrical stimulation of the auricular vagus nerve (aVNS) is an emerging electroceutical technology in the field of bioelectronic medicine with applications in therapy. Artificial modulation of the afferent vagus nerve - a powerful entrance to the brain - affects a large number of physiological processes implicating interactions between the brain and body. Engineering aspects of aVNS determine its efficiency in application. The relevant safety and regulatory issues need to be appropriately addressed. In particular, <i>in silico</i> modeling acts as a tool for aVNS optimization. The evolution of personalized electroceuticals using novel architectures of the closed-loop aVNS paradigms with biofeedback can be expected to optimally meet therapy needs. For the first time, two international workshops on aVNS have been held in Warsaw and Vienna in 2017 within the scope of EU COST Action "European network for innovative uses of EMFs in biomedical applications (BM1309)." Both workshops focused critically on the driving physiological mechanisms of aVNS, its experimental and clinical studies in animals and humans, <i>in silico</i> aVNS studies, technological advancements, and regulatory barriers. The results of the workshops are covered in two reviews, covering physiological and engineering aspects. The present review summarizes on engineering aspects - a discussion of physiological aspects is provided by our accompanying article (Kaniusas et al., 2019). Both reviews build a reasonable bridge from the rationale of aVNS as a therapeutic tool to current research lines, all of them being highly relevant for the promising aVNS technology to reach the patient.
ELEVATED LEVELS OF PETITE FORMATION IN STRAINS OF <i>SACCHAROMYCES CEREVISIAE</i> RESTORED TO RESPIRATORY COMPETENCE. II. ORGANIZATION OF MITOCHONDRIAL GENOMES IN STRAINS HAVING HIGH AND MODERATE FREQUENCIES OF PETITE MUTANT FORMATION (1985)

Restriction enzyme analysis of aberrant mtDNA molecules in restored strains of Saccharomyces cerevisiae that displays an elevated level of petite formation has shown the occurrence of novel junction fragments and nonstoichiometric amounts for some unaltered bands. Five aberrant mitochondrial genomes from high-frequency petite-forming (hfp) strains (greater than 60% petites per generation) contain like-oriented duplications and single copy regions. High-frequency petite formation is postulated to arise from increased intramolecular recombination between duplicated segments. Mitochondrial DNA structures in two other hfp strains cannot be easily interpreted and might arise from intramolecular recombination. Mitochondria DNA from moderate-frequency petite-forming (mfp) strains (5-16% petites per generation) contains inverted duplications in two cases. The elevated petite formation is postulated to arise from homologous recombination between directly repeated sequences. In mtDNA from one mfp strain, deletion end-points have been shown to overlap. Such deletion endpoint overlap is postulated to be required for the maintenance of the tandem duplication in hfp strains. Two regions of the wild-type mtDNA (between cyb and oli2 and between SrRNA and oxi2) appear to be dispensable for mitochondrial function.
Diffraction Tomography Using Arbitrary Transmitter and Receiver Surfaces (1984)

The theory of diffraction tomography for two-dimensional objects within the Born approximation is presented for cases where the scattered field is measured over arbitrarily shaped boundaries surrounding the object. Reconstruction algorithms are presented for both plane wave (parallel beam) and cylindrical wave (fan beam) insonification. Special attention is devoted to cases where the measurement and source boundaries are either lines or circles. The theory and algorithms presented are shown to be readily extended to the case of three-dimensional objects.
High-dose helium-implanted single-crystal silicon: Annealing behavior (1998)

The modifications induced in single-crystal silicon by implanted helium have been investigated by ion beam techniques. The damage has been detected by 2 MeV He+4 backscattering in channeling conditions and the helium in-depth distribution by 7 and 8 MeV N++15 elastic recoil scattering. The samples prepared by implanting 2×1016 cm−2 helium ions at 20 keV in silicon wafers held either at 77 K (LNT sample) or at 300 K (RT sample) have been heat treated for 2 h in the 100–800 °C temperature range. In the as-implanted LNT sample the damage maximum is at 130±20 nm and shifts in-depth to 180±10 nm after annealing at 200 °C, in the as-implanted RT sample, the damage maximum is already located at 180±10 nm. In the 250–500 °C temperature range, the LNT and RT samples follow the same annealing path with only slight differences in the temperature values; in both cases, the dechanneling signal increases and reaches a maximum value of nonregistered silicon atoms of 2.2–2.5×1022 at/cm3. In the same temperature range, the helium signal becomes narrower, builds up in a region centered on 220±20 nm and no appreciable loss of helium can be detected. The growth of the damage is consistent with the creation of cracks and a etherogenous distribution of bubbles filled with high pressure helium which stress the lattice; for the channeling Rutherford backscattering technique, their action is similar to silicon interstitials. At temperatures above 500 °C, helium is released from the samples; this process is associated with a decrease of the damage and the formation and increase in size of voids. At 900 °C empty voids with a diameter around 20 nm are found.
Downstream of Phosphatidylinositol-3 Kinase, a Multifunctional Signaling Molecule, and Its Regulation in Cell Responses (1998)

Phosphatidylinositol (PI)-3 kinase is an enzyme that phosphorylates the D-3 position of PI and its derivatives. It is activated immediately after growth factor or differentiation factor stimulation, suggesting that PI-3 kinase is involved in signal transduction of the stimulation. PI-3 kinase appears to play various important roles including signaling to the nucleus, vesicle transport, and rearrangement of the cytoskeleton since many cell responses which require these events are affected by inhibition or activation of PI-3 kinase. To understand how PI-3 kinase can act in such multiple ways, it is important to identify the factors downstream of PI-3 kinase. In this review, we discuss the factors downstream of PI-3 kinase and the methods used to identify them. Recent studies revealed that some proteins involved in vesicle transport or in rearrangement of the cytoskeleton are regulated by the phospholipids generated by PI-3 kinase, implying the mechanism by which PI-3 kinase regulates these cell responses.
Fusogenic potential of prokaryotic membrane lipids. (2001)

Development of protective immunity against many pathogens, particularly viruses, requires fine orchestration of both humoral- and cell mediated-immunity. The immunization of animals with soluble antigens usually leads to the induction of humoral immune responses. In contrast, the activation of a cell-mediated immune response against exogenous antigens has always been a challenge, requiring special strategies to expose them to the proteasome, a multifunctional protease complex in the cytosol of the target cells. The degradation of the protein by the cytosolic proteolytic system forms a cardinal step for the induction of cytotoxic T lymphocytes (CTLs). In the present study, we report that a potent primary CTL response against a soluble protein, ovalbumin, can be induced in mice by encapsulating it in the liposomes comprised of Escherichia coli membrane lipids. These lipids were shown to induce strong membrane-membrane fusion as evident from resonance energy transfer and content mixing assays. Furthermore, the fusion of these liposomes with living cells (J774 A1) was demonstrated to result in effective transfer of a fluorescent lipid probe to the plasma membrane of the cells. Moreover, ricin A, a protein synthesis inhibitor that does not cross plasma membrane, was demonstrated to gain access to the cytosol when it was encapsulated in these liposomes. Finally, the liposomes were demonstrated to behave like efficient vehicles for the in vivo delivery of the antigens to the target cells resulting in the elicitation of antigen reactive CD8+ T cell responses.
Different Foci for the Regulation of the Activity of the KefB and KefC Glutathione-gated K+ Efflux Systems (1999)

KefB and KefC are glutathione-gated K+ efflux systems in Escherichia coli, and the proteins exhibit strong similarity at the level of both primary sequence and domain organization. The proteins are maintained closed by glutathione and are activated by binding of adducts formed between glutathione and electrophiles. By construction of equivalent mutations in each protein, this study has analyzed the control over inactive state of the proteins. A UV-induced mutation in KefB, L75S, causes rapid spontaneous K+ efflux but has only a minor effect on K+ efflux via KefC. Similarly amino acid substitutions that cause increased spontaneous activity in KefC have only small effects in KefB. Exchange of an eight amino acid region from KefC (HALESDIE) with the equivalent sequence from KefB (HELETAID) has identified a role for a group of acidic residues in controlling KefC activity. The mutations HELETAID and L74S in KefC act synergistically, and the activity of the resultant protein resembles that of KefB. We conclude that, despite the high degree of sequence similarity, KefB and KefC exhibit different sensitivities to the same site-specific mutations.
Poly(methyl methacrylate) copolymers containing dipyrrolylquinoxaline receptors for the colorimetric detection of halide anion salts (2011)

Described herein is the synthesis of a dipyrrolylquinoxaline (DPQ) monomeric species containing methacrylamide functionality, and its subsequent copolymerisation with methyl methacrylate (MMA). The resulting copolymers were drop casted onto glass substrates, and the resulting thin films displayed distinct colorimetric change upon exposure to hydrofluoric acid (HF) vapour. Furthermore, glass substrates coated with the DPQ–MMA copolymer could be used as ‘dip sticks’ to test for trace acid in solution, turning from yellow to red upon immersion in an aqueous solution of HF. Analysis by UV–vis spectroscopic titration allowed the association constant (K a) for interaction with fluoride (as the tetrabutylammonium salt) to be calculated as 6.16 × 105 M− 1 in CH2Cl2. Polymer coatings of this type could find applications in the colorimetric detection of HF vapour, a common hazard associated with industrial processes, such as aluminium smelting.
Analysis of packet loss processes in high-speed networks (2002)

The exact distribution of the number of lost packets in a block of given size is obtained and compared with the distribution under the assumption of independent and identical packet loss probability (the i.i.d. distribution). Numerical examples show that the exact distribution may be worse for applications such as forward error correction.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Isonitrile, XIX. Die Kondensation von Carbonsäuren, Aldehyden und Isonitrilen mit primären aliphatischen Aminen, die einen abspaltbaren Alkyl‐ oder Alkenyl‐Rest tragen (1964)

Abstract Durch Kondensation von Carbonsäuren, Aldehyden und Isonitrilen mit β‐Amino‐carbonsäureestern oder resonanzstabilisierten primären Enaminen werden α‐[Acyl‐ alkyl (bzw. alkenyl)‐amino]‐carbonsäureamide erhalten, die durch schonende Behandlung mit Basen bzw. Säuren in α‐Acylamino‐carbonsäureamide übergeführt werden können. Die Vereinigung von 2.2‐Dimethyl‐ bzw. 2.2.5.5‐Tetramethyl‐Δ 3 ‐thiazolin mit Phthalylglycin und Isocyanessigsäure‐tert.‐butylester führt zu Tripeptid‐Derivaten, die sich vom Cystein und Penicillamin ableiten. Die Untersuchungen wurden als Vorversuche für Peptid‐Synthesen durch α‐Aminoalkylierung von Isonitrilen in Kombination mit Carbonsäuren 3) durchgeführt.
Civil War Time: From Grotius to the Global War on Terror (2017)

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Physiological and ecological studies on the oestrogenic isoflavones in subterranean clover ( <i>T. subterraneum</i> L.) IV. Effects of zinc deficiency in clover seedlings. (1967)

Results of a glasshouse experiment, conducted on an acutely zinc-deficient soil, are presented. At day 29, the cotyledons and unifoliate leaves of zinc-deficient plants showed higher isoflavone concentrations, and markedly higher total isoflavones per leaf, than did those of plants supplied with zinc. At day 47, however, when the "little leaf" condition was well advanced in the zinc-deficient plants, trifoliate leaves of the deficient plants were lower in isoflavone levels (and especially in isoflavones per leaf) than those of normal plants. The patterns of isoflavone distribution correspond with, and are thought to result from, effects of zinc deficiency in the seedling stage on photosynthetic accumulation in plant parts. It is considered that zinc deficiency in the field is unlikely to affect the incidence of "clover disease".
Quantitative measurement of EUV resist outgassing (2007)

The Mo/Si multilayer mirrors used for extreme ultraviolet (EUV) lithography can become contaminated during exposure in the presence of some hydrocarbons [1-3]. Because this leads to a loss in the reflectivity of the optics and throughput of the exposure tools, it needs to be avoided. Since photoresists are known to outgas during exposure to EUV radiation in a vacuum environment, the careful choice of materials is important to preserving the EUV optics. Work therefore has been performed to measure the species and quantities of molecules that outgas from EUV resists when exposed to EUV radiation [4-7].
<i>Hox</i> Genes: From Leukemia to Hematopoietic Stem Cell Expansion (2005)

Hox genes are clearly implicated in leukemia; however, neither the specificity of the leukemogenic potential among Hox genes of different paralog groups nor the role of the homeodomain is clear. We tested the leukemogenic potential of various NUP98-Hox fusion genes alone and with MEIS1. All genes tested had a significant overlapping effect in bone marrow cells in vitro. However, not all formed strong leukemogenic NUP98 fusion genes; but together with overexpression of MEIS1, all induced myeloid leukemia. This phenomenon was also seen with NUP98 fusions containing only the homeodomain of the corresponding Hox protein. We then exploited the strong transforming potential of NUP98-HOXD13 and NUP98-HOXA10 to establish preleukemic myeloid lines composed of early myeloid progenitors with extensive in vitro self-renewal capacity, short-term myeloid repopulating activity, and low propensity for spontaneous leukemic conversion. We also showed that MEIS1 can efficiently induce their conversion to leukemic stem cells, thus providing a novel model for the study of leukemic progression. In contrast to the leukemogenic effect of most of the Hox genes tested, HOXB4 has the ability to increase the self-renewal of hematopoietic stem cells without disrupting normal differentiation. On the basis of the discovery that the leukemogenic gene HOXA9 can also expand hematopoietic stem cells, we compared the ability of NUP98-Hox fusions to that of HOXB4 to trigger HSC expansion in vitro. Our preliminary results indicate that the expanding potential of HOXB4 is retained and even augmented by fusion to NUP98. Moreover, even greater expansion may be possible using Abd-B-like Hox fusions genes.
Isolation and characterisation of an oxygen, acid and bile resistant <i>Bifidobacterium animalis</i> subsp. <i>lactis</i> Qq08 (2010)

We isolated an aerotolerant bifidobacterium and identified it as Bifidobacterium animalis subsp. lactis Qq08. This strain has characteristics more favourable than the commercial probiotic strain, Bifidobacterium lactis Bb12.
Relationship between tumor size and disease stage in non-small cell lung cancer (2010)

There is a statistically significant relationship between tumor size and distribution of disease stage of primary NSCLC tumors: the smaller the tumor, the more likely the disease is N0M0 status.
Image processing by four-wave mixing in photorefractive GaAs (1987)

Three image processing experiments were performed by degenerate four-wave mixing in photorefractive GaAs. The experiments were imaging by phase conjugation, edge enhancement, and autocorrelation. The results show that undoped, semi-insulating, liquid-encapsulated Czochralski-grown GaAs crystals can be used as effective optical processing media despite their small electro-optic coefficient.