gebhart/patrepeval huggingface dataset:
Upregulation of signalase processing and induction of prM-E secretion by the flavivirus NS2B-NS3 protease: roles of protease components (1997)

Recently, we have shown that the ability of the flavivirus NS2B-NS3 protease complex to promote efficient signalase processing of the C-prM precursor, as well as secretion of prM and E, does not appear to depend strictly on cleavage of the precursor at its Lys-Arg-Gly dibasic site by the protease. We suggested that the association of the protease with the precursor via NS2B may be sufficient by itself for the above effects. To study the proposed association in more detail, we have developed an assay in which processing at the C-prM dibasic cleavage site is abolished by Lys-->Gly conversion. We constructed deletion mutants and chimeras of the West Nile (WN) flavivirus NS2B protein and expressed them in the context of [5'-C-->NS3(243)] containing either wild-type C-prM or its cleavage site mutant. All NS2B variants were able to form active protease complexes. Deletion of the carboxy-terminal cluster of hydrophobic amino acids in NS2B had no apparent effect on the formation of prM and prM-E secretion for the cassettes containing either wild-type or mutated C-prM precursor. Deletion of the amino-terminal hydrophobic cluster in NS2B did not affect prM-E secretion for the cassettes with wild-type C-prM but abrogated prM-E secretion for the cassettes with the mutated dibasic cleavage site in C-prM. Similarly, the NS2B-NS3(178) protease of Japanese encephalitis (JE) virus, when substituted for the WN virus NS2B-NS3(243) protease, was able to promote prM-E secretion for the cassette with the wild-type C-prM precursor but not with the mutated one. Replacement of the deleted amino-terminal hydrophobic cluster in the WN virus NS2B protein with an analogous JE virus sequence restored the ability of the protease to promote prM-E secretion. On the basis of these observations, roles of individual protease components in upregulation of C-prM signalase processing are discussed.
Study on reliability of commercially available hepatitis C virus antibody tests (1995)

The serodiagnosis of hepatitis C virus (HCV) infection was analyzed by a recombinant immunoblot assay (RIBA) with recombinant proteins encoded by the viral RNA isolated from our patients in Hamburg, Germany. The HCV RNA was amplified by PCR, and proteins encoded by the viral core and the NS3, NS4, and NS5 regions were expressed subsequently in Escherichia coli. The results obtained with our UKE RIBA were compared with the results of the Abbott HCV second-generation enzyme immunoassay (EIA). Serum samples from 270 patients, which were sent to us on the suspicion of HCV hepatitis and which were negative for hepatitis A virus and hepatitis B virus antibodies, were examined. In 227 cases (84.1%), there were identical positive (204 cases, 75.6%) or negative (23 cases, 8.5%) results in both tests. In 32 cases (11.9%), the reactive Abbott second-generation HCV EIA results could not be confirmed by the UKE RIBA and the HCV PCR. In follow-up studies conducted over 1 year, these results did not change. In three cases (1.1%), the UKE RIBA presented a positive result while the Abbott second-generation HCV EIA was negative. All three cases were positive in the HCV PCR and showed seroconversion in an HCV EIA 4 to 6 weeks later. In addition, 33 patient serum samples were examined by UKE RIBA in parallel with the Ortho RIBA 2.0. In three cases (9.1%), a positive Ortho RIBA 2.0 result could not be confirmed by the UKE RIBA and the HCV PCR. All three patients were free of complaints. The UKE RIBA showed also a smaller number of indeterminate results (3.0%) than the Ortho RIBA 2.0 (24.2%). This comparison study demonstrates that the commercially available HCV antibody tests should be further improved.
VACCINES: OUR INSURANCE FOR A HEALTHIER LIVING (2010)

In the 20th century, vaccination has been possibly the greatest revolution in health. Together with hygiene and antibiotics, vaccination led to the elimination of most childhood infectious diseases and contributed to prolong the disability- free life expectancy that in western societies increased from 50 to 78-85 years. In the 21st century, vaccination will eliminate the remaining childhood infectious diseases such as meningococcal meningitis, respiratory syncytial virus, group A streptococcus, and will address the health challenges of this century such as the aging society, antibiotic resistance, emerging infectious diseases and poverty. However, for this to happen we need to increase the public trust in vaccination so that vaccines can be perceived as the best insurance against most diseases across all ages.
Joint CTC-attention based end-to-end speech recognition using multi-task learning (2017)

Recently, there has been an increasing interest in end-to-end speech recognition that directly transcribes speech to text without any predefined alignments. One approach is the attention-based encoder-decoder framework that learns a mapping between variable-length input and output sequences in one step using a purely data-driven method. The attention model has often been shown to improve the performance over another end-to-end approach, the Connectionist Temporal Classification (CTC), mainly because it explicitly uses the history of the target character without any conditional independence assumptions. However, we observed that the performance of the attention has shown poor results in noisy condition and is hard to learn in the initial training stage with long input sequences. This is because the attention model is too flexible to predict proper alignments in such cases due to the lack of left-to-right constraints as used in CTC. This paper presents a novel method for end-to-end speech recognition to improve robustness and achieve fast convergence by using a joint CTC-attention model within the multi-task learning framework, thereby mitigating the alignment issue. An experiment on the WSJ and CHiME-4 tasks demonstrates its advantages over both the CTC and attention-based encoder-decoder baselines, showing 5.4-14.6% relative improvements in Character Error Rate (CER).
Unimolecular micelles: Synthesis and characterization of amphiphilic polymer systems (1999)

Unimolecular micelles were successfully synthesized from mucic acid, fatty acids, and poly(ethylene glycols) to create biocompatible polymers. These polymers consist of a core-shell structure that resembles conventional micellar structures but with significant thermodynamic stability in aqueous media. The core of the polymers provide a hydrophobic environment for drug encapsulation via hydrophobic interactions, whereas the shell provides excellent water solubility. The polymers were characterized by nuclear magnetic resonance, infrared and mass spectroscopies, as well as gel permeation chromatography, differential scanning calorimetry, and thermogravimetric and elemental analyses. Encapsulation ability was measured using high-pressure liquid chromatography to monitor lidocaine, a hydrophobic molecule. Encapsulation capabilities increased as lipophilicity of the core increased. To verify that encapsulation was caused by individual unimolecular micelles, surface tension and dynamic light scattering measurements were performed. The results indicated that these unimolecular micelles have great potential as drug carriers. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 703–711, 1999
CCL16 activates an angiogenic program in vascular endothelial cells (2003)

Besides regulating leukocyte trafficking in normal and injured tissues, several chemokines may positively or negatively regulate angiogenesis. Here we report that CCL16 activates an angiogenic program in vascular endothelial cells by activating CCR1. CCL16 induces dose-dependent random and directional migration of endothelial cells isolated from large vessels and liver capillaries without inducing their proliferation. It also promotes endothelial differentiation into capillary-like structures in an in vitro assay and is angiogenic in the chick chorionallantoic membrane. These angiogenic activities are neutralized by a specific antibody against CCL16. The direct angiogenic activity of CCL16 is further amplified by its ability to prime endothelium to a mitogen signal induced by vascular endothelial growth factor A and to raise their basal production of CXCL8 and CCL2, 2 other angiogenic chemokines. BX471 (R-N-[5-chloro-2-[2-[4(4-fluorophenyl) methyl]-2-methyl-1-piperazinyl]-2-oxoethoxy]phenyl] urea hydrochloric acid salt), a CCR1 antagonist, inhibits angiogenic properties of CCL16, whereas blocking of CCR8 or desensitizing CCR2, which are both well known receptors for CCL16, did not abolish endothelial activation. CCL16 may be specifically cross-linked to CCR1 expressed on endothelial cells. The largely restricted CCL16 expression in the liver suggests that this chemokine may play a role in hepatic vascular formation during development and in angiogenesis associated to hepatic diseases.
Evidence for Preorganization of the glmS Ribozyme Ligand Binding Pocket (2006)

We have examined the tertiary structure of the ligand-activated glmS ribozyme by a combination of methods with the aim of evaluating the magnitude of RNA conformational change induced by binding of the cofactor, glucosamine 6-phosphate (GlcN6P). Hydroxyl radical footprinting of a trans-acting ribozyme complex identifies several sites of solvent protection upon incubation of the RNA in Mg(2+)-containing solutions, providing initial evidence of the tertiary fold of the ribozyme. Under these folding conditions and at GlcN6P concentrations that saturate the ligand-induced cleavage reaction, we do not observe changes to this pattern. Cross-linking with short-wave UV light of the complex yielded similar overall results. In addition, ribozyme-substrate complexes cross-linked in the absence of GlcN6P could be gel purified and then activated in the presence of ligand. One of these active cross-linked species links the base immediately 3' of the cleavage site to a highly conserved region of the ribozyme core and could be catalytically activated by ligand. Combined with recent studies that argue that GlcN6P acts as a coenzyme in the reaction, our data point to a riboswitch mechanism in which ligand binds to a prefolded active site pocket and assists in catalysis via a direct participation in the reaction chemistry, the local influence on the geometry of the active site constituents, or a combination of both mechanisms. This mode of action is different from that observed for other riboswitches characterized to date, which act by inducing secondary and tertiary structure changes.
PHOTOCHEMICAL REDUCTION OF 5‐BROMOURACIL BY CYSTEINE DERIVATIVES AND COUPLING OF 5‐BROMOURACIL TO CYSTINE DERIVATIVES (1989)

Irradiation of pH 7, aqueous solutions of 5-bromouracil (BU) in the presence of cysteine peptide-like derivatives at 308 nm using a XeCl excimer laser yielded initial formation of only uracil (U) and the corresponding cystine derivative. Continued irradiation yielded an S-uracilylcysteinyl adduct as well as additional U and cystine derivative. Similar irradiation of a solution of BU and a cystine derivative yielded initial formation of U and the S-uracilylcysteinyl adduct. Formation of these products as well as secondary products of uracil photochemistry was observed upon irradiation of the respective solutions with 254 nm light. With 308 nm laser excitation, U-Cys adduct formation and reduction of BU to U are proposed to occur via initial electron transfer from the disulfide of the cystine derivative to triplet BU. The quantum yield of BU destruction with 308 nm excitation in the presence of cystine derivative is 1.1 X 10(-3). Reaction of triplet BU with the cysteine derivative does not yield U-Cys adduct but U and cystine derivative. A possible byproduct of reduction of triplet BU to U by a cysteinyl residue in a protein BU-DNA complex is a sulphenyl bromide which might yield a protein-DNA crosslink via nucleophilic substitution on sulfur by a nucleophilic site in DNA.
Biodegradable bone repair materials. Synthetic polymers and ceramics. (1986)

Many different materials have been used by orthopedic and maxillofacial surgeons to repair bony deficiencies. This review is limited to those materials that have been shown to be tissue-tolerant and biodegradable, and to include certain synthetic polymers and ceramics. There are many possible applications for these agents. Special terms and concepts are germane to an understanding of polymers and ceramics.
Characterization of Cytokine Expression in The Rectal Mucosa of Ulcerative Colitis: Correlation With Disease Activity (1999)

These findings suggest that in active UC, IL-4 is pivotal, in combination with other Th2-like cytokines. In contrast, Th1-like cytokines and IL-15 bear no definite relation to local inflammation of UC.
Effect of natural analogues oftrans-resveratrol on cytochromes P4501A2 and 2E1 catalytic activities (2006)

The aim was to assess the inhibitory effect of a series of naturally occurring trans-resveratrol analogues on cytochromes P450, namely CYP1A2 and CYP2E1, in vitro in order to analyse any structure-activity relationships. 3,5-Dimethoxy-4'-hydroxy-trans-stilbene (pterostilbene), 3,4',5-trimethoxy-trans-stilbene (TMS), 3,4'-dihydroxy-5-methoxy-trans-stilbene (3,4'-DH-5-MS) and 3,5-dihydroxy-4'-methoxy-trans-stilbene (3,5-DH-4'-MS) inhibited the activity of CYP1A2, with K(i) = 0.39, 0.79, 0.94 and 1.04 microM, respectively. Piceatannol (3,3',4,5'-tetrahydroxy-trans-stilbene) was the least potent inhibitor of CYP1A2 with a K(i) = 9.67 microM. Piceatannol and TMS in the concentration range 1-100 microM did not inhibit CYP2E1 activity. The activity of this enzyme likewise was not significantly influenced by pterostilbene and 3,5-DH-4'-MS with IC(50) > 100 microM, whereas 3,4'-DH-5-MS appeared to be a moderately potent, competitive inhibitor of CYP2E1 (K(i) = 42.6 microM). Structure-activity relationship analysis leads to the conclusion that the substitution of hydroxy groups of resveratrol with methoxy groups increases the inhibition of CYP1A2, yet the number and position of methylation are not essential. However, the 4'-hydroxy group in trans-resveratrol and its analogues may play an important role in the interaction with a binding site of CYP2E1.
Hypersecretion of corticotrophin-releasing hormone and arginine vasopressin in hypothyroid male rats as estimated with push-pull perfusion (1998)

The relationship between hypothyroidism and disturbance of the hypothalamo-hypophysial-adrenal axis was investigated using adult male rats. Hypothyroidism was produced by administration of 4-methyl-2-thiouracil (thiouracil) in the drinking water for 2 weeks. Hypothyroidism decreased adrenal weights to 57% of controls and plasma concentrations of corticosterone to 48% of controls. The changes in the weight of adrenals recovered to control levels by administration of thyroxine. The pituitary responsiveness to corticotrophin-releasing hormone (CRH) and arginine vasopressin (AVP) for ACTH release markedly increased in hypothyroid rats as compared with euthyroid rats. In vivo release of CRH and AVP in median eminence significantly increased in hypothyroid rats as compared with euthyroid rats. There were no significant differences in hypothalamic concentrations of CRH and AVP. These results indicate that hypothyroidism causes adrenal dysfunction directly and results in hypersecretion of ACTH mediated by increases in synthesis of CRH and AVP in the hypothalamus.
Immune evasion strategies of the primate lentiviruses (2001)

Individuals infected with human immunodeficiency virus (HIV) and macaques infected with simian immunodeficiency virus (SIV) make vigorous virus-specific antibody and cellular immune responses. Despite these responses, virus replication continues at all stages of infection and ultimately leads to immunological collapse, onset of opportunistic infections and death of infected hosts. Thus, the strategies by which HIV and SIV evade antiviral immune surveillance are fundamental to understanding lentiviral pathogenesis and crucial for our ability to develop effective strategies. It has become increasingly clear that the primate lentiviruses have evolved multiple and complementary mechanisms to circumvent host immune responses. Here we review these mechanisms of immune evasion considering contributions from both human and non-human primate systems.
Visual evoked potential-based acuity assessment in normal vision, artificially degraded vision, and in patients (2008)

The fully automated analysis avoided subjective problems in peak-trough assessment. The results provide quantitative limits to assess patients with possible malingering.
Changes in complementarity-determining regions significantly alter IgG binding to the neonatal Fc receptor (FcRn) and pharmacokinetics (2017)

A large body of data exists demonstrating that neonatal Fc receptor (FcRn) binding of an IgG via its Fc CH2-CH3 interface trends with the pharmacokinetics (PK) of IgG. We have observed that PK of IgG molecules vary widely, even when they share identical Fc domains. This led us to hypothesize that domains distal from the Fc could contribute to FcRn binding and affect PK. In this study, we explored the role of these IgG domains in altering the affinity between IgG and FcRn. Using a surface plasmon resonance-based assay developed to examine the steady-state binding affinity (K<sub>D</sub>) of IgG molecules to FcRn, we dissected the contributions of IgG domains in modulating the affinity between FcRn and IgG. Through analysis of a broad collection of therapeutic antibodies containing more than 50 unique IgG molecules, we demonstrated that variable domains, and in particular complementarity-determining regions (CDRs), significantly alter binding affinity to FcRn in vitro. Furthermore, a panel of IgG molecules differing only by 1-5 mutations in CDRs altered binding affinity to FcRn in vitro, by up to 79-fold, and the affinity values correlated with calculated isoelectric point values of both variable domains and CDR-L3. In addition, tighter affinity values trend with faster in vivo clearance of a set of IgG molecules differing only by 1-3 mutations in human FcRn transgenic mice. Understanding the role of CDRs in modulation of IgG affinity to FcRn in vitro and their effect on PK of IgG may have far-reaching implications in the optimization of IgG therapeutics.
Decoding India's Low Covid-19 Case Fatality Rate (2020)

India's case fatality rate (CFR) under Covid-19 is strikingly low, around 1.7% at the time of writing. The world average rate is far higher. Several observers have noted that this difference is at least partly due to India's younger age distribution. We use age-specific fatality rates from 17 comparison countries, coupled with India's distribution of Covid-19 cases, to “predict” India's CFR. In most cases, those predictions yield even lower numbers, suggesting that India's CFR is, if anything, too high rather than too low. We supplement the analysis with a decomposition exercise, and we additionally account for time lags between case incidence and death for a more relevant perspective under a growing pandemic. Our exercise underscores the importance of careful measurement and interpretation of the data, and emphasises the dangers of a misplaced complacency that could arise from an exclusive concern with aggregate statistics such as the CFR.
Oligomers with alternating thymidine and 2'-deoxytubercidin: duplex stabilization by a 7-deazapurine base (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOligomers with alternating thymidine and 2'-deoxytubercidin: duplex stabilization by a 7-deazapurine baseFrank Seela and Andreas KehneCite this: Biochemistry 1985, 24, 26, 7556–7561Publication Date (Print):December 17, 1985Publication History Published online1 May 2002Published inissue 17 December 1985https://pubs.acs.org/doi/10.1021/bi00347a008https://doi.org/10.1021/bi00347a008research-articleACS PublicationsRequest reuse permissionsArticle Views76Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Escherichia coliMalic Enzymes: Two Isoforms with Substantial Differences in Kinetic Properties, Metabolic Regulation, and Structure (2007)

Malic enzymes (MEs) catalyze the oxidative decarboxylation of malate in the presence of a divalent metal ion. In eukaryotes, well-conserved cytoplasmic, mitochondrial, and plastidic MEs have been characterized. On the other hand, distinct groups can be detected among prokaryotic MEs, which are more diverse in structure and less well characterized than their eukaryotic counterparts. In Escherichia coli, two genes with a high degree of homology to ME can be detected: sfcA and maeB. MaeB possesses a multimodular structure: the N-terminal extension shows homology to ME, while the C-terminal extension shows homology to phosphotransacetylases (PTAs). In the present work, a detailed characterization of the products of E. coli sfcA and maeB was performed. The results indicate that the two MEs exhibit relevant kinetic, regulatory, and structural differences. SfcA is a NAD(P) ME, while MaeB is a NADP-specific ME highly regulated by key metabolites. Characterization of truncated versions of MaeB indicated that the PTA domain is not essential for the ME reaction. Nevertheless, truncated MaeB without the PTA domain loses most of its metabolic ME modulation and its native oligomeric state. Thus, the association of the two structural domains in MaeB seems to facilitate metabolic control of the enzyme. Although the PTA domain in MaeB is highly similar to the domains of proteins with PTA activity, MaeB and its PTA domain do not exhibit PTA activity. Determination of the distinct properties of recombinant products of sfcA and maeB performed in the present work will help to clarify the roles of MEs in prokaryotic metabolism.