gebhart/patrepeval huggingface dataset:
Glycoproteins of Varicella-Zoster Virus and Their Herpes Simplex Virus Homologs (1991)

This report describes the glycoproteins of varicella-zoster virus (VZV) and their role as immunogens and discusses the relevance of studies of VZV to the selection of a glycoprotein subunit herpes simplex virus (HSV) vaccine. HSV types 1 and 2 and VZV are alpha-herpesviruses, which are characterized by common biologic features such as a relatively short replication cycle and a latent state, often in neurologic tissues. The three viruses also conserve several glycoprotein genes, including gB, gC, gE, gH, and gI. The known properties of the VZV glycoproteins closely resemble those of their homologous HSV counterparts and may provide further insight into biologic functions of the immunogens. In particular, VZV glycoproteins gpII and gpIII closely resemble their HSV homologs gB and gH in that all four harbor complement-independent neutralization epitopes.
Layer-Resolved Graphene Transfer via Engineered Strain Layers (2013)

The performance of optimized graphene devices is ultimately determined by the quality of the graphene itself. Graphene grown on copper foils is often wrinkled, and the orientation of the graphene cannot be controlled. Graphene grown on SiC(0001) via the decomposition of the surface has a single orientation, but its thickness cannot be easily limited to one layer. We describe a method in which a graphene film of one or two monolayers grown on SiC is exfoliated via the stress induced with a Ni film and transferred to another substrate. The excess graphene is selectively removed with a second exfoliation process with a Au film, resulting in a monolayer graphene film that is continuous and single-oriented.
<title>Robust image authentication method surviving JPEG lossy compression</title> (1997)

Image authentication verifies the originality of an image by detecting malicious manipulations. This goal is different from that of image watermarking which embeds into the image a signature surviving most manipulations. Existing methods for image authentication treat all types of manipulation equally (i.e., as unacceptable). However, some applications demand techniques that can distinguish acceptable manipulations (e.g., compression) from malicious ones. In this paper, we describe an effective technique for image authentication which can prevent malicious manipulations but allow JPEG lossy compression. The authentication signature is based on the invariance of the relationship between DCT coefficients of the same position in separate blocks of an image. This relationship will be preserved when these coefficients are quantized in a JPEG compression process. Our proposed method can distinguish malicious manipulations from JPEG lossy compression regardless of how high the compression ratio is. We also show that, in different practical cases, the design of authenticator depends on the number of recompression times and on whether the image is decoded into integral values in the pixel domain during the recompression process. Theoretical and experimental results indicate that this technique is effective for image authentication.
Expression of the Cell Adhesion Molecule CD146/MCAM in Non‐Small Cell Lung Cancer (2002)

Expression of MCAM is observed in a variety of human malignancies. We aimed to determine the rate of MCAM expression in our non-small cell lung cancer (NSCLC) collection and to clarify its correlation with clinicopathological parameters and patient survival. 85 NSCLC were analysed immunohistochemically using a monoclonal MCAM antibody (clone N1238) on an NSCLC tissue micro array. The staining was semiquantitatively scored. We found MCAM expression in 51% of NSCLC, preferentially squamous cell carcinomas (p=0.004). No other correlations to tumour size, grade, or stage were found. Univariate survival analysis showed no significant differences of MCAM positive and negative tumours. In adenocarcinomas however, MCAM positivity was significantly associated with shorter patient survival (p=0.016). We conclude, that MCAM is expressed in a high proportion of NSCLC and might be predictive of shortened patient survival in adenocarcinomas of the lung. Colour figure can be viewed on http://www.esacp.org/acp/2003/25-2/kristiansen.htm
Post- and pre-processing in coding of image sequences using filters with motion compensated history (2003)

To increase the performance of image coding of sequences it is beneficial to apply temporal prefiltering before coding to increase redundancy. To reduce the subjective impact of coding artifacts also temporal postfiltering can be applied after decoding. A problem with both of these techniques however (and of the more general techniques of image sequence enhancement using temporal filters) is that severe distortion may appear in moving objects. The author presents a method to avoid these artifacts of temporal filtering by introducing movement compensated temporal filtering. This technique yields an anisotropic, non-stationary 3-dimensional transfer function, which locally 'tracks' moving objects. The effect is that the problem of unsharp moving objects is significantly reduced, which allows for much lower cut-off frequencies than stationary filters do. The approach works both with FIR- and IIR-type filters. If a linear phase FIR filter is used for postfiltering, combined with a sampling rate increase, it can be seen as a motion compensated interpolator.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
INHIBITORS OF THE BIOSYNTHESIS AND PROCESSING OF N-LINKED OLIGOSACCHARIDE CHAINS (1987)

A number of glycoproteins have oligosaccharides linked to protein in a GlcNAc----asparagine bond. These oligosaccharides may be either of the complex, the high-mannose or the hybrid structure. Each type of oligosaccharides is initially biosynthesized via lipid-linked oligosaccharides to form a Glc3Man9GlcNAc2-pyrophosphoryl-dolichol and transfer of this oligosaccharide to protein. The oligosaccharide portion is then processed, first of all by removal of all three glucose residues to give a Man9GlcNAc2-protein. This structure may be the immediate precursor to the high-mannose structure or it may be further processed by the removal of a number of mannose residues. Initially four alpha 1,2-linked mannoses are removed to give a Man5 - GlcNAc2 -protein which is then lengthened by the addition of a GlcNAc residue. This new structure, the GlcNAc- Man5 - GlcNAc2 -protein, is the substrate for mannosidase II which removes the alpha 1,3- and alpha 1,6-linked mannoses . Then the other sugars, GlcNAc, galactose, and sialic acid, are added sequentially to give the complex types of glycoproteins. A number of inhibitors have been identified that interfere with glycoprotein biosynthesis, processing, or transport. Some of these inhibitors have been valuable tools to study the reaction pathways while others have been extremely useful for examining the role of carbohydrate in glycoprotein function. For example, tunicamycin and its analogs prevent protein glycosylation by inhibiting the first step in the lipid-linked pathway, i.e., the formation of Glc NAc-pyrophosphoryl-dolichol. These antibiotics have been widely used in a number of functional studies. Another antibiotic that inhibits the lipid-linked saccharide pathway is amphomycin, which blocks the formation of dolichyl-phosphoryl-mannose. In vitro, this antibiotic gives rise to a Man5GlcNAc2 -pyrophosphoryl-dolichol from GDP-[14C]mannose, indicating that the first five mannose residues come directly from GDP-mannose rather than from dolichyl-phosphoryl-mannose. Other antibodies that have been shown to act at the lipid-level are diumycin , tsushimycin , tridecaptin, and flavomycin. In addition to these types of compounds, a number of sugar analogs such as 2-deoxyglucose, fluoroglucose , glucosamine, etc. have been utilized in some interesting experiments. Several compounds have been shown to inhibit glycoprotein processing. One of these, the alkaloid swainsonine , inhibits mannosidase II that removes alpha-1,3 and alpha-1,6 mannose residues from the GlcNAc- Man5GlcNAc2 -peptide. Thus, in cultured cells or in enveloped viruses, swainsonine causes the formation of a hybrid structure.(ABSTRACT TRUNCATED AT 400 WORDS)
Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery (2005)

The Shigella bacteria cause bacillary dysentery, which remains a significant threat to public health. The genus status and species classification appear no longer valid, as compelling evidence indicates that Shigella, as well as enteroinvasive Escherichia coli, are derived from multiple origins of E.coli and form a single pathovar. Nevertheless, Shigella dysenteriae serotype 1 causes deadly epidemics but Shigella boydii is restricted to the Indian subcontinent, while Shigella flexneri and Shigella sonnei are prevalent in developing and developed countries respectively. To begin to explain these distinctive epidemiological and pathological features at the genome level, we have carried out comparative genomics on four representative strains. Each of the Shigella genomes includes a virulence plasmid that encodes conserved primary virulence determinants. The Shigella chromosomes share most of their genes with that of E.coli K12 strain MG1655, but each has over 200 pseudogenes, 300 approximately 700 copies of insertion sequence (IS) elements, and numerous deletions, insertions, translocations and inversions. There is extensive diversity of putative virulence genes, mostly acquired via bacteriophage-mediated lateral gene transfer. Hence, via convergent evolution involving gain and loss of functions, through bacteriophage-mediated gene acquisition, IS-mediated DNA rearrangements and formation of pseudogenes, the Shigella spp. became highly specific human pathogens with variable epidemiological and pathological features.
Conformational Similarity and Systematic Displacement of Complementarity Determining Region Loops in High Resolution Antibody X-ray Structures (1995)

Comparison of seven high resolution x-ray structures shows that the conformations of canonical complementarity determining region (CDR) loops, which are shared by these antibodies, are very similar. However, large spatial displacements (up to 2.7 A) of the essentially identical CDR loops become evident when the antibody beta-sheet frameworks, to which the loops are attached, are least-squares superposed. The loop displacements follow, and amplify, small positional differences in framework/loop splice points. Intradomain structural variability and, to a lesser extent, domain-domain orientation appear to cause the observed loop divergences. The results suggest that the selection of framework regions for loop grafting procedures is more critical than previously thought.
Antinuclear antibodies: clinical correlations and biologic significance. (1992)

Several trends become evident from the foregoing discussion. As the different ANA antigenic specificities have been identified, they have often been found to be highly conserved polypeptides that subserve very basic cellular functions that are carried out in the nucleus, nucleolus, and ribosomes. The reasons why only 30 or so basic cellular proteins become the targets of an autoimmune response in patients with connective tissue disease at the exclusions of the other 10,000 macromolecules that exist inside cells remain a mystery. However, some insight into this enigma might be provided by the mechanism of molecular mimicry (Table 9). The possibility that highly conserved immunogenic molecules that are expressed by infectious pathogens can trigger an immune response in a genetically predisposed human host that cross-reacts with cellular autoantigens is a well documented phenomenon in disorders such as rheumatic fever. This mechanism is now being mentioned with increasing frequency in discussions pertaining to the pathogenesis of autoimmune connective tissue diseases. Another trend relates to the increasing sensitivity of the newer assays that have been developed to detect ANA. When highly purified or recombinant autoantigens are used in versatile assays such as ELISA, radioimmunoassays, or immunoprecipitation, the frequency with which certain autoantibodies can be detected in patient subgroups can go up significantly. For example, with classical immunodiffusion, anti-Ro/SS-A antibodies can be detected in 25% of unselected patients with SLE, whereas with an ELISA based on affinity purified Ro/SS-A antigen, 50% of patients with SLE are found to have elevated levels of this autoantibody specificity. As is often the case, we pay for increased sensitivity in a laboratory test with decreased specificity. With immunodiffusion, virtually no normal individuals have anti-Ro/SS-A antibodies, but with the ELISA as many as 10% of normals have elevated anti-Ro/SS-A binding levels. Thus, the incremental diagnostic value of this newer anti-Ro/SS-A assay could be questioned. The true clinical value of this new laboratory technology will become more evident when these more sophisticated ANA assays are used together in a panel-like fashion to profile a given patient's autoimmune response at the very onset of his illness. Preliminary work has already begun in this area. This approach, if well standardized, could have significant diagnostic and prognostic value. Another benefit of this newer technology will be the ability to measure antibody binding levels to individual autoepitopes--limited portions of an autoantigen's amino acid sequence that represent single antibody binding sites. It is possible that certain patterns of clinical disease could be linked to autoantibody production against individual autoepitopes rather than whole autoantigenic molecules. This area is only now beginning to be explored.
Bacterial Two-component and Hetero-heptameric Pore-forming Cytolytic Toxins: Structures, Pore-forming Mechanism, and Organization of the Genes (2004)

Staphylococcal gamma-hemolysin (Hlg), leukocidin (Luk), and Panton-Valentine leukocidin (PVL) are two-component and hetero-oligomeric pore-forming cytolytic toxins (or cytolysin), that were first identified in bacteria. No information on the existence of hetero-oligomeric pore-forming cytolytic toxins in bacteria except for staphylococcal strains is available so far. Hlg (Hlg1 of 34 kDa/Hlg2 of 32 kDa) effectively lyses erythrocytes from human and other mammalian species. Luk (LukF of 34 kDa/LukS of 33 kDa) is cytolytic toward human and rabbit polymorphonuclear leukocytes and rabbit erythrocytes, and PVL (LukF-PV of 34 kDa/LukS-PV of 33 kDa) reveals cytolytic activity with a high cell specificity to leukocytes. Hlg1 is identical to LukF and that the cell specificities of the cytolysins are determined by Hlg2 and LukS. Based on the primary and 3-dimensional structures of the toxin components, Hlg, Luk, and PVL are thought to form a family of proteins. In the first chapter of this article, we describe the molecular basis of the membrane pore-forming nature of Hlg, Luk, and PVL. We also describe a requirement of the phosphorylation of LukS and LukS-PV by protein kinase for their leukocytolytic activity besides their pore formation on human leukocytes.Recently, the assembly mechanism of the LukF and Hlg2 monomers into pore-forming hetero-oligomers of Hlg on human erythrocyte membranes has been clarified for the first time by our study using a single-molecular fluorescence imaging technique. We estimated 11 sequential equilibrium constants for the assembly pathway which includes the beginning with membrane binding of monomers, proceeds through single pore oligomerization, and culminates in the formation of clusters of the pores. In the second chapter of this article, we refer to an assembly mechanism of LukF and Hlg2 on human erythrocytes as well as the roles of the membranes of the target cells in pore formation by Hlg. The LukF, LukS, and Hlg2 proteins are derived from the Hlg locus (hlg), and have been found in 99% of clinical isolates of Staphylococcus aureus. In contrast, LukF-PV and LukS-PV are derived from the PVL locus (pvl) which is distinct from the hlg locus, and only a small percentage of clinically isolated S. aureus strains carries pvl. Recently, we discovered pvl on the genome of lysogenic bacteriophages, psiPVL, and determined the entire gene of the phage. We also demonstrated the phage conversion of S. aureus leading to the production of PVL through the discovery of a PVL-carrying temperate phage, psiSLT, from a clinical isolate of S. aureus. In the third chapter of this article, we discuss genetic analyses of the Hlg, Luk, and PVL genes. We also discuss the current status of knowledge of the genetic organization of PVL-converting phages in order to achieve an understanding of their molecular evolution.
Geometry-Dependent Stripe Rearrangement Processes Induced by Strain on Preordered Microwrinkle Patterns (2005)

A preordered microwrinkle pattern on a metal-capped surface of a soft elastomer is employed to elucidate the elementary buckling phenomenon during strain-induced stripe rearrangement processes. The preordered one-dimensional stripe tends to align perpendicular to the direction of strain reversibly when lateral compressive strain is applied on the substrate at some angle phi with respect to the stripe orientation. For any value of strain, the film surface can be decomposed in domains containing stripes with two different orientations, namely the original and applied strain orientations. As strain is increased, the domains of the second type of stripes progressively grow and invade the whole surface. Interestingly, the domain shapes during growth are composed of parallelogram units that simply depend on phi and stripe wavelength. Moreover, domain growth proceeds in characteristic directions depending on the shape of the domain unit.
기술보고 : 우리나라 지하수 개발가능량 산정의 현황과 전망 (2015)

우리나라 지하수 개발가능량의 현황을 기출간된 지하수 관리 기본계획 보고서 내용을 기반으로 정리했다. 또한 지하수 개발가능량의 결정적인 요소인 지하수 함양량 산정기법을 검토하였다. 최종적으로 일정기간 수행된 지하수 기초조사 보고서에 나타난 지역별 지하수 개발가능량 산정기법을 검토, 요약했다. 지하수 개발가능량의 개선을 위해서는 개선된 기법(물수지 분석, 개선된 지하수위 변동법)의 적용과 함께 지속가능한 지하수 관리개념의 도입이 필요할 것으로 판단된다.
Decision making, the P3, and the locus coeruleus--norepinephrine system. (2005)

Psychologists and neuroscientists have had a long-standing interest in the P3, a prominent component of the event-related brain potential. This review aims to integrate knowledge regarding the neural basis of the P3 and to elucidate its functional role in information processing. The authors review evidence suggesting that the P3 reflects phasic activity of the neuromodulatory locus coeruleus-norepinephrine (LC-NE) system. They discuss the P3 literature in the light of empirical findings and a recent theory regarding the information-processing function of the LC-NE phasic response. The theoretical framework emerging from this research synthesis suggests that the P3 reflects the response of the LC-NE system to the outcome of internal decision-making processes and the consequent effects of noradrenergic potentiation of information processing.
Tumour necrosis factor inhibitors: risks and benefits in patients with rheumatoid arthritis (2004)

Rheumatoid arthritis (RA) is the most common form of inflammatory arthritis and can, if left untreated, result in significant disability and early death. It is also associated with large direct and indirect costs to the individual and to society. Early and aggressive disease modifying anti-rheumatic drug (DMARD) treatment of patients at risk of erosive disease has improved the outcome in the majority, but not all, RA patients. Tumour necrosis factor (TNF) appears to be a key mediator of the inflammatory and destructive process in RA, and consequently inhibitors of TNF action have been tested in randomized controlled trials in patients with RA. The results of these studies have suggested that TNF inhibitors are potent DMARD particularly when combined with methotrexate. They appear well tolerated with the commonest adverse events related to their parenteral route of administration, and the serious but rare side-effects being various infections, notably tuberculosis, multiple sclerosis, and worsening of cardiac failure. Treatment costs are high and range from $15 000 to $25 000 per patient per year. Etanercept, adalimumab and infliximab have recently been subsidised under the Pharmaceutical Benefits Scheme in Australia for patients with severe DMARD-resistant RA. The availability of TNF inhibitors in RA represents a significant advance in the treatment of patients with severe RA. (Intern Med J 2004; 34: 687−693)
Pigment Epithelium-Derived Factor: A Potent Inhibitor of Angiogenesis (1999)

In the absence of disease, the vasculature of the mammalian eye is quiescent, in part because of the action of angiogenic inhibitors that prevent vessels from invading the cornea and vitreous. Here, an inhibitor responsible for the avascularity of these ocular compartments is identified as pigment epithelium-derived factor (PEDF), a protein previously shown to have neurotrophic activity. The amount of inhibitory PEDF produced by retinal cells was positively correlated with oxygen concentrations, suggesting that its loss plays a permissive role in ischemia-driven retinal neovascularization. These results suggest that PEDF may be of therapeutic use, especially in retinopathies where pathological neovascularization compromises vision and leads to blindness.
Effects of a New Oral Hypoglycaemic Agent (CS‐045) on Metabolic Abnormalities and Insulin Resistance in Type 2 Diabetes (1994)

The effects of a thiazolidinedione antidiabetic agent (CS-045) on diabetic metabolic abnormalities were studied in a double-blind clinical trial. Fourteen patients with Type 2 diabetes were selected according to study criteria. Eight were treated with oral CS-045 at 400 mg daily, and six were given placebo. A multi-step, hyperinsulinaemic, euglycaemic clamp study, with simultaneous plasma free fatty acid study, and glucagon tolerance test were performed before and after administration of drug. Following 3 months of treatment with CS-045, there were significant decreases in the mean levels of fasting plasma glucose (from 9.18 +/- 0.95 to 7.78 +/- 0.44 mmol l-1), postprandial plasma glucose (from 11.8 +/- 1.23 to 10.36 +/- 1.06 mmol l-1), and haemoglobin A1c (from 9.3 +/- 0.4 to 6.8 +/- 0.4%). Insulin sensitivity also improved (1st step: from 3.12 +/- 0.33 to 4.70 +/- 0.47 mg kg-1 min-1 (p < 0.01); 2nd step: from 5.61 +/- 0.63 to 7.54 +/- 0.58 mg kg-1 min-1 (p < 0.01); 3rd step: from 9.21 +/- 0.67 to 11.10 +/- 0.87 mg kg-1 min-1). The fasting free fatty acid level decreased significantly from 0.28 +/- 0.04 to 0.22 +/- 0.02 g l-1. The residual free fatty acid level (%) under insulin infusion clamp conditions decreased significantly from 63.7 +/- 9.7 to 45.0 +/- 9.2%. CS-045 treatment was associated with decrease in total cholesterol, total triglycerides, and increase in HDL cholesterol. Basal C-peptide immunoreactivity level decreased, but there was no change in the peak C-peptide immunoreactivity value.(ABSTRACT TRUNCATED AT 250 WORDS)
Co-Morbid Obsessive–Compulsive Disorder and Attention Deficit Hyperactivity Disorder: Neurobiological Commonalities and Treatment Implications (2019)

OPINION article Front. Psychiatry, 13 August 2019Sec. Psychopharmacology Volume 10 - 2019 | https://doi.org/10.3389/fpsyt.2019.00557
The relationship between Cho/NAA and glioma metabolism: implementation for margin delineation of cerebral gliomas (2012)

HGG and LGG exhibit different spectroscopic patterns. Using (1)H-MRSI to guide the extent of resection has the potential to improve the clinical outcome of glioma surgery.