gebhart/patrepeval huggingface dataset:
Production of avirulent mutants of Mycobacterium bovis with vaccine properties by the use of illegitimate recombination and screening of stationary-phase cultures (2002)

A better tuberculosis vaccine is urgently required to control the continuing epidemic. Molecular techniques are now available to produce a better live vaccine than BCG by producing avirulent strains of the Mycobacterium tuberculosis complex with known gene deletions. In this study, 1000 illegitimate recombinants of Mycobacterium bovis were produced by illegitimate recombination with fragments of mycobacterial DNA containing a kanamycin resistance gene. Eight recombinant strains were selected on the basis of their inability to grow when stationary-phase cultures were inoculated into minimal medium. Five of these recombinants were found to be avirulent when inoculated into guinea pigs. Two of the avirulent recombinants produced vaccine efficacy comparable to BCG against an aerosol challenge in guinea pigs with M. bovis. One of these recombinants had an inactivated glnA2 gene encoding a putative glutamine synthetase. Transcriptional analysis showed that inactivation of glnA2 did not affect expression of the downstream glnE gene. The other recombinant had a block of 12 genes deleted, including the sigma factor gene sigG. Two avirulent recombinants with an inactivated pckA gene, encoding phosphoenolpyruvate carboxykinase which catalyses the first step of gluconeogenesis, induced poor protection against tuberculosis. It is clear that live avirulent strains of the M. tuberculosis complex vary widely in their ability as vaccines to protect against tuberculosis. Improved models may be required to more clearly determine the difference in protective effect between BCG and potential new tuberculosis vaccines.
Mildly Oxidized LDL Induces Expression of Group IIa Secretory Phospholipase A 2 in Human Monocyte–Derived Macrophages (2000)

Phospholipase A(2)s (PLA(2)s) constitute a family of enzymes that hydrolyze fatty acids of membrane phospholipids, thus initiating the synthesis of proinflammatory mediators. Various PLA(2)s have been detected in human atherosclerotic arteries (advanced lesions); however, only the secretory group of PLA(2) has been shown to specifically hydrolyze low density lipoprotein (LDL)-associated phospholipids and, as such, may play a potential role in atherogenesis. In the present study, we investigated the expression pattern of group IIa, IV, and V PLA(2)s in human macrophages, which are the key cells involved in the onset and perpetuation of atherosclerosis. Immunohistochemical staining by double labeling showed that the secretory nonpancreatic PLA(2) (snpPLA(2)) is detectable in macrophages in the intima of early atherosclerotic lesions. Reverse transcription-polymerase chain reaction analysis of RNA extracted from human monocytes clearly showed that expression of group IV PLA(2) was enhanced during differentiation into macrophages, with an onset of induction at days 2 to 3 of differentiation. Group V snpPLA(2) was constitutively expressed on differentiation, whereas the detection of group IIa snpPLA(2) was dependent on both differentiation and subsequent stimulation of macrophages. Indeed, the transcription of group IIa snpPLA(2) in macrophages was induced by treatment with minimally modified or mildly oxidized LDL, whereas native, extensively oxidized, or acetylated LDL had no effect. To our knowledge, this is the first report describing induction of group IIa snpPLA(2) expression in human monocyte-derived macrophages. The mRNA levels of cytosolic PLA(2) group IV and snpPLA(2) group V remained unchanged on LDL treatment. Thus, our results show that the expression of distinct PLA(2) enzymes is regulated not only during differentiation of monocytes into macrophages but also on exposure of macrophages to distinct LDL species. Consequently, our results indicate a potential role for both cytosolic and secretory PLA(2) enzymes in inflammation and in macrophage functions related to atherosclerosis, with a specific role for group IIa snpPLA2 in LDL scavenging.
Genome-wide expression analysis upon constitutive activation of the HacA bZIP transcription factor in Aspergillus niger reveals a coordinated cellular response to counteract ER stress (2012)

The results indicate that the constitutive activation of the HacA leads to a coordinated regulation of the folding and secretion capacity of the cell, but with consequences on growth and fungal physiology to reduce secretion stress.
Sound localization with a neural network trained with the multiple extended Kalman algorithm (2002)

A three-layer neural network is used to solve the problem of extracting relative azimuth and elevation positional information from signals detected by two spatially separate, directional receivers. This is analogous to the ability of owls to localize the position of sound based solely on the properties of the signals reaching their ears. A simple model of the acoustical environment was used to generate simulated data for training the network. The neural network was trained using the multiple extended Kalman algorithm (MEKA). MEKA enabled the network to be trained without constant user intervention for adjustment of the critical parameters of the model.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Role of gap junctions in the propagation of the cardiac action potential (2004)

Gap junctions play a pivotal role for the velocity and the safety of impulse propagation in cardiac tissue. Under physiologic conditions, the specific subcellular distribution of gap junctions together with the tight packaging of the rod-shaped cardiomyocytes underlies anisotropic conduction, which is continuous at the macroscopic scale. However, when breaking down the three-dimensional network of cells into linear single cell chains, gap junctions can be shown to limit axial current flow and to induce ‘saltatory’ conduction at unchanged overall conduction velocities. In two- and three-dimensional tissue, these discontinuities disappear due to lateral averaging of depolarizing current flow at the activation wavefront. During gap junctional uncoupling, discontinuities reappear and are accompanied by slowed and meandering conduction. Critical gap junctional uncoupling reduces conduction velocities to a much larger extent than does a reduction of excitability, which suggests that the safety for conduction is higher at any given conduction velocity for gap junctional uncoupling. In uniformly structured tissue, gap junctional uncoupling is accompanied by a parallel decrease in conduction velocity. However, this is not necessarily the case for non-uniform structures like tissue expansion where partial uncoupling paradoxically increases conduction velocity and has the capacity to remove unidirectional conduction blocks. Whereas the impact of gap junctions on impulse conduction is generally assessed from the point of view of cell coupling among cardiomyocytes, it is possible that other cell types within the myocardium might be coupled to cardiomyocytes as well. In this context, it has been shown that fibroblasts establish successful conduction between sheets of cardiomyocytes over distances as long as 300 μm. This might not only explain electrical synchronization of heart transplants but might be of importance for cardiac diseases involving fibrosis. Finally, the intriguing fact that sodium channels are clustered at the intercalated disc recently rekindled the provocative question of whether gap junctions alone are responsible for impulse propagation or whether electric field mechanisms might account for conduction as well. Whereas computer simulations show the feasibility of conduction in the absence of gap junctional coupling, a definite answer to this question must await further investigations into the biophysical properties of the intercalated disc.
Crosswalks, metadata harvesting, federated searching, metasearching: using metadata to connect users and information (2008)

Since the turn of the millennium, instantaneous access to a wide variety\nof content via the Web has ceased to be considered ???bleeding-edge technology???\nand instead has become expected. In fact, from 2000 to the\ntime of this writing, there has been continued exponential growth in the\nnumber of digital projects providing online access to a range of information\nresources: Web pages, full-text articles and books, cultural heritage\nresources (including images of works of art, architecture, and material\nculture), and other intellectual content, including born digital objects.\nUsers increasingly expect that the Web will serve as a portal to the entire\nuniverse of knowledge. Recently, Google Scholar, Yahoo! and OCLC???s\nWorldCat (a union catalog of the holdings of national and international\nlibraries) have joined forces to direct users to the closest library that owns\nthe book they are seeking, whether it is available in print or online or\nboth. Global access to the universe of traditional print materials and\ndigital resources has become more than ever the goal of many institutions\nthat create and/or manage digital resources.
Neutronics Characteristics of Cermet and Ceramic Driver Fuels for the Fast Test Reactor (FTR) (1967)

The neutronics characteristics of four possible driver fuels for the Fast Test Reactor (FTR) are compared. The fuels investigated are PuO2-SS and UO2-SS cermets and PuO2-238UO2 and UO2-238UO2 ceramics. Since a high flux is of paramount importance in a test reactor, low-inventory plutonium-fueled cores are found to be quite attractive for use in the FTR. For core volumes of approximately 600 liters, cermet fuels offer a higher neutron flux and a larger shutdown coefficient than oxide ceramic fuels. If the latter fuels are used, BeO could be added to enhance the Doppler coefficient.
Serum macrophage migration‐inhibitory factor as a diagnostic and prognostic biomarker for gastric cancer (2009)

Serum MIF level, which correlates with gastric MIF expression, is a better molecular marker than CEA in diagnosing gastric cancer in patients presenting with dyspepsia. A combination of serum MIF and CEA predicts 5-year survival better than the individual test.
Effect of commonly used cosmetic preservatives on skin resident microflora dynamics (2021)

Human skin is populated by various microorganisms, the so-called microbiota, such as bacteria, viruses, yeasts, fungi, and archaea. The skin microbiota is in constant contact with the surrounding environment which can alter its eubiotic state. Recently it has been also observed that the application of cosmetic products can alter the balance of the skin microbiota. This effect may be attributed to many factors including the residual activity of the preservatives on the skin. In the present work, we studied the effect of eleven preservatives commonly found in cosmetic products on Propionibacterium acnes, Staphylococcus epidermidis, and Staphylococcus aureus in vitro using 3D skin models and culture-dependent methods. Also, the effect on Histone deacetylase 3 (HDAC3) has been investigated. Among tested combinations, three resulted as the best suitable for restoring a pre-existing dysbiosis since they act moderately inhibiting C. acnes and strongly S. aureus without simultaneously inhibiting the growth of S. epidermidis. The other four combinations resulted as the best suitable for use in topical products for skin and scalp in which it is necessary to preserve the eubiosis of the microbiota. Some of the tested were also able to increase HDAC3 expression. Taking together these data highlight the role of preservatives of skin resident microflora dynamics and could provide a reference for correctly choice preservatives and dosage in cosmetic formulations to preserve or restore homeostasis of skin microbiota.
Oxidative Stress, Prooxidants, and Antioxidants: The Interplay (2014)

Oxidative stress is a normal phenomenon in the body. Under normal conditions, the physiologically important intracellular levels of reactive oxygen species (ROS) are maintained at low levels by various enzyme systems participating in the in vivo redox homeostasis. Therefore, oxidative stress can also be viewed as an imbalance between the prooxidants and antioxidants in the body. For the last two decades, oxidative stress has been one of the most burning topics among the biological researchers all over the world. Several reasons can be assigned to justify its importance: knowledge about reactive oxygen and nitrogen species production and metabolism; identification of biomarkers for oxidative damage; evidence relating manifestation of chronic and some acute health problems to oxidative stress; identification of various dietary antioxidants present in plant foods as bioactive molecules; and so on. This review discusses the importance of oxidative stress in the body growth and development as well as proteomic and genomic evidences of its relationship with disease development, incidence of malignancies and autoimmune disorders, increased susceptibility to bacterial, viral, and parasitic diseases, and an interplay with prooxidants and antioxidants for maintaining a sound health, which would be helpful in enhancing the knowledge of any biochemist, pathophysiologist, or medical personnel regarding this important issue.
Characterization of arsenate-, selenate- and nitrate-reducing activities in Bacillus sp. SF-1 (2004)

A gram-positive and facultative anaerobic bacterium, Bacillus sp. SF-1, which was isolated from selenium-polluted sediment, can grow on lactate as an electron donor and selenate, arsenate or nitrate as an alternate electron acceptor in the absence of oxygen. This strain seems to be a promising agent for bioremediation of selenium/arsenic. In an effort to characterize the reductase systems in strain SF-1, arsenate, selenate and nitrate reduction activities were investigated with washed-cell suspensions and crude cell extracts from cells grown on arsenate, selenate and nitrate. These reductase activities were induced individually by the respective electron acceptors. Tungstate, which is a typical inhibitory antagonist of molybdenum-containing dissimilatory reductases, strongly inhibited reduction of arsenate, selenate and nitrate in the anaerobic growth cultures. These results suggested that strain SF-1 catalyzes the reduction of arsenate, selenate and nitrate by distinct terminal reductases containing molybdenum as a cofactor. This may be an advantage to utilize SF-1 in the bioremediation precesses where contaminants exist in mixture.
Vessel damage mechanisms by ultrasound or shock wave pulses (2006)

Edwin L. Carstensen has been one of the pioneers investigating not only the thresholds for bioeffects of ultrasound, but also determining mechanisms for these bioeffects, especially when air cavities are involved. Previous studies have demonstrated that hemorrhage or endothelial layer damage can occur when the blood vessels are exposed to lithotripter shock waves or to ultrasound in the presence of echo contrast agents. The presence of bubbles is often necessary for the damage to occur. Two main hypotheses describing the mechanism of vessel damage by acoustically excited microbubbles have been proposed. The vessel could be damaged by the high pressures and/or temperatures generated by the violent collapse of cavitation bubbles. Alternatively, the vessel could rupture upon bubble expansion. Here, a simple model is presented for vessel rupture upon bubble expansion and calculations are presented for parameters corresponding to two recently published experimental observations of vessel rupture and of endothelial cell damage to try to distinguish between these two mechanisms.
Improved Out-of-Hospital Cardiac Arrest Survival Through the Inexpensive Optimization of an Existing Defibrillation Program (1999)

An inexpensive, multifaceted system optimization approach to rapid defibrillation can lead to significant improvements in survival after cardiac arrest in a large BLS-D EMS system.
Sorting Out Pandoraâ€™s Box: Discerning the Dynamic Roles of Liver Microenvironment in Oncolytic Virus Therapy for Hepatocellular Carcinoma (2014)

Oncolytic viral therapies have recently found their way into clinical application for hepatocellular carcinoma (HCC), a disease with limited treatment options and poor prognosis. Adding to the many intrinsic challenges of in vivo oncolytic viral therapy, is the complex microenvironment of the liver, which imposes unique limitations to the successful delivery and propagation of the virus. The normal liver milieu is characterized by an intricate network of hepatocytes and non-parenchymal cells including Kupffer cells, stellate cells, and sinusoidal endothelial cells, which can secrete anti-viral cytokines, provide a platform for non-specific uptake, and form a barrier to efficient viral spread. In addition, natural killer cells are greatly enriched in the liver, contributing to the innate defense against viruses. The situation is further complicated when HCC arises in the setting of underlying hepatitis virus infection and/or hepatic cirrhosis, which occurs in more than 90% of clinical cases. These conditions pose further inhibitory effects on oncolytic virus (OV) therapy due to the presence of chronic inflammation, constitutive cytokine expression, altered hepatic blood flow, and extracellular matrix deposition. In addition, OVs can modulate the hepatic microenvironment, resulting in a complex interplay between virus and host. The immune system undoubtedly plays a substantial role in the outcome of OV therapy, both as an inhibitor of viral replication, and as a potent mechanism of virus-mediated tumor cell killing. This review will discuss the particular challenges of oncolytic viral therapy for HCC, as well as some potential strategies for modulating the immune system and synergizing with the hepatic microenvironment to improve therapeutic outcome.
New cerium cobalt borocarbide synthesized from eutectic metal flux mixture (2017)

Cerium cobalt borocarbide grown from Ce/Co eutectic flux has a partially disordered structure containing cobalt squares capped with borocarbide chains.
Interaction Of Fibrinogen With Platelets In Plasma (1981)

Fibrinogen binds to specific receptors on washed human platelets and these sites are induced by ADP. This interaction is assumed to be the basis for the participation of the molecule in ADP-stimulated platelet aggregation, but fibrinogen binding to platelets in plasma has not been directly demonstrated. In this study, we have characterized the binding of 125 I-fibrinogen to platelets in the platelet rich plasma (PRP) of afibrinogene- mic patients. In either citrated or heparinized PRP, association of fibrinogen with platelets was demonstrable and was dependent on ADP dose. This binding was time dependent and reached equilibrium in 10 to 15 min. At 22°C, the rate constants of association were kon = 0.9×10-6 M-1 min-1 in plasma compared to kon = 0.6×l0-6M-1 min-1 in Tyrode’s buffer indicating that initial rate of reaction was similar in both milieu. The kinetics of binding in plasma were the same at 37°C and 22°C but fewer molecules were bound at the higher temperature. In the PRP, saturable binding of fibrinogen to the platelet was achieved at concentrations greater than 0.5 μM. A linear Scatchard plot was derived which indicated a single class of binding site with an affinity constant of Ka = 1.8×106 M-1 and 32,000 fibrinogen molecules were maximally bound per platelet. These values are essentially identical to those obtained with washed platelets. In buffer, platelet-bound fibrinogen becomes progressively nondissociab1e , and this stabilization occurred to a partial extent in plasma. In sum, these results establish that the previously defined steps in ADP-induced binding of fibrinogen to platelet occur in plasma.
Discrimination of U-14 Soccer Players by Level and Position (2010)

Adolescence is often viewed as a critical period for selection in youth soccer. The present study compared the characteristics of regionally selected and non-selected under-14 players (U-14) as a group and by position. Players were classified as local (n=69) and regional (n=45). Weight, height, skinfolds, functional capacities, soccer skills and goal orientation were measured and skeletal age was assessed with the Fels method. Factorial ANOVA was used to test the effect of selection, position and respective interaction terms, while discriminant analysis was used to identify the variables that contributed to selection. Selected players had an advanced maturity status (F=24.97, p<0.01), were heavier (F=30.67, p<0.01) and taller (F=35.07, p<0.01); performed better in explosive power (F=21.25, p<0.01), repeated sprints (F=20.04, p<0.01) and ball control (F=3.69, p<0.05); and were more ego oriented (F=13.29, p<0.01). The 2 competitive groups did not differ in agility, aerobic endurance, dribbling, shooting, passing, and task orientation. Position-related variation was negligible. The percentage of players who were correctly classified in the original groups was slightly lower when the analysis was performed for the total sample (86%) than by position (86-90%). Future research on talent identification and selection should adopt a multidimensional approach including variables related to the physiological, perceptual, cognitive and tactical demands.
Phosphorylated Ser/Arg-rich proteins: limiting factors in the assembly of 200S large nuclear ribonucleoprotein particles. (1996)

We have previously shown that specific nuclear pre-mRNA transcripts and their splicing products, as well as the general population of nuclear poly(A)+ RNA, are packaged in large nuclear ribonucleoprotein (InRNP) particles that sediment at the 200S region in sucrose gradients. The InRNP particles contain all uridine-rich small nuclear ribonucleoprotein complexes required for pre-mRNA splicing, as well as protein splicing factors. In this paper we show that all of the phosphorylated, mAb 104 detectable, Ser/Arg-rich essential splicing factors (SR proteins) in the nucleoplasm are integral components of the InRNP particles, whereas only part of the essential splicing factor U2AF65 (U2 snRNP auxiliary factor) and the polypyrimidine tract binding protein (PTB) are associated with these particles. This finding suggests a limiting role for SR proteins in the assembly of the InRNP particles. We further show that the structural integrity of InRNP particles is sensitive to variations in the phosphorylation levels of the SR proteins.