Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 19

Search results for: Leonard Chimaobi Agim

19 The Effects of Some Organic Amendments on Sediment Yield, Splash Loss, and Runoff of Soils of Selected Parent Materials in Southeastern Nigeria

Authors: Leonard Chimaobi Agim, Charles Arinzechukwu Igwe, Emmanuel Uzoma Onweremadu, Gabreil Osuji

Abstract:

Soil erosion has been linked to stream sedimentation, ecosystem degradation, and loss of soil nutrients. A study was conducted to evaluate the effect of some organic amendment on sediment yield, splash loss, and runoff of soils of selected parent materials in southeastern Nigeria. A total of 20 locations, five from each of four parent materials namely: Asu River Group (ARG), Bende Ameki Group (BAG), Coastal Plain Sand (CPS) and Falsebedded Sandstone (FBS) were used for the study. Collected soil samples were analyzed with standard methods for the initial soil properties. Rainfall simulation at an intensity of 190 mm hr-1was conducted for 30 minutes on the soil samples at both the initial stage and after amendment to obtain erosion parameters. The influence of parent material on sediment yield, splash loss and runoff based on rainfall simulation was tested for using one way analyses of variance, while the influence of organic material and their combinations were a factorially fitted in a randomized complete block design. The organic amendments include; goat dropping (GD), poultry dropping (PD), municipal solid waste (MSW) and their combinations (COA) applied at four rates of 0, 10, 20 and 30 t ha-1 respectively. Data were analyzed using analyses of variance suitable for a factorial experiment. Significant means were separated using LSD at 5 % probability levels. Result showed significant (p ≤ 0.05) lower values of sediment yield, splash loss and runoff following amendment. For instance, organic amendment reduced sediment yield under wet and dry runs by 12.91 % and 26.16% in Ishiagu, 40.76% and 45.67%, in Bende, 16.17% and 50% in Obinze and 22.80% and 42.35% in Umulolo respectively. Goat dropping and combination of amendment gave the best results in reducing sediment yield.

Keywords: organic amendment, parent material, rainfall simulation, soil erosion

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18 Collation between the Architecture of the Churches and Housing from Antiquity to the Present Day

Authors: Shaloom Mbambu Kabeya, Léonard Kabeya Mukeba

Abstract:

Churches, cathedrals and castles beaten from antiquity to modern times were relevant from that time to the present day, and preserved as cultural heritage. Our predecessors as François 1er1, Michelangelo2, and Giotto3 left us traces. Gustave Eiffel4, Hector Guimard5 did not decrease their time to show modernization (evolution) in architecture. Plagiarism is a brake on architectural development, construction works of spirits is necessary architecture. This work explains the relationship between ancient and modern architecture. It also shows the power of mathematics in modern architecture.

Keywords: architectural modernization, heritage, mathematical architecture, materials

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17 Top-K Shortest Distance as a Similarity Measure

Authors: Andrey Lebedev, Ilya Dmitrenok, JooYoung Lee, Leonard Johard

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Top-k shortest path routing problem is an extension of finding the shortest path in a given network. Shortest path is one of the most essential measures as it reveals the relations between two nodes in a network. However, in many real world networks, whose diameters are small, top-k shortest path is more interesting as it contains more information about the network topology. Many variations to compute top-k shortest paths have been studied. In this paper, we apply an efficient top-k shortest distance routing algorithm to the link prediction problem and test its efficacy. We compare the results with other base line and state-of-the-art methods as well as with the shortest path. Then, we also propose a top-k distance based graph matching algorithm.

Keywords: graph matching, link prediction, shortest path, similarity

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16 Thermosalient Effect of an Organic Aminonitrile and its Derivatives

Authors: Lukman O. Alimi, Vincent J. Smith, Leonard J. Barbour

Abstract:

The thermosalient effect is an extremely rare propensity of certain crystalline solids for self-actuation by elastic deformation or a ballistic event1. Thermosalient compounds, colloquially known as ‘jumping crystals’ are promising materials for fabrication of actuators that are also being considered as materials for clean energy conversion because of their capabilities to convert thermal energy into mechanical motion directly. Herein, an organic aminonitrile and its derivatives have been probed by a combination of structural, microscopic and thermoanalytical techniques. Crystals of these compounds were analysed by means of single crystal XRD and hotstage microscopy in the temperature range of 100 to 298 K and found to exhibit the thermosalient effect. We also carried out differential scanning calorimetric analysis at the temperature corresponding to that at which the crystal jumps as observed under a hotstage microscope.

Keywords: aminonitrile, jumping crystal, self actuation, thermosalient effect

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15 Implementation and Performance Analysis of Data Encryption Standard and RSA Algorithm with Image Steganography and Audio Steganography

Authors: S. C. Sharma, Ankit Gambhir, Rajeev Arya

Abstract:

In today’s era data security is an important concern and most demanding issues because it is essential for people using online banking, e-shopping, reservations etc. The two major techniques that are used for secure communication are Cryptography and Steganography. Cryptographic algorithms scramble the data so that intruder will not able to retrieve it; however steganography covers that data in some cover file so that presence of communication is hidden. This paper presents the implementation of Ron Rivest, Adi Shamir, and Leonard Adleman (RSA) Algorithm with Image and Audio Steganography and Data Encryption Standard (DES) Algorithm with Image and Audio Steganography. The coding for both the algorithms have been done using MATLAB and its observed that these techniques performed better than individual techniques. The risk of unauthorized access is alleviated up to a certain extent by using these techniques. These techniques could be used in Banks, RAW agencies etc, where highly confidential data is transferred. Finally, the comparisons of such two techniques are also given in tabular forms.

Keywords: audio steganography, data security, DES, image steganography, intruder, RSA, steganography

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14 Preliminary Seismic Hazard Mapping of Papua New Guinea

Authors: Hadi Ghasemi, Mark Leonard, Spiliopoulos Spiro, Phil Cummins, Mathew Moihoi, Felix Taranu, Eric Buri, Chris Mckee

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In this study the level of seismic hazard in terms of Peak Ground Acceleration (PGA) was calculated for return period of 475 years, using modeled seismic sources and assigned ground-motion equations. The calculations were performed for bedrock site conditions (Vs30=760 m/s). From the results it is evident that the seismic hazard reaches its maximum level (i.e. PGA≈1g for 475 yr return period) at the Huon Peninsula and southern New Britain regions. Disaggregation analysis revealed that moderate to large earthquakes occurring along the New Britain Trench mainly control the level of hazard at these locations. The open-source computer program OpenQuake developed by Global Earthquake Model foundation was used for the seismic hazard computations. It should be emphasized that the presented results are still preliminary and should not be interpreted as our final assessment of seismic hazard in PNG.

Keywords: probabilistic seismic hazard assessment, Papua New Guinea, building code, OpenQuake

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13 Implementation of Elliptic Curve Cryptography Encryption Engine on a FPGA

Authors: Mohamad Khairi Ishak

Abstract:

Conventional public key crypto systems such as RSA (Ron Rivest, Adi Shamir and Leonard Adleman), DSA (Digital Signature Algorithm), and Elgamal are no longer efficient to be implemented in the small, memory constrained devices. Elliptic Curve Cryptography (ECC), which allows smaller key length as compared to conventional public key crypto systems, has thus become a very attractive choice for many applications. This paper describes implementation of an elliptic curve cryptography (ECC) encryption engine on a FPGA. The system has been implemented in 2 different key sizes, which are 131 bits and 163 bits. Area and timing analysis are provided for both key sizes for comparison. The crypto system, which has been implemented on Altera’s EPF10K200SBC600-1, has a hardware size of 5945/9984 and 6913/9984 of logic cells for 131 bits implementation and 163 bits implementation respectively. The crypto system operates up to 43 MHz, and performs point multiplication operation in 11.3 ms for 131 bits implementation and 14.9 ms for 163 bits implementation. In terms of speed, our crypto system is about 8 times faster than the software implementation of the same system.

Keywords: elliptic curve cryptography, FPGA, key sizes, memory

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12 Optimization of Process Parameters for Peroxidase Production by Ensifer Species

Authors: Ayodeji O. Falade, Leonard V. Mabinya, Uchechukwu U. Nwodo, Anthony I. Okoh

Abstract:

Given the high utility of peroxidase in several industrial processes, the search for novel microorganisms with enhanced peroxidase production capacity is of keen interest. This study investigated the process conditions for optimum peroxidase production by Ensifer sp, new ligninolytic proteobacteria with peroxidase production potential. Also, some agricultural residues were valorized for peroxidase production under solid state fermentation. Peroxidase production was optimum at an initial medium pH 7, incubation temperature of 30 °C and agitation speed of 100 rpm using alkali lignin fermentation medium supplemented with guaiacol as the most effective inducer and ammonium sulphate as the best inorganic nitrogen. Optimum peroxidase production by Ensifer sp. was attained at 48 h with specific productivity of 12.76 ± 1.09 U mg⁻¹. Interestingly, probable laccase production was observed with optimum specific productivity of 12.76 ± 0.45 U mg⁻¹ at 72 h. The highest peroxidase yield was observed with sawdust as solid substrate under solid state fermentation. In conclusion, Ensifer sp. possesses the capacity for enhanced peroxidase production that can be exploited for various biotechnological applications.

Keywords: catalase-peroxidase, enzyme production, peroxidase, polymerase chain reaction, proteobacteria

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11 Food Security in Nigeria: An Examination of Food Availability and Accessibility in Nigeria

Authors: Okolo Chimaobi Valentine, Obidigbo Chizoba

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As a basic physiology need, the threat to sufficient food production is the threat to human survival. Food security has been an issue that has gained global concern. This paper looks at the food security in Nigeria by assessing the availability of food and accessibility of the available food. The paper employed multiple linear regression technique and graphic trends of growth rates of relevant variables to show the situation of food security in Nigeria. Results of the tests revealed that population growth rate was higher than the growth rate of food availability in Nigeria for the earlier period of the study. Commercial bank credit to the agricultural sector, foreign exchange utilization for food and the Agricultural Credit Guarantee Scheme Fund (ACGSF) contributed significantly to food availability in Nigeria. Food prices grew at a faster rate than the average income level, making it difficult to access sufficient food. It implies that prior to the year 2012; there was insufficient food to feed the Nigerian populace. However, continued credit to the food and agricultural sector will ensure sustained and sufficient production of food in Nigeria. Microfinance banks should make sufficient credit available to the smallholder farmer. The government should further control and subsidize the rising price of food to make it more accessible by the people.

Keywords: food, accessibility, availability, security

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10 Entrepreneurship as a Strategy for National Development and Attainment of Millennium Development Goals (MDGs)

Authors: Udokporo Emeka Leonard

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The thrust of this paper is to examine how entrepreneurship can assist in the attainment of the first goal among the MDGs – eradication of extreme poverty and hunger in Nigeria. The paper discusses how national development can be driven through employment creation and wealth generation that can lead to reduction in widespread poverty so as to attain one crucial target, in fewer years. The task before Nigeria is certainly a herculean one; it is, in fact a race against time. However, in view of the clear and present danger that the increasing rate of poverty portends for our democracy and our nation, is a race we must; for it is a time bomb on our hands. The paper has been structured into sections; with the introduction as section one. Section two discusses the concept of entrepreneurship; Section three examines the link between entrepreneurship and economic development, while section four examines the challenges facing entrepreneurship in Nigeria. In section five, measures and recommendations to boost entrepreneurship that can drive economic development that translates into poverty reduction and employment creation in Nigeria are suggested. This work is a literature review with some understanding of current trends and situations. It outlines some of the difficulties facing entrepreneurship in Nigeria as the operating environment, inadequate understanding and skewed incentive. It also makes recommendations on possible ways to significantly reduce poverty in 2015.

Keywords: development, entrepreneur, Nigeria, poverty

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9 Enhanced Peroxidase Production by Raoultella Species

Authors: Ayodeji O. Falade, Leonard V. Mabinya, Uchechukwu U. Nwodo, Anthony I. Okoh

Abstract:

Given the high-utility of peroxidase, its production in large amount is of utmost importance. Over the years, actinomycetes have been the major peroxidase-producing bacteria. Consequently, other classes of bacteria with peroxidase production potentials are underexplored. This study, therefore, sought to enhance peroxidase production by a Raoultella species, a new ligninolytic proteobacteria strain, by determining the optimum culture conditions (initial pH, incubation temperature and agitation speed) for peroxidase production under submerged fermentation using the classical process of one variable at a time and supplementing the fermentation medium with some lignin model and inorganic nitrogen compounds. Subsequently, the time-course assay was carried out under optimized conditions. Then, some agricultural residues were valorized for peroxidase production under solid state fermentation. Peroxidase production was optimal at initial pH 5, incubation temperature of 35 °C and agitation speed of 150 rpm with guaiacol and ammonium chloride as the best inducer and nitrogen supplement respectively. Peroxidase production by the Raoultella species was optimal at 72 h with specific productivity of 16.48 ± 0.89 U mg⁻¹. A simultaneous production of a non-peroxide dependent extracellular enzyme which suggests probable laccase production was observed with specific productivity of 13.63 ± 0.45 U mg⁻¹ while sawdust gave the best peroxidase yield under solid state fermentation. In conclusion, peroxidase production by the Raoultella species was increased by 3.40-fold.

Keywords: enzyme production, ligninolytic bacteria, peroxidase, proteobacteria

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8 Cytolethal Distending Toxins in Intestinal and Extraintestinal E. coli

Authors: Katarína Čurová, Leonard Siegfried, Radka Vargová, Marta Kmeťová, Vladimír Hrabovský

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Introduction: Cytolethal distending toxins (CDTs) represent intracellular acting proteins which interfere with cell cycle of eukaryotic cells. They are produced by Gram-negative bacteria with afinity to mucocutaneous surfaces and could play a role in the pathogenesis of various diseases. CDTs induce DNA damage probably through DNAse activity, which causes cell cycle arrest and leads to further changes (cell distension and death, apoptosis) depending on the cell type. Five subtypes of CDT (I to V) were reported in E. coli. Methods: We examined 252 E. coli strains belonging to four different groups. Of these strains, 57 were isolated from patients with diarrhea, 65 from patients with urinary tract infections (UTI), 65 from patients with sepsis and 65 from patients with other extraintestinal infections (mostly surgical wounds, decubitus ulcers and respiratory tract infections). Identification of these strains was performed by MALDI-TOF analysis and detection of genes encoding CDTs and determination of the phylogenetic group was performed by PCR. Results: In this study, we detected presence of cdt genes in 11 of 252 E. coli strains tested (4,4 %). Four cdt positive E. coli strains were confirmed in group of UTI (6,15 %), three cdt positive E. coli strains in groups of diarrhea (5,3 %) and other extraintestinal infections (4,6 %). The lowest incidence, one cdt positive E. coli strain, was observed in group of sepsis (1,5 %). All cdt positive E. coli strains belonged to phylogenetic group B2. Conclusion: CDT-producing E. coli are isolated in a low percentage from patients with intestinal and extraintestinal infections, including sepsis and our results correspond with these studies. A weak prevalence of cdt genes suggests that CDTs are not major virulence factors but in combination with other virulence factors may increase virulence potential of E. coli. We suppose that all 11 cdt positive E. coli strains represent real pathogens because they belong to the phylogenetic group B2 which is pathogenic lineage for bacteria E. coli.

Keywords: cytolethal distending toxin, E. coli, phylogenetic group, extraintestinal infection, diarrhea

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7 Perceived Effects of Alcohol Abuse on Ordinary Level Students at Gatsi Secondary School

Authors: Chimeri Muzano Leonard

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The study was carried out to investigate the perceptions of male and female Ordinary Level students on the effects of alcohol abuse at Gatsi Secondary School. The study showed that alcohol abuse has academic, social, psychological and health effects on Ordinary Level students. The negative effects comprises of death, dropping out, poor grades, poor concentration, risky behaviors, impairment of the brain and central nervous system , risky behaviors and Impairment of reproductive functioning Only students who enrolled for Ordinary Level in the 2014 academic year participated in this study. Fifty students (25 males and 25 females) were randomly selected to participate in the study. A formal survey questionnaire was used to collect data. The respondents were asked to use a scale of 0 (totally disagree) to 10 (completely agree) to indicate the extent to which they agreed with each perception. The Statistical Package for Social Sciences (SPSS) version 19.0 was used for data analysis. The Mann Whitney U test was used to test for the significance of differences in the perceptions of male and female students. No statistically significant differences were detected between males and females in most of their perceptions regarding the effects of alcohol abuse on Ordinary Level students. However, there were three perceptions found to be significantly different between male and female. They comprises of “Peers influence one to drink alcohol”, “Alcohol abuse is a major problem among male students compared to their female peers” and “ Female students should not drink beer”.It was evident from this study that Gatsi Secondary School needs to implement more effective interventions that combat alcohol abuse. A deeper analysis of the issues that predispose Ordinary Level students to alcohol abuse should inform the interventions. Consequently, unravelling the problem of negative effects of alcohol abuse was desirable because of its potential usefulness in developing strategies that might help curb the problem and presumably improve the performance of Ordinary Level students and above all the quality of education at Gatsi Secondary School.

Keywords: perceived effects, alcohol, Gatsi Secondary School, alcohol abuse

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6 Local Remedies to Hangover in Iligan City, Philippines: An Alcohol Consumer Welfare-Concerned Study

Authors: Lindsay Crystabelle A. Gillamac, Lemuel Roy Amarillo, Al Leonard Joseph B. Aca-Ac, Felipe V. Lula Jr.

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Hangover is the unpleasant psychological and physiologic effects after heavy consumption of alcoholic beverages. In awareness of the need to have a remedy for hangover occurrence in Iligan City, the authors aimed to determine the most preferred and effective local remedy to the hangover and inform people, bars and food establishments that there are available remedies to the hangover in the locality. The study utilizes qualitative data gathered through an interview on four different age groups with 50 random individuals each group as to what symptom determines they are experiencing the hangover. Then, quantitative data gathered through an online and written survey was done as to what local hangover remedy do they intake after drinking to ameliorate the most experienced symptom provided from the first assessment. After data tabulation of hangover symptoms on different age groups, we have found out that the most common determinant that you have a hangover has a headache. Thus, we queried the respondents again to what was effective the most in relieving them of a headache and their other felt symptoms depending on their varying age groups. The results of the evaluations showed that most respondents from different age groups preferred Halang-halang Soup, a spicy beef soup in the locality. As part of the hospitality industry concerned with welfare of customers, Bars in Iligan City should include on their menu these hang-over remedies in anticipation of guest needs given the fact that there are no more stores open at late hours in Iligan City. Placards should also be posted within the bar area to orient the guests about hang-over cures available inside the bar. Bartenders and other staff being directly in-contact with guests should take part in orienting guests about these aforementioned remedies. Added to that, we would like to promote Halang-halang Soup as a Health beneficial cuisine in the Philippines and help in the growth of the Tourism Industry of Iligan City by making the Halang-halang place a tourist destination.

Keywords: alcohol, alcohol consumption, alcohol hangover, anticipation of needs, bar, cure, hangover, headache, hospitality industry, local remedy, menu, menu development, menu improvement, remedy, Philippines

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5 Impact of Diabetes Mellitus Type 2 on Clinical In-Stent Restenosis in First Elective Percutaneous Coronary Intervention Patients

Authors: Leonard Simoni, Ilir Alimehmeti, Ervina Shirka, Endri Hasimi, Ndricim Kallashi, Verona Beka, Suerta Kabili, Artan Goda

Abstract:

Background: Diabetes Mellitus type 2, small vessel calibre, stented length of vessel, complex lesion morphology, and prior bypass surgery have resulted risk factors for In-Stent Restenosis (ISR). However, there are some contradictory results about body mass index (BMI) as a risk factor for ISR. Purpose: We want to identify clinical, lesional and procedural factors that can predict clinical ISR in our patients. Methods: Were enrolled 759 patients who underwent first-time elective PCI with Bare Metal Stents (BMS) from September 2011 to December 2013 in our Department of Cardiology and followed them for at least 1.5 years with a median of 862 days (2 years and 4 months). Only the patients re-admitted with ischemic heart disease underwent control coronary angiography but no routine angiographic control was performed. Patients were categorized in ISR and non-ISR groups and compared between them. Multivariate analysis - Binary Logistic Regression: Forward Conditional Method was used to identify independent predictive risk factors. P was considered statistically significant when <0.05. Results: ISR compared to non-ISR individuals had a significantly lower BMI (25.7±3.3 vs. 26.9±3.7, p=0.004), higher risk anatomy (LM + 3-vessel CAD) (23% vs. 14%, p=0.03), higher number of stents/person used (2.1±1.1 vs. 1.75±0.96, p=0.004), greater length of stents/person used (39.3±21.6 vs. 33.3±18.5, p=0.01), and a lower use of clopidogrel and ASA (together) (95% vs. 99%, p=0.012). They also had a higher, although not statistically significant, prevalence of Diabetes Mellitus (42% vs. 32%, p=0.072) and a greater number of treated vessels (1.36±0.5 vs. 1.26±0.5, p=0.08). In the multivariate analysis, Diabetes Mellitus type 2 and multiple stents used were independent predictors risk factors for In-Stent Restenosis, OR 1.66 [1.03-2.68], p=0.039, and OR 1.44 [1.16-1.78,] p=0.001, respectively. On the other side higher BMI and use of clopidogrel and ASA together resulted protective factors OR 0.88 [0.81-0.95], p=0.001 and OR 0.2 [0.06-0.72] p=0.013, respectively. Conclusion: Diabetes Mellitus and multiple stents are strong predictive risk factors, whereas the use of clopidogrel and ASA together are protective factors for clinical In-Stent Restenosis. Paradoxically High BMI is a protective factor for In-stent Restenosis, probably related to a larger diameter of vessels and consequently a larger diameter of stents implanted in these patients. Further studies are needed to clarify this finding.

Keywords: body mass index, diabetes mellitus, in-stent restenosis, percutaneous coronary intervention

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4 Implementation of an Accessible State-Wide Trauma Education Program

Authors: Christine Lassen, Elizabeth Leonard, Matthew Oliver

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The management of trauma is often complex and outcomes dependent on clinical expertise, effective teamwork, and a supported trauma system. The implementation of a statewide trauma education program should be accessible to all clinicians who manage trauma, but this can be challenging due to diverse individual needs, trauma service needs and geography. The NSW Institute of Trauma and Injury Management (ITIM) is a government funded body, responsible for coordinating and supporting the NSW Trauma System. The aim of this presentation is to describe how education initiatives have been implemented across the state. Simulation: In 2006, ITIM developed a Trauma Team Training Course - aimed to educate clinicians on the technical and non-technical skills required to manage trauma. The course is now independently coordinated by trauma services across the state at major trauma centres as well as in regional and rural hospitals. ITIM is currently in the process of re-evaluating and updating the Trauma Team Training Course to allow for the development of new resources and simulation scenarios. Trauma Education Evenings: In 2013, ITIM supported major trauma services to develop trauma education evenings which allowed the provision of free education to staff within the area health service and local area. The success of these local events expanded to regional hospitals. A total of 75 trauma education evenings have been conducted within NSW, with over 10,000 attendees. Wed-Based Resources: Recently, ITIM commenced free live streaming of the trauma education evenings which have now had over 3000 live views. The Trauma App developed in 2015 provides trauma clinicians with a centralised portal for trauma information and works on smartphones and tablets that integrate with the ITIM website. This supports pre-hospital and bedside clinical decisions and allows for trauma care to be more standardised, evidence-based, timely, and appropriate. Online e-Learning modules have been developed to assist clinicians, reduce unwarranted clinical variation and provide up to date evidence based education. The modules incorporate clinically focused education content with summative and formative assessments. Conclusion: Since 2005, ITIM has helped to facilitate the development of trauma education programs for doctors, nurses, pre-hospital and allied health clinicians. ITIM has been actively involved in more than 100 specialized trauma education programs, seminars and clinical workshops - attended by over 12,000 staff. The provision of state-wide trauma education is a challenging task requiring collaboration amongst numerous agencies working towards a common goal – to provide easily accessible trauma education.

Keywords: education, simulation, team-training, trauma

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3 Persistent Ribosomal In-Frame Mis-Translation of Stop Codons as Amino Acids in Multiple Open Reading Frames of a Human Long Non-Coding RNA

Authors: Leonard Lipovich, Pattaraporn Thepsuwan, Anton-Scott Goustin, Juan Cai, Donghong Ju, James B. Brown

Abstract:

Two-thirds of human genes do not encode any known proteins. Aside from long non-coding RNA (lncRNA) genes with recently-discovered functions, the ~40,000 non-protein-coding human genes remain poorly understood, and a role for their transcripts as de-facto unconventional messenger RNAs has not been formally excluded. Ribosome profiling (Riboseq) predicts translational potential, but without independent evidence of proteins from lncRNA open reading frames (ORFs), ribosome binding of lncRNAs does not prove translation. Previously, we mass-spectrometrically documented translation of specific lncRNAs in human K562 and GM12878 cells. We now examined lncRNA translation in human MCF7 cells, integrating strand-specific Illumina RNAseq, Riboseq, and deep mass spectrometry in biological quadruplicates performed at two core facilities (BGI, China; City of Hope, USA). We excluded known-protein matches. UCSC Genome Browser-assisted manual annotation of imperfect (tryptic-digest-peptides)-to-(lncRNA-three-frame-translations) alignments revealed three peptides hypothetically explicable by 'stop-to-nonstop' in-frame replacement of stop codons by amino acids in two ORFs of the lncRNA MMP24-AS1. To search for this phenomenon genomewide, we designed and implemented a novel pipeline, matching tryptic-digest spectra to wildcard-instead-of-stop versions of repeat-masked, six-frame, whole-genome translations. Along with singleton putative stop-to-nonstop events affecting four other lncRNAs, we identified 24 additional peptides with stop-to-nonstop in-frame substitutions from multiple positive-strand MMP24-AS1 ORFs. Only UAG and UGA, never UAA, stop codons were impacted. All MMP24-AS1-matching spectra met the same significance thresholds as high-confidence known-protein signatures. Targeted resequencing of MMP24-AS1 genomic DNA and cDNA from the same samples did not reveal any mutations, polymorphisms, or sequencing-detectable RNA editing. This unprecedented apparent gene-specific violation of the genetic code highlights the importance of matching peptides to whole-genome, not known-genes-only, ORFs in mass-spectrometry workflows, and suggests a new mechanism enhancing the combinatorial complexity of the proteome. Funding: NIH Director’s New Innovator Award 1DP2-CA196375 to LL.

Keywords: genetic code, lncRNA, long non-coding RNA, mass spectrometry, proteogenomics, ribo-seq, ribosome, RNAseq

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2 Risk and Protective Factors for the Health of Primary Care-Givers of Children with Autism Spectrum Disorders or Intellectual Disability: A Narrative Review and Discussion

Authors: Jenny Fairthorne, Yuka Mori, Helen Leonard

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Background: Primary care-givers of children with autism spectrum disorder (ASD) or intellectual disability (ID) have poorer health and quality of life (QoL) than primary care-givers (hereafter referred to as just care-givers) of typically developing children. We aimed to review original research which described factors impacting the health of care-givers of children with ASD or ID and to discuss how these factors might influence care-giver health. Methods: We searched Web of Knowledge, Medline, Scopus and Google Scholar using selections of words from each of three groups. The first comprised terms associated with ASD and ID and included autism, pervasive development disorder, intellectual disability, mental retardation, disability, disabled, Down and Asperger. The second included terms related to health such as depression, physical, mental, psychiatric, psychological and well-being. The third was terms related to care-givers such as mother, parent and care-giver. We included an original paper in our review if it was published between 1st January 1990 and 31st December, 2016, described original research in a peer-reviewed journal and was written in English. Additional criteria were that the research used a study population of 15 persons or more; described a risk or protective factor for the health of care-givers of a child with ASD, ID or a sub-type (such as ASD with ID or Down syndrome). Using previous research, we developed a simple and objective five-level tool to assess the strength of evidence provided by the reviewed papers. Results: We retained 33 papers. Factors impacting primary care-giver health included child behaviour, level of support, socio-economic status (SES) and diagnostic issues. Challenging child behaviour, the most commonly identified risk factor for poorer care-giver health and QoL was reported in ten of the studies. A higher level of support was associated with improved care-giver health and QoL. For example, substantial evidence indicated that family support reduced care-giver burden in families with a child with ASD and that family and neighbourhood support was associated with improved care-giver mental health. Higher socio-economic status (SES) was a protective factor for care-giver health and particularly maternal health. Diagnostic uncertainty and an unclear prognosis are factors which can cause the greatest concern to care-givers of children with ASD and those for whom a cause of their child’s ID has not been identified. We explain how each of these factors might impact caregiver health and how they might act differentially in care-givers of children with different types of ASD or ID (such as Down syndrome and ASD without ID). Conclusion: Care-givers of children with ASD may be more likely to experience many risk factors and less likely to experience the protective factors we identified for poorer mental health. Interventions to reduce risk factors and increase protective factors could pave the way for improved care-giver health. For example, workshops to train care-givers to better manage challenging child behaviours and earlier diagnosis of ASD (and particularly ASD without ID) would seem likely to improve care-giver well-being. Similarly, helping to expand support networks might reduce care-giver burden and stress leading to improved health.

Keywords: autism, caregivers, health, intellectual disability, mothers, review

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1 Clinical Presentation and Immune Response to Intramammary Infection of Holstein-Friesian Heifers with Isolates from Two Staphylococcus aureus Lineages

Authors: Dagmara A. Niedziela, Mark P. Murphy, Orla M. Keane, Finola C. Leonard

Abstract:

Staphylococcus aureus is the most frequent cause of clinical and subclinical bovine mastitis in Ireland. Mastitis caused by S. aureus is often chronic and tends to recur after antibiotic treatment. This may be due to several virulence factors, including attributes that enable the bacterium to internalize into bovine mammary epithelial cells, where it may evade antibiotic treatment, or evade the host immune response. Four bovine-adapted lineages (CC71, CC97, CC151 and ST136) were identified among a collection of Irish S. aureus mastitis isolates. Genotypic variation of mastitis-causing strains may contribute to different presentations of the disease, including differences in milk somatic cell count (SCC), the main method of mastitis detection. The objective of this study was to investigate the influence of bacterial strain and lineage on host immune response, by employing cell culture methods in vitro as well as an in vivo infection model. Twelve bovine adapted S. aureus strains were examined for internalization into bovine mammary epithelial cells (bMEC) and their ability to induce an immune response from bMEC (using qPCR and ELISA). In vitro studies found differences in a variety of virulence traits between the lineages. Strains from lineages CC97 and CC71 internalized more efficiently into bovine mammary epithelial cells (bMEC) than CC151 and ST136. CC97 strains also induced immune genes in bMEC more strongly than strains from the other 3 lineages. One strain each of CC151 and CC97 that differed in their ability to cause an immune response in bMEC were selected on the basis of the above in vitro experiments. Fourteen first-lactation Holstein-Friesian cows were purchased from 2 farms on the basis of low SCC (less than 50 000 cells/ml) and infection free status. Seven cows were infected with 1.73 x 102 c.f.u. of the CC97 strain (Group 1) and another seven with 5.83 x 102 c.f.u. of the CC151 strain (Group 2). The contralateral quarter of each cow was inoculated with PBS (vehicle). Clinical signs of infection (temperature, milk and udder appearance, milk yield) were monitored for 30 days. Blood and milk samples were taken to determine bacterial counts in milk, SCC, white blood cell populations and cytokines. Differences in disease presentation in vivo between groups were observed, with two animals from Group 2 developing clinical mastitis and requiring antibiotic treatment, while one animal from Group 1 did not develop an infection for the duration of the study. Fever (temperature > 39.5⁰C) was observed in 3 animals from Group 2 and in none from Group 1. Significant differences in SCC and bacterial load between groups were observed in the initial stages of infection (week 1). Data is also being collected on cytokines and chemokines secreted during the course of infection. The results of this study suggest that a strain from lineage CC151 may cause more severe clinical mastitis, while a strain from lineage CC97 may cause mild, subclinical mastitis. Diversity between strains of S. aureus may therefore influence the clinical presentation of mastitis, which in turn may influence disease detection and treatment needs.

Keywords: Bovine mastitis, host immune response, host-pathogen interactions, Staphylococcus aureus

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