gebhart/patrepeval huggingface dataset:
Application of MALDI‐TOF MS to lysine‐producing Corynebacterium glutamicum (2001)

In the present work, a novel comprehensive approach of (13)C-tracer studies with labeling measurements by MALDI-TOF MS, and metabolite balancing was developed to elucidate key fluxes in the central metabolism of lysine producing Corynebacterium glutamicum during batch culture. MALDI-TOF MS methods established allow the direct quantification of labeling patterns of low molecular mass Corynebacterium products from 1 microL of diluted culture supernatant. A mathematical model of the central Corynebacterium metabolism was developed, that describes the carbon transfer through the network via matrix calculations in a generally applicable way and calculates steady state mass isotopomer distributions of the involved metabolites. The model was applied for both experimental planning of tracer experiments and parameter estimation. Metabolic fluxes were calculated from stoichiometric data and from selected mass intensity ratios of lysine, alanine, and trehalose measured by MALDI-TOF MS in tracer experiments either with 1-(13)C glucose or with mixtures of (13)C6/(12)C6 glucose. During the phase of maximum lysine production C. glutamicum ATCC 21253 exhibited high relative fluxes into the pentose phosphate pathway of 71%, a highly reversible glucose-6-phosphate isomerase, significant backfluxes from the tricarboxylic acid cycle to the pyruvate node consuming the lysine precursor oxaloacetate, 36% net flux of anaplerotic carboxylation and 63% contribution of the dehydrogenase branch in the lysine biosynthetic pathway. Due to the straightforward and simple measurements of selected labeling patterns by MALDI-TOF MS sensitively reflecting the flux parameters of interest, the presented approach has an excellent potential to extend metabolic flux analysis from single experiments with enormous experimental effort to a broadly applied technique.
Effect of Spore-bearing Lactic Acid-forming Bacteria ( Bacillus coagulans SANK 70258) Administration on the Intestinal Environment, Defecation Frequency, Fecal Characteristics and Dermal Characteristics in Humans and Rats (2002)

The effects of spore-bearing lactic acid-forming bacteria ( Bacillus coagulans SANK 70258) on intestinal flora and decomposition products in the intestine, as well as on various dermal characteristics were determined in healthy humans and rats. Improvement of fecal shape, change of fecal color from dark brown to yellowish brown, decrease of fecal odor and fecal pH and an increase in defecation frequency in persons whose defecation frequency was relatively low were observed after administration. The number of intestinal bifidobacteria significantly ( p <0.05) increased, whereas the number of intestinal Clostridium perfringens significantly ( p <0.05) decreased after administration compared with the values before the intake. The concentrations of intestinal ammonia, indole and p -cresol decreased. The activities of &#103 -glucuronidase and tryptophanase decreased significantly compared with the levels during the control period ( p <0.05). The spore-bearing lactic acid-forming bacilli group was given B. coagulans SANK 70258, while kept on a basic diet adjusted to 60% protein. Protein was supplied by casein. After removing back hair, the rats were exposed to radiation of UV-B 0.5 MED once a day. Two weeks after the start of radiation, measurements were made for the number of exanthema (the number of flare and papula). The number of exanthema decreased as constipation alleviated as a result of the intake of B. coagulans SANK 70258. In experiment 2, improvement of fecal shape, change of fecal color from dark brown to yellowish brown, decrease of fecal odor, the fecal pH and increase in defecation frequency of persons whose frequency was relatively low were observed after administration. The number of intestinal bifidobacteria significantly ( p <0.05) increased, whereas the number of intestinal C. perfringens significantly ( p <0.05) decreased after administration compared with the values before the intake. The concentrations of intestinal ammonia, indole and p -cresol content decreased. The activity of &#103 -glucuronidase and tryptophanase decreased significantly ( p <0.05) compared with the levels during the control period. The number of comedones decreased as constipation was alleviated as a result of the intake of B. coagulans SANK 70258. These results indicate that the administration of B. coagulans SANK 70258 improves the intestinal environment, defecation frequency, fecal characteristics and dermal characteristics.
Airborne house dust particles and diesel exhaust particles as allergen carriers (1998)

Soot particles in airborne house dust may act as carriers of several allergens in indoor air. Furthermore, DEP has the ability to bind all the four allergens investigated under aqueous conditions in vitro.
Isolation of the receptor for IgG from a human monocyte cell line (U937) and from human peripheral blood monocytes. (1982)

The Fc receptors for IgG from a human monocyte line (U937) and from highly purified human peripheral blood monocytes were solubilized, purified, and partially characterized. Both sources of cells gave indistinguishable results. Two molecules (or sets of molecules), one of about 72,000 mol wt and the other of 40,000-43,000 mol wt were discerned on autoradiograms of sodium dodecyl sulfate (SDS)-polyacrylamide gels analyzing acid eluates from Sepharose-IgG columns over which detergent lysates of radioiodinated cells had been passed. The larger of the two molecules, p72, accounted for greater than or equal to 90% of the radioactivity. This component was noted to be heterodisperse both by size on SDS gels and by charge on isoelectric focusing gels. The charge heterogeneity, being virtually eliminated by neuraminidase and tunicamycin, was probably due to variable glycosylation. Several lines of evidence indicated that p72 is probably all or part of the Fc receptor: (a) radiolabeling of this molecule using chloroglycouril was blocked by IgG of the Fc receptor; (b) in soluble form this molecule expressed ligand specificity identical to the in situ receptor; (c) the molecule was not recovered from affinity adsorbants bearing proteins that do not bind to the Fc receptors, nor (d) from a human T cell line that does not bear Fc receptors. The smaller of the two molecules isolated, p40-43, is at least in part actin. Its relationship to p72 is not understood.
Extracellular Vesicles Containing P301L Mutant Tau Accelerate Pathological Tau Phosphorylation and Oligomer Formation but Do Not Seed Mature Neurofibrillary Tangles in ALZ17 Mice (2016)

In Alzheimer's disease, the distribution of neurofibrillary tangles, a histological hallmark comprised of phosphorylated forms of the protein tau, follows a distinct pattern through anatomically connected brain regions. The well-documented correlation between the severity of tau pathology and disease progression implies a prion-like seeding and spreading mechanism for tau. Experimentally, this has been addressed in transgenic mice by the injection of protein lysates isolated from brains of transgenic mice or patients with tauopathies, including AD, that were shown to behave like seeds, accelerating tau pathology and tangle formation in predisposed mice. More specifically, in vivo data suggest that brain lysates from mice harboring the P301S mutation of tau can seed protein aggregation when injected into the hippocampi of human wild-type tau transgenic ALZ17 mice. Here, we compared the seeding potential of lysates and extracellular vesicles enriched for exosomes (EVs) from wild-type and human P301L tau transgenic rTg4510 mouse brains. We show that transgenic EVs cause increased tau phosphorylation and soluble oligomer formation in a manner comparable to that of freely available proteins in brain lysates, a prerequisite for the formation of mature protein aggregates.
Selective Encoding for Recognizing Unreliably Localized Faces (2015)

Most existing face verification systems rely on precise face detection and registration. However, these two components are fallible under unconstrained scenarios (e.g., mobile face authentication) due to partial occlusions, pose variations, lighting conditions and limited view-angle coverage of mobile cameras. We address the unconstrained face verification problem by encoding face images directly without any explicit models of detection or registration. We propose a selective encoding framework which injects relevance information (e.g., foreground/background probabilities) into each cluster of a descriptor codebook. An additional selector component also discards distractive image patches and improves spatial robustness. We evaluate our framework using Gaussian mixture models and Fisher vectors on challenging face verification datasets. We apply selective encoding to Fisher vector features, which in our experiments degrade quickly with inaccurate face localization, our framework improves robustness with no extra test time computation. We also apply our approach to mobile based active face authentication task, demonstrating its utility in real scenarios.
Oligothymidylate analogues having stereoregular, alternating methylphosphonate/phosphodiester backbones. Synthesis and physical studies. (1980)

Two decathymidylate analogues, d-(TpTp)4TpT-isomer 1 and isomer 2, having stereoregular, alternating methylphosphonate/phosphodiester backbones were prepared. The phosphodiester linkages of d-(TpTp)4TpT are cleaved slowly by snake venom phosphodiesterase in a stepwise manner, while slow random cleavage occurs with micrococcal nuclease which hydrolyzes isomer 2 faster than isomer 1. The CD spectra of isomer 1 and d-(Tp)9T are identical suggesting they have similar conformations, while that of isomer 2 shows an overall reduction of [theta]. Isomer 1 forms a 1T . 1A complex with poly(dA) and both 1T . 1A and 2T . 1A complexes with poly(rA), while isomer 2 forms a 2T . 1A complex of low thermal stability with poly(dA) and no complex with poly(rA). The Tm values of the partially nonionic d-(TpTp)4TpT . polynucleotide complexes are less dependent on salt concentration than are those of d-(Tp)9T. The stoichiometry and CD spectra of the complexes suggest that poly(dA) . isomer 1 duplex assumes a B-type geometry while isomer 2 . poly(dA) . isomer 2 triplex and the isomer 1 . poly(rA) complexes have an A-type geometry. Although there are no apparent differences between steric restrictions to rotation about the backbones of either isomer 1 or 2, or steric restrictions to complex formation, the results suggest that the configuration of the methylphosphate linkage controls: 1) interaction with nucleases, 2) oligomer conformation, and 3) interaction with polynucleotides. The latter effects may result from differences in solvation of the two isomers.
Differences in complement activation between complement-resistant and complement-sensitive Moraxella (Branhamella) catarrhalis strains occur at the level of membrane attack complex formation (1994)

The mechanism of resistance to human complement-mediated killing in Moraxella catarrhalis was studied by comparing different complement-sensitive and complement-resistant M. catarrhalis strains in a functional bystander hemolysis assay and an enzyme-linked immunosorbent assay (ELISA) for soluble terminal complement complexes. Complement-resistant stains appeared to activate complement to the same extent as, or even slightly better than, complement-sensitive strains. This indicates that complement-resistant strains do not inhibit classical or alternative pathway activation but interfere with complement at the level of membrane attack complex formation. A clear difference in dose-response curves for resistant and sensitive strains was observed both in the bystander hemolysis assay and in the ELISA. Complement-resistant strains showed optimum curves, whereas complement-sensitive strains gave almost linear curves. We conclude that resistant strains bind and/or inactivate one of the terminal complement components or intermediates involved in membrane attack complex formation. Trypsin, known to abolish complement resistance, changed the optimum dose-response curve of a resistant strain to a linear one, which strongly suggests that complement resistance is mediated by an M. catarrhalis-associated protein. This protein acts directly or through the binding of a terminal complement inhibitor present in serum.
Noninvasive Tests in Patients with Stable Coronary Artery Disease (2001)

This Journal feature begins with a case vignette highlighting a common clinical problem. Evidence supporting various strategies is then presented, followed by a review of formal guidelines, when they exist. The article ends with the authors' clinical recommendations.A 58-year-old woman presents with chest discomfort while walking that is suggestive of coronary disease. She first noted the discomfort after beginning an exercise program three weeks earlier. The pain occurs within a few minutes after the beginning of exercise and resolves with rest. The physical examination and electrocardiogram are unremarkable. How should this patient be evaluated?The Clinical ProblemIn patients with known or suspected coronary artery disease, diagnosis and risk stratification can be aided by noninvasive tests for myocardial ischemia. The most commonly used tests are exercise electrocardiography, myocardial perfusion imaging, and stress echocardiography. Guidelines for choosing . . .
The Neuropeptide Alpha-Melanocyte-Stimulating Hormone Inhibits Experimental Arthritis in Rats (1994)

alpha-Melanocyte-stimulating hormone (alpha-MSH) modulates inflammatory processes in models of acute inflammation and in models of sepsis/septic shock/adult respiratory-distress syndrome (ARDS). Because this neuropeptide inhibits actions of cytokines and other mediators of imflammation that are also believed to underlie aspects of chronic inflammation, tests were performed to compare the effects of repeated administration of the peptide with those of prednisolone and saline on the development of adjuvant arthritis in rats. alpha-MSH (50 micrograms), injected i.p. twice daily, markedly inhibited the clinical and histological signs of experimental arthritis and moderated the weight loss observed in control animals. Prednisolone (100 mg/kg), given twice per day, prevented development of arthritis but caused marked and progressive weight loss. The results confirm the potent anti-inflammatory influence of alpha-MSH, in this case in a model of chronic inflammation that has immune components.
Matrix-assisted laser desorption/ionization mass spectrometry of acidic glycoconjugates facilitated by the use of spermine as a co-matrix (1998)

Negative-ion matrix-assisted laser desorption/ionization mass spectra of sialyated glycoconjugates were acquired employing 2,5-dihydroxybenzoic acid (DHB) in conjunction with spermine as a co-matrix. The addition of spermine to DHB permitted an improved crystal formation as well as a higher analyte solubility. Moreover, DHB/spermine appears to minimize alkali adduct formation, thus allowing the sample analysis without desalting. The combined matrix permitted the analysis of complex sialylated and sialylated/fucosylated structures down to the femotomole range. The ability to use such a matrix also facilitates determination of the sialic acid linkages (in combination with a specific enzyme cleavage). The matrix also appears suitable for studies on gangliosides.
The physiological roles of secretin and its receptor. (2013)

Secretin is secreted by S cells in the small intestine and affects the function of a number of organ systems. Secretin receptors (SR) are expressed in the basolateral domain of several cell types. In addition to regulating the secretion of a number of epithelia (e.g., in the pancreas and biliary epithelium in the liver), secretin exerts trophic effects in several cell types. In this article, we will provide a comprehensive review on the multiple roles of secretin and SR signaling in the regulation of epithelial functions in various organ systems with particular emphasis in the liver. We will discuss the role of secretin and its receptor in health and biliary disease pathogenesis. Finally, we propose future areas of research for the further evaluation of the secretin/secretin receptor axis in liver pathophysiology.
Altered levels of plasma neuron‐derived exosomes and their cargo proteins characterize acute and chronic mild traumatic brain injury (2019)

Neuron-derived exosomes (NDEs) were enriched by anti-L1CAM antibody immunoabsorption from plasmas of subjects ages 18-26 yr within 1 wk after a sports-related mild traumatic brain injury (acute mTBI) ( n = 18), 3 mo or longer after the last of 2-4 mTBIs (chronic mTBI) ( n = 14) and with no recent history of TBI (controls) ( n = 21). Plasma concentrations of NDEs, assessed by counts and levels of extracted exosome marker CD81, were significantly depressed by a mean of 45% in acute mTBI ( P < 0.0001), but not chronic mTBI, compared with controls. Mean CD81-normalized NDE levels of a range of functional brain proteins were significantly abnormal relative to those of controls in acute but not chronic mTBI, including ras-related small GTPase 10, 73% decrease; annexin VII, 8.8-fold increase; ubiquitin C-terminal hydrolase L1, 2.5-fold increase; AII spectrin fragments, 1.9-fold increase; claudin-5, 2.7-fold increase; sodium-potassium-chloride cotransporter-1, 2.8-fold increase; aquaporin 4, 8.9-fold increase (3.6-fold increase in chronic mTBI); and synaptogyrin-3, 3.1-fold increase (1.3-fold increase in chronic mTBI) (all acute mTBI proteins P < 0.0001). In chronic mTBI, there were elevated CD81-normalized NDE levels of usually pathologic β-amyloid peptide 1-42 (1.6-fold, P < 0.0001), P-T181-tau (2.2-fold, P < 0.0001), P-S396-tau (1.6-fold, P < 0.01), IL-6 (16-fold, P < 0.0001), and prion cellular protein (PRPc) (5.1-fold, P < 0.0001) with lesser or greater (IL-6, PRPc) increases in acute mTBI. Increases in NDE levels of most neurofunctional proteins in acute, but not chronic, mTBI, and elevations of most NDE neuropathological proteins in chronic and acute mTBI delineated phase-specificity. Longitudinal studies of more mTBI subjects may identify biomarkers predictive of and etiologically involved in mTBI-induced neurodegeneration.-Goetzl, E. J., Elahi, F. M., Mustapic, M., Kapogiannis, D., Pryhoda, M., Gilmore, A., Gorgens, K. A., Davidson, B., Granholm, A.-C., Ledreux, A. Altered levels of plasma neuron-derived exosomes and their cargo proteins characterize acute and chronic mild traumatic brain injury.
Highly stereoselective synthesis of (−)-monatin, a high-intensity sweetener, using chelation-controlled nitrone cycloaddition (2003)

Synthesis of (-)-monatin was achieved by chelation-controlled cycloaddition of nitrone 2 with allyl alcohol 3a in the presence of MgBr2-OEt2.
Cloning and expression of a cDNA encoding epitopes shared by 15- and 60-kilodalton proteins of Cryptosporidium parvum sporozoites (1993)

A cDNA (CP15/60) encoding epitopes of Cryptosporidium parvum 15- and 60-kDa sporozoite proteins was isolated and expressed in Escherichia coli toward the goal of developing an immunogen for producing high-titer anticryptosporidial colostrum. Antisera prepared in rats to native C. parvum 15-kDa protein and used to identify the CP15/60 bacteriophage clone recognized both 15- and 60-kDa in vitro translation products derived from sporozoite RNA. Antisera specific for recombinant CP15/60 antigen recognized native 15- and 60-kDa C. parvum sporozoite proteins by immunoblotting and identified both surface and internal antigens on C. parvum sporozoites by immunofluorescence staining. Northern (RNA) and Southern blot hybridization experiments using sporozoite RNA and DNA indicated that CP15/60 DNA is transcribed as a single 1.4-kb RNA species from a single-copy gene. Recombinant CP15/60 antigen was recognized by hyperimmune colostrum from cows immunized with C. parvum oocyst-sporozoite protein and by convalescent-phase sera from C. parvum-infected calves.
Activation of the lymphotoxin beta receptor by cross-linking induces chemokine production and growth arrest in A375 melanoma cells (1997)

The lymphotoxin beta receptor (LT beta R) was originally described as a transcribed sequence encoded on human chromosome 12p, with homology to the TNF receptor family. Subsequently, a recombinant LT beta R was shown to bind LT alpha LT beta heteromeric complexes. In this study, we have shown that LT beta R is expressed in a variety of tissues and cell lines of monocytic lineage, as well as in fibroblast and human melanoma cell lines. Unlike other members of the TNF receptor family, LT beta R is not expressed by peripheral blood T cells. A chimeric fusion protein consisting of the extracellular domain of LT beta R fused to the Fc region of human IgG1 was used to develop mAbs against LT beta R. Cross-linking LT beta R on A375 melanoma cells with these Abs generated an antiproliferative signal. In addition, the IL-8 and RANTES chemokines, early indicators of inflammation, were secreted by the A375 melanoma line and the WI38VA13 fibroblast line in response to cross-linking of LT beta R. These same activities could be induced by membrane-bound and soluble LT beta and LT alpha LT beta oligomers.
4‐O‐Phosphoryl‐l‐threonine, a substrate of the pdxC(serC) gene product involved in vitamin B6 biosynthesis (1996)

The Escherichia coli pdxC(serC) gene codes for a transaminase (EC 2.6.1.52). The gene is involved in both pyridoxine (vitamin B6) and serine biosynthesis and was overexpressed as a MalE/PdxC(SerC) fusion protein. The fusion protein was purified by affinity chromatography on an amylose resin and hydrolyzed in the presence of protease factor Xa. Both the fusion protein and the PdxC(SerC) protein were characterized (K(M) value, turnover number, optimum pH). Both enzymes used 4-O-phosphoryl-L-threonine rather than 4-hydroxy-L-threonine as a substrate indicating that the phosphorylated rather than the non-phosphorylated amino acid is involved in pyridoxine biosynthesis. Pyridoxal phosphate was shown to be the cofactor for both enzymes and therefore seems to be involved in its own biosynthesis.
Analysis of minimal radial basis function network algorithm for real-time identification of nonlinear dynamic systems (2000)

A performance analysis is presented of the minimal resource allocating network (MRAN) algorithm for online identification of nonlinear dynamic systems. Using nonlinear time-invariant and time-varying identification benchmark problems, MRAN&apos;s performance is compared with the online structural adaptive hybrid learning (ONSAHL) algorithm. Results indicate that the MRAN algorithm realises networks using fewer hidden neurons than the ONSAHL algorithm, with better approximation accuracy. Methods for improving the run-time performance of MRAN for real-time identification of nonlinear systems are developed. An extension to MRAN is presented, which utilises a winner neuron strategy and is referred to as the extended minimum resource allocating network (EMRAN). This modification reduces the computation load for MRAN and leads to considerable reduction in the identification time, with only a small increase in the approximation error. Using the same benchmark problems, results show that EMRAN is well suited for fast online identification of nonlinear plants.
A Novel Drug for Treatment of Necrotizing Soft-Tissue Infections (2014)

clinicaltrials.gov Identifier: NCT01417780.