gebhart/patrepeval huggingface dataset:
Multiscale structural similarity for image quality assessment (2025)

The structural similarity image quality paradigm is based on the assumption that the human visual system is highly adapted for extracting structural information from the scene, and therefore a measure of structural similarity can provide a good approximation to perceived image quality. This paper proposes a multi-scale structural similarity method, which supplies more flexibility than previous single-scale methods in incorporating the variations of viewing conditions. We develop an image synthesis method to calibrate the parameters that define the relative importance of different scales. Experimental comparisons demonstrate the effectiveness of the proposed method.
Allosteric Coupling between the Lid and Interdomain Linker in DnaK Revealed by Inhibitor Binding Studies (2008)

The molecular chaperone DnaK assists protein folding and refolding, translocation across membranes, and regulation of the heat shock response. In Escherichia coli, the protein is a target for insect-derived antimicrobial peptides, pyrrhocoricins. We present here the X-ray crystallographic analysis of the E. coli DnaK substrate-binding domain in complex with pyrrhocoricin-derived peptide inhibitors. The structures show that pyrrhocoricins act as site-specific, dual-mode (competitive and allosteric) inhibitors, occupying the substrate-binding tunnel and disrupting the latch between the lid and the beta-sandwich. Our structural analysis revealed an allosteric coupling between the movements of the lid and the interdomain linker, identifying a previously unknown mechanism of the lid-mediated regulation of the chaperone cycle.
Computational simulation of the turbocharger rotor mechanical noise (2016)

The article describes the computational model of turbocharger rotor including slide bearings and a subsequent application of multibody software for simulation of the turbocharger rotordynamics. The new developed simulation tool is based on the software enabling simulations of multibody nonlinear transient dynamics. The rotor is modelled as a flexible structure based on the Timoshenko’s beam nonlinear theory suitable for an effective solution in the time domain. The computational model incorporates journal and axial slide bearing models. Theoretical background of the journal bearing computational models, based on the numerical solution of the Reynolds equation, is presented. The simulation capabilities and possible results are demonstrated on the tractor diesel engine turbocharger rotor supported by fully floating ring bearings.
Isolation and the 5'-end nucleotide sequence of Bacillus licheniformis alpha-amylase gene (1984)

We have isolated and determined the 5'-end nucleotide sequence of the alpha-amylase gene from Bacillus licheniformis ATCC 14580. The alpha-amylase produced by this strain is thermostable and of liquefying type. The gene was originally cloned in a bacteriophage lambda 1059 vector. A subclone containing a 5.3 X 10(3)-base insert in pBR322 was further characterized. The nucleotide sequence coding for the 5' end of the structural gene together with the sequence coding for the upstream control regions was determined. The deduced N-terminal amino acid sequence was identical with the previously published amino acid sequence of B. licheniformis alpha-amylase. There was also very strong homology to the N-terminal sequence of Bacillus amyloliquefaciens alpha-amylase. The Mr of the thermostable alpha-amylase, as determined in vitro in a cell-free transcription/translation system of Escherichia coli, was about 55 000.
PRODEN: A new program for calculating integrated projected populations (1990)

Abstract Two new computational methods for the evaluation and partitioning of projected, planar, and averaged slab electron densities, implemented in the program PRODEN, are presented. The new algorithms for the projection, demarcation, and integration of electron densities are described and evaluated in terms of speed and numerical accuracy. Integrated Projected Populations are analyzed and some of the advantages and limitations of the methods are discussed.
Cardiac Myotrophin Exhibits rel/NF-κB Interacting Activity in Vitro (1996)

Myotrophin is a soluble-12 kilodalton protein isolated from hypertrophied spontaneously hypertensive rat and dilated cardiomyopathic human hearts. We have recently cloned the gene coding for myotrophin and expressed it in Escherichia coli. In the present study, the expression of myotrophin gene was analyzed, and at least seven transcripts have been detected in rat heart and in other tissues. We have further analyzed the primary structure of myotrophin protein and identified significant new structural and functional domains. Our analysis revealed that one of the ankyrin repeats of myotrophin is highly homologous specifically to those of myotrophin is highly homologous specifically to those of I kappa B alpha/rel ankyrin repeats. In addition, putative consensus phosphorylation sites for protein kinase C and casein kinase II, which were observed in I kappa B alpha proteins, were identified in myotrophin. To verify the significance of these homologies, kappa B gel shift assays were performed with Jurkat T cell nuclear extract proteins and the recombinant myotrophin. Results of these assays indicate that the recombinant myotrophin has the ability to interact with NF-kappa B/rel proteins as revealed by the formation of ternary protein-DNA complexes. While myotrophin-specific antibodies inhibited the formation of these complexes, rel-specific p50 and p65 antibodies supershifted these complexes. Thus, these results clearly indicate that the myotrophin protein to be a unique rel/NF-kappa B interacting protein.
Cloning, sequencing and expression of GroEL-like protein gene of Vibrio parahaemolyticus. (2004)

Vibrio parahaemolyticus is an important enteropathogen in regions where much seafood is consumed. Substantial quantity of GroEL-like protein is produced during the heat shock of V. parahaemolyticus and located in periplasmic and extracellular fractions. In this study, the GroEL-like protein gene of this pathogen was cloned and sequenced and its properties were analyzed. The open reading frame consisted of 1647 bp, encoded a 57.6-kDa GroEL-like protein of 548 amino acids. The amino acid sequence, hydrophobicity and antigenic pattern of V. parahaemolyticus GroEL-like protein were similar to the GroEL proteins of other vibrios, Escherichia coli and Salmonella enterica Typhi. The groEL-like gene of V. parahaemolyticus was cloned into the pQE-30 expression vector and the expression of a His-tagged GroEL-like protein was rapidly induced by isopropyl-beta-D-thiogalactopyranoside, largely in an insoluble form. The results of this study facilitate the study of the functions of the GroEL-like protein of V. parahaemolyticus.
The peroxisome proliferator-activated receptorγ (PPARγ) as a regulator of monocyte/macrophage function (1999)

Peroxisome proliferator-activated receptors (PPARs) are ligand-dependent transcription factors of the nuclear hormone receptor super-family, which includes the steroid, retinoid, and thyroid hormone receptors. The PPARs can be activated by fatty acids and their eicosanoid metabolites, and have until recently been considered primarily to regulate genes involved in glucose and lipid homeostasis. In the past year there has been an explosive increase in research implicating PPARgamma in macrophage biology, cell cycle regulation, and atherosclerosis. This review describes recent insights into the role of PPARgamma in the macrophage lineage, and its potential function in the regulation of inflammatory responses and atherosclerosis.
TLR2 as an essential molecule for protective immunity against Toxoplasma gondii infection (2003)

To investigate the role of the Toll-like receptor (TLR) family in host defense against Toxoplasma gondii, we infected TLR2-, TLR4- and MyD88-deficient mice with the avirulent cyst-forming Fukaya strain of T. gondii. All TLR2- and MyD88-deficient mice died within 8 days, whereas all TLR4-deficient and wild-type mice survived after i.p. infection with a high dose of T. gondii. Peritoneal macrophages from T. gondii-infected TLR2- and MyD88-deficient mice did not produce any detectable levels of NO. T. gondii loads in the brain tissues of TLR2- and MyD88-deficient mice were higher than in those of TLR4-deficient and wild-type mice. Furthermore, high levels of IFN-gamma and IL-12 were produced in peritoneal exudate cells (PEC) of TLR4-deficient and wild-type mice after infection, but low levels of cytokines were produced in PEC of TLR2- and MyD88-deficient mice. On the other hand, high levels of IL-4 and IL-10 were produced in PEC of TLR2- and MyD88-deficient mice after infection, but low levels of cytokines were produced in PEC of TLR4-deficient and wild-type mice. The most remarkable histological changes with infiltration of inflammatory cells were observed in lungs of TLR2-deficient mice infected with T. gondii, where severe interstitial pneumonia occurred and abundant T. gondii were found.
Cholera toxin B subunit as a carrier protein to stimulate a mucosal immune response. (1984)

Horseradish peroxidase (HRP) was covalently coupled to the binding subunit of cholera toxin (CTB) via a two-step glutaraldehyde procedure. The HRP-CTB conjugate was characterized by physiochemical as well as immunochemical methods. Mice were immunized intraduodenally with the HRP-CTB conjugate, with HRP alone, or with a mixture of uncoupled CTB and HRP. The functionally active dose of CTB was 50 micrograms and the HRP dose was in the 30- to 90-micrograms range. Both IgA and IgG antibody responses were measured in serum, intestinal washes, and bile by using a solid phase immunoradiometric assay. Mice immunized with the HRP-CTB conjugate showed a significantly higher level of IgA anti-HRP in intestinal washes and bile, as well as increased levels of serum IgG anti-HRP. Animals that received only HRP or the mixture of CTB and HRP had reduced levels of HRP-specific antibody of either class in both gut washes and bile. The IgA anti-HRP responses in the gut washes were 33- to 120-fold higher when the conjugate was used as the immunogen in comparison with immunization with the CTB + HRP or the HRP alone. Vaccines to stimulate mucosal immunity to any antigenic determinant might thus be prepared by covalent conjugation to effective mucosal immunogens such as CTB.
Synthesis and Antiviral Activity of the Carbocyclic Analogues of (E)-5-(2-Halovinyl)-2'-deoxyuridines and (E)-5-(2-Halovinyl)-2'-deoxycytidines (1985)

The carbocyclic analogues of the potent and selective antiherpes agents (E)-5-(2-bromovinyl)-2'-deoxyuridine (BVDU), (E)-5-(2-iodovinyl)-2'-deoxyuridine (IVDU), and (E)-5-(2-bromovinyl)-2'-deoxycytidine (BVDC) were synthesized by conventional methods with use of carbocyclic 2'-deoxyuridine as starting material. C-BVDU, C-IVDU, and C-BVDC were equally selective, albeit slightly less potent, in their antiherpes action than BVDU, IVDU, and BVDC. Although resistant to degradation by pyrimidine nucleoside phosphorylases, C-BVDU did not prove more effective than BVDU in the systemic (oral, intraperitoneal) or topical treatment of HSV-1 infections in mice.
Sympathetic Hyperactivity—A Hidden Enemy in Chronic Kidney Disease Patients (2007)

Chronic kidney disease is often characterized by the presence of sympathetic hyperactivity. The aim of this brief review is to summarize available knowledge on the pathogenesis of sympathetic hyperactivity and to discuss its clinical relevance, the consequences of this knowledge for the choice of treatment, and the yet unresolved issues.
Radiation hardening of optical fibre links by photobleaching with light of shorter wavelength (1996)

The influence of additionally injected short-wavelength photobleaching light on the radiation hardness of Ge-doped graded index fibres working at 1300 nm wavelength is investigated. Predictions are complicated by the fact that more efficient shortwave bleaching light experiences higher radiation-induced loss. Promising results are found for low fibre temperatures (/spl lsim/-50/spl deg/C) and bleaching light of about 835 nm wavelength.
Electrochromic Behavior of a Self-Propagating Molecular-Based Assembly (2009)

A metallo-supramolecular network undergoes reversible redox chemistry on indium-tin oxide (ITO) coated glass substrates with concurrent color change. The switching time, long-term stability, and coloration efficiency are competitive with polymeric materials such as the industrially important PEDOT.
Synthesis of 5,7‐disubstituted‐4‐β‐D‐ribofuranosylpyrazolo[4,3‐d]‐pyrimidines and 2,4‐disubstituted‐1‐β‐D‐ribofuranosylpyrrolo[3,2‐d]‐pyrimidines as congeners of uridine and cytidine (1992)

Abstract The synthesis of the congeners of uridine and cytidine in the pyrazolo[4,3‐ d ]pyrimidine and pyrrolo[3,2‐ d ]‐pyrimidine ring system is described. Glycosylation of the trimethylsilyl (TMS) derivative of pyrazolo[4,3‐ d )pyrimidine‐5,7(1 H ,4 H ,6 H )‐dione (4) with either 1‐bromo‐ or 1‐ O ‐acetyl‐2,3,5‐tri‐ O ‐benzoyl‐D‐ribofuranose 5 and 6 , respectively in the presence of a Lewis acid catalyst gave the protected nucleoside 7 , which on debenzoylation afforded the uridine analogue 4‐β‐D‐ribofuranosylpyrazolo[4,3‐ d ]pyrimidine‐5,7(1 H ,6 H )‐dione (8). Thiation of 7 gave 13 , which on deprotection yielded 4‐β‐D‐ribofuranosyl‐5‐oxopyrazolo[4,3‐ d ]pyrimidine‐7(1 H ,‐6 H )‐thione (14). Ammonolysis of 13 gave a low yield of the cytidine analogue 15. A chlorination of 7 , followed by amination furnished an alternative route to 15. A similar glycosylation of TMS‐4 with 2,3,5‐tri‐ O ‐benzyl‐α‐D‐arabinofuranosyl chloride (16) gave mainly the N4 glycosylated product 17 , which on debenzylation furnished 4‐β‐D‐arabinofuranosylpyrazolo[4,3‐ d ]pyrimidine‐5,7(1 H ,6 H )‐dione (18). 7‐Amino‐4‐β‐D‐arabinofuranosylpyrazolo[4,3‐ d ]pyrimidin‐5(1 H )‐one (23) was prepared from 17 via the pyridinium chloride intermediate 21. Condensation of the TMS derivative of pyrrolo[3,2‐ d ]pyrimidine‐2,4(1 H ,3 H ,5 H )‐dione (24) with 6 , followed by deprotection of the reaction product gave 1‐β‐D‐ribofuranosylpyrrolo[3,2‐ d ]pyrimidine‐2,4(3 H ,5 H )‐dione (26). Similarly, TMS‐24 was reacted with 16 to give a mixture of the blocked nucleosides 31 and 32 , which on debenzylation afforded a mixture of two isomeric compounds 34 and 35. 1‐β‐D‐Arabinofuranosylpyrrolo[3,2‐ d ]pyrimidine‐2,4(3 H ,5 H )‐dione (34) was converted to the ara‐C analogue 38 via the 3‐nitrotriazolyl intermediate 36. The structure of 38 was confirmed by single crystal X‐ray diffraction studies.
Pd/C-catalyzed reactions of HMF: decarbonylation, hydrogenation, and hydrogenolysis (2014)

The diverse reactivity of 5-hydroxymethylfural (HMF) in Pd/C-catalyzed reactions is described with emphasis on the role of additives that affect selectivity.
Preparation of a Promising Angiogenesis PET Imaging Agent: 68Ga-Labeled c(RGDyK)–Isothiocyanatobenzyl-1,4,7-Triazacyclononane-1,4,7-Triacetic Acid and Feasibility Studies in Mice (2008)

Stable (68)Ga-NOTA-RGD was obtained in a straightforward manner at a high yield and showed a high affinity for alpha(v)beta(3) integrin, specific uptake by angiogenic muscles, a high level of uptake by tumors, and rapid renal excretion. (68)Ga-NOTA-RGD was found to be a promising radioligand for the imaging of angiogenesis.
Structural polymorphism of the human monocyte 40 kilodalton Fc receptor for IgG. (1987)

The 40 kD monocyte Fc receptor for IgG is capable of binding murine IgG1 and of supporting an IgG1 anti-T3 T lymphocyte proliferative response among approximately 80% of Caucasian individuals (responders), whereas the 40 kD Fc receptor on monocytes of the remaining individuals (nonresponders) is incapable of interacting with murine IgG1. By using a monoclonal antibody (mab IV3) that reacts with the 40 kD receptor, we found that the monocyte 40 kD receptors from responder and nonresponder individuals cannot be distinguished by either electrophoretic mobility on SDS-polyacrylamide gels, or by the number of receptors per cell as determined by indirect immunofluorescence. However, isoelectric focussing of the purified radioiodinated 40 kD receptor revealed that the monocyte receptor from all of four nonresponder individuals evaluated has a single distinctive pattern of multiple, regularly spaced bands, whereas the pattern of the 40 kD monocyte receptor from 11 responder individuals is of two sorts. One (seen in four of 11 responders) consists of multiple, regularly spaced bands that are asynchronous with the nonresponder pattern, and the other (seen in seven of 11 responders) consists of multiple bands that correspond in mobility to all of the bands of both of the other two patterns. The incidence of these three patterns suggests that the 40 kD Fc receptor is encoded by a single structural gene with two alleles, both of which are expressed.
Pupil Dilation With Intra-Cameral Lidocaine Versus Topical Midriatics During Phacoemulsification (2014)

Intra-cameral preservative-free lidocaine 1% supply adequate midriasis during cataract surgery by itself.
Trimerization of collagen IX α-chains does not require the presence of the COL1 and NC1 domains (2007)

Collagen IX is a heterotrimer of three alpha-chains, which consists of three COL domains (collagenous domains) (COL1-COL3) and four NC domains (non-collagenous domains) (NC1-NC4), numbered from the C-terminus. Although collagen IX chains have been shown to associate via their C-terminal NC1 domains and form a triple helix starting from the COL1 domain, it is not known whether chain association can occur at other sites and whether other collagenous and non-collagenous regions are involved. To address this question, we prepared five constructs, two long variants (beginning at the NC4 domain) and three short variants (beginning at the COL2 domain), all ending at the NC2 domain (or NC2 replaced by NC1), to study association and selection of collagen IX alpha-chains. Both long variants were able to associate with NC1 or NC2 at the C-terminus and form various disulfide-bonded trimers, but the specificity of chain selection was diminished compared with full-length chains. Trimers of the long variant ending at NC2 were shown to be triple helical by CD. Short variants were not able to assemble into disulfide-bonded trimers even in the presence of both conserved cysteine residues from the COL1-NC1 junction. Our results demonstrate that collagen IX alpha-chains can associate in the absence of COL1 and NC1 domains to form a triple helix, but the COL2-NC2 region alone is not sufficient for trimerization. The results suggest that folding of collagen IX is a co-operative process involving multiple COL and NC domains and that the COL1-NC1 region is important for chain specificity.
Oral vanadyl sulfate improves hepatic and peripheral insulin sensitivity in patients with non-insulin-dependent diabetes mellitus. (1995)

We examined the in vivo metabolic effects of vanadyl sulfate (VS) in non-insulin-dependent diabetes mellitus (NIDDM). Six NIDDM subjects treated with diet and/or sulfonylureas were examined at the end of three consecutive periods: placebo for 2 wk, VS (100 mg/d) for 3 wk, and placebo for 2 wk. Euglycemic hyperinsulinemic (30 mU/m2.min) clamps and oral glucose tolerance tests were performed at the end of each study period. Glycemic control at baseline was poor (fasting plasma glucose 210 +/- 19 mg/dl; HbA1c 9.6 +/- 0.6%) and improved after treatment (181 +/- 14 mg/dl [P < 0.05], 8.8 +/- 0.6%, [P < 0.002]); fasting and post-glucose tolerance test plasma insulin concentrations were unchanged. After VS, the glucose infusion rate during the clamp was increased (by approximately 88%, from 1.80 to 3.38 mg/kg.min, P < 0.0001). This improvement was due to both enhanced insulin-mediated stimulation of glucose uptake (rate of glucose disposal [Rd], +0.89 mg/kg.min) and increased inhibition of HGP (-0.74 mg/kg.min) (P < 0.0001 for both). Increased insulin-stimulated glycogen synthesis (+0.74 mg/kg.min, P < 0.0003) accounted for > 80% of the increased Rd after VS, and the improvement in insulin sensitivity was maintained after the second placebo period. The Km of skeletal muscle glycogen synthase was lowered by approximately 30% after VS treatment (P < 0.05). These results indicate that 3 wk of treatment with VS improves hepatic and peripheral insulin sensitivity in insulin-resistant NIDDM humans. These effects were sustained for up to 2 wk after discontinuation of VS.
The Human Hepatic Cytochromes P450 Involved in Drug Metabolism (1992)

The cytochromes P450 are a superfamily of hemoproteins that catalyze the metabolism of a large number of xenobiotics and endobiotics. The type and amount (i.e., the animal's phenotype) of the P450s expressed by the animal, primarily in the liver, thus determine the metabolic response of the animal to a chemical challenge. A majority of the characterized P450s involved in hepatic drug metabolism have been identified in experimental animals. However, recently at least 12 human drug-metabolizing P450s have been characterized at the molecular and/or enzyme level. The characterization of these P450s has made it possible to "phenotype" microsomal samples with respect to their relative levels of the various P450s and their metabolic capabilities. The purpose of this review is to compare and contrast the human P450s involved in drug metabolism with their related forms in the rat and other experimental species.
Oxidation of methanol by the yeast, Pichia pastoris. Purification and properties of the alcohol oxidase. (1980)

The enzymes of methanol oxidation were investigated in a new yeast strain, Pichia pastoris IFP 206, with high yield (0.42g cell per g of methanol). The following enzymes were detected in cell free extracts of P. pastoris: alcohol oxidase, catalase, formaldehyde and formate dehydrogenases. The alcohol oxidase was purified from cell free extracts of P. pastoris containing high amount of the enzyme (33%) with a good yield (55%). The preparation was homogenous by immunochemical methods. The enzyme had a molecular weight of 675, 000 and was composed of eight identical subunits of M.W. 80, 000. Each subunit contained one FAD. The N-terminal sequence was found to be: Ala-Ile-Pro-Glu-Glu-Phe-Asp-Ile-Leu-Val-Leu-Gly- The protein had 65 free -SH groups per molecule. The optimum temperature for the enzyme activity was 37°C and the activation energy was 11.1 kcal/mol. Optimum pH was 7.5 and the enzyme activity was unstable at acidic pH. The apparent Km for methanol were 1.4 and 3.1mM at oxygen concentrations of 0.19 and 0.93 mat. Similarly, the apparent Kms for oxygen were 0.40 and 1.0mM at methanol concentrations of 1, 10 and 100ma. The enzyme oxidized primary alcohols with short carbon chains like ethanol and propanol. Inhibition of enzyme activity by hydrogen peroxide was a consequence of the oxidation of essential -SH groups. The inhibition was reversed by reducing agents.
Secondary building units, nets and bonding in the chemistry of metal–organic frameworks (2009)

This critical review presents a comprehensive study of transition-metal carboxylate clusters which may serve as secondary building units (SBUs) towards construction and synthesis of metal-organic frameworks (MOFs). We describe the geometries of 131 SBUs, their connectivity and composition. This contribution presents a comprehensive list of the wide variety of transition-metal carboxylate clusters which may serve as secondary building units (SBUs) in the construction and synthesis of metal-organic frameworks. The SBUs discussed here were obtained from a search of molecules and extended structures archived in the Cambridge Structure Database (CSD, version 5.28, January 2007) which included only crystals containing metal carboxylate linkages (241 references).