Search results for: arithmetic coding

Authors: Batul Kagalwala

Abstract:

The nervous system is made up of complex delicate structures such as the spinal cord, peripheral nerves and the brain. These are prone to various types of injury ranging from neurodegenerative diseases to trauma leading to diseases like Parkinson's, Alzheimer's, multiple sclerosis, amyotrophic lateral sclerosis (ALS), multiple system atrophy etc. Unfortunately, because of the complicated structure of nervous system, spontaneous regeneration, repair and healing is seldom seen due to which brain damage, peripheral nerve damage and paralysis from spinal cord injury are often permanent and incapacitating. Hence, innovative and standardized approach is required for advance treatment of neurological injury. Nigella sativa (N. sativa), an annual flowering plant native to regions of southern Europe and Asia; has been suggested to have neuroprotective and anti-seizures properties. Neuroregeneration is found to occur in damaged cells when treated using extract of N. sativa. Due to its proven health benefits, lots of experiments are being conducted to extract all the benefits from the plant. The flowers are delicate and are usually pale blue and white in color with small black seeds. These seeds are the source of active components such as 30–40% fixed oils, 0.5–1.5% essential oils, pharmacologically active components containing thymoquinone (TQ), ditimoquinone (DTQ) and nigellin. In traditional medicine, this herb was identified to have healing properties and was extensively used Middle East and Far East for treating diseases such as head ache, back pain, asthma, infections, dysentery, hypertension, obesity and gastrointestinal problems. Literature studies have confirmed the extract of N. sativa seeds and TQ have inhibitory effects on inducible nitric oxide synthase and production of nitric oxide as well as anti-inflammatory and anticancer activities. Experimental investigation will be conducted to understand which ingredient of N. sativa causes neuroregeneration and roots to its healing property. An aqueous/ alcoholic extract of N. sativa will be made. Seed oil is also found to have used by researchers to prepare such extracts. For the alcoholic extracts, the seeds need to be powdered and soaked in alcohol for a period of time and the alcohol must be evaporated using rotary evaporator. For aqueous extracts, the powder must be dissolved in distilled water to obtain a pure extract. The mobile phase will be the extract while the suitable stationary phase (substance that is a good adsorbent e.g. silica gels, alumina, cellulose etc.) will be selected. Different ingredients of N. sativa will be separated using High Performance Liquid Chromatography (HPLC) for treating damaged cells. Damaged brain cells will be treated individually and in different combinations of 2 or 3 compounds for different intervals of time. The most suitable compound or a combination of compounds for the regeneration of cells will be determined using DOE methodology. Later the gene will also be determined and using Polymerase Chain Reaction (PCR) it will be replicated in a plasmid vector. This plasmid vector shall be inserted in the brain of the organism used and replicated within. The gene insertion can also be done by the gene gun method. The gene in question can be coated on a micro bullet of tungsten and bombarded in the area of interest and gene replication and coding shall be studied. Investigation on whether the gene replicates in the organism or not will be examined.

Keywords: black cumin, brain cells, damage, extract, neuroregeneration, PCR, plasmids, vectors

Procedia PDF Downloads 646

Authors: Katarzyna Lubecka, Kirsty Flower, Megan Beetch, Lucinda Kurzava, Hannah Buvala, Samer Gawrieh, Suthat Liangpunsakul, Tracy Gonzalez, George McCabe, Naga Chalasani, James M. Flanagan, Barbara Stefanska

Abstract:

Hepatocellular carcinoma (HCC), the most prevalent type of primary liver cancer, is the second leading cause of cancer death worldwide. Late onset of clinical symptoms in HCC results in late diagnosis and poor disease outcome. Approximately 85% of individuals with HCC have underlying liver cirrhosis. However, not all cirrhotic patients develop cancer. Reliable early detection biomarkers that can distinguish cirrhotic patients who will develop cancer from those who will not are urgently needed and could increase the cure rate from 5% to 80%. We used Illumina-450K microarray to test whether blood DNA, an easily accessible source of DNA, bear site-specific changes in DNA methylation in response to HCC before diagnosis with conventional tools (pre-diagnostic). Top 11 differentially methylated sites were selected for validation by pyrosequencing. The diagnostic potential of the 11 pyrosequenced probes was tested in blood samples from a prospective cohort of cirrhotic patients. We identified 971 differentially methylated CpG sites in pre-diagnostic HCC cases as compared with healthy controls (P < 0.05, paired Wilcoxon test, ICC ≥ 0.5). Nearly 76% of differentially methylated CpG sites showed lower levels of methylation in cases vs. controls (P = 2.973E-11, Wilcoxon test). Classification of the CpG sites according to their location relative to CpG islands and transcription start site revealed that those hypomethylated loci are located in regulatory regions important for gene transcription such as CpG island shores, promoters, and 5’UTR at higher frequency than hypermethylated sites. Among 735 CpG sites hypomethylated in cases vs. controls, 482 sites were assigned to gene coding regions whereas 236 hypermethylated sites corresponded to 160 genes. Bioinformatics analysis using GO, KEGG and DAVID knowledgebase indicate that differentially methylated CpG sites are located in genes associated with functions that are essential for gene transcription, cell adhesion, cell migration, and regulation of signal transduction pathways. Taking into account the magnitude of the difference, statistical significance, location, and consistency across the majority of matched pairs case-control, we selected 11 CpG loci corresponding to 10 genes for further validation by pyrosequencing. We established that methylation of CpG sites within 5 out of those 10 genes distinguish cirrhotic patients who subsequently developed HCC from those who stayed cancer free (cirrhotic controls), demonstrating potential as biomarkers of early detection in populations at risk. The best predictive value was detected for CpGs located within BARD1 (AUC=0.70, asymptotic significance ˂0.01). Using an additive logistic regression model, we further showed that 9 CpG loci within those 5 genes, that were covered in pyrosequenced probes, constitute a panel with high diagnostic accuracy (AUC=0.887; 95% CI:0.80-0.98). The panel was able to distinguish pre-diagnostic cases from cirrhotic controls free of cancer with 88% sensitivity at 70% specificity. Using blood as a minimally invasive material and pyrosequencing as a straightforward quantitative method, the established biomarker panel has high potential to be developed into a routine clinical test after validation in larger cohorts. This study was supported by Showalter Trust, American Cancer Society (IRG#14-190-56), and Purdue Center for Cancer Research (P30 CA023168) granted to BS.

Keywords: biomarker, DNA methylation, early detection, hepatocellular carcinoma

Procedia PDF Downloads 289

Authors: Norma Kok, Diemo Masuko, Thandokazi Dlongwana, Komala Pillay

Abstract:

CONTEXT: While many school principals have been outstanding teachers and have inherent leadership potential, many have not had access to the quality of leadership development or support that empowers them to produce high-quality education outcomes in extremely challenging circumstances. Further, school leaders in under-served communities face formidable challenges arising from insufficient infrastructure, overcrowded classrooms, socio-economic challenges within the community, and insufficient parental involvement, all of which put a strain on principals’ ability to lead their schools effectively. In addition few school leaders have access to other supportive networks, and many do not know how to build and leverage social capital to create opportunities for their schools and learners. Moreover, we know that fostering parental involvement in their children’s learning improves a child’s morale, attitude, and academic achievement across all subject areas, and promotes better behaviour and social adjustment. Citizen Leader Lab facilitates the Partners for Possibility (PfP) programme to provide leadership development and support to school leaders serving under-resourced communities in South Africa to create effective environments of learning. This is done by creating partnerships between school leaders and private-sector business leaders over a 12-month period. (185) OBJECTIVES: To explore school leaders’ perceptions of their leadership capacities and changes at their schools after being exposed to a year-long leadership development training programme. METHODS: School leaders gained new leadership capacities e.g. resilience, improved confidence, communication and conflict resolution skills - catalysing into improved cultures of collaborative decision-making and environments for enhanced teaching and learningprogramme based on the 70:20:10 model whereby: 10% of learning comes from workshops, 20% of learning takes place through peer learning and 70% of learning occurs through experiential learning as partnerships work together to identify and tackle challenges in targeted schools. Participants completed a post-programme questionnaire consisting of structured and unstructured questions and semi-structured interviews were conducted with them and their business leader. The interviews were audio-recorded, transcribed and thematic content analysis was undertaken. The analysis was inductive and emerging themes were identified. A code list was generated after coding was undertaken using computer software (Dedoose). Quantitative data gathered from surveys was aggregated and analysed. RESULTS: School leadership found the programme interesting and rewarding. They gained new leadership capacities such as resilience, improved confidence, communication and conflict resolution skills - catalyzing into improved cultures of collaborative decision-making and environments for enhanced teaching and learning. New networks resulted in tangible outcomes such as upgrades to school infrastructure, water and sanitation, vegetable gardens at schools resulting in nutrition for learners and/or intangible outcomes such as skills for members of school management teams (SMTs). Collaborative leadership led to SMTs being more aligned, efficient, and cohesive; and teachers being more engaged and motivated. Notable positive changes at the school inspired parents and community members to become more actively involved in the school and in their children’s education. CONCLUSION: The PfP programme leads to improved leadership capacities and improved school culture which leads to improved teaching and learning and new resources for schools.

Keywords: collaborative decision-making, collaborative leadership, community involvement, confidence

Procedia PDF Downloads 75

Authors: Kalaumari Mayoral-Peña, Ana I. Montejano-Montelongo, Josué Reyes-Muñoz, Gonzalo A. Ortiz-Mancilla, Mayrin Rodríguez-Cruz, Víctor Hernández-Villalobos, Jesús A. Guzmán-López, Santiago García-Jacobo, Iván Licona-Vázquez, Grisel Fierros-Romero, Rosario Flores-Vallejo

Abstract:

The group B-lactamic antibiotics include some of the most frequently used small drug molecules against bacterial infections. Nevertheless, an alarming decrease in their efficacy has been reported due to the emergence of antibiotic-resistant bacteria. Infections caused by bacteria expressing extended Spectrum B-lactamases (ESBLs) are difficult to treat and account for higher morbidity and mortality rates, delayed recovery, and high economic burden. According to the Global Report on Antimicrobial Resistance Surveillance, it is estimated that mortality due to resistant bacteria will ascend to 10 million cases per year worldwide. These facts highlight the importance of developing low-cost and readily accessible detection methods of drug-resistant ESBLs bacteria to prevent their spread and promote accurate and fast diagnosis. Bacterial detection is commonly done using molecular diagnostic techniques, where PCR stands out for its high performance. However, this technique requires specialized equipment not available everywhere, is time-consuming, and has a high cost. Loop-Mediated Isothermal Amplification (LAMP) is an alternative technique that works at a constant temperature, significantly decreasing the equipment cost. It yields double-stranded DNA of several lengths with repetitions of the target DNA sequence as a product. Although positive and negative results from LAMP can be discriminated by colorimetry, fluorescence, and turbidity, there is still a large room for improvement in the point-of-care implementation. DNA origami is a technique that allows the formation of 3D nanometric structures by folding a large single-stranded DNA (scaffold) into a determined shape with the help of short DNA sequences (staples), which hybridize with the scaffold. This research aimed to generate DNA origami structures using LAMP products as scaffolds to improve the sensitivity to detect ESBLs in point-of-care diagnosis. For this study, the coding sequence of the CTM-X-15 ESBL of E. coli was used to generate the LAMP products. The set of LAMP primers were designed using PrimerExplorerV5. As a result, a target sequence of 200 nucleotides from CTM-X-15 ESBL was obtained. Afterward, eight different DNA origami structures were designed using the target sequence in the SDCadnano and analyzed with CanDo to evaluate the stability of the 3D structures. The designs were constructed minimizing the total number of staples to reduce costs and complexity for point-of-care applications. After analyzing the DNA origami designs, two structures were selected. The first one was a zig-zag flat structure, while the second one was a wall-like shape. Given the sequence repetitions in the scaffold sequence, both were able to be assembled with only 6 different staples each one, ranging between 18 to 80 nucleotides. Simulations of both structures were performed using scaffolds of different sizes yielding stable structures in all the cases. The generation of the LAMP products were tested by colorimetry and electrophoresis. The formation of the DNA structures was analyzed using electrophoresis and colorimetry. The modeling of novel detection methods through bioinformatics tools allows reliable control and prediction of results. To our knowledge, this is the first study that uses LAMP products and DNA-origami in combination to delect ESBL-producing bacterial strains, which represent a promising methodology for diagnosis in the point-of-care.

Keywords: beta-lactamases, antibiotic resistance, DNA origami, isothermal amplification, LAMP technique, molecular diagnosis

Procedia PDF Downloads 205

Authors: Yimer Mohammed Assen, Abiyot Legesse Kura, Engida Esyas Dube, Asebe Regassa Debelo, Girma Kelboro Mensuro, Lete Bekele Gure

Abstract:

Climate change has posed severe threats to many cultural landscapes of UNESCO world heritage sites recently. The UNESCO State of Conservation (SOC) reports categorized flooding, temperature increment, and drought as threats to cultural landscapes. This study aimed to examine variations and trends of rainfall and temperature extreme events and their threats to the UNESCO-designated Konso Cultural Landscape in southern Ethiopia. The study used dense merged satellite-gauge station rainfall data (1981-2020) with spatial resolution of 4km by 4km and observed maximum and minimum temperature data (1987-2020). Qualitative data were also gathered from cultural leaders, local administrators, and religious leaders using structured interview checklists. The spatial patterns, coefficient of variation, standardized anomalies, trends, and magnitude of change of rainfall and temperature extreme events both at annual and seasonal levels were computed using the Mann-Kendall trend test and Sen’s slope estimator under the CDT package. The standard precipitation index (SPI) was also used to calculate drought severity, frequency, and trend maps. The data gathered from key informant interviews and focus group discussions were coded and analyzed thematically to complement statistical findings. Thematic areas that explain the impacts of extreme events on the cultural landscape were chosen for coding. The thematic analysis was conducted using Nvivo software. The findings revealed that rainfall was highly variable and unpredictable, resulting in extreme drought and flood. There were significant (P<0.05) increasing trends of heavy rainfall (R10mm and R20mm) and the total amount of rain on wet days (PRCPTOT), which might have resulted in flooding. The study also confirmed that absolute temperature extreme indices (TXx, TXn, and TNx) and the percentile-based temperature extreme indices (TX90p, TN90p, TX10p, and TN10P) showed significant (P<0.05) increasing trends which are signals for warming of the study area. The results revealed that the frequency as well as the severity of drought at 3-months (katana/hageya seasons) was more pronounced than the 12-months (annual) time scale. The highest number of droughts in 100 years is projected at a 3-months timescale across the study area. The findings also showed that frequent drought has led to loss of grasses which are used for making traditional individual houses and multipurpose communal houses (pafta), food insecurity, migration, loss of biodiversity, and commodification of stones from terrace. On the other hand, the increasing trends of rainfall extreme indices resulted in destruction of terraces, soil erosion, loss of life and damage of properties. The study shows that a persistent decline in farmland productivity, due to erratic and extreme rainfall and frequent drought occurrences, forced the local people to participate in non-farm activities and retreat from daily preservation and management of their landscape. Overall, the increasing rainfall and temperature extremes coupled with prevalence of drought are thought to have an impact on the sustainability of cultural landscape through disrupting the ecosystem services and livelihood of the community. Therefore, more localized adaptation and mitigation strategies to the changing climate are needed to maintain the sustainability of Konso cultural landscapes as a global cultural treasure and to strengthen the resilience of smallholder farmers.

Keywords: adaptation, cultural landscape, drought, extremes indices

Procedia PDF Downloads 13