Abstract Introduction: Abdominal wall defects (AWD) are a common problem that can become difficult to manage, especially when the defect is large and resources are limited (silo and TPN). Methods: Retrospectively, 85 medical records of patients who have been admitted to TMC over a decade (2005 - 2015) were studied. The defects have been categorized into three groups: omphalocele minor, omphalocele major and gastroschisis. The aim is compare the outcomes within these three groups between developed and developing nations. Results: Out of 85 neonates with abdominal wall defects, 50 are males and 35 are females. 58 patients had omphalocele minor, 16 omphalocele major and 11 with gastroschisis. Associated congenital anomalies are reported in 45% of omphalocele groups (1 and 2) and in 27% of gastroschisis group. Post-operative morbidity rate among the omphalocele groups (1 and 2) is 27.37%, and 54.54% among gastroschisis group. Mortality rate among the group one is 3.45%, group two 12.5%, and group three 27.27%. The mortality rate among the two patients who received devices was 50%. Conclusion: Omphalocele can be treated effectively in the developing world; however, gastroschisis cases need more sophisticated supportive measures to reach the reported rates.

Libya is a lower middle-income country with no national surveillance system for hospital-acquired infections (HAIs). We assessed the prevalence of hospital-acquired infections and antimicrobial use in adult intensive care units (ICUs) in Libya. Objective: Evaluate drug resistance of bacteria isolated from equipment placed close to patients in an Intensive Care Unit of a Central hospital in Gharian.

Three-dimensional (3D) cell culture systems have gained increasing interest in drug discovery and tissue engineering due to a number of advantages in providing more physiologically relevant information and potentially more predictive data for in vivo tests. Extracellular matrix (ECM) proteins have been developed over in recent years to simulate a natural microenvironment for cells cultured in vitro. Conventional cell culture or 2D cell culture form monolayers of cells on a solid surface, which is typically polystyrene or glass, whereas a 3D culture system employ a porous growth matrix on which the cells grow. The transition from cell culture on a flat surface 2D to a 3D model in vitro is expected to mimic more realistic culture environments. However, the major limitation of 2D culture is their lack of structural architecture and stroma and not all types of normal epithelial cell are able to adhere and grow on 2D culture. For this study, two different immortal cell lines were used (HeLa and HaCaT cells) and two commercial 3D substrates (Collagen Rat Tail and Geltrex) were used, in order to evaluate how the transition from 2D to 3D affects viability, cell cycle, live/dead cell, responses to the drug exposure and bio-spectroscopy studies. The viability of cells were monitored with the aid of the Alamar Blue assay, cellular morphology was monitored with confocal microscopy, cell cycle and cell death studies were performed with flow cytometry and viability of 3D culture in bio-spectroscopy performed with Raman spectroscopy. The viability studies showed apparent differences between the 2D and 3D culture systems, the differences attributed in part to the physical transition from 2D to a 3D environment causing alterations to effective resazurin concentration, uptake and conversion rates. This was verified by flow cytometry, in which no significant differences in viable cell numbers between 2D and 3D systems was ii observed. Cell cycle analysis revealed cellular function could be altered by growth on the 3D substrates and the alterations were noted to be dependent on 3D membrane concentration. The use of 3D culture matrices has been widely interpreted to result in “improved viability levels” or “reduced” toxicity or cellular “resistance” compared to cells cultured on traditional 2D systems. Cells were grown on the different substrates (Collagen and CaF2), confirming that the in vitro cell culture environment impacts significantly on the cell cycle. The live cell in vitro Raman spectroscopic analysis of cells on the 2D CaF2 and 3D Collagen substrates was performed and data were analysed using principal component analysis (PCA). The spectroscopic analysis revealed differences in profiles which reflect the differences in cell cycle for both in vitro culture environments. In particular, the Raman spectra of cells grown on CaF2 show indicators of cell stress, which are also associated with cell cycle arrest at the G0/G1 phase. Doxorubicin still induced apoptosis with no difference in the population levels in 3D and 2D culture of apoptotic, necrotic and live cells. Also, cells grown on both substrates were arrested at G0/G1 phase by the Doxorubicin, Raman spectra collected from cells grown in Collagen showed that, Doxorubicin is clearly seen to be present in the nucleolus, nucleus and cytoplasm of the HaCaT cells. Statistical analysis, consisting of principal components analysis (PCA) was used to highlight the Doxorubicin interaction with HaCaT cells grown in 3D cultures. The results of this study show that Cellular health and viability levels were not altered by culture in 3D environments, but their normal cycle could be altered verified by the cell cycle studies performed and these variations must be accounted for in studies employing 3D membranes. The Raman spectra of cells grown on CaF2 show indicators of cell stress, which are also associated with cell cycle arrest at the G0/G1 phase. The bioavailability or effective concentration of the cytotoxicity assay and the chemotherapeutic agent are both affected by the iii absorptive nature of the matrix. Despite the differences in the cell cycle in cells grown in 2D and 3D cultures, the efficacies and ultimate effect of the drug on all the cultured cells are the same regardless of culture environment and the variations in the cell cycle for cells grown on different substrates must be accounted for in vitro cellular screening in particular when screening cell cycle dependant toxicants. This study has shown that the use of 3D culture systems has the potential to make a significant impact in the Raman spectroscopy field in particular Collagen is a cost effective substrate replacement for more expensive options. 

DNA, RNA, and protein are represented as strings in bioinformatics for this reason string processing is the cornerstone in the field of bioinformatics and these problems take a variety of manifestations each of which has a specific meaning. This topic will shed some light on some traditional string problems such as: local sequence alignment problem, global sequence alignment problem, exact pattern matching problem, approximate pattern matching problem, finding all maximal palindromes problem, finding all tandem repeats problem, finding all tandem arrays problem, etc. There are quite rich researches for these problems. This paper, will propose the major algorithms in this respect which implemented in BioQt.

The in vitro cell culture environment can impact on cell biochemistry and cell cycle. The manifestation of such substrate-induced changes in cell cycle in the Raman microspectroscopic profiles of cell cultures is investigated at the level of nucleolus, nucleus and cytoplasm. HeLa immortalised human cervical cells and HaCaT dermal cells were cultured on three different substrates, conventional polystyrene cell culture dishes, CaF2 slides as a commonly used Raman substrate, and glass slides coated with Collagen Rat Tail, as a mimic of the extra cellular matrix (ECM) environment. A cell cycle study, based on percentage DNA content, as determined using Propidium Iodide staining and monitored by flow cytometry, was performed on cells of both types, grown on the different substrates, confirming that the in vitro cell culture environment impacts significantly on the cell cycle. Live cell in vitro Raman spectroscopic analysis of cells on the 2D CaF2 and 3D Collagen substrates was performed and data was analysed using principal components analysis (PCA). The spectroscopic analysis revealed differences in profiles which reflect the differences in cell cycle for both in vitro culture environments. In particular, the Raman spectra of cells 2 grown on CaF2 show indicators of cell stress, which are also associated with cell cycle arrest at the G0/G1 phase. This work contributes to the field of Raman spectroscopic analysis by providing a fresh look at the significance of the effect of in vitro culture environment to cell cycle and the sensitivity of Raman spectroscopy to such differences in cell metabolism. 

In this study, the cellular viability and function of immortalized human cervical and dermal cells are monitored and compared in conventional 2D and two commercial 3D membranes, Collagen and Geltrex, of varying working concentration and volume. Viability was monitored with the aid of the Alamar Blue assay, cellular morphology was monitored with confocal microscopy, and cell cycle studies and cell death mechanism studies were performed with flow cytometry. The viability studies showed apparent differences between the 2D and 3D culture systems, the differences attributed in part to the physical transition from 2D to 3D environment causing alterations to effective resazurin concentration, uptake and conversion rates, which was dependent on exposure time, but also due to the effect of the membrane itself on cellular function. These effects were verified by flow cytometry, in which no significant differences in viable cell numbers between 2D and 3D systems were observed after 24 h culture. The results showed the observed effect was different after shorter exposure periods, was also dependent on working concentration of the 3D system and could be mediated by altering the culture vessel size. Cell cycle analysis revealed cellular function could be altered by growth on the 3D substrates and the alterations were noted to be dependent on 3D membrane concentration. The use of 3D culture matrices has been widely interpreted to result in “improved viability levels” or “reduced” toxicity or cellular “resistance” compared to cells cultured on traditional 2D systems. The results of this study show that cellular health and viability levels are not altered by culture in 3D environments, but their normal cycle can be altered as indicated in the cell cycle studies performed and such variations must be accounted for in studies employing 3D membranes for in vitro cellular screening.

BACKGROUND AND PURPOSE: A thorough knowledge of fetal growth and development is key to understanding both the normal and abnormal fetal MR imaging findings. We investigated the size and signal intensity of the normal pituitary gland and the intrasphenoidal ossification around the Rathke pouch in formalin-fixed fetuses on MR imaging.

MATERIALS AND METHODS: Thirty-two fetuses with undamaged brains were included in this study (mean age, 19.93 weeks; age range, 12–31 weeks). Visual inspection of the pituitary and ossification around the Rathke pouch in the sphenoid bone or the postsphenoid ossification was conducted. The extent of pituitary and postsphenoid ossification, pituitary/pons signal ratio, and postsphenoidal ossification/sphenoid bone signal ratio was compared according to gestational age.

RESULTS: The pituitary gland was identified as a hyperintense intrasellar structure in all cases, and postsphenoid ossification was identified as an intrasphenoidal hyperintense area in 27 of the 32 cases (84%). The mean pituitary/pons signal ratio was 1.13 ± 0.18 and correlated weakly with gestational age (R2 = 0.243), while the mean postsphenoid ossification/sphenoid bone signal ratio was 2.14 ± 0.56 and did not show any increase with gestational age (R2 = 0.05). No apparent change in the size of pituitary hyperintensity was seen with gestational age (R2 = 0.001). Postsphenoid ossification showed an increase in size with gestational age (R2 = 0.307).

CONCLUSIONS: The fetal pituitary gland was hyperintense on T1-weighted images and the pituitary/pons ratio and extent of postsphenoid ossification correlated weakly with gestational age.

The interest in the use of 3D matrices for in vitro analysis, with a view to increasing the relevance of in vitro studies and reducing the dependence on in vivo studies, has been growing in recent years. Cells grown in a 3D in vitro matrix environment have been reported to exhibit significantly different properties to those in a conventional 2D culture environment. However, comparison of 2D and 3D cell culture models have recently been noted to result in differing responses of cytotoxic assays, without any associated change in viability. The effect was attributed to differing conversion rates and effective concentrations of the resazurin assay in 2D and 3D environments, rather than differences in cellular metabolism. In this study, the efficacy of a chemotherapeutic agent, doxorubicin, is monitored and compared in conventional 2D and 3D collagen gel exposures of immortalized human cervical cells. Viability was monitored with the aid of the Alamar Blue assay and drug internalisation was verified using confocal microscopy. Drug uptake and retention within the collagen matrix was monitored by absorption spectroscopy. The viability studies showed apparent differences between the 2D and 3D culture systems, the differences attributed in part to the physical transition from 2D to a 3D environment causing alterations to dye resazurin uptake and conversion rates. The use of 3D culture matrices has widely been interpreted to result in “reduced” toxicity or cellular “resistance” to the chemotherapeutic agent. The results of this study show that the reduced efficiency of the drug to cells grown in the 3D environment can be accounted for by a sequential reduction of the effective concentration of the test compound and assay. This is due to absorption within the collagen gel inducing a higher uptake of both drug and assay thereby influencing the toxic impact of the drug and conversion rate of resazurin, and. The increased effective surface area of the cell exposed to the drug and assay in the 3D environment. The effect was noted to be higher after shorter exposure periods and should be accounted for in in vitro 2D and 3D culture environment comparisons.

Bioinformatics is a multi-disciplinary science focusing on the applications of computational methods and mathematical statistics to molecular biology. Choosing bioinformatics as specialization gives an opportunity to get involved with the most interesting computational techniques dealing with biological data to contribute to cure and diagnose some of genetic disorders that affect biological machines. The purpose of this library (which defines namespace BioQt), is to provide a set of routines for handling biological sequence data for Qt/C++ users (the full source code available on https://github.com/alrawab/BioQt). This thesis will shed the light on some modules of BioQt SDK such as exact string matching problem, Microsatellite Repeats, Palindromic sequences and sequence alignment algorithms (Longest Common Subsequence, Needleman-Wunsch and Smith-Waterman). This thesis examines and evaluates these challenging problems in bioinformatics by using Qt/C++.

Purpose

To investigate the diffusion tensor imaging parameters of the optic radiation and surrounding structures using the high-resolution readout-segmented diffusion tensor imaging method.

Materials and methods

Coronal readout-segmented diffusion tensor images were acquired in 15 healthy volunteers. On three slices of each image, eigenvalue 1, fractional anisotropy, radial diffusivity, apparent diffusion coefficient, and signal intensity on T2-weighted images were measured in the lateral inferior longitudinal fasciculus, external and internal layers of the optic radiation, and the tapetum within regions of interest delineated by two independent observers. Profile curve analysis of regions of interest across the optic radiation and surrounding structures was performed for a representative typical case.

Results

Significant differences in fractional anisotropy, radial diffusivity and apparent diffusion coefficient were observed between external and internal layers of the optic radiation, while there was no significant difference in eigenvalue 1. In fractional anisotropy maps, two low signal bands were observed between the inferior longitudinal fasciculus, the optic radiation and the tapetum. Profile curve analysis showed a minimum on the fractional anisotropy and eigenvalue 1 images and a maximum in the radial diffusivity image.

Conclusion

Readout-segmented diffusion tensor imaging revealed significant differences in the diffusion tensor imaging parameters between internal and external layers of the optic radiation.