Miracle-dz/UniFAR-FTUs huggingface dataset:
Physiological Responses of Plant Growth Promoting Rhizobacteria, Biochar and Chemical Fertilizer Under Salinity Stress

This research work is conducted to evaluate the physiological responses of phosphate solubilizing rhizobacteria (Pseudomonas sp.), biochar and N-fertilizer under salt stress. Biochar and fertilizer are mixed in soil (5:1) while Pseudomonas sp. is applied as seed soaking at 106 cells/ml prior to seed sowing. Salt stress with 150mM NaCl is applied for three days (3d) at three (3) leaf stage. The obtained results depicted significant effect of Pseudomonas sp. on root fresh weight and leaf area both under unstressed and salt stress conditions followed by biochar. Treatment with biochar and Pseudomonas sp. resulted in increased root fresh weight, leaf area, chlorophyll fluorescence and decreased osmotic potential by 60% particularly under salt stress. On the contrary, fertilizer treatment is found to be ineffective on seed germination (results not presented here), however increased chlorophyll content by 77%. Under salt stress, fertilizer treatment increased the osmotic potential of leaves. The combined treatments of fertilizer with Pseudomonas and biochar significantly increased root fresh weight, chlorophyll content and leaf area under salt stress. It is inferred that combined application of biochar and Pseudomonas can augment the effects of N-fertilizer on plants.
Esterase 2 as a fluorescent biosensor for the detection of organophosphorus compounds: docking and electronic insights from molecular dynamics

ABSTRACT Organophosphorus compounds (OP) are mainly used in agriculture as pesticides. Unfortunately, each year many rural workers are intoxicated by these compounds and, many times, the diagnosis of the exact molecule causing the intoxication can be tardy, exposing the patients to a huge risk of death. One way of preventing this delay is the use of enzymatic biosensors like the enzyme Esterase 2 from Alicyclobacillus acidocaldarius (AaEST2), which is an efficient fluorescent biosensor for OP identification. However, although this enzyme has been well studied experimentally, the complete understanding of the energy transfer processes that occur between AaEST2 and OPs is still obscure, making it difficult the accurate identification of the OP. In order to better understand this process, we applied in this work molecular docking and molecular dynamics studies, together with the Förster fluorescence resonance energy transfer (FRET) theory, to achieve a better understanding of the fluorescence profiles that are described in the literature and correlate them to individual OPs. Our results suggest that the pesticides chlorpyrifos, diazinon, parathion and paraoxon are all capable of quenching the residue Trp85 from AaEST2, triggering fluorescence. This supports our hypothesis that AaEST2 can be used as a fluorescent biosensor for the detection of organophosphorus compounds.
Surface chemistry, rheology and microstructure of as-received SHCa-1 hectorite gels

Abstract The zeta potential and yield-stress behaviour of gels prepared from as-received SHCa-1 hectorite (Ht) containing 50 wt. % impurities, mainly of calcite, dolomite and quartz, were characterized. The zeta potential is negative in the pH range 4–12. At pH <5, reaction of CaCO3 producing CO2 and Ca2+ increased the solution conductivity significantly and reduced the zeta potential. The buffering effect due to this chemical reaction was also observed in the yield stress–pH characterization below pH 8. Low yield stress was observed below pH 6 and above pH 12. The yield stress peaked at pH ~8, where Ht displayed a zeta potential of –20 mV. The relationship between maximum yield stress and Ht content (wt.%) was linear and was not affected by impurities. The ageing behaviour was characterized by an initial phase of rapid yield-stress increase and then by a phase of gradual increase. The Leong model performed better than the two-parameter glassy polymer ageing model in describing this ageing behaviour. However, the empirical power law model was more accurate. The timescale of the ageing process is long, lasting several days. An open cellular microstructure was observed to form in the gels. Impurities appeared not to interact with or bind to the Ht platelets.
Competition between the purine and pyrimidine triple helix motifs in an oligonucleotide system

Triple helices are classified into two groups according to the composition and orientation of the third strand, namely the pyrimidine motif and the purine motif. These motifs constitute tWQ separate fields of research. It was proposed, based on the alternative design rules, that the two motifs can in fact lead to competing structures. An oligonucleotide system has been designed to demonstrate this competition. Systematic variation of it's components gIVe insight into the requirements for optimal binding of a third strand. A palindromic, homopyrimidine oligonucleotide of 22 bases was designed to form an overlapping 9-base, Watson-Crick (WC), duplex with a partly complementary 22-base purine-rich oligonucleotide. This leaves two free 3' extensions under conditions when only the duplex is stable. If the conditions, however, favour triplex formation the pyrimidine tail can compete with the purine-rich tail as third strand for the duplex forming Hoogsteen or reverse-Hoogsteen hydrogen bonding respectively with the purines in the WC double strand. The underlying triplexes and core duplex were synthesised and characterised as controls. The technique of UV-melting was used to establish phase diagrams (Tm vs pH) to characterise the boundary conditions under which each construct is stable. The effect of pH, counterions, sequence composition and mutations (local base exchange) were evaluated from a comparison of the melting temperatures and the behaviour of the I phase boundaries. The technique of gel-retardation electrophoresis was used to distinguish the duplex from the control purine triplex. This thesis shows that the purine and pyrimidine motifs can compete for the same purine strand of the core double helix and can be converted into each other by just change in pH in the presence of magnesium ions. By systematically replacing thymine with adenine within the reverse-Hoogsteen strand a linear increase in the stability (Tm) of the purine motif is observed. The following trend arises for the increase in stability of the purine motif, listing the most to least preferred triads: A-AT> T-AT = I-AT> C-AT where C is considered a mismatch. These results allow one to specify the rules required for a rational approach to the design of oligonucleotide third strands.
PERFORMANCE EVALUATION OF MLP AND RBF CLASSIFIERS FOR HANDWRITTEN CHARACTER RECOGNITION USING HYBRID FEATURES

For evaluating the accuracy and capability of MLP (Multi Layer Perceptron) and RBF (Radial Basis Function) classifier algorithms; projection profile features for the character images are extracted and are merged with the binarization features after pre-processing every character image, and the combined features thus obtained are used to train both the classifiers (MLP and RBF Network) selected for performing character recognition task. Simulation studies are examined extensively and the proposed hybrid features are found to deliver the recognition accuracy of 93.46% when used with RBF Network as a classifier which is better than the 88.76% accuracy obtained when used with MLP Network as a classifier.
Mechanistic study of the formation of ring-retaining and ring-opening products from the oxidation of aromatic compounds under urban atmospheric conditions.

Aromatic hydrocarbons make up a large fraction of anthropogenic volatile organic compounds and contribute significantly to the production of tropospheric ozone and secondary organic aerosol (SOA). Four toluene and four 1,2,4-trimethylbenzene (1,2,4-TMB) photooxidation experiments were performed in an environmental chamber under relevant polluted conditions (NO x ~ 10ppb). An extensive suite of instrumentation including two proton-transfer-reaction mass spectrometers (PTR-MS) and two chemical ionisation mass spectrometers ( NH 4 + CIMS and I- CIMS) allowed for quantification of reactive carbon in multiple generations of hydroxyl radical (OH)-initiated oxidation. Oxidation of both species produces ring-retaining products such as cresols, benzaldehydes, and bicyclic intermediate compounds, as well as ring-scission products such as epoxides and dicarbonyls. We show that the oxidation of bicyclic intermediate products leads to the formation of compounds with high oxygen content (an O : C ratio of up to 1.1). These compounds, previously identified as highly oxygenated molecules (HOMs), are produced by more than one pathway with differing numbers of reaction steps with OH, including both auto-oxidation and phenolic pathways. We report the elemental composition of these compounds formed under relevant urban high-NO conditions. We show that ring-retaining products for these two precursors are more diverse and abundant than predicted by current mechanisms. We present the speciated elemental composition of SOA for both precursors and confirm that highly oxygenated products make up a significant fraction of SOA. Ring-scission products are also detected in both the gas and particle phases, and their yields and speciation generally agree with the kinetic model prediction.
Traditional vegetable salad (ulam) of Borneo as source of functional food

1, Awang-Kanak, F. and 1, 3, *Abu Bakar, M.F. Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (UTHM), Hub Pendidikan Tinggi Pagoh, KM1, Jalan Panchor, 84600, Muar, Johor, Malaysia Preparatory Centre for Science and Technology, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia Center of Research for Sustainable Uses of Natural Resources, Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (UTHM), Hub Pendidikan Tinggi Pagoh, KM1, Jalan Panchor, 84600, Muar, Johor, Malaysia
Simplified in-house kit formulation of 99mTc-TRODAT-1 with high radiolabeling efficiency for routine clinical use. Westmead Hospital Experience

Objective: The tropane derivative, TRODAT-1 when labelled with 99mTc has been shown to bind dopamine transporter (DAT) with high affinity and selectivity. In this study, we have modified the in-house formulation of TRODAT-1 cold kit. We investigated if the labeling procedure could be improved by using a block heater and thus be more efficient and consistent than using autoclaving or boiling water-bath methods described elsewhere. Methods: Briefly, 1mg of TRODAT-1 was dissolved in 100µl of ethanolic-HCl. To this solution 500µg SnCl2, 160mg sodium glucoheptonate, 19mg EDTA were added and mixed. The bulk solution containing TRODAT-1 was aseptically dispensed in 1.0mL aliquots and stored at -80°C. TRODAT-1 was radiolabelled by adding 1.4GBq of 99mTc-pertechneate in 3ml saline and heated for 30min at 100oC using a block heater enclosed with a lid. The radiochemical purity (RCP) was analysed using Instant Thin Layer Chromatography-Silica Gel (ITLC-SG) with 0.9% Sodium Chloride as the solvent and High Performance Liquid Chromatography (HPLC) was performed using 0.1% Trifluoroacetic acid (TFA) / Water (H2O) & Acetonitrile (ACN). As proof of concept, biodistribution of 99mTc-TRODAT-1 was studied in a rabbit model. Animals were injected with 30MBq of 99mTc-TRODAT-1 and images were acquired at 60 min post-injection with a Single-photon emission computed tomography (SPECT), Siemens Symbia camera. Results: Previous studies have used autoclaving method or a boiling water bath for radiolabeling TRODAT-1 with 99mTc. These methods have some limitation including the evaporating of water during boiling, uncontrollable temperatures, variable yield and increased possibility of contamination. To ensure consistent temperature and eliminate the possibility of contamination we used a block heater. The percentage of RCP of 99mTc-TRODAT-1 by ITLC-SG was >99% and reproducible. The retention time by HPLC for labeled product was 16.18min and for free 99mTc was 2.5min. Animal biodistribution studies showed brain hippocampus uptake of 0.32±0.08 %ID/g at 60min post-injection. Conclusions: This study describes a simple formulation and method of preparation for 99mTc-TRODAT-1, which is reproducible with radiochemical purity (RCP >99%). The pre-clinical results in rabbits indicated specific binding to dopamine receptors and therefore has the potential for use in DAT imaging in patients.
OOCFA2: a PDA-based higher-order flow analysis for object-oriented programs

values in-use. Something else to notice in the performance data is that memory usage and run time do not necessarily correlate with the breadth of paths explored (as seen in Table 1c). Indeed, even though the MATSim tests featured far less breadth in paths explored than with DaCapo, they ran for longer and used more memory. Of course, this shouldn’t be very surprising considering that all sorts of other factors could influence the performance far more than mere path-breadth: number of starting points (as discussed above); path-depth; complex manipulation of large, trackable state; etc. In this case, it is actually a factor of MATSim having more starting points and, moreover, doing much more array manipulation with trackable concrete values.
A 1.57-GHz fully integrated very low-phase-noise quadrature VCO

A very low-phase-noise quadrature voltage-controlled oscillator is presented, featuring an inherently better figure of merit than existing architectures. Through an improved circuit schematic and a special layout technique, the phase noise of the circuit can be lowered. The circuit draws 15 mA from a 2-V supply. The phase noise is -133.5 dBc/Hz at 600 kHz and the tuning range is 24% wide at a center frequency of 1.57 GHz.
Mechanical metamaterial with negative Poisson’s ratio based on circular honeycomb core

Mechanical metamaterials are artificial structures with mechanical properties defined by their structure rather than their composition. As a new type of metamaterials with unique mechanical properties and promising prospects, mechanical metamaterials have attracted great attention and become a new hot spot in the field of metamaterials. Mechanical metamaterials with negative Poisson’s ratio can exhibit novel mechanical properties such as excellent resistance capability of bending deformation and indentation. This type of materials have good prospects in many applications such as variant flexible wing skin. In this article, we adopt the design method of mechanical metamaterials to improve the structure of traditional honeycomb core and propose a new type of circular honeycomb core unit to obtain negative Poisson’s ratio. The advantage of circular honeycomb core is that this new structure is more stable than traditional concave hexagon honeycomb core. We established the corresponding mechanical model of this structure and adopted energy method to study the dependencies of structure parameters for its effective elastic modulus. The bending strain energy was taken into consideration while the tension and shear strain energy were ignored because they are very small compared with the bending strain energy. Then the expressions of effective elastic modulus in the directions of X and Y axis can be established in the condition of small deformation. In order to verify the validity of theoretical results, finite-element simulation method was employed to our study and we adopted periodic structure as the finite-element simulation model and aluminium alloy as the base material. The results of theory and the simulation have good agreements, and we found that its effective elastic modulus E x is mainly depending on its height h and thickness t while E y is mainly depending on its radius r and thickness t . And the thickness t may bring about deviation between theory and the simulation when it increases. The Poisson’s ratio of this material was also investigated through finite-element simulation method and different values of structure parameters were selected. Among these structure parameters, when h =35 mm, r ³ 21 mm and h =40 mm, r ³ 24 mm or h =45 mm, r ³ 26 mm, negative Poisson’s ratio can be obtained. The results indicate that the composite structure based on circular honeycomb core units can achieve negative Poisson’s ratio, which can be controlled by structure parameters. The excellent mechanical performance of light-weight and its negative Poisson’s ratio make circular honeycomb core a promising candidate as engineering material. And our study may pave a useful path to mechanical metamaterials with negative Poisson’s ratio.
3D MODELLING AND RAPID PROTOTYPING FOR CARDIOVASCULAR SURGICAL PLANNING – TWO CASE STUDIES

Abstract. In the last years, cardiovascular diagnosis, surgical planning and intervention have taken advantages from 3D modelling and rapid prototyping techniques. The starting data for the whole process is represented by medical imagery, in particular, but not exclusively, computed tomography (CT) or multi-slice CT (MCT) and magnetic resonance imaging (MRI). On the medical imagery, regions of interest, i.e. heart chambers, valves, aorta, coronary vessels, etc., are segmented and converted into 3D models, which can be finally converted in physical replicas through 3D printing procedure. In this work, an overview on modern approaches for automatic and semiautomatic segmentation of medical imagery for 3D surface model generation is provided. The issue of accuracy check of surface models is also addressed, together with the critical aspects of converting digital models into physical replicas through 3D printing techniques. A patient-specific 3D modelling and printing procedure (Figure 1), for surgical planning in case of complex heart diseases was developed. The procedure was applied to two case studies, for which MCT scans of the chest are available. In the article, a detailed description on the implemented patient-specific modelling procedure is provided, along with a general discussion on the potentiality and future developments of personalized 3D modelling and printing for surgical planning and surgeons practice.
In vitro cytotoxic and in vivo anxiolytic study of methanolic crude extract of Streculia villosa seeds

We have aimed to evaluate the in vitro cytotoxic and in vivo anxiolytic and sedative activities of the methanolic extract of Sterculia villosa roxb seeds. The dried powder of the seeds was extracted with methanol which was then tested to ascertain the neuropharmacological and cytotoxic potentials. The methanolic extract of Sterculia villosa roxb were subjected to Brine Shrimp lethality bioassay for possible cytotoxicity having LC 50 of 8. 672μg/ml. However, fractions produced concentration dependent increase in percent of mortality of Brine Shrimp nauplii indicates the presence of cytotoxic property. We also have studied for possible sedative and anxiolytic activity of the methanolic seed extract of Sterculia villosa roxb in mice. This study includes hole cross, open field, thiopental- sodium induced sleeping time and elevated-plus maze (EPM) tests at the dose of 200 mg/kg while on the peripheral and central nervous system the extract mild to moderately decreased the locomotor activity of mice in hole cross, open field and EPM test. However, the extract moderately has minimized the onset of sleep and slightly has maximized the duration of sleep while administered with thiopental sodium.
Preliminary Study of Ancient DNA from a 215-year-old Grapevine Herbarium

Simón de Rojas Clemente y Rubio (1777 to 1827) is considered the father of modern ampelography. He developed the first scientific method for describing grapevine varieties through the examination of material he collected in Andalusia between 1802 and 1804. The Royal Botanical Garden in Madrid conserves the material he collected and preserved (leaves and shoots). This herbarium, the oldest of all grapevine variety herbaria, is invaluable for ampelographic and other studies (such as genetic diversity, molecular characterization, or viticultural history studies) and provides unique insight into early 19th century (the pre-phylloxera era) grapevine cultivation. The present work reports a DNA extraction protocol and a redefining of the simple sequence repeat primers routinely used in grapevine characterization, which allowed successful amplification of the ancient DNA extracted from Clemente’s herborized material.
Computation and analysis of atmospheric carbon dioxide annual mean growth rates from satellite observations during 2003–2016

Abstract. The growth rate of atmospheric carbon dioxide (CO2) reflects the net effect of emissions and uptake resulting from anthropogenic and natural carbon sources and sinks. Annual mean CO2 growth rates have been determined from satellite retrievals of column-averaged dry-air mole fractions of CO2, i.e. XCO2, for the years 2003 to 2016. The XCO2 growth rates agree with National Oceanic and Atmospheric Administration (NOAA) growth rates from CO2 surface observations within the uncertainty of the satellite-derived growth rates (mean difference ± standard deviation: 0.0±0.3 ppm year−1; R: 0.82). This new and independent data set confirms record-large growth rates of around 3 ppm year−1 in 2015 and 2016, which are attributed to the 2015–2016 El Niño. Based on a comparison of the satellite-derived growth rates with human CO2 emissions from fossil fuel combustion and with El Niño Southern Oscillation (ENSO) indices, we estimate by how much the impact of ENSO dominates the impact of fossil-fuel-burning-related emissions in explaining the variance of the atmospheric CO2 growth rate. Our analysis shows that the ENSO impact on CO2 growth rate variations dominates that of human emissions throughout the period 2003–2016 but in particular during the period 2010–2016 due to strong La Niña and El Niño events. Using the derived growth rates and their uncertainties, we estimate the probability that the impact of ENSO on the variability is larger than the impact of human emissions to be 63 % for the time period 2003–2016. If the time period is restricted to 2010–2016, this probability increases to 94 %.
Exploring nanofibrous self-assembling peptide hydrogels using mouse myoblast cells for three-dimensional bioprinting and tissue engineering applications

Abstract Injured skeletal muscles which lose more than 20% of their volume, known as volumetric muscle loss, can no longer regenerate cells through self-healing. The traditional solution for recovery is through regenerative therapy. As the technology of three-dimensional (3D) bioprinting continues to advance, a new approach for tissue transplantation is using biocompatible materials arranged in 3D scaffolds for muscle repair. Ultrashort self-assembling peptide hydrogels compete as a potential biomaterial for muscle tissue formation due to their biocompatibility. In this study, two sequences of ultrashort peptides were analyzed with muscle myoblast cells (C2C12) for cell viability, cell proliferation, and differentiation in 3D cell culture. The peptides were then extruded through a custom-designed robotic 3D bioprinter to create cell-laden 3D structures. These constructs were also analyzed for cell viability through live/dead assay. Results showed that 3D bioprinted structures of peptide hydrogels could be used as tissue platforms for myotube formation – a process necessary for muscle repair.