Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigation of the Role of MERISTEM-DEFECTIVE (MDF) in Arabidopsis thaliana Root Development

Due to their sessile nature, plants have evolved to employ a sophisticated network of genetic and hormonal signalling pathways in order to modulate their development and responses to changing environmental conditions. Understanding these mechanisms is an important objective for plant developmental biologists and crop breeders, especially in the context of food security and climate change. Plant roots present an important target for trait optimisation due to their essential role in water and nutrient uptake from the soil. This thesis focuses on the regulatory role of splicing in root growth and development. Splicing is one of the processes involved in the generation of mature RNA, and is catalysed by a macromolecular complex known as the spliceosome. Many different components are involved in this process, potentially including the putative splicing factor gene MERISTEM-DEFECTIVE (MDF), which has been found to have a role in the organisation and maintenance of root meristems. Using Arabidopsis thaliana, this gene was investigated in order to further understand the underlying molecular mechanisms of root formation. To investigate the potential function of this putative splicing factor in the catalytic activation of the spliceosome, a yeast two-hybrid screen was conducted to explore protein-protein interactions between MDF and orthologs of human and yeast proteins known to interact with their MDF counterparts. No positive interactions were identified however, potentially due to the nature of the experimental setup. Indirect MDF-dependent regulation of root meristem-related genes was also briefly addressed. Downstream targets of MDF were examined through investigation of splicing-related genes differentially expressed and mis-spliced in mdf mutants, with a potential link identified between one of these genes, SR34, and root-specific stress responses.
Protein Molecular Motif Comparison Studies on Lung and Colon Cancer Genes (CHRNA3 and MLH1) using In-silico Protocols

INTRODUCTION Worldwide, lung cancer is the most common cancer among men in terms of both incidence and mortality, and among women has the third highest incidence, and is second after breast cancer in mortality. In 2012, there were 1.82 million new cases globally, and 1.56 million deaths due to lung cancer, representing 19.4% of all deaths from cancer. The highest rates are in North America, Europe and East Asia, with over a third of new cases in 2012 in China. Rates in Africa and South Asia are much lower [1]. The population segment most likely to develop lung cancer is people aged over 50 who have a history of smoking. In contrast to the mortality rate in men, which began declining more than 20 years ago, women's lung cancer mortality rates have been rising over the last decades, and are just recently beginning to stabilize [2]. In the USA, the lifetime risk of developing lung cancer is 8% in men and 6% in women [3]. Globally more than 1 million people get colorectal cancer every year [4] resulting in about 715,000 deaths as of 2010 up from 490,000 in 1990 [5]. As of 2012 it is the second most common cause of cancer in women (9.2% of diagnoses) and the third most common in men (10.0%) with it being the fourth most common cause of cancer death after lung, stomach, and liver cancer. Colorectal cancer was 10% of cancers in men and 9.2% of cancers in women. It is more common in developed than developing countries [6]. Globally incidences vary 10-fold with highest rates in the Australia, New Zealand, Europe and the US and lowest rates in Africa and South-Central Asia [7].
AN IMPROVED DISCRETIZATION METHOD FOR BOUNDED CONVECTIVE SCHEMES ON UNSTRUCTURED CO-LOCATED GRIDS

In comparison to structured grids, a more refined discretisation of convective transport on unstructured grids is required to account for their complex topologies. In particular, and with reference to the given cell–face, the far upwind node is not readily available on unstructured grids. Also, the solution accuracy can be affected by numerical diffusion caused by skewness of the grid. In this paper, a novel method is introduced for the far upwind node reconstruction in the framework of the cell–centred finite–volume discretisation. The main idea is to form an upwind–biased stencil with a local axis that connects the central cell node and the geometric cell–face centre. Note that central and downwind cells share the given cell–face. Instead of the actual downwind node, its projection onto the local axis is used. In the previous methods, the local axis has been defined along the line connecting the central and downwind nodes. These methods can not mitigate the grid skewness error whereas by its definition the new method bypasses the issue of grid skewness. The present method is applied to several test cases, covering transport of a scalar step-profile, laminar vortex shedding from a circular cylinder and turbulent flows in two engine intake ports. Depending on the test–case, the high resolution convective schemes such as MINMOD, the modified SMART and bounded central differencing scheme are employed. The latter is selected for large eddy simulations of one of engine ports. The preceding schemes are formulated for non–uniform grids, and they obey the well known convective boundedness criteria. The used grid types also varied, including triangular, polyhedral and Cartesian cut–cell shapes. The convergence properties and accuracy of the new method are scrutinised against the previous one. For all cases, the bounded numerical solution is ensured, and the improved convergence rate of the new method is noted. The accuracy of results predicted by both methods is established through comparisons with either analytical or experimental and numerical results from literature.
Stability of BDF-ADI Discretizations

We present new results on absolute stability for BDF-ADI (Backward differentiation formula Alternating Direction Implicit) methods applied to a linear advection and diffusion equations. Unconditional absolute stability of the BDF2-ADI method is proven for advection and diffusion separately, as well as to the BDF3-ADI method for the purely-diffusive case. Conditional absolute stability of the BDF4-ADI is also proven for the purely-diffusive case, and stability regions for BDF3-ADI and BDF4ADI are given in terms of the PDE coefficients and numerical parameters. Lastly, numerical experiments are presented to support the theoretical results and conjectures. These experiments also suggest future work.
Universal Loop assembly (uLoop): open, efficient, and species-agnostic DNA fabrication

Standardised Type IIS DNA assembly methods are becoming essential for biological engineering and research. Although a ‘common syntax’ has been proposed to enable higher interoperability between DNA libraries, Golden Gate (GG)-based assembly systems remain specific to target organisms. Furthermore, these GG assembly systems become laborious and unnecessarily complicated beyond the assembly of 4 transcriptional units. Here, we describe “universal Loop” (uLoop) assembly, a simple system based on Loop assembly that enables hierarchical fabrication of large DNA constructs (> 30 kb) for any organism of choice. uLoop comprises two sets of four plasmids that are iteratively used as odd and even levels to compile DNA elements in an exponential manner (4n-1). The elements required for transformation/maintenance in target organisms are also assembled as standardised parts, enabling customisation of host-specific plasmids. Thus, this species-agnostic method decouples efficiency of assembly from the stability of vectors in the target organism. As a proof-of-concept, we show the engineering of multi-gene expression vectors in diatoms, yeast, plants and bacteria. These resources will become available through the OpenMTA for unrestricted sharing and open-access.
Survey and Relative Occurrence of Rodent Species at Kafr El-Sheikh Governorate

The present investigation was carried out for determination rodent species surveillance and their relative occurrence at three sites i.e. (animal production research station, poultry farm and farmers' houses) at Kafr El-Sheikh district, Kafr El-Sheikh Governorate during 2015 and 2016 years. Surveyed rodent species were Norway rat, Rattus norvegicus, white bellied rat, Rattus rattus frugivorus and house mouse Mus musculus. Average numbers of trap indices were 0.27 and 0.21 during 1 and 2 years, respectively. The highest values of trap indices were 0.40 and 0.39 during August in 2015 and 2016, respectively. The total number of rodent species recorded through animal production research station during two successive years 2015 and 2016 were 136 and 65 individuals, respectively. The total number of rodent species in the poultry farm were 77 and 93 individuals, respectively. On the other hand, in the farmers' houses the total numbers were 109 and 95 individuals, in 2015 and 2016 respectively. Norway rat, R. norvegicus was the most dominant species in these location. In animal production station, the maximum numbers of rodent species are (19) individuals in August 2015 and (9) individuals in March and August 2016. The highest total number of rodents in poultry farm was recorded in May 2015 with (10) individuals and in August 2016 with (18) individuals. In farmers’ houses, the lowest numbers were recorded during winter months in January and February 2015 while January was the lowest in 2016, since no rats were caught during it.
Controlling signal-to-noise ratio effects in the measurement of speech intelligibility in fluctuating maskers

The measurement of speech intelligibility in noise is often complicated by floor and ceiling effects. Because of this, adaptive methods are often used to determine the signal-to-noise ratio (SNR) required for a fixed performance level. Unfortunately, such methods relinquish control of the test SNR, confounding data interpretation when the effect of interest is SNRdependent. For example, the intelligibility improvement afforded by glimpsing the target speech during brief dips in the level of a fluctuating masker is highly SNR-dependent. Thus, comparisons of performance in stationary and fluctuating maskers are susceptible to SNR confounds. Various methods of controlling SNR differences in the measurement of speech intelligibility are discussed, including the development and validation of a standardized intelligibility testing procedure that uses a variable response set size to control SNR differences. The application of these techniques to studies of hearing loss or simulated hearing loss demonstrate that impaired listeners may retain the ability to listen in the dips of a fluctuating masker to a much greater extent than previously thought.
Chromosomal characterization of the bonytongue Arapaima gigas (Osteoglossiformes: Arapaimidae)

The mitotic chromosomes of the pirarucu Arapaima gigas inhabiting the middle Araguaia River and collected in the municipality of Araguaiana (MT, Brazil) were studied. The chromosomes were analyzed through Giemsa staining, C-banding, Ag-NOR staining and in situ hybridization using an 18S rRNA gene probe. The karyotype had 2n=56 comprising 14 biarmed and 14 uniarmed chromosome pairs in both sexes. No cytologically distinguishable sex chromosome was identified. A single NOR-bearing chromosome pair was detected by Ag-NOR staining and confirmed by 18S rDNA- FISH. Faint constitutive heterochromatin was C-banded in the centromeric region of some chromosomes.
Introgression of ‘Ogura’ cytoplasm in cabbage alters its nutritional quality and antioxidant activities

Ogura-based cytoplasmic male sterility (CMS) system is widely used for hybrid seed production in Brassica vegetables. The adverse effects associated with the introgression of Ogura cytoplasm on nutritional quality of cabbage are still unknown. Therefore, the effect of Ogura cytoplasm introgression on different quality traits in 17 lines of cabbage (Brassica oleracea var. capitata L.) was investigated. Experimental results revealed that introgression of Ogura cytoplasm altered different quality traits significantly. In general, the concentration of different nutritional compounds increased 3–5 times in some lines, while a 4–5-fold reduction was noticed in others. However, a drastic elevation in the concentration of cupric ion reducing antioxidant capacity (CUPRAC) and ferric reducing ability of plasma (FRAP) was observed in the CMS lines RRMA (29 times) and 5A (78 times), respectively. On the other hand, the amount of CUPRAC, anthocyanin and lycopene reduced severely in the CMS lines 9A (27 times), 1A (44 times) and CH2A (16 times), respectively. This alteration in different quality traits might be attributed to compatible / incompatible nucleo-cytoplasmic and mitochondrial gene interactions associated with the introgression of alien cytoplasm. Therefore, best performing CMS lines, viz. RRMA, RJA, PMA, 208A and 5A, with increased concentration of different nutritional compounds may be utilized in future breeding programs for quality improvement in cabbage. The positive correlations obtained between different quality traits offer the chances for selection of the genotypes with superior multiple quality traits. Further, outcomes of principal component analysis (PCA) and cluster analysis will aid in selection of suitable parental lines for quality F1 hybrid development in cabbage.
ESTIMATION AND COMPARISON OF ANOPHELES MACULIPENNIS S.L. (DIPTERA: CULICIDAE) SURVIVAL RATES WITH LIGHT-TRAP AND INDOOR RESTING DATA

main vector of malaria in Europe and Palearctic region is Anopheles maculipennis complex. In order to determine the survival rate of An. maculipennis s.l. this study was carried out in Garaboteh (Zanjan province, Iran) in July 2003. In this study anophelines were sampled for 31 consecutive days from five fixed animal shelters and five light traps. Out of 24481 collected An. maculipennis s.l. , 19703 (80.48%) were female. Relative density of female anopheline with 95% CI was 74.25-78.48 and 49.16-52.36 in light traps (LT) and pyrethrum space spray catch (PSC), respectively. A significant differ- ence was in mean parous rate in LT (0.46) and PSC (0.50) samples (P 0.92) between parous and total females. Also there was significant correlation between nulliparous females and males in LT (r=0.96) and PSC (r=0.87) samples and with increasing anopheline abundance ratio of male/nulliparous significantly decreased (r=-0.35, P<0.05). Due to simplicity and feasibility of using graphical and para- metric method, it can be placed in entomological surveys for monitoring parity, age structure and survival rate of vector anopheline in the world.
An innovative ecological hybrid refrigeration cycle for high power refrigeration facility

Searching for new refrigerants is one of the most significant scientific problems in refrigeration. There are ecological refrigerants commonly known: H2O and CO2. H2O and CO2 known as natural refrigerants, but they have problems:a high freezing point of H2O and a low triple point of CO2. These problems can be solved by the application of a hybrid sorption-compression refrigeration cycle. The cycle combines the application possibility of H2O in the high temperature sorption stage and the low temperature application of CO2 in the compression stage. This solution gives significant energy savings in comparison with the two-stage compressor cycle and with the one-stage transcritical CO2 cycle. Besides, the sorption cycle may be powered by low temperature waste heat or renewable heat. This is an original idea of the authors. In the paper an analysis of the possible extension of this solution for high capacity industrial refrigeration is presented. The estimated energy savings as well as TEWI (Total Equivalent Warming Impact) index for ecological gains are calculated.
A Qualitative Exploration of Infection Prevention and Control Guidance for Australian Paramedics

Introduction The paramedic work setting in Australia presents challenges for applying recommended infection prevention and control (IPC) practices. Our study had two aims: to describe the guidance provided across a range of documents used by Australian ambulance services; and to explore the views of health experts regarding the adequacy of guidance on IPC practices for Australian paramedics. Methods Content analysis was used to evaluate the degree of alignment between IPC operating procedures from four state ambulance services and the IPC guidelines issued by the National Health and Medical Research Council (NHMRC) in 2010. Semi-structured interviews were conducted to explore perspectives of 14 experts about IPC practices among paramedics and IPC guidance provided to them. Results While the ambulance operating procedures aligned well with the NHMRC IPC guidelines, we identified differences in the nature of advice provided that could lead to differing practices by paramedics across Australia. Experts identified several domains of IPC practices by paramedics that would benefit from closer scrutiny and/or more specific guidance, including hand and environmental hygiene, governance and surveillance, environmental challenges, vehicle design, cultural barriers and communication with state health regulators. Conclusion Our study has further highlighted unique challenges faced by paramedics in adhering to recommended IPC practices while providing healthcare in the mobile primary emergency environment. Two recommendations arise from our research. First, there is a need to adapt the current national risk-based framework for IPC in Australia to paramedicine. Second, that targeted research into staff compliance is required to identify the key barriers and enablers to the uptake of IPC practices in paramedicine.
Taylor rules for monetary policy in a closed economy

This paper studies monetary stabilization policies in a DSGE model with Calvo type nominal …xities and imperfect competition. We model Monetary policy to follow alternative Taylor-type rules. We …nd that the monetary authority can guarantee the joint stabilization of in‡ation and output through the baseline Taylor rule (Taylor 1993) with strong enough reaction to in‡ation and no reaction to the output gap. Moreover, we …nd that the joint stabilization of in‡ation and output requires neither the estimation of unobservable variables nor the optimal choice of reaction coe¢ cients. Given that reaction coe¢ cients always guarantee Blanchard-Kahn conditions a good monetary policy can be implemented through an operational Taylor type rule which responds to observed targets already known with certainty at the time of monetary policy action.
PRODUCTION OF TURKISH DELIGHT WITH POMEGRANATE AND EFFECT OF VACUUM PACKING ON SHELF LIFE

Usage possibilities of pomegranate in Turkish delight industry were investigated in this study. Different variety Turkish delights were produced and Hicaz pomegranate was used as fruit. Sultan Turkish delight with Hicaz pomegranate among the Turkish delights was the most suitable for production. Therefore, Sultan Turkish delight with Hicaz pomegranate was produced and analyzed. Fruits in product were damaged and It was difficult to shape to the product when ratio of fruits in product increased. Usage of pomegranate seeds in the range of 17-19% was optimum for Sultan delight production. Sultan Turkish delights with Hicaz pomegranate were packed in vacuum and non-vacuum packaging. They were be stored 6 months and the product characteristics were be analyzed by physical, chemical and sensorial techniques. Products packaged with vacuum were damaged in the second month during storage time. In these products, dry matter, ash, sucrose, invert sugar, acidity (as citric acid), pH in the first day and second month 86.39-85.54%, 0.29-0.28%, 81.98-79.48%, 51.45-52.65%, 1.74-1.92%, 4.79-4.24 respectively. Dry matter, ash, sucrose, invert sugar, acidity (as citric acid), pH of products packaged with non-vacuum ranged from 86.42-94.65%, 0.29-0.30%, 77.60-82.01%, 51.47-52.86%, 1.74-2.18%, 3.39-4.83 respectively.
Investigating dual Ca2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation

The ryanodine receptors (RyR) are essential to calcium signaling in striated muscles. A deep understanding of the complex Ca2+-activation/inhibition mechanism of RyRs requires detailed structural and dynamic information for RyRs in different functional states (e.g., with Ca2+ bound to activating or inhibitory sites). Recently, high-resolution structures of the RyR isoform 1 (RyR1) were solved by cryo-electron microscopy, revealing the location of a Ca2+ binding site for activation. Toward elucidating the Ca2+-modulation mechanism of RyR1, we performed extensive molecular dynamics simulation of the core RyR1 structure in the presence and absence of bound and solvent Ca2+ (total simulation time is > 5 microseconds). In the presence of solvent Ca2+, Ca2+ binding to the activating site enhanced dynamics of RyR1 with higher inter-subunit flexibility, asymmetric inter-subunit motions, outward domain motions and partial pore dilation, which may prime RyR1 for subsequent channel opening. In contrast, the solvent Ca2+ alone reduced dynamics of RyR1 and led to inward domain motions and pore contraction, which may cause inhibition. Combining our simulation with the map of disease mutation sites in RyR1, we constructed a wiring diagram of key domains coupled via specific hydrogen bonds involving the mutation sites, some of which were modulated by Ca2+ binding. The rich structural and dynamic information gained from this study will guide future mutational and functional studies of RyR1 activation and inhibition by Ca2+. Statement of Significance The ryanodine receptors (RyR) are key players in calcium signaling, and make prominent targets for drug design owning to their association with many diseases of cardiac and skeletal muscles. However, the molecular mechanism of their activation and inhibition by Ca2+ remains elusive for the lack of high-resolution structural and dynamic information. Recent solutions of RyR1 structures by cryo-EM have paved the way for structure-based investigation of this important receptor by atomistic molecular simulation. This study presented, to our knowledge, the most extensive MD simulation of RyR1 core structure. Our simulation has offered new insights to the dual modulation mechanism of Ca2+, in which Ca2+ binding to the activating site primes RyR1 activation by elevating its dynamics while solvent Ca2+ inhibits RyR1 by reducing its dynamics. Additionally, our simulation has yielded a new wiring diagram of the allosterically coupled RyR1 domains informed by disease mutations.
APPLICATION OF FLOW CYTOMETRY FOR ESTIMATION OF NUCLEAR DNA CONTENT IN

A method was established and proposed to be the standard protocol for estimating the genome size of oil palm [Elaeis guineensis and its intraspecific hybrids, E. oleifera and oleifera x guineensis (O x G) interspecific hybrids]. The method used is laser-sourced flow cytometry. Oil palm Frond -1 leaflets, LBO1 lysis buffer and Glycine max cv. Polanka (as external standard) were used for the DNA content estimation. The 2C DNA contents of E. guineensis for the different fruit types were: dura (D) = 4.10 ± 0.20, pisifera (P) = 3.64 ± 0.28 and tenera (DxP) = 3.83 ± 0.31 pg. A simple average gave the DNA content for E. guineensis as 3.86