gebhart/patrepeval huggingface dataset:
Essential Role of Selenium in the Catalytic Activities of Mammalian Thioredoxin Reductase Revealed by Characterization of Recombinant Enzymes with Selenocysteine Mutations (2000)

Mammalian thioredoxin reductases (TrxR) are dimers homologous to glutathione reductase with a selenocysteine (SeCys) residue in the conserved C-terminal sequence -Gly-Cys-SeCys-Gly. We removed the selenocysteine insertion sequence in the rat gene, and we changed the SeCys(498) encoded by TGA to Cys or Ser by mutagenesis. The truncated protein having the C-terminal SeCys-Gly dipeptide deleted, expected in selenium deficiency, was also engineered. All three mutant enzymes were overexpressed in Escherichia coli and purified to homogeneity with 1 mol of FAD per monomeric subunit. Anaerobic titrations with NADPH rapidly generated the A(540 nm) absorbance resulting from the thiolate-flavin charge transfer complex characteristic of mammalian TrxR. However, only the SeCys(498) --> Cys enzyme showed catalytic activity in reduction of thioredoxin, with a 100-fold lower k(cat) and a 10-fold lower K(m) compared with the wild type rat enzyme. The pH optimum of the SeCys(498) --> Cys mutant enzyme was 9 as opposed to 7 for the wild type TrxR, strongly suggesting involvement of the low pK(a) SeCys selenol in the enzyme mechanism. Whereas H(2)O(2) was a substrate for the wild type enzyme, all mutant enzymes lacked hydroperoxidase activity. Thus selenium is required for the catalytic activities of TrxR explaining the essential role of this trace element in cell growth.
Cytokines and immunity to viral infections (1997)

In this review, we discuss two broad approaches we have taken to study the role of cytokines and chemokines in antiviral immunity. Firstly, recombinant vaccinia viruses were engineered to express genes encoding cytokines and chemokines of interest. Potent antiviral activity was mediated by many of these encoded factors, including IL-2, IL-12, IFN-gamma, TNF-alpha, CD40L, Mig and Crg-2. In some cases, host defense mechanisms were induced (IL-2, IL-12, Mig and Crg-2), whilst for others, a direct antiviral effect was demonstrated (IFN-gamma, TNF-alpha and CD40L). In sharp contrast, vector-directed expression of IL-4, a type 2 factor, greatly increased virus virulence, due to a downregulation of host type 1 immune responses. Our second experimental approach involved the use of strains of mice deficient for the production of particular cytokines or their receptors, often in combination with our engineered viruses. Mice deficient in either IFN-gamma, IFN-gamma R, IFN-alpha/beta R, TNFRs, CD40 or IL-6 were, in general, highly susceptible to poxvirus infection. Surprisingly, not only the TNFR1, but also the TNFR2, was able to mediate the antiviral effects of TNF-alpha in vivo, whilst the antiviral activity observed following CD40-CD40L interaction is a newly defined function which may involve apoptosis of infected cells. Through the use of perforin-deficient mice, we were able to demonstrate a requirement for this molecule in the clearance of some viruses, such as ectromelia virus, whilst for others, such as vaccinia virus, perforin was less important but IFN-gamma was essential.
High-performance Sagnac interferometer using cooled detectors for infrared LWIR hyperspectral imaging (2007)

An interferometric spectrometer is proposed for low resource LWIR hyperspectral imaging. Scaling from an uncooled LWIR HSI system, we find that signal to noise ratios of 1000 or higher can be achieved with cooled detectors and uncooled optics. Signal flux is high enough to collect high quality data at very high rates (500Hz and above). Sensitivity is limited by the full well of the detector and the spectral resolution for scenes at typical temperatures.
Comparison of rates of virus isolation from leukocyte populations separated from blood by conventional and Ficoll-Paque/Macrodex methods (1979)

One hundred fifty-two blood specimens, largely from immunocompromised patients, were collected in heparinized Vacutainer tubes and divided into paired aliquots of equal volume. Buffy-coat preparations, containing mixed leukocyte and separate mononuclear and polymorphonuclear leukocyte populations were obtained by treatment of blood with conventional and Ficoll-Paque/Macrodex (F-P/M) methods. The development of cytopathic effect in monolayers of WI-38 fibroblasts inoculated with cell suspensions derived from the two methods was used to assess virus infectivity. Twice as many virus isolations were obtained using F-P/M. Of those viruses isolated by both conventional and F-P/M, the development of cytopathic effect was more extensive using the latter method. Moreover, a greater variety of viruses was isolated using F-P/M method, as compared to the conventional method. The F-P/M method is no more time consuming than conventional procedures, is readily adaptable for use in the diagnostic virology laboratory, requires only minimal additional cost, and is a particularly suitable and effective means of monitoring viremia.
Amplification and expression of the β‐glucuronidase gene in maize plants by vectors based on maize streak virus (1994)

Maize streak virus (MSV) is a geminivirus infecting monocotyledonous plants. Its genome consists of one molecule of circular, single‐stranded DNA of 2.7 kb. The viral DNA can be efficiently introduced into maize plants by agroinfection which results in systemic infection. To explore the potential of MSV as a replicative gene vector, a reporter gene coding for β‐glucuronidase (GUS) was inserted into the non‐coding region of the viral genome. The resulting construct (MSV—GUS) of about 5.9 kb was still able to replicate in cells of maize plants although it was unable to induce viral symptoms. This replication led to a five to 10‐fold increase in the mean number of GUS‐positive spots per plant as compared with infections with the GUS gene without the MSV replicon. MSV—D—GUS, which differed from MSV—GUS by the deletion of genes V1 and V2 encoding a putative movement protein and the coat protein, respectively, also replicated and produced even more GUS‐positive spots. In both MSV—GUS‐ and MSV—D—GUS‐infected plants, the GUS‐positive spots were located mainly on the veins of leaves whose primodia had already developed at the time of inoculation and never on the leaves developing later. Thus, neither viral construct was able to move systemically, most probably because the DNAs were too large to be packaged.
Rapid Commun. Mass Spectrom.10. 1629-1637 (1996) Matrix-assisted Laser Desorption/Ionisation Mass Spectrometry in Milk Science (1997)

The interpretation of the mass spectra of new phosphorus containing organic compounds is presented. In these compounds, the phosphorylated hydrazono group, >C = N-NH-P(X)(OR)2, (X = O, S; R = CH3, C2H5), is condensed on the annular carbon from the 3-methyl-2(3H)benzoxazolone ring. Elucidation of the fragmentation pathways was aided by exact mass measurements and the observation of metastable transitions. © 1997 John Wiley & Sons, Ltd.
Detection of native‐like models for amino acid sequences of unknown three‐dimensional structure in a data base of known protein conformations (1992)

We present an approach which can be used to identify native-like folds in a data base of protein conformations in the absence of any sequence homology to proteins in the data base. The method is based on a knowledge-based force field derived from a set of known protein conformations. A given sequence is mounted on all conformations in the data base and the associated energies are calculated. Using several conformations and sequences from the globin family we show that the native conformation is identified correctly. In fact the resolution of the force field is high enough to discriminate between a native fold and several closely related conformations. We then apply the procedure to several globins of known sequence but unknown three dimensional structure. The homology of these sequences to globins of known structures in the data base ranges from 49 to 17%. With one exception we find that for all globin sequences one of the known globin folds is identified as the most favorable conformation. These results are obtained using a force field derived from a data base devoid of globins of known structure. We briefly discuss useful applications in protein structural research and future development of our approach.
Prioritization strategies for pandemic influenza vaccine in 27 countries of the European Union and the Global Health Security Action Group: a review (2007)

In the majority of the countries the establishment of vaccine priority groups, ranking and underlying rationales are in line with WHO recommendations. In most public plans the criteria by which prioritized groups are identified are not easily recognizable. Clarity however, may be necessary to assure public acceptability of the prioritization. Ethical experts, results of modelling exercises could play an increasing role in the future decision making process.
Mechanisms of Autoimmunity (2004)

Autoantibodies and autoreactive T cells, which exist even in healthy individuals, are usually regulated by a mechanism called immunological tolerance. For example, peripheral T cells are subject to various types of regulatory mechanisms, including clonal deletion, anergy, clonal ignorance, and T cells with regulatory functions. It is believed that autoimmune response may initiate when such regulated immune responses are pathologically activated by a certain trigger, probably a limited antigenic stimulation. Thereafter, other factors that promote autoimmune responses combine to develop an autoimmune disease. It is esti- mated that T cells are closely involved in these reactions.
Expression of TLR-2, TLR-4, NOD2 and pNF-κB in a Neonatal Rat Model of Necrotizing Enterocolitis (2007)

These results show that this rat model of NEC induced mucosal injury, leading to a highly responsive IEC phenotype and suggesting that alterations in the innate immune system participates in the pathogenesis of NEC and are enhanced by prematurity.
Magnetic Properties of Fe3Pt Invar Alloy (1979)

Magnetization, magnetostriction and magnetic anisotropy of Fe 3 Pt Invar alloys were investigated by changing the degree of long range order. The anomalous behaviour was found in magnetostriction and magnetic torque curves in the ordered Fe 3 Pt alloy at low temperatures. These anomalies are interpreted in terms of the reversible martensitic transformation caused by magnetic energy change.
Improved affinity of a chicken single-chain antibody to avian infectious bronchitis virus by site-directed mutagenesis of complementarity-determining region H3 (2011)

Affinity maturation of antibodies using random or site-directed mutagenesis provides the potential to change the properties of antibodies in vitro . We used site-directed mutagenesis to improve the binding affinity of an anti-avian infectious bronchitis virus (IBV) single-chain antibody ZL.80 with low affinity. Twelve highly variable residues in the third heavy chain complementarity-determining region (CDR H3) of ZL.80 were mutated to alanine, to determine their contributions to antigen binding. Only mutations at Cys H105, Asp H106 and Val H108 inhibited its binding to IBV in indirect enzyme-linked immunosorbent assays. These three sites were then substituted with tyrosine, arginine and serine, because these were considered to be beneficial to protein-protein interactions. The mutant Val H108 Tyr demonstrated a 12.9-fold increase in affinity compared to parental ZL.80. This study demonstrates that the affinity of single-chain variable fragments can be improved by a single amino acid substitution in the CDR H3 with no change in specificity, indicating that tyrosine could play an important role in antigen binding. Key words: Single-chain variable fragments (scFvs), affinity maturation, avian infectious bronchitis virus (IBV), third heavy chain complementarity-determining region (CDR H3).
A uniform system for microRNA annotation (2003)

MicroRNAs (miRNAs) are small noncoding RNA gene products about 22 nt long that are processed by Dicer from precursors with a characteristic hairpin secondary structure. Guidelines are presented for the identification and annotation of new miRNAs from diverse organisms, particularly so that miRNAs can be reliably distinguished from other RNAs such as small interfering RNAs. We describe specific criteria for the experimental verification of miRNAs, and conventions for naming miRNAs and miRNA genes. Finally, an online clearinghouse for miRNA gene name assignments is provided by the Rfam database of RNA families.
Temperature calibration of CMOS magnetic vector probe for contactless angle measurement system (2002)

This paper reports on the offset behavior of an integrated CMOS magnetotransistor vector probe. For the first time, measurement results on the temperature dependence of the offset and on its time stability are presented. They encourage the realization of a temperature calibrated angle measurement system. This system consists of a two dimensional magnetic sensor integrated with circuitry on a single chip in combination with a small permanent magnet. It exhibits 1/spl deg/ resolution and 3/spl deg/ accuracy.
Lipid tucaresol as an adjuvant for methamphetamine vaccine development (2014)

The immunopotentiator tucaresol was modified for incorporation into liposomes, where it was found to be a superior adjuvant to MPLA for vaccination against methamphetamine.
Gut bacterial tyrosine decarboxylases restrict levels of levodopa in the treatment of Parkinson’s disease (2019)

Human gut microbiota senses its environment and responds by releasing metabolites, some of which are key regulators of human health and disease. In this study, we characterize gut-associated bacteria in their ability to decarboxylate levodopa to dopamine via tyrosine decarboxylases. Bacterial tyrosine decarboxylases efficiently convert levodopa to dopamine, even in the presence of tyrosine, a competitive substrate, or inhibitors of human decarboxylase. In situ levels of levodopa are compromised by high abundance of gut bacterial tyrosine decarboxylase in patients with Parkinson's disease. Finally, the higher relative abundance of bacterial tyrosine decarboxylases at the site of levodopa absorption, proximal small intestine, had a significant impact on levels of levodopa in the plasma of rats. Our results highlight the role of microbial metabolism in drug availability, and specifically, that abundance of bacterial tyrosine decarboxylase in the proximal small intestine can explain the increased dosage regimen of levodopa treatment in Parkinson's disease patients.
Synthesis of Na 0.5 K 0.5 NbO 3 Piezoelectrics by a Solution Coating Approach (2008)

The solution coating method is shown to provide more homogeneous mixing of the starting powders and purer (Na 0.5 K 0.5 )NbO 3 (NKN) powder than the conventional method thereby rendering cold isostatic pressing unnecessary. Sintering NKN with potassium copper niobate (KCN) by uniaxial pressing gave a relative bulk density of 92%, d 33 coefficient of 112 pC/N and a loss factor of 1% after 6 h at 1100°C. In contrast, the conventional method yielded 84% relative bulk density and a 31% loss factor after 6 h at 1100°C and the sample was too porous to allow for dielectric and piezoelectric measurements.
Complexity-effective multicore coherence (2012)

Much of the complexity and overhead (directory, state bits, invalidations) of a typical directory coherence implementation stems from the effort to make it "invisible" even to the strongest memory consistency model. In this paper, we show that a much simpler, directory-less/broadcast-less, multicore coherence can outperform a directory protocol but without its complexity and overhead. Motivated by recent efforts to simplify coherence, we propose a hardware approach that does not require any application guidance. The cornerstone of our approach is a dynamic, application-transparent, write-policy (write-back for private data, write-through for shared data), simplifying the protocol to just two stable states. Self-invalidation of the shared data at synchronization points allows us to remove the directory (and invalidations) completely, with just a data-race-free guarantee from software. This leads to our main result: a virtually costless coherence that outperforms a MESI directory protocol (by 4.8%) while at the same time reducing shared cache and network energy consumption (by 14.2%) for 15 parallel benchmarks, on 16 cores.
NIDDM and Its Metabolic Control Predict Coronary Heart Disease in Elderly Subjects (1994)

The aim of this study was to evaluate whether noninsulin-dependent diabetes (NIDDM) and its metabolic control and duration predict coronary heart disease (CHD) events during a 3.5-year follow-up in a randomly selected Finnish population sample 65-74 years of age at baseline. Of 1,298 subjects participating in the baseline study, 1,069 were nondiabetic and 229 had NIDDM. During the follow-up, 3.4% of nondiabetic and 14.8% of NIDDM subjects died from CHD or had a nonfatal myocardial infarction (MI). The impact of NIDDM on CHD mortality and morbidity was more marked in women than in men. Odds ratios (ORs) and their 95% confidence intervals for CHD death and nonfatal MI in women with NIDDM compared with women with normal glucose tolerance were 11.7 (3.8-36.4) and 4.7 (3.6-6.1). In men, the corresponding ORs were 0.43 (0.1-1.9) and 1.4 (0.6-3.2). In multiple logistic regression analyses including all study subjects, NIDDM (P < 0.01), male sex (P < 0.05), and previous MI (P < 0.01) predicted CHD death (n = 45). NIDDM (P < 0.01), male sex (P < 0.05), previous MI (P < 0.05), current smoking (P < 0.001), systolic blood pressure (P < 0.001), and low high-density lipoprotein cholesterol (P < 0.01) predicted all CHD events (CHD death or nonfatal MI) (n = 107). In NIDDM subjects, only glycated hemoglobin A1c (GHbA1c) at baseline (P < 0.01) and duration of diabetes (P < 0.05) predicted CHD death (n = 15) and all CHD events (n = 33). There was a significant increase in the risk of CHD death and all CHD events in NIDDM subjects with GHbA1c levels higher than 7.0% compared with diabetic subjects with lower GHbA1c (ORs 4.3 [1.1-16.7] and 2.2 [1.0-5.1]). In conclusion, NIDDM and its metabolic control and the duration of diabetes are important predictors of CHD in elderly subjects, particularly in women.
Infrared Light‐Emitting Diode Radiation Causes Gravitropic and Morphological Effects in Dark‐Grown Oat Seedlings (1996)

Oat (Avena sativa cv Seger) seedlings were irradiated with IR light-emitting diode (LED) radiation passed through a visible-light-blocking filter. Infrared LED irradiated seedlings exhibited differences in growth and gravitropic response when compared to seedlings grown in darkness at the same temperature. Thus, the oat seedlings in this study were able to detect IR LED radiation. These findings call into question the use of IR LED as a safe-light for some photosensitive plant response experiments. These findings also expand the defined range of wavelengths involved in radiation-gravity (light-gravity) interactions to include wavelengths in the IR region of the spectrum.
[Reduction of radical cavities by homologous cartilage chips]. (1985)

The article reviews, first of all, the common obliteration methods of radical cavities. This is followed by a description of the author's own technique which has been practiced for the last 13 years. This method employs preserved (Cialit solution 1:5000) homologous septal cartilage chips, shaped into small cubes of 3-4 mm. size. The chips are implanted in obscure districts (apical mastoid, sinus dura angle) of radical cavities for primary or secondary (old cavities) partial obliteration, as shown in Figs. 1 and 2. Crushed homologous septal cartilage plates and temporal muscle fascia are placed additionally on the chips. The effect is the construction of a small, easy-care cavity, which can be appreciated at a glance. Statistical results of 314 cases (170 cases of primary obliteration, 144 old cavities) are presented. Chips in cavities are well tolerated. Chips were partially rejected in 13 cases only, whereas in 3 cases they were completely rejected. A permanent dry cavity and dry ear was achieved in 86% of the cases. Cholesteatoma recurred in 5 cases. The homologous cartilage technique is contraindicated in fistulas on the labyrinth or fenestra, as well as in exposed facial nerve or dehiscence of the facial nerve canal, in case of healed fistula of the dura, and in dissection of the sinus sigmoideus. In these cases, autologous cartilage (tragus, cavum conchae) must be implanted. One of the most important advantages of this method is that there is no crumpling up of the obliterated areas and no retractions over a longer period of time, compared with other relevant techniques (i.e., pedicled subcutis muscle grafts or free tissue flaps).
Performance of dual-gate GaAs MESFETs as gain-controlled low-noise amplifiers and high-speed modulators (1975)

A dual-gate GaAs MESFET with maximum gain of 18 dB at 10 GHz and minimum noise figure of 4 dB with 12 dB associated gain will be described. Variation of second gate potential has been found to yield gain modulation with a 44 dB dynamic range and 70 ps risetime.
Quorum sensing inhibitors: a bargain of effects (2006)

Many opportunistic pathogenic bacteria rely on quorum sensing (QS) circuits as central regulators of virulence expression. In Pseudomonas aeruginosa, QS-regulated gene expression contributes to the formation and maintenance of biofilms and their tolerance to conventional antimicrobials and the host innate immune system. Therefore, QS is an obvious target for a novel class of antimicrobial drugs which would function to efficiently block reception of the cognate QS signals in vivo, and thereby be capable of inducing chemical attenuation of pathogens. As QS is not directly involved in processes essential for growth of the bacteria, inhibition of QS does not impose harsh selective pressure for development of resistance as with antibiotics. Numerous chemical libraries of both natural and synthetic origin have been screened and several QS-inhibitory compounds have been identified. In animal pulmonary infection models, such inhibitors have proven able to significantly improve clearing of the infecting bacteria and reduce mortality. In addition, several enzymes that are able to inactivate the bacterial QS signal molecules have been identified. This inactivation leads to blockage of QS-mediated virulence of plant pathogens in several models.
Characterization of Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) Trafficking Reveals a Novel Lysosomal Targeting Mechanism via Amyloid Precursor-like Protein 2 (APLP2) (2013)

Proprotein convertase subtilisin/kexin type 9 (PCSK9) regulates low density lipoprotein receptor protein levels by diverting it to lysosomes. Monoclonal antibody therapeutics aimed to neutralize PCSK9 have been shown to successfully lower serum LDL levels; however, we previously found that such therapeutic antibodies are subject to PCSK9-mediated clearance. In this study, we discovered that PCSK9 interacts via its C-terminal domain directly and in a pH-dependent manner with amyloid precursor protein as well as its closely related family member, amyloid precursor protein-like protein 2. Furthermore, we determined that amyloid precursor protein-like protein-2, but not amyloid precursor protein, is involved in mediating postendocytic delivery of PCSK9 to lysosomes and is therefore important for PCSK9 function. Based on our data, we propose a model for a lysosomal transport complex by which a soluble protein can target another protein for degradation from the luminal side of the membrane by bridging it to a lysosomally targeted transmembrane protein.