Miracle-dz/UniFAR-FTUs huggingface dataset:
Perancangan Alat Penghitung Benih Ikan Berbasis Sensor Optik

Freshwater fish is one of important commodities for the people of Indonesia. High level of freshwater fish consumption in Indonesia leads to an enormous amount of freshwater fish embankment business. These freshwater fish embankment business are supported by fries cultivation business. One of the activities on the fries cultivation business is trading activity where the traded fries counting process is important. One of the problems on the counting process is that the counting process is done manually which is tend to be done inaccurately and time consuming. A proposed solution to alleviate this problem is the development of fries counter device by using optical sensor technology. The counter device consists of mechanical and electronics systems. The device is designed as a plastic box with three distribution pipes where on each pipe there is a transparent part installed with the optical sensor. Based on the testing results the optical sensor can be utilized as the counter sensor with accuracy result 91.4%.
Influence of different planting methods on growth, productivity and root characteristics of BT cotton in south-west Punjab

Field experiment was conducted during Kharif 2016-17 and 2017-18, at the Krishi Vigyan Kendra, Bathinda, Punjab Agricultural University, Ludhiana to study the growth, productivity and quality and root characteristics of Bt Cotton under different planting methods viz. T1: Cotton sowing drill (Three tynes), T2: Cotton sowing drill (Four tynes), T3: Ridge sowing and T4: Bed maker Bt sowing machine. The results concluded that bed maker Bt sowing machine treatment showed significantly higher plant height, dry matter accumulation, number of monopodial branches/plant, number of sympodial branches/plant, number of bolls/plant and average boll weight over cotton sowing drill (Three tynes) and cotton sowing drill (Four tynes) and it was at par with ridge sowing. Bed maker Bt sowing machine treatment gave significantly higher cotton yield (12.3%) over cotton sowing drill (Three tynes) but it was statistically similar with ridge sowing. Maximum ginning out turn (GOT), seed index and lint index was noticed in bed maker Bt sowing machine treatment.
Statistical inference for the evolutionary history of cancer genomes

Recent years have produced a large amount of work on inference about cancer evolution from mutations identified in cancer samples. Much of the modeling work has been based on classical models of population genetics, generalized to accommodate time-varying cell population size. Reverse-time genealogical views of such models, commonly known as coalescents, have been used to infer aspects of the past of growing populations. Another approach is to use branching processes, the simplest scenario being the linear birth-death process (lbdp), a binary fission Markov age-dependent branching process. A genealogical view of such models is also available. The two approaches lead to similar but not identical results. Inference from evolutionary models of DNA often exploits summary statistics of the sequence data, a common one being the so-called Site Frequency Spectrum (SFS). In a sequencing experiment with a known number of sequences, we can estimate for each site at which a novel somatic mutation has arisen, the number of cells that carry that mutation. These numbers are then grouped into sites which have the same number of copies of the mutant. SFS can be computed from the statistics of mutations in a sample of cells, in which DNA has been sequenced. In this paper, examine how the SFS based on birth-death processes differ from those based on the coalescent model. This may stem from the different sampling mechanisms in the two approaches. However, we also show mathematically and computationally that despite this, they can be made quantitatively comparable at least for the range of parameters typical for tumor cell populations. We also present a model of tumor evolution with selective sweeps, based on coalescence, and demonstrate how it may help in understanding the past history of tumor as well the influence of data pre-processing. We illustrate the theory with applications to several examples of The Cancer Genome Atlas tumors.
Neural signatures of model-free learning when avoiding harm to self and other

Moral behaviour requires learning how our actions help or harm others. Theoretical accounts of learning propose a key division between ‘model-free’ algorithms that efficiently cache outcome values in actions and ‘model-based’ algorithms that prospectively map actions to outcomes, a distinction that may be critical for moral learning. Here, we tested the engagement of these learning mechanisms and their neural basis as participants learned to avoid painful electric shocks for themselves and a stranger. We found that model-free learning was prioritized when avoiding harm to others compared to oneself. Model-free prediction errors for others relative to self were tracked in the thalamus/caudate at the time of the outcome. At the time of choice, a signature of model-free moral learning was associated with responses in subgenual anterior cingulate cortex (sgACC), and resisting this model-free influence was predicted by stronger connectivity between sgACC and dorsolateral prefrontal cortex. Finally, multiple behavioural and neural correlates of model-free moral learning varied with individual differences in moral judgment. Our findings suggest moral learning favours efficiency over flexibility and is underpinned by specific neural mechanisms.
Do natural disturbances have significant effects on sandy beach macrofauna of Southeastern Brazil?

The role of morphodynamic features such as grain size, swash climate and wave action on the macrofauna of beaches are well-known. However, few studies have investigated natural disturbances as potential drivers of temporal community variations. In southeastern Brazil, we sampled the intertidal macrofauna of two sandy beaches to test whether seasonal disturbances as the frequency of storm wave events (SWE) and rainfall have significant influence on their composition and abundance. The macrofauna assemblage differed significantly between the rainy and the dry seasons, but rainfall was not the main driver of community changes, although both beaches are in the vicinity of extensive river plumes. Actually, SWE explained most macrofauna richness overtime, with positive effects. Our results point to the importance of learning more about the effects of poorly studied disturbances on macrofaunal communities, and based on them we strongly recommend including these seasonal phenomena when monitoring sandy beaches.
Using Spatial Regression to Model Potentially Toxic Metal (PTM) Mobility Based on Physicochemical Soil Properties

Mining processes generate waste rock, tailings, and slag that can increase potentially toxic metal (PTM) concentrations in soils. Un-reclaimed, abandoned mine sites are particularly prone to leaching these contaminants, which may accumulate and pose significant environmental and public health concerns. The characterization and spatial delineation of PTMs in soils is vital for risk assessment and soil reclamation. Bumpus Cove, a once active mining district of eastern Tennessee, is home to at least 47 abandoned, un-reclaimed mines, all permanently closed by the 1950s. This study evaluated soil physicochemical properties, determined the spatial extent of PTMs (Zn, Mn, Cu, Pb, and Cd), and examined the influence of soil properties on PTM distribution in Bumpus Cove, TN. Soil samples (n = 52) were collected from a 0.67 km2study area containing 6 known abandoned Pb, Zn, and Mn mines at the headwaters of Bumpus Cove Creek. Samples were analyzed for Zn, Mn, Cu, Pb, and Cd by microwave-assisted acid digestion and flame atomic absorption spectrometry (FAAS) (12–1,354 mg/kg Zn, 6–2,574 mg/kg Mn, 1–65 mg/kg Cu, 33–2,271 mg/kg Pb, and 7–40 mg/kg Cd). Of the measured PTMs, only Pb exceeds permissible limits in soils. In addition to the PTM analyses, soil physical (texture, moisture content, and bulk density) and chemical (pH, cation exchange capacity (CEC), and total organic carbon (TOC)) properties were evaluated. Spatially weighted multivariate regression models developed for all PTMs using soil physicochemical properties produced improved results over ordinary least squares (OLS) regression models. Models for Zn (R2 = 0.71) and Pb (R2 = 0.69) retained covariatesepH, moisture content, and CEC (Zn), and pH and CEC (Pb). This study will help define PTM concentration and transport and provide a reference for state and local entities responsible for contaminant monitoring in Bumpus Cove, TN.
Genetic Diversity in FUB Genes of Fusarium oxysporum f. sp. cubense Suggests Horizontal Gene Transfer

Fusaric acid (FA) is an important secondary metabolite of many Fusarium species and involved in the wilt symptoms caused in banana by Fusarium oxysporum f. sp. cubense (Foc). To investigate the evolution characteristics of the 12 Foc FA biosynthetic genes (FUB), coding sequences of the 12 FUB genes and three housekeeping genes, EF-1α/RPB1/RPB2 (translation elongation factor-1α/RNA polymerase II subunit I/RNA polymerase II subunit II), were subjected to genetic diversity analysis, phylogenetic analysis, recombination detection, and selective pressure analysis. The results of selective pressure analysis showed that the 15 genes were mainly subjected to negative selection. However, a significantly higher number of silent mutations, which could not be simply explained by selective pressure difference, were observed in the 12 FUB genes in Foc than in the three housekeeping genes. Infraspecies phylogeny and recombination detection analysis showed that significantly more horizontal gene transfer (HGT) events (normalized) had occurred in the FUB genes than in the three housekeeping genes. In addition, many of these events involved outgroup isolates and significantly increased the genetic diversity of FUB genes in Foc. The infraspecies phylogenetic analysis suggested that the polyphyletic phylogeny proposed for Foc requires further discussion, and the divergence of race 1, race 4, and the common ancestor of several F. oxysporum (Fo) isolates pathogenic to nonbanana plants should have diverged over a short period. Finally, our results suggest that the FUB genes in Fo should have benefited from HGT to gain a relatively high genetic diversity to respond to different host plants and environments despite mainly being subject to negative selection.
Individuation of parts of a single object and multiple distinct objects relies on a common neural mechanism in inferior intraparietal sulcus

Object identification and enumeration rely on the ability to distinguish, or individuate, objects from the background. Does multiple object individuation operate only over bounded, separable objects or does it operate equally over connected features within a single object? While previous fMRI experiments suggest that connectedness affects the processing and enumeration of objects, recent behavioral and EEG studies demonstrated that parallel individuation occurs over both object parts and distinct objects. However, it is unclear whether individuation of object parts and distinct objects relies on a common or independent neural mechanisms. Using fMRI-based multivariate pattern analyses, we here demonstrate that activity patterns in inferior and superior intraparietal sulci (IPS) encode numerosity independently of whether the individuated items are connected parts of a single object or distinct objects. Lateral occipital cortex is more sensitive to perceptual aspects of the two stimulus types and the targets of the stimuli, suggesting a dissociation between ventral and dorsal areas in representing perceptual object properties and more general information about numerosity, respectively. Our results suggest that objecthood is not a necessary prerequisite for parallel individuation in IPS. Rather, our results point toward a common individuation mechanism that selects targets over a flexible object hierarchy, independently of whether the targets are distinct separable objects or parts of a single object.
Evaluation of hygienic quality of ferment of local beer dolo used as condiment in Burkina Faso

Rabile is a ferment of local beer called “dolo” in Burkina Faso. It is used for local beer production and as condiment in sauces. Its process of production could be a source of contamination. So the quality of ferment needs to be guaranteed for consumers’ health. The aim of the study was to control the hygienic quality of local ferment consumed in Burkina Faso. A total of 70 samples were purchased in seven localities of Burkina Faso. The standard plate count method was used for microbial analysis. The results show that aerobic mesophilic flora varied from 8.34 ± 0.72 to 10.07 ± 0.51 log10 UFC.g-1; yeast and mold from 7.24 to 8.28 log10 UFC.g-1; Staphylococcus aureus from 4.08 to 4.76 log10 UFC.g-1; Enterococci from 3.47 to 4.61 log10 UFC.g-1 and total coliform from 2.12 to 2.32 log10 UFC.g-1. Salmonella spp. and Shiguella spp. were not detected in any of the samples. So, 100% of the samples from Ouahigouya were contaminated with sulphite reducing bacteria (BRS). All the samples analyzed were contaminated by S. aureus and Enterococci. The hygienic control of the ferment showed that the contamination caused by food borne pathogens can lead to food poisoning. Pearson correlation matrix of microorganisms’ distribution in the samples showed highest positive correlation between Enterococci and sulphite reducing bacteria at r = 0.888. Analysis of principal components exhibited the variability of microbial groups with 94.312% cumulative values of the variance and Eigen values ranging between 0.492 and 3.695. The data suggested that traditional beer ferments samples collected were not suitable in quality and there is need to ameliorate the process of production. Key words: Local ferment, dolo, hygienic quality, food, Burkina Faso.
Experimental Co-infection of Low Pathogenic Avian Influenza Virus (H9N2) and Escherichia Coli in SPF Broiler Chickens.

The work was implemented to evaluate the pathogenicity of H9N2 when co-infected with the E.coli. Avian influenza H9N2 virus strain A/chicken/Egypt/1618F/2016 which was isolated from Luxor province during 2016 and E.coli serotype O78 were used in this research. Sixty SPF birds were divided into 6 groups of ten birds each. At age 21 days, group 1 was inoculated with H9N2 only, group 2 received E.coli and three days later received H9N2, group 3 inoculated with H9N2 and after three days received E.coli, group 4 was challenged with E.coli and H9N2 at the same time, group 5 was inoculated with E.coli only, and group 6 was designed as a negative group. Clinical signs, postmortem examination, and serological examination were monitored for 15 days. The H9N2 virus presence was assessed in tracheal and cloacal swabs using real-time PCR. The most severe signs and lesions were observed in groups (3, and 4), with also high mortality rate than other groups with a percentage of 20%. Groups 3, and 4 showed a longer duration in virus shedding in the tracheal and cloacal samples. The hemagglutination inhibition test, group 4 showed high HI antibody titer against AIV-H9N2 antigen than other groups, while group 2 showed the lowest HI antibody titer against AIV-H9N2 antigen than other groups that received only the H9N2 virus. In conclusion, the outcomes of this study revealed that the infection of H9N2 with E.coli can exacerbate the clinical outcomes and mortality rates which leads to higher economic losses in chicken flocks.
The role of bacteria in paralytic shellfish poisoning

Historically the production of paralytic shellfish toxins (PST), has been attributed to dinoflagellates. However, in the last decade, increasing evidence has been presented to indicate the involvement of a wide range of bacterial species including cyanobacteria and heterotrophic bacteria (Gallacher et al., 1997). Several studies investigating bacteria capable of PST production, have identified bacteria associated with dinoflagellates are capable of autonomous PST production (Gallacher et al., 1997). However, more recent research has focussed on the effects of these bacteria on toxin production by dinoflagellates, for which the production of bacterial-free (axenic) cultures is essential to identify whether dinoflagellates are capable of autonomous toxin production, in the absence of bacteria. Many different methods to produce axenic algal cultures have been published, including washing methods and the addition of bacteriolytic compounds. However, efforts to generate axenic dinoflagellate cultures, have been hampered not only by difficulties in removing associated bacteria, but also by the lack of effective methods for assessing the presence of certain bacteria. Traditionally, the absence of bacterial growth on marine media was considered acceptable proof for axenic status. However, as the numbers of bacteria determined by culture methods falls short of numbers detected using microscopy (Akagi et al., 1977), culture methods alone have been deemed inadequate to determine the axenic status of algal cultures. In this study, the production of an axenic dinoflagellate culture was vital, firstly, to assess the effect on dinoflagellate toxin production following removal of all associated bacteria, and secondly, to identify whether original toxicity was restored when the microflora was replaced. Methods to assess the axenic nature of cultures combined traditional methods of culturing, with epifluorescence microscopy, the method now frequently relied upon for axenic confirmation. However, molecular techniques were also included, which allowed the axenic status of dinoflagellate cultures to be confidently determined. The availability of molecular techniques also enabled an assessment of the bacterial diversity associated with original dinoflagellate cultures to be conducted, with culture-based and non culture-based identification systems adopted. This investigation indicated that a diverse range of bacteria were associated with cultures, although discrepancies between the two detection methods were noted. Results from the assessment of axenic dinoflagellate cultures confirmed the need for molecular methods, as bacterial DNA was identified in cultures which were considered axenic cultures using media assessment and epifluorescence microscopy. (Abstract shortened by ProQuest.).
Impact of global warming on insects: are tropical species more vulnerable than temperate species?

The magnitude and ecological impact of climate change varies with latitude. Several recent models have shown that tropical ectotherms face the greatest risk from warming because they currently experience temperatures much closer to their physiological optimum than temperate taxa. Even a small increase in temperature may thus result in steep fitness declines in tropical species but increased fitness in temperate species. This prediction, however, is based on a model that does not account for latitudinal differences in activity periods. Temperate species in particular may often experience considerably higher temperatures than expected during the active season. Here, we integrate data on insect warming tolerance and temperature-dependent development to re-evaluate latitudinal trends in thermal safety margins after accounting for latitudinal trends in insect seasonal activity. Our analyses suggest that temperate and tropical species differ far less in thermal safety margins than commonly assumed, and thus face a similar risk from warming.
Seed Priming: An old empirical technique with new contemporary perspectives in respect to Pisum sativum L: A review

Pea is a small duration pulse crop which gives a different performance in field emergence and seed yield at different soil type and environment. Major factors that deteriorate pea yield are a fungal infection at germination, low nodules formation and slow food stimulation process to seeds. For surpassing such a problem, seed priming is the best solution. Seed priming is of many types depending upon the priming material like chemicals, bio-agents, water, nanoparticles, radiations, growth hormones and many more. Using different priming technique, seed’s hormonal and metabolomic process can be altered and managed in a positive way, resulting in better germination and appropriate plant stand with greater biological and seed yield. This review deals with different priming techniques and their effect on pea crop’s germination, phenological and yield attributing traits for getting good crop establishment and better yield performance.
Wood–Moisture Relationships Studied with Molecular Simulations: Methodological Guidelines

This paper aims at providing a methodological framework for investigating wood polymers using atomistic modeling, namely, molecular dynamics (MD) and grand canonical Monte Carlo (GCMC) simulations. Atomistic simulations are used to mimic water adsorption and desorption in amorphous polymers, make observations on swelling, mechanical softening, and on hysteresis. This hygromechanical behavior, as observed in particular from the breaking and reforming of hydrogen bonds, is related to the behavior of more complex polymeric composites. Wood is a hierarchical material, where the origin of wood-moisture relationships lies at the nanoporous material scale. As water molecules are adsorbed into the hydrophilic matrix in the cell walls, the induced fluid–solid interaction forces result in swelling of these cell walls. The interaction of the composite polymeric material, that is the layer S2 of the wood cell wall, with water is known to rearrange its internal material structure, which makes it moisture sensitive, influencing its physical properties. In-depth studies of the coupled effects of water sorption on hygric and mechanical properties of different polymeric components can be performed with atomistic modeling. The paper covers the main components of knowledge and good practice for such simulations.
In Silico Screening of Circulating MicroRNAs as Potential Biomarkers for the Diagnosis of Ovarian Cancer

Current screening tests for the diagnosis of ovarian cancer (OC) face enduring challenges. However, microRNAs (miRNAs) are stable in the circulation and may be promising molecular biomarkers for OC prediction. Circulating miRNA expression profiles in OC were analyzed using sequencing data from the Gene Expression Omnibus database. Differentially expressed miRNAs were generated from GSE94533, of which some were selected as candidate miRNAs based on an electronic search of the literature and comprehensive evaluation. A meta-analysis was preformed to integrate an evaluation index for these miRNAs in diagnosing OC patients. An independent validation set (GSE106817) was also conducted to further confirm the roles of these miRNAs. We identified four MIR200 members (MIR200A, MIR200B, MIR200C, and MIR429) and MIR25 as being differentially expressed among malignant or benign ovarian tumor patients and healthy controls. In the meta-analysis, these five miRNAs yielded a pooled area under the receiver operating characteristic (ROC) curve (AUC) of 0.78 (sensitivity: 64%, specificity: 88%) in discriminating OC from healthy controls, while the four MIR200 members demonstrated a summary AUC of 0.81 (sensitivity: 92%, specificity: 69%) in differing OC cases from patients with benign disease. In the validation set, differential expression and ROC curve analyses of these miRNAs were consistent except for MIR25. The circulating MIR200 family has the potential to become reliable and noninvasive biomarkers for OC diagnosis. Studies with larger cohorts are warranted to validate the applicability of these miRNAs.