Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating structural network disruption in multiple sclerosis

Multiple sclerosis (MS) is an inflammatory, demyelinating and neurodegenerative disease of the central nervous system (CNS). Conventional whole brain magnetic resonance imaging (MRI) measures do not sufficiently explain disability in MS. Network science provides a powerful approach to study brain organizational principles and in combination with graph theory has revealed fundamental connectivity patterns in neurological conditions including MS. The overarching aim of this thesis is to investigate structural network disruption in MS evaluating the potential of brain networks analyses as novel biomarkers in MS pathology. The results of this thesis add to the current scientific knowledge. In particular, by applying an optimised structural network reconstruction pipeline we demonstrated that network metrics explain disability better in MS over and above conventional non- network metrics. In addition, in the absence of any longitudinal network studies, we developed a longitudinal network pipeline which we then applied to our longitudinal data. These findings demonstrated for the first time that baseline structural network metrics are predictors of future deep grey matter atrophy and increased lesion load. Finally, we applied a data-driven network decomposition approach detecting progressive weakening of connections that is linked to the severity of MS subtypes suggesting that these techniques are sensitive to pathology. The results presented here highlight the potential of network-based approaches as complementary methods for disease biomarkers to better predict disease course and monitor treatment effects. We believe that these findings may provide a framework for future studies with the aim to bridge the gap between imaging and symptomatology.
Molecular mutation characteristics of mismatch and homologous recombination repair genes in gastrointestinal cancer

Gastrointestinal cancer is one of the most common types of cancer with high mortality rates. Mutations in several genes are reportedly involved in the progression of gastrointestinal cancer, including tumor protein 53 (TP53), APC regulator of WNT signaling pathway (APC), KRAS proto-oncogene GTPase (KRAS) and erb-b2 receptor tyrosine kinase 2 (ERBB2). Most notably, there are numerous mutations in DNA repair genes, including mismatch repair (MMR) and homologous recombination (HR) genes. The focus of the present study was to investigate the effects of MMR and HR gene mutations on genomic instability in gastrointestinal cancer. Using targeted capture and massively parallel genomic sequencing, 137 gastrointestinal cancer patients were analyzed for somatic single-nucleotide variants (SNVs) and insertion-deletion (indel) mutations in the exon regions of 183 cancer driver genes, including 4 MMR genes [MutL homolog MLH1, MLH2, MLH6 and PMS1 homolog 2, mismatch repair system component (PMS2)] and 15 HR genes [BRCA1 DNA repair associated (BRCA1), BRCA2 DNA repair associated (BRCA2), ATM serine/threonine kinase (ATM), phosphatase and tensin homolog, BLM RecQ like helicase, FA complementation group A, FA complementation group C, FA complementation group D2, FA complementation group E, FA complementation group F, FA complementation group G, nibrin, partner and localizer of BRCA2 and Werner syndrome RecQ like helicase]. A number of frequently mutated genes, including but not limited to, mechanistic target of rapamycin kinase, neurofibromin 1, APC and, in particular, DNA repair genes, including PMS2, ATM and BRCA2, were identified. Frequency analysis was performed based on the SNVs and indels in the 183 genes to indirectly indicate the relative status of genomic instability in each patient. Correlation analysis suggested that MMR and HR gene mutations directly affected the count of SNVs and indels. Overall, 56 of the gastrointestinal cancer patients (40%) were found to have an inactivation mutation (stopgain/frameshift/splicing) in one or more of the four MMR genes, whereas 112 patients (82%) harbored at least one HR gene inactivation mutation. In addition, patients with MMR or HR inactivation variants had more SNVs and indels compared with patients with no such mutations. No other clinical characteristics (including sex and age) appeared to have a statistically significant impact. Further analysis indicated that different MMR or HR genes exerted distinct effects on genomic instability. The results obtained in the current study may lay a foundation for investigations into the tumorigenic process and for the development of novel therapeutic strategies for the treatment of gastrointestinal cancer.
The Frequency of Meningitis Cases in Zagazig Fever Hospital: A Cross-sectional Study

Background and study aim: Meningitis is the inflammation of meninges and can be life-threatening in some cases. The study aimed to determine the frequency and clinical presentations of the meningitis cases in ZagazigFeverHospital to put recommendations to assist in improving the preventive and management measure-ments for meningitis. Patients and Methods: A cross-section study included all of 70 meningitis patients in ZagazigFeverHospital, who fulfilled the selection criteria, over a period of one year from September 2016 to September 2017. The data collection sheet included demographic, clinical assessments, diagnostic lumbar puncture with CSF analysis. Results: The majority of meningitis cases were males (57.1%), from urban areas (67.1%), aged less than ten years or more than forty years, and diagnosed in winter (42.9%), especially in February. According to the CSF culture results, patients were classified into two groups; 87.1% as aseptic meningitis (group A) and 12.8% as bacterial meningitis (group B). Neisseria meningitides was the common cause of bacterial meningitis. The death rate was (11.4%), and the old age was a significant risk factor for mortality (P= 0.02). Conclusion: Meningitis is a real health problem in Al Sharkia Governorate; Neisseria meningitides was the common cause of septic meningitis. Health authorities in Al Sharkia governorate should focus their preventive efforts on the age group 40 years.
Dynamic security enhancement of power systems using mean-variance mapping optimization

In this paper, a preventive control action that involves both generation rescheduling and load curtailment is proposed for enhancing the dynamic security of large interconnected power systems. The control action is formulated as a security-constrained optimization problem that is solved by mean-variance mapping optimization (MVMO) integrated with a self-adaptive penalization technique and artificial neural networks to develop a fast and effective methodology. The proposed methodology is applied to a 16-generator 68-bus test system to solve the security-constrained optimization problem with both continuous and discrete decision variables. To find a proper and cost-effective solution for the control actions within an acceptable time, dynamic security assessment methodology based on artificial neural networks is integrated into the optimization process for predicting the violations of security constraints brought about by the candidate solutions. The proposed method effectively integrates a variety of popular heuristic optimization algorithms, including MVMO, differential evolution, particle swarm optimization, genetic algorithms, big bang–big crunch, and artificial bee colony. MVMO outperforms all the others in various aspects such as reliability and robustness.
Application-layer versus Network-layer Multicast: Networking Load, Link Stress, and Distribution Delay

Multicast is the task of disseminating a message from a source to a set of destinations. If supported by the network and switches, multicast can be performed at the network layer. The alternative solution is application-layer multicast (ALM) which disseminates the message through a set of unicast communications. ALM is simple to implement and does not require switches to support multicast. This, however, comes at some price including higher networking load, and slower message dissemination compared to network-layer multicast (NLM). This work analyzes some of these costs/penalties. We show that when ALM is done carefully, its networking load can be bounded to three times that of any NLM, irrespective of the network topology, the number of destination nodes, and the message size. In addition, it can be ensured that ALM does not put significant stress/pressure on any physical link in any network topology. We also analyze how slower ALM is compared to NLM. We implement an ALM algorithm in Amazon EC2 and show that the distribution delay increases slightly as the number of destination nodes increases. Deciding on what layer to use for multicasting depends on the trade-offs one is willing to make. The results presented in this work helps in making such a decision.
Comparative analysis of ML POS on Arabic tweets

One of the challenges of natural language processing is social media text like tweets. Conversational text in contrast to genres that are highly edited (standard language) which traditional NLP tools have been developed for contains many syntactic patterns and non-standard lexical items. These are the outcomes of dialectal variation, diversity in topic, orthography, unintended errors, conversational errors and creative language use. The fact that twitter text is characterized by idiosyncratic style, noise and linguistic errors makes it difficult to part-of-speech tag. The aim of this paper is to design and implement models of speech tagging for Arabic tweets by investigating numerous models of machine learning like K-Nearest Neighbour, Naïve Bayes and Decision tree models. In this paper, a novel Arabic Twitter corpus is introduced while assessing various state-of-the-art POS taggers which retrained on the given corpus. A state-of-the-art accuracy of 87.97% is achieved when tagging twitter.
Role of vacuum assisted closure in the management of infected wound in Orthopaedics

Background and Objective: Wounds are a major source of morbidity, lead to considerable disability, and are associated with increased mortality; therefore, they have a significant impact on public health and the expenditure of healthcare resources. Vacuum-assisted closure (VAC) uses negative pressure to assist wound healing. Negative pressure drains fluid from the wound, thus removing the substrate for growth of microorganisms. Negative pressure may also accelerate granulation tissue formation and promote angiogenesis. The mechanical stimulation of cells by tensile forces may also play a role by increasing cellular proliferation and protein synthesis. Negative pressure wound therapy (NPWT) involves the use of a negative pressure therapy or suction device to aspirate and remove fluids, debris, and infectious materials from the wound bed to promote the formation of granulation tissue. Materials and Methods: A total of 30 post-operative infected wound cases presented in between December 2016 to August 2018 were taken for study. Each case was examined clinically in systematic manner as per the proforma drafted. VAC dressing was done and all cases were followed up to discharge and subsequently for a follow up on 10 th day. Results: In our clinical study of 30 cases managed by VAC dressing, 30% of the cases were of post-operative infected wounds of radius & ulna, 13.3% humerus, 23.3% femur, 23.3% tibia, 3.3% spine, 3.3% calcaneum, 3.3% metatarsals. By the completion of VAC therapy none of the cases required a revision surgery or implant removal. There is a progression of healthy healing in all the cases (100%). Commonest organisms isolated were Staphylococcus, Pseudomonas and Proteus. Interpretation and Conclusion: In our study VAC therapy enhanced granulation tissue formation leading to better wound healing, and faster recovery. VAC is thus a promising new technology in the field of wound healing with multiple applications in a variety of wounds and can be used in both acute and chronic wounds, salvage procedures or as an adjuvant therapy to improve the results of various surgical procedures.
naemia among breastfeeding infants (0-6 months) and associated factors in a low income urban setting of Kenya

Controversies surrounding exclusive breastfeeding for the first six months of life and the risk of developing anaemia exist. Studies worldwide have indicated uncertainties on the way forward given the World Health Organization’s firm stand on exclusive breastfeeding as the most appropriate practice for infants less than six months old. In Kenya, research on anaemia status of infants below six months old is scanty. The main objective of the study was to determine the prevalence of anaemia and its associated factors among breastfeeding infants 0-6 months old in Kangemi Slums, Kenya. One hundred and thirty nine (139) breastfeeding infants aged 0-6 months and their respective mothers were recruited into a cross-sectional study. Infants’ blood was drawn from the heel while mothers’ blood was from a finger prick. Anaemia was assessed using HemoCue ® (Hemo-control, EKF-diagnostic GmbH, Barleben/Magdeburg, Germany) and defined as haemoglobin levels <11.0 and <12.0g/dl for infants and mothers, respectively. Logistic regression was used to model the associations. Anaemia prevalence (35.3%) was of moderate public health significance and was not statistically different between exclusively (36.8%) and nonexclusively (28%) breastfed infants (χ 2 =0.702, 1df, p=0.402). There was no significant difference in mean haemoglobin levels between infants exclusively and those nonexclusively breastfed (t=-1.040, p=0.300). A reduced estimated relative risk of anaemia (OR=0.713, 0.95 CI: 0.34-1.50) was observed among infants <4 months versus 4-6 months old. Key factors of significant positive association with anaemia among the infants included maternal nutritional status (Body Mass Index (p=0.015), haemoglobin levels (p=0.018)) and proportion of household income spent on food (p=0.026). This study concluded that there is a likelihood of exclusively breastfed infants below 6 months to be anaemic in Kenya to the extent of moderate public health significance and special attention is warranted. The study reveals maternal nutritional status, haemoglobin levels and proportion of household income as key predictors of anaemia in infants. Keywords: anaemia, exclusive breastfeeding, infants, low income, associated factors
Visit-to-visit variability in low-density lipoprotein cholesterol is associated with adverse events in non-obstructive coronary artery disease

Objective: A higher visit-to-visit variability in low-density lipoprotein cholesterol (LDL-C) is associated with an increased frequency of cardiovascular events. We investigated the association between the visit-to-visit LDL-C variability and all-cause mortality, myocardial infarction (MI), and coronary revascularization in a population with non-obstructive coronary artery disease (CAD). Methods: From this retrospective cohort of individuals who underwent coronary angiography from 2006 to 2010, a total of 2.012 consecutive patients with non-obstructive CAD, who underwent three or more LDL-C determinations during the first 2 years, were identified and followed up for 5 years. The variability in the visit-to-visit LDL-C was measured by standard deviation (SD) and coefficient of variation (CV). The risk of all-cause mortality and composite endpoints, MI, and coronary revascularization were evaluated by a multivariable Cox regression analysis. Results: During a 5-year follow-up, a total of 99 (4.92%) mortality cases and 154 (7.65%) cases of composite endpoints were observed. The percentage of subjects who experienced mortality or composite endpoints was higher in those with a higher LDL-C-SD or LDL-C-CV level. The association between the LDL-C variability and clinical endpoints was regardless of possible confounding factors. Conclusion: Among the patients with non-obstructive CAD, a higher visit-to-visit LDL-C variability is associated with increasing all-cause mortality or composite endpoints during the long-term follow-up. (Anatol J Cardiol 2019; 22: 117-24)
Outcome of Conservative Management in the Treatment of Symptomatic Spondylolysis and Grade I Spondylolisthesis.

BACKGROUND Bracing (thoraco-lumbar-sacral orthosis) has been accepted as mainstay of treatment for symptomatic spondylolysis (SP) and grade I spondylolisthesis (SPL1). However, increasing costs and patient noncompliance can make bracing prohibitive and difficult to manage. The purpose of this study was to determine if SP and SPL1 can be effectively treated using physical therapy and other non-bracing conservative management techniques in order to relieve pain and restore physical function. METHODS We performed a cross-sectional study in which patients who presented from June 1, 2004, to May 1, 2015, with symptomatic SP and SPL1 who were treated with nonbracing conservative management, entailing a universal 6-week physical therapy program and restriction of offending activity, were considered for the study. Physical therapy included core strengthening activities, hamstrings stretching, and spine range of motion exercises. Patients meeting inclusion criteria were contacted via phone interview and asked to complete an Oswestry Disability Questionnaire (ODQ) in order to generate a disability score to assess their current pain and daily function. Patients were then stratified into groups based on their level of disability as denoted by their disability score; minimal disability = disability score of 0% to 19.9%, moderate disability = 20% to 39.9%, severe disability = 40% to 59.9%, crippled = 60% to 79.9%, and bed bound or exaggerating = 80% to 100%. RESULTS Fourty-six patients were identified as meeting inclusion criteria (28 with SP and 18 with SPL1). Twenty-three of 46 were successfully contacted and agreed to complete the ODQ (10/23 with SP and 13/23 with SPL1). Twenty-two of 23 (96%) patients had a minimal disability score (0% to 19.9%), One of 23 (4%) patients had a moderate disability score (20% to 39.9%), and 18/23 (78%) patients had a disability score of zero, denoting no pain or limitation of function. CONCLUSION The results of this study suggest that, in patients with symptomatic spondylolysis and grade I spondylolisthesis, pain relief and restoration of function can be achieved using conservative management techniques without use of a brace.
Bewerten der Symptomlast von COPD-Patienten in der Praxis

Bei der COPD adaptieren wir die Behandlung im Gegensatz zum Asthma nicht an Ergebnisse quantitativer Messungen, sondern an die Symptome und die Zahl stattgefundener Exazerbationen. Zur Messung der Symptomatologie wird der COPD-Assessment-Test (CAT) oder der COPD Control Questionaire (CCQ) favorisiert, alternativ der Modified British Medical Research Council (mMRC), der nur eine Graduierung der Dyspnoe vornimmt. Letzterer kann schnell und ohne großen Aufwand verwendet werden. Die vorliegende Studie untersucht, wie sich der mMRC und die FEV1 in der täglichen Praxisarbeitverhalten bzw. bewähren. 2017 wurden in 1914 deutschen Praxen bei maximal 15 Patienten pro Praxis Geschlecht, Alter, Grund für den Praxisbesuch, Morgenmedikation (ja/nein), der Grad der Dyspnoe (mMRC) und die FEV1 ermittelt. 26.230 Patienten (52% männlich, 2% ohne Angabe) konnten eingeschlossen werden. Der Hauptgrund für den Praxisbesuch war ein Folgerezept (57%) oder Beschwerden (49%), wobei auch beide Gründe angegeben werden konnten. Die Morgenmedikation war bei 78% erfolgt, von denen 45% wegen Beschwerden und/oder 62% wegen Folgerezept die Praxis aufgesucht hatten. Bei 20% ohne Morgenmedikation lag die Motivation für den Praxisbesuch bei 61% in Beschwerden und/oder bei 39% im Folgerezept, 2% kamen ohne Angabe. Patienten ohne Morgenmedikation waren eher jünger, hatten leichtere Atemflusslimitierung und suchten die Praxis etwas häufiger wegen Beschwerden auf als ältere Patienten mit Morgenmedikation und stärkerer Atemflusslimitierung. Im mMRC nahm der Anteil der Patienten mit Zunahme der Luftnot ab. Die meisten Patienten hatten eine mittlere Atemflusslimitierung (24% leicht, 23% schwer und 5% sehr schwer). FEV1 und mMRC zeigten eine sehr gute Korrelation (Korrelationskoeffizient nach Spearman = 0,59). So lange wir über keine quantitative Möglichkeit zur Therapiebeurteilung verfügen, sollte der Methode der Vorzug gegeben werden, die leicht in der Praxis verwendet werden kann und deswegen akzeptiert und genutzt wird. Der mMRC zeigte eine gute Korrelation mit der FEV1 und kann im täglichen Praxisleben einfach und schnell bei gutem Resultat eingesetzt werden.
PET Theranostics for Molecular Imaging and Radioimmunotherapy of Pancreatic Cancer

Epidermal growth factor receptor (EGFR) is overexpressed in up to 90% of pancreatic cancer tumours. Panitumumab is an antibody that targets EGFR and can be radiolabeled for molecular imaging and radioimmunotherapy (RIT). This thesis aimed to develop a “theranostic” agent that could be used for both imaging and treatment of pancreatic tumours. The first study demonstrated the ability of Cu-panitumumab F(ab′)2 fragments to visualize patient-derived orthotopic pancreatic cancer xenograft mouse models with PET/CT imaging and showed the superiority of panitumumab F(abʹ)2 over IgG or Fab fragments. Next, studies were performed involving metal-chelating polymers (MCPs) to allow antibodies to carry up to 20-fold more chelation sites compared to antibodies directly derivatized with chelators for Cu-radiolabeling, thereby amplifying radiation delivered per antibody. This work demonstrated that the presence of pendant PEG chains on MCPs resulted in longer blood circulation times compared to MCPs without pendant PEG chains. The next study demonstrated that Cu-panitumumab F(ab′)2 was useful in RIT when combined with radiosensitizing agents in pancreatic cancer xenograft mouse models. Tumour regression was not achieved so the final investigation compared Cu and Lupanitumumab F(abʹ)2, which have similar β-emission energies but Lu has double the abundance of β-emissions compared to Cu. Cu-RIT and Lu-RIT were compared to external γ-irradiation to determine their relative biological effectiveness (RBE) in four pancreatic cancer cell lines, with different EGFR overexpression and proliferation rates. This work demonstrated that the degree of EGFR overexpression did not predict responsiveness of cells to RIT with Cuor Lu-RIT. Also, fast growing cells responded very well to Cu-RIT while slow growing cells responded extremely poorly, while proliferation rate did not correlate with response to Lu-
Comparative study of the clinical profile of chronic dacryocystitis and chronic rhinosinusitis after external dacryocystorhinostomy

Purpose To compare the clinical profile of patients with chronic dacryocystitis (CDC) with and without associated chronic rhinosinusopathies who had been submitted to external dacryocystorhinostomy (EDCR). Methods This was a retrospective, observational, and longitudinal study that included all patients diagnosed with CDC who were submitted to EDCR at the Antonio Pedro University Hospital. Patients were divided into two groups, with and without rhinosinusopathies (Group I and Group II, respectively). The following variables were assessed to compare the Group I and Group II: age, ethnicity, epiphora, discharge by expression of the lacrimal sac, duration of the CDC, and previous history of CDC exacerbation. Results The study included a total of 78 patients, 22 patients (28.2%) in Group I and 56 patients (71.8%) in Group II. The mean age was 64.3 (±19.7) years. In Group I and II predominated elderly, female, and White (p=0.93, p=0.38, p=0.77). In relation to the clinical characteristics, most of the patients presented epiphora and discharge by compression of the lacrimal sac in both Groups (p=0.61, p=0.44). In relation to a previous history of exacerbations of the CDC, six patients in Group I and four patients in Group II presented it as purulent discharge (p=0.04). Conclusion Chronic rhinosinusopathies may favor episodes of exacerbations of chronic dacryocystitis in particular with the presence of purulent discharge.