Miracle-dz/UniFAR-FTUs huggingface dataset:
SAPH‐ire TFx: A Machine Learning Recommendation Model and Webtool for the Prediction of Functional Post‐Translational Modifications

Post‐translational Modifications (PTMs), chemical or proteinaceous covalent alterations to the side chains of amino acid residues in proteins, are a rapidly expanding feature class of significant importance in cell biology. Due to a high burden of experimental proof and the lack of effective means for experimentalists to prioritize PTMs by functional significance, currently less than ~2% of all PTMs have an assigned biological function. Here, we describe a new artificial neural network model, SAPH‐ire TFx for the functional prediction of experimentally observed eukaryotic PTMs. Unlike previous functional PTM prioritization models, SAPH‐ire TFx is trained to emphasize metrics that maximally capture the range of diverse feature sets comprising the functional modified eukaryotic proteome. The model of was generated through systematic evaluation of input features, model architectures, training procedures, and interpretation metrics using a 2018 training dataset of 430,750 PTMs containing 7,480 PTMs with literature‐supported evidence of biological function. The resulting model was used to classify an expanded 2019 dataset of 512,015 PTMs (12,867 known functional) containing 102,475 PTMs unencountered in the original dataset. Model output from the 2019 extended dataset was benchmarked against pre‐existing prediction models, revealing superior performance in classification of functional and/or disease‐linked PTM sites, including drawing attention to PTMs that were previously thought inconsequential. Finally, a dynamic web interface provides customizable graphical and tabular visualization of PTM and SAPH‐ire TFx data within the context of all modifications within a protein family, exposing several metrics by which important functional PTMs can be identified for investigation.
Long-term changes in temperature around Australia

Coarse long-term temperature data around Australia from 1870 and fine-scale temperature measurements from the three long-term stations since the 1940s confirm a strong warming trend over the past 100 years, with the strongest warming in the Southeast and the Southwest. This background warming signal is propagating throughout the ecosystem, impacting the physical, chemical and biological characteristics of Australia’s marine environment. 1 CSIRO Oceans and Atmosphere, Queensland Biosciences Precinct (QBP), St Lucia, QLD, Australia 2 Centre for Applications in Natural Resource Mathematics (CARM), School of Mathematics and Physics, The University of Queensland, St Lucia, QLD, Australia 3 Oceans Graduate School, The University of Western Australia, Perth, WA, Australia 4 UWA Oceans Institute, The University of Western Australia, Perth, WA, Australia State and Trends of Australia’s Oceans Report
The Impact of Wood Fuel Energy on Economic Growth in Sub-Saharan Africa: Dynamic Macro-Panel Approach

This study estimates the impact of wood fuel consumption on economic growth in 19 sub-Saharan African countries over the 1979-2017 period. The study employs dynamic macro-panel estimators, which comprises pooled mean group (PMG), mean group (MG), and dynamic fixed effects (DFE). The estimated result reveals that PMG is the most efficient estimator among the three estimators based on the Hausman h-test. The results from PMG model reveal that wood fuel consumption has significant negative impact on economic growth. Also, when an interaction term between labor and wood fuel consumption was included in the model and estimated, the coefficient of wood fuel consumption yields negative and significant coefficient. This suggests that the interaction term has a negative and significant effect on economic growth. These results unveil that wood fuel consumption negatively and significantly affect economic growth, both directly and indirectly. The policy recommendations from this study are as follows: (1) Governments of these countries should provide adequate and affordable modern fuels to the populace; especially rural dwellers to decrease the use of wood fuel for cooking and heating (2) policy makers should intensify awareness campaign on the risk and danger wood fuel poses to economic growth so as to discourage its use and (3) policy makers should provide adequate solar powered stoves and solar-powered room heaters as cheap substitutes to the use of wood fuel for cooking and heating. These recommendations will assist in negating the negative effects of wood fuel consumption on economic growth of the region.
Influence of host (Alnus and Myrica) genotype on infectivity, N2 fixation, spore formation and hydrogenase activity in Frankia.

Nine species of Alnus, two of them represented by several provenances, and Myrica gale were inoculated with a 'local source' of Frankia. The inoculum is an effective (N2 -fixing), spore-Forming type of Frankia that lacks H, uptake (hydrogenase) activity in symbiosis with A. incana. Despite their wide geographical origin (Europe, China, North America) and their various taxonomie grouping within the genus, all Alnus species/provenances formed Infixing nodules. In all studied nodules Frankia had the phenotype Spore+ . None of the studied symbioses had hydrogenase activity. The Frankia inoculum was infective also on M. gale, and gave effective nodules without hydrogenase activity. Unlike some other spore-forming types of symbiotic Frankia, all studied symbiotic phenotypes of the 'local source' of Frankia were thus stable characters not influenced by the various host genotypes included in the study.
Triple Band Reject Frequency Selective Surface with Application to 2.4 GHz Band

— This paper presents the development of a frequency selective surface, FSS, with three bands of rejection, with the central bandwidth applied to the 2.4 GHz frequency band. Despite the fact that the main applications are in the 2.4 GHz frequency band, as emphasized in this paper, to reduce costs with scale production, it is interesting to note when the same FSS can be used for different applications such as wireless and cellular communications (1.71 GHz-1.93 GHz) and radio frequency localization (3.1 GHz-3.3GHz). The three rejection bands are obtained from the association of crossed- dipoles and matryoshka ring geometries. For each geometry the initial design equations are proposed. The procedure to obtain the matryoshka geometry is described step by step. Numerical results are presented for each geometry, and also to the associated geometries, considering different incident angles ( θ =0°, 15°, 30° and 45°). The current distribution of each resonant frequency was shown, making it possible to visualize the respective excited geometry. After the numerical results, we verified that the resonant frequencies associated to the respective geometry remained practically unchanged even for the associated geometries. A FSS prototype with the associated geometries was designed, fabricated, and characterized, with a very good agreement between numerical and experimental results, obtaining an attenuation of at least 15 dB in the 2.4 GHz frequency band.
At a crossroads? Offender rehabilitation in Australian prisons

This article presents a commentary on the current status of offender rehabilitation in Australian prisons. Prompted by recent debates concerning the value of rehabilitation programs in reducing rates of re-imprisonment, it considers the current evidence to support the effectiveness of Australian correctional programs highlighting the importance of the prison social climate, the intensity and quality of treatment and the need for psychological treatment to be integrated within broader models of rehabilitation and reintegration.
PCA likelihood ratio test approach for attributed social networks monitoring

Abstract One of the most important factors in building and changing communication mechanisms in social networks is considering features of the members of social networks. Most of the existing methods in network monitoring don’t consider effects of features in network formation mechanisms and others don’t lead to reliable results when the features abound or when there are correlations among them. In this article, we combined two methods principal component analysis (PCA) and likelihood method to monitor the underlying network model when the features of individuals abound and when some of them have high correlations with each other.
Series active power filter supplied by fuel cell for mitigating power quality issues

In this paper, the combination of the series active power filter (SAPF) with a fuel cell (FC) source is deliberated. The FC based on the SAPF aims to compensate voltage deviations or disturbances that occur in the system caused by power quality issues. The proposed system consists of a fuel cell source connected to the DC l ink through two DC-DC converters, the first extracts the maximum power of the FC source through pulse width modulation (PWM) signals generated from the maximum power point tracker (MPPT) controller. Thus, the second converter is used to regulate the high voltage side of the converter through closed control loops, in addition to a voltage source inverter (VSI) and a series injection transformer. Despite of fluctuations of the DC link during the compensation of the needed energy, MPPT and closed control loops generate PWM signals to the switching devices of DC-DC boost converters in order to extract maximum fuel cell power and to maintain the bus voltage within its limits and around its reference values respectively. The proposed topology is simulated in MATLAB/Simulink software, where simulation results show that the proposed FC based SAPF can efficiently reduce problems of voltage sags-wells and harmonics.
Automation of NA Marker Measurements

Quality and productivity of Nucleic Acid (NA) based marker measurement by means of the polymerase chain reaction (PCR) is significantly improved with a higher degree of automation. The application of new instruments and innovative system concepts allows PCR to be established as a truly routine NA marker measuring tool in the diagnostic laboratory. The COBAS AmpliPrep instrument (Roche Diagnostics) automates the entire specimen preparation process of nucleic acid isolation either based on probe capture technology or on extraction method with glass particles. The compatibility of this front end workstation with various back end PCR systems like the COBAS AMPLICOR analyzer, LightCycler instrument and COBAS TaqMan instrument (all of them Roche Diagnostics) offers flexibility for various assays to be performed in the molecular diagnostic laboratory. In addition, the combination with COBAS TaqMan 96 analyzer and in particular, the connection of both those instruments with the docking station (Roche Diagnostics) represents the first fully automated PCR system with a continuous workflow from the sample input to result without any manual operator interaction. COBAS, AMPLICOR, AMPLILINK, AmpliPrep, TaqMan, and LightCycler are trademarks of a member of the Roche Group
Exploring sustainable healthcare waste management implementation in teaching hospitals in Malaysia

There are growing expectations for healthcare organizations to take active steps and introduce sustainable approaches to healthcare waste management (HCWM). This study investigated sustainable healthcare waste management (SHCWM) in two university teaching hospitals in Malaysia. The objectives of the study were to identify current practices and SHCWM initiatives as well as examine the t raining and knowledge of hospital staff on sustainable healthcare waste management . Following a questionnaire survey of 243 senior hospital staff, the study found that sustainable healthcare waste management initiatives were being implemented in the healthcare facilities (HCFs) surveyed. Descriptive statistics using frequency distributions and mean rank analysis were used to analyze data from the 243 respondents. The findings revealed that proper segregation and sorting, purchasing supplies that generate less hazardous waste, education/awareness about material reuse and recycling, purchasing environmentally friendly products, and encouraging material reuse and recycling through reward were the five initiatives perceived to be most implemented at the HCFs. The study also found that majority of the respondents received training and were highly knowledgeable about the health and environmental risks of HCW as well as SHCWM aspects such as waste minimization. The findings from this study provide an overview of SHCWM in particularly large teaching hospitals in Malaysia and suggests further research for a more comprehensive and wider understanding of SHCWM in HCFs in Malaysia.
Inhibitor susceptibility of the cyanide-resistant pathway in Candida albicans

The cytochrome chain which is sensitive to cyanide is the main electron transport pathway in respiration of eukaryotic organisms. However, an alternative , cyanideresistant respiratory pathway has been known to appear prevalently in a number of higher plants and eukaryotic microorganisms under certain physiological circumstances1,2)although a new hypothesis, based on a cycling of fatty acids and free fatty acid peroxy radicals, was recently proposed for the cyanide-resistant pathway in plant mitochondria3,4). The occurrence of the cyanide-resistant oxygen uptake phenomenon in the pathogenic fungus Candida albicans has been documented in several reports5-10). We reported previously that an alternative, cyanideresistant pathway was induced in yeast-form cells of C. albicans upon aging treatment and that although aged cells possessed two respiratory pathways, the cyanide-resistant one operated fully when the cytochrome one was blocked9,10). To reveal further differences in the inhibitor susceptibility of both pathways, effects of some respiratory inhibitors on oxygen uptake of C. albicans cells were examined before and after aging treatment in this study.
Characterization of Selected Jackfruit Germplasm Accessions for Fruit Shape Through Morphological and Marker Based Assay

The study involved characterization of Jackfruit accessions with obloid (round) versus ellipsoid fruit shape. The morphological characterization was based on tree, fruit and seed descriptors. The Jackfruit accessions exhibited wide range of differences. The dominant tree growth habit was erect type, with medium to low branching density and branching pattern was irregular in most of the trees. With respect to fruit rind weight, it was more than fifty to sixty per cent in accessions with obloid fruit, than ellipsoid fruits. The rind weight ranged from thirty to forty per cent of the total fruit weight. Based on fruit and flake quality characters, the accessions such as Allilugatta 5, Kumaraswamy, Manipur Parmesh and Swarna in obloid fruits and Ashoka Red, Ashoka Yellow, Byrachandra, Janagere and NSP in ellipsoid fruits have been identified for commercial purpose. Among ten RAPD primers screened, two primers showed higher PIC value (0.24) viz., OPA 4 and OPAH 4. Similarly among ten ISSR markers screened, ISSR - 868 (0.31) showed higher PIC value. These can be used effectively to probe the genetic variations among the Jackfruit accessions.
Retention of Surgically Implanted Ultrasonic Transmitters in the Brown Bullhead Catfish

Abstract Our objective was to compare the ability of brown bullheads Ameiurus nebulosus to tolerate the implantation of ultrasonic transmitters with different coatings. A total of 14 brown bullheads were surgically implanted with ultrasonic transmitters; 7 transmitters were coated with paraffin wax and 7 with Scotchcast, an inert epoxy resin. Six brown bullheads were held as controls with no surgical procedures. Fish were held for 75 d in a flow-through, gravity-filtered series of tanks and monitored for transmitter expulsion, growth (i.e., percent relative weight change), condition (i.e., relative weight), and mortality. All fish with paraffin-coated implants retained their transmitters for the duration of the experiment, whereas two fish with Scotchcast implants expelled their transmitters within 50 d. All fish in the experiment survived, and the implanted fish exhibited growth and condition similar to those of the controls. On the basis of these results, we conclude that brown bullheads tolerate implan.
Evaluating Collapse Fragility Curves for Existing Buildings Retrofitted Using Seismic Isolation

Few studies have investigated so far the collapse capacity of buildings with base-isolation. In such studies, preliminary considerations have been drawn based on a number of assumptions regarding: (i) the methodology used for assessing the collapse capacity, (ii) the collapse conditions and failure modes assumed for both superstructure and isolation system, and (iii) the numerical modeling assumptions. The main results pointed out that the collapse conditions of base-isolated buildings may occur for intensity levels slightly higher than those associated with the design earthquake. In this paper, further developments are made through the use of enhanced models for the description of the behavior of a rubber-based isolation system and the assumption of more rational collapse conditions. Collapse fragility functions, in terms of mean and dispersion values, are proposed for two archetypes representative of existing buildings retrofitted using the seismic isolation technique. The collapse margin ratio (median collapse capacity Sa,C, namely the spectral acceleration associated to a probability of exceedance equal to 50%, divided by the design spectral acceleration at the collapse prevention limit state) has been evaluated for each examined case-study. Values ranging from 1.10 to 1.45 were found.
Seismic Azimuthal Anisotropy for the Southeastern Tibetan Plateau Extracted by Wave Gradiometry Analysis

Wave Gradiometry (WG) is a dense array data processing method used to extract seismic velocity and other properties of the earth. In this study, we propose using WG for a plane wave field to measure azimuthal anisotropy by fitting the phase velocities from different back azimuths. We applied this new method to the Temporary Western Sichuan Array and obtained the isotropic and azimuthal anisotropy for period bands centered at T = 20, 40, and 60 s in the southeast Tibetan Plateau. Our results show that the fast orientations of anisotropy are well consistent with the strikes of the fault system and orogenic belt. The weak anisotropic magnitude in the northern part of the south Chuandian subblock and a consistence of fast orientation in boundary fault zone (BFZ) at different periods may be attributed to anisotropic relics associated with the Emeishan Large Igneous Province. Comparing our results with those of previous studies, we found that our anisotropic results are consistent with anisotropic structures measured by the Pms phase in the plateau area, while a systematical angular difference exists in the BFZ, Sichuan Basin, and south Chuandian subblock where high Rayleigh wave phase velocity was observed. The Lijiang‐Xiaojin fault and Longmenshan fault appear to form a deep‐rooted strong boundary at the lithospheric scale, as they serve as a boundary for anisotropic structures, isotropic velocity, and the other three WG parameters.
Synthesis and Properties of Fluorinated Polyimides from Rigid and Twisted Bis(Trifluoromethyl)Benzidine for Flexible Electronics

Fluorinated polyimides were prepared from the twisted benzidine monomer containing two trifluoromethyl (CF3) groups on one aromatic ring. The diamine monomer having a rigid and nonplanar structure was polymerized with typical dianhydride monomers including BPDA, BTDA, ODPA, 6-FDA, and PMDA, to obtain the corresponding polyimides. Most polyimides are soluble in organic solvents due to their twisted chain structure and can be solution cast into flexible and tough films. These films have a UV-vis absorption cut-off wavelength at 354–398 nm and a light transparency of 34–90% at a wavelength of 550 nm. They also have tensile strengths of 92–145 MPa and coefficients of thermal expansion (CTE) of 6.8–63.1 ppm/°C. The polymers exhibited high thermal stability with 5% weight loss at temperatures ranging from 535 to 605°C in nitrogen and from 523 to 594°C in air, and high glass temperature (Tg) values in the range of 345–366°C. Interestingly, some of the soluble polyimides showed thermo-responsive behaviors in organic solvents presumably due to the multiple hydrogen bondings with unsymmetrically positioned two CF3 groups along the polymer chains.
Lyophilization of Avocado (Persea americana Mill.): Effect of Freezing and Lyophilization Pressure on Antioxidant Activity, Texture, and Browning of Pulp

Effects of both previous freezing (−26 and −80°C) and lyophilization (0.12, 0.37, and 1.07 mbar) conditions on drying kinetics, antioxidant activity, texture, and browning index of avocado pulp were evaluated. Vacuum pressure was found to have less effect on the lyophilization process than previous freezing temperature. Samples frozen initially at − 80°C required a longer lyophilization time. The best fittings for the drying kinetics of the avocado were obtained using the Page equation. The processing directly affected the antioxidant activity of the avocado pulp. Both the lipophilic and the hydrophilic fraction of the freeze-dried pulp decreased antioxidant activity, regardless of the applied pressure or freezing type. The hardness of the fresh avocado (0.93 N) was higher than the freeze-dried samples frozen in a conventional freezer (0.49 N) and their adhesion was greater than all of the freeze-dried samples. Freeze-dried pulps showed higher browning index than fresh avocado pulp (135.3).
Genetic Mapping Using Genotyping‐by‐Sequencing in the Clonally Propagated Cassava

Cassava (Manihot esculenta L.) is one of the most important food crops in the tropics, but yields are far below their potential. The gene pool of cas- sava contains natural genetic diversity relevant to many important breeding goals, but breeding progress has been slow, partly because of insuf- ficient genomic resources. As a first step toward implementing genomewide genetic studies that will facilitate rapid genetic gain through breed- ing, we genotyped-by-sequencing a set of 182 full-sibs population of cassava that segregated in several traits: resistance to the cassava mosaic disease (CMD) and yield under CMD pressure; increased carotenoid content in storage roots; color of stem exterior and anthocyanin pigmen- tation in the petioles, inner root skin, and api- cal leaves. Employing a rare-cutting restriction enzyme, PstI, in a genotyping-by-sequencing (GBS) library preparation, we obtained 2478 segregating single nucleotide polymorphisms (SNPs), of which 1257 passed standard filter - ing for missing genotypes and deviation from expected genotypic frequencies. We mapped 772 SNPs across 19 linkage groups and anchored 313 unique scaffolds from the version 4.1 of the cassava genome assembly. Most of the stud- ied morphological traits as well as resistance to CMD and root carotenoid content showed quali- tative inheritance. As expected, quantitative trait loci analysis for these traits revealed single loci surrounded by small confidence intervals. Yield under CMD was associated with the CMD resis- tance locus. We show that GBS is a powerful genotyping tool that provides a sufficient number of markers for unraveling the genetic architecture of Mendelian traits in cassava in addition to the development of a robust genetic map that can help anchor unassembled genomic scaffolds.