gebhart/patrepeval huggingface dataset:
An HASApf–redoxin complex causing asymmetric catalytic oxidation via the regenerative formation of a reactive oxygen species (2015)

A PP (pea)-HASApf-redoxin complex eluted from encapsulated PP gel with aeration displays asymmetric oxidation activity over 200 times greater than that of a similar protein expressed by E. coli cells. The intermediate spin, identified in the ESR spectrum, appears at g = 4.3 and g = 2.0, suggesting that an iron electron-transfer system for the asymmetric oxidation of secondary alcohols may be successfully created by the PP-HASApf-redoxin complex (39 kDa). FTIR experiments provided values νs(SO2) ≈ 950-1050 cm(-1) and νas(SO2) ≈ 1100-1200 cm(-1) for metal-bound sulfinate S-O and Fe-O vibrations. The sulfur and iron detected by physicochemical inspection (IC/ICP-AES) may facilitate the electron transport of a sulfate-iron complex (e.g., rubredoxin (6 kDa) or ferredoxin (9 kDa)) to the HASApf (21 kDa). The observations are consistently acceptable; i.e., the oxygen-driven PP-HASApf-redoxin complex functions regenerate via the successive asymmetric catalytic event - Fe(ii) + O2 → Fe(iii)-O-O(-) → Fe(iv) = O (oxidizing rac- or rac-) → Fe(ii) + H2O. Therefore, the use of a raw biomaterial as a PP-HASApf-redoxin complex-catalytic system for asymmetric oxidation is an important novelty, despite the apparent difficulties in working with pure dehydrogenase enzymatic/redox-cofactor systems for biotransformation.
Adverse Effects of Clinical Intervention on the Complement System (1991)

Adverse effects, due to activation of the complement (C) system and consequent generation of biologically active peptides, may occur during any form of extracorporeal processing of blood or plasma. Studies of the biocompatibility of dialyzer membranes have provided new insight into the mechanisms of C activation in extracorporeal circuits. The use of hemodialyzers, bypass oxygenators and on-line processing of plasma, by filtration or adsorption on columns, may all lead to activation of the alternative pathway of C and injurious reactions. The mechanisms by which drugs or drug metabolites interact with the C system, thereby inducing pseudoallergic reactions, have been only partly clarified. However, several drugs appear to interfere with the function of regulator proteins in the C system. Long-term administration of drugs that inhibit the covalent binding reaction of C3/C4 may contribute to development of drug-induced systemic lupus erythematosus in predisposed patients. Administration of high doses of immunoglobulins can cause anaphylactoid reactions which may involve C activation. Adverse reactions, seen after treatment with certain recombinant proteins, may also be associated with C activation.
Measuring the adequacy of hemodialysis access (1996)

Vascular access morbidity is still an important problem. The risk of thrombosis increases in prosthetic grafts as the access flow decreases below 600 ml/min, whereas native arteriovenous accesses can maintain patency at much lower flows, in some cases flows below those needed to deliver adequate dialysis. Intra-access pressures are also dissipated differently in the two access types. These differences between native and prosthetic grafts determine the utility of the monitoring techniques that are useful for detecting stenosis and assessing function in the two access types. Modern non-urea methods for measuring access recirculation are therefore useful in native but not in graft hemoaccesses. Direct or indirect intra-access pressure measurements and direct flow measurements are most useful in grafts to detect and then correct lesion before thrombosis.
Proteolytic inactivation of blood coagulation factor IX by thrombin (1985)

Coagulation factor IX is a vitamin K-dependent glycoprotein that circulates in blood as a precursor of a serine protease. Incubation of human factor IX with human alpha-thrombin resulted in a time and enzyme concentration-dependent cleavage of factor IX yielding a molecule composed of a heavy chain (mol wt 50,000) and a doublet light chain (mol wt 10,000). The proteolysis of factor IX by thrombin was significantly inhibited by physiological levels of calcium ions. Under nondenaturing conditions, the heavy and light chains of thrombin-cleaved factor IX remained strongly associated, but these chains were readily separated by gel filtration in the presence of denaturants. Amino-terminal sequence analyses of the isolated heavy and light chains of thrombin-cleaved human factor IX indicated that thrombin cleaved peptide bonds at Arg327-Val328 and Arg338-Ser339 in this molecule. Comparable cleavages were observed in bovine factor IX by bovine thrombin and occurred at Arg319-Ser320 and Arg339-Ser340. Essentially, a complete loss of factor IX procoagulant activity was associated with its cleavage by thrombin. Furthermore, thrombin-cleaved factor IX neither developed coagulant activity after treatment with factor XIa nor inhibited the coagulant activity of native factor IX. These data indicate that thrombin cleaves factor IX near its active site serine residue, rendering it incapable of activating factor X. Whether or not this reaction occurs in vivo is unknown.
A method for making group inferences from functional MRI data using independent component analysis (2001)

Independent component analysis (ICA) is a promising analysis method that is being increasingly applied to fMRI data. A principal advantage of this approach is its applicability to cognitive paradigms for which detailed models of brain activity are not available. Independent component analysis has been successfully utilized to analyze single-subject fMRI data sets, and an extension of this work would be to provide for group inferences. However, unlike univariate methods (e.g., regression analysis, Kolmogorov-Smirnov statistics), ICA does not naturally generalize to a method suitable for drawing inferences about groups of subjects. We introduce a novel approach for drawing group inferences using ICA of fMRI data, and present its application to a simple visual paradigm that alternately stimulates the left or right visual field. Our group ICA analysis revealed task-related components in left and right visual cortex, a transiently task-related component in bilateral occipital/parietal cortex, and a non-task-related component in bilateral visual association cortex. We address issues involved in the use of ICA as an fMRI analysis method such as: (1) How many components should be calculated? (2) How are these components to be combined across subjects? (3) How should the final results be thresholded and/or presented? We show that the methodology we present provides answers to these questions and lay out a process for making group inferences from fMRI data using independent component analysis.
Group B Erythrocytes Enzymatically Converted to Group O Survive Normally in A, B, and O Individuals (1982)

With an alpha-galactosidase, B erythrocytes can be converted to blood group O under conditions that neither impair their viability in vitro nor affect their ability to survive normally after transfusion to individuals of groups O, A, and B. Such an approach has the potential for producing enzymatically converted group O cells for use in transfusion therapy. It should also be possible to convert A cells to group O by using the appropriate alpha-N-acetylgalactosaminidase.
Status of Cryogenic Refractive Index Measurements (1985)

This review paper summarizes and identifies the sources of cryogenic refractive index measurements in the infrared. Representative refractive index versus temperature and wave-length data are presented for the following materials: germanium, silicon, hot-pressed cadmium telluride (Irtran 6), hot-pressed zinc sulfide (Irtran 2), polycrystalline cadmium telluride, cesium iodide, cesium bromide, zinc selenide, and birefringent thallium arsenic selenide. The measurement techniques and the errors associated with the measurements are discussed, and the need for additional measurements is delineated.© (1980) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Comparison of Skin Staples With Sutures for Anastomosis of the Small Intestine in Dogs (2000)

Skin stapling devices can be used to create technically simple, rapid, and safe end-to-end anastomoses in canine jejunum.
Mutations of the Type A Domain of Complement Factor B That Promote High-Affinity C3b-Binding (1999)

Factor B is a zymogen that carries the catalytic site of the complement alternative pathway convertases. During C3 convertase assembly, factor B associates with C3b and is cleaved at a single site by factor D. The Ba fragment is released, leaving the active complex, C3bBb. During the course of this process, the protease domain becomes activated. The type A domain of factor B, also part of Bb, is similar in structure to the type A domain of the complement receptor and integrin, CR3. Previously, mutations in the factor B type A domain were described that impair C3b-binding. This report describes "gain of function" mutations obtained by substituting factor B type A domain amino acids with homologous ones derived from the type A domain of CR3. Replacement of the betaA-alpha1 Mg2+ binding loop residue D254 with smaller amino acids, especially glycine, increased hemolytic activity and C3bBb stability. The removal of the oligosaccharide at position 260, near the Mg2+ binding cleft, when combined with the D254G substitution, resulted in increased affinity for C3b and iC3b, a C3b derivative. These findings offer strong evidence for the direct involvement of the type A domain in C3b binding, and are suggestive that steric effects of the D254 sidechain and the N260-linked oligosaccharide may contribute to the regulation of ligand binding.
Allelic diversity of simple sequence repeats among elite inbred lines of cultivated sunflower (2002)

Simple sequence repeat (SSR) markers were developed for cultivated sunflower (Helianthus annuus L.) from the DNA sequences of 970 clones isolated from genomic DNA libraries enriched for (CA)n,, (CT)n, (CAA)n, (CATA)n, or (GATA)n. The clones harbored 632 SSRs, of which 259 were unique. SSR markers were developed for 130 unique SSRs by designing and testing primers for 171 unique SSRs. Of the total, 74 SSR markers were polymorphic when screened for length polymorphisms among 16 elite inbred lines. The mean number of alleles per locus was 3.7 for dinucleotide, 3.6 for trinucleotide, and 9.5 for tetranucleotide repeats and the mean polymorphic information content (PIC) scores were 0.53 for dinucleotide, 0.53 for trinucleotide, and 0.83 for tetranucleotide repeats. Cluster analyses uncovered patterns of genetic diversity concordant with patterns produced by RFLP fingerprinting. SSRs were found to be slightly more polymorphic than RFLPs. Several individual SSRs were significantly more polymorphic than RFLP and other DNA markers in sunflower (20% of the polymorphic SSR markers had PIC scores ranging from 0.70 to 0.93). The newly developed SSRs greatly increase the supply of sequence-based DNA markers for DNA fingerprinting, genetic mapping, and molecular breeding in sunflower; however, several hundred additional SSR markers are needed to routinely construct complete genetic maps and saturate the genome.
In vitro multispecies Lubbock chronic wound biofilm model (2008)

Multispecies biofilms are becoming increasingly recognized as the naturally occurring state in which bacteria reside. One of the primary health issues that is now recognized to be exacerbated by biofilms are chronic, nonhealing wounds such as venous leg ulcers, diabetic foot ulcers, and pressure ulcers. Arguably three of the most important species associated with multispecies biofilms that our group sees clinically are Pseudomonas aeruginosa, Enterococcus faecalis, and Staphylococcus aureus. This study was conducted to address the need for a chronic pathogenic biofilm laboratory model that allows for cooperative growth of these three organisms. We have developed a novel media formulation, simple laboratory system, quantitative polymerase chain reaction for monitoring population dynamics, and methods for objectively and subjectively measuring biofilm formation. The Lubbock chronic wound pathogenic biofilm withstood treatment with a 50-fold higher concentration of bleach than that which was completely bacteriocidal for fully turbid planktonic cultures. The Lubbock chronic wound pathogenic biofilm when treated with biofilm effectors such as gallium nitrate and triclosan responded with selective inhibition of Pseudomonas aeruginosa or Staphylococcus aureus, respectively, as has been reported in the literature. The ability of this 24-hour model to react as predicted using known biofilm effectors suggests that it will lend itself to future work in the development and testing of first-generation chronic wounds pathogenic biofilm therapeutics. We have defined a realistic in vitro multispecies biofilm model simulating the functional characteristics of chronic pathogenic biofilms and developed effective tools for its characterization and analyses.
Design of Tissue-engineered Nanoscaffold Through Self-assembly of Peptide Amphiphile (2006)

In order to mimic in vivo topography of the native tissue created by extracellular matrix (ECM) components, which make up all soft tissues, the surface features of each biomaterial should be considered as a nanodimensional structure. In this study, an artificial ECM was designed to mimic the nanostructured topography created by ECM components in native tissue. The proliferation and differentiation of mesenchymal stem cells (MSCs) was investigated in a three dimensional (3-D) network of nanofibers formed by the self-assembly of peptide amphiphile (PA) molecules. PA was synthesized by standard solid phase chemistry that ends with the alkylation of the NH 2 terminus of the peptide. The sequence of arginine-glycine-aspartic acid (RGD) was included in peptide design as well. A 3-D network of nanofibers was formed by mixing MSC suspensions in a media with dilute aqueous solution of PA. The attachment, proliferation and osteogenic differentiation of MSCs were influenced by the self-assembled PA nanofibers as the cell scaffold and the values were significantly high compared with those in the static culture (2-D tissue culture plate).
Click Chemistry for Rapid Labeling and Ligation of RNA (2010)

The copper(I)-promoted azide-alkyne cycloaddition reaction (click chemistry) is shown to be compatible with RNA (with free 2'-hydroxyl groups) in spite of the intrinsic lability of RNA. RNA degradation is minimized through stabilization of the Cu(I) in aqueous buffer with acetonitrile as cosolvent and no other ligand; this suggests the general possibility of "ligandless" click chemistry. With the viability of click chemistry validated on synthetic RNA bearing "click"-reactive alkynes, the scope of the reaction is extended to in-vitro-transcribed or, indeed, any RNA, as a click-reactive azide is incorporated enzymatically. Once clickable groups are installed on RNA, they can be rapidly click labeled or conjugated together in click ligations, which may be either templated or nontemplated. In click ligations the resultant unnatural triazole-linked RNA backbone is not detrimental to RNA function, thus suggesting a broad applicability of click chemistry in RNA biological studies.
Localization of alpha type II calcium calmodulin-dependent protein kinase at glutamatergic but not gamma-aminobutyric acid (GABAergic) synapses in thalamus and cerebral cortex. (1996)

The alpha subunit of type II calcium/calmodulin-dependent protein kinase (CAM II kinase-alpha) plays an important role in longterm synaptic plasticity. We applied preembedding immunocytochemistry (for CAM II kinase-alpha) and postembedding immunogold labeling [for glutamate or gamma-aminobutyric acid (GABA)] to explore the subcellular relationships between transmitter-defined axon terminals and the kinase at excitatory and inhibitory synapses in thalamus and cerebral cortex. Many (but not all) axon terminals ending in asymmetric synapses contained presynaptic CAM II kinase-alpha immunoreactivity; GABAergic terminals ending in symmetric synapses did not. Postsynaptically, CAM II kinase-alpha immunoreactivity was associated with postsynaptic densities of many (but not all) glutamatergic axon terminals ending on excitatory neurons. CAM II kinase-alpha immunoreactivity was absent at postsynaptic densities of all GABAergic synapses. The findings show that CAM II kinase-alpha is selectively expressed in subpopulations of excitatory neurons and, to our knowledge, demonstrate for the first time that it is only associated with glutamatergic terminals pre- and postsynaptically. CAM II kinase-alpha is unlikely to play a role in plasticity at GABAergic synapses.
Prevalence of HNPCC in a Series of Consecutive Patients on the First Endoscopic Diagnosis of Colorectal Cancer: A Multicenter Study (1999)

Modifying the criteria makes it easier to identify new mutations or confirm the existence of those already known, as well as allowing preventative treatment in relatives who are apparently healthy.
DIRECTIONAL NEURITE OUTGROWTH AND AXONAL DIFFERENTIATION OF EMBRYONIC HIPPOCAMPAL NEURONS ARE PROMOTED BY A NEURITE OUTGROWTH DOMAIN OF THE B2‐CHAIN OF LAMININ (1996)

Molecular cues involved in directional neurite outgrowth and axonal differentiation of embryonic hippocampal neurons were studied on substrates coated in a striped 5 microns pattern with synthetic peptides from a neurite outgrowth (RDIAEIIKDI, P1543) and cell attachment (CDPGYIGSR, P364) domain of the B2- and B1-chains of laminin, respectively. Both peptides supported neuronal attachment, but only the B2-chain-derived P1543 promoted expression of a mature neuronal phenotype. Directional neurite outgrowth and axonal differentiation of embryonic hippocampal neurons were selectively induced by striped substrates of the B2-chain-derived P1543. Axonal differentiation was determined by expression of a phosphorylated epitope of the 200 kDa neurofilament protein in the longer "axonal" neurite of the bipolar embryonic hippocampal neurons. Ethanol (100 mM), a neuroactive compound known to delay neuronal development, impaired both directional neurite outgrowth and expression of a phosphorylated epitope of the 200 kDa neurofilament protein on a patterned P1543 substratum. The present results provide direct evidence that a 10 amino acid peptide (P1543), derived from a neurite outgrowth domain of the B2-chain of laminin, may be an axonal guidance and differentiation factor for embryonic hippocampal neurons in vitro.
Design of Logic-Compatible Embedded Flash Memories for Moderate Density On-Chip Non-Volatile Memory Applications (2013)

University of Minnesota Ph.D. dissertation. December 2013. Major: Electrical Engineering. Advisor: Chris H. Kim. 1 computer file (PDF); xx, 129 pages.
Optimization and enhancement of H− ions in a magnetized sheet plasma (2000)

Several schemes to improve the efficiency of extraction of H− ions from a magnetized sheet plasma source are reported. Parameters that affect the optimization of the extraction process such as plasma electrode position relative to the core plasma, plasma electrode bias, extraction electrode bias, neutral gas pressure, and discharge current were investigated. The negative hydrogen ion current density extracted from pure hydrogen plasma under optimum conditions was 0.15 A/m2. Enhancement of the H− current density has been observed by as much as 73.3% when argon was mixed with hydrogen at a 10%/90% ratio. The addition of argon raised the electron density by ten times and increased the electron temperature by 40% at the center of the sheet plasma. These plasma parameters were of comparable value with and without argon at the periphery of the sheet. The existence of high-energy electrons at the core and the presence of cold electrons at the periphery of the sheet plasma conform to ideal conditions of H−production of a volume source. The increase in H− current density with the addition of argon correlates well with the product of electron density and the square root of electron temperature at the center of the sheet plasma.
Inhibition of propionibacterium acnes by bacteriocin-like inhibitory substances (BLIS) produced by Streptococcus salivarius. (2006)

We report the in vitro inhibition of Propionibacterium acnes (P. acnes) by a bacteriocin-like inhibitory substance (BLIS-like substance) produced by Streptococcus salivarius (S. salivarius). Bacteriocins are proteinaceous substances produced by bacteria that are capable of inhibiting the growth of similar bacterial strains. Unlike classical antibiotics, they have a relatively narrow spectrum of killing activity, resulting in a reduction in the intensity of selection for resistance. These findings suggest that BLIS may potentially be used for its anti-P. acnes activity in the treatment of acne.
High-throughput screening of filamentous fungi using nanoliter-range droplet-based microfluidics (2016)

Filamentous fungi are an extremely important source of industrial enzymes because of their capacity to secrete large quantities of proteins. Currently, functional screening of fungi is associated with low throughput and high costs, which severely limits the discovery of novel enzymatic activities and better production strains. Here, we describe a nanoliter-range droplet-based microfluidic system specially adapted for the high-throughput sceening (HTS) of large filamentous fungi libraries for secreted enzyme activities. The platform allowed (i) compartmentalization of single spores in ~10 nl droplets, (ii) germination and mycelium growth and (iii) high-throughput sorting of fungi based on enzymatic activity. A 10(4) clone UV-mutated library of Aspergillus niger was screened based on α-amylase activity in just 90 minutes. Active clones were enriched 196-fold after a single round of microfluidic HTS. The platform is a powerful tool for the development of new production strains with low cost, space and time footprint and should bring enormous benefit for improving the viability of biotechnological processes.