gebhart/patrepeval huggingface dataset:
The essential role of fumarate reductase in haem-dependent growth stimulation of Bacteroides fragilis (2003)

Haem is required for optimal growth of the bacterial anaerobe Bacteroides fragilis. Previous studies have shown that growth in the presence of haem is coincident with increased yields of ATP from glucose, expression of b-type cytochromes and expression of fumarate reductase activity. This paper describes the identification of the genes that encode the cytochrome, iron-sulfur cluster protein and flavoprotein of the B. fragilis fumarate reductase. These genes, frdC, frdA and frdB, respectively, are organized in an operon. Nonpolar, in-frame deletions of frdC and frdB were constructed in the B. fragilis chromosome. These mutant strains had no detectable fumarate reductase or succinate dehydrogenase activity. In addition, the frd mutant strains showed a threefold increase in generation time, relative to the wild-type strain. Growth of these mutant strains was fully restored to the wild-type rate by the introduction of a B. fragilis replicon containing the entire frd operon. Growth of the frd mutant strains was partially restored by supplementing the growth medium with succinate, indicating that the frd gene products function as a fumarate reductase. During growth on glucose, the frd mutant strains showed a threefold decrease in cell mass yield, relative to the wild-type strain. These data indicate that fumarate reductase is important for both energy metabolism and succinate biosynthesis in B. fragilis.
국채선물의 가격변동성과 수량 및 미결제수량간의 동학분석: 이변량 GARCH-M 모형의 적용 (2003)

이 논문은 한국선물거래소에서 거래되는 국채선물의 경우 선물가격의 변화와 거래수량변화의 조건부 평균과 분산에서의 상관관계를 이변량 GARCH-M 모형을 이용하여 분석하고 있다. 조건부 평균에서의 상관관계는 전체표본, 채권시가평가제도의 도입 전후, 국채선물옵션의 도입 전후로 나누어 분석하고 있고, 조건부 분산을 고려하는 경우에는 전체표본, 채권시가평가제도의 도입 후, 국채선물옵션의 도입 전에서 선물가격의 변화와 거래수량변화간의 상관관계를 분석하고 있다. 이변량 GARCH-M모형의 추정을 통한 선도-지연관계에 대한 결과는 거래수량은 가격변화에 선도하는 어떠한 정보도 보유하지 못한 것으로 나타났다. 그리고 가격변화는 수량변화에 선도하지 못하는 것으로 나타났고, 미결제수량변화에는 선도효과가 있음을 보여주고 있다.
Photolabile Protecting Groups for Nucleosides: Mechanistic Studies of the 2-(2-Nitrophenyl)ethyl Group (2001)

The photochemistry of several 2-(2-nitrophenyl)ethyl-caged compounds including caged thymidine nucleosides was studied by nanosecond laser flash photolysis and stationary illumination experiments with quantitative HPLC analysis for quantum yields and product distribution. Effects of solvent basicity and acidity were investigated by varying the H2O content and HCl concentration, respectively, in MeCN/H2O mixtures. For all compounds 1 – 7 investigated, intramolecular H abstraction by the nitro group from the exocyclic α-position with respect to the aryl moiety was found to be the primary process. The protolytic dissociation equilibrium of the resulting aci-nitro compound was kinetically characterized in the 0.1 – 10 μs time region. In general, two reaction channels compete for the aci-nitro compound and its anion: β-elimination of the caged compound occurs from the anion, while from the undissociated aci-nitro compound, a nitrosobenzene derivative is formed with no release of the caged compound. The yield ratio of these two reaction channels can be controlled through shifts in the protolytic dissociation equilibrium of the aci-nitro compound. In solutions with either low basicity (H2O-free MeCN) or high acidity (higher concentration of HCl in H2O/MeCN), two as yet unidentified products are formed, each one specifically for one of the mentioned conditions.
Lysophospholipids Are Potential Biomarkers of Ovarian Cancer (2004)

LPA, LPI, LPC, and S1P appear useful as diagnostic and prognostic biomarkers of ovarian cancer.
A randomised controlled trial of the effectiveness of providing free fluoride toothpaste from the age of 12 months on reducing caries in 5-6 year old children. (2002)

This study demonstrates that a programme distributing free toothpaste containing 1,450 ppmF provides a significant clinical benefit for high caries risk children living in deprived, non-fluoridated districts.
From Diagnosis and Classification to Complications and Therapy: DCCT Part II? (1994)

I have long been concerned about our approach to diagnosing diabetes. While one can readily agree that an elevated blood glucose level is a key component of diabetes, I strenuously argue that the cause of that blood glucose elevation is also of critical importance, i.e., a deficiency in insulin action. Diabetes is, after all, an endocrine disease, and it has always disturbed me as to how little diagnostic attention is paid to the concentration of the hormone involved. This is, I believe, unlike virtually all other endocrine diseases. Instead of measuring insulin (along with glucose), we have become obsessed with the oral glucose tolerance test (OGTT), which I view as a highly variable test of an unnatural gastronomic excess.
Gene-Transferred Oligoclonal T Cells Predominantly Persist in Peripheral Blood from an Adenosine Deaminase-Deficient Patient during Gene Therapy (2001)

Adenosine deaminase (ADA) deficiency is the primary cause of severe combined immunodeficiency disease and has become a focus for developing innovative approaches to gene therapy. We previously described successful treatment of a Japanese ADA-deficient patient by periodic infusions of genetically modified autologous T lymphocytes transduced with a retroviral vector containing human ADA cDNA. In order to investigate whether polyclonality was restored by the gene therapy and whether the gene-transduced T lymphocytes persisted in the peripheral blood of the patient, we analyzed the T cell clonotype using a T cell receptor-specific RT-PCR/SSCP method. Oligoclonal T cell expansion was observed in every Vbeta family, and the expanded T cell clones were stable throughout the periodic gene therapy. Some of these T cell clones are likely carrying the vector, since they were identical to the clones selected by G418 resistance. Therefore, although it is uncertain when oligoclonal T cells started to expand and what percentage of the oligoclones carries the vector, the peripheral blood of the patient administered the gene therapy included oligoclonal T cells, some of which were identical to the ADA-gene-transduced clones.
Subcutaneous heparin treatment increases survival in small cell lung cancer (1994)

These results confirm the value of anticoagulant treatment in SCLC, already suspected for warfarin and now proven for heparin, but the modes of administration and the biologic explanations for this activity still warrant further investigation.
Synthesis and use of labelled nudeoside phosphoramidite building blocks bearing a reporter group: biotinyl, dinitrophenyl, pyrenyl and dansyl (1989)

The synthesis of protected nucleoside phosphoramidites bearing various markers such as biotinyl, dinitrophenyl, dansyl and pyrenyl groups are reported. These labelled deoxynucleosides phosphoramidites were used for solid phase oligonucleotide synthesis in the same way than the usual protected phosphoramidities without any change in the synthetic cycle and the deprotection step. The new labelled building blocks described herein have been used in conjunction with the labile base protected phosphoramidites ('PAC phosphoramidites') which allowed mild ammonia deprotection, especially recommended for the dinitrophenyl-labelled oligonucleotides. Multiple labelling (i.e. 10 to 20 biotins) can be efficiently and easily performed, on the same oligonucleotide which results in an increase of sensitivity. The polylabelled oligonucleotides are chemically well defined and gave increased signal and low background coloration for in situ hybridisation. The modified oligonucleotides can still be kinased in the normal way as the reporter groups are on the heterocycles.
Properties and evolutionary relationships of the Marek's disease virus homologues of protein kinase, glycoprotein D and glycoprotein I of herpes simplex virus (1991)

The deduced amino acid sequences of the open reading frames (ORFs) mapping in the short unique segment (US) of Marek's disease virus (MDV) reported in the accompanying paper have been analysed using computer programs to determine their relationships to herpesvirus proteins. Analysis of the catalytic domains of protein kinases showed that the MDV kinase (MDV PK) was closely related to the alphaherpesvirus protein kinase mapping in US. The results also showed that the MDV PK was more closely related to the cellular kinases that control cell division than to the proto-oncogenes c-src and c-mos and it was predicted that the MDV PK would phosphorylate serine/threonine. The MDV homologue of herpes simplex virus (HSV) glycoprotein D (gD) contained several residues that were conserved in mammalian herpesviruses. In particular, six cysteines were perfectly aligned in all the gDs and there were numerous conservative substitutions. Although only approximately 65% of the MDV homologue of glycoprotein I (gI) of HSV has been sequenced, it was clear that a significant number of amino acid residues including four cysteines were conserved in the gI homologues of MDV and mammalian herpesviruses. Further analysis suggested that MDV gD was more closely related to the gDs of pseudorabies virus (PRV) and equine herpesvirus 1 than to the gD of HSV-1 and HSV-2. It was noted that HSV-2 glycoprotein G (gG), PRV gX and MDV gD were related and that MDV ORF4 was related to MDV gD and probably to HSV-1 gG. The results have shown a clear relationship between the genes of MDV and their counterparts in mammalian alphaherpesviruses and are consistent with the idea that MDV glycoprotein genes in US might have arisen by a process of gene duplication and independent evolution.
Inverted repeat nucleotide sequences in the genomes of Marek disease virus and the herpesvirus of the turkey. (1982)

The DNAs of two herpesvirus, the oncogenic Marek disease virus and the serologically related herpesvirus of the turkey, were studied by electron microscopy. On the basis of fold-back molecules observed in single-stranded DNA from both viruses, structures have been derived from the overall nucleotide sequence arrangement in their genomes. Although differing in molecular weight, the genomes of Marek disease virus and turkey herpesvirus are both constructed according to the same plan--two regions of unique nucleotide sequence, each enclosed by inverted repeat sequence. The genome structure of these viruses therefore closely resembles that of herpes simplex virus rather than the biologically more similar herpesvirus Epstein--Barr virus, H. saimiri, and H. ateles.
Ganglioside GM3 Inhibits Matrix Metalloproteinase-9 Activation and Disrupts Its Association with Integrin (2003)

Gangliosides GM3 and GT1b both inhibit epithelial cell adhesion and migration on fibronectin. GT1b binds to integrin alpha5beta1 and blocks the integrin-fibronectin interaction; GM3 does not interact with integrin, and its effect is poorly understood. We evaluated the effects of endogenous modulation of GM3 expression on epithelial cell motility on several matrices and the mechanism of these effects. Endogenous accumulation of GM3 decreased cell migration on fibronectin, types I, IV, and VII collagen matrices; depletion of GM3 dramatically increased cell migration, regardless of matrix. GM3 overexpression and depletion in vitro correlated inversely with the expression and activity of matrix metalloproteinase-9; consistently, the cell migration stimulated by GM3 depletion is reversed by inhibition of matrix metalloproteinase-9 activity. Accumulation and depletion of GM3 in epithelial cells grown on fibronectin also correlated inversely with epidermal growth factor receptor and mitogen activated protein kinase phosphorylation and with Jun expression. Ganglioside depletion facilitated the co-immunoprecipitation of matrix metal-loproteinase-9 and integrin alpha5beta1, while endogenous accumulation of GM3, but not GT1b, blocked the co-immunoprecipitation. These data suggest modulation of epidermal growth factor receptor signaling and dissociation of integrin/matrix metalloproteinase-9 as mechanisms for the GM3-induced effects on matrix metalloproteinase-9 function.
Tenascin‐C, GLUT‐1, and syndecan‐2 expression in juvenile nasopharyngeal angiofibroma: Correlations to vessel density and tumor stage (2012)

The immunoexpression of stromal TNC correlated with vascular density and higher tumors stage, which supports the idea of TNC having a role in the tumorigenesis of JNA putatively by promoting angiogenesis.
Nucleotide sequence of the G protein gene of human respiratory syncytial virus reveals an unusual type of viral membrane protein. (1985)

The major surface glycoprotein (G) of human respiratory syncytial (RS) virus has an estimated mature Mr of 84,000-90,000. Among a library of cDNA clones prepared from RS virus mRNAs, we identified clones that hybridized to a message that encoded a Mr 36,000 polypeptide that was specifically immunoprecipitated with anti-G antiserum. The amino acid sequence of the G protein backbone was determined by nucleotide sequence analysis of several of the cDNA clones. It contains a combination of structural features that make it unique among the known viral glycoproteins. The G mRNA is 918 nucleotides long and contains a single major open reading frame that encodes a polypeptide having 298 amino acid residues with a Mr of 32,587, a finding consistent with the Mr 36,000 estimate for the in vitro translation product of the G mRNA. This suggests that greater than 50% of the molecular weight of the mature glycoprotein may be contributed by carbohydrate. Glycosylation of G is largely resistant to tunicamycin, an inhibitor of the attachment of N-linked oligosaccharides, suggesting that the majority of the carbohydrate residues are attached via O-glycosidic bonds. In accordance with this, serine and threonine residues, the acceptor sites for O-linked oligosaccharides, comprise 30.6% of the total amino acid composition. There are also four potential acceptor sites for N-linked oligosaccharides. The amino acid sequence lacks both an NH2-terminal hydrophobic signal sequence and a COOH-terminal hydrophobic region. Instead, a strongly hydrophobic region is located between amino acid residues 38 and 66. This region may serve as both the signal to insert the nascent polypeptide through the membrane and as the membrane anchor site.
Gene therapy and the hemophilias. (1994)

Gene therapy for hemophilia A and B, now in the developmental stage, holds promise of a therapeutic revolution, resulting in amelioration or cure of the hemorrhagic diatheses. The genes for factor VIII and IX have been cloned, and vectors for the transfer of their cDNA into cells have been developed. Although viral and nonviral constructs containing the hemophilia gene have been used, most often modified retroviruses or adenoviruses have been employed. Cells that have been targeted for genetic modification to produce the antihemophilic proteins include hepatocytes, muscle cells, endothelial cells, keratinocytes, and fibroblasts. The delivery system may be (1) ex vivo, with implantation of modified cultured hemophilic cells in the donor, either in tissues or in semipermeable capsules, or (2) in vivo, the vector being delivered directly to target cells, genetically modifying them in situ. Successful in vivo therapy has been demonstrated in a hemophilic animal model, with conversion to a less severe hemophilic state.
Unexpected Changes in the Population of Coordination Isomers for the Lanthanide Ion Complexes of DOTMA–Tetraglycinate (2016)

Lanthanide complexes with DOTA-tetraglycinate (DOTA-(gly)4) heavily favor the square antiprismatic (SAP) coordination isomer in aqueous solution, a structural feature that has made them useful as water-based paraCEST agents. In an effort to create amide-based paraCEST agents with rapid water exchange rates, we prepared the analogous tetraglycinate complexes with DOTMA, a ligand known to favor the twisted square antiprismatic (TSAP) coordination structures. Unexpectedly, NMR investigations show that the LnDOTMA-(gly)4 complexes, like the LnDOTA-(gly)4 complexes, also favor the SAP isomers in solution. This observation led to density functional theory (DFT) calculations in order to identify the energy terms that favor the SAP structures in lanthanide complexes formed with macrocyclic DOTA- and DOTMA-tetraamide ligands. The DFT calculations revealed that, regardless the nature of the ligand, the TSAP isomers present more negative hydration energies than the SAP counterparts. The extent to which the TSAP isomer is stabilized varies, however, depending on the ligand structure, resulting in different isomeric populations in solution.
Opioids in the systemic hemodynamic and renal responses to stress in spontaneously hypertensive rats. (1989)

Endogenous opioid peptides have been implicated in the regulation of cardiovascular and renal function. We tested this hypothesis by examining whether the opioid antagonist naloxone alters the cardiovascular or renal responses produced by environmental stress (air stress) in conscious spontaneously hypertensive rats (SHR). Before naloxone administration, air stress produced significant increases in heart rate, mean arterial pressure, and renal sympathetic nerve activity, and it caused a decrease in urinary sodium excretion. After intravenous and intracerebroventricular administration of naloxone, the air stress-induced pressor and antinatriuretic responses were inhibited. Subsequent studies with a different opioid antagonist, the quaternary compound naltrexone methylbromide, also showed inhibition of the air stress-induced pressor and antinatriuretic responses and demonstrated opioid receptor specificity of this inhibition. Furthermore, since only intracerebroventricular and not intravenous administration of naltrexone methylbromide inhibited the pressor and antinatriuretic responses to air stress, a central nervous system site of action was established. The opioid antagonists caused inhibition of the pressor and antinatriuretic responses to air stress without affecting the air stress-induced increase in renal sympathetic nerve activity. Our investigations indicate that central endogenous opioid peptides contribute to the pressor and antinatriuretic responses that occur in conscious SHR during acute environmental stress.
Monoclonal Antibodies to Bluetongue Virus Define Two Neutralizing Epitopes and a Hemagglutinating Epitope (1990)

Monoclonal antibodies were used to characterize neutralizing epitopes on VP2 of bluetongue virus serotype 10 (BTV-10). Six neutralizing monoclonal antibodies that immune precipitated VP2 demonstrated two distinct patterns of reactivity in the competitive enzyme-linked immune absorbent assay (ELISA). These results suggest that there are at least two distinct domains of neutralization on VP2 of BTV. Monoclonal antibodies defining the two domains were serotype-restricted in plaque neutralization, immune precipitation or ELISA. One of the two neutralizing domains also demonstrated significant hemagglutinating activity. Both cattle and sheep infected with BTV-10 produce antibodies to the two neutralizing epitopes.
Photo-Realistic Single Image Super-Resolution Using a Generative Adversarial Network (2016)

Despite the breakthroughs in accuracy and speed of single image super-resolution using faster and deeper convolutional neural networks, one central problem remains largely unsolved: how do we recover the finer texture details when we super-resolve at large upscaling factors? The behavior of optimization-based super-resolution methods is principally driven by the choice of the objective function. Recent work has largely focused on minimizing the mean squared reconstruction error. The resulting estimates have high peak signal-to-noise ratios, but they are often lacking high-frequency details and are perceptually unsatisfying in the sense that they fail to match the fidelity expected at the higher resolution. In this paper, we present SRGAN, a generative adversarial network (GAN) for image super-resolution (SR). To our knowledge, it is the first framework capable of inferring photo-realistic natural images for 4x upscaling factors. To achieve this, we propose a perceptual loss function which consists of an adversarial loss and a content loss. The adversarial loss pushes our solution to the natural image manifold using a discriminator network that is trained to differentiate between the super-resolved images and original photo-realistic images. In addition, we use a content loss motivated by perceptual similarity instead of similarity in pixel space. Our deep residual network is able to recover photo-realistic textures from heavily downsampled images on public benchmarks. An extensive mean-opinion-score (MOS) test shows hugely significant gains in perceptual quality using SRGAN. The MOS scores obtained with SRGAN are closer to those of the original high-resolution images than to those obtained with any state-of-the-art method.
Addition of oligonucleotides to the 5′-terminus of DNA by T4 RNA ligase (1979)

Bacteriophage T4-induced RNA ligase catalyzes the controlled template-independent addition of RNA to the 5'-phosphoryl end of large DNA molecules. Restriction enzyme-generated fragments of Co1E1 DNA with completely basepaired or cohesive ends and linear single-stranded øX174 viral DNA were all good substrates. DNA molecules from 10 to 6000 nucleotides long were quantitatively joined in an hour to a number of different RNA homopolymers. The most efficient of these was A(pA)5; I(pI)5 and C(pC)5 were also utilized while U(pU)5 was not. The optimum ribohomopolymer length was six nucleotides. Joining of ribohomopolymers between 10 and 20 nucleotides long occurred at approximately 1/2 the maximal rate and a trimer was the shortest substrate. Thus RNA ligase provides a method for generating extensions of predetermined length and base composition at the 5'-end of large DNA molecules that complements the available procedures for extending the 3'-hydroxyl terminus of DNA.
Importance of the superficial tissue layer for the indentation stiffness of articular cartilage (2002)

Indentation testing is a widely used technique for nondestructive mechanical analysis of articular cartilage. Although cartilage shows an inhomogeneous, layered structure with anisotropic mechanical properties, most theoretical indentation models assume material homogeneity and isotropy. In the present study, quantitative polarized light microscopy (PLM) measurements from canine cartilage were utilized to characterize thickness and structure of the superficial, collageneous tissue layer as well as to reveal its relation to experimental indentation measurements. In addition to experimental analyses, a layered, transversely isotropic finite element (FE) model was developed and the effect of superficial (tangential) tissue layer with high elastic modulus in the direction parallel to articular surface on the indentation response was studied. The experimental indentation stiffness was positively correlated with the relative thickness of the superficial cartilage layer. Also the optical retardation, which reflects the degree of parallel organization of collagen fibrils as well as collagen content, was related to indentation stiffness. FE results indicated effective stiffening of articular cartilage under indentation due to high transverse modulus of the superficial layer. The present results suggest that indentation testing is an efficient technique for the characterization of the superficial degeneration of articular cartilage.