Miracle-dz/UniFAR-FTUs huggingface dataset:
An Empirical Study for Vietnamese Constituency Parsing with Pre-training

Constituency parsing is an important task that gets more attention in natural language processing. In this work, we use a span-based approach for Vietnamese constituency parsing. Our method follows the self-attention encoder architecture and a chart decoder using a CKY-style inference algorithm. We present analyses of the experiment results of the comparison of our empirical method using pre-training models XLM-R and PhoBERT on both Vietnamese datasets VietTreebank and NIIVTB1. The results show that our model with XLM-R archived the significantly F1-score better than other pre-training models, VietTreebank at 81.19% and NIIVTB1 at 85.70%.
Forecasting Forest Inventory Using Imputed Tree Lists for LiDAR Grid Cells and a Tree-List Growth Model

A method to forecast forest inventory variables derived from light detection and ranging (LiDAR) would increase the usefulness of such data in future forest management. We evaluated the accuracy of forecasted inventory from imputed tree lists for LiDAR grid cells (20 × 20 m) in spruce (Picea sp.) plantations and tree growth predicted using a locally calibrated tree-list growth model. Tree lists were imputed by matching measurements from a library of sample plots with grid cells based on planted species and the smallest sum of squared difference between six inventory variables. Total and merchantable basal area, total and merchantable volume, Lorey’s height, and quadratic mean diameter increments predicted using imputed tree lists were highly correlated (0.75–0.86) with those from measured tree lists in 98 validation plots. Percent root mean squared error ranged from 12.8–49.0% but was much lower (4.9–13.5%) for plots with ≤10% LiDAR-derived error for all plot-matched variables. When compared with volumes from 15 blocks harvested 3–5 years after LiDAR acquisition, average forecasted volume differed by only 1.5%. To demonstrate the novel application of this method for operational management decisions, annual commercial thinning was planned at grid-cell resolution from 2018–2020 using forecasted inventory variables and commercial thinning eligibility rules.
Exploitation of lettuce waste flour to increase bread functionality: effect on physical, nutritional, sensory properties and on consumer response

Phenol and fibre-rich flour obtained by air-drying and grinding of lettuce waste was partially substituted (26, 53, 170 and 575 g kg ) to wheat flour to produce functional bread. The addition of flour progressively decreased dough leavening capacity while increased bread moisture and firmness. Lettuce waste flour significantly increased the polyphenolic content (up to 3.4 g GAE kg ) of bread samples and enhanced their antioxidant activity by 200%. Bread containing 170 and 575 g kg 1 of lettuce waste flour presented sensory properties and consumer acceptability comparable to those of commercial wholemeal bread with similar rye bran content. Bread containing at least 170 g kg 1 of lettuce waste flour could be associated to nutritional claims related to its enhanced fibre content (>30 g kg ). Data obtained by conjoint analysis demonstrate the possibility of increasing consumer preference for lettuce waste flour bread by proper nutritional (fibre content) and sustainability (lettuce waste valorisation) claims.
Local Ecological Knowledge and Fire Management: What Does the Public Understand?

As ﬁre management agencies seek to implement more ﬂexible ﬁre management strategies, local understanding and support for these strategies become increasingly important. One issue associated with implementing more ﬂexible ﬁre management strategies is educating local populations about ﬁre management and identifying what local populations know or do not know related to ﬁre management. This study used survey data from three 2010 wildland ﬁres to understand how ecological knowledge and education level affected ﬁre management perception and understanding. Results indicated that increased accuracy in identifying ecological conditions was associated with higher proﬁciencies in the identiﬁcation of ﬁre management strategies used for wildﬁres. Education levels were not signiﬁcantly related to public perception of ﬁre management but were related to signiﬁcant differences in accurately identifying ecological conditions. Results suggest that education may play a mediating role in understanding complex wildﬁre issues but is not associated with a better understanding of ﬁre management.
A Point-Cloud Deep Learning Framework for Prediction of Fluid Flow Fields on Irregular Geometries

We present a novel deep learning framework for flow field predictions in irregular domains when the solution is a function of the geometry of either the domain or objects inside the domain. Grid vertices in a computational fluid dynamics (CFD) domain are viewed as point clouds and used as inputs to a neural network based on the PointNet architecture, which learns an end-to-end mapping between spatial positions and CFD quantities. Using our approach, (i) the network inherits desirable features of unstructured meshes (e.g., fine and coarse point spacing near the object surface and in the far field, respectively), which minimizes network training cost; (ii) object geometry is accurately represented through vertices located on object boundaries, which maintains boundary smoothness and allows the network to detect small changes between geometries; and (iii) no data interpolation is utilized for creating training data; thus accuracy of the CFD data is preserved. None of these features are achievable by extant methods based on projecting scattered CFD data into Cartesian grids and then using regular convolutional neural networks. Incompressible laminar steady flow past a cylinder with various shapes for its cross section is considered. The mass and momentum of predicted fields are conserved. For the first time, our network generalizes the predictions to multiple objects as well as an airfoil, even though only single objects and no airfoils are observed during training. The network predicts the flow fields hundreds of times faster than our conventional CFD solver, while maintaining excellent to reasonable accuracy.
IN SILICO DOCKING STUDIES OF GALLIC ACID STRUCTURAL ANALOGUES AS BCL-XL INHIBITOR IN CANCER

Objective: Apoptosis, or programed cell death, forms an important part of the cellular regulation machinery. The Bcl-2 protein family, comprising proapoptotic and antiapoptotic members, forms an important part of the cells internal apoptotic pathway. Overexpression of the antiapoptotic members of the family in a number of cancer cell lines renders them immune to apoptosis and the ability to survive under conditions of cellular stress. Inhibition of the antiapoptotic members of the Bcl-2 family like Bcl-XL is, therefore, an interesting target for the development of anticancer therapy. Methods: The structure of antiapoptotic Bcl-XL receptor (1YSG) was taken from PDB database. The 23-dimensional structure of gallic acid analogs was designed. The Lipinski properties of gallic acid analogs were calculated using molsoft. Docking studies have been carried out through Autodock 4.0 software. Results: Molecular docking analysis with gallic acid and their structural analogs showed propyl gallate, benzyl gallate, diallyl gallate, phenyl ethyl gallate, and allyl gallate are more interactive and binding strongly than gallic acid at active site of Bcl-XL. Conclusion: Further these five compounds should be considered as potential candidates for Bcl-XL inhibitor. Keywords: Apoptosis, Bcl-2, Antiapoptotic Bcl-XL receptor, Gallic acid, Docking studies.
Free energy calculations of protein-water complexes with Gromacs

We used GFP(Green Fluorescent Protein) to understand its basic structure, adding solvent water around the GFP, minimize and equilibrating it using molecular dynamics simulation with Gromacs. Gromacs is an open source software and widely used in molecular dynamics simulation of biological molecules such as proteins, and nucleic acids (DNA AND RNA-molecules). We employ the CHARMM (Chemistry at HARvard Molecular Mechanics) program for the force fields which enable the potential energy of a molecular system to be calculated rapidly. In this particular simple molecular mechanics interaction fields (CHARMM), the force fields consists of stretching energy, bending energy and torsion energy. The non-bond interaction energy is modeled by Lennard-Jones potential. The pdb2gmx gromacs command is implemented to obtained the basic coordinate file and topology for the particular system from the GFP PDB file (1gfl.pdb). We enclosed water molecule in a rhombic dodecahedron box having size 0.5nm, and protein are embedded in solvent water. The steepest descent method (first-order minimization) are implemented to calculate the local energy minimum with 104-steps. The stability of protein with solvent water molecule are analyzed by measuring the root-mean square displacement (RMSD) of all atoms. It was shown with help of figure that RMSD initially increases rapidly in the first part of simulation, but become stable around 0.14nm, roughly the resolution of the X-ray structure. The difference is partly due to the moving and vibration of atoms around an equilibrium structure. Secondary structure of GFP protein is presented with the help of DSSP-program.
Estimation of Antibacterial Activity of Plants Extracts from Phyllanthus Emblica, Terminalia Chebula and Eucalyptus Globulus Against Oral Pathogens

Dental caries and periodontal disease are the most common oral infections in humans. These diseases are primarily treated with antimicrobial drugs; however, the rise in antimicrobial resistance necessitates the investigation of plant-based phytocompounds as antimicrobial agents. This study investigated the phytochemicals present in three plants, Phyllanthus emblica, Terminalia chebula and Eucalyptus globulus, as well as their antibacterial effect on the cariogenic bacteria, Staphylococcus aureus (MTCC 3160), Escherichia coli (MTCC 1655) and Streptococcus mutans (MTCC 890). Fruits of Phylanthus emblica, Terminalia chebula and leaves of Eucalyptus globulus were extracted in aqueous, ethanol and methanol solvents. These extracts were tested for phytochemical compounds. Antibacterial activity was evaluated using agar disc diffusion method. The minimum inhibitory concentration (MIC) was measured via 96-well turbidimetric method. Results of preliminary qualitative phytochemical study of extracts revealed the presence of tannins and terpinoids in all the three plants. Antibacterial activity assay showed that the plant extracts were more active against gram-positive bacteria than gram-negative bacteria. The most susceptible bacteria was S. aureus. The bacterial strains tested were more susceptible to methanol extracts followed by ethanol and the least effective was aqueous extract. These findings indicate that Phyllanthus emblica, Terminalia chebula and Eucalyptus globulus extracts have potential antibacterial activity against oral pathogens such as S. aureus, S. mutans and E.coli and could be potentially used treatment of dental carries.
The Subcellular Compartment for Endoplasmic Reticulum-Associated Degradation of Exogenous Antigens from dendritic cells

Dendritic cells (DCs) have the unique ability of processing and presenting exogenous antigens upon major histocompatibility class I (MHC I) molecules. This ability is called antigen cross-presentation (CP) and plays not only in the activation of naive CD8 + T into anti-infectious and anti-tumoral cytotoxic CD8 + T cells, but also in the inactivation of self-acting naive T cells by T cell anergy or T cells deletion. Since antigen CP was first described more than four decades ago, so many numbers of studies, by using a variety of sources of antigens and antigen-presenting cells (APCs), had been carried out to solve the cellular process of CP. There are accumulating in vivo and in vitro evidences that endoplasmic reticulum (ER)-associated degradation (ERAD) acts as a key player in CP. But for all these efforts, the precious molecular mechanisms for CP are still remained to be elucidated. It may be partially because there are several pathways for CP running alongside with each other and each cell uses these several pathways redundantly responding against environmental conditions. Here, we review the intracellular transport routes for exogenous antigens and the subcellular compartment in which exogenous antigens undergo ERAD.
Plant DNA barcodes: Applications today and in the future

DNA barcodes have provided a new biological tool for organismal biologists to increase their understanding of the natural world. Over the last decade four plant DNA barcode markers, rbcL, matK, trnH‐psbA, and ITS2, have been developed, tested, and used to address basic questions in systematics, ecology, evolutionary biology and conservation, including community assembly, species interaction networks, taxonomic discovery, and assessing priority areas for environmental protection. Forensic investigators have also applied these plant DNA barcodes in the regulatory areas of traffic in endangered species and monitoring commercial products, such as foods and herbal supplements. Major challenges ahead will focus on building the global plant DNA barcode library and adopting genomic sequencing technologies for a more efficient and cost‐effective workflow in applying these genetic identification markers to additional fields of biological and commercial endeavors.
Mycoplasma pneumoniae a Chlamydia pneumoniae: původci respiračních infekcí a jejich vztah k některým chronickým onemocněním

13 www.prakticka-medicina.cz Respirační infekce jsou stále v popředí zájmu kliniků, mikrobiologů a epidemiologů, poněvadž jsou v komunitě nejčastější skupinou onemocnění s různým stupněm závažnosti. V jejich etiologii se uplatňuje celá řada původců, pře devším velké množství virů, z bakteriálních agens mají dominantní význam Streptococcus pneumoniae, Haemophilus influenzae a nověji Moraxella catarrhalis. Mykoplasmata a chlamydie jsou ne zcela přesně zařazeny do společné skupiny intracelulárních původců respiračních infekcí, někdy označovaných jako „atypické infekce“. Ve způsobu parazitismu na úkor hostitelských buněk se odlišují.
Étude de l'influence du phosphore sur l'activité fermentaire, la protéosynthèse et les teneurs en ATP de contenus de rumen dans différents systèmes de culture continus

The aim of this study was to determine phosphorus (P) requirements for the two main aspects of rumen metabolism: microbial digestion of the diet and microbial protein synthesis. A process for the extraction of adenosine trisphosphate (ATP) has been designed. RNA assay and the incorporation of heavy nitrogen (15N) were used to quantify microbial growth. The results permitted the two continuous culture systems to be compared and pointed out the difference between the nitrogen metabolism of free bacteria and that of bacteria bound to solid particles. The amount of P needed to degrade cellulose compounds and for ATP synthesis was higher than the growth requirement estimated to be 3. 6g of P/kg of digestible organic matter in the rumen.
A call for viewshed ecology: Advancing our understanding of the ecology of information through viewshed analysis

There has been rapid increase of interest in the role that information acquisition plays in ecological process and in shaping life histories and their evolution. Compared to auditory and olfactory cues, the range at which visual cues are likely to be informative to animals is particularly sensitive to the spatial structure of the environment. However, quantification of and accounting for availability of visual information in fundamental and applied ecological research remains extremely limited. We argue that a comprehensive understanding of animal behaviour in a spatial context would greatly benefit from objective quantification of the area an animal can potentially obtain visual information from and therefore draw broad attention to viewshed analysis. This analysis identifies all cells of a gridded surface that are connected by lines‐of‐sight to a viewpoint, hence, providing information on how much of the environment surrounding a location can be seen. Although heavily used in non‐ecological disciplines including civil planning and archaeology, viewshed analysis has seldom been applied in an ecological context. Here, we highlight the opportunity to make use of viewshed approaches in conjunction with three‐dimensional remote sensing data and data from animal tracking to make major progress in understanding how visual information influences animal spatial behaviour, ecology and evolution.
Effect of Conventional or Plant-Based Diets on the Productivity of Broiler Chickens

The study was conducted to investigate the gross responses, meat yield traits and excreta/litter quality of broilers fed diets based on only plant ingredients or conventional diets containing animal protein. A total of 320 day-old male broiler chicks (Cobb 500) was distributed randomly into five treatments (T 1 , T 2 , T 3 , T 4 and T 5 ), each replicated eight times with eight chicks per replicate in a completely randomized block design. Diets T 1 and T 2 were formulated with entirely plant ingredients, whereas diets T 3 and T 4 were conventional, and contained both plant and animal ingredients. Diet T 5 was used as control, basically contained plant ingredients except for tallow mixer. All diets were iso-energetic and iso-nitrogenous in nature, cold-pelleted and fed the birds ad libitum from d1-35 days. Live weight up to 35d was improved (P 0.05) on day 35. Mortality was unaffected (P>0.05) between treatment. Excreta pH values and the concentration of ammonia were not influenced (P>0.05) by treatment. Higher (P 0.05) by dietary treatments. Birds fed conventional diets (T 3 and T 4 ) demonstrated increased (P<0.01) abdominal fat content compared to other dietary treatments. Breast weight (%) tended to be increased (P<0.08) in the birds when the birds fed on plant-based diet (T 1 ). In conclusion, the productivity of broilers fed conventional diets was better than those fed on plant-based diets only.
Type I-E CRISPR-Cas system as an immune system in a eukaryote

Defense against viruses and other mobile genetic elements (MGEs) is important in many organisms. The CRISPR-Cas systems found in bacteria and archaea constitute adaptive immune systems that acquire the ability to recognize MGEs by introducing nucleic acid samples, spacers, in the CRISPR locus. The CRISPR is transcribed and processed, and the produced CRISPR RNAs guide Cas proteins to degrade matching nucleic acid sequences. No CRISPR-Cas system is found to occur naturally in eukaryotic cells but here we demonstrate interference by type I-E CRISPR-Cas system from Escherichia coli introduced in Saccharomyces cerevisiae. The designed CRISPR arrays are properly expressed and processed in S. cerevisiae. Targeted plasmids display reduced transformation efficiency, indicative of DNA cleavage. Unlike e.g. Cas9-based systems, which can be used to inactivate MGEs in eukaryotes by introducing specific mutations, type I-E systems processively degrade the target. The type I-E system thus allows for defense without knowledge of MGE gene function. The reconstituted CRISPR-Cas system in S. cerevisiae can also function as a basic research platform for testing the role of various factors in the interference process.
Opposite Accumulation Patterns of Two Glycoside Hydrolase Family 3 α-L-Arabinofuranosidase Proteins in Avocado Fruit during Ripening

Avocado fruit ripen with ethylene production after harvest and the flesh becomes soft and edible due to degradation of cell wall polysaccharides during ripening. α-L-Arabinofuranosidase is a hydrolytic enzyme known to digest arabinose-containing cell wall polysaccharides. It has been shown that its activity increased with fruit ripening. However, our previous study showed that an α-L-arabinofuranosidase gene (PaArf/Xyl3A) is expressed in the avocado fruit before ethylene production. In addition, the transcripts were detected in some organs in which the level of ethylene was extremely low. These results indicate that the gene expression is independent of ethylene. In the present study, we carried out immunoblot analyses of α-L-arabinofuranosidase at the protein level. Using a polyclonal antibody raised against Japanese pear α-L-arabinofuranosidase, two αL-arabinofuranosidase proteins with molecular masses of 72 kDa and 68 kDa, presumably belonging to glycoside hydrolase family 3, were detected in ripening avocado fruit. The protein levels in ethylene or 1methylcyclopropene (1-MCP)-treated fruits were examined and the results indicated that the two proteins responded to ethylene in opposite ways; the 68 kDa protein showed a temporary accumulation, whereas the 72 kDa protein exhibited dissipation possibly caused by a loss of stability. The total enzyme activity of α-Larabinofuranosidase was elevated faster in the ethylene-treated fruit throughout ripening and was slower in the 1-MCP-treated fruit, suggesting the existence of another α-L-arabinofuranosidase, which did not crossreact with the antibody and was positively regulated by ethylene, in ripening avocado fruit.
Genetic diversity in a structured family of six generations of ornamental chili peppers (capsicum annuum)

The genus Capsicum has been used as an ornamental plant, but there are only a few commercial cultivars for this purpose available in Brazil. The aim of this study was to analyze the genetic diversity in a structured family of six generations of ornamental pepper based on quantitative and qualitative data, separately and integrated in the same analysis. These studies are part of the Capsicum breeding program developed at Universidade Federal da ParaA­ba and Universidade Federal de ViA§osa. Six generations (P1, P2, F1, F2, BC1, and BC2) of ornamental pepper, belonging to the germplasm bank of Universidade Federal da ParaA­ba, were evaluated. Two accessions of ornamental pepper plants belonging to the germplasm bank of UFPB (01 and 132) were chosen based on an earlier diallel study. Ten plants of each parent and F1, 72 plants of backcross 1 (BC1), 75 plants of backcross 2 (BC2), and 147 plants of the segregating F2 generation were studied. Analysis of genetic diversity was performed for all generations. Quantitative data were subjected to cluster analysis by Tocherâs method. Multi-traits were analyzed based on the arithmetic complement of the index of coincidence. The matrices of quantitative and multi-categorical traits were summed, and data were subjected to cluster analysis by Tocherâs optimized method. The relative importance of the traits was evaluated by Singh (1981)âs method. High genetic variability was determined in F2 and backcrosses by three cluster analyses, showing that parents 01 and 132 differ for the evaluated traits. According to the relative importance of traits, those that most contributed to genetic divergence were number of seeds per fruit, number of fruits per plant, days to flowering and days to fruiting.