gebhart/patrepeval huggingface dataset:
The transmembrane domain of glycophorin A as studied by cross-linking using photoactivatable phospholipids. (1982)

Glycophorin A, the major sialoglycoprotein of the human erythrocyte, consists of a NH2-terminal carbohydrate-rich region exposed to the outside, a hydrophobic region which forms a transmembrane bridge, and a COOH-terminal hydrophilic region extending into the cytoplasm. With the aim of further defining the membrane-embedded region, the protein has been reconstituted into vesicles formed from dimyristoylphosphatidylcholine and phospholipids containing photosensitive carbene precursors. The photosensitive groups were incorporated either at the omega-position of sn-2 fatty acyl chain or the polar head group of lecithins. Following photolysis, covalent cross-linking (1-2%) of the photoactivatable phospholipids to the protein was demonstrated. Degradation and sequence analysis showed that in the case of phospholipids containing photoactivatable groups in the fatty acyl chains most of the covalent cross-linking involved the carboxyl group of Glu-70. Therefore, the latter residue must be within the bilayer. This conclusion was supported by the reaction of the membrane-permeant [14C] dicyclohexylcarbodiimide with glycophorin reconstituted into vesicles. The same residue was labeled. Photolysis of glycophorin vesicles containing phospholipids with photolabels in the polar head group gave products in which the cross-links were present in peptide fragments (residues 62-81 and 82-96). These results define the probable boundaries of the membrane-embedded segment of glycophorin A. Corresponding experiments with erythrocyte ghosts gave similar results.
Feature structures, unification and finite-state transducers (1998)

We present a new framework for describing morphological models which combines several types of descriptions in a single unified declarative language: simple morphological rules relate strings to feature structures; rules can be grouped into inheritance hierarchies of paradigms; rules can be composed for describing simple agglutinative morphology; they can also be combined to describe more complex morphotactic structures. Rules are compiled as extended finite-state transducers where left projections are characters and right projections are feature structures: unification is used instead of concatenation to compute the output of a transduction.
Glutamate dehydrogenase activity in lactobacilli and the use of glutamate dehydrogenase-producing adjunct Lactobacillus spp. cultures in the manufacture of cheddar cheese (2006)

The study was undertaken to investigate the occurrence of glutamate dehydrogenase activity in different species of lactobacilli, and to determine, in a series of cheese-making trials, the effects of glutamate dehydrogenase-producing adjunct cultures on sensory attribute development during the maturation of cheddar cheese.The presence of dehydrogenase activity with glutamate as substrate was monitored in cell lysates of >100 strains from 30 different species of lactobacilli using a qualitative colorimetric plate screening assay. Activity was detectable in 25 of the 29 representative species obtained from culture collections and in 12 of the 13 non-starter species isolated from cheese. There were pronounced interspecies and strain differences in the occurrence, level and pyridine nucleotide specificity of the glutamate dehydrogenase activity detected. Among the non-starter lactobacilli the highest frequency of enzyme occurrence and activity was detected in the Lactobacillus plantarum isolates. The establishment of glutamate dehydrogenase-producing adjunct strains in the predominant population of lactobacilli in the cheese curd affected the formation of a number of volatile compounds in ripening cheddar cheese, while the presence of Lact. plantarum strains, in particular, was associated with an intensification and acceleration of aroma and flavour development during the maturation period.Glutamate dehydrogenase formation by lactobacilli is a strain-dependent metabolic attribute, and adjunct cultures expressing the activity that are able to proliferate during cheese ripening have a positive impact on the rate of development and the intensity of cheddar cheese aroma and flavour development.It has been demonstrated that some strains of glutamate dehydrogenase-producing lactobacilli have potential use as adjunct cultures to accelerate and intensify aroma and flavour formation during the manufacture of cheddar and, by analogy, other similar varieties of cheese. The importance of phenotypic discriminative monitoring of the dominant lactobacilli present during ripening to confirm adjunct establishment and population complexity was highlighted as was the requirement to establish the metabolic attributes of the non-starter population in uninoculated control cheeses in comparative trials.
Acellular Bovine Pericardia with Distinct Porous Structures Fixed with Genipin as an Extracellular Matrix (2004)

A cell extraction process was employed to remove the cellular components from bovine pericardia. Various porous structures of the acellular tissues were then created, using acetic acid and collagenase, and subsequently fixed with genipin. The biological response and tissue regeneration pattern for each studied group were evaluated in a growing rat model. One month postoperatively, fibroblasts, neoconnective tissue fibrils, and neocapillaries were observed in the acellular, acetic acid-treated, and collagenase-treated tissues to fill the pores within the implanted samples, indicating that these tissue samples were being regenerated. The neoconnective tissue fibrils were identified to be neocollagen fibrils and neoglycosaminoglycans. On the other hand, no tissue regeneration was observed in the cellular tissue throughout the entire course of the study; tissue regeneration was limited to the outer most layer of the acellular tissue. In contrast, the areas of tissue regeneration in the acetic acid-treated and collagenase-treated tissues were expanded with increasing duration of implantation. However, 1 year postoperatively there were still numerous inflammatory cells observed in the acetic acid-treated tissue, whereas inflammatory cells in the collagenase-treated tissue had almost disappeared. These results indicated that tissue regeneration patterns within acellular tissues were significantly affected by their porous structures.
Scalable, Lightweight, Integrated and Quick-to-Assemble (SLIQ) Hyperdrives for Functional Circuit Dissection (2017)

Independently adjustable multielectrode arrays are routinely used to interrogate neuronal circuit function, enabling chronic <i>in vivo</i> monitoring of neuronal ensembles in freely behaving animals at a single-cell, single spike resolution. Despite the importance of this approach, its widespread use is limited by highly specialized design and fabrication methods. To address this, we have developed a Scalable, Lightweight, Integrated and Quick-to-assemble multielectrode array platform. This platform additionally integrates optical fibers with independently adjustable electrodes to allow simultaneous single unit recordings and circuit-specific optogenetic targeting and/or manipulation. In current designs, the fully assembled platforms are scalable from 2 to 32 microdrives, and yet range 1-3 g, light enough for small animals. Here, we describe the design process starting from intent in computer-aided design, parameter testing through finite element analysis and experimental means, and implementation of various applications across mice and rats. Combined, our methods may expand the utility of multielectrode recordings and their continued integration with other tools enabling functional dissection of intact neural circuits.
Relationship between antitumor effect and metabolites of 5-fluorouracil in combination treatment with 5-fluorouracil and guanosine in ascites sarcoma 180 tumor system. (1983)

The antitumor activity of 5-fluorouracil (FUra) against ascites Sarcoma 180 was significantly enhanced by coadministration of guanosine, and slightly by adenosine, but not by cytidine or uridine. In advanced ascites Sarcoma 180, guanosine also enhanced the action of FUra, but adenosine, uridine, and cytidine did not. The potentiation of antitumor activity by guanosine was reversed by addition of cytidine. The antitumor activity of FUra was significantly potentiated when guanosine was administered either 0 to 15 min before or 5 min after FUra. Changes in metabolites of FUra after potentiation by guanosine were investigated. Total radioactivity in the plasma was significantly decreased 10 min after the combined administration of [6-14C]FUra (3 mg/kg i.p.) and guanosine (100 mg/kg i.p.) in comparison with that of [6-14C]FUra alone and was slightly decreased by coadministration of [6-14C]FUra and adenosine. Conversely, it was significantly increased by uridine or cytidine. The decrease in total radioactivity in the plasma caused by guanosine was completely reversed by addition of cytidine. FUra, 5-fluorouridine, alpha-fluoro-beta-ureidopropionic acid, and alpha-fluoro-beta-alanine were found in the plasma. Intact FUra accounted for about 55% of the total radioactivity. The proportion of metabolites of [6-14C]FUra was not changed by coadministration of [6-14C]FUra and guanosine, adenosine, or cytidine, but the proportion of FUrd was increased by uridine. In the ascitic fluid, the total radioactivity derived from [6-14C]FUra was decreased by its combined administration with guanosine, and it was reversed by addition of cytidine. This pattern was similar to that in the plasma. The main FUra compound was intact FUra itself (90%), and 5-fluorouridine accounted for 1% of the total radioactivity in the ascitic fluid. On the other hand, total radioactivity of [6-14C]FUra in the tumor cells was significantly and slightly increased by guanosine and adenosine, respectively. Total radioactivity after [6-14C]FUra in combination with uridine or cytidine was less than that after [6-14C]FUra alone. Incorporation of [6-14C]FUra into RNA was increased about 3.7 times by its combination with guanosine in comparison with FUra alone, and it was increased 2.0, 0.6, and 0.7 times by adenosine, uridine, and cytidine, respectively. Moreover, FUra-nucleotides were significantly increased by guanosine. The increased radioactivity in RNA and FUra-nucleotides of tumor cells caused by guanosine was completely reversed by cytidine. These changes in incorporation into tumor cells were comparable to those in antitumor activity against ascites Sarcoma 180. The potentiation of antitumor activity of FUra by guanosine was considered to be due to an increase in incorporation of FUra into FUra-nucleotides and RNA in the tumor cells.
Regulation of JAK3 expression and activation in human B cells and B cell malignancies (1995)

Members of the Janus family (JAK) of protein tyrosine kinases are critical enzymes in signaling pathways via hematopoietin receptors. We have cloned JAK3, which unlike other known family members (JAK1, JAK2, and TYK2) is preferentially expressed in hematopoietic cells but not in a variety of other cells. Functionally, JAK3 and JAK1 are coupled to the receptors for IL-2, IL-4, IL-7, IL-9, and IL-15 in T cells and NK cells. Because of the importance of IL-2, IL-4, and IL-7 in B cell physiology, we sought to determine whether JAK3 was also present in B lymphocytes and whether it was involved in signaling via cytokines that are important for B cell development and function. In this report, we demonstrate that JAK3 is expressed in normal human peripheral blood B cells at levels that are comparable to those in T cells. In addition, the levels were found to be markedly up-regulated following stimulation with staphylococcal protein A Cowan and anti-CD40 Abs. In addition, IL-4 and IL-7 induced the rapid tyrosine phosphorylation of JAK3 and JAK1, and IL-4 activated both JAK3 and JAK1 phosphotransferase activity. JAK3 protein was also detected in immature B cell lines, but not in more well differentiated cell lines. Additionally, JAK3 was detected in lysates from bone marrow lymphoblasts of patients with B cell precursor acute lymphocytic leukemia and cell lines derived from human B cell lymphomas. Together, these data suggest that the regulation of JAK3 expression and activity is likely to be important in B cell development and function.
Discrete Analysis for Antialiased Lines (2000)

This paper presents a new fast and smooth antialiasing technique. Drawing straight line is the graphic tool’s main primitive. Previous antialiasing techniques improve smoothness but slow down computation.
Regulation of Effector Treg Cells in Murine Lupus (2016)

This study revealed the existence of mechanisms that, by acting on IRF-4, can fine-tune the function and survival of effector Treg cells in lupus. These findings suggest that the existence of a powerful effector Treg cell compartment that successfully survives in an unfavorable inflammatory environment could limit disease development.
Transthyretin as both a Sensor and a Scavenger of β-Amyloid Oligomers (2013)

Transthyretin (TTR) is a homotetrameric transport protein, assembled from monomers that each contain two four-stranded β-sheets and a short α-helix and loop. In the tetramer, the "inner" β-sheet forms a hydrophobic pocket while the helix and loop are solvent-exposed. β-Amyloid (Aβ) aggregates bind to TTR, and the level of binding is significantly reduced in mutants L82A (on the loop) and L110A (on the inner β-sheet). Protection against Aβ toxicity was demonstrated for wild-type TTR but not L82A or L110A, providing a direct link between TTR-Aβ binding and TTR-mediated cytoprotection. Protection is afforded at substoichiometric (1:100) TTR:Aβ molar ratios, and the level of binding of Aβ to TTR is highest for partially aggregated materials and decreased for freshly prepared or heavily aggregated Aβ, suggesting that TTR binds selectively to soluble toxic Aβ aggregates. A novel technique, nanoparticle tracking, is used to show that TTR arrests Aβ aggregation by both preventing formation of new aggregates and inhibiting growth of existing aggregates. TTR tetramers are normally quite stable; tetrameric structure is necessary for the protein's transport functions, and mutations that decrease tetramer stability have been linked to TTR amyloid diseases. However, TTR monomers bind more Aβ than do tetramers, presumably because the hydrophobic inner sheet is solvent-exposed upon tetramer disassembly. Wild-type and L110A tetramers, but not L82A, were destabilized upon being co-incubated with Aβ, suggesting that binding of Aβ to L82 triggers tetramer dissociation. Taken together, these results suggest a novel mechanism of action for TTR: the EF helix/loop "senses" the presence of soluble toxic Aβ oligomers, triggering destabilization of TTR tetramers and exposure of the hydrophobic inner sheet, which then "scavenges" these toxic oligomers and prevents them from causing cell death.
Metabolism of isoprenaline in dog and man (1972)

1. The metabolism of isoprenaline has been studied in man and dog following intravenous and oral or intra-duodenal administration.2. Intravenous isoprenaline was excreted largely unchanged in urine in both species. Only one-third of the radioactivity in urine was in the form of the O-methyl metabolite.3. After oral doses in man or intraduodenal doses in dogs, plasma radioactivity was almost entirely as conjugated isoprenaline and this metabolite accounted for more than 80% of radioactivity in urine.4. Catechol-O-methyl transferase may be less important than Uptake(2) in limiting the pharmacological action of isoprenaline.5. Pharmacological response (heart-rate increase) was related to plasma concentration of isoprenaline only after rapid intravenous injections. In dogs, following prolonged infusion or intraduodenal doses, heart rate returned to base-line values when plasma concentrations of isoprenaline were high.
Facial Recognition from Volume Rendered Magnetic Resonance Imaging Data (2009)

Three-dimensional (3-D) reconstructions of computed tomography (CT) and magnetic resonance (MR) brain imaging studies are a routine component of both clinical practice and clinical and translational research. A side effect of such reconstructions is the creation of a potentially recognizable face. The Health Insurance Portability and Accountability Act of 1996 (HIPAA) Privacy Rule requires that individually identifiable health information may not be used for research unless identifiers that may be associated with the health information including ldquoFull face photographic images and other comparable imagesrdquo are removed (de-identification). Thus, a key question is: Are reconstructed facial images comparable to full-face photographs for the purpose of identification? To address this question, MR images were selected from existing research repositories and subjects were asked to pair an MR reconstruction with one of 40 photographs. The chance probability that an observer could match a photograph with its 3-D MR image was 1 in 40 (0.025), and we considered 4 successes out of 40 (4/40, 0.1) to indicate that a subject could identify persons' faces from their 3-D MR images. Forty percent of the subjects were able to successfully match photographs with MR images with success rates higher than the null hypothesis success rate. The Blyth-Still-Casella 95% confidence interval for the 40% success rate was 29%-52%, and the 40% success rate was significantly higher (P< 0.001) than our null hypothesis success rate of 1 in 10 (0.10).
Continuous 24-hour assessment of the neural regulation of systemic arterial pressure and RR variabilities in ambulant subjects. (1990)

In this study, we tested the hypothesis that the neural control of circulation in humans undergoes continuous but in part predictable changes throughout the day and night. Dynamic 24-hour recordings were obtained in two groups of ambulant subjects. In 18 hospitalized patients free to move, direct high-fidelity arterial pressures and electrocardiograms were recorded, and in an additional 28 nonhospitalized subjects, only electrocardiograms were obtained. Spectral analysis of systolic arterial pressure and of RR interval variabilities provided quantitative markers of sympathetic and vagal control of the sinus node and of sympathetic modulation of vasomotor tone. With this approach, the low-frequency (approximately 0.1 Hz) component of RR interval and systolic arterial pressure variabilities is considered a marker primarily of sympathetic activity, whereas the high-frequency (approximately 0.25 Hz) component of RR interval variability, related to respiration, seems to be a marker primarily of vagal activity. We observed a pronounced and consistent reduction in the markers of sympathetic activity and an increase in those of vagal activity during the night. In the invasive studies, while the subjects were still lying in bed after waking up, the markers of sympathetic activity rose rapidly and concomitantly with a simultaneous vagal withdrawal. Noninvasive studies confirmed the early morning rise of the markers of sympathetic activity and the circadian pattern of sympathovagal balance. These data indicate that the ominously increased rate of cardiovascular events in the morning hours may reflect the sudden rise of sympathetic activity and the reduction of vagal tone.
Typing of Chlamydia trachomatis by restriction endonuclease analysis of the amplified major outer membrane protein gene (1991)

A procedure was developed for characterization of Chlamydia trachomatis strains by using restriction endonuclease analysis of amplified genes of the major outer membrane protein (MOMP). Reference strains of the 15 serovars (A through K and L1 through L3) and clinical isolates were tested. The nucleotide sequences of the MOMP genes of each of the 15 serovars were arbitrarily constructed by using the sequences of the four variable domains known for each serovar and the constant domains of serovar L1. Computer analysis of these sequences indicated that two restriction digestions performed in parallel, one with AluI and the other with IIpaII, followed by HinfI and EcoRI, would allow the theoretical differentiation of 13 serovars. Serovars Ba and L1 presented the same theoretical restriction profile. Our typing method consisted of polymerase chain reaction amplification of a fragment of about 1,200 bp of the MOMP gene, followed by restriction endonuclease digestion with the aforementioned enzymes. From the 15 serovars, we obtained 14 different patterns; 13 profiles were serovar specific, while serovars B and Ba presented the same pattern. Application of this typing method to C. trachomatis strains isolated from clinical material gave the same results as the immunotyping method for 14 of 17 strains. Furthermore, restriction endonuclease analysis detected differences within a serovar. This method seems to be promising for epidemiological studies.
Application of broadband radar to volumetric sensing and distance measurement (1998)

States that broadband radar is a relatively recent technology which is finding many new applications such as sensing the position and movement of objects in and around vehicles, fluid level measurement in storage tanks, and detecting intruders. Its advantages over competing technologies (ultrasonics, optical and conventional radar) include: low cost implementation; very low power consumed and radiated; accurate position information; unobtrusive, i.e. radar can be mounted within a sealed plastic enclosure; tolerant of dust, spray and other contaminants. Describes the application of broadband radar to consumer, automotive and industrial sensing, and illustrates how a sensor can be used in two modes, first to sense intrusion within a volume and, second, to provide a distance measuring capability.
Effects of social determinants on food choice and skipping meals among Turkish adolescents. (2008)

Human papilloma virus-induced recurrent laryngeal papillomatosis is considered a troublesome and dangerous disease, because it can cause airway obstruction. Better understanding of metabolic pathways followed under pathological conditions can contribute to improved therapies by which growth and recurrence may be obviated. Part I of this study presents a clinically relevant total lipid fatty acid profile for papilloma cells, analyzed by gas liquid chromatography and a phosholipid red blood cell profile for RLP patients, analyzed by thin layer chromatography. In the papilloma cells virus interference with delta-6 and delta 5- desaturase activities is prevalent and the n-9 FA metabolic pathway is followed. It is plausible that up-regulated fatty acid synthase and 9 desaturase activities occur, since enhanced saturated fatty acids and monounsaturated fatty acid levels are also prevalent. High saturated fatty acid levels are known for their propensity to interfere with delta-6 and delta-5 desaturase activities and this is reflected in the blood profile of the RLP patients. It is also known that enhanced saturated fatty acid levels can contribute to enhanced cyclooxygenase-2 activity. Furthermore, cumulative oxidative stress with an oxidative burst is responsible for complete exhaustion of exogenous dietary arachidonic acid intake in these patients. The role of linoleic acid needs to be defined. The dietary intakes of lipids and micronutrients in RLP patients and a rationale for adjuvant FA therapy in the management of these patients are discussed in parts II and III of the study.