Miracle-dz/UniFAR-FTUs huggingface dataset:
Cellular Degradation of Free and Inhibitor-bound Tissue-type Plasminogen Activator

Summary The low density lipoprotein receptor-related protein (LRP) is a multiligand clearance receptor that removes free tissue-type plasminogen activator (t-PA) or complexes of t-PA with plasminogen activator inhibitor type 1 (PAI-1) from the blood circulation or the pericellular space. Co-receptors are essential for LRP-mediated clearance of several ligands (e.g. glycosaminoglycans for thrombin/protease nexin and lipoprotein lipase, and the urokinase receptor for urokinase/PAI-1 complexes). The present study was undertaken to investigate whether LRP-mediated t-PA clearance requires a co-receptor as well. In five cell lines from different organs and species degradation of t-PA and t-PA/PAI-1 was mediated by LRP (or LRP-like receptors). No degradation of t-PA and t-PA/PAI-1 occurred in THP-1 or U-937 human monocyte-like cells, despite the presence of functional LRP. As glycosaminoglycans can bind t-PA and PAI-1 we investigated whether they are involved in t-PA/PAI-1 degradation. Pre-treatment of COS cells or HT1080 cells with chlorate, an inhibitor of glycosaminoglycan sulfation, did not decrease t-PA/PAI-1 degradation. Furthermore, CHO cells genetically deficient in glycosaminoglycans efficiently degraded t-PA/PAI-1. Thus it is unlikely that glycosaminoglycans are co-receptors for degradation of t-PA or t-PA/PAI-1. This study indicates that THP-1 and U-937 cells lack a critical component (co-receptor? ) for the LRP-mediated degradation of t-PA. Abbreviations: LRP, low density lipoprotein receptor-related protein; PAI-1, plasminogen activator inhibitor type 1; RAP, receptor-associated protein; t-PA, tissue-type plasminogen activator; u-PA, urokinase; u-PAR, urokinase receptor.
Evaluation of PCR-RFLP (based on ITS-1 and HaeIII) for the detection of Leishmania species, using Greek canine isolates and Jordanian clinical material

Abstract It is possible to detect and distinguish Leishmania parasites using PCR-RLFP — a combination of PCR and analysis of the fragment-length polymorphism seen when the amplicons are digested with one or more restriction enzymes. In the present study, clinical samples from 24 Jordanians suspected to have cutaneous leishmaniasis and cultures set up using leishmanial parasites from five Greek dogs were investigated using PCR, in which the internal-transcribed-spacer-1 (ITS1) region of the parasites' ribosomal-RNA gene was amplified, followed by HaeIII digestion of the resulting amplicons. The cultures, which were all maintained in Leibowitz L-15 medium with 20% foetal calf serum, were each investigated as serial dilutions. Using the PCR-RLFP analysis, each culture was identified as L. donovani and each was found positive for this parasite with a mean sensitivity of 66%–100% (depending on the culture dilution tested), a specificity of 100%, a mean positive predictive value of 100%, and a negative predictive value of 74.6%–100%. When simulated clinical samples, created by mixing human blood with known numbers of L. donovani promastigotes, were investigated, the PCR-RFLP gave optimal results (with a value of 100% each for sensitivity, specificity and positive and negative predictive values). When the real clinical samples (25 lesion aspirates and 20 samples of peripheral blood from 24 Jordanian patients) were investigated using the molecular method, 20 (84%) of the patients were found to have lesion aspirates that were PCR-RFLP-positive for L. major (although, by microscopy, only six were found to have amastigote-positive lesion aspirates). None of the blood samples from the Jordanian patients, however, was found PCR-positive.
Wnt Gradient Formation Requires Retromer Function in Wnt-Producing Cells

Wnt proteins function as morphogens that can form long-range concentration gradients to pattern developing tissues. Here, we show that the retromer, a multiprotein complex involved in intracellular protein trafficking, is required for long-range signaling of the Caenorhabditis elegans Wnt ortholog EGL-20. The retromer functions in EGL-20–producing cells to allow the formation of an EGL-20 gradient along the anteroposterior axis. This function is evolutionarily conserved, because Wnt target gene expression is also impaired in the absence of the retromer complex in vertebrates. These results demonstrate that the ability of Wnt to regulate long-range patterning events is dependent on a critical and conserved function of the retromer complex within Wnt-producing cells.
Characterization of lipids and antioxidant capacity of novel nutraceutical egg products developed with omega-3-rich oils.

BACKGROUND Cardiovascular disease has had an unquestioned status of the number one cause of death in the US since 1921. Omega-3 polyunsaturated fatty acids (ω-3 PUFAs) have cardio-protective benefits. However, egg is typically a poor source of ω-3 PUFAs and, in general, the American diet is low in these cardio-protective fatty acids. Novel, nutritionally enhanced egg products were developed by substituting yolk with ω-3 PUFA-rich flaxseed, menhaden, algae, or krill oil. Experimental egg products matched composition of hen egg (whole egg). The experimental egg products, mixed whole egg, and a liquid egg product (Egg Beaters) were microwave-cooked and compared. RESULTS Although fat, protein, and moisture contents of experimental egg products matched (P > 0.05) mixed whole egg, experimental egg products had more (P < 0.05) ω-3 PUFAs, lower (P < 0.05) ω-6/ω-3 ratio, and depending on oil added, a higher (P < 0.05) unsaturated/saturated fatty acids ratio compared to mixed whole egg. Triglycerides were the main lipid class in all experimental egg products except those developed with krill oil, which had even more phospholipids than mixed whole egg. Analysis of thiobarbituric acid reactive substances showed that lipid oxidation of experimental egg products was lower (P < 0.05) or similar (P > 0.05) to mixed whole egg, except for experimental egg products with krill oil. However, peroxide value showed that all egg samples had minimal oxidation. Experimental egg products developed with menhaden or flaxseed oil had the highest (P < 0.05) concentration of the antioxidant, ethyoxquin compared to all other egg samples. However, experimental egg products with krill oil likely contained a natural antioxidant, astaxanthin. CONCLUSION This study demonstrated an alternative approach to developing novel, nutraceutical egg products. Instead of dietary modification of chicken feed, yolk substitution with ω-3 PUFAs oils resulted in enhancement of ω-3 PUFAs beyond levels possible to achieve by modifying chicken feed.
Functional characterization of Delta3,Delta2-enoyl-CoA isomerases from rat liver.

The degradation of unsaturated fatty acids by beta-oxidation involves Delta(3),Delta(2)-enoyl-CoA isomerases (enoyl-CoA isomerases) that catalyze 3-cis --> 2-trans and 3-trans --> 2-trans isomerizations of enoyl-CoAs and the 2,5 --> 3,5 isomerization of dienoyl-CoAs. An analysis of rat liver enoyl-CoA isomerases revealed the presence of a monofunctional enoyl-CoA isomerase (ECI) in addition to mitochondrial enoyl-CoA isomerase (MECI) in mitochondria, whereas peroxisomes contain ECI and multifunctional enzyme 1 (MFE1). Thus ECI, which previously had been described as peroxisomal enoyl-CoA isomerase, was found to be present in both peroxisomes and mitochondria. This enzyme seems to be identical with mitochondrial long-chain enoyl-CoA isomerase (Kilponen, J.M., Palosaari, P.M., and Hiltunen, J.K. 1990. Biochem. J. 269, 223-226). All three hepatic enoyl-CoA isomerases have broad chain length specificities but are distinguishable by their preferences for one of the three isomerization reactions. MECI is most active in catalyzing the 3-cis --> 2-trans isomerization; ECI has a preference for the 3-trans --> 2-trans isomerization, and MFE1 is the optimal isomerase for the 2,5 --> 3,5 isomerization. A functional characterization based on substrate specificities and total enoyl-CoA isomerase activities in rat liver leads to the conclusion that the 3-cis --> 2-trans and 2,5 --> 3,5 isomerizations in mitochondria are catalyzed overwhelmingly by MECI, whereas ECI contributes significantly to the 3-trans --> 2-trans isomerization. In peroxisomes, ECI is predicted to be the dominant enzyme for the 3-cis --> 2-trans and 3-trans --> 2-trans isomerizations of long-chain intermediates, whereas MFE1 is the key enzyme in the 2,5 --> 3,5 isomerization.
Regions of the Herpes Simplex Virus Scaffolding Protein That Are Important for Intermolecular Self-Interaction

ABSTRACT The herpes simplex virus type 1 (HSV-1) scaffolding protein encoded by gene UL26.5 promotes the formation of the icosahedral capsid shell through its association with the major capsid protein VP5 and through intermolecular interactions with itself. Inside the capsid shell, the UL26.5 product together with the maturational protease, a minor protein, form a spherical structure which is broken down and released from the capsid during packaging of the viral genome. Selected residues from four internal regions of the HSV-1 scaffolding protein that have significant conservation of amino acids within the scaffolding proteins of alphaherpesviruses were mutated, and the properties of the proteins were examined. Only the HSV-1 scaffolding protein with mutations in the conserved N-terminal domain showed reduced interaction with the varicella-zoster virus homologue in a cell-based immunofluorescence assay, providing the first evidence that this domain in the HSV-1 protein is likely to be involved in intermolecular self-interaction. Scaffolding protein with mutations in this domain or in either of two other domains failed to assemble into scaffold-like particles but retained the ability to self-interact, although the aggregates were significant smaller than most of the aggregates formed by the wild-type protein. These results suggest that there are multiple domains involved in the intermolecular self-association of the HSV-1 scaffolding protein that can act independently of one another. This conclusion was supported by the observation that none of the mutant proteins with lesions in an individual domain, including a protein with mutations in a central region previously implicated in self-interaction (A. Pelletier, F. Dô, J. J. Brisebois, L. Lagacé, and M. G. Cordingley, J. Virol. 71:5197–5208, 1997), interfered with capsid assembly in a baculovirus expression system. A protein mutated in the central region and another conserved domain, both of which had been predicted to form coiled coils, was impaired for capsid formation but still retained the capacity to interact with VP5.
Analysis of Fusion Junctions of Circularized Chromosomes in Streptomyces griseus

ABSTRACT A filamentous soil bacterium, Streptomyces griseus2247, carries a 7.8-Mb linear chromosome. We previously showed by macrorestriction analysis that mutagenic treatments easily caused deletions at both ends of its linear chromosome and changed the chromosome to a circular form. In this study, we confirmed chromosomal circularization by cloning and sequencing the junction fragments from two deletion mutants, 404-23 and N2. The junction sequences were compared with the corresponding right and left deletion end sequences in the parent strain, 2247. No homology and a 6-bp microhomology were found between the two deletion ends of the 404-23 and N2 mutants, respectively, which indicate that the chromosomal circularization was caused by illegitimate recombination without concomitant amplification. The circularized chromosomes were stably maintained in both mutants. Therefore, the chromosomal circularization might have occurred to prevent lethal deletions, which otherwise would progress into the indispensable central regions of the chromosome.
Accuracy of Macular Ganglion-Cell Complex Thickness to Total Retina Thickness Ratio to Detect Glaucoma in White Europeans

Purpose:The aim of this study was to evaluate the diagnostic accuracy of macular ganglion-cell complex (GCC) thickness to total retinal thickness ratio (G/T ratio), a parameter found particularly accurate in Japanese eyes to detect glaucoma and recently proposed for the RTVue-100 Fourier-domain optical coherence tomography (RTVue-100 OCT), and to compare the diagnostic accuracy of this parameter to that of parameters provided by the instrument software in European eyes. Methods:Retinal nerve fiber layer thickness (RNFLT) and macular GCC thickness parameters of 1 randomly selected eye of 177 white European patients (50 healthy, 28 ocular hypertensive, 33 preperimetric glaucoma, and 66 perimetric glaucoma eyes) were measured with an RTVue-100 OCT. Results:The RNFLT and GCC parameter values of the healthy group were significantly higher than those of the various other groups (P<0.001 for all comparisons). For all separation (normal vs. all other eyes; normal vs. preperimetric and perimetric glaucoma eyes; and normal vs. perimetric glaucoma eyes) average RNFLT, inferior RNFLT, average GCC, and inferior GCC showed consistently higher area under receiver operating characteristics curve (AUROC) than G/T ratio. In the normal versus perimetric glaucoma separation, the AUROC values were 0.977, 0.982, 0.969, 0.976, and 0.959 for average RNFLT, inferior RNFLT, average GCC, inferior GCC, and G/T ratio, respectively. Conclusions:In contrast to Japanese eyes, in white Europeans G/T ratio does not improve separation of glaucomatous and healthy eyes.
An adenovirus-simian immunodeficiency virus env vaccine elicits humoral, cellular, and mucosal immune responses in rhesus macaques and decreases viral burden following vaginal challenge

Six female rhesus macaques were immunized orally and intranasally at 0 weeks and intratracheally at 12 weeks with an adenovirus type 5 host range mutant (Ad5hr)-simian immunodeficiency virus SIVsm env recombinant and at 24 and 36 weeks with native SIVmac251 gp120 in Syntex adjuvant. Four macaques received the Ad5hr vector and adjuvant alone; two additional controls were naive. In vivo replication of the Ad5hr wild-type and recombinant vectors occurred with detection of Ad5 DNA in stool samples and/or nasal secretions in all macaques and increases in Ad5 neutralizing antibody in 9 of 10 macaques following Ad administrations. SIV-specific neutralizing antibodies appeared after the second recombinant immunization and rose to titers > 10,000 following the second subunit boost. Immunoglobulin G (IgG) and IgA antibodies able to bind gp120 developed in nasal and rectal secretions, and SIV-specific IgGs were also observed in vaginal secretions and saliva. T-cell proliferative responses to SIV gp140 and T-helper epitopes were sporadically detected in all immunized macaques. Following vaginal challenge with SIVmac251, transient or persistent infection resulted in both immunized and control monkeys. The mean viral burden in persistently infected immunized macaques was significantly decreased in the primary infection period compared to that of control macaques. These results establish in vivo use of the Ad5hr vector, which overcomes the host range restriction of human Ads for rhesus macaques, thereby providing a new model for evaluation of Ad-based vaccines. In addition, they show that a vaccine regimen using the Ad5hr-SIV env recombinant and gp120 subunit induces strong humoral, cellular, and mucosal immunity in rhesus macaques. The reduced viral burden achieved solely with an env-based vaccine supports further development of Ad-based vaccines comprising additional viral components for immune therapy and AIDS vaccine development.
Pyruvate-Carbon Dioxide Exchange Reaction of Desulfovibrio desulfuricans

Suh, Byungse (University of Kansas, Lawrence), and J. M. Akagi. Pyruvate-carbon dioxide exchange reaction of Desulfovibrio desulfuricans. J. Bacteriol. 91:2281–2285. 1966. —The pyruvate-CO2 exchange reaction, catalyzed by Desulfovibrio desulfuricans, required the presence of phosphate and coenzyme A. However, the requirement for phosphate disappeared when the concentration of coenzyme A was increased to a level of 3.8 × 10−3m. Passing crude extracts through a diethylaminoethyl-cellulose column and an Amberlite CG-50 ion-exchange column, to remove ferredoxin and cytochrome c3, resulted in a marked decrease in exchange activity; full activity was restored by the addition of ferredoxin or cytochrome c3. Fe++ or Co++ stimulated the exchange of CO2 into pyruvate.
The effects of an oral care practice on incidence of pneumonia among ventilator patients in ICUs of selected hospitals in Isfahan, 2010

Background: Oral care plays an inevitable role in health and well-being of patients in intensive care units (ICUs). Poor oral care causes colonization of respiratory pathogens and secondary respiratory infections. Ventilator-associated pneumonia occurs in patients on mechanical ventilation for more than 48 hours. It results in prolonged duration of mechanical ventilation, mortality and health expenses. The present study aimed to review the effects of an oral care practice on the incidence of ventilator-associated pneumonia in patients on mechanical ventilation admitted in ICUs. Materials and Methods: This was a clinical trial study conducted in the ICUs of selected hospitals in Isfahan during 2010. We randomly divided 54 patients into the intervention and control groups. Intubation was performed during the 48 hours before the study. The intervention group received an oral care practice along with brushing and the control group received routine oral care twice daily. The incidence of ventilator-associated pneumonia was diagnosed through clinical pulmonary infection score (CPIS). Findings: The two groups were compared in terms of underlying criteria (APACHE-II). The incidence of ventilator-associated pneumonia did not statistically differ between the intervention and control groups (37% vs. 48.1%; p = 0.41). Conclusions: The results of the present study showed that brushing and standard oral care practice had no effects on ventilator-associated pneumonia. Therefore, the incidence of such complication might be affected by many different factors.
Genome-Based Analysis and Gene Dosage Studies Provide New Insight into 3-Hydroxy-4-Methylvalerate Biosynthesis in Ralstonia eutropha

ABSTRACT Recombinant Ralstonia eutropha strain PHB−4 expressing the broad-substrate-specificity polyhydroxyalkanoate (PHA) synthase 1 from Pseudomonas sp. strain 61-3 (PhaC1Ps) synthesizes a PHA copolymer containing the branched side-chain unit 3-hydroxy-4-methylvalerate (3H4MV), which has a carbon backbone identical to that of leucine. Mutant strain 1F2 was derived from R. eutropha strain PHB−4 by chemical mutagenesis and shows higher levels of 3H4MV production than does the parent strain. In this study, to understand the mechanisms underlying the enhanced production of 3H4MV, whole-genome sequencing of strain 1F2 was performed, and the draft genome sequence was compared to that of parent strain PHB−4. This analysis uncovered four point mutations in the 1F2 genome. One point mutation was found in the ilvH gene at amino acid position 36 (A36T) of IlvH. ilvH encodes a subunit protein that regulates acetohydroxy acid synthase III (AHAS III). AHAS catalyzes the conversion of pyruvate to 2-acetolactate, which is the first reaction in the biosynthesis of branched amino acids such as leucine and valine. Thus, the A36T IlvH mutation may show AHAS tolerance to feedback inhibition by branched amino acids, thereby increasing carbon flux toward branched amino acid and 3H4MV biosynthesis. Furthermore, a gene dosage study and an isotope tracer study were conducted to investigate the 3H4MV biosynthesis pathway. Based on the observations in these studies, we propose a 3H4MV biosynthesis pathway in R. eutropha that involves a condensation reaction between isobutyryl coenzyme A (isobutyryl-CoA) and acetyl-CoA to form the 3H4MV carbon backbone.
Modeling Multi-level Incentives in Health Care: A Multiscale Decision Theory Approach

Financial incentives offered by payers to health care providers and patients have been identified as a key mechanism to lower costs while improving quality of care. How to effectively design incentive programs that can align the varying objectives of health care stakeholders, as well as predict programs’ performance and stakeholders’ decision response is an unresolved research challenge. The objective of this study is to establish a novel approach based on multiscale decision theory (MSDT) that can effectively model and efficiently analyze such incentive programs, and the complex health care system in general. The MSDT model captures the interdependencies of stakeholders, their decision processes, uncertainties, and how incentives impact decisions and outcomes at the payer, hospital, physician, and patient level. In the first part of this thesis, we study the decision processes of agents pertaining to the investment and utilization of imaging technologies. We analyze the payer-hospital-physician relationships and later extend the model to include radiologist and patient as major stakeholders in the second part of this thesis. We focus on a specific incentive program, the Medicare Shared Savings Program (MSSP) for Accountable Care Organizations (ACOs). The multi-level interactions between agents are mathematically formulated as a sequential non-cooperative game. We derive the equilibrium solutions using the subgame perfect Nash equilibrium (SPNE) concept and the backward induction principle, and determine the conditions under which the MSSP incentive leads to the desired outcomes of cost reduction and quality of care improvements. In the third part of this thesis, we study the multilevel decision making in chronic disease management. We model and analyze patients’ and physicians’ decision processes as a general-sum stochastic game with perfect information and switching control structure. We incorporate the Health Belief Model (HBM) as the theoretical foundation to capture the behavioral aspect of agents. We analyze how incentives and interdependencies affect patients’ engagement in health-promoting activities and physicians’ delivery of primary care services. We show that a re-alignment of incentives can improve the effectiveness of chronic disease management.
SUPPRESSOR OF FRIGIDA3 Encodes a Nuclear ACTIN-RELATED PROTEIN6 Required for Floral Repression in Arabidopsisw⃞

Flowering traits in winter annual Arabidopsis thaliana are conferred mainly by two genes, FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). FLC acts as a flowering repressor and is regulated by multiple flowering pathways. We isolated an early-flowering mutant, suppressor of FRIGIDA3 (suf3), which also shows leaf serration, weak apical dominance, and infrequent conversion of the inflorescence shoot to a terminal flower. The suf3 mutation caused a decrease in the transcript level of FLC in both a FRI-containing line and autonomous pathway mutants. However, suf3 showed only a partial reduction of FLC transcript level, although it largely suppressed the late-flowering phenotype. In addition, the suf3 mutation caused acceleration of flowering in both 35S-FLC and a flc null mutant, indicating that SUF3 regulates additional factor(s) for the repression of flowering. SUF3 is highly expressed in the shoot apex, but the expression is not regulated by FRI, autonomous pathway genes, or vernalization. SUF3 encodes the nuclear ACTIN-RELATED PROTEIN6 (ARP6), the homolog of which in yeast is a component of an ATP-dependent chromatin-remodeling SWR1 complex. Our analyses showed that SUF3 regulates FLC expression independent of vernalization, FRI, and an autonomous pathway gene, all of which affect the histone modification of FLC chromatin. Subcellular localization using a green fluorescent protein fusion showed that Arabidopsis ARP6 is located at distinct regions of the nuclear periphery.