Miracle-dz/UniFAR-FTUs huggingface dataset:
Laser Excitation Studies of the Product Release Steps in the Catalytic Cycle of the Light-driven Enzyme, Protochlorophyllide Oxidoreductase*

The latter stages of the catalytic cycle of the light-driven enzyme, protochlorophyllide oxidoreductase, have been investigated using novel laser photoexcitation methods. The formation of the ternary product complex was initiated with a 6-ns laser pulse, which allowed the product release steps to be kinetically accessed for the first time. Subsequent absorbance changes associated with the release of the NADP+ and chlorophyllide products from the enzyme could be followed on a millisecond timescale. This has facilitated a detailed kinetic and thermodynamic characterization for the interconversion of all the various bound and unbound product species. Initially, NADP+ is released from the enzyme in a biphasic process with rate constants of 1210 and 237 s–1. The rates of both phases show a significant dependence on the viscosity of the solvent and become considerably slower at higher glycerol concentrations. The fast phase of this process exhibits no dependence on NADP+ concentration, suggesting that conformational changes are required prior to NADP+ release. Following NADP+ release, the NADPH rebinds to the enzyme with a maximum rate constant of ∼72 s–1. At elevated temperatures (>298 K) chlorophyllide is released from the enzyme to yield the free product with a maximum rate constant of 20 s–1. The temperature dependencies of the rates of each of these steps were measured, and enthalpies and entropies of activation were calculated using the Eyring equation. A comprehensive kinetic and thermodynamic scheme for these final stages of the reaction mechanism is presented.
A first look at mobile Ad-Blocking apps

Online advertisers, third party trackers and analytics services are constantly tracking user activities as they access web services through their web browsers or mobile apps. While, web browser plugins disabling and blocking Ads (often associated tracking/analytics scripts), e.g. AdBlock Plus[3] have been well studied and are relatively well understood, an emerging new category of apps in the tracking mobile eco-system, referred as the mobile Ad-Blocking apps, received very little to no attention. With the recent significant increase of the number of mobile Ad-Blockers and the exponential growth of mobile Ad-Blocking apps' popularity, this paper aims to fill in the gap and study this new category of players in the mobile ad/tracking eco-system. This paper presents the first study of Android Ad-Blocking apps (or Ad-Blockers), analysing 97 Ad-Blocking mobile apps extracted from a corpus of more than 1.5 million Android apps on Google Play. While the main (declared) purpose of the apps is to block advertisements and mobile tracking services, our data analysis revealed the paradoxical presence of third-party tracking libraries and permissions to access sensitive resources on users' mobile devices, as well as the existence of embedded malware code within some mobile Ad-Blockers. We also analysed user reviews and found that even though a fraction of users raised concerns about the privacy and the actual performance of the mobile Ad-Blocking apps, most of the apps still attract a relatively high rating.
Transient atrial mechanical dysfunction (stunning) after cardioversion of atrial fibrillation and flutter.

BACKGROUND Conversion of atrial fibrillation (AFib) and flutter (AFlt) to sinus rhythm results in a transient mechanical dysfunction of atria (atrial stunning). Methods used as a means of assessing atrial stunning, atrial stunning after conversion of atrial fibrillation/flutter, and the cause, mechanisms, determinants of the extent, and drugs affecting atrial stunning were examined. METHODS Studies on the subject, identified through a comprehensive literature search, were thoroughly evaluated. RESULTS AND CONCLUSIONS Left atrial (LA) stunning has been reported with all modes of conversion of AFib/AFlt to sinus rhythm. The incidence of LA stunning is 38% to 80%. Spontaneous echocardiographic contrast, LA appendage (LAA) flow velocities and emptying fraction, transmitral inflow velocity of atrial wave (A-wave), time-velocity integral of A-wave, and atrial filling fraction have been used as means of assessing LA stunning. The data on right atrial (RA) stunning are limited, but parallel findings have been reported in the right atrium. Atrial stunning does not develop after the unsuccessful attempts of cardioversion or on delivery of electric current to the heart without AFib/AFlt, and it is a function of the underlying AFib/AFlt manifesting at the restoration of sinus rhythm. Tachycardia-induced atrial myopathy and chronic atrial hibernation are suggested mechanisms. Duration of preceding AFib/AFlt, atrial size, and underlying heart disease are determinants of the extent of atrial stunning. Verapamil, dofetilide, and acetylstrophenathidine have been shown to attenuate or protect from atrial stunning in animal or small human studies. A comprehensive knowledge of atrial stunning would be helpful in selecting the patients for, and the duration of, anticoagulation therapy after cardioversion.
Neuroprotective Therapy

The concept of neuroprotection relies on the principle that delayed neuronal injury occurs after ischemia. The phenomenon of the "ischemic cascade" has been described, and each step along this cascade provides a target for therapeutic intervention. In animal models of global and focal cerebral ischemia, numerous preclinical studies have demonstrated various agents to be neuroprotective at different steps along this cascade. A wide variety of drugs has also been studied in humans. Ten classes of neuroprotective agents have reached phase III efficacy trials but have shown mixed results. They include calcium channel antagonists, NMDA receptor antagonists, lubeluzole, CDP-choline, the free radical scavenger tirilizad, anti-intercellular adhesion molecule-1 (ICAM-1) antibody, GM-1 ganglioside, clomethiazole, the sodium channel antagonist fosphenytoin, and piracetam. In the future, clinicians may have an armamentarium of treatments for acute ischemic stroke at their disposal, with a combination of agents directed at different sites in the ischemic cascade being the ultimate goal.
Characteristic Chromatogram: A Method of Discriminate and Quantitative Analysis for Quality Evaluation of Uncaria Stem with Hooks

Abstract It remains a challenge to establish new monographs for herbal drugs derived from multiple botanical sources. Specifically, the difficulty involves discriminating and quantifying these herbs with components whose levels vary markedly among different samples. Using Uncaria stem with hooks as an example, a characteristic chromatogram was proposed to discriminate its five botanical origins and to quantify its characteristic components in the chromatogram. The characteristic chromatogram with respect to the components of Uncaria stem with hooks with the five botanical origins was established using 0.02% diethylamine and acetonitrile as the mobile phase. The total analysis time was 50 min and the detection wavelength was 245 nm. Using the same chromatogram parameters, the single standard to determine multicomponents method was validated to simultaneously quantify nine indole alkaloids, including vincosamide, 3α-dihydrocadambine, isocorynoxeine, corynoxeine, isorhynchophylline, rhynchophylline, hirsuteine, hirsutine, and geissoschizine methyl ether. The results showed that only the Uncaria stem with hooks from Uncaria rhynchophylla, the most widely used in the herbal market, showed the presence of these nine alkaloids. The conversion factors were 1.27, 2.32, 0.98, 1.04, 1.00, 1.02, 1.26, 1.33, and 1.25, respectively. The limits of quantitation were lower than 700 ng/mL. The total contents of 31 batches of Uncaria stem with hooks were in the range of 0.1 – 0.6%, except for Uncaria hirsuta Havil and Uncaria sinensis (Oliv.) Havil. The results also showed that the total content of indole alkaloids tended to decrease with an increase in the hook diameter. This showed that the characteristic chromatogram is practical for controlling the quality of traditional Chinese medicines with multiple botanical origins.
A Nanosystem of Amphiphilic Oligopeptide-Drug Conjugate Actualizing Both αvβ3 Targeting and Reduction-Triggered Release for Maytansinoid

To design a prodrug-based self-assembling nanosystem with both ligand targeting and stimuli-responsive features, and elucidate the superiority of each targeting strategy and the synergistic effect between them, we synthesized four small molecule amphiphilic peptide-drug conjugates (APDCs) using maytansinoid (DM1) as a cytotoxic agent, cRGDfK as a homing peptide, and disulfide (SS) or thioether (SMCC) as linker. Owing to their amphiphilicity, the APDCs could self-assemble into nanoparticles (APDC@NPs) which were evaluated in vitro in three different cell lines and in vivo in tumor-bearing C57BL/6 mice. The RSSD@NPs showed the strongest interaction with αvβ3 integrin, highest cell uptake and intracellular free drug level, and best antitumor efficacy in vitro and in vivo, while it shared the same goodness with other test nanosystems in terms of high drug loading, EPR effect and free of potentially toxic polymers. Especially, the in vivo efficacy of RSSD@NPs was 2 fold of free DM1 which is too cytotoxic to be a drug, while the active targeted APDC@NPs demonstrated acceptable system, tissue and blood compatibility. In αvβ3-positive cells or tumors, the RGD targeting contributed much more than disulfide in anticancer effect. The maximum synergism of the two strategies reached to 22 fold in vitro and 3 fold in vivo. Generally, the active targeting, prodrug and nanosystem could significantly decrease the toxicity of free DM1 and improve its therapy outcome via combining active targeting, prodrug and nanopreparation, especially the dual targeting strategies and their synergism.
Mapping of Proton Relaxation Near Superparamagnetic Iron Oxide Particle–Loaded Polymer Threads for Magnetic Susceptibility Difference Quantification

ObjectivesConventional radiological methods, including magnetic resonance imaging (MRI), fail to visualize polymeric surgical mesh implants because of small thread dimensions and material characteristics. For MRI delineation of such meshes, superparamagnetic iron oxide particles (SPIOs) are integrated in the mesh polymer. Usually, if SPIOs are used as an intravenous contrast agent, they increase the R1 and R2 of adjacent protons. It can be assumed that embedding SPIOs in polymers alters their molecular dynamics. The aim of this study was to investigate the influence of SPIO integration in polymer on the relaxation of adjacent protons. Materials and MethodsPolymer threads were placed in an agarose phantom. At 1.5 T, R1, R2, and R2* maps were calculated from multi inversion-recovery spin echo, multi–spin echo, and multi–gradient echo images, respectively. The threads were aligned parallel or orthogonal to B0. ResultsNo impact of SPIO on proton R1 and R2 was observed. R2* was increased by the SPIO-loaded threads. R1 and R2 amplitude maps showed a magnetic susceptibility difference of 0.97 ppm/(mg SPIO/g polymer) around SPIO-loaded threads. ConclusionsIn contrast to SPIO in aqueous solutions, polymer-embedded SPIO do not affect proton R1 and R2. However, embedded SPIO generate strong local static magnetic field gradients. Thus, SPIO integration is suitable to control the magnetic susceptibility of polymer threads. This can be exploited to visualize implanted polymer-based meshes in MRI using R2* susceptible sequences. Because no impact on R1 and R2 of adjacent protons by SPIO embedded in mesh threads was observed, structures adjacent to implanted meshes will be observable in R1 and R2 maps.
Glut-1 Expression Correlates with Basal-like Breast Cancer.

INTRODUCTION Glucose transporter 1 (Glut-1) is a facilitative glucose transporter expressed in many cancers including breast cancer. Basal-like breast cancer (BLBC) is a high-risk disease associated with poor prognosis and lacks the benefit of targeted therapy. The aim of this study was to characterize the immunohistochemical (IHC) expression of Glut-1 in patients with BLBC compared with non-BLBC. MATERIALS AND METHODS We identified 523 cases of invasive breast carcinoma from our database. The clinicopathologic findings and the biologic markers including estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (Her2) status were reviewed. IHC stains for cytokeratin 5/6 (CK5/6), epidermal growth factor receptor (EGFR), p53, and Glut-1 were performed on tissue microarray using standard procedures. BLBC was defined as ER-,PR-, Her2-, and CK5/6+ and/or EGFR+. RESULTS Of informative cases, 14.7% were categorized as BLBC versus 85.3% as non-BLBC. Glut-1 was expressed in 42 (76.4%) of 55 BLBCs, whereas only 55 (23.8%) of 231 non-BLBCs showed immunostaining for Glut-1 (P < .001). Overall, Glut-1 expression was significantly associated with high histologic grade, ER negativity, PR negativity, CK5/6 positivity, EGFR expression, and high p53 expression (P < .001). However, there was no correlation between Glut-1 immunostaining and patient's outcome. CONCLUSIONS Our results show that Glut-1 is significantly associated with BLBC and might be a potential therapeutic target for this aggressive subgroup of breast cancer, and this warrants further investigations.
Prediction of in vivo drug-drug interactions from in vitro data: impact of incorporating parallel pathways of drug elimination and inhibitor absorption rate constant.

AIMS Success of the quantitative prediction of drug-drug interactions via inhibition of CYP-mediated metabolism from the inhibitor concentration at the enzyme active site ([I]) and the in vitro inhibition constant (K(i)) is variable. The aim of this study was to examine the impact of the fraction of victim drug metabolized by a particular CYP (f(mCYP)) and the inhibitor absorption rate constant (k(a)) on prediction accuracy. METHODS Drug-drug interaction studies involving inhibition of CYP2C9, CYP2D6 and CYP3A4 (n = 115) were investigated. Data on f(mCYP) for the probe substrates of each enzyme and k(a) values for the inhibitors were incorporated into in vivo predictions, alone or in combination, using either the maximum hepatic input or the average systemic plasma concentration as a surrogate for [I]. The success of prediction (AUC ratio predicted within twofold of in vivo value) was compared using nominal values of f(mCYP) = 1 and k(a) = 0.1 min(-1). RESULTS The incorporation of f(mCYP) values into in vivo predictions using the hepatic input plasma concentration resulted in 84% of studies within twofold of in vivo value. The effect of k(a) values alone significantly reduced the number of over-predictions for CYP2D6 and CYP3A4; however, less precision was observed compared with the f(mCYP). The incorporation of both f(mCYP) and k(a) values resulted in 81% of studies within twofold of in vivo value. CONCLUSIONS The incorporation of substrate and inhibitor-related information, namely f(mCYP) and k(a), markedly improved prediction of 115 interaction studies with CYP2C9, CYP2D6 and CYP3A4 in comparison with [I]/K(i) ratio alone.
Gene transfer of human heme oxygenase into coronary endothelial cells potentially promotes angiogenesis

Heme oxygenase (HO‐1) is a stress protein that has been suggested to participate in defense mechanisms against agents that induce oxidative injury such as hemoglobin/heme, hypoxia‐ischemia and cytokines. Overexpression of HO‐1 in endothelial cells (EC) might, therefore, protect against oxidative stress produced under these pathological conditions, by generation of CO, a vasodilator, and bilirubin, which has antioxidant properties that enhance blood vessel formation to counteract hypoxia‐induced injury. A plasmid containing the cytomegalovirus promoter (pCMV) neomycin human HO‐1 gene complexed to cationic liposomes, lipofectin, was used to transfect rabbit coronary microvessel EC. Cells transfected with human HO‐1 gene demonstrated a twofold increase in HO activity and maintained a similar phenotype as in the nontransfected cells. Cell number in transfected cells with human HO‐1 gene increased by about 45%, as compared to nontransfected or those transfected with control pCMV. Transfected and nontransfected EC revealed a similar response to basic fibroblast growth factor (bFGF) in capillary formation. However, transfected cells with the human HO‐1 gene exhibited a twofold increase in blood vessel formation. The angiogenic response of EC to overexpression of HO‐1 gene provides direct evidence that the inductive form of HO‐1 following injury represents an important tissue adaptive mechanism for moderating the severity of cell damage produced in inflammatory reaction sites of hemorrhage, thrombosis and hypoxic‐ischemia. Thus, HO‐1 may participate in the regulation of EC activation, proliferation and angiogenesis. J. Cell. Biochem. 68:121–127, 1998. © 1998 Wiley‐Liss, Inc.
Mucoid phenotype of Klebsiella pneumoniae is a plasmid-encoded virulence factor

We have previously reported that the presence of a 180-kilobase plasmid encoding production of aerobactin was correlated with the virulence of Klebsiella pneumoniae K1 and K2 isolates. This work demonstrates that a variant of a K2 strain which has lost this plasmid, pKP100, becomes avirulent. Labeling of this plasmid with the mobilizable, replication-defective element pME28, used here as a mobilizable transposon, allowed the transfer of this plasmid into a plasmidless derivative. Virulence was restored upon reacquisition of this tagged plasmid, pKP101. In addition to aerobactin production, another phenotype could be correlated with the presence of this virulence plasmid: the mucoid phenotype of the bacterial colonies. Both wild-type and plasmidless strains are encapsulated, but only the former presented mucoid colonies. Participation of this phenotype in the virulence of K. pneumoniae was demonstrated by constructing a mutant altered in the plasmid gene encoding this phenotype. The resulting strain demonstrated a 1,000-fold decrease in virulence. Introduction of the recombinant plasmid pKP200 carrying the gene encoding this mucoid phenotype into Escherichia coli HB101 also led to the production of a mucoid phenotype. Rocket immunoelectrophoresis demonstrated that in E. coli this phenotype was due to the production of colanic acid. On the other hand, neither the overproduction of K2 capsular polysaccharide nor the presence of colanic acid was detected in mucoid strains of K. pneumoniae. We conclude that this mucoid phenotype is definitely an important virulence factor of K. pneumoniae. It is due to the plasmid-encoded production of a substance which is different from colanic acid and the capsular polysaccharide of K. pneumoniae.
The Potential Use of Methotrexate in the Treatment of Cutaneous Leishmaniasis: In Vitro Assays against Sensitive and Meglumine Antimoniate-resistant Strains of Leishmania tropica

Background: The present study aimed to evaluate the effect of methotrexate (MTX) alone and in combination with meglumine antimoniate (MA, Glucantime) against sensitive and MA-resistant Leishmania tropica stages in vitro. Methods: The present study was carried out in 2014 in Leishmaniasis Research Center at School of Medicine, Kerman University of Medical sciences, Kerman, Iran. The effects of MTX alone and along with MA on promastigote and amastigote stages of sensitive (SS) and MA-resistant (RS) L. tropica strains have been evaluated using a colorimetric MTT assay and in a macrophage model, respectively. In addition, the inhibitory effect of MTX on the Leishmania invasion of murine macrophages was assessed in promastigotes of both strains of L. tropica. Sensitive and MA resistant L. tropica are referred to those isolates that are responsive or non-responsive to one or two courses of treatment by MA systemically and/or intralesionally, respectively. Results: The findings of OD and IC50 showed that MTX plus MA (SS: 16.1 μg/ml, RS: 39.8 μg/ml) had a higher anti-leishmanial effect than MA (SS: 52.2 μg/ml, RS: 170 μg/ml) or MTX alone (SS: 22.2 μg/ml, RS: 51.4 μg/ml) on promastigotes of both strains of L. tropica. The MTX plus MA caused a significant decrease (P<0.05) in the mean infection rate (MIR) and the mean number of amastigotes in each macrophage compared with positive control. Infectivity of promastigotes is significantly (P<0.05) reduced when it was preincubated with MTX. Conclusion: This study indicated high potency and a synergistic effect of MTX on MA in inhibiting the growth rateof promastigote and amastigote stages of sensitive and meglumine antimoniate-resistant L. tropica. Further works are needed to evaluate the anti-leishmanial effects of MTX on L. tropica using a clinical setting.
Cost-utility analysis of vortioxetine versus agomelatine, bupropion SR, sertraline and venlafaxine XR after treatment switch in major depressive disorder in Finland

ABSTRACT Background: To assess the cost-utility of vortioxetine versus relevant comparators (agomelatine, bupropion SR, sertraline, and venlafaxine XR) in the finnish setting in major depressive disorder (MDD) patients with inadequate response to selective serotonin- /serotonin–norepinephrine reuptake inhibitors. Methods: A one-year analysis was conducted using a decision tree with a Markov state transition component. The health states were remission, relapse and recovery. A Finnish healthcare payer perspective was adopted. Results: Vortioxetine was less costly and more effective versus all comparators in both direct and societal perspectives. Vortioxetine reduced the average annual direct costs by 4% versus venlafaxine XR and 8% versus sertraline. The greater efficacy associated with vortioxetine was translated into a higher percentage of patients in remission and recovery. The model was most sensitive to changes in remission rates at 8 weeks. Conclusion: This cost-utility analysis showed vortioxetine to be a good alternative for MDD patients switching therapy in Finland.
Cloning and Stable Expression of cDNA Coding For Platelet Endothelial Cell Adhesion Molecule -1 (PECAM-1, CD31) in NIH-3T3 Cell Line.

PURPOSE PECAM-1 (CD31) is a glycoprotein expressed on endothelial and bone marrow precursor cells. It plays important roles in angiogenesis, maintenance and integration of the cytoskeleton and direction of leukocytes to the site of inflammation. We aimed to clone the cDNA coding for human CD31 from KG1a for further subcloning and expression in NIH-3T3 mouse cell line. METHODS CD31 cDNA was cloned from KG1a cell line after total RNA extraction and cDNA synthesis. Pfu DNA polymerase-amplified specific band was ligated to pGEMT-easy vector and sub-cloned in pCMV6-Neo expression vector. After transfection of NIH-3T3 cells using 3 μg of recombinant construct and 6 μl of JetPEI transfection reagent, stable expression was obtained by selection of cells by G418 antibiotic and confirmed by surface flow cytometry. RESULTS 2235 bp specific band was aligned completely to human CD31 reference sequence in NCBI database. Transient and stable expression of human CD31 on transfected NIH-3T3 mouse fibroblast cells was achieved (23% and 96%, respectively) as shown by flow cytometry. CONCLUSION Due to murine origin of NIH-3T3 cell line, CD31-expressing NIH-3T3 cells could be useful as immunogen in production of diagnostic monoclonal antibodies against human CD31, with no need for purification of recombinant proteins.