Data management tools for NFFA-EUROPE project

This thesis discusses and presents some developments toward new data services within the EU NFFAEUROPE project. The work performed originates by the need to rationalize and organize large scientific data-sets using a FAIR approach. The activity leverages on results obtained in previous MHPC work and tackle some of the issues about FAIR principle that are coming out due to an increase in size of variety of the original datasets. More specifically the overall goal of the thesis is to setup well organized data services to manage all the SEM images coming from different sources and partner within the NFFA-EUROPE project. The specific goals within this thesis are the following; \u2022 Creation of python application to collect and enrich metadata for SEM images coming from different sources. \u2022 Develop a massive parallel processing approach to be able to reduce time in collecting metadata on a large amount of images. \u2022 Plan and develop of an easy to setup and portable computational ecosystem to accomplish the above goal based on Kubernetes and Spark, with the idea to easily deploy in on different computational infrastructure. \u2022 Measure performance on different computational infrastructure of the massive data processing

Does obesity affect the plasma level of Plasminogen Activator Inhibitor-1? And does CO2 pneumoperitoneum affect it?

AbstractBackgroundThis prospective controlled study was designed to evaluate the effect of obesity on the plasma level of Plasminogen Activator Inhibitor-1 (PAI-1) and also to evaluate the effect of CO2 pneumoperitoneum on the plasma level of PAI-1 in patients underwent laparoscopic surgery.MethodsThe study included two groups; first group (non obese) included 30 patients with normal average BMI underwent laparoscopic cholecystectomy while the second group included 30 obese patients with BMI>30kg/m2 underwent laparoscopic band ligation or fundoplication surgery. Five ml of venous blood was collected from each patient in the non obese group once before induction of anesthesia while three venous blood samples (5ml) were collected from each patient in the obese group as follows: first sample was taken before induction of anesthesia to compare it with the non obese group, second sample was taken after 1h of CO2 insufflations (to know the effect of CO2 insufflations on PAI-1 level) and third sample was taken 1week after surgery (to know the remaining effect in the postoperative period).ResultsThe level of PAI-1 was significantly high (5.423±2.5ng/ml) in the obese patients compared to non obese patients (1.4±0.641ng/ml) (P value=0.001). The level of PAI-1 was significantly high after CO2 insufflations compared to baseline level (6.396±2.542ng/ml vs. 5.423±2.5ng/ml) in obese group (P value=0.001). And this level also showed significant increase up to 1week (6.01±2.492ng/ml vs. 5.423±2.5ng/ml) (P value=0.028) in the obese group.ConclusionThe PAI-1 level was higher in obese patients when compared to non obese patients. PAI-1 level was elevated after CO2 insufflations and this elevation did not reach base line level up to 1week after laparoscopic surgery

Antioxidant Role of Vitamin C in Alleviating the Reproductive Toxicity of Lead Acetate in Male Rats

Environmental pollution with heavy metals represents global problem. One of these heavy metals is the lead acetate that emits from many industries such as paint, ceramics, lead containing pipes and plastics led to a manifold rise in the occurrence of free lead in biological systems and the environment. Exposure to lead acetate affects most of the body’s organs especially testes since it has a unique vascular system. Therefore, the present study aimed to evaluate the protective effect of vitamin C against lead acetate induced testicular toxicity in rats. Thirty male adult albino rats were used in this study. They were equally divided into three groups; group I "control group", group II "lead acetate treated group" and group III "lead acetate and vitamin C treated group". Administration of lead acetate (20 mg /kg body weight for 8 successive weeks) resulted in a significant decrease in serum level of testosterone. It also led to a significant increase in the testicular tissue homogenate concentration of MDA and a significant decrease in GSH concentration and catalase activity. Administration of vitamin C (20 mg/kg body weight) with lead acetate for 8 successive weeks succeeded in improving semen quality and antioxidant enzyme concentrations of testes. It can be concluded that lead acetate testicular toxicity in rats led to disturbance in serum level of the main male reproductive hormone and increased testicular contents of oxidative markers and decreased the antioxidant markers. The use of vitamin C improved these changes.  &nbsp

Immune response of the chicken in determination of virulence profiles of Salmonella enterica

Salmonella enterica subspecies enterica (S. enterica) infection remains a global problem in a wide range of animals and in man. Poultry-derived food is a common source of human infection with the non-host-adapted Salmonella strains while fowl typhoid and pullorum disease are serious diseases in poultry. Development of novel immune-based control strategies against Salmonella infection necessitates a better understanding of the host-pathogen interactions at the cellular level. This study characterizes, in vitro and in vivo, the immune responses that develop following infection of avian species with typhoid and non-typhoid Salmonella serotypes. Salmonella serovars Typhimurium, Enteritidis, Hadar and Infantis showed a greater level of invasion and/or uptake characters to both chicken macrophages (HD11) and chicken kidney epithelial cells (CKC), when compared with S. Pullorum or S. Gallinarum. Nitrate and reactive oxygen species were greater in Salmonella-infected HD11 cells compared with the non-infected controls. HD11 cells revealed higher mRNA gene expression for CXCLi2 (IL-8), IL-6 and iNOS genes in response to S. Enteritidis infection when compared to S. Pullorum-infected cells. S. Typhimurium- and S. Hadar-infected HD11 showed higher gene expression for CXCLi2 versus S. Pullorum-infected cells. Higher mRNA gene expression levels of pro-inflammatory cytokine IL-6, chemokines CXCLi1 (K60) and CXCLi2 and iNOS genes were detected in S. Typhimurium- and S. Enteritidis-infected CKC followed by S. Hadar and S. Infantis while no significant changes were observed in S. Pullorum or S. Gallinarum-infected CKC. Epithelial cell response and production of pro-inflammatory cytokines and chemokines were greatly influenced by Salmonella virulence markers, including Salmonella pathogenicity island type-1 (SPI-1), SPI-2 and bacterial flagella. In chicken infections, S. Enteritidis and S. Infantis colonized the caeca more efficiently than S. Gallinarum and S. Pullorum. High numbers of B-lymphocytes and macrophages were observed in the caecal tonsils of infected birds. S. Enteritidis infection in newly hatched birds elicited the expression of CXCLi1 and CXCLi2 chemokines in the caecal tonsils, while S. Gallinarum up-regulated the expression of LITAF. In older chickens, S. Enteritidis infection resulted in a significantly higher expression of CXCLi2, iNOS, LITAF and IL-10 while S. Pullorum appeared to down-regulate CXCLi1 expression in the caecal tonsils. Data from spleens showed either no expression or down-regulation of the tested genes. In conclusion, data from the present study provide further insights on the interaction of Salmonella with poultry, and while both S. Typhimurium and S. Enteritidis are strong inflammatory serotypes, S. Pullorum and S. Gallinarum are not

Evaluation of stool and urine parameters correlation to CRP and D-dimer in COVID-19 infected adults and their contact children

Aim: Aim is to depict suggestive urine and stool parameters in asymptomatic suspected contact children living with COVID-19 infected adults. These parameters will facilitate identifying  children who deserve the confirmatory diagnosis of COVID-19 by PCR test.  Methods: Study was conducted in the National Hepatology and Tropical Medicine Research institute (NHTMRI) Cairo, Egypt. It included 66 mild COVID-19 adult patients (group1) and their 82 asymptomatic contact children (group 2). Results:  In group 1, both C reactive protein (CRP) and D-dimer levels were significantly high. C reactive protein was significantly positively correlated with urinary microalbumin> 30, albumin/ creatinine ratio and urine pus >10 cells / HPF and significantly negatively correlated with vitamin C. D-dimer was significantly negatively correlated with vitamin C. In group 2, CRP and D-dimer were significantly negatively correlated with urine specific gravity (SG), urinary vitamin C. CRP was significantly negatively correlated with stool pus > 10 cells/ HPF, while D-dimer was significantly positively correlated with stool occult blood.   Receiver Operating Curve (ROC) analysis revealed that urine SG showed the highest area under the curve (AUC); 0.859, 0.96, sensitivity of 100%, 100% and specificity of 71.8%, 77.8% with reference to D-dimer and CRP; respectively. Conclusions: In contact children of adult COVID-19 proved infection, urine SG, stool occult blood and stool pus > 10 cells/ HPF can be feasible tool for suspected COVID-19 infection, based on its results COVID-19 PCR request can be an imperative option to confirm the diagnosis; particularly in developing countries where detection of COVID -19 by PCR is not readily feasible.COVID19; urine; stool; childre

Immune response of the chicken in determination of virulence profiles of Salmonella enterica

Salmonella enterica subspecies enterica (S. enterica) infection remains a global problem in a wide range of animals and in man. Poultry-derived food is a common source of human infection with the non-host-adapted Salmonella strains while fowl typhoid and pullorum disease are serious diseases in poultry. Development of novel immune-based control strategies against Salmonella infection necessitates a better understanding of the host-pathogen interactions at the cellular level. This study characterizes, in vitro and in vivo, the immune responses that develop following infection of avian species with typhoid and non-typhoid Salmonella serotypes. Salmonella serovars Typhimurium, Enteritidis, Hadar and Infantis showed a greater level of invasion and/or uptake characters to both chicken macrophages (HD11) and chicken kidney epithelial cells (CKC), when compared with S. Pullorum or S. Gallinarum. Nitrate and reactive oxygen species were greater in Salmonella-infected HD11 cells compared with the non-infected controls. HD11 cells revealed higher mRNA gene expression for CXCLi2 (IL-8), IL-6 and iNOS genes in response to S. Enteritidis infection when compared to S. Pullorum-infected cells. S. Typhimurium- and S. Hadar-infected HD11 showed higher gene expression for CXCLi2 versus S. Pullorum-infected cells. Higher mRNA gene expression levels of pro-inflammatory cytokine IL-6, chemokines CXCLi1 (K60) and CXCLi2 and iNOS genes were detected in S. Typhimurium- and S. Enteritidis-infected CKC followed by S. Hadar and S. Infantis while no significant changes were observed in S. Pullorum or S. Gallinarum-infected CKC. Epithelial cell response and production of pro-inflammatory cytokines and chemokines were greatly influenced by Salmonella virulence markers, including Salmonella pathogenicity island type-1 (SPI-1), SPI-2 and bacterial flagella. In chicken infections, S. Enteritidis and S. Infantis colonized the caeca more efficiently than S. Gallinarum and S. Pullorum. High numbers of B-lymphocytes and macrophages were observed in the caecal tonsils of infected birds. S. Enteritidis infection in newly hatched birds elicited the expression of CXCLi1 and CXCLi2 chemokines in the caecal tonsils, while S. Gallinarum up-regulated the expression of LITAF. In older chickens, S. Enteritidis infection resulted in a significantly higher expression of CXCLi2, iNOS, LITAF and IL-10 while S. Pullorum appeared to down-regulate CXCLi1 expression in the caecal tonsils. Data from spleens showed either no expression or down-regulation of the tested genes. In conclusion, data from the present study provide further insights on the interaction of Salmonella with poultry, and while both S. Typhimurium and S. Enteritidis are strong inflammatory serotypes, S. Pullorum and S. Gallinarum are not

Polymorphism of Prolactin Gene and Its Association with Egg Production Trait in Four Commercial Chicken Lines

Δε διατίθεται περίληψη στα ελληνικάBroodiness is a behavioral trait observed in most common breeds of domestic fowl and due to its fundamental role in avian reproduction, it has been of great interest to poultry scientists, breeders and producers of hatching eggs. Prolactin gene (PRL) is generally accepted as crucial to the onset and maintenance of broodiness in birds and thus plays a crucial role in egg production. Therefore, the present study aimed to screen the Single Nucleotides Polymorphisms (SNPs) of prolactin gene in four commercial chicken lines namely Hubbard F15, Lohmann, Cobb500, and Avian48 using PCR and direct sequencing. A total number of forty chickens (ten females from each of the four commercial chicken lines) were used. Blood samples were collected aseptically from brachial (wing) vein of the chickens for genomic DNA extraction. PCR reaction was done using five pairs of primers, one sense (F) and one antisense (R) primer for each of the five exons of prolactin gene. Finally, DNA sequencing and Single Nucleotide Polymorphisms (SNPs) analysis was done using Laser gene Megalign program. The results showed three SNPs in Hubbard F15 chicken line; one synonymous SNP at the position 3838 bp (ACC/ACT-transition) in exon 2 while in exon 5, two SNPs were detected; one non-synonymous single nucleotide polymorphism at the position 7921bp (CCT/TCT-transition) which results in amino acid changes at codon positions 169 (P/S), and one synonymous single nucleotide polymorphism at the position 8187 bp T/ C. The study concluded that this SNP in PRL gene could be used as the potential molecular markers for egg production traits in chicken

Surgical treatment of displaced intra-articular calcaneal fracture using a single small lateral approach

The objective of this study was to evaluate the outcome of semi-open reduction and minimal internal fixation through a single small lateral approach as a minimally invasive technique for treatment of displaced intra-articular calcaneal fractures. This prospective study was conducted on eighteen patients (16 men and 2 women). The average age was 37.7 (22–55). The most common cause of injury was a fall from height in fourteen patients. Patients were operated on within a mean time of 4.8 days of admission (1–11 days) and were followed up for an average period of 24.1 months (6–39 months). Patients were evaluated clinically using the Creighton-Nebraska Heath Foundation Assessment score of Crosby and Fitzgibbons (J Bone Joint Surg (Am) 72-A:852–859, 1990). The scoring system proposed by Knirk and Jupiter was used for radiological assessment of the posterior subtalar joint (Knirk and Jupiter in J Bone Joint Surg (Am) 68-A: 647–659, 1986). The skin incision healed in all cases without necrosis, infection, or sural nerve injury. All fractures healed after an average of 8 weeks (7–10 weeks), and patients returned to the routine daily activities after an average time of 4.3 months (3–7 months). In conclusion, semi-open reduction and minimal internal fixation through a small lateral approach is an effective treatment for carefully selected cases of displaced intra-articular calcaneal fractures

Molecular characterization of cytochrome P450 1B1 and effect of benzo(a) pyrene on its expression in Nile tilapia (Oreochromis niloticus)

Cytochrome P4501 (CYP1) family enzymes are most active in hydroxylating a variety of environmental contaminants including Polyaromatic Hydrocarbons (PAH), planar polychlorinated biphenyls and arylamines. CYP1B which belongs to the cytochrome  P450 superfamily of genes, is involved in the oxidation of endogenous and exogenous compounds, and could potentially be a useful biomarker in fish for exposure to arylhydrocarbon receptors (AhR) ligands. In this study, a new complementary   DNA (cDNA) of the CYP1B subfamily encoding 1B1 was isolated from Nile tilapia (Oreochromis niloticus) liver after intracoelomic injection with benzo (a) pyrene (BaP). The full-length cDNA was 2107 base pair (bp) long and contained a 5' noncoding region of 29 bp, an open reading frame of 1527 bp coding for 508 amino acids and a stop codon, and a 3' noncoding region of 551 bp, respectively. The deduced amino acid sequence of Nile tilapia CYP1B1 shows similarities of 79.7, 70.3, 65.7, 65.4, 65.0, and 63.7% with Plaice CYP1B1, Japanese eel CYP1B1, zebra fish CYP1B1, common carp CYP1B1, common carp CYP1B2 and  Channel catfish CYP1B1, respectively. The phylogenetic tree based on the amino acid sequences clearly shows tilapia CYP1B1  and Plaice CYP1B1 to be more closely related to each other than to the other CYP1B subfamilies. Furthermore, real-time PCR  was used for measuring BaP induction of CYP1B1 mRNA in different organs of tilapia (O. niloticus), using β-actin gene as internal control, and the results revealed that there was a large increase in CYP1B1 mRNA in liver (22.8), intestine (2.0) and muscles (1.3).Keywords: Oreochromis niloticus, benzo (a) pyrene, CYP1B1 cDNA, sequence analysis, real-time PCR