Bacterial production of human discoidin domain receptor 2 (DDR2) kinase and its gatekeeper mutants to assess activation by phosphorylation

Discoidin domain receptor 2 (DDR2) belongs to a subfamily of receptor tyrosine kinases (RTKs) known as discoidin domain receptors (DDRs). DDRs are characterized by an extracellular discoidin homology domain and being activated by collagen resulting in a delayed but sustained activation. DDR2 overexpression was reported in some tumors, atherosclerosis as well as a number of inflammatory and fibrotic conditions. Recently 3 kinase inhibitor drugs (imatinib, nilotinib and dasatinib) were reported to inhibit DDR2 kinase activity suggesting it might have a role in their therapeutic effect. However minimal information is available on DDR2 downstream signaling. Identification of DDR2 substrates is essential to understand the molecular mechanisms underlying the associated diseases and predict side effects and resistance to kinase inhibitors. Identification of kinase substrates is a challenging task as all kinases use ATP to phosphorylate their substrates in addition to the low stoichiometry of phosphorylation events. Kevan Shokat lab designed a chemical genetic approach for substrate identification, where kinases are engineered to accept synthetic ATP analogs (A*TP) and kinase inhibitors that do not bind to the wild types (analog sensitive kinases). The first aim of the present study was to construct a series of kinase domain mutations and a functional analog sensitive kinase to help in the identification of DDR2 substrates. Currently DDR2 protein is produced in insect and mammalian cells, which are expensive and time-consuming expression systems. The second aim was to develop a protocol for DDR2 kinase production using the less demanding bacterial system. A series of analog sensitive, drug resistant, activating and kinase dead mutations were constructed and the kinase domains were expressed in Rosetta pLysS bacterial strain as glutathione-S-transferase (GST) fusion proteins. The proteins were produced in soluble forms with milligram yields. However preliminary kinase and autophosphorylation reactions of the purified proteins revealed low kinase activities. The results show that if the bacterial expression system is to be pursued, in vitro activation using the upstream Src kinase or Src co-expression is essential to produce a highly active DDR2 kinase

Encapsulation of essential oils in chitosan nanoparticle formulations and Investigation on their antioxidant and antibacterial properties.

Peppermint oil (PO) and Green Tea oil (GTO) are two essential oils (EOs) were encapsulated in chitosan nanoparticles (CS NPs) via two-steps method (emulsification followed by ionic gelation). Encapsulation of GTO and PO in CS NPs were investigated through different characterization techniques such as; Fourier transform infrared (FT-IR) spectroscopy, powder X-ray diffraction (XRD). Both NPs (CS/PO NPs and CS/GTO NPs) showed a spherical shape with 20-90 nm size range as detected by Transmission electron microscopy (TEM). Thermogravimetric analysis (TGA) was used to study the thermal stability of both bulk and encapsulated EOs that showed an enhancement in the thermal stability of both encapsulated EOs by about 2.18 and 1.75 folds for PO and GTO, respectively. Through UV-vis spectroscopy, both encapsulation efficiency (EE%), loading capacity (LC%) and in-vitro release were estimated. EE% of CS/PO NPs and CS/GTO NPs were about 82-78% and 22-81%, respectively, when the initial EO amount was 0.25–1 w/w CS. Whereas, the loading capacity (LC%) of CS/PO NPs and CS/GTO NPs were about 8-22% and 2.2-23%, respectively for the initial EO amount was 0.25–1 w/w CS. The in-vitro release studies of both EOs showed an initial rapid release profile followed by a slow release at two different pH conditions: acidic pH (acetate buffer) and neutral pH (phosphate buffer saline). Furthermore, the stability of the total phenolic contents (TPC) of both EOs in CS NPs was studied using Folin–Ciocalteu reagent. The antioxidant activity of both pure and encapsulated PO and GTO was evaluated by 2,2-diphenyl-1-picrylhydrazyl radical (DPPH). The antioxidant activities of CS/PO NPs and CS/GTO NPs were improved by about 2 and 2.4 folds, respectively. Finally, agar dilution and colony counting method were used to study the antibacterial activity of pure and encapsulated PO and GTO against Gram positive (Staphylococcus aureus) and Gram negative (Escherichia coli) bacteria. In case of Gram positive bacteria, encapsulated PO showed an enhanced antibacterial activity by about 39.63%, while encapsulated GTO showed an improvement in antibacterial activity by about 57.5% on the other hand, against Gram negative bacteria, encapsulated PO showed an enhanced antibacterial activity by about 3%, while encapsulated GTO showed an improvement in antibacterial activity by about 1.8%

Performance Evaluation of Checkpoint/Restart Techniques

Distributed applications running on a large cluster environment, such as the cloud instances will have shorter execution time. However, the application might suffer from sudden termination due to unpredicted computing node failures, thus loosing the whole computation. Checkpoint/restart is a fault tolerance technique used to solve this problem. In this work we evaluated the performance of two of the most commonly used checkpoint/restart techniques (Distributed Multithreaded Checkpointing (DMTCP) and Berkeley Lab Checkpoint/Restart library (BLCR) integrated into the OpenMPI framework). We aimed to test their validity and evaluate their performance in both local and Amazon Elastic Compute Cloud (EC2) environments. The experiments were conducted on Amazon EC2 as a well-known proprietary cloud computing service provider. Results obtained were reported and compared to evaluate checkpoint and restart time values, data scalability and compute processes scalability. The findings proved that DMTCP performs better than BLCR for checkpoint and restart speed, data scalability and compute processes scalability experiments

The Development of a Predictive Theory of Science Education Based Upon Information Processing Theory

This thesis describes the establishment of a new predictive theory for science education which can give direction to the improvement and transformation of science teaching at all levels. It is based upon Information Processing Theory. It has the ability to predict performance in science on the basis of independent psychological tests and to provide a framework for understanding how scientific learning takes place. The development of the theory has resulted from empirical work on 529 school pupils at "0" Grade (age 16) and on 440 Glasgow University students, through two series of experiments in addition to two confirmatory studies in the U.S.A. and Egypt. The first series related to students performance in individual questions, and the second related to students over-all performance in conventional examinations. Throughout this empirical work, a constant pattern has emerged showing that the students' holding-thinking space limited their ability to solve problems of different complexity. As soon as there was an overload on students' holding-thinking space, their performance fell away. In addition, the students' holding-thinking space is considered to be a good predictor for success in the conventional "0" Grade examinations, as well as the university examinations not only in chemistry, but also in physics, biology and mathematics. Where the theory and the empirical measurements have not agreed exactly, further investigation has been done to examine the disparities. In some cases new understanding has occurred which has allowed the theory to be modified. This thesis illustrates the importance of the teaching of learning strategies. In fact, it raises the teaching of strategies on to a par with the teaching of content. Three ways of successfully reducing the load on the students' holding-thinking space have been described and tested. The effect of the limitation of students' perceptual fields and of holding-thinking space on learning and problem solving tasks is also explored. The theory, which has been established in this thesis, answered some of the questions that educators have concerning students' limitations in learning and in problem solving. The outworking of this theory in terms of instructional methods, design of computer programs, books and laboratory experiences, is forming the basis of several follow-up studies

Haematological and biochemical observations in four pure breeds of rabbits and their crosses under Egyptian environmental conditions

The present study was conducted to evaluate 16 crosses between 4 breeds of rabbits from a physiological point of view. The breeds tested were Baladi Red (BR), Chinchilla Giganta (ChG), French Giant Papillon (FGP) and Simenwar (S). A total number of 6144 blood samples were collected to detect the effect of crossing, age of kits, month of kindling and sex effects. The traits evaluated were: haematological parameters; red blood cell count (RBCs), haemoglobin concentration (Hb), haematocrit value (Ht%), biochemical parameters of plasma; total protein (TP), albumin (Alb), globulin concentration (Glo), albumin/globulin ratio (Alb/Glo) and triglycerides (TG). BR or its crosses, using BR sires or BR dams, showed the highest value of RBCs, Hb and Ht%. Crossbred rabbits obtained from mating BR and FGP rabbits had the highest Glo values. Rabbits which were born in May-June months had the highest values of TP and its fractions (Alb and Glo). Age of kits had a highly significant effect (P<0.001) on RBCs, Hb, Ht%, TP and TG. Moreover, Glo and Alb/Glo ratio (P<0.01) and Alb (P<0.05) were also significantly affected. Sex had no significant effect on all studied parameters. Significant positive correlations were found between TP and each final body weight, total weight gain, total feed intake, carcass weight and dressing percentage, while significant negative correlation was found with feed conversion.Abdel-Azeem, A.; Abdel-Azim, A.; Darwish, A.; Omar, E. (2010). Haematological and biochemical observations in four pure breeds of rabbits and their crosses under Egyptian environmental conditions. World Rabbit Science. 18(2). doi:10.4995/WRS.2010.18.1318

A Multidimensionality Reduction Approach to Rainfall Prediction

The rainfall has an impact on various fields and industries, including transportation, construction, tourism, health, and wildlife preservation. Accurate rainfall prediction is essential for mitigating the negative impact of rainfall on these sectors. However, previous studies on rainfall prediction have been mainly based on datasets from North America, Europe, Australia, and Central Asia, covering different periods. This study proposes using weather datasets covering the past 5 to 10 years to capture recent patterns in weather data. Additionally, the curse of dimensionality can impact model performance and lead to overfitting. Therefore, this study proposes utilizing dimensionality reduction techniques to ensure that only the significant features are used for rainfall prediction. Multiple Linear Regression (MLR) with dimensionality reduction is applied to improve the accuracy of rainfall prediction. The experimental result shows that UMAP+MLR and t-SNE+MLR have lower MSEs of 57.27 and 56.74 and higher r2 scores of 0.130 and 0.138, respectively. The proposed approach can be valuable in optimizing resource utilization and mitigating the impacts of rainfall on various fields and industries. The source code for our research is available on GitHub repository: https://github.com/Prasanjit-Dey/Dimension_Reduction

Serum calprotectin as a diagnostic marker of late onset sepsis in full-term neonates

Background: Calprotectin, a complex of two calcium-binding proteins that belong to the S100 protein family, is abundant in the cytosolic fraction of neutrophils. A high level of calprotectin reportedly exists in extracellular fluid during various inflammatory conditions, but its role in neonatal sepsis was investigated only in one study as a marker of sepsis in very low birth weight neonates. Objective: This study aimed to measure the serum calprotectin level by ELISA in full-term neonates with late onset neonatal sepsis, its correlations with other laboratory markers of sepsis as interleukin-6, C-reactive protein (CRP), total leucocytic count and platelet count and its relation to the outcome of cases. Methods: This study comprised 48 full-term neonates with gestational ages of 37 to 42 weeks with manifestations of late onset neonatal sepsis admitted to the neonatal intensive care unit, Minia University Hospital during the period from February, 2011 to December, 2011 and 40 healthy neonates, age and sex matched as a control group. Serum levels of calprotectin, IL6 and CRP were measured for all neonates recruited in this study. Results: Serum calprotectin levels were significantly higher in term neonates with late onset neonatal sepsis than controls (3.77±1.85 μg/ml and 0.70±0.33 μg/ml respectively, P-value = 0.000). Cases with positive blood cultures and poor outcomes had the highest levels of calprotectin (5.8±0.61 μg/ml and 6.1±0.42 μg/ml respectively). Significant positive correlations were found between calprotectin levels and IL6 (P-value =0.000, r=0.92), C-reactive protein (p=0.000,r=0.95) and total leucocytic count (P-value =0.000, r=0.72), and negative correlations were found between its level and platelet count (P-value =0.000, r=-0.87), gestational age (P-value =0.014, r=-0.35) and body weight (P-value=0.018, r=-0.34). No significant differences were observed between males and females as regards calprotectin levels (3.96±2.10 μg/ml vs 3.55±1.52 μg/ml, P-value=0.444). Conclusions: Serum calprotectin levels are significantly higher in full-term neonates with late onset neonatal sepsis. Its levels correlated well with other laboratory markers of sepsis and neonatal mortality. It is a sensitive diagnostic marker for late onset neonatal sepsis.Keywords: Calprotectin, IL6, Full-term, Late-onset sepsisEgypt J Pediatr Allergy Immunol 2012;10(1):19-2

Evaluation of the diagnostic value of brain natriuretic peptide for detection of left ventricular systolic dysfunction and pulmonary hypertension in patients with acute exacerbation of chronic obstructive pulmonary disease

Background: One of the most critical health concerns of our day is acute deterioration of chronic obstructive lung disease (COPD). Detecting concurrent heart illness in these individuals might be challenging.Objective: Aims of this study were determining the diagnostic value of B-type natriuretic peptide (BNP) levels in the identification of acute COPD exacerbations (AECOPD) that were linked with left ventricular (LV) dysfunction and pulmonary hypertension. Methods: a prospective study of 100 patients with acute COPD exacerbations was done. All research participants were subjected to history taking, clinical examination, laboratory testing, blood gas analysis, echocardiography, and NT-pro BNP plasma level estimation.Results: Receiver operating characteristic (ROC) curve for BNP as a diagnostic for LV systolic dysfunction showed that area under the curve (AUC) was 0.923 at cut off point of 72.1 ng/ml with sensitivity of 93.3% and specificity of 84.6% (P&lt;0.001).Conclusion: Heart failure is confirmed when the average natriuretic (NT)-BNP level in the left ventricle during AECOPD is higher than normal, which should prompt quick treatment for both conditions

Forecasting project schedule performance using probabilistic and deterministic models

AbstractEarned value management (EVM) was originally developed for cost management and has not widely been used for forecasting project duration. In addition, EVM based formulas for cost or schedule forecasting are still deterministic and do not provide any information about the range of possible outcomes and the probability of meeting the project objectives. The objective of this paper is to develop three models to forecast the estimated duration at completion. Two of these models are deterministic; earned value (EV) and earned schedule (ES) models. The third model is a probabilistic model and developed based on Kalman filter algorithm and earned schedule management. Hence, the accuracies of the EV, ES and Kalman Filter Forecasting Model (KFFM) through the different project periods will be assessed and compared with the other forecasting methods such as the Critical Path Method (CPM), which makes the time forecast at activity level by revising the actual reporting data for each activity at a certain data date. A case study project is used to validate the results of the three models. Hence, the best model is selected based on the lowest average percentage of error. The results showed that the KFFM developed in this study provides probabilistic prediction bounds of project duration at completion and can be applied through the different project periods with smaller errors than those observed in EV and ES forecasting models

MYCOBIOTA OF SOLARIZED AND UNSOLARIZED CUCUMBER SOILS AND ROLE OF SOLARIZATION IN CONTROLLING OF SCLEROTINIA SCLEROTIORUM (LIB.) de BARY UNDER GREENHOUSE CONDITIONS

Soil mycoflora play an important role in agri-cultural economy of a country. The current study was made to have the knowledge about soilborne fungi associated with cucumber crop in solarized and unsolarized soils. Solarization exerted various effects, some of which are biological, others are chemical and still others are physical. All together these changes affected directly or indirectly the mycoflora of the soil, especially the soilborne pathogenic ones. Forty-nine fungal species belong to thirty genera have been isolated from solarized and unsolarized soils. The diversity as well as the count was greatly affected by solarization. By comparison of the species lists of the fungal flora of solarized and unsolarized soils it was evident that soil fungi behave differently toward soil solar-ization, while some new species developed e.g. Absidia, Acrophialophora, Talaromyces, Glio-cladium, some remained unaffected e. g. Aspergil-lus, Penicillium, Chaetomium, Botryotrichum, still others disappeared e. g. Acremonium, Cephali-ophora, Eurotium and others. Regarding solariza-tion for controlling white cucumber rot caused by Sclerotinia sclerotiorum, the obtained data clearly show that solarization had led to a marked in-crease in the number of healthy plants up to 72.5%