Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimization of Start Codon Targeted Polymorphism PCR(SCoT-PCR) system in Vitis vinifera

The grape SCoT-PCR reaction system was optimized based on the L16(45) orthogonal experiment and single factor experiment design.The results showed that: the key factor was the dNTPs concentration in the orthogonal experiment,while in the single factor experiment,the key factors were the dNTPs and Mg2+ concentration;Based on the results,it was suggested that the optimal SCoT-PCR system for grape was: total 20 μL reaction system containing 2.0 mmol·L-1 Mg2+,0.3 mmol·L-1 dNTPs,1.0 U Taq polymerase,0.3 μmol·L-1 primer,and 30 ng DNA template.The PCR amplification profile was pre-denaturing at 94 ℃ for 5 min,,denaturing at 94 ℃ for 1 min,annealing at 54 ℃ for 1 min and extending at 72 ℃ for 2 min,34 cycles and extending at 72 ℃ for 8 min finally.The optimal reaction system was further verified in 20 grape varieties,which showed good stability and repeatability.The system provides a new technology for evaluation of genetic diversity,genomic analysis,construction of fingerprinting and molecular marker assisted breeding for the grape.
Novel Molecular Insights about Lactobacillar Sortase-Dependent Piliation

One of the more conspicuous structural features that punctuate the outer cell surface of certain bacterial Gram-positive genera and species is the sortase-dependent pilus. As these adhesive and variable-length protrusions jut outward from the cell, they provide a physically expedient and useful means for the initial contact between a bacterium and its ecological milieu. The sortase-dependent pilus displays an elongated macromolecular architecture consisting of two to three types of monomeric protein subunits (pilins), each with their own specific function and location, and that are joined together covalently by the transpeptidyl activity of a pilus-specific C-type sortase enzyme. Sortase-dependent pili were first detected among the Gram-positive pathogens and subsequently categorized as an essential virulence factor for host colonization and tissue invasion by these harmful bacteria. However, the sortase-dependent pilus was rebranded as also a niche-adaptation factor after it was revealed that “friendly” Gram-positive commensals exhibit the same kind of pilus structures, which includes two contrasting gut-adapted species from the Lactobacillus genus, allochthonous Lactobacillus rhamnosus and autochthonous Lactobacillus ruminis. This review will highlight and discuss what has been learned from the latest research carried out and published on these lactobacillar pilus types.
In vitro fermentation and immunomodulating characteristics of dietary fibres

Abstract Dietary fibres are a diverse group of substances, indigestible by human digestive enzymes, but (partially) fermentable in the human large intestine by the resident microbiota. Many health beneficial effects of fibres such as lowering blood cholesterol levels or increasing stool bulk have been reported. For some fibres, immunomodulating properties have been shown. Other studies investigate the degradation fate of fibres by the bacteria. In this PhD thesis BMDCs from TLR2/4 knock out mice were validated to be unresponsive to naturally present contaminants like LPS and proved to be a good tool to analyse the immune response of dietary fibres. A variety of 44 fibres, was tested on these immune cells and all fibres were found to modulated the immune system differently. Also, different immunomodulating properties of an oat and barley β-glucan having rather similar chemical structures, were found. The insoluble fraction of the β-glucans induced highest amounts of cytokines. As a consequence, sample preparation such as drying, dispersing and heating were shown to affect the immunomodulatory properties. The in vitro fermentation characteristics of barley β-glucan and sugar beet pectin and the immunomodulatory properties of their degradation products on BMDCs were compared and shown to be substrate and degradation product specific. This study showed, that glycosidic degradation products of both fibres induced higher amounts of cytokines than their intact polysaccharide. An in vitro batch fermentation of soluble, indigestible maltodextrins by human faecal inocula was monitored and the activity of carbohydrate degrading enzymes, produced by the microbiota, was analysed. Results revealed that the maltodextrin was only slowly and incompletely fermented, despite the high potential of microbial enzymes present to degrade typical starch linkages. Overall, this thesis showed that dietary fibres interact and influence the immune system dependent on their individual chemical fine structure. Additionally, an evaluation of the health impact of dietary fibres can only be complete when also glycosidic fermentation products are considered.
ANALISIS KEMAMPUAN PEMECAHAN MASALAH BERDASARKAN AKTIVITAS BELAJAR PADA MODEL PEMBELAJARAN PBL

Dalam kurikulum 2013 siswa dituntut untuk mengembangkan ketrampilan dalam pemecahan masalah matematika. Namun rendahnya ketrampilan pemecahan masalah yang dialami siswa menyebabkan kurang berkembangnya kemampuan pemecahan masalah dan aktivitas belajar menjadi rendah karena siswa cendrung meniru cara guru dalam menyelesaikan masalah dan kurang terlibat aktif dalam pembelajaran. Untuk mengatasi permasalahan tersebut diterapkan pembelajaran matematika model PBL (problem based learning). Model pembelajaran PBL (problem based learning) menawarkan bentuk pembelajaran yang melibatkan siswa secara aktif dalam pembelajaran. PBL (problem based learning) adalah model pembelajaran pada masalah autentik sehingga siswa dapat menyusun pengetahuan sendiri, serta menumbuhkembangkan ketrampilan yang lebih tinggi. Siswa memperoleh pengetahuan tersebut secara langsung melalui pengalaman sendiri. Supaya aktivitas belajar lebih meningkat, maka dilengkapi dengan penguatan tugas terstruktur. Melalui tugas terstruktur maka siswa akan lebih banyak memiliki kesempatan untuk berlatih mengembangkan ketrampilan pemecahan masalah matematika. Dengan demikian, pembelajaran PBL (problem based learning) yang dilengkapi dengan pemberian tugas terstruktur dapat meningkatkan kemampuan pemecahan masalah matematika siswa.
Deep Neural Language Model for Text Classification Based on Convolutional and Recurrent Neural Networks

iv ACKNOWLEDGEMENTS . vi TABLE OF CONTENTS . vii LIST OF TABLES . ix LIST OF FIGURES . x CHAPTER 1: INRTODUCTION . 1 1.1 Research Problem and Motivation . 7 1.2 Contributions . 9 CHAPTER 2: LITERATURE SURVEY . 11 2.1 Traditional Methods for Natural Language Processing . 11 2.1.1 N-gram Models . 13 2.1.2 Structured Language Models . 14 2.1. 3 Word Vector Representations . 15 2.2 Neural Networks: Basics and Definitions . 16 2.2.1 Neural Network Language Models (NNLMs) . 19 2.2.2 Feedforward Neural Network Based Language Models (FFNNLMs). 20 2.3 Deep Learning Background . 21 2.4 Deep Learning for Natural Language Processing . 22 2.4. 1 Windows-Based Neural Networks . 24 2.5 Convolutional Neural Networks (CNNs) . 26 2.5. 1 Pooling Layer . 27 2.6 Convolution Neural Networks for Natural Language Processing (CNNs-NLP) . 29 2.7 GoogLeNet: Inception Convolution Neural Networks . 31 2.8 Recurrent Neural Networks (RNNs) . 35 2.8. 1 Recurrent Neural Networks Based Language Models (RNNLMs) . 39 2.8. 2 The Problem of Long-Term Dependencies . 40 2.8. 3 Vanishing and Exploding Gradients . 42 2.9 Long Short-Term Memory (LSTM) . 43 2.10 Bidirectional Recurrent Neural Networks (BRNNs) . 45 2.11 Gated Recurrent Unite (GRU) . 46 2.12 Vector Representations of Words . 47 2.13 Combination of Convolution Neural Networks and Recurrent Neural Networks (CNNsRNNs) . 49 CHAPTER 3: RESEARCH PLAN . 51 3.1 Deep Neural Network Language Model for Text Classification . 51 3.2 The Embedding Layer . 51
How Social Impact Affects Smartphone Brand Loyalty

ABSTRACT Recently, we have seen strong smartphone brands are associated repeatedly with exceptional sales, such as buyers queuing at Apple Stores on the first day of product release while some others are not. However, what factors influence our decision on choosing a particular brand of smartphone? Finding answers of this question is meaningful to the academic field as well as the sales of smartphones. This study tends to understand how product functions and social aspects have relationships on the emergence of the aforementioned phenomenon through validating a proposed model based on the survey results. A total of 319 valid questionnaires from smartphone and nonsmartphone users in Taiwan were received by this study. Our study found social dimensions namely, convergence, innovation, and network externality were the antecedents for product utility, and these antecedents are indirectly influencing to brand loyalty. Some implications and suggestions for smartphone manufacturers/retailers, governments, and academics are also given.
Vibration–based structural damage identification

Many aerospace, civil and mechanical systems continue to be used despite ageing and the associated potential for damage accumulation. Therefore, the ability to monitor the structural health of these systems is becoming increasingly important. A wide variety of highly effective local non–destructive evaluation tools is available. However, damage identification based upon changes in vibration characteristics is one of the few methods that monitor changes in the structure on a global basis. A summary of developments in the field of global structural health monitoring that have taken place over the last thirty years is first presented. Vibration–based damage detection is a primary tool that is employed for this monitoring. Next, the process of vibration based damage detection will be described as a problem in statistical pattern recognition. This process is composed of three portions: (i) data acquisition and cleansing; (ii) feature selection and data compression; and (iii) statistical model development. Current research regarding feature selection and statistical model development will be emphasized with the application of this technology to a large–scale laboratory structure.
Parental consumption of ultra-processed, high-fat products has no association with childhood overweight/obesity: an epidemiological study among 10-12-years-old children in Greece.

BACKGROUND Overweight and obesity during childhood consist two of the most important public health issues in the 21st century. Consumption of high-fat processed food has been increased alarmingly. OBJECTIVE To examine the association between parental ultra-processed, high-fat products' consumption and childhood overweight/obesity. METHODS A cross-sectional survey, conducted among 422 children, aged 10-12 years, and their parents, during school years 2014-16. Parental and child data were collected through self-administered, anonymous and validated questionnaires. Among others, high-fat ultra-processed food consumption was also recorded. Children's weight status was based on gender- and age-specific tables derived from the International Obesity Task Force body mass index (BMI) cut-offs. RESULTS The prevalence of obesity in the reference population was 2.9%, whereas the prevalence of overweight was 19.3%. A strong correlation was observed between children's and their parents' BMI status (P < 0.001). Multi-adjusted data analysis revealed no association between parental intake of ultra-processed, high-fat products and children overweight/obesity. Similarly, when the data analysis accounted for family income and physical activity status of the children, the aforementioned results remained insignificant. CONCLUSION Despite the fact that parents' specific dietary habits seem not to affect their children's weight status, public health programs should consider parental nutrition education and mobilization as a preventive measure for childhood overweight/obesity.
Erratum: Regulation of imaginal disc cell size, cell number and organ size by Drosophila class I(A) phosphoinositide 3-kinase and its adaptor - (Current biology (1999) 9 (1019-1029))

In this Research Paper, which appeared in the 23 Sep tember 1999 issue of Current Biology, the axes in F igure 4a were incorrectly labelled. T h e axis labels should be ' N u m b e r of cells per clone ' for the x axis (not ' N u m b e r of clones ' as was publ ished) and ' N u m b e r of clones ' for the y axis (the publ i shed version had no label for this axis). T h e corrected version of the figure is shown here. (a) / Control ,
Understanding Public Library Services and Use: A Structural Equation Modeling Framework

This dissertation describes the process of fitting publicly available data from the 2015 Public Libraries Survey and 2015 American Community Survey to a structural equation model based on a theory of action for public libraries relating operating revenue to latent factors measuring service availability and library use within the context of matched community demographic data. The process of using theory-based data analysis to investigate publicly-available data is examined. Key findings include acceptable estimates of goodness-of-fit for hypothesized factors representing public library service availability and public library use, an inconsistent mediation effect of service availability on the relationship between public library operating revenue and public library use, and identification of disparities between local community descriptors associated with library revenue and local community descriptors associated with library use. Suggestions for further investigation of these disparities are presented.
Seasonal Variation of the Essential Oils of Salvia lavandulifolia: Antibacterial Activity

Abstract Spanish sage (Salvia lavandulifolia Vahl.) is an important medicinal plant native from the Iberian Peninsula being the species of the genus most commonly grown in this area. The seasonal variation of the essential oil chemical composition in organic cropping has been analysed. Besides, the antibacterial and antifungal activity of the essential oils has been evaluated. Essential oils extracted from aerial parts of the S. lavandulifolia by steam distillation show an important variation both on the yield and on the chemical composition during the different seasons. The main constituents of the oil were identified as 1,8-cineole (21.4–33.8 %), limonene (5.6–10.4 %), α-pinene (10.5–17.5 %), β-pinene (6.0–17.3 %), myrcene (t-10.0 %), camphor (6.1–9.4 %), and trans-caryophyllene (4.0–8.5 %), varying according to the seasons. According to our results essential oils coming from autumn and winter time produce the higher inhibition on the grow of most of the microorganism tested, and they are also more effective against Gram positive bacteria.
Bone Marrow Cells Differentiate in Cardiac Cell Lineages After Infarction Independently of Cell Fusion

Recent studies in mice have challenged the ability of bone marrow cells (BMCs) to differentiate into myocytes and coronary vessels. The claim has also been made that BMCs acquire a cell phenotype different from the blood lineages only by fusing with resident cells. Technical problems exist in the induction of myocardial infarction and the successful injection of BMCs in the mouse heart. Similarly, the accurate analysis of the cell populations implicated in the regeneration of the dead tissue is complex and these factors together may account for the negative findings. In this study, we have implemented a simple protocol that can easily be reproduced and have reevaluated whether injection of BMCs restores the infarcted myocardium in mice and whether cell fusion is involved in tissue reconstitution. For this purpose, c-kit–positive BMCs were obtained from male transgenic mice expressing enhanced green fluorescence protein (EGFP). EGFP and the Y-chromosome were used as markers of the progeny of the transplant.
Antibiotic resistance of Raouitella ornithinolytica strains isolatd from some cow's and buffalo's milk samples causing subclinical mastitis in Misan city

This study aims to monitored antibiotic resistance of Raouitella ornithinolytica strains' in clinical and subclinical mastitis infection in dairy cow's and buffalo's milk samples in different region of Misan City (in Suoth of Iraq) between the period from October 2015 to May 2016 . After samples collection cultivation and identification of bacterial strains were cultivated on MacConkey agar at 35c-+2c at 24 hours with Crystal Violet and urea agar.To further characterize the isolates distinguish between members of Enterobacteriaceae , the IMViC test was performed , methylene red (M),Voges - Proskauer (V) test. Typical results were using the API 20E. Pure cultures Enterobacteriaceae bacteria strains . We isolated eighteenth different kinds of Enterobacteriaceae strains from cows and buffalo milk samples were identified as Raoultella ornithinolytica ,which represent 44.4% of all isolated found. Many virulence factors expressed by Raoultella ornithinolytica were studied in vitro. All R. ornithinolytica isolates produced capsule . All isolates of R. ornithinolytica were resistant to Tetracycline , Ampicillin, Amikacin, Amoxicillin, Optochin , but they showed high sensitivity to Benzylpenicillin Dihydrostreptomycin sulfide 200mg The results indicated that total percentage of the infectivity of milk was Raoultella ornithinolytica (44.4%) most frequently followed by Klebsiella oxytoca (16.6%) , Sphingomonas paucimobilis and Escherichia coli (11.1%) with a small percentage of other Enterobacteriaceae species were also isolated. Quality of the milk was screened using white side test. Identification of the isolate was carried out depend on the morphology of colony and biochemical test . It is interesting to note the a some of our Raoultella ornithinolytica isolates were resistant to methicillin , and thes is resistance was 83% in Tetracycline , Ampicillin, Amikacin, Optochin, Amoxicillin , Benzylpenicillin-Dihydrostreptomycin sulfide. We detected the most resistance against five antibiotics Tetracycline , Ampicillin, Amikacin, Optochin, Amoxicillin . According to our knowledge through the date, we think that this study represented the first record of the occurrence of the antibiotics resistance of R. ornithinolytica isolates in bovine milk samples in Iraq.
Mechanical strain can increase segment number in live chick embryos

Physical cues, experienced during early embryonic development, can influence species-specific vertebral numbers. Here we show that mechanical stretching of live chicken embryos can induce the formation of additional somites and thereby modify early segmental patterning. Stretching deforms the somites, and results in a cellular reorganization that forms stable daughter somites. Cells from the somite core thereby undergo mesenchymal-to-epithelial transitions (MET), thus meeting the geometrical demand for more border cells. Using a Cellular Potts Model, we suggest that this MET occurs through lateral induction by the existing epithelial cells. Our results indicate that self-organizing properties of the somitic mesoderm generate phenotypic plasticity that allows it to cope with variations in the mechanical environment. This plasticity may provide a novel mechanism for explaining how vertebral numbers in species may have increased during evolution. Additionally, by preventing the formation of transitional vertebrae, these self-organization qualities of somites may be selectively advantageous.
The complete chloroplast genome sequence of rose-gold pussy willow, Salix gracilistyla Miq. (Salicaceae)

Abstract To understand genetic background of Salix gracilistyla Miq. , we presented its complete chloroplast genome which is 155,557 bp and has four sub regions: 84,530 bp of large single copy (LSC) and 16,218 bp of small single copy (SSC) regions are separated by 27,405 bp of inverted repeat (IR) regions including 130 genes (84 protein-coding gene, eight rRNAs, and 38 tRNAs). The overall GC content of the chloroplast genome is 36.7% and those in the LSC, SSC, and IR regions are 34.5%, 31.0%, and 41.9%, respectively. Phylogenetic trees show phylogenetic position of S. gracilistyla with low level of inter-species sequence variations.
Effects of fire rotation interval and overstory type on ambient soil temperatures in ponderosa pine forests in Arizona

Ambient soil temperatures were measured every four weeks from May 1986 to November 1986 at three depths under the organic forest floor in ponderosa pine (Pinus ponderosa Lawson & C. Lawson) forests in three stand types subjected to periodic prescribed burning. Temperatures at the organic layer – soil surface interface in sawtimber stands were higher and more variable than in pole and saplings stands. Temperature variability reached a maximum in the summer and decreased into the fall and early winter. Soil temperature variability decreased as depth below the surface increased. Three years after the low-intensity prescribed burns, soil temperatures in the burned stands were not significantly different from the those in the unburned controls, suggesting that any effect, though none was detected, of the low-intensity prescribed burns on soil temperature and belowground processes affected by temperature is short-lived in these stands.
PROFIL ASAM LEMAK RANTAI CABANG CAIRAN RUMEN YANG DISUPLEMENTASI LEGUMINOSA DALAM RANSUM BERBASIS INDEKS SINKRONISASI PROTEIN-ENERGI

The experiment was aimed to assess the use of the legume and synchronization index of protein and energy (SPE) in the diet of dairy cattles on branch chain volatile fatty acids (BCVFA) profile. The research was applied in In vitro technique. The research was used a Completely Randomized Design (CRD), factorially pattern (2x3), the first factor was the two species of legume (Sesbania and Leucaena) and the second factor was the three levels of the SPE index (0.4, 0.5, and 0.6), there were 6 treatments combination and replicates 4 times each. The results showed interaction between legumes with SPE index was highly significant (P 0,05) on iso valerat and valerat. Legume and SPE index respectively showed nonsignificant (P>0.05) on iso valerat and valerat. It can be concluded that Turi supplementation with high SPE index (0.6) gave the best effect on Branch Chain Volatile Fatty Acids (BCVFA) profile. Key words: Branch chain volatile fatty acids, Protein-energy synchronization index, Legume The experiment was aimed to assess the use of the legume and synchronization index of protein and energy (SPE) in the diet of dairy cattles on branch chain volatile fatty acids (BCVFA) profile. The research was applied in In vitro technique. The research was used a Completely Randomized Design (CRD), factorially pattern (2x3), the first factor was the two species of legume (Sesbania and Leucaena) and the second factor was the three levels of the SPE index (0.4, 0.5, and 0.6), there were 6 treatments combination and replicates 4 times each. The results showed interaction between legumes with SPE index was highly significant (P 0,05) on iso valerat and valerat. Legume and SPE index respectively showed nonsignificant (P>0.05) on iso valerat and valerat. It can be concluded that Turi supplementation with high SPE index (0.6) gave the best effect on Branch Chain Volatile Fatty Acids (BCVFA) profile. Key words: Branch chain volatile fatty acids, Protein-energy synchronization index, Legume