gebhart/patrepeval huggingface dataset:
Discrete Heterogeneous Quaternary Structure Formed by α/β-Peptide Foldamers and α-Peptides (2007)

The development of unnatural oligomers that adopt predictable secondary structures has led to increased interest in expanding the conformational repertoire of foldamers to include discrete, cooperatively folded tertiary and quaternary structures. Here we report the first examples of heterogeneous quaternary structure: stable tetrameric helix bundles incorporating both α-peptides and α/β-peptide foldamers. The results suggest that hydrophobic interactions in the core of the helix bundle contribute to the stability of the assembly, as do cyclic β-amino acid residues within the α/β-peptide. These observations demonstrate that secondary structural elements in well-folded tertiary or quaternary structures need not have the same backbone composition. Our findings highlight the prospect that diverse combinations of foldamer and α-peptide subunits could lead to folding and/or assembly behavior reminiscent of that necessary for complex protein function.
Headache Disorders: A Management Guide for Practitioners (1996)

Prevalence and Impact of Headache. Diagnosis and Classification of Headache Disorders. The Changing Headache, Secondary (Organic) Headache Disorders, And Diagnostic Testing. Pathophysiology of Headache. The History and Physical Exam. Pharmacological Treatment of Migraine. Nonpharmacological Measures and Physician Strategies for Improved Outcome of Therapy. Psychiatric Aspects of Primary Headache Disorders. Emergency Room Evaluation and Treatment. Inpatient Treatment of Primary Headache Disorders.
The cell wall components peptidoglycan and lipoteichoic acid from Staphylococcus aureus act in synergy to cause shock and multiple organ failure. (1995)

Although the incidence of Gram-positive sepsis has risen strongly, it is unclear how Gram-positive organisms (without endotoxin) initiate septic shock. We investigated whether two cell wall components from Staphylococcus aureus, peptidoglycan (PepG) and lipoteichoic acid (LTA), can induce the inflammatory response and multiple organ dysfunction syndrome (MODS) associated with septic shock caused by Gram-positive organisms. In cultured macrophages, LTA (10 micrograms/ml), but not PepG (100 micrograms/ml), induces the release of nitric oxide measured as nitrite. PepG, however, caused a 4-fold increase in the production of nitrite elicited by LTA. Furthermore, PepG antibodies inhibited the release of nitrite elicited by killed S. aureus. Administration of both PepG (10 mg/kg; i.v.) and LTA (3 mg/kg; i.v.) in anesthetized rats resulted in the release of tumor necrosis factor alpha and interferon gamma and MODS, as indicated by a decrease in arterial oxygen pressure (lung) and an increase in plasma concentrations of bilirubin and alanine aminotransferase (liver), creatinine and urea (kidney), lipase (pancreas), and creatine kinase (heart or skeletal muscle). There was also the expression of inducible nitric oxide synthase in these organs, circulatory failure, and 50% mortality. These effects were not observed after administration of PepG or LTA alone. Even a high dose of LTA (10 mg/kg) causes only circulatory failure but no MODS. Thus, our results demonstrate that the two bacterial wall components, PepG and LTA, work together to cause systemic inflammation and multiple systems failure associated with Gram-positive organisms.
Detection of 60° phase defects on alternating PSMs (1998)

In this paper we present results of an algorithm that has been developed which is sensitive to phase defects of 60 degrees on i-line alternating PSMs. This algorithm consists of microcode and software, which can be loaded into existing inspection hardware. The algorithm works in die-to-die inspection mode and uses both transmitted and reflected light images to maximize sensitivity. Isolated phase defects as well as phase defects close to chrome edges were inspected. In addition, the algorithm is able to detect missing and mis-aligned shifter edges. A programmed phase defect test plate was developed to characterize defect detection sensitivity. Detection of 60 degrees defects smaller than 0.75 micrometers has been demonstrated with this algorithm. Defect sensitivity characterization and actual production plate effect results are shown. Finally, recent results showing the application of the algorithm to the inspection of Deep-UV multiphase reticles using a shorter inspection wavelength are presented.
Identification of amino acid residues required for Ras p21 target activation. (1991)

The Krev-1 gene has been shown to suppress ras-mediated transformation in vitro. Both ras and Krev-1 proteins have identical effector domains (ras residues 32 to 40), which are required for biological activity and for the interaction of Ras p21 with Ras GTPase-activating protein (GAP). In this study, five amino acid residues flanking the ras effector domain, which are not conserved with the Krev-1 protein, were shown to be required for normal protein-protein interactions and biological activity. The substitution of Krev-1 p21 residues 26, 27, 30, 31, and 45 with the corresponding amino acid residues from Ras p21 resulted in a Krev-1 protein which had ras function in both mammalian and yeast biological assays. Replacement of these residues in Ras p21 with the corresponding Krev-1 p21 amino acids resulted in ras proteins which were impaired biologically or reduced in their affinity for in vitro GAP binding. Evaluation of these mutant ras proteins have implications for Ras p21-GAP interactions in vivo.
Simple Synthesis of Both Enantiomers of the C7-C12 Segment of Epothilones (1998)

Both enantiomers of the C7-C12 segment (3 and 4) of antitumor antibiotics epothilones (1and 2) were synthesized from methyl (R)- and (S)-3-hydroxy-2-methylpropionate (5 and 6) in five steps in a fair yield.
Malaria and the Red Cell (2002)

Because of the breakdown of malaria control programs, the constant emergence of drug resistant parasites, and, possibly, climatic changes malaria poses a major problem for the developing countries. In addition, because of the speed of international travel it is being seen with increasing frequency as an imported disease in non-tropical countries. This update explores recent information about the pathophysiology of the disease, its protean hematological manifestations, and how carrier frequencies for the common hemoglobin disorders have been maintained by relative resistance to the malarial parasite. In Section I, Dr. Louis Miller and colleagues consider recent information about the pathophysiology of malarial infection, including new information about interactions between the malarial parasite and vascular endothelium. In Section II, Dr. David Roberts discusses what is known about the complex interactions between red cell production and destruction that characterize the anemia of malaria, one of the commonest causes of anemia in tropical countries. In Section III, Dr. David Weatherall reviews recent studies on how the high gene frequencies of the thalassemias and hemoglobin variants have been maintained by heterozygote advantage against malaria and how malaria has shaped the genetic structure of human populations.
Recombinant subunit ORF2.1 antigen and induction of antibody against immunodominant epitopes in the hepatitis E virus capsid protein (2000)

A recombinant subunit antigen (ORF2.1), representing the carboxy-terminal 267 amino acids of the 660-amino-acid hepatitis E virus (HEV) capsid protein, was expressed in Escherichia coli and used for the immunisation of rats. Purified antigen formulated with either Aluminium Hydroxide Gel Adjuvant (Alum) or Titermax gave high and equivalent levels of antibody after three doses. Responses to two doses of 15, 75, or 150 microg antigen, formulated with Alum and given at 0 and 4 weeks, were also equivalent by 17 weeks after immunisation. Rats initially developed antibody to a wide range of linear epitopes in the ORF2.1 region, but by 27 weeks the predominant response detected by Western immunoblotting was restricted to the conformational epitope unique to ORF2.1 [Li et al. (1997) Journal of Medical Virology 52:289-300], a pattern that was also observed when comparing acute-phase patient serum samples with serum samples from convalescing patients. Antibody from immunised rats blocked the majority of patients' serum reactivity in enzyme-linked immunosorbent assay against both ORF2.1 (57-92% inhibition) and virus-like particles of HEV produced using the baculovirus system (74-97% inhibition). Together, these results suggest that the ORF2.1 subunit vaccine induces an antibody response against immunodominant, conformational epitopes in the viral capsid, which largely mimics that seen in convalescent patients, who are presumed to be immune to HEV infection.
Stability and Lifetime of Quadruply Hydrogen Bonded 2-Ureido-4[1H]-pyrimidinone Dimers (2000)

2-Ureido-4[1H]-pyrimidinones are known to dimerize via a strong quadruple hydrogen bond array. A detailed study of the dimerization constant and lifetime of the dimer is presented here. Excimer fluorescence of pyrene-labeled 2-ureido-4[1H]-pyrimidinone 1b was used to determine a dimerization constant Kdim of 6 × 107 M-1 in CHCl3, 1 × 107 M-1 in chloroform saturated with water, and 6 × 108 M-1 in toluene (all at 298 K). Under these conditions, the preexchange lifetime of the similar dimers of both 1d and 1e is 170 ms in CDCl3, 80 ms in wet CDCl3, and 1.7 s in toluene-d8, as determined by dynamic NMR spectroscopy. Association rate constants were calculated from the Kdim values and the preexchange lifetimes. The resulting values are significantly lower than the diffusion-controlled association rate constants calculated using the Stokes−Einstein and the Debeije equations. This difference is ascribed to a tautomeric equilibrium of the monomer between the dimerizing 4[1H]-pyrimidinone and nondimerizing 6[1H]-pyrimidinone tautomers, which is unfavorable for dimerization.
Role of appendix in the development of inflammatory bowel disease in TCR-alpha mutant mice. (1996)

T cell receptor-alpha mutant mice (TCR-alpha-/-), created by gene targeting of the TCR-alpha gene in embryonic stem cells, spontaneously develop inflammatory bowel disease (IBD) resembling human ulcerative colitis. Since gut-associated lymphoid tissue is likely to play an important role in the development of chronic intestinal inflammation, we examined the changes in the appendix lymphoid follicle (ALF) and Peyer's patches (PP) in these mice. We found the structure of the ALF to be remarkably similar to that of the PP in the small intestine; in both instances, lymphoid follicles covered by surface epithelium (dome-formation) were found. The amount of proliferation in the lymphoid follicles of the appendix estimated by in vivo incorporation of 5-bromo-2'deoxyuridine was more than two times that of PP in TCR-alpha-/- mice. ELISPOT assay showed an increase of IgA, IgG1, and IgG2a, but not IgM-secreting B cells in ALF of TCR-alpha-/- mice compared to TCR-alpha+/- control mice. Furthermore, TCR-alpha-/- mice revealed an increase of autoantibody-producing B cells against the cytoskeletal protein tropomyosin in ALF as compared to PP. When TCR-alpha-/- mice underwent appendectomy at a young age (3-5 wk), the number of mesenteric lymph nodes cells at 6-7 mo were markedly less than in the sham-operated TCR-alpha-/- mice. Furthermore, appendectomy at 1 mo of age suppressed the development of IBD, with only 3.3% of these mice developing IBD in the 6-7-mo period of observation. In contrast, approximately 80% of controls, including the sham-operated TCR-alpha-/- mice, developed IBD during this period. These results suggest that ALF, rather than PP, is the priming site of cells involved in the disease process and plays an important role in the development of IBD in TCR-alpha-/- mice.
Integrated Microchip Device with Electrokinetically Controlled Solvent Mixing for Isocratic and Gradient Elution in Micellar Electrokinetic Chromatography (1997)

A monolithic micromachined device is presented which allows on-chip adjustments of the content of organic modifier in the run buffer for fast, efficient MEKC separations. Isocratic and gradient conditions are controlled by proper setting of voltages applied to the buffer reservoirs of the microchip. The precision of this control is tested for gradients of various shapes (linear, concave, convex) by mixing pure buffer and buffer doped with a fluorescent dye. The effect of isocratic and gradient solvent changes on the MEKC separation of a mixture of coumarin dyes is demonstrated using methanol and acetonitrile as modifiers. Separations were carried out using a column length of 25 mm and a field strength of 660 V/cm with high resolution. Analysis times were as short as 33 s for methanol and under 22 s for acetonitrile. Gradients with both modifiers were executed within 10 s. Of the two modifiers, acetonitrile proved to have a more pronounced impact on the elution pattern of the test mixture. Only slight band broadening is observed for gradient runs as compared to isocratic runs using methanol. On the other hand, in the case of acetonitrile gradients, some of the peaks exhibit a focusing effect (as observed in HPLC gradients), yielding up to 100 000 plates.
Glycolytic enzymes associated with the cell surface of Streptococcus pneumoniae are antigenic in humans and elicit protective immune responses in the mouse (2004)

Streptococcus pneumoniae is a leading cause of otitis media, sinusitis, pneumonia, bacteraemia and meningitis worldwide. The drawbacks associated with the limited number of various capsular polysaccharides that can be included in the polysaccharide-based vaccines focuses much attention on pneumococcal proteins as vaccine candidates. We extracted an enriched cell wall fraction from S. pneumoniae WU2. Approximately 150 soluble proteins could be identified by 2D gel electrophoresis. The proteins were screened by 2D-Western blotting using sera that were obtained longitudinally from children attending day-care centres at 18, 30 and 42 months of age and sera from healthy adult volunteers. The proteins were further identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Seventeen proteins were antigenic in children and adults, of which 13 showed an increasing antibody response with age in all eight children analysed. Two immunogenic proteins, fructose-bisphosphate aldolase (FBA) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and a control protein with known low immunogenicity, heat shock protein 70 (DnaK), were expressed in Escherichia coli, purified and used to immunize mice. Mouse antibodies elicited to the recombinant (r) FBA and rGAPDH were cross-reactive with several genetically unrelated strains of different serotypes and conferred protection to respiratory challenge with virulent pneumococci. In addition, the FBA used in this study (NP_345117) does not have a human ortholog and warrants further investigation as a candidate for a pneumococcal vaccine. In conclusion, the immunoproteomics based approach utilized in the present study appears to be a suitable tool for identification of novel S. pneumoniae vaccine candidates.
A versatile low temperature synthetic route to Zintl phase precursors: Na4Si4, Na4Ge4 and K4Ge4 as examples (2009)

Na(4)Si(4) and Na(4)Ge(4) are ideal chemical precursors for inorganic clathrate structures, clusters, and nanocrystals. The monoclinic Zintl phases, Na(4)Si(4) and Na(4)Ge(4), contain isolated homo-tetrahedranide [Si(4)](4-) and [Ge(4)](4-) clusters surrounded by alkali metal cations. In this study, a simple scalable route has been applied to prepare Zintl phases of composition Na(4)Si(4) and Na(4)Ge(4) using the reaction between NaH and Si or Ge at low temperature (420 degrees C for Na(4)Si(4) and 270 degrees C for Na(4)Ge(4)). The method was also applied to K(4)Ge(4), using KH and Ge as raw materials, to show the versatility of this approach. The influence of specific reaction conditions on the purity of these Zintl phases has been studied by controlling five factors: the method of reagent mixing (manual or ball milled), the stoichiometry between raw materials, the reaction temperature, the heating time and the gas flow rate. Moderate ball-milling and excess NaH or KH facilitate the formation of pure Na(4)Si(4), Na(4)Ge(4) or K(4)Ge(4) at 420 degrees C (Na(4)Si(4)) or 270 degrees C (both M(4)Ge(4) compounds, M = Na, K). TG/DSC analysis of the reaction of NaH and Ge indicates that ball milling reduces the temperature for reaction and confirms the formation temperature. This method provides large quantities of high quality Na(4)Si(4) and Na(4)Ge(4) without the need for specialized laboratory equipment, such as Schlenk lines, niobium/tantalum containers, or an arc welder, thereby expanding the accessibility and chemical utility of these phases by making them more convenient to prepare. This new synthetic method may also be extended to lithium-containing Zintl phases (LiH is commercially available) as well as to alkali metal-tetrel Zintl compounds of other compositions, e.g. K(4)Ge(9).
Acuerdos de cooperacion en I + D en España: un analisis empírico. (1995)

En este trabajo se analiza una muestra de 102 acuerdos de cooperacion en I + D suscritos por empresas espanolas. El analisis de la misma confirma la existencia de ciertas caracteristicas distintivas de los acuerdos de I + D frente al resto, como su mayor numero de socios, el escaso peso de las empresas conjuntas y la mayor presencia de ayudas publicas. Asimismo, en el trabajo se presenta una distincion entre dos tipos de acuerdos de I +D: acuerdos cerrados y abiertos, identificando los factores que influyen para que se adopte uno u otro tipo de acuerdo.
A Vapochromic LED (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA Vapochromic LEDYoshihito Kunugi, Kent R. Mann, Larry L. Miller, and Christopher L. ExstromView Author Information Department of Chemistry, University of Minnesota Minneapolis, Minnesota 55455 Cite this: J. Am. Chem. Soc. 1998, 120, 3, 589–590Publication Date (Web):January 7, 1998Publication History Received20 October 1997Revised2 December 1997Published online7 January 1998Published inissue 1 January 1998https://pubs.acs.org/doi/10.1021/ja973627zhttps://doi.org/10.1021/ja973627zrapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views688Altmetric-Citations131LEARN 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 SUBJECTS:Aromatic compounds,Diodes,Ketones,Layers,Quantum mechanics Get e-Alerts
Involvement of Rho-Kinase in Cold Ischemia-Reperfusion Injury after Liver Transplantation in Rats (2004)

The present study demonstrates that Rho-kinase-mediated production of ROS and inflammatory cytokines are substantially involved in the pathogenesis of hepatocellular necrosis and apoptosis induced by cold I/R in vivo and that Rho-kinase may be regarded as a novel therapeutic target for the disorder.
Use of a new adhesive film for the preparation of multi-purpose fresh-frozen sections from hard tissues, whole-animals, insects and plants (2003)

A method for preparing thin fresh-frozen sections from large samples and hard tissues is described and the applications are shown. A new adhesive film is introduced to produce the frozen sections. The sample is frozen in a cooled hexane or liquid nitrogen, and then freeze-embedded with 4-5% carboxymethyl cellulose (CMC) in the coolant. A specially prepared adhesive film is fastened to the cut surface of the sample in order to support the section and cut slowly with a disposable tungsten carbide blade. The adhesive film is made of a thin plastic film and an adhesive before use. This method produces 2-microm thick fresh-frozen sections from a large sample, bone or tooth. The "film-section" i.e. the section attached to the adhesive film, can be used for many types of studies such as histology, general histochemistry, enzyme histochemistry, immunohistochemistry, in situ hybridization, elemental analysis, and autoradiography for water-soluble materials. Immunohistochemistry and in situ hybridization can be carried out with nonfixed and undecalcified sections. The section on the adhesive film can be transferred to a glass slide and mounted under a cover slip, and stained sections can be examined with an optical microscope at high magnification. This method is also useful for preparing frozen sections from samples of fish, insects, and plants. Furthermore, samples of particular areas can be collected from the film-section by means of a laser microdissection technique. The multiple possible applications of the adhesive film render it highly useful for studies in biological and medico-dental fields.
Conservative and Tiled Rasterization Using a Modified Triangle Set-Up (2005)

Several algorithms that use graphics hardware to accelerate processing require conservative rasterization in order to function correctly. Conservative rasterization stands for either overestimating or underestimating the size of the triangles. Overestimation is carried out by including all pixels that are at least partially overlapped by the triangle, whereas underestimation includes only the pixels that are fully inside the triangle. No or few algorithms for conservative rasterization have been described in the literature, and current hardware does not explicitly support it. Therefore, we present a simple algorithm, which requires only a small modification to the triangle set-up when edge functions are used. Furthermore, the same algorithm can be used for tiled rasterization, where all pixels in a tile (e.g., 8 × 8 pixels) are visited before moving to the next tile.
Polarization sensitive optical coherence tomography of the rabbit eye (1999)

A polarization-sensitive optical coherence tomography (PSOCT) system was used to acquire depth-resolved images of the Stokes parameters of light backreflected from ex vivo rabbit eyes. The light backreflected from the eye interferes with that from the reference arm and is coherently detected in two orthogonal polarization channels. The two signals are digitized and the four Stokes parameters (I, Q, U, and V) of the backreflected light are computed for light backreflected from each longitudinal/lateral position in the eye. From the measured Stokes parameters, an estimate of the relative phase retardation between the two orthogonal polarizations can be determined. Two eyes were enucleated, imaged within 6-h postmortem and histology performed. Images of the Stokes parameters of light backreflected from the corneal stroma show significant local variations in the polarization state, possibly due to local changes in stromal structure. Depth-resolved Stokes parameter images of light backreflected from the retina were also acquired. A birefringent layer was observed at the position consistent with the known location of the nerve fiber layer (NFL). The local thickness of the birefringent layer determined with PSOCT was in good agreement with values determined histologically.