gebhart/patrepeval huggingface dataset:
Molecular basis of antibody‐mediated neutralization and protection against flavivirus (2016)

Antibody-mediated humoral immunity plays a pivotal role in flavivirus control. Neutralizing antibodies targeting viral envelope (E) protein, provide protection against flaviviruses in vivo but can also promote virus infection by antibody-dependent enhancement when antibodies are weakly neutralizing or in subneutralizing concentrations. The molecular basis for antibody-mediated virus neutralization can be revealed by structural studies of monoclonal antibodies complexed with the E protein or virion. In addition, the flavivirus non-structural protein NS1 can also induce host antibody production, and some of these antibodies can provide protection against virus challenge. In this review, we summarize the known structures of flavivirus neutralizing or protective antibodies bound to their epitopes and describe the underlying molecular mechanisms. © 2016 IUBMB Life, 68(10):783-791, 2016.
Efficiency of Mammalian Selenocysteine Incorporation (2004)

Five components have thus far been identified that are necessary for the incorporation of selenocysteine (Sec) into approximately 25 mammalian proteins. Two of these are cis sequences, a SECIS element in the 3'-untranslated region and a Sec codon (UGA) in the coding region. The three known trans-acting factors are a Sec-specific translation elongation factor (eEFSec), the Sec-tRNA(Sec), and a SECIS-binding protein, SBP2. Here we describe a system in which the efficiency of Sec incorporation was determined quantitatively both in vitro and in transfected cells, and in which the contribution of each of the known factors is examined. The efficiency of Sec incorporation into a luciferase reporter system in vitro is maximally 5-8%, which is 6-10 times higher than that in transfected rat hepatoma cells, McArdle 7777. In contrast, the efficiency of Sec incorporation into selenoprotein P in vitro is approximately 40%, suggesting that as yet unidentified cis-elements may regulate differential selenoprotein expression. In addition, we have found that SBP2 is the only limiting factor in rabbit reticulocyte lysate but not in transfected rat hepatoma cells where SBP2 is found to be mostly if not entirely cytoplasmic despite having a strong putative nuclear localization signal. The significance of these findings with regard to the function of known Sec incorporation factors is discussed.
Identification of candidate endothelial cell autoantigens in systemic lupus erythematosus using a molecular cloning strategy: a role for ribosomal P protein P0 as an endothelial cell autoantigen (2000)

A panel of candidate endothelial autoantigens in SLE, which includes previously described autoantigens and novel targets, has been identified by a molecular cloning strategy. This novel molecular approach could also be applied to the identification of autoantigens in other autoimmune vascular diseases.
Evidence for the identity of human scatter factor and human hepatocyte growth factor. (1991)

Scatter factor (SF), a secretory protein of fibroblasts, dissociates and increases the motility of epithelial cells and may be involved in cell migration processes during embryogenesis and tumor progression. Hepatocyte growth factor (HGF), a protein isolated from serum of patients with liver failure, is a potent mitogen for hepatocytes and is thought to play a role in liver regeneration. Here we present structural and functional evidence that human SF and human HGF (and also the human lung fibroblast-derived mitogen) are identical proteins encoded by a single gene, since (i) no major difference could be found by protein sequencing, by cDNA analysis, and by immunological comparison and (ii) SF in fact acts as a hepatocyte growth factor--i.e., stimulates DNA synthesis of activity--i.e., dissociates and induces invasiveness of various epithelial cells. The human SF/HGF gene was localized to chromosome bands 7q11.2-21. These results have important consequences for further studies on the involvement of SF/HGF as a modulator of cellular growth and motility in embryonal, malignant, and regenerative processes.
Innate immunity and transcription of MGAT-III and Toll-like receptors in Alzheimer's disease patients are improved by bisdemethoxycurcumin (2007)

We have tested a hypothesis that the natural product curcuminoids, which has epidemiologic and experimental rationale for use in AD, may improve the innate immune system and increase amyloid-beta (Abeta) clearance from the brain of patients with sporadic Alzheimer's disease (AD). Macrophages of a majority of AD patients do not transport Abeta into endosomes and lysosomes, and AD monocytes do not efficiently clear Abeta from the sections of AD brain, although they phagocytize bacteria. In contrast, macrophages of normal subjects transport Abeta to endosomes and lysosomes, and monocytes of these subjects clear Abeta in AD brain sections. Upon Abeta stimulation, mononuclear cells of normal subjects up-regulate the transcription of beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase (MGAT3) (P < 0.001) and other genes, including Toll like receptors (TLRs), whereas mononuclear cells of AD patients generally down-regulate these genes. Defective phagocytosis of Abeta may be related to down-regulation of MGAT3, as suggested by inhibition of phagocytosis by using MGAT3 siRNA and correlation analysis. Transcription of TLR3, bditTLR4, TLR5, bditTLR7, TLR8, TLR9, and TLR10 upon Abeta stimulation is severely depressed in mononuclear cells of AD patients in comparison to those of control subjects. In mononuclear cells of some AD patients, the curcuminoid compound bisdemethoxycurcumin may enhance defective phagocytosis of Abeta, the transcription of MGAT3 and TLRs, and the translation of TLR2-4. Thus, bisdemethoxycurcumin may correct immune defects of AD patients and provide a previously uncharacterized approach to AD immunotherapy.
Scheme to Measure Packet Processing Time of a Remote Host through Estimation of End-Link Capacity (2013)

As transmission speeds increase faster than processing speeds, the packet processing time (PPT) of a host is becoming more significant in the measurement of different network parameters in which packet processing by the host is involved. The PPT of a host is the time elapsed between the arrival of a packet at the data-link layer and the time the packet is processed at the application layer (RFCs 2679 and 2681). To measure the PPT of a host, stamping the times when these two events occur is needed. However, time stamping at the data-link layer may require placing a specialized packet-capture card and the host under test in the same local network. This makes it complex to measure the PPT of remote end hosts. In this paper, we propose a scheme to measure the PPT of an end host connected over a single- or multiple-hop path and without requiring time stamping at the data-link layer. The proposed scheme is based on measuring the capacity of the link connected to the host under test. The scheme was tested on an experimental testbed and in the Internet, over a U.S. inter-state path and an international path between Taiwan and the U.S. We show that the proposed scheme consistently measures PPT of a host.
Production and characterization of monoclonal antibodies which affect RNA-dependent DNA polymerase activity of porcine retrovirus reverse transcriptase. (1988)

[in Japanese]
Visualization of Myocardial Perfusion Derived from Coronary Anatomy (2008)

Visually assessing the effect of the coronary artery anatomy on the perfusion of the heart muscle in patients with coronary artery disease remains a challenging task. We explore the feasibility of visualizing this effect on perfusion using a numerical approach. We perform a computational simulation of the way blood is perfused throughout the myocardium purely based on information from a three-dimensional anatomical tomographic scan. The results are subsequently visualized using both three-dimensional visualizations and bull's eye plots, partially inspired by approaches currently common in medical practice. Our approach results in a comprehensive visualization of the coronary anatomy that compares well to visualizations commonly used for other scanning technologies. We demonstrate techniques giving detailed insight in blood supply, coronary territories and feeding coronary arteries of a selected region. We demonstrate the advantages of our approach through visualizations that show information which commonly cannot be directly observed in scanning data, such as a separate visualization of the supply from each coronary artery. We thus show that the results of a computational simulation can be effectively visualized and facilitate visually correlating these results to for example perfusion data.
Summary of the key features of seven biomathematical models of human fatigue and performance. (2004)

Although all models appear to have been fundamentally influenced by the two-process model of sleep regulation by Borbély, there is considerable diversity among them in the number and type of input and output variables, and their stated goals and capabilities.
실업과 산출간의 균형 관계 (2021)

이 논문은 실업과 산출간에 안정적인 균형관계가 성립하는지를 살펴보고 있다. 구체적으로는 오쿤의 법칙이 성립하는지를 살펴보기 위해 이 논문은 PSS(2001)에 의해 개발된 ARDL방법을 사용한다. 이 방법은 비록 변수들간의 차분구조가 동일하지 않더라도 변수간들간에 공적분이 성립하는지를 살펴볼 수 있는 방법으로 알려져 있다. 이 논문에서 사용된 국내 실업률은 I(1)과정이지만 경제성장률은 I(0)이기 때문에 전통적인 방법에서는 공적분관계가 성립하지 않게 된다. 따라서 두 변수간의 안정적 관계의 성립여부를 고찰하기 위해서 이 논문은 ARDL방법을 통해서도 분석해보고 있다. 왜냐하면 두 변수는 이론적 측면에서는 안정적인 관계인 것으로 설명되고 있기 때문이다. ARDL모형 분석결과 국내 경제에서 실업률과 경제성장률간에는 안정적인 관계가 성립하는 것으로 나타났다. 하지만, 이 연구는 실업률과 경제성장률 두 변수에서만 주목하였는데 향후 노동생산성의 변화 같은 변수를 고려하여 실업률과 경제성장률간의 안정적 관계를 확대하여 분석할 필요가 있다.
The Datacycle architecture (1992)

A database system is, by one definition [4], "a system whose overall purpose is to maintain information and to make that information available on demand." Database systems have evolved as part of a response to the desire to separate concerns. That is, the "application" should be responsible for manipulation of information and for its presentation to a user, and the "database system" should perform application-independent data management operations.
Finding dots: Segmentation as popping out regions from boundaries (2010)

Many applications need to segment out all small round regions in an image. This task of finding dots can be viewed as a region segmentation problem where the dots form one region and the areas between dots form the other. We formulate it as a graph cuts problem with two types of grouping cues: short-range attraction based on feature similarity and long-range repulsion based on feature dissimilarity. The feature we use is a pixel-centric relational representation that encodes local convexity: Pixels inside the dots and outside the dots become sinks and sources of the feature vector. Normalized cuts on both attraction and repulsion pop out all the dots in a single binary segmentation. Our experiments show that our method is more accurate and robust than state-of-art segmentation algorithms on four categories of microscopic images. It can also detect textons in natural scene images with the same set of parameters.
HLA-DP4, the Most Frequent HLA II Molecule, Defines a New Supertype of Peptide-Binding Specificity (2002)

Among HLA-DP specificities, HLA-DP4 specificity involves at least two molecules, HLA-DPA1*0103/DPB1*0401 (DP401) and HLA-DPA1*0103/DPB1*0402 (DP402), which differ from each other by only three residues. Together, they are present worldwide at an allelic frequency of 20-60% and are the most abundant human HLA II alleles. Strikingly, the peptide-binding specificities of these molecules have never been investigated. Hence, in this study, we report the peptide-binding motifs of both molecules. We first set up a binding assay specific for the immunopurified HLA-DP4 molecules. Using multiple sets of synthetic peptides, we successfully defined the amino acid preferences of the anchor residues. With these assays, we were also able to identify new peptide ligands from allergens and viral and tumor Ags. DP401 and DP402 exhibit very similar patterns of recognition in agreement with molecular modeling of the complexes. Pockets P1 and P6 accommodate the main anchor residues and interestingly contain only two polymorphic residues, beta86 and beta11, respectively. Both positions are almost dimorphic and thus produce a limited number of pocket combinations. Taken together, our results support the existence of three main binding supertypes among HLA-DP molecules and should significantly contribute to the identification of universal epitopes to be used in peptide-based vaccines for cancer, as well as for allergic or infectious diseases.
Use of New Methods for Construction of Tightly Regulated Arabinose and Rhamnose Promoter Fusions in Studies of the Escherichia coli Phosphate Regulon (1998)

Escherichia coli genes regulated by environmental inorganic phosphate (Pi) levels form the phosphate (Pho) regulon. This regulation requires seven proteins, whose synthesis is under autogenous control, including response regulator PhoB, its partner, histidine sensor kinase PhoR, all four components of the Pi-specific transport (Pst) system (PstA, PstB, PstC, and PstS), and a protein of unknown function called PhoU. Here we examined the effects of uncoupling PhoB synthesis and PhoR synthesis from their normal controls by placing each under the tight control of the arabinose-regulated P(araB) promoter or the rhamnose-regulated P(rhaB) promoter. To do this, we made allele replacement plasmids that may be generally useful for construction of P(araB) or P(rhaB) fusions and for recombination of them onto the E. coli chromosome at the araCBAD or rhaRSBAD locus, respectively. Using strains carrying such single-copy fusions, we showed that a P(rhaB) fusion is more tightly regulated than a P(araB) fusion in that a P(rhaB)-phoR+ fusion but not a P(araB)-phoR+ fusion shows a null phenotype in the absence of its specific inducer. Yet in the absence of induction, both P(araB)-phoB+ and P(rhaB)-phoB+ fusions exhibit a null phenotype. These data indicate that less PhoR than PhoB is required for transcriptional activation of the Pho regulon, which is consistent with their respective modes of action. We also used these fusions to study PhoU. Previously, we had constructed strains with precise delta phoU mutations. However, we unexpectedly found that such delta phoU mutants have a severe growth defect (P. M. Steed and B. L. Wanner, J. Bacteriol. 175:6797-6809, 1993). They also readily give rise to compensatory mutants with lesions in phoB, phoR, or a pst gene, making their study particularly difficult. Here we found that, by using P(araB)-phoB+, P(rhaB)-phoB+, or P(rhaB)-phoR+ fusions, we were able to overcome the extremely deleterious growth defect of a Pst+ delta phoU mutant. The growth defect is apparently a consequence of high-level Pst synthesis resulting from autogenous control of PhoB and PhoR synthesis in the absence of PhoU.
Management of rheumatoid arthritis: the historical context. (2001)

We review the historical highlights of the management of rheumatoid arthritis (RA). Studies of nonsteroidal antiinflammatory drugs, disease modifying antirheumatic drugs, and biological agents over 5 decades were evaluated and summarized. There is emphasis on drug therapy as it has developed and evolved from empirical relief of symptoms with salicylates to targeted intervention in the immunoinflammatory process with tumor necrosis factor inhibitors. A therapeutic paradigm has been proposed to rationalize the use of the available therapies. If one accepts the thesis that both the acute and chronic consequences of RA are due to persistent misdirected and inadequately controlled inflammation that causes tissue destruction and loss of function, then prolonged complete control of the abnormal inflammatory process is the fundamental first step in the management of all patients with RA. Unfortunately, even with the newest therapeutic options to treat RA, most patients achieve only partial suppression of inflammation and many lose therapeutic benefit after an initial good response. The management of persistent or recurrent rheumatoid inflammation and disability continues to be a challenge. It remains to be determined whether the future addition of more potent specific interventions in the immunoinflammatory process will be able to solve this problem without disarming host defenses against infections and tumors.
Visual Sentiment Analysis by Attending on Local Image Regions (2017)

Visual sentiment analysis, which studies the emotional response of humans on visual stimuli such as images and videos, has been an interesting and challenging problem. It tries to understand the high-level content of visual data. The success of current models can be attributed to the development of robust algorithms from computer vision. Most of the existing models try to solve the problem by proposing either robust features or more complex models. In particular, visual features from the whole image or video are the main proposed inputs. Little attention has been paid to local areas, which we believe is pretty relevant to human's emotional response to the whole image. In this work, we study the impact of local image regions on visual sentiment analysis. Our proposed model utilizes the recent studied attention mechanism to jointly discover the relevant local regions and build a sentiment classifier on top of these local regions. The experimental results suggest that 1) our model is capable of automatically discovering sentimental local regions of given images and 2) it outperforms existing state-of-the-art algorithms to visual sentiment analysis.
Solubility diagram of the Cu–Ni nanosystem (2006)

The application of equilibrium thermodynamics to a nanosystem changes Gibbs's rule of geometrical thermodynamics. This fact leads to the necessity to reconsider the phase diagram and solubility curve concepts. The notions of 'solubility diagram', 'solidus', 'liquidus' are used to discuss the case of phase transition in Cu–Ni nanoparticles. It is shown that, in the limit where thermodynamic arguments remain valid, the solubility diagrams of nanoparticles are functions of their size and nucleation mode. This is demonstrated for different sizes.
Regulated expression of the human cytomegalovirus pp65 gene: octamer sequence in the promoter is required for activation by viral gene products (1989)

To better understand the regulation of late gene expression in human cytomegalovirus (CMV)-infected cells, we examined expression of the gene that codes for the 65-kilodalton lower-matrix phosphoprotein (pp65). Analysis of RNA isolated at 72 h from cells infected with CMV Towne or ts66, a DNA-negative temperature-sensitive mutant, supported the fact that pp65 is expressed at low levels prior to viral DNA replication but maximally expressed after the initiation of viral DNA replication. To investigate promoter activation in a transient expression assay, the pp65 promoter was cloned into the indicator plasmid containing the gene for chloramphenicol acetyltransferase (CAT). Transfection of the promoter-CAT construct and subsequent superinfection with CMV resulted in activation of the promoter at early times after infection. Cotransfection with plasmids capable of expressing immediate-early (IE) proteins demonstrated that the promoter was activated by IE proteins and that both IE regions 1 and 2 were necessary. Analysis of promoter deletion mutants indicated that the 5' minimal sequence required for activation is -61 from the CAP site (+1) and that an 8-base-pair sequence located at -51 to -58 is necessary for activation of the pp65 promoter. This sequence is repeated once at +93 and is found as an inverted repeat at +67. These studies suggest that interactions between IE proteins and this octamer sequence may be important for the regulation and expression of this CMV gene.
Editorial: 25-Hydroxycholesterol: a new life in immunology (2010)

Abstract A discussion on paper by Park and Scott revealing the signaling pathways leading to the synthesis of a potent immunoregulatory oxysterol by macrophage and dendritic cells.
A transdermal patch delivering the PTHrP1-34 analog, abaloparatide (BA058), dose-dependently increases spine and hip bmd compared to placebo (2014)

Searchable abstracts of presentations at key conferences on calcified tissues ISSN 2052-1219 (online)
Structure of Linkage Disequilibrium in Plants (2003)

Future advances in plant genomics will make it possible to scan a genome for polymorphisms associated with qualitative and quantitative traits. Before this potential can be realized, we must understand the nature of linkage disequilibrium (LD) within a genome. LD, the nonrandom association of alleles at different loci, plays an integral role in association mapping, and determines the resolution of an association study. Recently, association mapping has been exploited to dissect quantitative trait loci (QTL). With the exception of maize and Arabidopsis, little research has been conducted on LD in plants. The mating system of the species (selfing versus outcrossing), and phenomena such as population structure and recombination hot spots, can strongly influence patterns of LD. The basic patterns of LD in plants will be better understood as more species are analyzed.
RecA‐mediated SOS induction requires an extended filament conformation but no ATP hydrolysis (2008)

The Escherichia coli SOS response to DNA damage is modulated by the RecA protein, a recombinase that forms an extended filament on single-stranded DNA and hydrolyzes ATP. The RecA K72R (recA2201) mutation eliminates the ATPase activity of RecA protein. The mutation also limits the capacity of RecA to form long filaments in the presence of ATP. Strains with this mutation do not undergo SOS induction in vivo. We have combined the K72R variant of RecA with another mutation, RecA E38K (recA730). In vitro, the double mutant RecA E38K/K72R (recA730,2201) mimics the K72R mutant protein in that it has no ATPase activity. The double mutant protein will form long extended filaments on ssDNA and facilitate LexA cleavage almost as well as wild-type, and do so in the presence of ATP. Unlike recA K72R, the recA E38K/K72R double mutant promotes SOS induction in vivo after UV treatment. Thus, SOS induction does not require ATP hydrolysis by the RecA protein, but does require formation of extended RecA filaments. The RecA E38K/K72R protein represents an improved reagent for studies of the function of ATP hydrolysis by RecA in vivo and in vitro.
Buspirone: A Worldwide Update (1991)

Buspirone is an anxiolytic drug from the azapirone family of molecules. It differs chemically and pharmacologically from the benzodiazepines. Although its profile of efficacy is comparable with that of benzodiazepines, it produces less drowsiness, less psychomotor impairment, less alcohol potentiation, and has less potential for addiction or abuse. Buspirone also appears to have efficacy in major depressive disorders, in comparison with placebo, but its activity in panic disorders is less impressive. It may diminish alcohol dependence both in animals and in chronic alcoholics. Clinical studies in the elderly show no important difference from younger patients in safety and efficacy profile, pharmacokinetics, and dosage requirement. The drug appears to be well tolerated in primary care settings and to be free of adverse clinical interactions with many drugs that might be used concomitantly. However, because its pharmacology differs from that of conventional anxiolytics, patients need to be informed about both its gradual onset of action and absence of euphoria and immediate sedation.