gebhart/patrepeval huggingface dataset:
The IsdC Protein from Staphylococcus aureus Uses a Flexible Binding Pocket to Capture Heme (2008)

Staphylococcus aureus scavenges heme-iron from host hemoproteins using iron-regulated surface determinant (Isd) proteins. IsdC is the central conduit through which heme is passed across the cell wall and binds this molecule using a NEAr Transporter (NEAT) domain. NMR spectroscopy was used to determine the structure of IsdC in complex with a heme analog, zinc-substituted protoporphyrin IX (ZnPPIX). The backbone coordinates of the ensemble of conformers representing the structure exhibit a root mean square deviation to the mean structure of 0.53 +/- 0.11 angstroms. IsdC partially buries protoporphyrin within a large hydrophobic pocket that is located at the end of its beta-barrel structure. The central metal ion of the analog adopts a pentacoordinate geometry in which a highly conserved tyrosine residue serves as a proximal ligand. Consistent with the structure and its role in heme transfer across the cell wall, we show that IsdC weakly binds heme (K(D) = 0.34 +/- 0.12 microm) and that ZnPPIX rapidly dissociates from the protein at a rate of 126 +/- 30 s(-1). NMR studies of the apo-form of IsdC reveal that a 3(10) helix within the binding pocket undergoes a flexible to rigid transition as heme is captured. This structural plasticity may increase the efficiency of heme transfer across the cell wall by facilitating protein-protein interactions between apoIsdC and upstream hemoproteins.
Premature ageing in transgenic mice expressing different growth hormone genes. (1993)

Transgenic mice expressing various growth hormone genes have markedly reduced life spans, with few animals surviving beyond 12 months in some of the lines. Except for an increased incidence of mammary tumours in female mice expressing human growth hormones, pathological findings in debilitated or moribund transgenic mice resemble the well-documented degenerative changes that occur at a much greater chronological age in normal rodents. This study demonstrates that 10-month-old male transgenic mice expressing bovine growth hormone (known as 25-copy PEPCK. bGH transgenic mice) also show age-related changes in hypothalamic and striatal neurotransmitter metabolism that are not seen in normal litter mate controls until at least 24 months of age. Female mice and male mice with a lower circulating concentration of bGH (known as 5-copy PEPCK. bGH transgenic mice) live longer and fail to show the same magnitude of change in neurotransmitter synthesis and release. Although more work needs to be done to determine the physiological significance of these changes and to determine their relationship to the general effects of ageing on the CNS, transgenic mice expressing various growth hormone genes may provide an interesting and valuable model with which to study the ageing process.
Peptidyl .alpha.-ketoheterocyclic inhibitors of human neutrophil elastase. 3. In vitro and in vivo potency of a series of peptidyl .alpha.-ketobenzoxazoles (1995)

A series of peptidyl alpha-ketobenzoxazoles were synthesized and evaluated for their in vitro and in vivo inhibition of human neutrophil elastase (HNE). These compounds inhibit HNE by forming both a covalent bond between the ketone carbonyl carbon atom and the hydroxyl group of Ser-195 and a hydrogen bond between the benzoxazole nitrogen atom and His-57. Appending to the parent benzoxazole ring a variety of substituents which spanned a range of physicochemical properties had only a modest effect on in vitro potency (Ki = 3-0.4 nM). This apparent lack of a significant effect is believed to result from the fact that any increased ketone carbonyl activation by the ring substituent is counter balanced by a corresponding decrease in the hydrogen-bonding ability of the benzoxazole nitrogen atom. In contrast to the results in vitro, maximizing in vivo activity was critically dependent upon the choice of the benzoxazole ring substituent. Several substituted peptidyl alpha-ketobenzoxazoles effectively inhibited HNE-induced lung injury when administered intratracheally 24 h prior to the enzyme.
Sensory Stimulation-Guided Sacroiliac Joint Radiofrequency Neurotomy: Technique Based on Neuroanatomy of the Dorsal Sacral Plexus (2003)

A sensory stimulation-guided approach toward the identification and subsequent radiofrequency thermocoagulation of symptomatic sacral lateral branch nerves appears to offer significant therapeutic advantages over existing therapies for the treatment of chronic sacroiliac joint complex pain.
The effects of lifelong ubiquinone Q10 supplementation on the Q9 and Q10 tissue concentrations and life span of male rats and mice (1998)

The effect of lifelong oral supplementation with ubiquinone Q10 (10 mg/kg/day) was examined in Sprague-Dawley rats and C57/B17 mice. There were no significant differences in survival or life-span found in either rats or mice. Histopathologic examination of different rat tissues showed no differences between the groups. In Q10 supplemented rats, plasma and liver Q10 levels were 2.6 to 8.4 times higher at all age points than in control rats. Interestingly, in supplemented rats the Q9 levels also were significantly higher (p<0.05) in plasma and liver at ages 18 and 24 months. Neither Q9 nor Q10 levels were affected by supplementation in kidney, heart, or brain tissues. In spite of the significant changes in plasma and liver ubiquinone concentrations, lifelong Q10 supplementation did not prolong or shorten the lifespan of either rats or mice.
Genetic predictors for acute experimental cold and heat pain sensitivity in humans (2006)

The effects of TRPA1 variations on experimental short duration heat pain sensitivity may contribute to inter-individual variation in pain sensitivity in humans.
Effect of Deuterium Substitution in Sympathomimetic Amines on Adrenergic Responses (1961)

It was discovered that replacement of the alpha-hydrogens of tyramine and tryptamine by deuterium produces a marked intensification of the blood pressure effects and nictitating membrane contraction normally produced by these amines. The results are interpreted on the basis of kinetic isotope effects at the level of monoamine oxidase and clearly establish the importance of this enzyme in the limitation of responses when tyramine and tryptamine are involved. The observed deuterium isotope effects with alpha,alpha-bisdeuterotyramine (alpha,alpha-D(2)-tyramine) have been reproduced with only one of the optical isomers of monodeuterotyramine. This establishes that the enzyme displays a high degree of optical specificity. The use of l-bisdeuteronorepinephrine revealed that norepinephrine cannot be attacked by the enzyme at the effector cell level.
Base-Sensitivity of Arginine Alpha-Ketoamide Inhibitors of Serine Proteases (2009)

Serine protease enzymes use a serine hydroxyl group to catalyze hydrolysis of polypeptides. They are important in immunity, blood clotting, digestion, and as therapeutic or diagnostic targets for cancer, diabetes, stroke, inflammatory diseases, and viral infections. Their inhibitors typically possess an electrophile that reacts with the nucleophilic hydroxyl group of the catalytic serine. The a-ketoamide is a valuable electrophile in inhibitor discovery as it permits synthetic elaboration to both sides, unlike other electrophiles. Here we show that an a-ketoamide is unstable above pH 7 when adjacent to the C-terminus of arginine – the guanidine side chain condenses with the a-ketoamide at the keto group rather than the amide carbonyl to form a six-membered hemiaminal rather than a seven-membered lactam.
Secretion of apolipoprotein A-I in lipoprotein particles following transfection of the human apolipoprotein A-I gene into 3T3 cells. (1987)

Apolipoprotein A-I (apoA-I) is the major protein constituent of plasma high density lipoproteins (HDL). To examine apoA-I processing and secretion, the human apoA-I gene (2.2-kilobase PstI-PstI fragment) linked to the mouse metallothionein promoter was transfected by electroporation into NIH 3T3 fibroblasts along with the plasmid pSV2 neo, which confers neomycin resistance. Transfected cells were selected for neomycin resistance and screened for the ability to produce apoA-I by enzyme-linked immunosorbent assay. In the absence of lipids in the medium, selected 3T3 cells secreted apoA-I, mainly in the proprotein form, at density greater than 1.25 g/ml. Following incubation of cells with lipids, and subsequent washing with lipid-free medium, apoA-I was recovered in the HDL region (1.063-1.21 g/ml) as well as in the 1.21 g/ml infranatant. Examination of the HDL fraction by electron microscopy revealed round particles, 10-21 nm in diameter. These data indicate that human apoA-I secreted by transfected 3T3 fibroblasts can assemble into lipoprotein particles under the appropriate conditions.
Prophylactic and therapeutic efficacy of immunoglobulin G antibodies to Pseudomonas aeruginosa lipopolysaccharide against murine experimental corneal infection. (1997)

In an experimental model of P. aeruginosa keratitis, systematically delivered IgG antibodies directed against the O-side-chain antigens of P. aeruginosa, LPS conferred protection against severe corneal damage when administered both prophylactically and therapeutically.
The X window system (1990)

An overview of the X Window System is presented, focusing on the system substrate and the low-level facilities provided to build applications and to manage the desktop. The system provides high-performance, high-level, device-independent graphics. A hierarchy of resizable, overlapping windows allows a wide variety of application and user interfaces to be built easily. Network-transparent access to the display provides an important degree of functional separation, without significantly affecting performance, which is crucial to building applications for a distributed environment. To a reasonable extent, desktop management can be custom-tailored to individual environments, without modifying the base system and typically without affecting applications.
Fatty acid profile of skeletal muscle phospholipids in trained and untrained young men (2000)

Endurance trained (n = 14) and untrained young men (n = 15) were compared regarding the fatty acid profile of the vastus lateralis muscle after 8 wk on diets with a similar fatty acid composition. The skeletal muscle phospholipids in the trained group contained lower proportions of palmitic acid (16:0) (-12.4%, P < 0.001) and di-homo-gamma-linolenic acid [20:3(n-6)] (-15.3%, P = 0.018), a lower n-6-to-n-3 ratio (-42.0%, P = 0.015), higher proportions of stearic acid (18:0) (+9.8%, P = 0.004) and sum of n-3 polyunsaturated fatty acids (+33.8%, P = 0.009), and a higher ratio between 20:4(n-6) to 20:3(n-6) (+18.4%, P = 0.006) compared with those in the untrained group. The group differences in 16:0, 20:3(n-6), 18:0/16:0, and 20:4(n-6)/20:3(n-6) were independent of fiber-type distribution. The trained group also showed a lower proportion of 16:0 (-7.9%, P < 0.001) in skeletal muscle triglycerides irrespective of fiber type. In conclusion, the fatty acid profile of the skeletal muscle differed between trained and untrained individuals, although the dietary fatty acid composition was similar. This difference was not explained by different fiber-type distribution alone but appears to be a direct consequence of changes in fatty acid metabolism due to the higher level of physical activity.
Human saliva inactivates mutagenicity of carcinogens (1981)

Mutagenicities of AF-2, MNNG, 4NQO, aflatoxin B1, benzo [a] pyrene and Trp-P-1, with or without metabolic activation, were inactivated by treatment with human saliva to a great extent in the Ames test with Salmonella typhimurium test strains TA98 and TA100. Mutagenic activities of quercetin, pyrolysates of beef, salmon and sodium glutamate, and condensate of cigarette smoke were also decreased to some extent by saliva treatment, but no significant effect was found on the activity of MMS and pyrolysate of polypeptone. These effects showed individual variations. The inhibition of AF-2 mutagenicity by saliva varied with temperature in TA100 but not in TA98 cultures. Boiled saliva inactivated AF-2 mutagenicity in TA98 to some extent but not in TA100 cultures. Inactivation of AF-2 mutagenicity by saliva treatment was completed within 30 sec. Complex mechanisms may be involved in the inactivation of mutagenicity of carcinogens by saliva, including biochemical reactions with enzymes, vitamins, etc. and/or adsorption with high molecular weight substances in saliva such as proteins, bacterial cells, mucous materials, etc.
Electrospun PCL in Vitro: a Microstructural Basis for Mechanical Property Changes (2009)

Polymeric tissue-engineering scaffolds must provide mechanical support while host-appropriate cells populate the structure and deposit extracellular matrix (ECM) components specific to the organ targeted for replacement. Even though this concept is widely shared, changes in polymer modulus and other mechanical properties versus biological exposure are largely unknown. This work shows that specific interactions of biological milieu with electrospun scaffolds can exert control over scaffold modulus. The net effects of biological and non-biological environments on electrospun structures following 7 and 28 days of in vitro exposure are established. Reduction of modulus, ultimate tensile strength and elongation occurs without the apparent involvement of classic hydrolysis mechanisms. We describe this phenomenon as deposition-induced inhibition of nanofiber rearrangement. This phenomenon shows that both mechanical and morphological characterization of electrospun structure under load in biological environments is required to tailor scaffold design to pursue specific tissue-engineering goals.
Generation of Fiber-Mutant Recombinant Adenoviruses for Gene Therapy of Malignant Glioma (1998)

Recombinant adenovirus (Adv)-mediated gene transduction is a powerful technology for cancer gene therapy. In this article, we report the generation of a fiber-mutant Adv vector, using the Adv genomic DNA-terminal protein complex (DNA-TPC) cotransfection method. First, a fiber-mutant construct in a plasmid carrying the right-side two-thirds of the human adenovirus type 5 (Ad5) genome (pTR) was cotransfected with Ad5 DNA-TPC, yielding the recombinant Adv with the desired fiber mutation. The DNA-TPC from the mutant Adv was then utilized to produce a second-step recombinant Adv with an expression cassette in the place of E1. By this procedure, we generated a fiber mutant, F/K20, that has a linker and a stretch of 20 lysine residues added at the C terminus of the fiber. By using Adv carrying a reporter lacZ gene (AxCAZ2) with either F/K20 or wild-type fiber (F/wt), we examined the transduction efficiency of F/K20-Adv. No significant difference in the transduction efficiency between F/K20 and F/wt-Adv was observed for a human fibroblast line, WI-38, or various tumor cell lines, including melanoma, prostate, esophageal, and pancreatic cancer lines. In clear contrast, F/K20-Adv showed a remarkably enhanced efficiency in genetic transduction of human glioma cells. In all four human glioma lines tested, the multiplicities of infection (MOIs) for transduction of 50% of the population (ED50) were decreased with F/K20-Adv compared with F/wt-Adv: 7-fold for T98G, 14-fold for U251, 9-fold for U373, and 42-fold for U87 cells. Therefore, we attempted to apply F/K20-Adv for gene therapy of malignant glioma. Glioma cells infected with F/K20-Adv carrying genes for interleukin 2 or interleukin 12 produced a high level of each cytokine at a much lower MOI than did cells infected with F/wt-Adv. Infection with F/K20-Adv carrying the wild-type p53 tumor suppressor gene resulted in an enhanced level of p53 protein expression and an increased incidence of F/K20-Adv in transduction efficiency for malignant glioma, providing promising tools for gene therapy.
Treating stage IV pressure ulcers with negative pressure therapy: a case report. (1999)

Decubitus ulcers remain a significant healthcare concern today, especially in the elderly and immobile population. Following the observation of three Stage IV decubitus ulcers refractory to standard medical and surgical therapy for 10 months, a new vacuum-assisted closure device (V.A.C.) was initiated to speed wound healing. The V.A.C. was initiated in August 1996. The three Stage IV ulcers were located on the patient's right ischium, left ischium, and sacrum. On initiation, they measured 7 1/2 cm x 2 1/2 cm x 2 1/2 cm, 8 cm x 3 1/2 cm x 2 1/2 cm, and 3 1/2 cm x 2 cm x 2 cm respectively. The treatment consisted of insertion of sterile sponge into the wound bed connected to the negative pressure device by suction hose. The device operated at a negative pressure of 125 mm Hg with a 5-minute-on 2-minute-off-cycle. Dressing changes were performed every 48 hours during the treatment period. Successful closure of the sacral ulcer occurred in October 1996. The ischial ulcers were small enough to be taken off V.A.C. therapy in early November 1996. While we are encouraged by the results of this study, further additional clinical studies are warranted.
A Framework for Binding and Retrieving Class-Specific Information to and from Image Patterns Using Correlation Filters (2012)

We describe a template-based framework to bind class-specific information to a set of image patterns and retrieve that information by matching the template to a query pattern of the same class. This is done by mapping the class-specific information to a set of spatial translations which are applied to the set of image patterns from which a template is designed, taking advantage of the properties of correlation filters. The bound information is retrieved during matching with an authentic query by estimating the spatial translations applied to the images that were used to design the template. In this paper, we focus on the problem of binding information to biometric signatures as an application of our framework. Our framework is flexible enough to allow spreading the information to be bound over multiple pattern classes which, in the context of biometric key-binding, enables multiclass and multimodal biometric key-binding. We demonstrate the effectiveness of the proposed scheme via extensive numerical results on multiple biometric databases.
Rhodium-Catalyzed Asymmetric 1,4-Addition and Its Related Asymmetric Reactions (2003)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRhodium-Catalyzed Asymmetric 1,4-Addition and Its Related Asymmetric ReactionsTamio Hayashi and Kaori YamasakiView Author Information Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan Cite this: Chem. Rev. 2003, 103, 8, 2829–2844Publication Date (Web):July 24, 2003Publication History Received21 February 2003Published online24 July 2003Published inissue 1 August 2003https://pubs.acs.org/doi/10.1021/cr020022zhttps://doi.org/10.1021/cr020022zresearch-articleACS PublicationsCopyright © 2003 American Chemical SocietyRequest reuse permissionsArticle Views18933Altmetric-Citations1339LEARN 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:Catalysts,Chemical reactions,Ligands,Rhodium,Stereoselectivity Get e-Alerts
Production and Characterization of RNA Aptamers Specific for Amyloid Fibril Epitopes (2007)

One of the most fascinating features of amyloid fibrils is their generic cross-beta architecture that can be formed from many different and completely unrelated proteins. Nonetheless, amyloid fibrils with diverse structural and phenotypic properties can form, both in vivo and in vitro, from the same protein sequence. Here, we have exploited the power of RNA selection techniques to isolate small, structured, single-stranded RNA molecules known as aptamers that were targeted specifically to amyloid-like fibrils formed in vitro from beta(2)-microglobulin (beta(2)m), the amyloid fibril protein associated with dialysis-related amyloidosis. The aptamers bind with high affinity (apparent K(D) approximately nm) to beta(2)m fibrils with diverse morphologies generated under different conditions in vitro, as well as to amyloid fibrils isolated from tissues of dialysis-related amyloidosis patients, demonstrating that they can detect conserved epitopes between different fibrillar species of beta(2)m. Interestingly, the aptamers also recognize some other, but not all, amyloid fibrils generated in vitro or isolated from ex vivo sources. Based on these observations, we have shown that although amyloid fibrils share many common structural properties, they also have features that are unique to individual fibril types.
Direct evidence for a xylose metabolic pathway in Saccharomyces cerevisiae (1986)

Xylose transport, xylose reductase, and xylitol dehydrogenase activities are demonstrated in Saccharomyces cerevisiae. The enzymes in the xylose catabolic pathway necessary for the conversion of xylose to xylulose are present, although S. cerevisiae cannot grow on xylose as a sole carbon source. Xylose transport is less efficient than glucose transport, and its rate is dependent upon aeration. Xylose reductase appears to be a xylose inducible enzyme and xylitol dehydrogenase activity is constitutive, although both are repressed by glucose. Both xylose reductase and xylitol dehydrogenase activities are five- to tenfold lower in S. cerevisiae as compared to Candida utilis. In vivo conversion of (14)C-xylose in S. cerevisiae is demonstrated and xylitol is detected, although no significant levels of any other (14)C-labeled metabolites (e. g., ethanol) are observed.
Analysis of Restriction Fragment Length Polymorphisms in Deoxyribonucleic Acid (DNA) Recovered from Dried Bloodstains (1986)

Deoxyribonucleic acid (DNA) was recovered from dried bloodstains aged up to three years and shown to be of high molecular weight. DNA was digested with restriction endonucleases and fractionated by agarose gel electrophoresis. Following transfer to a filter, DNA was hybridized with two different radioactively labeled recombinant probes which recognize highly polymorphic regions in human DNA. The autoradiographic pattern observed was not altered by sample age, and the size of the alleles was consistent with those observed in the general population. Therefore, DNA of high molecular weight prepared from dried blood samples can be used for identification.